1037. Anzieta, JC; Williams-Jones, G; Ortiz, HD; Ruiz, MC.Investigating 10 yr of volcanoacoustic activity at Tungurahua Volcano, Ecuador, aided by machine learning.Seismological Research Letters, 2025, 96(2A): 949–967 Investigating 10 yr of volcanoacoustic activity at Tungurahua Volcano, Ecuador, aided by machine learning.
volcano, infrasound, Tungurahua, machine learning
Here, we present the results of applying diverse data processing and machine learning tools to investigate a very large dataset obtained from single station infrasonic recordings from the last 10 yr of the most recent period of explosive activity at Tungurahua volcano, Ecuador. To increase the quality and quantity of information extracted from the large data set and enhance pattern recognition, we combined traditional techniques with more recent ones. We divided the investigation into sequential steps: detection, discrimination, cleaning, and clustering. For the detection step, we tested the classical short‐term average/long‐term average algorithm and an algorithm specific for explosions detection called “Volcanic INfrasound Explosions Detector Algorithm (VINEDA)” and detected 118,516 events. To clean the detected signals from potential false positives, we used supervised classification that reduced the events to 75,483, and a catalog cleaning procedure using shallow learners including support vector machines, random forests, and a single layer neural network, trained using data from a manual catalog, to a final number of 36,359 events. This led to a sixfold increase in detected explosions compared to the manual catalog. Then, we applied hierarchical clustering to a well‐studied time window of activity using two independent difference metrics: dynamic time warping and waveform cross correlation and showed the insights and drawbacks from this approach. We showed that the different techniques were able to reveal repeating and striving events between selected different eruptive phases and associated them to possible changes in eruptive dynamics. Finally, to analyze the whole dataset at once we used a convolutional autoencoder network and obtained similar results to the classical clustering in a fraction of the time. We identified different families of explosions that appeared, sometimes intermittently, and revealed various potentially competing eruptive processes during the whole time period.Link DOI
1035. Aufrère, S; Williams-Jones, G; Moune, S; Morgan, D; Vigouroux, N; Russell, JK.Olivine time-capsules constrain the pre-eruptive history of Holocene basalts, Mount Meager Volcanic Complex, British Columbia, Canada.Journal of Petrology, 2024, 65: egae089 Olivine time-capsules constrain the pre-eruptive history of Holocene basalts, Mount Meager Volcanic Complex, British Columbia, Canada
basalt, cascade volcanic arc, diffusion chronometry, mount meager volcanic complex, olivine
The Canadian segment of the Cascade Volcanic Arc (i.e. the Garibaldi Volcanic Belt) comprises more than 100 eruptive centres, spanning the entire Quaternary period (Pleistocene to Holocene in age), and with deposits ranging in composition from alkaline basalt to rhyolite. At least one of the volcanoes is currently active; Mount Meager / Q̓welq̓welústen erupted explosively 2360 years BP and has ongoing fumarolic activity. Long-term forecasting of eruption frequency and style depends on reconstruction of the history and timescales of magmatic processes preceding previous volcanic eruptions. Utilising diffusion chronometry, we investigate the Mount Meager Volcanic Complex focusing on Holocene olivine-phyric basalts (Lillooet Glacier basalts) exposed by the retreat of the Lillooet Glacier. We identify two distinct olivine populations in samples of quenched, glassy basalt lavas that record different magmatic processes and histories. Glomerocrysts of Fo83 olivine phenocrysts, entrained and transported by a hot mafic input, form Population 1. These exhibit resorption and normally zoned outermost rim compositions of Fo76–78; a third of them also show interior reverse compositional zoning. A second population of skeletal microphenocrysts have the same composition as the phenocryst rims (i.e. Fo76–78) and are in equilibrium with the adjacent matrix glass. We estimate the pre-eruptive temperature-fO2 conditions in a shallow reservoir (100 MPa; ~3 km) for a melt with H2O content of 0.5–1 wt.% as ~1097–1106°C (± 30°C), and NNO + 0.5 (±1.1), respectively. Using these input parameters, we report Fe-Mg diffusion chronometry results for 234 normally zoned profiles from 81 olivine phenocrysts. Diffusion modelling of compositional profiles in oriented crystals indicates pre-eruptive magmatic residence times of 1 to 3 months. These remarkably short residence times in shallow reservoirs prior to eruption suggest very short periods of unrest may precede future eruptions.Website DOI
1033. Jones, TJ; Nyce Jr, H; Le Moigne, Y; Williams-Jones, G; Nyce, D.Rethinking natural hazards research and engagement to include co-creation with Indigenous communities.npj Natural Hazards, 2024, 1: 34 Rethinking natural hazards research and engagement to include co-creation with Indigenous communities
Co-creation, natural hazards, Indigenous Knowledge, volcano, Sii Aks
Indigenous peoples are widely affected by natural hazards and their history and knowledge can directly inform on past events and mitigation strategies. Here we show how effective co-creation of resources and bi-lateral knowledge exchange between natural hazard researchers and local Indigenous communities provides an effective,
equitable, and sustainable way to conduct research.Website DOI
1032. Unnsteinsson, T; Flowers, G; Williams-Jones, G.Formation and persistence of glaciovolcanic voids explored with analytical and numerical models.Journal of Glaciology, 2024, Formation and persistence of glaciovolcanic voids explored with analytical and numerical models
glacier, volcano, numerical model, Mt. Meager
One fifth of Earth’s volcanoes are covered by snow or ice and many have active geothermal systems that interact with the overlying ice. These glaciovolcanic interactions can melt voids into glaciers, and are subject to controls exerted by ice dynamics and geothermal heat output. Glaciovol11 canic voids have been observed to form prior to volcanic eruptions, which raised concerns when such features were discovered within Job Glacier on Qwelqwelústen (Mount Meager Volcanic Complex), British Columbia, Canada. In this study we model the formation, evolution, and steady-state morphol15 ogy of glaciovolcanic voids using analytical and numerical models. Analytical steady-state void geometries show cave height limited to one quarter of the ice thickness, while numerical model results suggest the void height h scales with ice thickness H and geothermal heat flux Q as h/H = aHbQc, with exponents b =-n/2 and c = 1/2 where n is the creep exponent. Applying this scaling to the glaciovolcanic voids within Job Glacier suggests the potential for total geothermal heat flux in excess of 10 MW. Our results show that relative changes in ice thickness are more influential in glaciovolcanic void formation and evolution than relative changes in geothermal heat flux.PDF DOI
1031. Anzieta, J, Pacheco, D, Williams-Jones, G, Ruiz, M.Cleaning volcano‑seismic event catalogues: a machine learning
application for robust systems and potential crises in volcano
observatories.Bulletin of Volcanology, 2023, 85: 59 Cleaning volcano‑seismic event catalogues: a machine learning
application for robust systems and potential crises in volcano
observatories
Volcano-seismic events, Volcano catalogues, Machine learning, Volcano observatories, Volcanic crises
Complete and precise volcano-seismic event catalogues are important not only for the statistical value that they possess for
describing past volcanic activity, but also because they constitute the input for automated systems that help monitor volcanic
activity in real time. Computer systems are valuable assets in the task of volcano-seismic event classification because in
theory they can have improved performance compared to humans due to speed, consistency, and unbiasedness. However, such
systems are trained with data from previously created catalogues of events, and as such, if catalogues have noise, the systems
will learn incorrectly. In this work, we propose the implementation of a methodology that is relatively easy and fast to apply
for the identification of potentially mislabeled events in a seismic event catalogue. We compare the results of applying the
procedure to two open catalogues from Cotopaxi and Llaima volcanoes. The first catalogue is believed to have an unknown
but potentially significant level of noise, while the other is assumed to be clean. We further validate our results for one of
the datasets with volcano observatory scientists in a blind-review fashion to demonstrate some of the hypotheses that can
arise in a catalogue with a presumably important level of noise. We conclude that the methodology is valid for identifying
potentially mislabeled seismic events and can help in assessing the quality of a given catalogue.PDF DOI
1028. Le Moigne, Y; Vigouroux, N; Russell, JK; Williams-Jones, G.Magmatic origin and storage conditions for the eruption of Tseax volcano, Northern Cordillera Volcanic Province, Canada.Chemical Geology, 2022, 588: 120648 Magmatic origin and storage conditions for the eruption of Tseax volcano, Northern Cordillera Volcanic Province, Canada.
Monogenetic volcano, Tseax volcano, Northern Cordilleran Volcanic Province, Basanite, Plumbing system
The Northern Cordilleran Volcanic Province (NCVP) is the most active volcanic belt in Canada, yet there are few detailed petrologic studies of the individual volcanoes. Tseax volcano is the southernmost volcanic centre of the NCVP, the second youngest (~ 1700 CE) eruption in Canada, and is one of Canada’s worst natural disasters killing up to ~ 2,000 Nisga’a First Nation people. We present a conceptual model for the origins, evolution and pre-eruptive storage of the Tseax magma which erupted ~ 0.5 km3 of volcanic material, mainly in the form of valley-filling lava flows. All Tseax products are alkali Fe- Ti- rich basanite-to-tephrite having trace element distributions similar to the other mafic NCVP lavas. Phenocrysts consist of plagioclase, olivine and titanomagnetite, often forming glomerocrysts suggesting co-crystallisation of these 3 mineral phases. Clinopyroxene is never observed as a phenocryst phase. The lavas have low Mg#’s implying they are fractionated relative to a mantle-derived ‘parent’ magma. Trace elements indicate the magma derives from melting of a fertile mantle source (i.e., (Nb/K)n ~1), most likely the upper asthenosphere. There is no evidence in the Tseax volcanic rocks for magma mixing or lithospheric contamination during ascent. The phenocryst assemblage suggests rapid ascent of a low viscosity magma to < 5.5 km where titanomagnetite becomes the first phase on the liquidus (~ 1133 °C). There the magma stalled for a very short period of time under P-T conditions where clinopyroxene did not reach saturation. Based on the size of the plagioclase phenocrysts, the magma stalled for less than a year and cooled down to 1094 - 1087 °C prior to eruption.Website DOI
1027. Le Moigne, Y; Williams-Jones, G; Vigouroux, N; Russell, JK.Chronology and eruption dynamics of the historic ~ 1700 CE eruption of Tseax Volcano, British Columbia, Canada.Frontiers in Earth Science, 2022, 10: 910451 Chronology and eruption dynamics of the historic ~ 1700 CE eruption of Tseax Volcano, British Columbia, Canada.
Tseax volcano; Monogenetic volcanism; Lava flow; Eruption dynamics; Indigenous knowledge
The eruption of Tseax volcano in ~1700 CE, in north-western British Columbia, is the second youngest volcanic event in Canada. It is also one of Canada’s worst natural disasters as it killed up to 2,000 people of the Nisga’a First Nation living there at the time. The eruption also significantly impacted the local environment by diverting the Nass River (the 3rd largest river in British Columbia). Within the Nisga’a culture, Adaawak stories preserve an observational account of the Tseax eruption. In this study, we establish the chronology of the eruption by integrating field observations, petrophysical data and Nisga’a oral and written histories. The Nisga’a stories corroborate the short duration and exceptional intensity of the eruption as recorded in the volcanic products. The eruption was divided in two main periods: (1) Period A and (2) Period B. (1) The eruption started in a typical Hawaiian style with low levels of lava fountaining that built up a spatter rampart. This pyroclastic edifice was breached by voluminous pāhoehoe lava flows erupted at high discharge rates. We estimate that almost half of the erupted flow volume (0.20 km3) erupted in Period A was emplaced at 800-1000 m3/s. The lava reached the Nass Valley, 20 km downstream of the volcano, in “swift currents”, diverted the Nass River and engulfed the former Nisga’a villages in only 1 to 3 days, thus likely being responsible for the reported fatalities. The discharge rates progressively diminished to 10-200 m3/s until the end of this first eruptive period, which lasted a few weeks to a few hundred days. (2) During Period B, two ‘a‘ā flows were erupted with discharge rates < 50 m3/s. This period was also characterised by a more explosive eruption style that built a 70 m high tephra cone overlapping with spatter rampart. In total, Period B lasted approximately 20 days. In total, the eruption produced 0.5 km3 of volcanic materials (mostly in the form of lava flows) on the order of weeks to a few months. The short duration of the eruption was probably inherent to the limited amount of melt produced in the mantle. However, the eruption of Tseax was similar in magnitude to the flank eruption on larger shield volcanoes such as Kīlauea’s Fissure 8 in 2018 or Mauna Loa in 1984.PDF DOI
1026. Warwick, R; Williams-Jones, G; Kelman, M; Witter, JB.A scenario-based volcanic hazard assessment for the Mount Meager Volcanic Complex, British Columbia.Journal of Applied Volcanology, 2022, 11:1-22 A scenario-based volcanic hazard assessment for the Mount Meager Volcanic Complex, British Columbia.
Mount Meager; Hazard scenarios; Pyroclastic density currents; Lahars; Tephra fall
The Mount Meager Volcanic Complex (Mount Meager) is a glacier-clad stratovolcanic system in southwestern British Columbia which last erupted over 2400 years ago (VEI 4). While this is Canada’s most recent major explosive eruption, most past research on Mount Meager has focused on its numerous and large volume landslides and thus the volcanic hazard characteristics remain understudied. Here we present a suite of scenario-based hazard maps and an assessment addressing a range of potential future explosive eruptions and associated hazards. In order to overcome limited knowledge of the eruptive history, numerical models have been used to simulate the primary syneruptive hazards of concern (dome-collapse pyroclastic density currents, lahars and tephra fallout) largely utilizing eruption parameters from analogous volcanoes, i.e., glacier-clad stratovolcanoes in a subduction zone setting. This study provides a framework for similar volcanic hazard studies where geologic data is limited, funds are minimal, and access is difficult. Furthermore, this sets the stage for recognizing volcanic hazards in the Canadian landscape, providing a resource to prepare for and mitigate potential impacts well in advance of a crisis situation. Website DOI
1025. Al-Shaer, A; Lyons, A; Ishikawa, Y; Hudson, BG; Boudko, SP; Forde, NR.Sequence-dependent mechanics of collagen reflect its structural and functional organization.Biophys. J., 2021, 120: 4013-4028 Sequence-dependent mechanics of collagen reflect its structural and functional organization
Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semi-flexible regions as found for fibril-forming collagens to a lengthy region of high flexibility toward its N-terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions, particularly when coinciding in multiple chains, significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain. DOI PubMed
1023. Almblad, H; Randall, TE; Liu, F; Leblanc, K; Groves, RA; Kittichotirat, W; Winsor, GL; Fournier, N; Au, E; Groizeleau, J; Rich, JD; Lou, YF; Granton, E; Jennings, LK; Singletary, LA; Winstone, TML; Good, NM; Bumgarner, RE; Hynes, MF; Singh, M; Stietz, MS; Brinkman, FSL; Kumar, A; Brassinga, AKC; Parsek, MR; Tseng, BS; Lewis, IA; Yipp, BG; MacCallum, JL; Harrison, JJ.Bacterial cyclic diguanylate signaling networks sense temperature.Nat. Commun., 2021, 12 Bacterial cyclic diguanylate signaling networks sense temperature
Many bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, we identify a thermosensory diguanylate cyclase (TdcA) that modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogen Pseudomonas aeruginosa. TdcA synthesizes c-di-GMP with catalytic rates that increase more than a hundred-fold over a ten-degree Celsius change. Analyses using protein chimeras indicate that heat-sensing is mediated by a thermosensitive Per-Arnt-SIM (PAS) domain. TdcA homologs are widespread in sequence databases, and a distantly related, heterologously expressed homolog from the Betaproteobacteria order Gallionellales also displayed thermosensitive diguanylate cyclase activity. We propose, therefore, that thermotransduction is a conserved function of c-di-GMP signaling networks, and that thermosensitive catalysis of a second messenger constitutes a mechanism for thermal sensing in bacteria. Many bacteria use the second messenger cyclic diguanylate (c-di-GMP) to control motility, biofilm production and virulence. Here, the authors identify a thermosensitive enzyme that synthesizes c-di-GMP and modulates temperature-dependent motility, biofilm development and virulence in the opportunistic pathogen Pseudomonas aeruginosa. DOI PubMed
1022. Almeida, P; Sandkam, BA; Morris, J; Darolti, I; Breden, F; Mank, JE.Divergence and Remarkable Diversity of the Y Chromosome in Guppies.Mol. Biol. Evol., 2021, 38: 619-633 Divergence and Remarkable Diversity of the Y Chromosome in Guppies
Poecilia reticulata; sex chromosomes; Y haplotypes; recombination suppression; linked-reads
The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence. DOI PubMed
1021. Alteen, MG; Tan, HY; Vocadlo, DJ.Monitoring and modulating O-GlcNAcylation: assays and inhibitors of O-GlcNAc processing enzymes.Curr. Opin. Struct. Biol., 2021, 68: 157-165 Monitoring and modulating O-GlcNAcylation: assays and inhibitors of O-GlcNAc processing enzymes
O-linked N-acetylglucosamine (O-GlcNAc) is protein modification that is emerging as a regulator of diverse aspects of cellular physiology. Aberrant O-GlcNAcylation has been linked to several diseases, spurring the creation of methods to detect and perturb the activity of the two enzymes that govern this modification - O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). Here we summarize assays used for these two enzymes. We also detail the latest structure-guided development of inhibitors of these two enzymes and touch on selected reports that underscore the utility of inhibitors as tools for uncovering the diverse roles of O-GlcNAc in cell function. Finally, we summarize recent reports on the potential therapeutic benefits of antagonizing these enzymes and comment on outstanding challenges within the field. DOI PubMed
1020. Atlas, WI; Ban, NC; Moore, JW; Tuohy, AM; Greening, S; Reid, AJ; Morven, N; White, E; Housty, WG; Housty, JA; Service, CN; Greba, L; Harrison, S; Sharpe, C; Butts, KIR; Shepert, WM; Sweeney-Bergen, E; Macintyre, D; Sloat, MR; Connors, K.Indigenous Systems of Management for Culturally and Ecologically Resilient Pacific Salmon (Oncorhynchus spp.) Fisheries.Bioscience, 2021, 71: 186-204 Indigenous Systems of Management for Culturally and Ecologically Resilient Pacific Salmon (Oncorhynchus spp.) Fisheries
traditional knowledge; salmon; sustainable fisheries; mixed-stock fisheries; Indigenous governance
Pacific salmon (Oncorhynchus spp.) are at the center of social-ecological systems that have supported Indigenous peoples around the North Pacific Rim since time immemorial. Through generations of interdependence with salmon, Indigenous Peoples developed sophisticated systems of management involving cultural and spiritual beliefs, and stewardship practices. Colonization radically altered these social-ecological systems, disrupting Indigenous management, consolidating authority within colonial governments, and moving most harvest into mixed-stock fisheries. We review Indigenous management of salmon, including selective fishing technologies, harvest practices, and governance grounded in multigenerational place-based knowledge. These systems and practices showcase pathways for sustained productivity and resilience in contemporary salmon fisheries. Contrasting Indigenous systems with contemporary management, we document vulnerabilities of colonial governance and harvest management that have contributed to declining salmon fisheries in many locations. We suggest that revitalizing traditional systems of salmon management can improve prospects for sustainable fisheries and healthy fishing communities and identify opportunities for their resurgence. DOI PubMed
1019. Bakkum, A; Donelan, JM; Marigold, DS.Savings in sensorimotor learning during balance-challenged walking but not reaching.J. Neurophysiol., 2021, 125: 2384-2396 Savings in sensorimotor learning during balance-challenged walking but not reaching
< em > adaptation <; em >; < em > internal model <; em >; < em > locomotion <; em >; < em > reaching <; em >
Safe and successful motor performance relies on the ability to adapt to physiological and environmental change and retain what is learned. An open question is what factors maximize this retention? One overlooked factor is the degree to which balance is challenged during learning. We propose that the greater need for control and/or perceived threat of falling or injury associated with balance-challenging tasks increases the value assigned to maintaining a learned visuomotor mapping (i.e., the new relationship between visual input and motor output). And we propose that a greater-valued mapping is a more retainable mapping, as it serves to benefit future motor performance. Thus, we tested the hypothesis that challenging balance enhances motor memory, reflected by greater recall and faster relearning (i.e., savings). Four groups of participants adapted to a novel visuomotor mapping induced by prism lenses while performing a reaching or walking task, with and without an additional balance challenge. We found that challenging balance did not disrupt visuomotor adaptation during reaching or walking. We then probed recall and savings by having participants repeat the adaptation protocol 1 wk later. For reaching, we found evidence of initial recall, though neither group demonstrated savings upon reexposure to the prisms. In contrast, both walking groups demonstrated significant initial recall and savings. In addition, we found that challenging balance significantly enhanced savings during walking. Taken together, our results demonstrate the robustness of motor memories formed during walking and highlight the potential influence of balance control on sensorimotor learning. NEW & NOTEWORTHY Most everyday tasks challenge our balance. Yet, this aspect of daily motor behavior is often overlooked in adaptation paradigms. Here, we show that challenging balance does not impair sensorimotor adaptation during precision reaching and walking tasks. Furthermore, we show that challenging balance enhances savings of a learned visuomotor mapping during walking. These results provide evidence for the potential performance benefits associated with learning during unconstrained, naturalistic behaviors. DOI PubMed
1018. Brain, M.J.; Moya, S.; Kincey, M.E.; Tunstall, N.; Petley, D.N.; Sepúlveda, S.A.Controls on post-seismic landslide behaviour in brittle rocks.Journal of Geophysical Research - Earth Surface, 2021, 126, e2021JF006242 Controls on post-seismic landslide behaviour in brittle rocks
DOI
1017. Christians, JK; Shergill, HK; Albert, AYK.Sex-dependent effects of prenatal food and protein restriction on offspring physiology in rats and mice: systematic review and meta-analyses.Biol. Sex Differ., 2021, 12 Sex-dependent effects of prenatal food and protein restriction on offspring physiology in rats and mice: systematic review and meta-analyses
Developmental origins; Developmental programming; Maternal nutrition; Malnutrition; Prenatal exposure
Background Males and females may experience different effects of early-life adversity on life-long health. One hypothesis is that male foetuses invest more in foetal growth and relatively less in placental growth, and that this makes them susceptible to poor nutrition in utero, particularly if nutrition is reduced part-way through gestation. Objectives Our objectives were to examine whether (1) food and/ or protein restriction in rats and mice has consistent sex-dependent effects, (2) sex-dependency differs between types of outcomes, and (3) males are more severely affected when restriction starts part-way through gestation. Data sources PubMed and Web of Science were searched to identify eligible studies. Study eligibility criteria Eligible studies described controlled experiments that restricted protein or food during gestation in rats or mice, examined physiological traits in offspring from manipulated pregnancies, and tested whether effects differed between males and females. Results Our search identified 292 articles, of which the full texts of 72 were assessed, and 65 were included for further synthesis. A majority (50) used Wistar or Sprague-Dawley rats and so these were the primary focus. Among studies in which maternal diet was restricted for the duration of gestation, no type of trait was consistently more severely affected in one particular sex, although blood pressure was generally increased in both sexes. Meta-analysis found no difference between sexes in the effect of protein restriction throughout gestation on blood pressure. Among studies restricting food in the latter half of gestation only, there were again few consistent sex-dependent effects, although three studies found blood pressure was increased in males only. Meta-analysis found that food restriction in the second half of gestation increased adult blood pressure in both sexes, with a significantly greater effect in males. Birthweight was consistently reduced in both sexes, a result confirmed by meta-analysis. Conclusions We found little support for the hypotheses that males are more affected by food and protein restriction, or that effects are particularly severe if nutrition is reduced part-way through gestation. However, less than half of the studies tested for sex by maternal diet interactions to identify sex-dependent effects. As a result, many reported sex-specific effects may be false positives. DOI PubMed
1016. Cojocaru, R; Unrau, PJ.Processive RNA polymerization and promoter recognition in an RNA World.Science, 2021, 371: 1225-+ Processive RNA polymerization and promoter recognition in an RNA World
Early life is thought to have required the self-replication of RNA by RNA replicases. However, how such replicases evolved and subsequently enabled gene expression remains largely unexplored. We engineered and selected a holopolymerase ribozyme that uses a sigma factor-like specificity primer to first recognize an RNA promoter sequence and then, in a second step, rearrange to a processive elongation form. Using its own sequence, the polymerase can also program itself to polymerize from certain RNA promoters and not others. This selective promoter-based polymerization could allow an RNA replicase ribozyme to define "self" from "nonself," an important development for the avoidance of replicative parasites. Moreover, the clamp-like mechanism of this polymerase could eventually enable strand invasion, a critical requirement for replication in the early evolution of life. DOI PubMed
1015. Cross, DJ; Huber, BR; Silverman, MA; Cline, MM; Gill, TB; Cross, CG; Cook, DG; Minoshima, S.Intranasal Paclitaxel Alters Alzheimer's Disease Phenotypic Features in 3xTg-AD Mice.J. Alzheimers Dis., 2021, 83: 379-394 Intranasal Paclitaxel Alters Alzheimer's Disease Phenotypic Features in 3xTg-AD Mice
Alzheimer's disease; axonal transport; cognitive impairment; intranasal drug administration; microtubule stabilization
Background: Microtubule stabilizing drugs, commonly used as anti-cancer therapeutics, have been proposed for treatment of Alzheimer's disease (AD); however, many do not cross the blood-brain barrier. Objective: This research investigated if paclitaxel (PTX) delivered via the intranasal (IN) route could alter the phenotypic progression of AD in 3xTg-AD mice. Methods: We administered intranasal PTX in 3XTg-AD mice (3xTg-AD n = 15, 10 weeks and n = 10, 44 weeks, PTX: 0.6 mg/kg or 0.9%saline (SAL)) at 2-week intervals. After treatment, 3XTg-AD mice underwent manganese-enhanced magnetic resonance imaging to measure in vivo axonal transport. In a separate 3XTg-AD cohort, PTX-treated mice were tested in a radial water tread maze at 52 weeks of age after four treatments, and at 72 weeks of age, anxiety was assessed by an elevated-plus maze after 14 total treatments. Results: PTX increased axonal transport rates in treated 3XTg-AD compared to controls (p <= 0.003). Further investigation using an in vitro neuron model of A beta-induced axonal transport disruption confirmed PTX prevented axonal transport deficits. Confocal microscopy after treatment found fewer phospho-tau containing neurons (5.25 +/- 3.8 versus 8.33 +/- 2.5, p < 0.04) in the CA1, altered microglia, and reduced reactive astrocytes. PTX improved performance of 3xTg-AD on the water tread maze compared to controls and not significantly different from WT (Day 5, 143.8 +/- 43 versus 91.5 +/- 77s and Day 12, 138.3 +/- 52 versus 107.7 +/- 75s for SAL versus PTX). Elevated plus maze revealed that PTX-treated 3xTg-AD mice spent more time exploring open arms (Open arm 129.1 +/- 80 versus 20.9 +/- 31s for PTX versus SAL, p <= 0.05). Conclusion: Taken collectively, these findings indicate that intranasal-administered microtubule-stabilizing drugs may offer a potential therapeutic option for treating AD. DOI PubMed
1012. Davies, SW; Putnam, HM; Ainsworth, T; Baum, JK; Bove, CB; Crosby, SC; Côté, IM; Duplouy, A; Fulweiler, RW; Griffin, AJ; Hanley, TC; Hill, T; Humanes, A; Mangubhai, S; Metaxas, A; Parker, LM; Rivera, HE; Silbiger, NJ; Smith, NS; Spalding, AK; Traylor-Knowles, N; Weigel, BL; Wright, RM; Bates, AE.Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science.PLoS. Biol., 2021, 19 Promoting inclusive metrics of success and impact to dismantle a discriminatory reward system in science
Success and impact metrics in science are based on a system that perpetuates sexist and racist "rewards" by prioritizing citations and impact factors. These metrics are flawed and biased against already marginalized groups and fail to accurately capture the breadth of individuals' meaningful scientific impacts. We advocate shifting this outdated value system to advance science through principles of justice, equity, diversity, and inclusion. We outline pathways for a paradigm shift in scientific values based on multidimensional mentorship and promoting mentee well-being. These actions will require collective efforts supported by academic leaders and administrators to drive essential systemic change. DOI PubMed
1011. Dinsdale, NL; Crespi, BJ.Endometriosis and polycystic ovary syndrome are diametric disorders.Evol. Appl., 2021, 14: 1693-1715 Endometriosis and polycystic ovary syndrome are diametric disorders
anogenital distance; endometriosis; folliculogenesis; polycystic ovary syndrome; testosterone
Evolutionary and comparative approaches can yield novel insights into human adaptation and disease. Endometriosis and polycystic ovary syndrome (PCOS) each affect up to 10% of women and significantly reduce the health, fertility, and quality of life of those affected. PCOS and endometriosis have yet to be considered as related to one another, although both conditions involve alterations to prenatal testosterone levels and atypical functioning of the hypothalamic-pituitary-gonadal (HPG) axis. Here, we propose and evaluate the novel hypothesis that endometriosis and PCOS represent extreme and diametric (opposite) outcomes of variation in HPG axis development and activity, with endometriosis mediated in notable part by low prenatal and postnatal testosterone, while PCOS is mediated by high prenatal testosterone. This diametric disorder hypothesis predicts that, for characteristics shaped by the HPG axis, including hormonal profiles, reproductive physiology, life-history traits, and body morphology, women with PCOS and women with endometriosis will manifest opposite phenotypes. To evaluate these predictions, we review and synthesize existing evidence from developmental biology, endocrinology, physiology, life history, and epidemiology. The hypothesis of diametric phenotypes between endometriosis and PCOS is strongly supported across these diverse fields of research. Furthermore, the contrasts between endometriosis and PCOS in humans parallel differences among nonhuman animals in effects of low versus high prenatal testosterone on female reproductive traits. These findings suggest that PCOS and endometriosis represent maladaptive extremes of both female life-history variation and expression of sexually dimorphic female reproductive traits. The diametric disorder hypothesis for endometriosis and PCOS provides novel, unifying, proximate, and evolutionary explanations for endometriosis risk, synthesizes diverse lines of research concerning the two most common female reproductive disorders, and generates future avenues of research for improving the quality of life and health of women. DOI PubMed
1010. Dominguez-Zamora, FJ; Marigold, DS.Motives driving gaze and walking decisions.Curr. Biol., 2021, 31: 1632-+ Motives driving gaze and walking decisions
To navigate complex environments, people must decide how to direct gaze to acquire relevant information and decide where, when, and how to move the body. Recent work supports the idea that gaze may be directed to reduce task-relevant environmental uncertainty and to ensure movement accuracy based on the cost (or effort) to move the body and maintain balance. During walking, these two factors may compete for gaze allocation and explain how we make decisions about where to step. Using a forced-choice walking paradigm, where we manipulated the visual uncertainty (simulating uncertain terrain characteristics) and motor cost associated with specific step-target choices, we examined the motives driving gaze and step decisions. We characterized each individual's distinct gaze behavior based on their sensitivity to changes in visual uncertainty, which predicted step-choice behavior when foot-placement accuracy was important to the task. We show that individuals who tended to look at both target choices as visual uncertainty increased prioritized stepping onto the more certain location after looking at it longer, even at the expense of increased motor cost. In contrast, individuals who tended to look at only one of the target choices as visual uncertainty increased preferred to step on the target that minimized motor cost. Overall, we demonstrate that how a person explores the environment with their eyes dictates where they step. These gaze and step decisions may relate to the value a person assigns to information gain, being certain of their actions, and conserving energy. DOI PubMed
1009. Dulvy, NK; Pacoureau, N; Rigby, CL; Pollom, RA; Jabado, RW; Ebert, DA; Finucci, B; Pollock, CM; Cheok, J; Derrick, DH; Herman, KB; Sherman, CS; VanderWright, WJ; Lawson, JM; Walls, RHL; Carlson, JK; Charvet, P; Bineesh, KK; Fernando, D; Ralph, GM; Matsushiba, JH; Hilton-Taylor, C; Fordham, SV; Simpfendorfer, CA.Overfishing drives over one-third of all sharks and rays toward a global extinction crisis.Curr. Biol., 2021, 31: 4773-+ Overfishing drives over one-third of all sharks and rays toward a global extinction crisis
The scale and drivers of marine biodiversity loss are being revealed by the International Union for Conservation of Nature (IUCN) Red List assessment process. We present the first global reassessment of 1,199 species in Class Chondrichthyes-sharks, rays, and chimeras. The first global assessment (in 2014) concluded that one-quarter (24%) of species were threatened. Now, 391 (32.6%) species are threatened with extinction. When this percentage of threat is applied to Data Deficient species, more than one-third (37.5%) of chondrichthyans are estimated to be threatened, with much of this change resulting from new information. Three species are Critically Endangered (Possibly Extinct), representing possibly the first globalmarine fish extinctions due to overfishing. Consequently, the chondrichthyan extinction rate is potentially 25 extinctions per million species years, comparable to that of terrestrial vertebrates. Overfishing is the universal threat affecting all 391 threatened species and is the sole threat for 67.3% of species and interacts with three other threats for the remaining third: loss and degradation of habitat (31.2% of threatened species), climate change (10.2%), and pollution (6.9%). Species are disproportionately threatened in tropical and subtropical coastal waters. Science-based limits on fishing, effective marine protected areas, and approaches that reduce or eliminate fishing mortality are urgently needed to minimize mortality of threatened species and ensure sustainable catch and trade of others. Immediate action is essential to prevent further extinctions and protect the potential for food security and ecosystem functions provided by this iconic lineage of predators. DOI PubMed
1008. Dunic, JC; Brown, CJ; Connolly, R; Turschwell, MP; Côté, IM.Long-term declines and recovery of meadow area across the world's seagrass bioregions.Glob. Change Biol., 2021, 27: 4096-4109 Long-term declines and recovery of meadow area across the world's seagrass bioregions
attribution; coastal ecosystems; global change; meta-analysis; reconstruction; seagrass; time series
As human impacts increase in coastal regions, there is concern that critical habitats that provide the foundation of entire ecosystems are in decline. Seagrass meadows face growing threats such as poor water quality and coastal development. To determine the status of seagrass meadows over time, we reconstructed time series of meadow area from 175 studies that surveyed 547 sites around the world. We found an overall trajectory of decline in all seven bioregions with a global net loss of 5602 km(2) (19.1% of surveyed meadow area) occurring since 1880. Declines have typically been non-linear, with rapid and historical losses observed in several bioregions. The greatest net losses of area occurred in four bioregions (Tropical Atlantic, Temperate North Atlantic East, Temperate Southern Oceans and Tropical Indo-Pacific), with declining trends being the slowest and most consistent in the latter two bioregions. In some bioregions, trends have recently stabilised or reversed. Losses, however, still outweigh gains. Despite consistent global declines, meadows show high variability in trajectories, within and across bioregions, highlighting the importance of local context. Studies identified 12 different drivers of meadow area change, with coastal development and water quality as the most commonly cited. Overall, however, attributions were primarily descriptive and only 10% of studies used inferential attributions. Although ours is the most comprehensive dataset to date, it still represents only one-tenth of known global seagrass extent, with conspicuous historical and geographic biases in sampling. It therefore remains unclear whether the bioregional patterns of change documented here reflect changes in the world's unmonitored seagrass meadows. The variability in seagrass meadow trajectories, and the attribution of change to numerous drivers, suggest we urgently need to improve understanding of the causes of seagrass meadow loss if we are to improve local-scale management. DOI PubMed
1007. Ens, NJ; Lim, EG; Howard, BR; Eastham, TM.A comparison of the predatory impacts of an invasive and native crab species using a functional response approach.Biol. Invasions, 2021, 23: 2329-2336 A comparison of the predatory impacts of an invasive and native crab species using a functional response approach
European green crab; Pacific oyster; Aquaculture; Carcinus maenas; Cancer productus; Crassostrea gigas
The European green crab (Carcinus maenas) is invasive on the West coast of North America, but the ecological consequences of this invasion remain poorly understood. Comparative functional response analysis has arisen as a method of elucidating ecological consequences of invasive species by comparing the impact of these species to native analogues. Through comparative functional response experiments of green crabs and native red rock crabs (Cancer productus) we found that green crab predation increased asymptotically (Type II functional response) when fed increasing densities of Pacific oysters (Magallana gigas), while red rock crab predation displayed a sigmoidal (Type III) response. At high oyster densities red rock crabs consume more Pacific oysters than green crabs do, due to their reduced handling time, though green crabs consume more Pacific oysters relative to their size than red rock crabs. However, compared to red rock crabs, green crabs consume more oysters at low prey densities, which implies that they have a larger, potentially destabilizing impact on low densities of Pacific oysters. As green crabs continue to spread across the West coast of North America, Pacific oysters will face increased predation pressure. Our results show the advantage of using functional response analysis to compare density dependent predation between an invasive species and a native species to predict the ecological consequences of invasions. DOI
1006. Finucci, B; Cheok, J; Ebert, DA; Herman, K; Kyne, PM; Dulvy, NK.Ghosts of the deep - Biodiversity, fisheries, and extinction risk of ghost sharks.Fish. Fish., 2021, 22: 391-412 Ghosts of the deep - Biodiversity, fisheries, and extinction risk of ghost sharks
by‐ catch; chimaera; chondrichthyan; data deficiency; holocephali; IUCN Red List; liver oil; sustainable fisheries
Ghost sharks (subclass Holocephali) remain a largely data-poor group of cartilaginous fishes. The general paucity of attention may partially be related to identification and unresolved taxonomic issues, occurrence in the deep oceans, and their low value and interest in fisheries (which some notable exceptions). Here, we synthesize and assess the extinction risk of all known extant ghost sharks (52 species) by applying the IUCN Red List of Threatened Species Categories and Criteria. Ghost sharks have a low proportion of threatened (8%) and Near Threatened (8%) species, with most species (69%) assessed as Least Concern. The group still exhibits some data deficiency (15%), and biological information is lacking for most species. Endemism is high, with 37% of species known from only one location or one country. Species richness was highest in the Northeast Atlantic, off the northwest coast of Africa (Morocco to Mauritania), the East China Sea, New Zealand and off the northwest coast of South America (Ecuador and Peru). Ghost sharks are predominately taken as by-catch, but some targeted fishing and/or retention for the liver oil trade occurs. Species-specific reporting, monitoring and management are required to assess population trends, and further investigation is needed on trade and use, particularly for higher risk species including the sicklefin chimaeras (genus Neoharriotta) and the American Elephantfish (Callorhynchus callorhynchus, Callorhinidae). DOI
1005. Flamarique, IN; Fujihara, R; Yazawa, R; Bolstad, K; Gowen, B; Yoshizaki, G.Disrupted eye and head development in rainbow trout with reduced ultraviolet (sws1) opsin expression.J. Comp. Neurol., 2021, 529: 3013-3031 Disrupted eye and head development in rainbow trout with reduced ultraviolet (sws1) opsin expression
AB5407; CRISPR; Cas9; fish; photoreceptor; retina; sws1 antiserum; visual opsin
Visual opsins are proteins expressed by retinal photoreceptors that capture light to begin the process of phototransduction. In vertebrates, the two types of photoreceptors (rods and cones) express one or multiple opsins and are distributed in variable patterns across the retina. Some cones form opsin retinal gradients, as in the mouse, whereas others form more demarcated opsin domains, as in the lattice-like mosaic retinas of teleost fishes. Reduced rod opsin (rh1) expression in mouse, zebrafish, and African clawed frog results in lack of photoreceptor outer segments (i.e., the cilium that houses the opsins) and, in the case of the mouse, to retinal degeneration. The effects of diminished cone opsin expression have only been studied in the mouse where knockout of the short-wavelength sensitive 1 (sws1) opsin leads to ventral retinal cones lacking outer segments, but no retinal degeneration. Here we show that, following CRISPR/Cas9 injections that targeted knockout of the sws1 opsin in rainbow trout, fish with diminished sws1 opsin expression exhibited a variety of developmental defects including head and eye malformations, underdeveloped outer retina, mislocalized opsin expression, cone degeneration, and mosaic irregularity. All photoreceptor types were affected even though sws1 is only expressed in the single cones of wild fish. Our results reveal unprecedented developmental defects associated with diminished cone opsin expression and suggest that visual opsin genes are involved in regulatory processes that precede photoreceptor differentiation. DOI PubMed
1004. Fremlin, KM; Elliott, JE; Martin, PA; Harner, T; Saini, A; Gobas, FAPC.Fugacity-Based Trophic Magnification Factors Characterize Bioaccumulation of Cyclic Methyl Siloxanes within an Urban Terrestrial Avian Food Web: Importance of Organism Body Temperature and Composition.Environ. Sci. Technol., 2021, 55: 13932-13941 Fugacity-Based Trophic Magnification Factors Characterize Bioaccumulation of Cyclic Methyl Siloxanes within an Urban Terrestrial Avian Food Web: Importance of Organism Body Temperature and Composition
terrestrial food web; cyclic methyl siloxanes; fugacity; trophic magnification; thermodynamic biomagnification; body temperature; endothermic and poikilothermic organisms
Trophic magnification of cyclic volatile methyl siloxanes (cVMS) in a terrestrial food web was investigated by measuring concentrations of octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), and dodecamethylcyclohexasiloxane (D6) and two reference chemicals within air and biota samples from an avian food web located in a mixed urban-agricultural landscape. Terrestrial trophic magnification factors derived from lipid normalized concentrations (TMFLs) for D5 and D6 were 0.94 (0.17 SE) and 1.1 (0.23 SE) and not statistically different from 1 (p > 0.05); however, the TMFL of D4 was 0.62 (0.11 SE) and statistically less than 1 (p < 0.001). TMFLs of PCB-153 and p,p'-DDE were 5.6 (2.2 SE) and 6.1 (2.8 SE) and statistically greater than 1 (p < 0.001). TMFLs of cVMS in this terrestrial system were similar to those reported in aquatic systems. However, trophic magnification factors derived on a fugacity basis (TMFFs), which recognize differences in body temperature and lipid composition between organisms, were greater than corresponding TMFLs primarily because a temperature-induced thermodynamic biomagnification of hydrophobic chemicals occurs when endothermic organisms consume poikilothermic organisms. Therefore, we recommend that biomagnification studies of food webs including endothermic and poikilothermic organisms incorporate differences in body temperature and tissue composition to accurately characterize the biomagnification potential of chemicals. DOI PubMed
1003. Galpern, P; Best, LR; Devries, JH; Johnson, SA.Wild bee responses to cropland landscape complexity are temporally-variable and taxon-specific: Evidence from a highly replicated pseudo-experiment.Agric. Ecosyst. Environ., 2021, 322 Wild bee responses to cropland landscape complexity are temporally-variable and taxon-specific: Evidence from a highly replicated pseudo-experiment
Landscape ecology; Landscape complexity; Pollination services; Prairie; Alberta, Canada; Phenology; Apoidea; Bombus
Wild bees may benefit from the restoration of natural areas in agricultural regions. The abundance and diversity of wild bee species responds to the amount of nesting and foraging habitat, but it is less clear how the distribution of these resources (e.g., the landscape complexity) may affect bees. We implemented a pseudo-experiment to disentangle the effects of three components of landscape complexity for wild bees in a Canadian Prairie cropland region. We used an algorithm to identify 146 sites that minimized correlations in indices of patch richness (i.e., the diversity in land cover types) and contagion (i.e., their degree of interspersion), and that collectively captured a cross-section of landscape contexts that differed in the relative proportion of cropland to other non-crop land covers. We trapped bees at these locations repeatedly over time (1119 unique collection events; equivalent to 10,471 trap-days over two consecutive years), identifying 22,493 bees of 213 taxa, in order to model trends for bees at different times of the season. We found that increasing patch richness may support a greater number of bee taxa, but individual bee taxa varied considerably in their response to components of landscape complexity. The effect on the total abundance of wild bees was temporally-variable, with the amount of cropland positively associated with abundance earlier in the season when mass-flowering crops are in bloom, and negatively later in the season when semi-natural areas are likely to provide the most forage. The response of bee abundance to contagion also varied temporally, and demonstrated a "humped" effect later in the growing season, suggesting there is an optimum in the complementary resources provided by adjacent habitat types. Our study shows that increasing the amount or diversity of non-crop land covers in this region is not likely to have a consistent effect for the majority of species across the season. We argue that modifying croplands to support wild bees is likely to be a complex task, requiring study of the functional responses to landscape of bee species present in the region, and their interactions with the phenological variability in resources. DOI
1002. Ghovanloo, MR; Choudhury, K; Bandaru, TS; Fouda, MA; Rayani, K; Rusinova, R; Phaterpekar, T; Nelkenbrecher, K; Watkins, AR; Poburko, D; Thewalt, J; Andersen, OS; Delemotte, L; Goodchild, SJ; Ruben, PC.Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity.J. Gen. Physiol., 2021, 153 Cannabidiol inhibits the skeletal muscle Nav1.4 by blocking its pore and by altering membrane elasticity
Cannabidiol (CBD) is the primary nonpsychotropic phytocannabinoid found in Cannabis sativa, which has been proposed to be therapeutic against many conditions, including muscle spasms. Among its putative targets are voltage-gated sodium channels (Navs), which have been implicated in many conditions. We investigated the effects of CBD on Nav1.4, the skeletal muscle Nav subtype. We explored direct effects, involving physical block of the Nav pore, as well as indirect effects, involving modulation of membrane elasticity that contributes to Nav inhibition. MD simulations revealed CBD's localization inside the membrane and effects on bilayer properties. Nuclear magnetic resonance (NMR) confirmed these results, showing CBD localizing below membrane headgroups. To determine the functional implications of these findings, we used a gramicidinbased fluorescence assay to show that CBD alters membrane elasticity or thickness, which could alter Nav function through bilayer-mediated regulation. Site-directed mutagenesis in the vicinity of the Nav1.4 pore revealed that removing the local anesthetic binding site with F1586A reduces the block of INa by CBD. Altering the fenestrations in the bilayer-spanning domain with Nav1.4-WWWW blocked CBD access from the membrane into the Nav1.4 pore (as judged by MD). The stabilization of inactivation, however, persisted in WWWW, which we ascribe to CBD-induced changes in membrane elasticity. To investigate the potential therapeutic value of CBD against Nav1.4 channelopathies, we used a pathogenic Nav1.4 variant, P1158S, which causes myotonia and periodic paralysis. CBD reduces excitability in both wild-type and the P1158S variant. Our in vitro and in silico results suggest that CBD may have therapeutic value against Nav1.4 hyperexcitability. DOI PubMed
1001. Ghovanloo, MR; Ruben, PC.Cannabidiol and Sodium Channel Pharmacology: General Overview, Mechanism, and Clinical Implications.Neuroscientist, 2021, Cannabidiol and Sodium Channel Pharmacology: General Overview, Mechanism, and Clinical Implications
voltage-gated sodium channels; cannabidiol; channelopathies; Dravet syndrome; myotonia
Voltage-gated sodium (Nav) channels initiate action potentials in excitable tissues. Altering these channels' function can lead to many pathophysiological conditions. Nav channels are composed of several functional and structural domains that could be targeted pharmacologically as potential therapeutic means against various neurological conditions. Mutations in Nav channels have been suggested to underlie various clinical syndromes in different tissues and in association with conditions ranging from epileptic to muscular problems. Treating those mutations that increase the excitability of Nav channels requires inhibitors that could effectively reduce channel firing. The main non-psychotropic constituent of the cannabis plant, cannabidiol (CBD), has recently gained interest as a viable compound to treat some of the conditions that are associated with Nav malfunctions. In this review, we discuss an overview of Nav channels followed by an in-depth description of the interactions of CBD and Nav channels. We conclude with some clinical implications of CBD use against Nav hyperexcitability based on a series of preclinical studies published to date, with a focus on Nav/CBD interactions. DOI PubMed
1000. Godwin, SC; Krkosek, M; Reynolds, JD; Bateman, AW.Bias in self-reported parasite data from the salmon farming industry.Ecol. Appl., 2021, 31 Bias in self-reported parasite data from the salmon farming industry
Caligus clemensi; environmental compliance; environmental management; environmental policy; industry data; Lepeophtheirus salmonis; Pacific salmon; policy implementation; salmon farms; salmon lice; sea lice; self‐ reported data
Many industries are required to monitor themselves in meeting regulatory policies intended to protect the environment. Self-reporting of environmental performance can place the cost of monitoring on companies rather than taxpayers, but there are obvious risks of bias, often addressed through external audits or inspections. Surprisingly, there have been relatively few empirical analyses of bias in industry self-reported data. Here, we test for bias in reporting of environmental compliance data using a unique data set from Canadian salmon farms, where companies monitor the number of parasitic sea lice on fish in open sea pens, in order to minimize impacts on wild fish in surrounding waters. We fit a hierarchical population-dynamics model to these sea-louse count data using a Bayesian approach. We found that the industry's monthly counts of two sea-louse species, Caligus clemensi and Lepeophtheirus salmonis, increased by a factor of 1.95 (95% credible interval: 1.57, 2.42) and 1.18 (1.06, 1.31), respectively, in months when counts were audited by the federal fisheries department. Consequently, industry sea-louse counts are less likely to trigger costly but mandated delousing treatments intended to avoid sea-louse epidemics in wild juvenile salmon. These results highlight the potential for combining external audits of industry self-reported data with analyses of their reporting to maintain compliance with regulations, achieve intended conservation goals, and build public confidence in the process. DOI PubMed
999. Greenberg, DA; Palen, WJ.Hydrothermal physiology and climate vulnerability in amphibians.Proc. R. Soc. B-Biol. Sci., 2021, 288 Hydrothermal physiology and climate vulnerability in amphibians
dehydration; desiccation; ecophysiology; frogs; global change; thermal performance
Concerns over the consequences of global climate change for biodiversity have spurred a renewed interest in organismal thermal physiology. However, temperature is only one of many environmental axes poised to change in the future. In particular, hydrologic regimes are also expected to shift concurrently with temperature in many regions, yet our understanding of how thermal and hydration physiology jointly affect performance and fitness is still limited for most taxonomic groups. Here, we investigated the relationship between functional performance, hydration state and temperature in three ecologically distinct amphibians, and compare how temperature and water loss can concurrently limit activity under current climate conditions. We found that performance was maintained across a broad range of hydration states in all three species, but then declines abruptly after a threshold of 20-30% mass loss. This rapid performance decline was accelerated when individuals were exposed to warmer temperatures. Combining our empirical hydrothermal performance curves with species-specific biophysical models, we estimated that dehydration can increase restrictions on species' activity by up to 60% compared to restriction by temperature alone. These results illustrate the importance of integrating species' hydration physiology into forecasts of climate vulnerability, as omitting this axis may significantly underestimate the effects of future climate change on Earth's biological diversity. DOI PubMed
998. Greenberg, DA; Pyron, RA; Johnson, LGW; Upham, NS; Jetz, W; Mooers, AO.Evolutionary legacies in contemporary tetrapod imperilment.Ecol. Lett., 2021, 24: 2464-2476 Evolutionary legacies in contemporary tetrapod imperilment
diversification; evolutionary age; extinction risk; extinction selectivity; phylogenetics; range dynamics; turnover; vertebrates
The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns - but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing similar to 30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life. DOI PubMed
996. Guzman, LM; Johnson, SA; Mooers, AO; M'Gonigle, LK.Using historical data to estimate bumble bee occurrence: Variable trends across species provide little support for community-level declines.Biol. Conserv., 2021, 257 Using historical data to estimate bumble bee occurrence: Variable trends across species provide little support for community-level declines
Occupancy models; Bumble bees& nbsp; species' declines
Bumble bees are globally important pollinators, especially in temperate regions, and evidence suggests that many species are declining. One recent high profile study by Soroye et al. (2020) applied occupancy models to dated historical collection data to quantify declines across North America and Europe. The authors modelled 66 species across a set of sites spanning both North America and Europe, rather than confining species to sites where they might be expected to occur. In addition, they inferred non-detections for time intervals where there is no evidence that the site was visited (by forcing every site to have exactly 3 visits in each era). We use simulated data to (i) investigate the validity of methods used in that study and (ii) test whether a multi-species framework that incorporates species' ranges and site visitation histories produces better estimates. We show that the method used by Soroye et al. (2020) yields biased estimates of declines, whereas our framework does not. We use such a model to provide revised and appreciably lower estimates for bumble bee community declines, with speciesspecific trends more closely matching classifications from IUCN. The species level trends we provide can help inform future species-at-risk assessments. Well-parameterized occupancy models may be a powerful tool for assessing species-wide trends using curated historical collection data. DOI
995. Guzman, LM; Trzcinski, MK; Barberis, IM; Cereghino, R; Srivastava, DS; Gilbert, B; Pillar, VD; de Omena, PM; MacDonald, AAM; Corbara, B; Leroy, C; Bautista, FO; Romero, GQ; Kratina, P; Debastiani, VJ; Gonialves, AZ; Marino, NAC; Farjalla, VF; Richardson, BA; Richardson, MJ; Dezerald, O; Piccoli, GCO; Jocque, M; Montero, G.Climate influences the response of community functional traits to local conditions in bromeliad invertebrate communities.Ecography, 2021, 44: 440-452 Climate influences the response of community functional traits to local conditions in bromeliad invertebrate communities
bromeliads; climatic variation; functional traits; local conditions; macroinvertebrates
Functional traits determine an organism's performance in a given environment and as such determine which organisms will be found where. Species respond to local conditions, but also to larger scale gradients, such as climate. Trait ecology links these responses of species to community composition and species distributions. Yet, we often do not know which environmental gradients are most important in determining community trait composition at either local or biogeographical scales, or their interaction. Here we quantify the relative contribution of local and climatic conditions to the structure and composition of functional traits found within bromeliad invertebrate communities. We conclude that climate explains more variation in invertebrate trait composition within bromeliads than does local conditions. Importantly, climate mediated the response of traits to local conditions; for example, invertebrates with benthic life-history traits increased with bromeliad water volume only under certain precipitation regimes. Our ability to detect this and other patterns hinged on the compilation of multiple fine-grained datasets, allowing us to contrast the effect of climate versus local conditions. We suggest that, in addition to sampling communities at local scales, we need to aggregate studies that span large ranges in climate variation in order to fully understand trait filtering at local, regional and global scales. DOI
994. Hepp, M; Palsson, E; Thomsen, SK; Green, DJ.Predicting the effects of reservoir water level management on the reproductive output of a riparian songbird.PLoS One, 2021, 16 Predicting the effects of reservoir water level management on the reproductive output of a riparian songbird
Dams and reservoirs alter natural water flow regimes with adverse effects on natural ecosystems. Quantifying and reducing these effects are important as global demands for energy and water, and the number of dams and reservoir, increase. However, costs and logistic constraints typically preclude experimental assessment of reservoir effects on the environment. We developed a stochastic individual-based model (IBM), parameterized using empirical data, to estimate the annual productivity of yellow warblers that breed in riparian habitat within the footprint of the Arrow Lakes Reservoir in British Columbia, Canada. The IBM incorporated information on breeding phenology, nest site selection, brood parasitism, daily nest survival, re-nesting probabilities and post-fledging survival. We used the IBM to estimate the effect of four different water management scenarios on annual productivity. We found that the IBM accurately estimated average nest success (0.39 +/- 0.10 SD), the proportion of females that produced at least one fledgling during a breeding season (0.56 +/- 0.11), and annual fledging success (2.06 +/- 0.43) under current conditions. The IBM estimated that reservoir operations currently reduce the annual productivity of this population by 37%, from an average of 1.62 to 1.06 independent young/female. Delaying when reservoir water levels reach 435m asl (the minimum elevation occupied by yellow warblers) by approximately 2 weeks was predicted to increase annual productivity to 1.44 independent young/female. The standardized effect on annual productivity of reducing the maximum elevation of the reservoir so that yellow warbler habitat is not inundated (Cohen's d = 1.52) or delaying when water is stored (Cohen's d = 0.83) was primarily driven by inundation effects on post-fledging survival. Reservoir operation effects on breeding birds will be species specific, but this IBM can easily be modified to allow the environmental impacts on the entire breeding bird community to be incorporated into water management decisions. DOI PubMed
993. Hoffarth, ER; Haatveit, KC; Kuatsjah, E; MacNeil, GA; Saroya, S; Walsby, CJ; Eltis, LD; Houk, KN; Garcia-Borras, M; Ryan, KS.A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases.Proc. Natl. Acad. Sci. U. S. A., 2021, 118 A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases
pyridoxal phosphate; oxidase; X-ray crystallography; water; molecular dynamics
The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the Pseudoalteromonas luteoviolacea indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4 ' carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases. DOI PubMed
992. Husak, JF; Fuxjager, MJ; Johnson, MA; Vitousek, MN; Donald, JW; Francis, CD; Goymann, W; Hau, M; Kircher, BK; Knapp, R; Martin, LB; Miller, ET; Schoenle, LA; Williams, TD.Life history and environment predict variation in testosterone across vertebrates.Evolution, 2021, 75: 1003-1010 Life history and environment predict variation in testosterone across vertebrates
Endocrine systems act as key intermediaries between organisms and their environments. This interaction leads to high variability in hormone levels, but we know little about the ecological factors that influence this variation within and across major vertebrate groups. We study this topic by assessing how various social and environmental dynamics influence testosterone levels across the entire vertebrate tree of life. Our analyses show that breeding season length and mating system are the strongest predictors of average testosterone concentrations, whereas breeding season length, environmental temperature, and variability in precipitation are the strongest predictors of within-population variation in testosterone. Principles from small-scale comparative studies that stress the importance of mating opportunity and competition on the evolution of species differences in testosterone levels, therefore, likely apply to the entire vertebrate lineage. Meanwhile, climatic factors associated with rainfall and ambient temperature appear to influence variability in plasma testosterone, within a given species. These results, therefore, reveal how unique suites of ecological factors differentially explain scales of variation in circulating testosterone across mammals, birds, reptiles, amphibians, and fishes. DOI PubMed
991. Jackson, EW; Wilhelm, RC; Johnson, MR; Lutz, HL; Danforth, I; Gaydos, JK; Hart, MW; Hewson, I.Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin.J. Virol., 2021, 95 Diversity of Sea Star-Associated Densoviruses and Transcribed Endogenous Viral Elements of Densovirus Origin
densovirus; parvovirus; sea star wasting disease; viral discovery; viral metagenomics; ssDNA viruses
A viral etiology of sea star wasting syndrome (SSWS) was originally explored with virus-sized material challenge experiments, field surveys, and metagenomics, leading to the conclusion that a densovirus is the predominant DNA virus associated with this syndrome and, thus, the most promising viral candidate pathogen. Single-stranded DNA viruses are, however, highly diverse and pervasive among eukaryotic organisms, which we hypothesize may confound the association between densoviruses and SSWS. To test this hypothesis and assess the association of densoviruses with SSWS, we compiled past metagenomic data with new metagenomic-derived viral genomes from sea stars collected from Antarctica, California, Washington, and Alaska. We used 179 publicly available sea star transcriptomes to complement our approaches for densovirus discovery. Lastly, we focus the study on sea star-associated densovirus (SSaDV), the first sea star densovirus discovered, by documenting its biogeography and putative tissue tropism. Transcriptomes contained only endogenized densovirus elements similar to the NS1 gene, while numerous extant densoviral genomes were recovered from viral metagenomes. SSaDV was associated with nearly all tested species from southern California to Alaska, and in contrast to previous work, we show that SSaDV is one genotype among a high diversity of densoviruses present in sea stars across the West Coast of the United States and globally that are commonly associated with grossly normal (i.e., healthy or asymptomatic) animals. The diversity and ubiquity of these viruses in sea stars confound the original hypothesis that one densovirus is the etiological agent of SSWS. IMPORTANCE The primary interest in sea star densoviruses, specifically SSaDV, has been their association with sea star wasting syndrome (SSWS), a disease that has decimated sea star populations across the West Coast of the United States since 2013. The association of SSaDV with SSWS was originally drawn from metagenomic analysis, which was further studied through field surveys using quantitative PCR (qPCR), with the conclusion that it was the most likely viral candidate in the metagenomic data based on its representation in symptomatic sea stars compared to asymptomatic sea stars. We reexamined the original metagenomic data with additional genomic data sets and found that SSaDV was 1 of 10 densoviruses present in the original data set and was no more represented in symptomatic sea stars than in asymptomatic sea stars. Instead, SSaDV appears to be a widespread, generalist virus that exists among a large diversity of densoviruses present in sea star populations. DOI PubMed
990. Jeng, SCY; Trachman, RJ; Weissenboeck, F; Truong, L; Link, KA; Jepsen, MDE; Knutson, JR; Andersen, ES; Ferre-D'Amare, AR; Unrau, PJ.Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET.RNA, 2021, 27: 433-444 Fluorogenic aptamers resolve the flexibility of RNA junctions using orientation-dependent FRET
RNA; fluorescent aptamer; FRET; riboswitch; helical junction; G-quadruplex
To further understand the transcriptome, new tools capable of measuring folding, interactions, and localization of RNA are needed. Although Forster resonance energy transfer (FRET) is an angle- and distance-dependent phenomenon, the majority of FRET measurements have been used to report distances, by assuming rotationally averaged donor-acceptor pairs. Angle-dependent FRET measurements have proven challenging for nucleic acids due to the difficulties in incorporating fluorophores rigidly into local substructures in a biocompatible manner. Fluorescence turn-on RNA aptamers are genetically encodable tags that appear to rigidly confine their cognate fluorophores, and thus have the potential to report angular-resolved FRET. Here, we use the fluorescent aptamers Broccoli and Mango-III as donor and acceptor, respectively, to measure the angular dependence of FRET. Joining the two fluorescent aptamers by a helix of variable length allowed systematic rotation of the acceptor fluorophore relative to the donor. FRET oscillated in a sinusoidal manner as a function of helix length, consistent with simulated data generated from models of oriented fluorophores separated by an inflexible helix. Analysis of the orientation dependence of FRET allowed us to demonstrate structural rigidification of the NiCo riboswitch upon transition metal-ion binding. This application of fluorescence turn-on aptamers opens the way to improved structural interpretation of ensemble and single-molecule FRET measurements of RNA. DOI PubMed
989. Kemp, JM; Whittaker, DG; Venkateshappa, R; Pang, ZK; Johal, R; Sergeev, V; Tibbits, GF; Mirams, GR; Claydon, TW.Electrophysiological characterization of the hERG R56Q LQTS variant and targeted rescue by the activator RPR260243.J. Gen. Physiol., 2021, 153 Electrophysiological characterization of the hERG R56Q LQTS variant and targeted rescue by the activator RPR260243
Human Ether-a`-go-go (hERG) channels contribute to cardiac repolarization, and inherited variants or drug block are associated with long QT syndrome type 2 (LQTS2) and arrhythmia. Therefore, hERG activator compounds present a therapeutic opportunity for targeted treatment of LQTS. However, a limiting concern is over-activation of hERG resurgent current during the action potential and abbreviated repolarization. Activators that slow deactivation gating (type I), such as RPR260243, may enhance repolarizing hERG current during the refractory period, thus ameliorating arrhythmogenicity with reduced early repolarization risk. Here, we show that, at physiological temperature, RPR260243 enhances hERG channel repolarizing currents conducted in the refractory period in response to premature depolarizations. This occurs with little effect on the resurgent hERG current during the action potential. The effects of RPR260243 were particularly evident in LQTS2-associated R56Q mutant channels, whereby RPR260243 restored WT-like repolarizing drive in the early refractory period and diastolic interval, combating attenuated protective currents. In silico kinetic modeling of channel gating predicted little effect of the R56Q mutation on hERG current conducted during the action potential and a reduced repolarizing protection against afterdepolarizations in the refractory period and diastolic interval, particularly at higher pacing rates. These simulations predicted partial rescue from the arrhythmic effects of R56Q by RPR260243 without risk of early repolarization. Our findings demonstrate that the pathogenicity of some hERG variants may result from reduced repolarizing protection during the refractory period and diastolic interval with limited effect on action potential duration, and that the hERG channel activator RPR260243 may provide targeted antiarrhythmic potential in these cases. DOI PubMed
988. Kim, B; Molina, R; Jensen, G; Poburko, D.A differentiated Ca2+ signalling phenotype has minimal impact on myocardin expression in an automated differentiation assay using A7r5 cells.Cell Calcium, 2021, 96 A differentiated Ca2+ signalling phenotype has minimal impact on myocardin expression in an automated differentiation assay using A7r5 cells
Smooth muscle; ImageJ; Microscopy; High-content analysis; Differentiation
Vascular smooth muscle cells are unusual in that differentiated, contractile cells possess the capacity to "dedifferentiate" into a synthetic phenotype that is characterized by being replicative, secretory, and migratory. One aspect of this phenotypic modulation is a shift from voltage-gated Ca2+ signalling in electrically coupled, differentiated cells to increased dependence on store-operated Ca2+ entry and sarcoplasmic reticulum Ca2+ release in synthetic cells. Conversely, an increased voltage-gated Ca2+ entry is seen when proliferating A7r5 smooth muscle cells quiesce. We asked whether this change in Ca2+ signalling was linked to changes in the expression of the phenotype-regulating transcriptional co-activator myocardin or alpha-smooth muscle actin, using correlative epifluorescence Ca2+ imaging and immunocytochemistry. Cells were cultured in growth media (DMEM, 10% serum, 25 mM glucose) or differentiation media (DMEM, 1% serum, 5 mM glucose). Coinciding with growth arrest, A7r5 cells became electrically coupled, and spontaneous Ca2+ signalling showed increasing dependence on L-type voltage-gated Ca2+ channels that were blocked with nifedipine (5 mu M). These synchronized oscillations were modulated by ryanodine receptors, based on their sensitivity to dantrolene (5 mu M). Actively growing cultures had spontaneous Ca2+ transients that were insensitive to nifedipine and dantrolene but were blocked by inhibition of the sarco-endoplasmic reticulum ATPase with cyclopiazonic acid (10 mu M). In cells treated with differentiation media, myocardin and alpha SMA immunoreactivity increased prior to changes in the Ca2+ signalling phenotype, while chronic inhibition of voltage-gated Ca2+ entry modestly increased immunoreactivity of myocardin. Stepwise regression analyses suggested that changes in myocardin expression had a weak relationship with Ca2+ signalling synchronicity, but not frequency or amplitude. In conclusion, we report a 96-well assay and analytical pipeline to study the link between Ca2+ signalling and smooth muscle differentiation. This assay showed that changes in the expression of two molecular differentiation markers (myocardin and alpha SMA) tended to precede changes in the Ca2+ signalling phenotype. DOI PubMed
986. Kong, KYS; Jeng, SCY; Rayyan, B; Unrau, PJ.RNA Peach and Mango: orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands.RNA, 2021, 27: 604-615 RNA Peach and Mango: orthogonal two-color fluorogenic aptamers distinguish nearly identical ligands
RNA; Mango; Peach; TO1-B; TO3-B; orthogonal aptamers; two-color imaging
Two-channel fluorogenic RNA aptamer-based imaging is currently challenging. While we have previously characterized the Mango series of aptamers that bind tightly and specifically to the green fluorophore TO1-Biotin, the next aim was to identify an effective fluorogenic aptamer partner for two-color imaging. A competitive in vitro selection for TO3-Biotin binding aptamers was performed resulting in the Peach I and II aptamers. Remarkably, given that the TO1-Biotin and TO3-Biotin heterocycles differ by only two bridging carbons, these new aptamers exhibit a marked preference for TO3-Biotin binding relative to the iM3 and Mango III A10U aptamers, which preferentially bind TO1-Biotin. Peach I, like Mango I and II, appears to contain a quadruplex core isolated by a GAA boolean AND A type tetraloop-like adaptor from its closing stem. Thermal melts of the Peach aptamers reveal that TO3-Biotin binding is cooperative, while TO1-Biotin binding is not, suggesting a unique and currently uncharacterized mode of ligand differentiation. Using only fluorescent measurements, the concentrations of Peach and Mango aptamers could be reliably determined in vitro. The utility of this orthogonal pair provides a possible route to in vivo two-color RNA imaging. DOI PubMed
985. Konno, RN; Nigam, N; Wakeling, JM.Modelling extracellular matrix and cellular contributions to whole muscle mechanics.PLoS One, 2021, 16 Modelling extracellular matrix and cellular contributions to whole muscle mechanics
Skeletal muscle tissue has a highly complex and heterogeneous structure comprising several physical length scales. In the simplest model of muscle tissue, it can be represented as a one dimensional nonlinear spring in the direction of muscle fibres. However, at the finest level, muscle tissue includes a complex network of collagen fibres, actin and myosin proteins, and other cellular materials. This study shall derive an intermediate physical model which encapsulates the major contributions of the muscle components to the elastic response apart from activation-related along-fibre responses. The micro-mechanical factors in skeletal muscle tissue (eg. connective tissue, fluid, and fibres) can be homogenized into one material aggregate that will capture the behaviour of the combination of material components. In order to do this, the corresponding volume fractions for each type of material need to be determined by comparing the stress-strain relationship for a volume containing each material. This results in a model that accounts for the micro-mechanical features found in muscle and can therefore be used to analyze effects of neuro-muscular diseases such as cerebral palsy or muscular dystrophies. The purpose of this study is to construct a model of muscle tissue that, through choosing the correct material parameters based on experimental data, will accurately capture the mechanical behaviour of whole muscle. This model is then used to look at the impacts of the bulk modulus and material parameters on muscle deformation and strain energy-density distributions. DOI PubMed
984. Kundra, S; Lam, LN; Kajfasz, JK; Casella, LG; Andersen, MJ; Abranches, J; Flores-Mireles, AL; Lemos, JA.c-di-AMP Is Essential for the Virulence of Enterococcus faecalis.Infect. Immun., 2021, 89 c-di-AMP Is Essential for the Virulence of Enterococcus faecalis
c-di-AMP; enterococcus; osmotic stress; pathogenesis; second messenger nucleotide; stress response; urinary tract infection
Second messenger nucleotides are produced by bacteria in response to environmental stimuli and play a major role in the regulation of processes associated with bacterial fitness, including but not limited to osmoregulation, envelope homeostasis, central metabolism, and biofilm formation. In this study, we uncovered the biological significance of c-di-AMP in the opportunistic pathogen Enterococcus faecalis by isolating and characterizing strains lacking genes responsible for c-di-AMP synthesis (cdaA) and degradation (dhhP and gdpP). Using complementary approaches, we demonstrated that either complete loss of c-di-AMP (Delta cdaA strain) or c-di-AMP accumulation (Delta dhhP, Delta gdpP, and Delta dhhP Delta gdpP strains) drastically impaired general cell fitness and virulence of E. Wallis. In particular, the Delta cdaA strain was highly sensitive to envelope-targeting antibiotics, was unable to multiply and quickly lost viability in human serum or urine ex vivo, and was virtually avirulent in an invertebrate (Galleria mellonella) and in two catheter-associated mouse infection models that recapitulate key aspects of enterococcal infections in humans. In addition to evidence linking these phenotypes to altered activity of metabolite and peptide transporters and inability to maintain osmobalance, we found that the attenuated virulence of the AcciaA strain also could be attributed to a defect in Delta cdaA pilus production and activity that severely impaired biofilm formation under both in vitro and in vivo conditions. Collectively, these results demonstrate that c-di-AMP signaling is essential for E. faecalis pathogenesis and a desirable target for drug development. DOI PubMed
983. Lajoie, K; Marigold, DS; Valdes, BA; Menon, C.The potential of noisy galvanic vestibular stimulation for optimizing and assisting human performance.Neuropsychologia, 2021, 152 The potential of noisy galvanic vestibular stimulation for optimizing and assisting human performance
Noisy galvanic vestibular stimulation; Non-invasive brain stimulation; Human performance; Assistive technology; Bilateral vestibulopathy; Parkinson's disease; Motor function
Noisy galvanic vestibular stimulation (nGVS) is an emerging non-invasive brain stimulation technique. It involves applying alternating currents of different frequencies and amplitudes presented in a random, or noisy, manner through electrodes on the mastoid bones behind the ears. Because it directly activates vestibular hair cells and afferents and has an indirect effect on a variety of brain regions, it has the potential to impact many different functions. The objective of this review is twofold: (1) to review how nGVS affects motor, sensory, and cognitive performance in healthy adults; and (2) to discuss potential clinical applications of nGVS. First, we introduce the technique. We then describe the regions receiving and processing vestibular information. Next, we discuss the effects of nGVS on motor, sensory, and cognitive function in healthy adults. Subsequently, we outline its potential clinical applications. Finally, we highlight other electrical stimulation technologies and discuss why nGVS offers an alternative or complementary approach. Overall, nGVS appears promising for optimizing human performance and as an assistive technology, though further research is required. DOI PubMed
982. Lange, EC; Travis, J; Hughes, KA; M'Gonigle, LK.Can You Trust Who You See? The Evolution of Socially Cued Anticipatory Plasticity.Am. Nat., 2021, 197: E129-E142 Can You Trust Who You See? The Evolution of Socially Cued Anticipatory Plasticity
social environment; phenotypic plasticity; alternative phenotypes; fluctuating environment; socially cued anticipatory plasticity
The social environment can affect development and fitness. However, we do not know how selection acts on individuals that cue developmental pathways using features of the social environment. Socially cued anticipatory plasticity (SCAP) is a hypothetical strategy whereby juveniles use social cues to alter development to match their adult phenotype to the social environment that they expect to encounter. While intuitively appealing, the evolution of such plasticity is a puzzle, because the cue changes when individuals use it. Can socially cued plasticity evolve when such a feedback occurs? We use individual-based simulations to model evolution of SCAP in an environment that fluctuates between favoring each of two discrete phenotypes. We found that socially cued plasticity evolved, but only when strong selection acted on survival rather than on fecundity differences between adult phenotypes. In this case, the social cue reliably predicted which phenotype would be favored on maturation. Surprisingly, costs to plasticity increased the range of conditions under which it was adaptive. In the absence of costs, evolution led to a state where SCAP individuals could not effectively respond to environmental changes. Costs to plasticity lowered the proportion of the population that used SCAP, which in turn increased the reliability of the social cue and allowed individuals that used socially cued plasticity to switch between the favored phenotypes more consistently. Our results suggest that the evolution of adaptive plasticity in response to social cues may represent a larger class of problems in which evolution is hard to predict because of feedbacks among critical processes. DOI PubMed
981. Li, CM; Beauregard-Lacroix, E; Kondratev, C; Rousseau, J; Heo, AJ; Neas, K; Graham, BH; Rosenfeld, JA; Bacino, CA; Wagner, M; Wenzel, M; Al Mutairi, F; Al Deiab, H; Gleeson, JG; Stanley, V; Zaki, MS; Kwon, YT; Leroux, MR; Campeau, PM.UBR7 functions with UBR5 in the Notch signaling pathway and is involved in a neurodevelopmental syndrome with epilepsy, ptosis, and hypothyroidism.Am. J. Hum. Genet., 2021, 108: 134-147 UBR7 functions with UBR5 in the Notch signaling pathway and is involved in a neurodevelopmental syndrome with epilepsy, ptosis, and hypothyroidism
The ubiquitin-proteasome system facilitates the degradation of unstable or damaged proteins. UBR1-7, which are members of hundreds of E3 ubiquitin ligases, recognize and regulate the half-life of specific proteins on the basis of their N-terminal sequences ("N-end rule"). In seven individuals with intellectual disability, epilepsy, ptosis, hypothyroidism, and genital anomalies, we uncovered bi-allelic variants in UBR7. Their phenotype differs significantly from that of Johanson-Blizzard syndrome (JBS), which is caused by bi-allelic variants in UBR1, notably by the presence of epilepsy and the absence of exocrine pancreatic insufficiency and hypoplasia of nasal alae. While the mechanistic etiology of JBS remains uncertain, mutation of both Ubr1 and Ubr2 in the mouse or of the C. elegans UBR5 ortholog results in Notch signaling defects. Consistent with a potential role in Notch signaling, C. elegans ubr-7 expression partially overlaps with that of ubr-5, including in neurons, as well as the distal tip cell that plays a crucial role in signaling to germline stem cells via the Notch signaling pathway. Analysis of ubr-5 and ubr-7 single mutants and double mutants revealed genetic interactions with the Notch receptor gene glp-1 that influenced development and embryo formation. Collectively, our findings further implicate the UBR protein family and the Notch signaling pathway in a neurodevelopmental syndrome with epilepsy, ptosis, and hypothyroidism that differs from JBS. Further studies exploring a potential role in histone regulation are warranted given clinical overlap with KAT6B disorders and the interaction of UBR7 and UBRS with histones. DOI PubMed
979. Liu, SY; Wang, YC; Xu, Q; Zhang, MJ; Chen, NS.Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation.BMC Genomics, 2021, 22 Comparative analysis of full-length mitochondrial genomes of five Skeletonema species reveals conserved genome organization and recent speciation
Harmful algal blooms; Skeletonema species; Mitochondrial genome; Comparative genomics; Molecular marker; Divergence time
Background Skeletonema species are prominent primary producers, some of which can also cause massive harmful algal blooms (HABs) in coastal waters under specific environmental conditions. Nevertheless, genomic information of Skeletonema species is currently limited, hindering advanced research on their role as primary producers and as HAB species. Mitochondrial genome (mtDNA) has been extensively used as "super barcode" in the phylogenetic analyses and comparative genomic analyses. However, of the 21 accepted Skeletonema species, full-length mtDNAs are currently available only for a single species, S. marinoi. Results In this study, we constructed full-length mtDNAs for six strains of five Skeletonema species, including S. marinoi, S. tropicum, S. grevillei, S. pseudocostatum and S. costatum (with two strains), which were isolated from coastal waters in China. The mtDNAs of all of these Skeletonema species were compact with short intergenic regions, no introns, and no repeat regions. Comparative analyses of these Skeletonema mtDNAs revealed high conservation, with a few discrete regions of high variations, some of which could be used as molecular markers for distinguishing Skeletonema species and for tracking the biogeographic distribution of these species with high resolution and specificity. We estimated divergence times among these Skeletonema species using 34 mtDNAs genes with fossil data as calibration point in PAML, which revealed that the Skeletonema species formed the independent clade diverging from Thalassiosira species approximately 48.30 Mya. Conclusions The availability of mtDNAs of five Skeletonema species provided valuable reference sequences for further evolutionary studies including speciation time estimation and comparative genomic analysis among diatom species. Divergent regions could be used as molecular markers for tracking different Skeletonema species in the fields of coastal regions. DOI PubMed
978. Loveland, JL; Giraldo-Deck, LM; Lank, DB; Goymann, W; Gahr, M; Kupper, C.Functional differences in the hypothalamic-pituitary-gonadal axis are associated with alternative reproductive tactics based on an inversion polymorphism.Horm. Behav., 2021, 127 Functional differences in the hypothalamic-pituitary-gonadal axis are associated with alternative reproductive tactics based on an inversion polymorphism
Alternative reproductive tactics; Testosterone; Androstenedione; HPG axis; GnRH challenge; Steroidogenic acute regulatory protein
The evolution of social behavior depends on genetic changes, yet, how genomic variation manifests itself in behavioral diversity is still largely unresolved. Chromosomal inversions can play a pivotal role in producing distinct behavioral phenotypes, in particular, when inversion genes are functionally associated with hormone synthesis and signaling. Male ruffs exhibit alternative reproductive tactics (ARTs) with an autosomal inversion determining two alternative morphs with clear behavioral and hormonal differences from the ancestral morph. We investigated hormonal and transcriptomic differences in the pituitary and gonads. Using a GnRH challenge, we found that the ability to synthesize testosterone in inversion carriers is severely constrained, whereas the synthesis of androstenedione, a testosterone precursor, is not. Inversion morphs were able to produce a transient increase in androstenedione following the GnRH injection, supporting the view that pituitary sensitivity to GnRH is comparable to that of the ancestral morph. We then performed gene expression analyses in a second set of untreated birds and found no evidence of alterations to pituitary sensitivity, gonadotropin production or gonad sensitivity to luteinizing hormone or follicle-stimulating hormone across morphs. Inversion morphs also showed reduced progesterone receptor expression in the pituitary. Strikingly, in the gonads, inversion morphs over expressed STAR, a gene that is located outside of the inversion and responsible for providing the cholesterol substrate required for the synthesis of sex hormones. In conclusion, our results suggest that the gonads determine morph-specific differences in hormonal regulation. DOI PubMed
977. Lucci, VEM; Inskip, JA; McGrath, MS; Ruiz, I; Lee, R; Kwon, BK; Claydon, VE.Longitudinal Assessment of Autonomic Function during the Acute Phase of Spinal Cord Injury: Use of Low-Frequency Blood Pressure Variability as a Quantitative Measure of Autonomic Function.J. Neurotrauma, 2021, 38: 309-321 Longitudinal Assessment of Autonomic Function during the Acute Phase of Spinal Cord Injury: Use of Low-Frequency Blood Pressure Variability as a Quantitative Measure of Autonomic Function
autonomic dysfunction; blood pressure variability; cardiac arrhythmia; cardiovascular control; and spinal cord injury
High-level spinal cord injury (SCI) can disrupt cardiovascular autonomic function. However, the evolution of cardiovascular autonomic function in the acute phase following injury is unknown. We evaluated the timing, severity, progression, and implications of cardiovascular autonomic injury following acute SCI. We tested 63 individuals with acute traumatic SCI (aged 48 +/- 2 years) at five time-points: <2 weeks, and 1, 3, 6-12, and >12 months post-injury. Supine beat-to-beat systolic arterial pressure (SAP) and R-R interval (RRI) were recorded and low-frequency variability (LF SAP and LF RRI) determined. Cross-spectral analyses were used to determine baroreflex function (low frequency) and cardiorespiratory interactions (high frequency). Known electrocardiographic (ECG) markers for arrhythmia and self-reported symptoms of cardiovascular dysfunction were determined. Comparisons were made with historical data from individuals with chronic SCI and able-bodied controls. Most individuals had high-level (74%) motor/sensory incomplete (63%) lesions. All participants had decreased LF SAP at <2 weeks (2.22 +/- 0.65 mm Hg-2). Autonomic injury was defined as high-level SCI with LF SAP <2 mm Hg-2. Two distinct groups emerged by 1 month: autonomically complete SCI with sustained low LF SAP (0.76 +/- 0.17 mm Hg-2) and autonomically incomplete SCI with increased LF SAP (5.46 +/- 1.0 mm Hg-2,p < 0.05). Autonomically complete injuries did not recover over time. Cardiovascular symptoms were prevalent and worsened with time, especially in those with autonomically complete lesions, and chronic SCI. Baroreflex function and cardiorespiratory interactions were impaired after SCI. Risk of arrhythmia increased immediately after SCI, and remained elevated throughout the acute phase. Acute SCI is associated with severe cardiovascular dysfunction. LF SAP provides a simple, non-invasive, translatable, quantitative assessment of autonomic function, and is most informative 1 month after injury. DOI PubMed
976. Magnuson, JR; Doesburg, SM; McNeil, CJ.Development and recovery time of mental fatigue and its impact on motor function.Biol. Psychol., 2021, 161 Development and recovery time of mental fatigue and its impact on motor function
Electroencephalography; Event related potentials; Frequency; Mental fatigue; motor function
Mental fatigue is commonplace but there is limited understanding of the neural underpinnings of its development, the time course of its recovery, and its impact on motor function. Hence, this study used neural (electroencephalography) and motor measures to investigate the development and recovery of mental fatigue. Twenty participants performed a 60-min N-back task, with neural activity compared within the task. Additionally, pretask neural and motor measures were compared to assessments beginning at 0, 30 and 60 min post-task. Alpha power increased during the task and was greater than baseline at 30 and 60 min post-task. Motor skills were impaired at similar to 10-17 min post-task but recovered at similar to 40-47 min. Using a unique combination of neural and motor measures, our results suggest that attentiveness and, possibly, selectiveness in inhibiting irrelevant information are impaired after an acute mentally-fatiguing task. Notably, recovery time differed for neural and motor measures. DOI PubMed
975. Mamashli, F; Kozhemiako, N; Khan, S; Nunes, AS; McGuiggan, NM; Losh, A; Joseph, RM; Ahveninen, J; Doesburg, SM; Hamalainen, MS; Kenet, T.Children with autism spectrum disorder show altered functional connectivity and abnormal maturation trajectories in response to inverted faces.Autism Res., 2021, 14: 1101-1114 Children with autism spectrum disorder show altered functional connectivity and abnormal maturation trajectories in response to inverted faces
autism spectrum disorder; functional connectivity; inverted faces; phase‐ amplitude coupling
The processing of information conveyed by faces is a critical component of social communication. While the neurophysiology of processing upright faces has been studied extensively in autism spectrum disorder (ASD), less is known about the neurophysiological abnormalities associated with processing inverted faces in ASD. We used magnetoencephalography (MEG) to study both long-range and local functional connectivity, with the latter assessed using local cross-frequency coupling, in response to inverted faces stimuli, in 7-18 years old individuals with ASD and age and IQ matched typically developing (TD) individuals. We found abnormally reduced coupling between the phase of the alpha rhythm and the amplitude of the gamma rhythm in the fusiform face area (FFA) in response to inverted faces, as well as reduced long-range functional connectivity between the FFA and the inferior frontal gyrus (IFG) in response to inverted faces in the ASD group. These group differences were absent in response to upright faces. The magnitude of functional connectivity between the FFA and the IFG was significantly correlated with the severity of ASD, and FFA-IFG long-range functional connectivity increased with age in TD group, but not in the ASD group. Our findings suggest that both local and long-range functional connectivity are abnormally reduced in children with ASD when processing inverted faces, and that the pattern of abnormalities associated with the processing of inverted faces differs from the pattern of upright faces in ASD, likely due to the presumed greater reliance on top-down regulations necessary for efficient processing of inverted faces. Lay Summary We found alterations in the neurophysiological responses to inverted faces in children with ASD, that were not reflected in the evoked responses, and were not observed in the responses to upright faces. These alterations included reduced local functional connectivity in the fusiform face area (FFA), and decreased long-range alpha-band modulated functional connectivity between the FFA and the left IFG. The magnitude of long-range functional connectivity between the FFA and the inferior frontal gyrus was correlated with the severity of ASD. DOI PubMed
974. Mann, ME; Hall, LJ; Dulvy, NK.Scientific impact in a changing world.Cell, 2021, 184: 1407-1408 Scientific impact in a changing world
Measuring scientific success has traditionally involved numbers and statistics. However, due to an increasingly uncertain world, more than ever we need to measure the effect that science has on real-world scenarios. We asked researchers to share their points of view on what scientific impact means to them and how impact matters beyond the numbers. PubMed
973. McKnight, EA; Swanson, H; Brahney, J; Hik, DS.The physical and chemical limnology of Yukon’s largest lake, Lhù’ààn Mân’ (Kluane Lake), prior to the 2016 ‘A’ą̈y Chù’ diversion.Arctic Science, 2021, The physical and chemical limnology of Yukon’s largest lake, Lhù’ààn Mân’ (Kluane Lake), prior to the 2016 ‘A’ą̈y Chù’ diversion
Limnology, Yukon Climate Change, Lhu'aan Man' (Kluane Lake); 'A'ay Chu' (Slims River); physical limnology; climate change; large northern lakes
Despite increasing evidence that large northern lakes are rapidly changing due to climate change, descriptive baseline studies of their physicochemical properties are largely lacking, limiting our ability to detect or predict change. This study represents a comprehensive scientific assessment of the limnology of Yukon’s largest lake: Lhù’ààn Mân’ (Kluane Lake), an important waterbody for local and First Nation communities, and key habitat for trout and salmon. Water sample and instrument data generated throughout 2015 describe distinct regions within the lake and their respective seasonal variability. A deep, glacially-influenced southern basin was characterized by cold, turbid, poorly stratified, unproductive, and nutrient-poor conditions; a shallower northwestern region (Tthe Kaala Daagur (Brooks/Little Arm)) was warmer, fully mixed, and more productive; a northeast region (’Ùha K’ènji (Talbot/Big Arm)) was clear and stratified with intermediate depth, temperature, productivity, and nutrient concentrations; and a central region had intermediate physicochemical conditions relative to the other three. This variability demonstrates the need for adequate spatial (within lake) and temporal (between seasons) monitoring of large northern lakes. In 2016, glacier recession within the watershed resulted in diversion of the lake’s primary inflow (‘A’ą̈y Chù’ (Slims River)). Our results, when used together with Indigenous knowledge, form a historical reference that enables assessments of the potential ecological consequences to Lhù’ààn Mân’.Link DOI
972. McRae, CJ; Huang, WB; Fan, TY; Côté, IM.Effects of thermal conditioning on the performance of Pocillopora acuta adult coral colonies and their offspring.Coral Reefs, 2021, 40: 1491-1503 Effects of thermal conditioning on the performance of <i>Pocillopora acuta</i> adult coral colonies and their offspring
Thermal pre-conditioning; Acclimation; Resilience; Climate change; Taiwan
Ocean warming induced by climate change is the greatest threat to the persistence of coral reefs globally. Given the current rate of ocean warming, there may not be sufficient time for natural acclimation or adaptation by corals. This urgency has led to the exploration of active management techniques aimed at enhancing thermal tolerance in corals. Here, we test the capacity for transgenerational acclimation in the reef-building coral <i>Pocillopora acuta</i> as a means of increasing offspring performance in warmer waters. We exposed coral colonies from a reef influenced by intermittent upwelling and constant warm-water effluent from a nuclear power plant to temperatures that matched (26 degrees C) or exceeded (29.5 degrees C) season-specific mean temperatures for three reproductive cycles; offspring were allowed to settle and grow at both temperatures. Heated colonies reproduced significantly earlier in the lunar cycle and produced fewer and smaller planulae. Recruitment was lower at the heated recruitment temperature regardless of parent treatment. Recruit survival did not differ based on parent or recruitment temperature. Recruits from heated parents were smaller and had lower maximum quantum yield (Fv/Fm), a measurement of symbiont photochemical performance. We found no direct evidence that thermal conditioning of adult P. acuta corals improves offspring performance in warmer water; however, chronic exposure of parent colonies to warmer temperatures at the source reef site may have limited transgenerational acclimation capacity. The extent to which coral response to this active management approach might vary across species and sites remains unclear and merits further investigation. DOI PubMed
971. Montgomery, A; Tam, F; Gursche, C; Cheneval, C; Besler, K; Enns, W; Manku, S; Rey, K; Hanson, PJ; Rose-John, S; McManus, BM; Choy, JC.Overlapping and distinct biological effects of IL-6 classic and trans-signaling in vascular endothelial cells.Am. J. Physiol.-Cell Physiol., 2021, 320: C554-C565 Overlapping and distinct biological effects of IL-6 classic and trans-signaling in vascular endothelial cells
cell signaling; endothelial cell; IL-6; inflammation; vascular injury
IL-6 affects tissue protective/reparative and inflammatory properties of vascular endothelial cells (ECs). This cytokine can signal to cells through classic and trans-signaling mechanisms, which are differentiated based on the expression of IL-6 receptor (IL-6R) on the surface of target cells. The biological effects of these IL-6-signaling mechanisms are distinct and have implications for vascular pathologies. We have directly compared IL-6 classic and trans-signaling in ECs. Human ECs expressed IL-6R in culture and in situ in coronary arteries from heart transplants. Stimulation of human ECs with IL-6, to model classic signaling, triggered the activation of phosphatidylinositol 3-kinase (PI3K)-Akt and ERK1/2 signaling pathways, whereas stimulation with IL-6 thorn sIL-6R, to model trans-signaling, triggered activation of STAT3, PI3K-Akt, and ERK1/2 pathways. IL-6 classic signaling reduced persistent injury of ECs in an allograft model of vascular rejection and inhibited cell death induced by growth factor withdrawal. When inflammatory effects were examined, IL-6 classic signaling did not induce ICAM or CCL2 expression but was sufficient to induce secretion of CXCL8 and support transmigration of neutrophil-like cells. IL-6 trans-signaling induced all inflammatory effects studied. Our findings show that IL-6 classic and trans-signaling have overlapping but distinct properties in controlling EC survival and inflammatory activation. This has implications for understanding the effects of IL-6 receptor-blocking therapies as well as for vascular responses in inflammatory and immune conditions. DOI PubMed
970. Moore, JW; Connors, BM; Hodgson, EE.Conservation risks and portfolio effects in mixed-stock fisheries.Fish. Fish., 2021, 22: 1024-1040 Conservation risks and portfolio effects in mixed-stock fisheries
diversity‐ stability; ecological portfolio effects; mixed‐ stock fishery; Pacific salmon; resilience; sustainable fisheries
Fish biodiversity sustains the resilience and productivity of fisheries, yet this biodiversity can be threatened by overharvest and depletion in mixed-stock fisheries. Thus, the biodiversity that provides benefits may also make sustainable resource extraction more difficult, a key challenge in fisheries management. We simulated a mixed-stock fishery to explore relationships between different dimensions of biodiversity and fishery performance relative to conservation and fishery objectives. Different dimensions of biodiversity (number of stocks, evenness, asynchrony among stocks, heterogeneity in stock productivity) exacerbated trade-offs between fishery and conservation objectives. For example, fisheries targeting stock-complexes with greater asynchrony, and to a lesser extent richness, had greater stability in harvest through time but also greater risks of overfishing weak stocks and reduced yield compared to less biodiverse stock-complexes. These trade-offs were ameliorated by increasing management control-the capacity of fishery managers to harvest specific stocks. To explore these trade-offs in real-world fisheries, we contrasted the fishing and population status of individual stocks within three major mixed-stock sockeye salmon (Oncorhynchus nerka, Salmonidae) fisheries-Bristol Bay, Fraser River, and Skeena River. In general, the fisheries with lower management control had individual stocks that were more often being over- or under-fished, compared with those with higher management control, though variation among regions in biodiversity, scale of management, and magnitude of habitat alteration likely also contribute to these relationships. Collectively, our findings emphasize that there is a need to extract less or regulate better in order to conserve and benefit from biodiversity in fisheries and other natural resource management systems. DOI
969. Pacoureau, N; Rigby, CL; Kyne, PM; Sherley, RB; Winker, H; Carlson, JK; Fordham, SV; Barreto, R; Fernando, D; Francis, MP; Jabado, RW; Herman, KB; Liu, KM; Marshall, AD; Pollom, RA; Romanov, EV; Simpfendorfer, CA; Yin, JS; Kindsvater, HK; Dulvy, NK.Half a century of global decline in oceanic sharks and rays.Nature, 2021, 589: 567-+ Half a century of global decline in oceanic sharks and rays
Overfishing is the primary cause of marine defaunation, yet declines in and increasing extinction risks of individual species are difficult to measure, particularly for the largest predators found in the high seas(1-3). Here we calculate two well-established indicators to track progress towards Aichi Biodiversity Targets and Sustainable Development Goals(4,5): the Living Planet Index (a measure of changes in abundance aggregated from 57 abundance time-series datasets for 18 oceanic shark and ray species) and the Red List Index (a measure of change in extinction risk calculated for all 31 oceanic species of sharks and rays). We find that, since 1970, the global abundance of oceanic sharks and rays has declined by 71% owing to an 18-fold increase in relative fishing pressure. This depletion has increased the global extinction risk to the point at which three-quarters of the species comprising this functionally important assemblage are threatened with extinction. Strict prohibitions and precautionary science-based catch limits are urgently needed to avert population collapse(6,7), avoid the disruption of ecological functions and promote species recovery(8,9). DOI PubMed
968. Pan, DM; Gu, JH; Zhang, J; Hu, YE; Liu, F; Iqbal, K; Cekic, N; Vocadlo, DJ; Dai, CL; Gong, CX.Thiamme2-G, a Novel O-GlcNAcase Inhibitor, Reduces Tau Hyperphosphorylation and Rescues Cognitive Impairment in Mice.J. Alzheimers Dis., 2021, 81: 273-286 Thiamme2-G, a Novel O-GlcNAcase Inhibitor, Reduces Tau Hyperphosphorylation and Rescues Cognitive Impairment in Mice
Alzheimer's disease; O-GlcNAcylation; OGA; OGA inhibitor; tau hyperphosphorylation; Thiamme2-G
Background: Abnormal hyperphosphorylation of microtubule-associated protein tau plays a pivotal role in Alzheimer's disease (AD). We previously found that O-GlcNAcylation inversely correlates to hyperphosphorylation of tau in AD brain, and downregulation of brain O-GlcNAcylation promotes tau hyperphosphorylation and AD-like neurodegeneration in mice. Objective: Herein we investigated the effect of increasing O-GlcNAcylation by using intermittent dosing with low doses of a potent novel O-GlcNAcase (OGA) inhibitor on AD-like brain changes and cognitive function in a mouse model of sporadic AD (sAD) induced by intracerebroventricular (ICV) injection of streptozotocin (STZ). Methods: STZ was injected into the lateral ventricle of C57BL/6J mice. From the second day, Thiamme2-G (TM2G) or saline, as a vehicle control, was orally administered to the ICV-STZ mice three times per week for five weeks. A separate group of ICV-saline mice treated with saline was used as a baseline control. Behavioral tests, including open field and novel object recognition, were conducted three weeks after the first dose of the TM2G or saline. Protein O-GlcNAcylation, tau hyperphosphorylation, synaptic proteins, and neuroinflammation in the mouse brain were assessed by western blotting. Results: ICV-STZ caused decreased protein O-GlcNAcylation. Enhancement of O-GlcNAcylation to moderate levels by using low-dose OGA inhibitor in ICV-STZ mice prevented STZ-induced body weight loss, rescued cognitive impairments, and restored AD-like pathologies, including hyperphosphorylation of tau and abnormalities in synaptic proteins and neuroinflammation. Conclusion: These findings suggest that moderately increasing protein O-GlcNAcylation by using lowdoses ofOGAinhibitor may be a suitable therapeutic strategy for sAD. DOI PubMed
966. Park, K; Li, CM; Tsiropoulou, S; Goncalves, J; Kondratev, C; Pelletier, L; Blacque, OE; Leroux, MR.CDKL kinase regulates the length of the ciliary proximal segment.Curr. Biol., 2021, 31: 2359-+ CDKL kinase regulates the length of the ciliary proximal segment
Cilia are organelles found throughout most unicellular eukaryotes and different metazoan cell types. To accomplish their essential roles in cell motility, fluid flow, and signaling, cilia are divided into subcompartments with variable structures, compositions, and functions. How these specific subcompartments are built remains almost completely unexplored. Here, we show that C. elegans CDKL-1, related to the human CDKL kinase family (CDKL1/CDKL2/CDKL3/CDKL4/CDKL5), specifically controls the length of the proximal segment, a ciliary subdomain conserved in evolution from Tetrahymena motile cilia to C. elegans chemosensory, mammalian olfactory, and photoreceptor non-motile cilia. CDKL-1 associates with intraflagellar transport (IFT), influences the distribution of the IFT anterograde motors heterotrimeric kinesin-II and homodimeric OSM-3-kinesin/KIF17 in the proximal segment, and shifts the boundary between the proximal and distal segments (PS/DS boundary). CDKL-1 appears to function independently from several factors that influence cilium length, namely the kinases DYF-5 (mammalian CILK1/MAK) and NEKL-1 (NEK9), as well as the depolymerizing kinesins KLP-13 (KIF19) and KLP-7 (KIF2). However, a different kinase, DYF-18 (CCRK), is needed for the correct localization and function of CDKL-1 and similarly influences the length of the proximal segment. Loss of CDKL-1, which affects proximal segment length without impairing overall ciliary microtubule structural integrity, also impairs cilium-dependent processes, namely cGMP-signaling-dependent body length control and CO2 avoidance. Collectively, our findings suggest that cilium length is regulated by various pathways and that the IFT-associated kinase CDKL-1 is essential for the construction of a specific ciliary compartment and contributes to development and sensory physiology. DOI PubMed
965. Patankar, JV; Muller, TM; Kantham, S; Acera, MG; Mascia, F; Scheibe, K; Mahapatro, M; Heichler, C; Yu, YQ; Li, W; Ruder, B; Gunther, C; Leppkes, M; Mathew, MJ; Wirtz, S; Neufert, C; Kuhl, AA; Paquette, J; Jacobson, K; Atreya, R; Zundler, S; Neurath, MF; Young, RN; Becker, C.E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis.Nat. Cell Biol., 2021, 23: 796-+ E-type prostanoid receptor 4 drives resolution of intestinal inflammation by blocking epithelial necroptosis
Inflammatory bowel diseases present with elevated levels of intestinal epithelial cell (IEC) death, which compromises the gut barrier, activating immune cells and triggering more IEC death. The endogenous signals that prevent IEC death and break this vicious cycle, allowing resolution of intestinal inflammation, remain largely unknown. Here we show that prostaglandin E2 signalling via the E-type prostanoid receptor 4 (EP4) on IECs represses epithelial necroptosis and induces resolution of colitis. We found that EP4 expression correlates with an improved IBD outcome and that EP4 activation induces a transcriptional signature consistent with resolution of intestinal inflammation. We further show that dysregulated necroptosis prevents resolution, and EP4 agonism suppresses necroptosis in human and mouse IECs. Mechanistically, EP4 signalling on IECs converges on receptor-interacting protein kinase 1 to suppress tumour necrosis factor-induced activation and membrane translocation of the necroptosis effector mixed-lineage kinase domain-like pseudokinase. In summary, our study indicates that EP4 promotes the resolution of colitis by suppressing IEC necroptosis. Patankar et al. identify E-type prostanoid receptor 4 as a negative regulator of tumour necrosis factor signalling and mixed-lineage kinase domain-like pseudokinase activation, thereby suppressing necroptosis of intestinal epithelial cells and promoting resolution of intestinal inflammation. DOI PubMed
964. Petrou, EL; Fuentes-Pardo, AP; Rogers, LA; Orobko, M; Tarpey, C; Jimenez-Hidalgo, I; Moss, ML; Yang, DY; Pitcher, TJ; Sandell, T; Lowry, D; Ruzzante, DE; Hauser, L.Functional genetic diversity in an exploited marine species and its relevance to fisheries management.Proc. R. Soc. B-Biol. Sci., 2021, 288 Functional genetic diversity in an exploited marine species and its relevance to fisheries management
phenology; population genomics; isolation by time; resource wave; Pacific herring
The timing of reproduction influences key evolutionary and ecological processes in wild populations. Variation in reproductive timing may be an especially important evolutionary driver in the marine environment, where the high mobility of many species and few physical barriers to migration provide limited opportunities for spatial divergence to arise. Using genomic data collected from spawning aggregations of Pacific herring (Clupea pallasii) across 1600 km of coastline, we show that reproductive timing drives population structure in these pelagic fish. Within a specific spawning season, we observed isolation by distance, indicating that gene flow is also geographically limited over our study area. These results emphasize the importance of considering both seasonal and spatial variation in spawning when delineating management units for herring. On several chromosomes, we detected linkage disequilibrium extending over multiple Mb, suggesting the presence of chromosomal rearrangements. Spawning phenology was highly correlated with polymorphisms in several genes, in particular SYNE2, which influences the development of retinal photoreceptors in vertebrates. SYNE2 is probably within a chromosomal rearrangement in Pacific herring and is also associated with spawn timing in Atlantic herring (Clupea harengus). The observed genetic diversity probably underlies resource waves provided by spawning herring. Given the ecological, economic and cultural significance of herring, our results support that conserving intraspecific genetic diversity is important for maintaining current and future ecosystem processes. DOI PubMed
963. Post, JR; Ward, HGM; Wilson, KL; Sterling, GL; Cantin, A; Taylor, EB.Assessing conservation status with extensive but low-resolution data: Application of frequentist and Bayesian models to endangered Athabasca River rainbow trout.Conserv. Biol., 2021, Assessing conservation status with extensive but low-resolution data: Application of frequentist and Bayesian models to endangered Athabasca River rainbow trout
Athabasca rainbow trout; conservation status thresholds; hierarchical Bayesian analysis; low-resolution data; population trend analysis; analisis bayesiano de jerarquias; analisis de tendencias poblacionales; datos de baja resolucion; trucha arcoiris de Athabasca; umbrales del estado de conservacion
Use of extensive but low-resolution abundance data is common in the assessment of species at-risk status based on quantitative decline criteria under International Union for Conservation of Nature (IUCN) and national endangered species legislation. Such data can be problematic for 3 reasons. First, statistical power to reject the null hypothesis of no change is often low because of small sample size and high sampling uncertainty leading to a high frequency of type II errors. Second, range-wide assessments composed of multiple site-specific observations do not effectively weight site-specific trends into global trends. Third, uncertainty in site-specific temporal trends and relative abundance are not propagated at the appropriate spatial scale. A common result is the propensity to underestimate the magnitude of declines and therefore fail to identify the appropriate at-risk status for a species. We used 3 statistical approaches, from simple to more complex, to estimate temporal decline rates for a designatable unit (DU) of rainbow trout in the Athabasca River watershed in western Canada. This DU is considered a native species for purposes of listing because of its genetic composition characterized as >0.95 indigenous origin in the face of continuing introgressive hybridization with introduced populations in the watershed. Analysis of abundance trends from 57 time series with a fixed-effects model identified 33 sites with negative trends, but only 2 were statistically significant. By contrast, a hierarchical linear mixed model weighted by site-specific abundance provided a DU-wide decline estimate of 16.4% per year and a 3-generation decline of 93.2%. A hierarchical Bayesian mixed model yielded a similar 3-generation decline trend of 91.3% and the posterior distribution showed that the estimate had a >99% probability of exceeding thresholds for an endangered listing. We conclude that the Bayesian approach was the most useful because it provided a probabilistic statement of threshold exceedance in support of an at-risk status recommendation. DOI PubMed
962. Price, MHH; Moore, JW; Connors, BM; Wilson, KL; Reynolds, JD.Portfolio simplification arising from a century of change in salmon population diversity and artificial production.J. Appl. Ecol., 2021, 58: 1477-1486 Portfolio simplification arising from a century of change in salmon population diversity and artificial production
artificial production; biodiversity loss; conservation genetics; fisheries; historical ecology; population diversity; portfolio effects; salmon abundance
Population and life-history diversity can buffer species from environmental variability and contribute to long-term stability through differing responses to varying conditions akin to the stabilizing effect of asset diversity on financial portfolios. While it is well known that many salmon populations have declined in abundance over the last century, we understand less about how different dimensions of diversity may have shifted. Specifically, how has diminished wild abundance and increased artificial production (i.e. enhancement) changed portfolios of salmon populations, and how might such change influence fisheries and ecosystems? We apply modern genetic tools to century-old sockeye salmon Oncorhynchus nerka scales from Canada's Skeena River watershed to (a) reconstruct historical abundance and age-trait data for 1913-1947 to compare with recent information, (b) quantify changes in population and life-history diversity and the role of enhancement in population dynamics, and (c) quantify the risk to fisheries and local ecosystems resulting from observed changes in diversity and enhancement. The total number of wild sockeye returning to the Skeena River during the modern era is 69% lower than during the historical era; all wild populations have declined, several by more than 90%. However, enhancement of a single population has offset declines in wild populations such that aggregate abundances now are similar to historical levels. Population diversity has declined by 70%, and life-history diversity has shifted: populations are migrating from freshwater at an earlier age, and spending more time in the ocean. There also has been a contraction in abundance throughout the watershed, which likely has decreased the spatial extent of salmon provisions to Indigenous fisheries and local ecosystems. Despite the erosion of portfolio strength that this salmon complex hosted a century ago, total returns now are no more variable than they were historically perhaps in part due to the stabilizing effect of artificial production. Policy implications. Our study provides a rare example of the extent of erosion of within-species biodiversity over the last century of human influence. Rebuilding a diversity of abundant wild populations-that is, maintaining functioning portfolios-may help ensure that watershed complexes like the Skeena are robust to global change. DOI
960. Queroue, M; Barbraud, C; Barraquand, F; Turek, D; Delord, K; Pacoureau, N; Gimenez, O.Multispecies integrated population model reveals bottom-up dynamics in a seabird predator-prey system.Ecol. Monogr., 2021, 91 Multispecies integrated population model reveals bottom-up dynamics in a seabird predator-prey system
Bayesian inference; demography; environmental variation; integrated population model; matrix population model; Nimble; predator-prey interactions
Assessing the effects of climate and interspecific relationships on communities is challenging because of the complex interplay between species population dynamics, their interactions, and the need to integrate information across several biological levels (individuals, populations, communities). Usually used to quantify single-species demography, integrated population models (IPMs) have recently been extended to communities. These models allow fitting multispecies matrix models to data from multiple sources while simultaneously accounting for uncertainty in each data source. We used multispecies IPMs accommodating climatic variables to quantify the relative contribution of climate vs. interspecific interactions on demographic parameters, such as survival and breeding success, in the dynamics of a predator-prey system. We considered a stage-structured predator-prey system combining 22 yr of capture-recapture data and population counts of two seabirds, the Brown Skua (Catharacta lonnbergi) and its main prey the Blue Petrel (Halobaena caerulea), both breeding on the Kerguelen Islands in the Southern Ocean. Our results showed that climate and predator-prey interactions drive the demography of skuas and petrels in different ways. The breeding success of skuas appeared to be largely driven by the number of petrels and to a lesser extent by intraspecific density dependence. In contrast, there was no evidence of predation effects on the demographic parameters of petrels, which were affected by oceanographic factors. We conclude that bottom-up mechanisms are the main drivers of this skua-petrel system. DOI
958. Rogowska, MD; Pena, UNV; Binning, N; Christians, JK.Recovery of the maternal skeleton after lactation is impaired by advanced maternal age but not by reduced IGF availability in the mouse.PLoS One, 2021, 16 Recovery of the maternal skeleton after lactation is impaired by advanced maternal age but not by reduced IGF availability in the mouse
Background Lactation results in substantial maternal bone loss that is recovered following weaning. However, the mechanisms underlying this recovery, and in particular the role of insulin-like growth factor 1 (IGF-I), is not clear. Furthermore, there is little data regarding whether recovery is affected by advanced maternal age. Methods Using micro-computed tomography, we studied bone recovery following lactation in mice at 2, 5 and 7 months of age. We also investigated the effects of reduced IGF-I availability using mice lacking PAPP-A2, a protease of insulin-like growth factor binding protein 5 (IGFBP-5). Results In 2 month old mice, lactation affected femoral trabecular and cortical bone, but only cortical bone showed recovery 3 weeks after weaning. This recovery was not affected by deletion of the Pappa2 gene. The amount of trabecular bone was reduced in 5 and 7 month old mice, and was not further reduced by lactation. However, the recovery of cortical bone was impaired at 5 and 7 months compared with at 2 months. Conclusions Recovery of the maternal skeleton after lactation is impaired in moderately-aged mice compared with younger mice. Our results may be relevant to the long-term effects of breastfeeding on the maternal skeleton in humans, particularly given the increasing median maternal age at childbearing. DOI PubMed
957. Sabal, MC; Boyce, MS; Charpentier, CL; Furey, NB; Luhring, TM; Martin, HW; Melnychuk, MC; Srygley, RB; Wagner, MC; Wirsing, AJ; Ydenberg, RC; Palkovacs, EP.Predation landscapes influence migratory prey ecology and evolution.Trends Ecol. Evol., 2021, 36: 737-749 Predation landscapes influence migratory prey ecology and evolution
Migratory prey experience spatially variable predation across their life cycle. They face unique challenges in navigating this predation landscape, which affects their perception of risk, antipredator responses, and resulting mortality. Variable and unfamiliar predator cues during migration can limit accurate perception of risk and migrants often rely on social information and learning to compensate. The energetic demands of migration constrain antipredator responses, often through context-dependent patterns. While migration can increase mortality, migrants employ diverse strategies to balance risks and rewards, including life history and antipredator responses. Humans interact frequently with migratory prey across space and alter both mortality risk and antipredator responses, which can scale up to affect migratory populations and should be considered in conservation and management. DOI PubMed
956. Sanchez, N; Simha, SN; Donelan, JM; Finley, JM.Using asymmetry to your advantage: learning to acquire and accept external assistance during prolonged split-belt walking.J. Neurophysiol., 2021, 125: 344-357 Using asymmetry to your advantage: learning to acquire and accept external assistance during prolonged split-belt walking
locomotion; mechanical work; metabolic cost; motor adaptation; split-belt walking
People can learn to exploit external assistance during walking to reduce energetic cost. For example, walking on a split-belt treadmill affords the opportunity for people to redistribute the mechanical work performed by the legs to gain assistance from the difference in belts' speed and reduce energetic cost. Though we know what people should do to acquire this assistance, this strategy is not observed during typical adaptation studies. We hypothesized that extending the time allotted for adaptation would result in participants adopting asymmetric step lengths to increase the assistance they can acquire from the treadmill. Here, participants walked on a split-belt treadmill for 45min while we measured spatiotemporal gait variables, metabolic cost, and mechanical work. We show that when people are given sufficient time to adapt, they naturally learn to step further forward on the fast belt, acquire positive mechanical work from the treadmill, and reduce the positive work performed by the legs. We also show that spatiotemporal adaptation and energy optimization operate over different timescales: people continue to reduce energetic cost even after spatiotemporal changes have plateaued. Our findings support the idea that walking with symmetric step lengths, which is traditionally thought of as the endpoint of adaptation, is only a point in the process by which people learn to take advantage of the assistance provided by the treadmill. These results provide further evidence that reducing energetic cost is central in shaping adaptive locomotion, but this process occurs over more extended timescales than those used in typical studies. NEW & NOTEWORTHY Split-belt treadmill adaptation can be seen as a process where people learn to acquire positive work from the treadmill to reduce energetic cost. Though we know what people should do to reduce energetic cost, this strategy is not observed during adaptation studies. We extended the duration of adaptation and show that people continuously adapt their gait to acquire positive work from the treadmill to reduce energetic cost. This process requires longer exposure than traditionally allotted. DOI PubMed
955. Schneider, M; Al-Shaer, A; Forde, NR.AutoSmarTrace: Automated chain tracing and flexibility analysis of biological filaments.Biophys. J., 2021, 120: 2599-2608 AutoSmarTrace: Automated chain tracing and flexibility analysis of biological filaments
Single-molecule imaging is widely used to determine statistical distributions of molecular properties. One such characteristic is the bending flexibility of biological filaments, which can be parameterized via the persistence length. Quantitative extraction of persistence length from images of individual filaments requires both the ability to trace the backbone of the chains in the images and sufficient chain statistics to accurately assess the persistence length. Chain tracing can be a tedious task, performed manually or using algorithms that require user input and/or supervision. Such interventions have the potential to introduce user-dependent bias into the chain selection and tracing. Here, we introduce a fully automated algorithm for chain tracing and determination of persistence lengths. Dubbed "AutoSmarTrace," the algorithm is built off a neural network, trained via machine learning to identify filaments within images recorded using atomic force microscopy. We validate the performance of AutoSmarTrace on simulated images with widely varying levels of noise, demonstrating its ability to return persistence lengths in agreement with input simulation parameters. Persistence lengths returned from analysis of experimental images of collagen and DNA agree with previous values obtained from these images with different chain-tracing approaches. Although trained on atomic-force-microscopy-like images, the algorithm also shows promise to identify chains in other single-molecule imaging approaches, such as rotary-shadowing electron microscopy and fluorescence imaging. DOI PubMed
954. Simha, SN; Wong, JD; Selinger, JC; Abram, SJ; Donelan, JM.Increasing the gradient of energetic cost does not initiate adaptation in human walking.J. Neurophysiol., 2021, 126: 440-450 Increasing the gradient of energetic cost does not initiate adaptation in human walking
energy optimization; explore-exploit; gait; motor learning
When in a new situation, the nervous system may benefit from adapting its control policy. In determining whether or not to initiate this adaptation, the nervous system may rely on some features of the new situation. Here, we tested whether one such feature is salient cost savings. We changed cost saliency by manipulating the gradient of participants' energetic cost landscape during walking. We hypothesized that steeper gradients would cause participants to spontaneously adapt their step frequency to lower costs. To manipulate the gradient, a mechatronic system applied controlled fore-aft forces to the waist of participants as a function of their step frequency as they walked on a treadmill. These forces increased the energetic cost of walking at high step frequencies and reduced it at low step frequencies. We successfully created three cost landscapes of increasing gradients, where the natural variability in participants' step frequency provided cost changes of 3.6% (shallow), 7.2% (intermediate), and 10.2% (steep). Participants did not spontaneously initiate adaptation in response to any of the gradients. Using metronomeguided walking-a previously established protocol for eliciting initiation of adaptation-participants next experienced a step frequency with a lower cost. Participants then adapted by -1.41 +/- 0.81 (P = 0.007) normalized units away from their originally preferred step frequency obtaining cost savings of 4.80% +/- 3.12%. That participants would adapt under some conditions, but not in response to steeper cost gradients, suggests that the nervous system does not solely rely on the gradient of energetic cost to initiate adaptation in novel situations. NEW & NOTEWORTHY People can adapt to novel conditions but often require cues to initiate the adaptation. Using a mechatronic system to reshape energetic cost gradients during treadmill walking, we tested whether the nervous system can use information present in the cost gradient to spontaneously initiate adaptation. We found that our participants did not spontaneously initiate adaptation even in the steepest gradient. The nervous system does not rely solely on the cost gradient when initiating adaptation. DOI PubMed
953. Skowron, P; Farooq, H; Cavalli, FMG; Morrissy, AS; Ly, M; Hendrikse, LD; Wang, EY; Djambazian, H; Zhu, H; Mungall, KL; Trinh, QM; Zheng, TN; Dai, SZ; Stucklin, ASG; Vladoiu, MC; Fong, V; Holgado, BL; Nor, C; Wu, XC; Abd-Rabbo, D; Berube, P; Wang, YC; Luu, B; Suarez, RA; Rastan, A; Gillmor, AH; Lee, JJY; Zhang, XY; Daniels, C; Dirks, P; Malkin, D; Bouffet, E; Tabori, U; Loukides, J; Doz, FP; Bourdeaut, F; Delattre, OO; Masliah-Planchon, J; Ayrault, O; Kim, SK; Meyronet, D; Grajkowska, WA; Carlotti, CG; de Torres, C; Mora, J; Eberhart, CG; Van Meir, EG; Kumabe, T; French, PJ; Kros, JM; Jabado, N; Lach, B; Pollack, IF; Hamilton, RL; Rao, AAN; Giannini, C; Olson, JM; Bognar, L; Klekner, A; Zitterbart, K; Phillips, JJ; Thompson, RC; Cooper, MK; Rubin, JB; Liau, LM; Garami, M; Hauser, P; Li, KKW; Ng, HK; Poon, WS; Gillespie, GY; Chan, JA; Jung, S; McLendon, RE; Thompson, EM; Zagzag, D; Vibhakar, R; Ra, YS; Garre, ML; Schuller, U; Shofuda, T; Faria, CC; Lopez-Aguilar, E; Zadeh, G; Hui, CC; Ramaswamy, V; Bailey, SD; Jones, SJ; Mungall, AJ; Moore, RA; Calarco, JA; Stein, LD; Bader, GD; Reimand, J; Ragoussis, J; Weiss, WA; Marra, MA; Suzuki, H; Taylor, MD.The transcriptional landscape of Shh medulloblastoma.Nat. Commun., 2021, 12 The transcriptional landscape of Shh medulloblastoma
Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN. Furthermore, we discover an extensive network of fusions in focally amplified regions encompassing GLI2, and several loss-of-function fusions in tumor suppressor genes PTCH1, SUFU and NCOR1. Molecular convergence on a subset of genes by nucleotide variants, copy number aberrations, and gene fusions highlight the key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma and open up opportunities for therapeutic intervention. Sonic Hedgehog medulloblastoma (Shh-MB) comprises four subtypes each with distinct clinical traits. Here the authors characterize the genome, transcriptome, and methylome of Shh-MB subtypes, revealing a complex fusion landscape and the molecular convergence of MYCN and cAMP signaling pathways. DOI PubMed
952. Smith, NS; Côté, IM.Biotic resistance on coral reefs? Direct and indirect effects of native predators and competitors on invasive lionfish.Coral Reefs, 2021, 40: 1127-1136 Biotic resistance on coral reefs? Direct and indirect effects of native predators and competitors on invasive lionfish
Competition; Consumptive effects; Groupers; Non-consumptive effects; Invasive species control
Biotic resistance is the ability of an ecological community to prevent or limit the establishment or success of non-indigenous species. Native species can confer resistance by outcompeting or directly consuming non-native invaders. The fear of being eaten could also limit invader success, but non-consumptive effects of native predators have rarely been documented as a source of biotic resistance. Here, we test whether native groupers on Caribbean coral reefs can promote biotic resistance to invasive Indo-Pacific lionfish through competition, consumption, and/or through non-consumptive effects. Stomach content analysis of more than 200 groupers, comprising five species, revealed no instances of predation on lionfish. To test for competitive and non-consumptive effects of groupers, we released tagged juvenile lionfish onto reef patches that varied in grouper densities and monitored lionfish behaviours over five weeks. At dawn, during peak grouper and lionfish hunting times, juvenile lionfish hid more on reefs with more grouper predators. Juvenile lionfish were also less active during the day on reefs with high grouper densities. Hiding and inactivity are incompatible with foraging and thus should result in lionfish eating fewer prey and having reduced somatic growth rates. Although there was no substantial effect of interspecific competition on lionfish behaviours, we found that lionfish swam greater distances with increasing densities of intraspecific competitors at dawn. We did not detect a cascading effect of grouper predators on smaller fishes, perhaps because the seasonal peak in prey fish recruitment masked the effects of lower lionfish predation. Fear of native predators by lionfish has the potential to reduce invader foraging success, although it might not fully mitigate the negative effects on native prey communities. Efforts to rebuild grouper populations throughout the Caribbean may still aid in controlling the lionfish invasion despite weak evidence of interspecific competition and lack of direct predation on lionfish, but further research is needed. At broader scales, our findings highlight that the global depletion of large predators can have implications beyond demographic effects on prey. DOI
951. Souza, IC; Morozesk, M; Azevedo, VC; Mendes, VAS; Duarte, ID; Rocha, LD; Matsumoto, ST; Elliott, M; Baroni, MV; Wunderlin, DA; Monferran, MV; Fernandes, MN.Trophic transfer of emerging metallic contaminants in a neotropical mangrove ecosystem food web.J. Hazard. Mater., 2021, 408 Trophic transfer of emerging metallic contaminants in a neotropical mangrove ecosystem food web
Trophodynamic; Estuarine food chains; Neotropical estuaries; Pollution pathway; Steel industry
Emerging metallic contaminants (EMCs) are of concern due their presence in aquatic ecosystems and the lack of environmental regulations in several countries. This study verifies the presence of EMCs in two neotropical mangrove estuarine ecosystems (Espirito Santo Brazil) by evaluating abiotic and biotic matrices across six trophic levels (plankton, oyster, shrimp, mangrove trees, crabs and fish) and hence interrogates the trophic transfer of these elements and their possible input sources. Using the oyster Crassostrea rhizophorae as a biomonitor, ten EMCs (Bi, Ce, La, Nb, Sn, Ta, Ti, W, Y and Zr) were determined. Bi input was from iron export and pelletizing industries; Ce, La and Y inputs were mainly associated with solid waste from steel production, while Zr, Nb and Ti were related to atmospheric particulate matter emissions. EMCs were detected at various trophic levels, showing biomagnification for most of them in the Santa Cruz estuary but biodilution in Vit ' oria Bay. These contrasting results between the estuaries could be attributed to different pollution degrees, needing further research to be fully understood. This is the first report demonstrating EMCs trophic pathways in situ, constituting an essential baseline for future research and safety regulations involving EMCs in the environment. DOI PubMed
950. Tavassoly, O; Pellitero, ED; Larroquette, F; Cai, E; Thomas, RA; Soubannier, V; Luo, W; Durcan, TM; Fon, EA.Pharmacological Inhibition of Brain EGFR Activation By a BBB-penetrating Inhibitor, AZD3759, Attenuates alpha-synuclein Pathology in a Mouse Model of alpha-Synuclein Propagation.Neurotherapeutics, 2021, 18: 979-997 Pharmacological Inhibition of Brain EGFR Activation By a BBB-penetrating Inhibitor, AZD3759, Attenuates alpha-synuclein Pathology in a Mouse Model of alpha-Synuclein Propagation
α -Synuclein; Parkinson’ s disease; Pre-formed fibrils; Propagation; EGFR-tyrosine-kinase inhibitor; AZD3759
Aggregation and deposition of alpha-synuclein (alpha-syn) in Lewy bodies within dopamine neurons of substantia nigra (SN) is the pathological hallmark of Parkinson's disease (PD). These toxic alpha-syn aggregates are believed to propagate from neuron-to-neuron and spread the alpha-syn pathology throughout the brain beyond dopamine neurons in a prion-like manner. Targeting propagation of such alpha-syn aggregates is of high interest but requires identifying pathways involving in this process. Evidence from previous Alzheimer's disease reports suggests that EGFR may be involved in the prion-like propagation and seeding of amyloid-beta. We show here that EGFR regulates the uptake of exogenous alpha-syn-PFFs and the levels of endogenous alpha-syn in cell cultures and a mouse model of alpha-syn propagation, respectively. Thus, we tested the therapeutic potentials of AZD3759, a highly selective BBB-penetrating EGFR inhibitor, in a preclinical mouse model of alpha-syn propagation. AZD3759 decreases activated EGFR levels in the brain and reduces phosphorylated alpha-synuclein (pSyn) pathology in brain sections, including striatum and SN. As AZD3759 is already in the clinic, this paper's results suggest a possible repositioning of AZD3759 as a disease-modifying approach for PD. DOI PubMed
949. Theodoridis, PR; Bokros, M; Marijan, D; Balukoff, NC; Wang, DZ; Kirk, CC; Budine, TD; Goldsmith, HD; Wang, ML; Audas, TE; Lee, S.Local translation in nuclear condensate amyloid bodies.Proc. Natl. Acad. Sci. U. S. A., 2021, 118 Local translation in nuclear condensate amyloid bodies
long noncoding RNA; hypoxia; acidosis; HSR; Hsp70
Biomolecular condensates concentrate molecules to facilitate basic biochemical processes, including transcription and DNA replication. While liquid-like condensates have been ascribed various functions, solid-like condensates are generally thought of as amorphous sites of protein storage. Here, we show that solid-like amyloid bodies coordinate local nuclear protein synthesis (LNPS) during stress. On stimulus, translationally active ribosomes accumulate along fiber-like assemblies that characterize amyloid bodies. Mass spectrometry analysis identified regulatory ribosomal proteins and translation factors that relocalize from the cytoplasm to amyloid bodies to sustain LNPS. These amyloidogenic compartments are enriched in newly transcribed messenger RNA by Heat Shock Factor 1 (HSF1). Depletion of stress-induced ribosomal intergenic spacer noncoding RNA (rIGSRNA) that constructs amyloid bodies prevents recruitment of the nuclear protein synthesis machinery, abolishes LNPS, and impairs the nuclear HSF1 response. We propose that amyloid bodies support local nuclear translation during stress and that solid-like condensates can facilitate complex biochemical reactions as their liquid counterparts can. DOI PubMed
948. Vakorin, VA; Nita, DA; Payne, ET; McBain, KL; Frndova, H; Go, C; Ribary, U; Abend, NS; Gallentine, WB; Nash, KB; Hutchison, JS; Parshuram, CS; Snead, OC; van Straaten, IECW; Stam, CJ; Doesburg, SM; Hahn, CD.Alterations in coordinated EEG activity precede the development of seizures in comatose children.Clin. Neurophysiol., 2021, 132: 1505-1514 Alterations in coordinated EEG activity precede the development of seizures in comatose children
Electroencephalography (EEG); Coma; Critically ill children; ICU; Brain connectivity
Objective: We aimed to test the hypothesis that computational features of the first several minutes of EEG recording can be used to estimate the risk for development of acute seizures in comatose critically-ill children. Methods: In a prospective cohort of 118 comatose children, we computed features of the first five minutes of artifact-free EEG recording (spectral power, inter-regional synchronization and cross-frequency coupling) and tested if these features could help identify the 25 children who went on to develop acute symptomatic seizures during the subsequent 48 hours of cEEG monitoring. Results: Children who developed acute seizures demonstrated higher average spectral power, particularly in the theta frequency range, and distinct patterns of inter-regional connectivity, characterized by greater connectivity at delta and theta frequencies, but weaker connectivity at beta and low gamma frequencies. Subgroup analyses among the 97 children with the same baseline EEG background pattern (generalized slowing) yielded qualitatively and quantitatively similar results. Conclusions: These computational features could be applied to baseline EEG recordings to identify critically-ill children at high risk for acute symptomatic seizures. Significance: If confirmed in independent prospective cohorts, these features would merit incorporation into a decision support system in order to optimize diagnostic and therapeutic management of seizures among comatose children. (c) 2021 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved. DOI PubMed
947. Watkins, HV; Yan, HF; Dunic, JC; Côté, IM.Research biases create overrepresented "poster children" of marine invasion ecology.Conserv. Lett., 2021, 14 Research biases create overrepresented "poster children" of marine invasion ecology
biological invasions; biotic introductions; introduced marine animals; invasion ecology; systematic review; taxonomic bias
Nonnative marine species are increasingly recognized as a threat to the world's oceans, yet are poorly understood relative to their terrestrial and freshwater counterparts. Here, we conducted a systematic review of 2,203 research articles on nonnative marine animals to determine whether the current literature reflects the known diversity of marine invaders, how much we know about these species, and how frequently their impacts are measured. We found that only 39% of nonnative animals listed in the World Register of Introduced Marine Species appeared in the peer-reviewed English literature. Of those, fewer than half were the subject of more than one study. There is currently little focus on the consequences of marine introductions: only 9.9% of studies quantified the impact of nonnative species. Finally, our knowledge of nonnative marine species is heavily limited by strong taxonomic biases consistent across all phyla, resulting in one or two disproportionately well-studied representatives for each phylum, which we refer to as the "poster children" of invasion. These gaps in the literature make it difficult to effectively triage the most detrimental invasive species for management and illustrate the challenges in achieving the global biodiversity goals of preventing and managing the introduction and establishment of invasive species. DOI
946. Wicke, K; Mooers, A; Steel, M.Formal Links between Feature Diversity and Phylogenetic Diversity.Syst. Biol., 2021, 70: 480-490 Formal Links between Feature Diversity and Phylogenetic Diversity
Evolutionary distinctiveness; feature diversity; phylogenetic diversity; shapley value
The extent to which phylogenetic diversity (PD) captures feature diversity (FD) is a topical and controversial question in biodiversity conservation. In this short paper, we formalize this question and establish a precise mathematical condition for FD (based on discrete characters) to coincide with PD. In this way, we make explicit the two main reasons why the two diversity measures might disagree for given data; namely, the presence of certain patterns of feature evolution and loss, and using temporal branch lengths for PD in settings that may not be appropriate (e.g., due to rapid evolution of certain features over short periods of time). Our article also explores the relationship between the "Fair Proportion" index of PD and a simple index of FD (both of which correspond to Shapley values in cooperative game theory). In a second mathematical result, we show that the two indices can take identical values for any phylogenetic tree, provided the branch lengths in the tree are chosen appropriately. DOI PubMed
945. Wilcox, KA; Wagner, MA; Reynolds, JD.Salmon subsidies predict territory size and habitat selection of an avian insectivore.PLoS One, 2021, 16 Salmon subsidies predict territory size and habitat selection of an avian insectivore
The annual migration and spawning event of Pacific salmon (Oncorhynchus spp.) can lead to cross-boundary delivery of marine-derived nutrients from their carcasses into adjacent terrestrial ecosystems. The densities of some passerine species, including Pacific wrens (Troglodytes pacificus), have been shown to be positively correlated with salmon abundance along streams in Alaska and British Columbia, but mechanisms maintaining these densities remain poorly understood. Riparian areas near salmon streams could provide higher quality habitat for birds through greater food availability and more suitable vegetation structure for foraging and breeding, resulting in wrens maintaining smaller territories. We examined relationships between salmon biomass and Pacific wren territory size, competition, and habitat selection along 11 streams on the coast of British Columbia, Canada. We show that male wren densities increase and territory sizes decrease as salmon-spawning biomass increases. Higher densities result in higher rates of competition as male wrens countersing more frequently to defend their territories along streams with more salmon. Wrens were also more selective of the habitats they defended along streams with higher salmon biomass; they were 68% less likely to select low-quality habitat on streams with salmon compared with 46% less likely at streams without salmon. This suggests a potential trade-off between available high-quality habitat and the cost of competition that structures habitat selection. Thus, the marine-nutrient subsidies provided by salmon carcasses to forests lead to higher densities of wrens while shifting the economics of territorial defence toward smaller territories being defended more vigorously in higher quality habitats. DOI PubMed
944. Wilkinson, LV; Alford, MA; Coleman, SR; Wu, BC; Lee, AHY; Blimkie, TM; Bains, M; Falsafi, R; Pletzer, D; Hancock, REW.Peptide 1018 inhibits swarming and influences Anr-regulated gene expression downstream of the stringent stress response in Pseudomonas aeruginosa.PLoS One, 2021, 16 Peptide 1018 inhibits swarming and influences Anr-regulated gene expression downstream of the stringent stress response in Pseudomonas aeruginosa
Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that causes considerable human morbidity and mortality, particularly in nosocomial infections and individuals with cystic fibrosis. P. aeruginosa can adapt to surface growth by undergoing swarming motility, a rapid multicellular movement that occurs on viscous soft surfaces with amino acids as a nitrogen source. Here we tested the small synthetic host defense peptide, innate defense regulator 1018, and found that it inhibited swarming motility at concentrations as low as 0.75 mu g/ml, well below the MIC for strain PA14 planktonic cells (64 mu g/ml). A screen of the PA14 transposon insertion mutant library revealed 29 mutants that were more tolerant to peptide 1018 during swarming, five of which demonstrated significantly greater swarming than the WT in the presence of peptide. Transcriptional analysis (RNA-Seq) of cells that were inoculated on swarming plates containing 1.0 mu g/ml peptide revealed differential expression of 1,190 genes compared to cells swarming on plates without peptide. Furthermore, 1018 treatment distinctly altered the gene expression profile of cells when compared to that untreated cells in the centre of the swarm colonies. Peptide-treated cells exhibited changes in the expression of genes implicated in the stringent stress response including those regulated by anr, which is involved in anaerobic adaptation, indicative of a mechanism by which 1018 might inhibit swarming motility. Overall, this study illustrates potential mechanisms by which peptide 1018 inhibits swarming surface motility, an important bacterial adaptation associated with antibiotic resistance, virulence, and dissemination of P. aeruginosa. DOI PubMed
943. Wilson, K; Grzywacz, D; Cory, JS; Donkersley, P; Graham, RI.Trans-generational viral transmission and immune priming are dose-dependent.J. Anim. Ecol., 2021, 90: 1560-1569 Trans-generational viral transmission and immune priming are dose-dependent
baculovirus; immune priming; outbreak pest; vertical transmission; virus triggering
It is becoming increasingly apparent that trans-generational immune priming (i.e. the transfer of the parental immunological experience to its progeny resulting in offspring protection from pathogens that persist across generations) is a common phenomenon not only in vertebrates, but also invertebrates. Likewise, it is known that covert pathogenic infections may become 'triggered' into an overt infection by various stimuli, including exposure to heterologous infections. Yet, rarely have both phenomena been explored in parallel. Using as a model system the African armyworm Spodoptera exempta, an eruptive agricultural pest and its endemic dsDNA virus (Spodoptera exempta nucleopolyhedrovirus, SpexNPV), the aim of this study was to explore the impact of parental inoculating-dose on trans-generational pathogen transmission and immune priming (in its broadest sense). Larvae were orally challenged with one of five doses of SpexNPV and survivors from these treatments were mated and their offspring monitored for viral mortality. Offspring from parents challenged with low viral doses showed evidence of 'immune priming' (i.e. enhanced survival following SpexNPV challenge); in contrast, offspring from parents challenged with higher viral doses exhibited greater susceptibility to viral challenge. Most offspring larvae died of the virus they were orally challenged with; in contrast, most offspring from parents that had been challenged with the highest doses were killed by the vertically transmitted virus (90%) and not the challenge virus. These results demonstrate that the outcome of a potentially lethal virus challenge is critically dependent on the level of exposure to virus in the parental generation-either increasing resistance at very low parental viral doses (consistent with trans-generational immune priming) or increasing susceptibility at higher parental doses (consistent with virus triggering). We discuss the implications of these findings for understanding both natural epizootics of baculoviruses and for using them as biological control agents. DOI PubMed
942. Wilson, KL; Bailey, CJ; Davies, TD; Moore, JW.Marine and freshwater regime changes impact a community of migratory Pacific salmonids in decline.Glob. Change Biol., 2021, Marine and freshwater regime changes impact a community of migratory Pacific salmonids in decline
Bayesian; ecosystem change; fisheries; population dynamics; salmon; time-series; watersheds
Marine and freshwater ecosystems are increasingly at risk of large and cascading changes from multiple human activities (termed "regime shifts"), which can impact population productivity, resilience, and ecosystem structure. Pacific salmon exhibit persistent and large fluctuations in their population dynamics driven by combinations of intrinsic (e.g., density dependence) and extrinsic factors (e.g., ecosystem changes, species interactions). In recent years, many Pacific salmon have declined due to regime shifts but clear understanding of the processes driving these changes remains elusive. Here, we unpacked the role of density dependence, ecosystem trends, and stochasticity on productivity regimes for a community of five anadromous Pacific salmonids (Steelhead, Coho Salmon, Pink Salmon, Dolly Varden, and Coastal Cutthroat Trout) across a rich 40-year time-series. We used a Bayesian multivariate state-space model to examine whether productivity shifts had similarly occurred across the community and explored marine or freshwater changes associated with those shifts. Overall, we identified three productivity regimes: an early regime (1976-1990), a compensatory regime (1991-2009), and a declining regime (since 2010) where large declines were observed for Steelhead, Dolly Varden, and Cutthroat Trout, intermediate declines in Coho and no change in Pink Salmon. These regime changes were associated with multiple cumulative effects across the salmon life cycle. For example, increased seal densities and ocean competition were associated with lower adult marine survival in Steelhead. Watershed logging also intensified over the past 40 years and was associated with (all else equal) >= 97% declines in freshwater productivity for Steelhead, Cutthroat, and Coho. For Steelhead, marine and freshwater dynamics played approximately equal roles in explaining trends in total productivity. Collectively, these changing environments limited juvenile production and lowered future adult returns. These results reveal how changes in freshwater and marine environments can jointly shape population dynamics among ecological communities, like Pacific salmon, with cascading consequences to their resilience. DOI PubMed
941. Wong, S; Bigman, JS; Dulvy, NK.The metabolic pace of life histories across fishes.Proc. R. Soc. B-Biol. Sci., 2021, 288 The metabolic pace of life histories across fishes
allometry; Bergmann's rule; gill oxygen limitation theory; metabolic theory of ecology; temperature-size rule
All life acquires energy through metabolic processes and that energy is subsequently allocated to life-sustaining functions such as survival, growth and reproduction. Thus, it has long been assumed that metabolic rate is related to the life history of an organism. Indeed, metabolic rate is commonly believed to set the pace of life by determining where an organism is situated along a fast-slow life-history continuum. However, empirical evidence of a direct interspecific relationship between metabolic rate and life histories is lacking, especially for ectothermic organisms. Here, we ask whether three life-history traits-maximum body mass, generation length and growth performance-explain variation in resting metabolic rate (RMR) across fishes. We found that growth performance, which accounts for the trade-off between growth rate and maximum body size, explained variation in RMR, yet maximum body mass and generation length did not. Our results suggest that measures of life history that encompass trade-offs between life-history traits, rather than traits in isolation, explain variation in RMR across fishes. Ultimately, understanding the relationship between metabolic rate and life history is crucial to metabolic ecology and has the potential to improve prediction of the ecological risk of data-poor species. DOI PubMed
940. Zhang, LS; Zhou, AG; Sun, BR; Chen, KS; Yu, HZ.Functional and versatile superhydrophobic coatings via stoichiometric silanization.Nat. Commun., 2021, 12 Functional and versatile superhydrophobic coatings via stoichiometric silanization
Superhydrophobic coatings have tremendous potential for applications in different fields and have been achieved commonly by increasing nanoscale roughness and lowering surface tension. Limited by the availability of either ideal nano-structural templates or simple fabrication procedures, the search of superhydrophobic coatings that are easy to manufacture and are robust in real-life applications remains challenging for both academia and industry. Herein, we report an unconventional protocol based on a single-step, stoichiometrically controlled reaction of long-chain organosilanes with water, which creates micro- to nano-scale hierarchical siloxane aggregates dispersible in industrial solvents (as the coating mixture). Excellent superhydrophobicity (ultrahigh water contact angle >170 degrees and ultralow sliding angle <1<degrees>) has been attained on solid materials of various compositions and dimensions, by simply dipping into or spraying with the coating mixture. It has been demonstrated that these complete waterproof coatings hold excellent properties in terms of cost, scalability, robustness, and particularly the capability of encapsulating other functional materials (e.g. luminescent dyes). Artificial superhydrophobic coatings that are simple to prepare and practical to use are sought after. Here, the authors create versatile, complete-waterproof coatings based on a single-step, stoichiometrically controlled reaction of organosilanes with water. DOI PubMed
939. Arevalo-Cortes, A; Mejia-Jaramillo, AM; Granada, Y; Coatsworth, H; Lowenberger, C; Triana-Chavez, O.The Midgut Microbiota of Colombian Aedes aegypti Populations with Different Levels of Resistance to the Insecticide Lambda-cyhalothrin.Insects, 2020, 11 The Midgut Microbiota of Colombian Aedes aegypti Populations with Different Levels of Resistance to the Insecticide Lambda-cyhalothrin
Aedes aegypti; microbiome; lambda-cyhalothrin; insecticide resistance
Simple Summary Aedes aegypti is a mosquito capable of transmitting many viral diseases such as dengue, Zika, and chikungunya. Since no effective treatments are available for these viruses, eliminating the mosquito with insecticides is vital to combat these diseases. However, the mosquito can generate resistance to the insecticide by changing its genes or its physiology. It has been recognized that the type of bacteria that live inside the mosquito's gut can contribute to this resistance. In this study, we evaluated Ae. aegypti mosquitoes from six locations in Colombia to determine if they are resistant to lambda-cyhalothrin insecticide, and we analyze their gut microbiota. We observed resistance in five of the six areas. We compared the gut microbiota from susceptible and resistant mosquitoes and found specific bacteria in resistant mosquitoes that may play a role in insecticide resistance. Overall, our findings contribute to the understanding of insecticide resistance in Ae. aegypti that will generate alternatives for interventions to control this mosquito in Colombia. Insecticide resistance in Aedes aegypti populations is a problem that hinders vector control and dengue prevention programs. In this study, we determined the susceptibility of Ae. aegypti populations from six Colombian regions to the pyrethroid lambda-cyhalothrin and evaluated the presence of the V1016I mutation in the sodium channel gene, which has been broadly involved in the resistance to this insecticide. The diversity of the gut microbiota of these mosquito populations was also analyzed. Only mosquitoes from Bello were susceptible to lambda-cyhalothrin and presented a lower allelic frequency of the V1016I mutation. Remarkably, there was not an important change in allelic frequencies among populations with different resistance ratios, indicating that other factors or mechanisms contributed to the resistant phenotype. Treatment of mosquitoes with antibiotics led us to hypothesize that the intestinal microbiota could contribute to the resistance to lambda-cyhalothrin. Beta diversity analysis showed significant differences in the species of bacteria present between susceptible and resistant populations. We identified 14 OTUs of bacteria that were unique in resistant mosquitoes. We propose that kdr mutations are important in the development of resistance to lambda-cyhalothrin at low insecticide concentrations but insect symbionts could play an essential role in the metabolization of pyrethroid insecticides at higher concentrations, contributing to the resistant phenotype in Ae. aegypti. DOI PubMed
938. Baltayeva, J; Konwar, C; Castellana, B; Mara, DL; Christians, JK; Beristain, AG.Obesogenic diet exposure alters uterine natural killer cell biology and impairs vasculature remodeling in mice.Biol. Reprod., 2020, 102: 63-75 Obesogenic diet exposure alters uterine natural killer cell biology and impairs vasculature remodeling in mice
pregnancy; natural killer cell; uterus; decidua; placenta; diet-induced obesity; spiral artery remodeling; high-fat/high-sucrose diet; gene expression; gene microarray
Prepregnancy obesity associates with adverse reproductive outcomes that impact maternal and fetal health. While obesity-driven mechanisms underlying adverse pregnancy outcomes remain unclear, local uterine immune cells are strong but poorly studied candidates. Uterine immune cells, particularly uterine natural killer cells (uNKs), play central roles in orchestrating developmental events in pregnancy. However, the effect of obesity on uNK biology is poorly understood. Using an obesogenic high-fat/high-sugar diet (HFD) mouse model, we set out to examine the effects of maternal obesity on uNK composition and establishment of the maternal-fetal interface. HFD exposure resulted in weight gain-dependent increases in systemic inflammation and rates of fetal resorption. While HFD did not affect total uNK frequencies, HFD exposure did lead to an increase in natural cytotoxicity receptor-1 expressing uNKs as well as overall uNK activity. Importantly, HFD-associated changes in uNK coincided with impairments in uterine artery remodeling in mid but not late pregnancy. Comparison of uNK mRNA transcripts from control and HFD mice identified HFD-directed changes in genes that play roles in promoting activity/cytotoxicity and vascular biology. Together, this work provides new insight into how obesity may impact uNK processes central to the establishment of the maternal-fetal interface in early and mid pregnancy. Moreover, these findings shed light on the cellular processes affected by maternal obesity that may relate to overall pregnancy health. Summary sentence High-fat diet promotes uterine NK cell activation in pregnancy and associates with impaired vascular remodeling within the uterus and drives altered uterine NK gene expression. DOI PubMed
937. Belanger, CR; Lee, AHY; Pletzer, D; Dhillon, BK; Falsafi, R; Hancock, REW.Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media.Proc. Natl. Acad. Sci. U. S. A., 2020, 117: 33519-33529 Identification of novel targets of azithromycin activity against Pseudomonas aeruginosa grown in physiologically relevant media
azithromycin; host-mimicking media; RNA-Seq; Pseudomonas aeruginosa; antibiotic susceptibility
Pseudomonas aeruginosa causes severe multidrug-resistant infections that often lead to bacteremia and sepsis. Physiologically relevant conditions can increase the susceptibility of pathogens to antibiotics, such as azithromycin (AZM). When compared to minimal-inhibitory concentrations (MICs) in laboratory media, AZM had a 16-fold lower MIC in tissue culture medium with 5% Mueller Hinton broth (MHB) and a 64-fold lower MIC in this tissue culture medium with 20% human serum. AZM also demonstrated increased synergy in combination with synthetic host-defense peptides DJK-5 and IDR-1018 under host-like conditions and in a murine abscess model. To mechanistically study the altered effects of AZM under physiologically relevant conditions, global transcriptional analysis was performed on P. aeruginosa with and without effective concentrations of AZM. This revealed that the arn operon, mediating arabinosaminylation of lipopolysaccharides and related regulatory systems, was down-regulated in host-like media when compared to MHB. Inactivation of genes within the arn operon led to increased susceptibility of P. aeruginosa to AZM and great increases in synergy between AZM and other antimicrobial agents, indicating that dysregulation of the arn operon might explain increased AZM uptake and synergy in host-like media. Furthermore, genes involved in central and energy metabolism and ribosome biogenesis were dysregulated more in physiologically relevant conditions treated with AZM, likely due to general changes in cell physiology as a result of the increased effectiveness of AZM in these conditions. These data suggest that, in addition to the arn operon, there are multiple factors in host-like environments that are responsible for observed changes in susceptibility. DOI PubMed
936. Brachmann, CG; Hernandez-Ramirez, G; Hik, DS.CH4 uptake along a successional gradient in temperate alpine soils.Biogeochemistry, 2020, 147: 109-123 CH4 uptake along a successional gradient in temperate alpine soils
Columbia mountains; Methane; Soil fluxes; Alpine; Deglaciated terrain, treelike
The effects of climate change appear to be amplified in mountains compared with lowland areas, with rapid changes in plant community composition, soil properties, and increased substrate for biological development following retreat of glaciers. Associated soil gaseous fluxes in alpine ecosystems contribute to the global balance of greenhouse gases, but methane and carbon dioxide soil fluxes and their controls are not well known. We used a dynamic closed-chamber method to measure methane and carbon dioxide fluxes along a successional gradient during the peak growing season in the North Selkirk Mountains, British Columbia, Canada. Soil physico-chemical properties, vegetation cover, and topographic variables were quantified to determine mechanisms influencing these fluxes. Mean methane uptake ranged from - 155 mu g CH4-C m(- 2) h(-1) in well vegetated sites to zero in recently deglaciated terrain. Soil total carbon (TC) and water content were the primary drivers of methane uptake. Sites with TC greater than 4% and moisture below 0.22 water fraction by volume (w.f.v) corresponded to the strongest methane sinks. Increased vegetation cover and relatively drier soil conditions, anticipated with future climate change, suggest that methane uptake may increase in these alpine ecosystems. DOI
934. Cawte, AD; Unrau, PJ; Rueda, DS.Live cell imaging of single RNA molecules with fluorogenic Mango II arrays.Nat. Commun., 2020, 11:1283 Live cell imaging of single RNA molecules with fluorogenic Mango II arrays
RNA molecules play vital roles in many cellular processes. Visualising their dynamics in live cells at single-molecule resolution is essential to elucidate their role in RNA metabolism. RNA aptamers, such as Spinach and Mango, have recently emerged as a powerful background-free technology for live-cell RNA imaging due to their fluorogenic properties upon ligand binding. Here, we report a novel array of Mango II aptamers for RNA imaging in live and fixed cells with high contrast and single-molecule sensitivity. Direct comparison of Mango II and MS2-tdMCP-mCherry dual-labelled mRNAs show marked improvements in signal to noise ratio using the fluorogenic Mango aptamers. Using both coding (beta-actin mRNA) and long non-coding (NEAT1) RNAs, we show that the Mango array does not affect cellular localisation. Additionally, we can track single mRNAs for extended time periods, likely due to bleached fluorophore replacement. This property makes the arrays readily compatible with structured illumination super-resolution microscopy.Website DOI PubMed
933. Colijn, C; Corander, J; Croucher, NJ.Designing ecologically optimized pneumococcal vaccines using population genomics.NAT. MICROBIOL, 2020, Designing ecologically optimized pneumococcal vaccines using population genomics
Streptococcus pneumoniae (the pneumococcus) is a common nasopharyngeal commensal that can cause invasive pneumococcal disease (IPD). Each component of current protein-polysaccharide conjugate vaccines (PCVs) generally induces immunity specific to one of the approximately 100 pneumococcal serotypes, and typically eliminates it from carriage and IPD through herd immunity. Overall carriage rates remain stable owing to replacement by non-PCV serotypes. Consequently, the net change in IPD incidence is determined by the relative invasiveness of the pre- and post-PCV-carried pneumococcal populations. In the present study, we identified PCVs expected to minimize the post-vaccine IPD burden by applying Bayesian optimization to an ecological model of serotype replacement that integrated epidemiological and genomic data. We compared optimal formulations for reducing infant-only or population-wide IPD, and identified potential benefits to including non-conserved pneumococcal carrier proteins. Vaccines were also devised to minimize IPD resistant to antibiotic treatment, despite the ecological model assuming that resistance levels in the carried population would be preserved. We found that expanding infant-administered PCV valency is likely to result in diminishing returns, and that complementary pairs of infant- and adult-administered vaccines could be a superior strategy. PCV performance was highly dependent on the circulating pneumococcal population, further highlighting the advantages of a diversity of anti-pneumococcal vaccination strategies. Here the authors have developed a framework to predict which Streptococcus pneumoniae serotypes would be best targeted by vaccination, of children and adults, to prevent the post-vaccine emergence of similarly virulent strains, thereby minimizing the pneumococcal disease burden. DOI PubMed
932. Côté, IM; Mills, SC.Degrees of honesty: cleaning by the redlip cleaner wrasse Labroides rubrolabiatus.Coral Reefs, 2020, 39: 1693-1701 Degrees of honesty: cleaning by the redlip cleaner wrasse <i>Labroides rubrolabiatus</i>
Cleaning symbiosis; Mutualism; Interspecific interactions; Cleanerfish; Coral reefs
Cleaning symbioses among coral reef fishes are highly variable. Cleanerfishes vary in how much they cooperate with (i.e. remove only ectoparasites) or cheat (i.e. bite healthy tissue, scales or mucus) on their fish clients. As a result, clients use various strategies to enforce cooperation by cleaners (e.g. punishment or partner choice), and cleaners use tactile stimulation to manipulate cheated client behaviour. We provide the first detailed observations of cleaning behaviour of the redlip cleaner wrasse <i>Labroides rubrolabiatus</i> and ask where interactions with this cleanerfish lie on the continuum of cleanerfish honesty, client control, and cleanerfish manipulation. Ninety per cent of redlip cleaner wrasses took jolt-inducing cheating bites from their clients, but they did so at a very low rate (similar to 2 jolts per 100 s inspection). Retaliatory chases by clients were uncommon. Three-quarters (30 of 40) of cleaner wrasses used tactile stimulation on their clients, but rarely did so to reconcile with cheated clients. Instead, the majority (70%) of tactile stimulation events targeted a passing client that then stopped for inspection. The relationship between redlip cleaner wrasses and their clients appears to be less conflictual than those documented in otherLabroidescleanerfishes. Future studies should test whether this low level of conflict is consistent across space and time and is underpinned by a preference for ectoparasites over other client-gleaned items. As an active cleaner that appears to take few cheating bites from their clients,L. rubrolabiatushas the potential to be as important a driver of fish health and community structure on coral reefs as its better-known relatives. DOI
931. Crespi, BJ.The blind men and the elephant: What is missing cognitively in the study of cumulative technological evolution.Behav. Brain Sci., 2020, 43 The blind men and the elephant: What is missing cognitively in the study of cumulative technological evolution
I describe and explain (1) evidence regarding a key role for autism spectrum cognition in human technology; (2) tradeoffs of autistic cognition with social skills; and (3) a model of how cumulative technological culture evolves. This model involves positive feedback whereby increased technical complexity selects for enhanced social learning of mechanistic concepts and skills, leading to further advances in technology. DOI PubMed
930. Delaney, Sean P.; Julian, Lisa M.; Pietrobon, Adam; Yockell-Lelièvre, Julien; Doré, Carole; Wang, Ting T.; Doyon, Valerie C.; Raymond, Angela; Patten, David A.; Kristof, Arnold S.; Harper, Mary-Ellen; Sun, Hongyu; Stanford, William L.Human pluripotent stem cell modeling of tuberous sclerosis complex reveals lineage-specific therapeutic vulnerabilities.bioRxiv, 2020, Human pluripotent stem cell modeling of tuberous sclerosis complex reveals lineage-specific therapeutic vulnerabilities
mTORC1 hyperactivation resulting from inactivating TSC2 mutations underlie the multi-system tumor disorder tuberous sclerosis complex (TSC) and the rare pulmonary neoplasm lymphangioleiomyomatosis (LAM). Mutation-bearing neural precursor cells (NPCs) lead to the formation of TSC brain tumors during development, while the cell of origin of TSC mesenchymal tumors such as LAM is unknown. We report the first model of multi-system TSC cell types, characterized by NPCs and neural crest cells (NCCs) differentiated in parallel from multiple engineered TSC2−/− human pluripotent stem cell (hPSC) lines. These cells successfully model defining phenotypes of neural and mesenchymal TSC, with transcriptomic signatures reflecting those observed in patient tumors, thus establishing TSC2−/− NCCs as a powerful model of LAM. Employing this rich cellular and transcriptomic resource, we identified lineage-specific catabolic signaling mechanisms that drive divergent cell behavior and therapeutic sensitivities that, in turn, demonstrate the power of employing lineage-specific stem cell models to dissect multi-system diseases.Website DOI
929. Dulvy, NK; Yan, HF.Conservation: Goldilocks Nations for Restoring Reef Sharks.Curr. Biol., 2020, 30: R1415-R1418 Conservation: Goldilocks Nations for Restoring Reef Sharks
The first baited, video-based global survey of coral reef sharks reveals widespread depletion and functional extinction from eight nations. The authors identify priority 'Goldilocks' nations with the necessary combination of governance and shark abundance to recover depleted shark populations. DOI PubMed
928. Gibeau, P; Bradford, MJ; Palen, WJ.Can the creation of new freshwater habitat demographically offset losses of Pacific salmon from chronic anthropogenic mortality?PLoS One, 2020, 15 Can the creation of new freshwater habitat demographically offset losses of Pacific salmon from chronic anthropogenic mortality?
Over 1 billion USD are devoted annually to rehabilitating freshwater habitats to improve survival for the recovery of endangered salmon populations. Mitigation often requires the creation of new habitat (e.g. habitat offsetting) to compensate population losses from human activities, however offsetting schemes are rarely evaluated. Anadromous Pacific salmon are ecologically, culturally, and economically important in the US and Canada, and face numerous threats from degradation of freshwater habitats. Here we used a matrix population model of coho salmon (Oncorhynchus kisutch) to determine the amount of habitat offsetting needed to compensate mortality (2-20% per year) caused by a range of development activities. We simulated chronic mortality to three different life stages (egg, parr, smolt/adult), individually and simultaneously, to mimic impacts from development, and evaluated if the number of smolts produced from constructed side-channels demographically offset losses. We show that under ideal conditions, the typical size of a constructed side-channel in the Pacific Northwest (PNW) (3405 m(2)) is sufficient to compensate for only relatively low levels of chronic mortality to either the parr or smolt/adult stages (2-7% per year), but populations do not recover if mortality is >10% per year. When we assumed lower productivity (e.g.; 25(th) percentile), we found that constructed channels would need to be 2.5-4.5 fold larger as compared to the typical size built in the PNW, respectively, to maintain population sizes. Moreover, when we imposed mortality to parr and smolt/adult stages simultaneously, we found that constructed side-channels would need to be between 1.8- and 2.3- fold larger that if the extra chronic mortality was imposed to one life stage only. We conclude that habitat offsetting has the potential to mitigate chronic mortality to early life stages, but that realistic assumptions about productivity of constructed side-channels and cumulative effects of anthropogenic disturbances on multiple life stages need to be considered. DOI PubMed
927. Halley, AC; Baldwin, MKL; Cooke, DF; Englund, M; Krubitzer, L.Distributed Motor Control of Limb Movements in Rat Motor and Somatosensory Cortex: The Sensorimotor Amalgam Revisited.Cereb. Cortex, 2020, 30: 6296-6312 Distributed Motor Control of Limb Movements in Rat Motor and Somatosensory Cortex: The Sensorimotor Amalgam Revisited
sensorimotor; stimulation; motor; rat; evolution
Which areas of the neocortex are involved in the control of movement, and how is motor cortex organized across species? Recent studies using long-train intracortical microstimulation demonstrate that in addition to M1, movements can be elicited from somatosensory regions in multiple species. In the rat, M1 hindlimb and forelimb movement representations have long been thought to overlap with somatosensory representations of the hindlimb and forelimb in S1, forming a partial sensorimotor amalgam. Here we use long-train intracortical microstimulation to characterize the movements elicited across frontal and parietal cortex. We found that movements of the hindlimb, forelimb, and face can be elicited from both M1 and histologically defined S1 and that representations of limb movement types are different in these two areas. Stimulation of S1 generates retraction of the contralateral forelimb, while stimulation of M1 evokes forelimb elevation movements that are often bilateral, including a rostral region of digit grasping. Hindlimb movement representations include distinct regions of hip flexion and hindlimb retraction evoked from S1 and hip extension evoked from M1. Our data indicate that both S1 and M1 are involved in the generation of movement types exhibited during natural behavior. We draw on these results to reconsider how sensorimotor cortex evolved. DOI PubMed
926. Hipfner, JM; Prill, MM; Studholme, KR; Domalik, AD; Tucker, S; Jardine, C; Maftei, M; Wright, KG; Beck, JN; Bradley, RW; Carle, RD; Good, TP; Hatch, SA; Hodum, PJ; Ito, M; Pearson, SF; Rojek, NA; Slater, L; Watanuki, Y; Will, AP; Bindoff, AD; Crossin, GT; Drever, MC; Burg, TM.Geolocator tagging links distributions in the non-breeding season to population genetic structure in a sentinel North Pacific seabird.PLoS One, 2020, 15 Geolocator tagging links distributions in the non-breeding season to population genetic structure in a sentinel North Pacific seabird
We tested the hypothesis that segregation in wintering areas is associated with population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and on 13 colonies in the eastern Pacific Ocean (California to Alaska), and deployed light-level geolocator tags on 12 eastern Pacific colonies to delineate wintering areas. Geolocator tags were deployed previously on one colony in Japan. There was strong genetic differentiation between populations in the eastern vs. western Pacific Ocean, likely due to two factors. First, glaciation over the North Pacific in the late Pleistocene might have forced a southward range shift that historically isolated the eastern and western populations. And second, deep-ocean habitat along the northern continental shelf appears to act as a barrier to movement; abundant on both sides of the North Pacific, the rhinoceros auklet is virtually absent as a breeder in the Aleutian Islands and Bering Sea, and no tagged birds crossed the North Pacific in the non-breeding season. While genetic differentiation was strongest between the eastern vs. western Pacific, there was also extensive differentiation within both regional groups. In pairwise comparisons among the eastern Pacific colonies, the standardized measure of genetic differentiation (F-ST) was negatively correlated with the extent of spatial overlap in wintering areas. That result supports the hypothesis that segregation in the non-breeding season is linked to genetic structure. Philopatry and a neritic foraging habit probably also contribute to the structuring. Widely distributed, vulnerable to anthropogenic stressors, and exhibiting extensive genetic structure, the rhinoceros auklet is fully indicative of the scope of the conservation challenges posed by seabirds. DOI PubMed
925. Jin, SW; Mwimanzi, FM; Mann, JK; Bwana, MB; Lee, GQ; Brumme, CJ; Hunt, PW; Martin, JN; Bangsberg, DR; Ndung'u, T; Brumme, ZL; Brockman, MA.Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5.PLoS Pathog., 2020, 16 Variation in HIV-1 Nef function within and among viral subtypes reveals genetically separable antagonism of SERINC3 and SERINC5
HIV Nef counteracts cellular host restriction factors SERINC3 and SERINC5, but our understanding of how naturally occurring global Nef sequence diversity impacts these activities is limited. Here, we quantify SERINC3 and SERINC5 internalization function for 339 Nef clones, representing the major pandemic HIV-1 group M subtypes A, B, C and D. We describe distinct subtype-associated hierarchies for Nef-mediated internalization of SERINC5, for which subtype B clones display the highest activities on average, and of SERINC3, for which subtype B clones display the lowest activities on average. We further identify Nef polymorphisms that modulate its ability to counteract SERINC proteins, including substitutions in the N-terminal domain that selectively impair SERINC3 internalization. Our findings demonstrate that the SERINC antagonism activities of HIV Nef differ markedly among major viral subtypes and between individual isolates within a subtype, suggesting that variation in these functions may contribute to global differences in viral pathogenesis. Author summary Cellular restriction factors dampen viral replication and reduce pathogenesis. In response, HIV has evolved a variety of mechanisms to counteract restriction factors, including the ability of its Nef protein to internalize Serine incorporator (SERINC) proteins 3 and 5 from the infected cell surface, thereby enhancing infectivity of viral particles. Nef displays substantial sequence diversity, but how this impacts SERINC antagonism remains unclear. To examine this, we used cell culture models to measure SERINC internalization function for 339 participant-derived Nef clones, representing four globally relevant HIV-1 group M subtypes. We observed significant variability in Nef function among circulating viral strains and subtypes. We also identified naturally occurring Nef mutations that modulate its ability to counteract SERINC proteins, including some that selectively impair SERINC3 internalization. These findings uncover viral features that may contribute to global differences in HIV pathogenesis and provide new insight into the interactions between Nef and SERINC restriction factors that can inform future mechanistic studies. DOI PubMed
924. Kankaanpaa, T; Vesterinen, E; Hardwick, B; Schmidt, NM; Andersson, T; Aspholm, PE; Barrio, IC; Beckers, N; Bety, J; Birkemoe, T; DeSiervo, M; Drotos, KHI; Ehrich, D; Gilg, O; Gilg, V; Hein, N; Hoye, TT; Jakobsen, KM; Jodouin, C; Jorna, J; Kozlov, MV; Kresse, JC; Leandri-Breton, DJ; Lecomte, N; Loonen, M; Marr, P; Monckton, SK; Olsen, M; Otis, JA; Pyle, M; Roos, RE; Raundrup, K; Rozhkova, D; Sabard, B; Sokolov, A; Sokolova, N; Solecki, AM; Urbanowicz, C; Villeneuve, C; Vyguzova, E; Zverev, V; Roslin, T.Parasitoids indicate major climate-induced shifts in arctic communities.Glob. Change Biol., 2020, 26: 6276-6295 Parasitoids indicate major climate-induced shifts in arctic communities
Arctic; climate change; DNA barcoding; Dryas; food webs; functional traits; host-parasitoid interactions; insect herbivory; pollinators
Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a widespread habitat,Dryasheathlands, and describe parasitoid community composition in terms of larval host use (i.e., parasitoid use of herbivorous Lepidoptera vs. pollinating Diptera) and functional groups differing in their closeness of host associations (koinobionts vs. idiobionts). Of the latter, we expect idiobionts-as being less fine-tuned to host development-to be generally less tolerant to cold temperatures, since they are confined to attacking hosts pupating and overwintering in relatively exposed locations. To further test our findings, we assess whether similar climatic variables are associated with host abundances in a 22 year time series from Northeast Greenland. We find sites which have experienced a temperature rise in summer while retaining cold winters to be dominated by parasitoids of Lepidoptera, with the reverse being true for the parasitoids of Diptera. The rate of summer temperature rise is further associated with higher levels of herbivory, suggesting higher availability of lepidopteran hosts and changes in ecosystem functioning. We also detect a matching signal over time, as higher summer temperatures, coupled with cold early winter soils, are related to high herbivory by lepidopteran larvae, and to declines in the abundance of dipteran pollinators. Collectively, our results suggest that in parts of the warming Arctic,Dryasis being simultaneously exposed to increased herbivory and reduced pollination. Our findings point to potential drastic and rapid consequences of climate change on multitrophic-level community structure and on ecosystem functioning and highlight the value of collaborative, systematic sampling effort. DOI PubMed
923. Kent, BAP; Dashtgard, SE; Huang, CQ; MacEachern, JA; Gibson, HD; Cathyl-Huhn, G.Initiation and early evolution of a forearc basin: Georgia Basin, Canada.Basin Res., 2020, 32: 163-185 Initiation and early evolution of a forearc basin: Georgia Basin, Canada
coal; forearc basins; Late Cretaceous; sequence stratigraphy; stratigraphy; T-R sequences; transgression
The lower Nanaimo Group was deposited in the (forearc) Georgia Basin, Canada and records the basin's initiation and early depositional evolution. Nanaimo Group strata are subdivided into 11 lithostratigraphic units, which are identified based on lithology, paleontology, texture and position relative to both the basal nonconformity and to each other. Significant topography on the basal nonconformity, however, has resulted in assignment of lithostratigraphic units that are not time correlative, and hence, cannot reliably be used to accurately reconstruct basin evolution. Herein, we present a sequence stratigraphic framework for lower Nanaimo Group strata in the Comox Sub-Basin (northern Georgia Basin) that integrates both facies analysis and maximum depositional ages (MDAs) derived from detrital zircon. This stratigraphic framework is used to define significant sub-basin-wide surfaces that bound depositional units and record the evolution of the basin during its early stages of development. Seven distinct depositional phases are identified in the lower 700 m of the lower Nanaimo Group. Depositional phases are separated by marine flooding surfaces, regressive surfaces, or disconformities. The overall stratigraphy reflects net transgression manifested as an upwards transition from braided fluvial conglomerates to marine mudstones. Transgression was interrupted by periods of shoreline progradation, and both facies analysis and MDAs reveal a disconformity in the lowermost part of the Nanaimo Group in the Comox Sub-Basin. Stratigraphic reconstruction of the Comox Sub-Basin reveals two dominant depocenters (along depositional strike) for coarse clastics (sandstones and conglomerates) during early development of the Georgia Basin. The development and position of these depocenters is attributed to subduction/tectonism driving both subsidence in the north-northwest and uplift in the central Comox Sub-Basin. Our work confirms that in its earliest stages of development, the Georgia Basin evolved from an underfilled, ridged forearc basin that experienced slow and stepwise drowning to a shoal-water ridged forearc basin that experienced rapid subsidence. We also propose that the Georgia Basin is a reasonable analogue for ridged forearc basins globally, as many ridged forearcs record similar depositional histories during their early evolution. DOI
922. Kozhemiako, N; Nunes, AS; Samal, A; Rana, KD; Calabro, FJ; Hamalainen, MS; Khan, S; Vaina, LM.Neural activity underlying the detection of an object movement by an observer during forward self-motion: Dynamic decoding and temporal evolution of directional cortical connectivity.Prog. Neurobiol., 2020, 195 Neural activity underlying the detection of an object movement by an observer during forward self-motion: Dynamic decoding and temporal evolution of directional cortical connectivity
Optic flow; Flow parsing; Magnetoencephalography; Neural decoding; Dynamic Granger causality
Relatively little is known about how the human brain identifies movement of objects while the observer is also moving in the environment. This is, ecologically, one of the most fundamental motion processing problems, critical for survival. To study this problem, we used a task which involved nine textured spheres moving in depth, eight simulating the observer's forward motion while the ninth, the target, moved independently with a different speed towards or away from the observer. Capitalizing on the high temporal resolution of magnetoencephalography (MEG) we trained a Support Vector Classifier (SVC) using the sensor-level data to identify correct and incorrect responses. Using the same MEG data, we addressed the dynamics of cortical processes involved in the detection of the independently moving object and investigated whether we could obtain confirmatory evidence for the brain activity patterns used by the classifier. Our findings indicate that response correctness could be reliably predicted by the SVC, with the highest accuracy during the blank period after motion and preceding the response. The spatial distribution of the areas critical for the correct prediction was similar but not exclusive to areas underlying the evoked activity. Importantly, SVC identified frontal areas otherwise not detected with evoked activity that seem to be important for the successful performance in the task. Dynamic connectivity further supported the involvement of frontal and occipital-temporal areas during the task periods. This is the first study to dynamically map cortical areas using a fully data-driven approach in order to investigate the neural mechanisms involved in the detection of moving objects during observer's self-motion. DOI PubMed
921. Kozhemiako, N; Nunes, AS; Vakorin, V; Iarocci, G; Ribary, U; Doesburg, SM.Alterations in Local Connectivity and Their Developmental Trajectories in Autism Spectrum Disorder: Does Being Female Matter?Cereb. Cortex, 2020, 30: 5166-5179 Alterations in Local Connectivity and Their Developmental Trajectories in Autism Spectrum Disorder: Does Being Female Matter?
autism spectrum disorder; developmental trajectories; fMRI; local connectivity; resting-state networks; sex differences
Autism spectrum disorder (ASD) is diagnosed more often in males with a ratio of 1:4 females/males. This bias is even stronger in neuroimaging studies. There is a growing evidence suggesting that local connectivity and its developmental trajectory is altered in ASD. Here, we aim to investigate how local connectivity and its age-related trajectories vary with ASD in both males and females. We used resting-state fMRI data from the ABIDE I and II repository: males (n=102) and females (n=92) with ASD, and typically developing males (n=104) and females (n=92) aged between 6 and 26. Local connectivity was quantified as regional homogeneity. We found increases in local connectivity in participants with ASD in the somatomotor and limbic networks and decreased local connectivity within the default mode network. These alterations were more pronounced in females with ASD. In addition, the association between local connectivity and ASD symptoms was more robust in females. Females with ASD had the most distinct developmental trajectories of local connectivity compared with other groups. Overall, our findings of more pronounced local connectivity alterations in females with ASD could indicate a greater etiological load for an ASD diagnosis in this group congruent with the female protective effect hypothesis. DOI PubMed
920. Le Moigne, Y, Zurek, JM, Williams-Jones, G, Lev, E; Calahorrano-Di Patre, A; Anzieta, JC.Standing waves in high speed lava channels: A tool for constraining lava flow dynamics and eruptive parameters.Journal of Volcanology and Geothermal Research, 2020, 401, 106944 Standing waves in high speed lava channels: A tool for constraining lava flow dynamics and eruptive parameters
Standing waves; Hydraulic jumps; Supercritical flow; Lava viscosity; Lava flow; Basalt; Real time monitoring
Estimates of the rheological properties of lava flows are essential for understanding their emplacement and for hazard assessment. Despite being a well-known phenomenon in water hydraulics, the formation and presence of standing waves in lava channels is poorly understood. Standing waves, generally located near the vent area, have been frequently described at high speed channelized lava flows. They are interpreted as hydraulic jumps indicating a flow under supercritical conditions. Identifying standing waves therefore offers an opportunity to apply open channel hydraulic theory for supercritical flows in order to determine important eruption parameters such as discharge rate and apparent viscosity. We use the length and amplitude of standing waves to reconstruct flow dynamics from both observational data and video analysis. The geometry of these standing waves allows us to extract the physical properties of the channelized lava (velocity, discharge rate, apparent viscosity), to estimate the channel depth and constrain the flow regime. With the rapid advances in technology, scientists can deploy equipment to enable low-cost real time monitoring of these phenomena and constrain eruption discharge rate and apparent viscosity, key parameters for volcanic hazard assessment and mitigation.PDF DOI
919. Le Moigne, Y; Williams-Jones, G; Russell, JK; Quane, S.Physical volcanology of Tseax volcano, British Columbia, Canada.Journal of Maps, 2020, 16(2), 363-375 Physical volcanology of Tseax volcano, British Columbia, Canada
Tseax volcano; lava flow; mapping; DEM; bathymetry
Tseax volcano erupted ∼ 250 years ago in NW British Columbia, Canada producing tephra deposits and lava flows. Field mapping has defined the stratigraphy of Tseax and the lava flow morphologies. Aerial photogrammetry and bathymetry surveys were used to create a high resolution digital elevation model of the volcano to facilitate mapping and estimates of erupted material volumes. Tseax volcano (∼ 10.4 ± 0.7 × 106 m3) comprises an outer
breached spatter rampart and an inner conical tephra cone. Tseax is associated with a 32 km long and 0.49 ± 0.08 km3 basanite-to-tephrite lava flow field covering ∼ 36 km2 and divided into 4 distinct lava flows with heterogeneous surface morphologies. We present a volcanological map of Tseax volcano at a scale of 1:22,500. This will serve as supporting information for further research on the eruptive history of Tseax volcano and the lava flow field emplacement.PDF DOI
918. Lee, J; Worrall, LJ; Vuckovic, M; Rosell, FI; Gentile, F; Ton, AT; Caveney, NA; Ban, F; Cherkasov, A; Paetzel, M; Strynadka, NCJ.Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site.Nat. Commun., 2020, 11 Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M-pro) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 angstrom resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 angstrom resolution and in its product bound state at 2.0 angstrom resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M-pro inhibition. The SARS-CoV-2 main protease (M-pro) is one of two cysteine proteases essential for viral replication. Here, the authors determine the crystal structure of an M-pro acyl intermediate with its native C-terminal autocleavage sequence and the structure of a product bound active site mutant (C145A), which are of interest for antiviral drug development. DOI PubMed
917. Leung, B; Hargreaves, AL; Greenberg, DA; McGill, B; Dornelas, M; Freeman, R.Clustered versus catastrophic global vertebrate declines.Nature, 2020, 588 Clustered versus catastrophic global vertebrate declines
Recent analyses have reported catastrophic global declines in vertebrate populations(1,2). However, the distillation of many trends into a global mean index obscures the variation that can inform conservation measures and can be sensitive to analytical decisions. For example, previous analyses have estimated a mean vertebrate decline of more than 50% since 1970 (Living Planet Index(2)). Here we show, however, that this estimate is driven by less than 3% of vertebrate populations; if these extremely declining populations are excluded, the global trend switches to an increase. The sensitivity of global mean trends to outliers suggests that more informative indices are needed. We propose an alternative approach, which identifies clusters of extreme decline (or increase) that differ statistically from the majority of population trends. We show that, of taxonomic-geographic systems in the Living Planet Index, 16 systems contain clusters of extreme decline (comprising around 1% of populations; these extreme declines occur disproportionately in larger animals) and 7 contain extreme increases (around 0.4% of populations). The remaining 98.6% of populations across all systems showed no mean global trend. However, when analysed separately, three systems were declining strongly with high certainty (all in the Indo-Pacific region) and seven were declining strongly but with less certainty (mostly reptile and amphibian groups). Accounting for extreme clusters fundamentally alters the interpretation of global vertebrate trends and should be used to help to prioritize conservation efforts. In the geographically and taxonomically divided systems of vertebrates in the Living Planet Index, a small percentage of clusters showed extreme declines or increases, whereas most vertebrate populations across all systems showed no mean global trend. DOI PubMed
916. Lowney, AM; Flower, TP; Thomson, RL.Kalahari skinks eavesdrop on sociable weavers to manage predation by pygmy falcons and expand their realized niche.Behav. Ecol., 2020, 31: 1094-1102 Kalahari skinks eavesdrop on sociable weavers to manage predation by pygmy falcons and expand their realized niche
alarm call; antipredator behavior; communities; ecological engineers; heterospecific eavesdropping; mixed-species groups
Eavesdropping on community members has immediate and clear benefits. However, little is known regarding its importance for the organization of cross-taxa community structure. Furthermore, the possibility that eavesdropping could allow species to coexist with a predator and access risky foraging habitat, thereby expanding their realized niche, has been little considered. Kalahari tree skinks (Trachylepis spilogaster) associate with sociable weaver (Philetairus socius) colonies as do African pygmy falcons (Polihierax semitorquatus), a predator of skinks and weavers. We undertook observational and experimental tests to determine if skinks eavesdrop on sociable weavers to mitigate any increase in predation threat that associating with weaver colonies may bring. Observations reveal that skinks use information from weavers to determine when predators are nearby; skinks were more active, more likely to forage in riskier habitats, and initiated flight from predators earlier in the presence of weavers compared with when weavers were absent. Playback of weaver alarm calls caused skinks to increase vigilance and flee, confirming that skinks eavesdrop on weavers. Furthermore, skinks at sociable weaver colonies were more likely to flee than skinks at noncolony trees, suggesting that learning is mechanistically important for eavesdropping behavior. Overall, it appears that eavesdropping allows skinks at colony trees to gain an early warning signal of potential predators, expand their realized niche, and join communities, whose predators may otherwise exclude them. DOI
915. Mathewes, RW; Greenwood, DR; Love, RL.The Kanaka Creek fossil flora (Huntingdon Formation), British Columbia, Canada - paleoenvironment and evidence for Paleocene age using palynology and macroflora.Can. J. Earth Sci., 2020, 57: 348-365 The Kanaka Creek fossil flora (Huntingdon Formation), British Columbia, Canada - paleoenvironment and evidence for Paleocene age using palynology and macroflora
Paleocene; paleobotany; palynology; paleoclimate; Huntingdon Formation; Kanaka Creek
Paleogene sediments of the Huntingdon Formation, a correlative to the Chuckanut Formation of neighbouring Washington State, USA, are exposed in the Greater Vancouver area, British Columbia, Canada. Palynology and plant macrofossils suggest the Kanaka Creek section is Paleocene rather than Eocene in age. Detrital zircon dating is less decisive, yet indicates the Kanaka rocks are no older than Maastrichtian. Analyses of plant macro- and micro-fossils suggest an early to middle Paleocene age for the Kanaka fossil flora. Paleocene indicators include macrofossils such as Platanus bella, Archeampelos, Hamamelites inequalis, and Ditaxocladus, and pollen taxa such as Paraalnipollenites, Triporopollenites mullensis, and Duplopollis. Paleogene taxa such as Woodwardia maxonii, Macclintockia, and Glyptostrobus dominate the flora. Fungal spores including the Late Cretaceous Pesavis parva and the Paleogene Pesavis tagluensis are notable age indicators. Physiognomy of 41 angiosperm leaf morphotypes from Kanaka Creek yields mean annual temperatures in the microthermal to lower mesothermal range (11.2 +/- 4.3 to 14.6 +/- 2.7 degrees C from leaf margin analysis; 14.8 +/- 2.1 degrees C from Climate Leaf Analysis Multivariate Program), with mild winters (cold month mean temperature 3.9 +/- 3.4 degrees C). Paleoclimate was cooler than the upper Paleocene and Eocene members of the Chuckanut Formation. Mean annual precipitation is estimated at similar to 140 cm with large uncertainties. The Kanaka paleoflora is reconstructed as a mixed conifer-broadleaf forest, sharing common taxa with other western North American Paleocene floras and growing in a temperate moist climate. Kanaka Creek is a rare coastal Paleocene plant locality that provides new insights into coastal vegetation and climate prior to the Paleocene-Eocene Thermal Maximum. DOI
914. McGuire, BE; Hettle, AG; Vickers, C; King, DT; Vocadlo, DJ; Boraston, AB.The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of alpha-1,3-galactosidic linkages in lambda-carrageenan and blood group antigens.J. Biol. Chem., 2020, 295: 18426-18435 The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of alpha-1,3-galactosidic linkages in lambda-carrageenan and blood group antigens
glycoside hydrolase; carrageenan; blood group antigen; galactosidase; Pseudoalteromonas; X-ray crystal structure; glycoside hydrolase; X-ray crystallography; enzyme structure; structural biology; galactose
alpha-Linked galactose is a common carbohydrate motif in nature that is processed by a variety of glycoside hydrolases from different families. Terminal Gal alpha 1-3Gal motifs are found as a defining feature of different blood group and tissue antigens, as well as the building block of the marine algal galactan lambda-carrageenan. The blood group B antigen and linear alpha-Gal epitope can be processed by glycoside hydrolases in family GH110, whereas the presence of genes encoding GH110 enzymes in polysaccharide utilization loci from marine bacteria suggests a role in processing lambda-carrageenan. However, the structure-function relationships underpinning the alpha-1,3-galactosidase activity within family GH110 remain unknown. Here we focus on a GH110 enzyme (PdGH110B) from the carrageenolytic marine bacterium Pseudoalteromonas distincta U2A. We showed that the enzyme was active on Gal alpha 1-3Gal but not the blood group B antigen. X-ray crystal structures in complex with galactose and unhydrolyzed Gal alpha 1-3Gal revealed the parallel beta-helix fold of the enzyme and the structural basis of its inverting catalytic mechanism. Moreover, an examination of the active site reveals likely adaptations that allow accommodation of fucose in blood group B active GH110 enzymes or, in the case of PdGH110, accommodation of the sulfate groups found on lambda-carrageenan. Overall, this work provides insight into the first member of a predominantly marine clade of GH110 enzymes while also illuminating the structural basis of alpha-1,3-galactoside processing by the family as a whole. DOI
913. Mull, CG; Yopak, KE; Dulvy, NK.Maternal Investment, Ecological Lifestyle, and Brain Evolution in Sharks and Rays.Am. Nat., 2020, 195: 1056-1069 Maternal Investment, Ecological Lifestyle, and Brain Evolution in Sharks and Rays
brain evolution; brain organization; oviparity; viviparity; shark; ray
Across vertebrates increased maternal investment (via increased pre- and postnatal provisioning) is associated with larger relative brain size, yet it remains unclear how brain organization is shaped by life history and ecology. Here, we tested whether maternal investment and ecological lifestyle are related to variation in brain size and organization across 100 chondrichthyans. We hypothesized that brain size and organization would vary with the level of maternal investment and habitat depth and complexity. We found that chondrichthyan brain organization varies along four main axes according to (1) absolute brain size, (2) relative diencephalon and mesencephalon size, (3) relative telencephalon and medulla size, and (4) relative cerebellum size. Increased maternal investment is associated with larger relative brain size, while ecological lifestyle is informative for variation between relative telencephalon and medulla size and relative cerebellum size after accounting for the independent effects of reproductive mode. Deepwater chondrichthyans generally provide low levels of yolk-only (lecithotrophic) maternal investment and have relatively small brains, predominantly composed of medulla (a major portion of the hindbrain), whereas matrotrophic chondrichthyans-which provide maternal provisioning beyond the initial yolk sac-found in coastal, reef, or shallow oceanic habitats have relatively large brains, predominantly composed of telencephalon (a major portion of the forebrain). We have demonstrated, for the first time, that both ecological lifestyle and maternal investment are independently associated with brain organization in a lineage with diverse life-history strategies and reproductive modes. DOI PubMed
911. Peters, CH; Watkins, AR; Poirier, OL; Ruben, PC.E1784K, the most common Brugada syndrome and long-QT syndrome type 3 mutant, disrupts sodium channel inactivation through two separate mechanisms.J. Gen. Physiol., 2020, 152 E1784K, the most common Brugada syndrome and long-QT syndrome type 3 mutant, disrupts sodium channel inactivation through two separate mechanisms
Inheritable and de novo variants in the cardiac voltage-gated sodium channel, Nav1.5, are responsible for both long-QT syndrome type 3 (LQT3) and Brugada syndrome type 1 (BrS1). Interestingly, a subset of Nav1.5 variants can cause both LQT3 and BrS1. Many of these variants are found in channel structures that form the channel fast inactivation machinery, altering the rate, voltage dependence, and completeness of the fast inactivation process. We used a series of mutants at position 1784 to show that the most common inheritable Nav1.5 variant, E1784K, alters fast inactivation through two separable mechanisms: (1) a charge-dependent interaction that increases the noninactivating current characteristic of E1784K; and (2) a hyperpolarized voltage dependence and accelerated rate of fast inactivation that decreases the peak sodium current. Using a homology model built on the NavPaS structure, we find that the charge-dependent interaction is between E1784 and K1493 in the DIII-DIV linker of the channel, five residues downstream of the putative inactivation gate. This interaction can be disrupted by a positive charge at position 1784 and rescued with the K1493E/E1784K double mutant that abolishes the noninactivating current. However, the double mutant does not restore either the voltage dependence or rates of fast inactivation. Conversely, a mutant at the bottom of DIVS4, K1641D, causes a hyperpolarizing shift in the voltage dependence of fast inactivation and accelerates the rate of fast inactivation without causing an increase in noninactivating current. These findings provide novel mechanistic insights into how the most common inheritable arrhythmogenic mixed syndrome variant, E1784K, simultaneously decreases transient sodium currents and increases noninactivating currents, leading to both BrS1 and LQT3. DOI PubMed
910. Precht, WF; Aronson, RB; Gardner, TA; Gill, JA; Hawkins, JP; Hernandez-Delgado, EA; Jaap, WC; McClanahan, TR; McField, MD; Murdoch, TJT; Nugues, MM; Roberts, CM; Schelten, CK; Watkinson, AR; Côté, IM.The timing and causality of ecological shifts on Caribbean reefs.Adv. Mar. Biol., 2020, 87: 331-360 The timing and causality of ecological shifts on Caribbean reefs
Caribbean reefs have experienced unprecedented changes in the past four decades. Of great concern is the perceived widespread shift from coral to macroalgal dominance and the question of whether it represents a new, stable equilibrium for coral-reef communities. The primary causes of the shift-grazing pressure (top-down), nutrient loading (bottom-up) or direct coral mortality (side-in)-still remain somewhat controversial in the coral-reef literature. We have attempted to tease out the relative importance of each of these causes. Four insights emerge from our analysis of an early regional dataset of information on the benthic composition of Caribbean reefs spanning the years 1977-2001. First, although three-quarters of reef sites have experienced coral declines concomitant with macroalgal increases, fewer than 10% of the more than 200 sites studied were dominated by macroalgae in 2001, by even the most conservative definition of dominance. Using relative dominance as the threshold, a total of 49 coral-to-macroalgae shifts were detected. This total represents similar to 35% of all sites that were dominated by coral at the start of their monitoring periods. Four shifts (8.2%) occurred because of coral loss with no change in macroalgal cover, 15 (30.6%) occurred because of macroalgal gain without coral loss, and 30 (61.2%) occurred owing to concomitant coral decline and macroalgal increase. Second, the timing of shifts at the regional scale is most consistent with the side-in model of reef degradation, which invokes coral mortality as a precursor to macroalgal takeover, because more shifts occurred after regional coral-mortality events than expected by chance. Third, instantaneous observations taken at the start and end of the time-series for individual sites showed these reefs existed along a continuum of coral and macroalgal cover. The continuous, broadly negative relationship between coral and macroalgal cover suggests that in some cases coral-to-macroalgae phase shifts may be reversed by removing sources of perturbation or restoring critical components such as the herbivorous sea urchin Diadema antillarum to the system. The five instances in which macroalgal dominance was reversed corroborate the conclusion that macroalgal dominance is not a stable, alternative community state as has been commonly assumed. Fourth, the fact that the loss in regional coral cover and concomitant changes to the benthic community are related to punctuated, discrete events with known causes (i.e. coral disease and bleaching), lends credence to the hypothesis that coral reefs of the Caribbean have been under assault from climate-change-related maladies since the 1970s. DOI PubMed
909. Richard, K; Schonhofer, C; Giron, LB; Rivera-Ortiz, J; Read, S; Kannan, T; Kinloch, NN; Shahid, A; Feilcke, R; Wappler, S; Imming, P; Harris, M; Brumme, ZL; Brockman, MA; Mounzer, K; Kossenkov, AV; Abdel-Mohsen, M; Andrae-Marobela, K; Montaner, LJ; Tietjen, I.The African natural product knipholone anthrone and its analogue anthralin (dithranol) enhance HIV-1 latency reversal.J. Biol. Chem., 2020, 295: 14084-14099 The African natural product knipholone anthrone and its analogue anthralin (dithranol) enhance HIV-1 latency reversal
drug-drug synergy; histone deacetylase (HDAC); human immunodeficiency virus (HIV); latency reversal; molecular pharmacology; natural product; protein kinase C (PKC); viral reservoirs; drug discovery; histone deacetylase inhibitor (HDAC inhibitor) (HDI)
A sterilizing or functional cure for HIV is currently precluded by resting CD4(+)T cells that harbor latent but replication-competent provirus. The "shock-and-kill" pharmacological ap-proach aims to reactivate provirus expression in the presence of antiretroviral therapy and target virus-expressing cells for elimination. However, no latency reversal agent (LRA) to date effectively clears viral reservoirs in humans, suggesting a need for new LRAs and LRA combinations. Here, we screened 216 compounds from the pan-African Natural Product Library and identified knipholone anthrone (KA) and its basic building block anthralin (dithranol) as novel LRAs that reverse viral latency at low micromolar concentrations in multiple cell lines. Neither agent's activity depends on protein kinase C; nor do they inhibit class I/II histone deacetylases. However, they are differentially modulated by oxidative stress and metal ions and induce distinct patterns of global gene expression from established LRAs. When applied in combination, both KA and anthralin synergize with LRAs representing multiple functional classes. Finally, KA induces both HIV RNA and protein in primary cells from HIV-infected donors. Taken together, we describe two novel LRAs that enhance the activities of multiple "shock-and-kill" agents, which in turn may inform ongoing LRA combination therapy efforts. DOI PubMed
907. Saunders, LJ; Fitzsimmons, PN; Nichols, JW; Gobas, FAPC.In vitro-in vivo extrapolation of hepatic and gastrointestinal biotransformation rates of hydrophobic chemicals in rainbow trout.Aquat. Toxicol., 2020, 228 In vitro-in vivo extrapolation of hepatic and gastrointestinal biotransformation rates of hydrophobic chemicals in rainbow trout
Bioaccumulation; Biotransformati on; Animal alternatives; In vitro-in vivo extrapolation; Intestinal metabolism; Rainbow trout
Hepatic in vitro biotransformation assays, in combination with in vitro-in vivo extrapolation (IVIVE) and bioaccumulation modeling, can be used to support regulatory bioaccumulation assessments. In most applications, however, these methods ignore the possibility of extrahepatic metabolism. Here we evaluated intestinal biotransformation in rainbow trout using 59 fractions prepared from the upper intestinal (GIT) epithelium. Measured levels of activity determined using standard substrates for phase I and phase II biotransformation enzymes were within 2-fold of activities measured in hepatic 59 fractions. In vitro intrinsic clearance rates for 2-ethylhexyl-4-methoxycinnamate (EHMC; an organic sunscreen agent) and two polycyclic aromatic hydrocarbons (pyrene [PYR] and benzo(a)pyrene [BAP]) were significantly higher in liver 59 fractions than in GIT 59 fractions. For octocrylene (OCT; a second sunscreen agent), however, in vitro intrinsic clearance rates were higher in GIT 59 fractions compared to liver 59 fractions. An existing 'liver only' IVIVE model was expanded to consider biotransformation in both the liver and GIT. Relevant IVIVE scaling factors were developed by morphological, histological, and biochemical evaluation of trout intestines. For chemicals biotransformed at higher rates by hepatic 59 fractions (i.e., BAP, PYR, EHMC), the 'liver & GIT' model yielded whole-body biotransformation rate DOI PubMed
906. Sherman, CS; Heupel, MR; Johnson, M; Kaimuddin, M; Qamar, LMS; Chin, A; Simpfendorfer, CA.Repeatability of baited remote underwater video station (BRUVS) results within and between seasons.PLoS One, 2020, 15 Repeatability of baited remote underwater video station (BRUVS) results within and between seasons
Baited remote underwater video stations (BRUVS) are increasingly being used to evaluate and monitor reef communities. Many BRUVS studies compare multiple sites sampled at single time points that may differ from the sampling time of another site. As BRUVS use grows in its application to provide data relevant to sustainable management, marine protected area success, and overall reef health, understanding repeatability of sampling results is vital. We examined the repeatability of BRUVS results for the elasmobranch community both within and between seasons and years, and explored environmental factors affecting abundances at two sites in Indonesia. On 956 BRUVS, 1139 elasmobranchs (69% rays, 31% sharks) were observed. We found consistent results in species composition and abundances within a season and across years. However, elasmobranch abundances were significantly higher in the wet season. The elasmobranch community was significantly different between the two sites sampled, one site being more coastal and easily accessed by fishermen. Our results demonstrate that while BRUVS are a reliable and repeatable method for surveying elasmobranchs, care must be taken in the timing of sampling between different regions to ensure that any differences observed are due to inherent differences amongst sampling areas as opposed to seasonal dissimilarities. DOI PubMed
905. van der Burght, SN; Rademakers, S; Johnson, JL; Li, CM; Kremers, GJ; Houtsmuller, AB; Leroux, MR; Jansen, G.Ciliary Tip Signaling Compartment Is Formed and Maintained by Intraflagellar Transport.Curr. Biol., 2020, 30: 4299-+ Ciliary Tip Signaling Compartment Is Formed and Maintained by Intraflagellar Transport
Primary cilia are ubiquitous antenna-like organelles that mediate cellular signaling and represent hotspots for human diseases termed ciliopathies. Within cilia, subcompartments are established to support signal transduction pathways, including Hedgehog signaling. How these compartments are formed and maintained remains largely unknown. Cilia use two mechanisms, a trafficking system and a diffusion barrier, to regulate the trafficking of proteins into, within, and out of cilia. The main ciliary trafficking machinery, intraflagellar transport (IFT), facilitates bidirectional transport of cargo, including signaling proteins, from the base (basal body) to the tip of the axoneme [1]. Anterograde IFT to the tip relies on kinesins, and cytoplasmic dynein enables retrograde transport back [2, 3]. To help confine proteins to cilia, a subdomain immediately distal to the basal body, called the transition zone (TZ), acts as a diffusion barrier for both membrane and soluble proteins [4-6]. Here, we show that in Caenorhabditis elegans a salt-sensing receptor-type guanylate cyclase, GCY-22, accumulates at a high concentration within a subcompartment at the distal region of the cilium. Targeting of GCY-22 to the ciliary tip is dynamic, requiring the IFT system. Disruption of the TZ barrier or IFT trafficking causes GCY-22 protein mislocalization and defects in the formation and maintenance of the ciliary tip compartment. Structure-function studies uncovered GCY-22 protein domains needed for entry and tip localization. Together, our findings provide mechanistic insights into the formation and maintenance of a novel subdomain at the cilium tip that contributes to the behavioral response to NaCl. DOI PubMed
904. Venugopal, S; Schiavi, F; Moune, S; Bolfan-Casanova, N; Druitt, T; Williams-Jones, G.Melt inclusion vapour bubbles: the hidden reservoir for major, trace and volatile elements.Nature Scientific Reports, 2020, 10, 9034 Melt inclusion vapour bubbles: the hidden reservoir for major, trace and volatile elements.
Olivine-hosted melt inclusions (MIs) provide samples of magmatic liquids and their dissolved volatiles from deep within the plumbing system. Inevitable post-entrapment modifcations can lead to signifcant compositional changes in the glass and/or any contained bubbles. Re-heating is a common technique to reverse MI crystallisation; however, its efect on volatile contents has been assumed to be minor. We test this assumption using crystallised and glassy basaltic MIs, combined with Raman spectroscopy and 3D imaging, to investigate the changes in fuid and solid phases in the bubbles before and after re-heating. Before re-heating, the bubble contains CO2 gas and anhydrite (CaSO4) crystallites. The rapid difusion of major and volatile elements from the melt during re-heating creates new phases within the bubble: SO2, gypsum, Fe-sulphides. Vapour bubbles hosted in naturally glassy MIs similarly contain a plethora of solid phases (carbonates, sulphates, and sulphides) that account for up to 84% of the total MI sulphur, 80% of CO2, and 14% of FeO. In both re-heated and naturally glassy MIs, bubbles sequester major and volatile elements that are components of the total magmatic budget and represent a “loss” from the glass. Analyses of the glass alone signifcantly underestimates the original magma composition and storage parameters.PDF DOI
903. Wang, YK; Niu, G; Wang, Q; Roy, S; Dai, LY; Wu, HP; Sun, YX; Song, SN; Song, ZT; Xie, YH; Ye, ZG; Meng, XJ; Ren, W.Reliable resistive switching of epitaxial single crystalline cubic Y-HfO2 RRAMs with Si as bottom electrodes.Nanotechnology, 2020, 31 Reliable resistive switching of epitaxial single crystalline cubic Y-HfO2 RRAMs with Si as bottom electrodes
epitaxial HfO2; Y doping; RRAM; resistive switching; conduction mechanism
Previous studies have mainly focused on the resistive switching (RS) of amorphous or polycrystalline HfO2-RRAM. The RS of single crystalline HfO2 films has been rarely reported. Yttrium doped HfO2 (YDH) thin films were fabricated and successful Y incorporation into HfO2 was confirmed by x-ray photoemission spectroscopy. A pure cubic phase of YDH and an abrupt YDH/Si interface were obtained and verified by x-ray diffraction, Raman spectroscopy and transmission electron microscopy. A Pt/YDH/n(++)-Si heterostructure using Si as the bottom electrode was fabricated, which shows stable RS with an ON/OFF ratio of 100 and a reliable data retention (10(4) s). The electron transport mechanism was investigated in detail. It indicates that hopping conduction is dominating when the device is at a high resistance state, while space charge limited conduction acts as the dominant factor at a low resistance state. Such behavior, which is different from devices using TiN or Ti as electrodes, was attributed to the Y doping and specific YDH/Si interface. Our results demonstrate a proof of concept study to use highly doped Si as bottom electrodes along with single crystalline YDH as insulator layer for such RRAM applications as wireless sensors and synaptic simulation. DOI PubMed
901. Williams-Jones, G; Barendregt, RW; Russell, JK; Le Moigne, Y; Enkin, RJ; Gallo R.The age of the Tseax volcanic eruption, British Columbia, Canada.Canadian Journal of Earth Sciences, 2020, The age of the Tseax volcanic eruption, British Columbia, Canada
Tseax volcano; lava flow; tephra cone; paleomagnetism; radiocarbon dating; geochemistry
A recent volcanic eruption occurred at Tseax volcano that formed a series of tephra cones in northwestern British Columbia, Canada. The explosive to effusive eruption also formed a 32 km sequence of Fe-rich Mg-poor basanite–trachybasalt lavas covering 40 km2. Oral stories of the Nisg_a’a Nation report that the eruption may have caused as many as 2000 fatalities. The actual eruption date and question of whether there was one or multiple eruptive episodes in the 14th and 18th centuries are, as of yet, unresolved. New radiocarbon dating of wood charcoal from immediately beneath vent-proximal tephra deposits and complementary age information suggest an eruption in 1675–1778 CE (95.4% probability) was responsible for the formation of the tephra cone. New paleomagnetic and geochemical data from the tephra cone and lava flows suggest there is, in fact, no statistically significant difference in time between the explosive and effusive deposits and that they formed during a single eruptive episode.PDF DOI
900. Williamson, SN; Zdanowicz, C; Anslow, FS; Clarke, GKC; Copland, L; Danby, RK; Flowers, GE; Holdsworth, G; Jarosch, AH; Hik, DS.Evidence for Elevation-Dependent Warming in the St. Elias Mountains, Yukon, Canada.J. Clim., 2020, 33: 3253-3269 Evidence for Elevation-Dependent Warming in the St. Elias Mountains, Yukon, Canada
The climate of high midlatitude mountains appears to be warming faster than the global average, but evidence for such elevation-dependent warming (EDW) at higher latitudes is presently scarce. Here, we use a comprehensive network of remote meteorological stations, proximal radiosonde measurements, downscaled temperature reanalysis, ice cores, and climate indices to investigate the manifestation and possible drivers of EDW in the St. Elias Mountains in subarctic Yukon, Canada. Linear trend analysis of comprehensively validated annual downscaled North American Regional Reanalysis (NARR) gridded surface air temperatures for the years 1979-2016 indicates a warming rate of 0.028 degrees C a(-1) between 5500 and 6000 m above mean sea level (MSL), which is similar to 1.6 times larger than the global-average warming rate between 1970 and 2015. The warming rate between 5500 and 6000 m MSL was similar to 1.5 times greater than the rate at the 2000-2500 m MSL bin (0.019 degrees C a(-1)), which is similar to the majority of warming rates estimated worldwide over similar elevation gradients. Accelerated warming since 1979, measured by radiosondes, indicates a maximum rate at 400 hPa (similar to 7010 m MSL). EDW in the St. Elias region therefore appears to be driven by recent warming of the free troposphere. MODIS satellite data show no evidence for an enhanced snow albedo feedback above 2500 m MSL, and declining trends in sulfate aerosols deposited in high-elevation ice cores suggest a modest increase in radiative forcing at these elevations. In contrast, increasing trends in water vapor mixing ratio at the 500-hPa level measured by radiosonde suggest that a longwave radiation vapor feedback is contributing to EDW. DOI
899. Wong, KKL.First person - Kenneth Kin Lam Wong.J. Cell Sci., 2020, 133 First person - Kenneth Kin Lam Wong
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Kenneth Kin Lam Wong is first author on `Hyperpolarized mitochondria accumulate in Drosophila Hipk-overexpressing cells to drive tumor-like growth', published in JCS. Kenneth is a PhD student in the lab of Dr Esther Verheyen at the Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada, investigating the crosstalk between cell signaling and metabolism in tumor cells. DOI
898. Wong, KKL; Liao, JZ; Shih, CRY; Harden, N; Verheyen, EM.Hyperpolarized mitochondria accumulate in Drosophila Hipk-overexpressing cells to drive tumor-like growth.J. Cell Sci., 2020, 133 Hyperpolarized mitochondria accumulate in Drosophila Hipk-overexpressing cells to drive tumor-like growth
Drosophila; Hipk; Myc; ROS; Energetics; Mitochondria
Both functional and dysfunctional mitochondria are known to underlie tumor progression. Here, we establish use of the proto-oncogene Drosophila Homeodomain-interacting protein kinase (Hipk) as a new tool to address this paradox. We find that, in Hipk-overexpressing tumor-like cells, mitochondria accumulate and switch from fragmented to highly fused interconnected morphologies. Moreover, elevated Hipk promotes mitochondrial membrane hyperpolarization. These mitochondria! changes are at least in part driven by the upregulation of Myc. Furthermore, we show that the altered mitochondrial energetics, but not morphology, is required for Hipk-induced tumor-like growth, because knockdown of pdsw (also known as nd-pdsw, NDUFB10 in mammals; a Complex I subunit) abrogates the growth. Knockdown of ATPsyn beta (a Complex V subunit), which produces higher levels of reactive oxygen species (ROS) than pdsw knockdown, instead synergizes with Hipk to potentiate JNK activation and the downstream induction of matrix metalloproteinases. Accordingly, ATPsyn beta knockdown suppresses Hipk-induced tumor-like growth only when ROS scavengers are co-expressed. Together, our work presents an in vivo tumor model featuring the accumulation of hyperfused and hyperpolarized mitochondria, and reveals respiratory complex subunit-dependent opposing effects on tumorigenic outcomes. This article has an associated First Person interview with the first author of the paper. DOI
897. Zellman, CO; Vu, D; Williams, VE.Adjacent functional group effects on the assembly of columnar liquid crystals.Can. J. Chem., 2020, 98: 379-385 Adjacent functional group effects on the assembly of columnar liquid crystals
supramolecular chemistry; liquid crystal; physical organic chemistry; self-assembly
Although the impact of individual functional groups on the self-assembly of columnar liquid crystal phases has been widely studied, the effect of varying multiple substituents has received much less attention. Herein, we report a series of dibenzo[a,c]phenazines containing an alcohol or ether adjacent to an electron-withdrawing ester or acid. With one exception, these difunctional mesogens form columnar phases. The phase behavior appeared to be dominated by the electron-withdrawing substituent; transition temperatures were similar to derivatives with these groups in isolation. In most instances, the addition of an electron-donating group ortho to an ester or acid suppressed the melting temperature and elevated the clearing temperature, leading to broader liquid crystal thermal ranges. This effect was more pronounced for derivatives functionalized with longer chain hexyloxy groups. These results suggest a potential strategy for controlling the phase ranges of columnar liquid crystals and achieving room temperature mesophases. DOI
896. Bird, BM; Geniole, SN; Procyshyn, TL; Ortiz, TL; Carre, JM; Watson, NV.Effect of exogenous testosterone on cooperation depends on personality and time pressure.Neuropsychopharmacology, 2019, 44 Effect of exogenous testosterone on cooperation depends on personality and time pressure
The social heuristic hypothesis posits that human cooperation is an intuitive response that is expressed especially under conditions of time-constraint. Conversely, it proposes that for individuals given an opportunity for reflection, cooperation is more likely to be curtailed by an optimizing process calibrated to maximize individual benefit in a given situation. Notably, the steroid hormone testosterone has also been implicated in intuitive decision-making, including both prosocial and anti-social behaviors, with effects strongest in men with particular dispositional characteristics. This raises the possibility that increased testosterone may augment the effects predicted by the social heuristic hypothesis, particularly among men higher in specific dispositional characteristics (dominance, impulsivity, independent self-construal: high risk for testosterone-induced antisocial behavior). Here, in a testosterone administration study with a relatively large sample of men (N = 400), we test this possibility in a double-blind, placebo-controlled paradigm, with men randomly assigned to play a one-shot public goods game either under time-pressure (forced intuition) or with a time delay (forced reflection). Results revealed that within the placebo group, time-pressure (versus forced delay) increased cooperation among low risk men, but decreased cooperation among high risk men. Testosterone further moderated this pattern by abolishing the time-pressure effect in low risk men and-in high risk men-reversing the effect by selectively reducing offers (compared to placebo) under forced delay. This is the first evidence that testosterone and personality can interact with time-pressure and delay to predict human cooperation. DOI PubMed
895. Brandl, SJ; Tornabene, L; Goatley, CHR; Casey, JM; Morais, RA; Côté, IM; Baldwin, CC; Parravicini, V; Schiettekatte, NMD; Bellwood, DR.Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning.Science, 2019, 364: 1189 Demographic dynamics of the smallest marine vertebrates fuel coral reef ecosystem functioning
How coral reefs survive as oases of life in low-productivity oceans has puzzled scientists for centuries. The answer may lie in internal nutrient cycling and/or input from the pelagic zone. Integrating meta-analysis, field data, and population modeling, we show that the ocean's smallest vertebrates, cryptobenthic reef fishes, promote internal reef fish biomass production through extensive larval supply from the pelagic environment. Specifically, cryptobenthics account for two-thirds of reef fish larvae in the near-reef pelagic zone despite limited adult reproductive outputs. This overwhelming abundance of cryptobenthic larvae fuels reef trophodynamics via rapid growth and extreme mortality, producing almost 60% of consumed reef fish biomass. Although cryptobenthics are often overlooked, their distinctive demographic dynamics may make them a cornerstone of ecosystem functioning on modern coral reefs. DOI PubMed
894. Bruno, JF; Côté, IM; Toth, LT.Climate Change, Coral Loss, and the Curious Case of the Parrotfish Paradigm: Why Don't Marine Protected Areas Improve Reef Resilience?Annual Review of Marine Science, 2019, 11 Climate Change, Coral Loss, and the Curious Case of the Parrotfish Paradigm: Why Don't Marine Protected Areas Improve Reef Resilience?
coral reef; disturbance; parrotfish; resilience; resistance; climate change
Scientists have advocated for local interventions, such as creating marine protected areas and implementing fishery restrictions, as ways to mitigate local stressors to limit the effects of climate change on reef-building corals. However, in a literature review, we find little empirical support for the notion of managed resilience. We outline some reasons for why marine protected areas and the protection of herbivorous fish (especially parrotfish) have had little effect on coral resilience. One key explanation is that the impacts of local stressors (e.g., pollution and fishing) are often swamped by the much greater effect of ocean warming on corals. Another is the sheer complexity (including numerous context dependencies) of the five cascading links assumed by the managed-resilience hypothesis. If reefs cannot be saved by local actions alone, then it is time to face reef degradation head-on, by directly addressing anthropogenic climate change-the root cause of global coral decline. DOI PubMed
893. Caicedo, P.A., I.M. Serrato, S. Zim, G. Dimopoulos, C. Lowenberger, and C.B. Ocampo.Immune response-related genes associated to blocking midgut dengue virus infection in Aedes aegypti strains that differ in susceptibility to Dengue-2 Virus.Insect Science, 2019, 26, 635–648 Immune response-related genes associated to blocking midgut dengue virus infection in Aedes aegypti strains that differ in susceptibility to Dengue-2 Virus.
Aedes aegypti; dengue virus; innate immune response; knockdown; microarray; vector competence
Aedes (Stegomyia) aegypti, the principal global vector of dengue viruses, has differences in its susceptibility to dengue virus infection. We compared the global expression of genes in the midguts of Colombian Ae. aegypti dengue-susceptible (Cali-S) and dengue-refractory (Cali-MIB) field derived strains after ingesting either a sugarmeal, a bloodmeal, or a bloodmeal containing dengue virus serotype 2 (DENV-2). Microarray-based transcriptome analysis among treatments indicated a total of 4725 transcripts with differential expression between the two strains. Eleven genes were selected from different functional groups based on their significant up or down expression levels as well as reports in the literature suggesting they are associated with dengue virus elimination. We measured mRNA abundance of these 11 genes at 0, 8, 24, and 36 h postinfection using quantitative real time PCR (qPCR) to confirm the microarray results and assess any temporal patterns. Four genes were selected (Gram-negative binding protein-GNBP [AAEL009176], Niemann Pick Type-C2-NPC2 [AAEL015136], Keratinocyte lectin [AAEL009842], and Cathepsin-b [AAEL007585]) for knockdown experiments using RNA interference (RNAi) methodology to determine the phenotype (DENV-2 susceptible or refractory). Silencing GNBP, Cathepsin-b and Keratinocyte lectin reduced the percentage of mosquitoes with disseminated virus in the Cali-S strain to 8%, 20%, and 12% respectively compared with 96% in the controls. Silencing of NPC2 increased the percentage of mosquitos with disseminated virus infections in Cali-MIB to 66% compared with 35% in the controls. This study provides insight into genes that may contribute to the Cali-S susceptible and Cali-MIB refractory phenotypes in Ae. aegypti. DOI PubMed
892. Cantalapiedra, JL; Aze, T; Cadotte, MW; Dalla Riva, GV; Huang, D; Mazel, F; Pennell, MW; Rios, M; Mooers, AO.Conserving evolutionary history does not result in greater diversity over geological time scales.Proc. R. Soc. B-Biol. Sci., 2019, 286 Conserving evolutionary history does not result in greater diversity over geological time scales
conservation; phylogenetic diversity; diversification; macroevolution
Alternative prioritization strategies have been proposed to safeguard biodiversity over macroevolutionary time scales. The first prioritizes the most distantly related species-maximizing phylogenetic diversity (PD)-in the hopes of capturing at least some lineages that will successfully diversify into the future. The second prioritizes lineages that are currently speciating, in the hopes that successful lineages will continue to generate species into the future. These contrasting schemes also map onto contrasting predictions about the role of slow diversifiers in the production of biodiversity over palaeontological time scales. We consider the performance of the two schemes across 10 dated species-level palaeo-phylogenetic trees ranging from Foraminifera to dinosaurs. We find that prioritizing PD for conservation generally led to fewer subsequent lineages, while prioritizing diversifiers led to modestly more subsequent diversity, compared with random sets of lineages. Importantly for conservation, the tree shape when decisions are made cannot predict which scheme will be most successful. These patterns are inconsistent with the notion that long-lived lineages are the source of new species. While there may be sound reasons for prioritizing PD for conservation, long-term species production might not be one of them. DOI PubMed
891. Cenzer, M; M'Gonigle, LK.Local adaptation in dispersal in multi-resource landscapes.Evolution, 2019, 73: 648-660 Local adaptation in dispersal in multi-resource landscapes
Competition; divergence; migration rate; movement; polymorphism; spatial autocorrelation
The distribution of resources in space has important consequences for the evolution of dispersal-related traits. Dispersal moderates patterns of gene flow and, consequently, the potential for local adaptation to spatially differentiated resource types. We lack both models and experiments that evaluate how dispersal evolves in landscapes with multiple resources. Here, we investigate the evolution of dispersal in landscapes that contain two resource types that differ in their spatial autocorrelations. Individuals may possess ecological traits that give them a fitness advantage on one or the other resource. We find that resources differing in their spatial autocorrelation select for different optimal dispersal strategies and, further, that some multi-resource landscapes can support the stable coexistence of distinct dispersal strategies. Whether divergence in dispersal strategies between resource specialists occurs depends on the underlying structure of the resources and the degree of linkage between dispersal strategies and ecological specialization. This work indicates that the spatial autocorrelation of resources is an important factor in determining when evolutionary branching is likely to occur, and sheds light on when secondary isolating mechanisms should arise between locally adaptedspecialists. DOI PubMed
890. Christians, JK; Lennie, KI; Wild, LK; Garcha, R.Effects of high-fat diets on fetal growth in rodents: a systematic review.Reprod. Biol. Endocrinol., 2019, 17: 39 Effects of high-fat diets on fetal growth in rodents: a systematic review
Developmental origins; Fetal growth; Maternal nutrition; Obesity
Background: Maternal nutrition during pregnancy has life-long consequences for offspring. However, the effects of maternal overnutrition and/ or obesity on fetal growth remain poorly understood, e.g., it is not clear why birthweight is increased in some obese pregnancies but not in others. Maternal obesity is frequently studied using rodents on high-fat diets, but effects on fetal growth are inconsistent The purpose of this review is to identify factors that contribute to reduced or increased fetal growth in rodent models of maternal overnutrition. Methods: We searched Web of Science and screened 2173 abstracts and 328 full texts for studies that fed mice or rats diets providing similar to 45% or similar to 60% calories from fat for 3 weeks or more prior to pregnancy. We identified 36 papers matching the search criteria that reported birthweight or fetal weight. Results: Studies that fed 45% fat diets to mice or 60% fat diets to rats generally did not show effects on fetal growth. Feeding a 45% fat diet to rats generally reduced birth and fetal weight. Feeding mice a 60% fat diet for 4-9 weeks prior to pregnancy tended to increase in fetal growth, whereas feeding this diet for a longer period tended to reduce fetal growth. Conclusions: The high-fat diets used most often with rodents do not closely match Western diets and frequently reduce fetal growth, which is not a typical feature of obese human pregnancies. Adoption of standard protocols that more accurately mimic effects on fetal growth observed in obese human pregnancies will improve translational impact in this field.Website DOI PubMed
889. Chua, MD; Liou, CH; Bogdan, AC; Law, HT; Yeh, KM; Lin, JC; Siu, LK; Guttman, JA.Klebsiella pneumoniae disassembles host microtubules in lung epithelial cells.Cell Microbiol., 2019, 21 Klebsiella pneumoniae disassembles host microtubules in lung epithelial cells
Klebsiella pneumoniae raises significant concerns to the health care industry as these microbes are the source of widespread contamination of medical equipment, cause pneumonia as well as other multiorgan metastatic infections and have gained multidrug resistance. Despite soaring mortality rates, the host cell alterations occurring during these infections remain poorly understood. Here, we show that during in vitro and in vivo K. pneumoniae infections of lung epithelia, microtubules are severed and then eliminated. This destruction does not require direct association of K. pneumoniae with the host cells, as microtubules are disassembled in cells that are distant from the infecting bacteria. This microtubule dismantling is dependent on the K. pneumoniae (Kp) gene ytfL as non-pathogenic Escherichia coli expressing Kp ytfL disassemble microtubules in the absence of K. pneumoniae itself. Our data points to the host katanin catalytic subunit A like 1 protein (KATNAL1) and the katanin regulatory subunit B1 protein (KATNB1) as the gatekeepers to the microtubule severing event as both proteins localise specifically to microtubule cut sites. Infected cells that had either of these proteins knocked out maintained intact microtubules. Taken together, we have identified a novel mechanism that a bacterial pathogen has exploited to cause microtubule destruction within the host epithelia. DOI PubMed
888. Cook, KV; Reid, AJ; Patterson, DA; Robinson, KA; Chapman, JM; Hinch, SG; Cooke, SJ.A synthesis to understand responses to capture stressors among fish discarded from commercial fisheries and options for mitigating their severity.Fish. Fish., 2019, 20 A synthesis to understand responses to capture stressors among fish discarded from commercial fisheries and options for mitigating their severity
air exposure; by-catch; fish handling; injury; mortality; physiology
Discarding non-target fish from commercial fisheries is controversial and has been a persistent concern for fisheries managers globally. Discard management strategies typically begin by understanding mortality rates among discarded fish, a challenging task given the dynamic, highly context-specific nature of fisheries. An alternative is to develop our knowledge of how stressors operate by first understanding the causes of mortality that drive this context dependence. Particularly relevant to mitigation efforts is an understanding of how fish respond to the physical factors of fishing, such as the gear itself and methods of fishing and handling the gear. We provide a synthesis of how commercial fishing methods may influence discard mortality and outline means by which capture-induced stress and injury can be mitigated for common commercial gear types, emphasizing method variants or alternatives during capture, handling, and release that could improve survival. This synthesis identifies exhaustion and injury as the most detrimental and ubiquitous stressors experienced by discarded fish, with few options for mitigating their effects. Trawls and hanging net fisheries are identified as the most harmful gears for by-catch, characterized by high stress regardless of method variants and limited options for mitigation. Irrespective of gear type and type of stressor, minimizing durations of capture and handling and encouragement of good handling behaviour (e.g., during landing and sorting) will reduce the magnitude of stress and injury in fish, and ultimately increase survival. DOI
887. Craig, L; Forest, KT; Maier, B.Type IV pili: dynamics, biophysics and functional consequences.Nat. Rev. Microbiol., 2019, 17: 429-440 Type IV pili: dynamics, biophysics and functional consequences
The surfaces of many bacteria are decorated with long, exquisitely thin appendages called type IV pili (T4P), dynamic filaments that are rapidly polymerized and depolymerized from a pool of pilin subunits. Cycles of pilus extension, binding and retraction enable T4P to perform a phenomenally diverse array of functions, including twitching motility, DNA uptake and microcolony formation. On the basis of recent developments, a comprehensive understanding is emerging of the molecular architecture of the T4P machinery and the filament it builds, providing mechanistic insights into the assembly and retraction processes. Combined microbiological and biophysical approaches have revealed how T4P dynamics influence self-organization of bacteria, how bacteria respond to external stimuli to regulate T4P activity for directed movement, and the role of T4P retraction in surface sensing. In this Review, we discuss the T4P machine architecture and filament structure and present current molecular models for T4P dynamics, with a particular focus on recent insights into T4P retraction. We also discuss the functional consequences of T4P dynamics, which have important implications for bacterial lifestyle and pathogenesis. DOI PubMed
886. Crespi, B; Dinsdale, N; Read, S; Hurd, P.Spirituality, dimensional autism, and schizotypal traits: The search for meaning.PLoS One, 2019, 14 Spirituality, dimensional autism, and schizotypal traits: The search for meaning
The relationships of spirituality with human social cognition, as exemplified in autism spectrum and schizophrenia spectrum cognitive variation, remain largely unstudied. We quantified non-clinical levels of autism spectrum and schizotypal spectrum traits (using the Autism Quotient and the Schizotypal Personality Questionnaire-Brief Revised) and dimensions of spirituality (using the Hardt Spirituality Questionnaire) in a large sample of undergraduate students. We tested in particular the hypothesis, based on the diametrical model of autism and psychosis, that autism should be negatively associated, and positive schizotypal traits should be positively associated, with spirituality. Our primary findings were threefold. First, in support of the diametric model, total Spirituality score was significantly negatively correlated with total Autism Quotient score, and significantly positively correlated with Positive Schizotypal traits (the Schizotypal Personality Cognitive-Perceptual subscale), as predicted. Second, these associations were driven mainly by opposite patterns regarding the Search for Meaning Spirituality subscale, which was the only subscale that was significantly negatively associated with autism, and significantly positively associated with Positive Schizotypal traits. Third, Belief in God was positively correlated with Positive Schizotypal traits, but was uncorrelated with autism traits. The opposite findings for Search for Meaning can be interpreted in the contexts of well-supported cognitive models for understanding autism in terms of weak central coherence, and understanding Positive Schizotypal traits in terms of enhanced salience. DOI PubMed
885. Darolti, I; Wright, AE; Sandkam, BA; Morris, J; Bloch, NI; Farre, M; Fuller, RC; Bourne, GR; Larkin, DM; Breden, F; Mank, JE.Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers.Proc. Natl. Acad. Sci. U. S. A., 2019, 116: 19031-19036 Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers
Y degeneration; dosage compensation; recombination; poeciliids
Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing Glade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation. DOI PubMed
884. Dhanda, AS; Lulic, KT; Vogl, AW; Mc Gee, MM; Chiu, RH; Guttman, JA.Listeria Membrane Protrusion Collapse: Requirement of Cyclophilin A for Listeria Cell-to-Cell Spreading.J. Infect. Dis., 2019, 219 Listeria Membrane Protrusion Collapse: Requirement of Cyclophilin A for Listeria Cell-to-Cell Spreading
cell-to-cell spread; cyclophilin A; Listeria; Listeria monocytogenes
Background. Listeria generate actin-rich tubular protrusions at the plasma membrane that propel the bacteria into neighboring cells. The precise molecular mechanisms governing the formation of these protrusions remain poorly defined. Methods. In this study, we demonstrate that the prolyl cis-trans isomerase (PPIase) cyclophilin A (CypA) is hijacked by Listeria at membrane protrusions used for cell-to-cell spreading. Results. Cyclophilin A localizes within the F-actin of these structures and is crucial for their proper formation, as cells depleted of CypA have extended actin-rich structures that are misshaped and are collapsed due to changes within the F-actin network. The lack of structural integrity within the Listeria membrane protrusions hampers the microbes from spreading from CypA null cells. Conclusions. Our results demonstrate a crucial role for CypA during Listeria infections. DOI PubMed
883. Escasa, SR; Harrison, RL; Mowery, JD; Bauchan, GR; Cory, JS.The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa.PLoS One, 2019, 14 The complete genome sequence of an alphabaculovirus from Spodoptera exempta, an agricultural pest of major economic significance in Africa
Spodoptera exempta nucleopolyhedrovirus (SpexNPV) is a viral pathogen of the African armyworm, Spodoptera exempta (Lepidoptera: Noctuidae), a significant agricultural pest of cereal crops in Africa. SpexNPV has been evaluated as a potential insecticide for control of this pest and has served as the subject of research on baculovirus pathology and transmission. Occlusion bodies (OBs) of SpexNPV isolate 244.1 were examined, and the nucleotide sequence of the genome was determined and characterized. SpexNPV-244.1 OBs consisted of irregular polyhedra with a size and appearance typical for alphabaculoviruses. Virions within the polyhedra contained 1-8 nucleocapsids per unit envelope. The SpexNPV-244.1 genome was comprised of a 129,528 bp circular sequence, in which 139 ORFs were annotated. Five homologous regions (hrs) consisting of a variable number of 28-bp imperfect palindromes were identified in the genome. The genome sequence contained the 38 core genes of family Baculoviridae, as well as three ORFs unique to the SpexNPV sequence and one ORF that was apparently acquired by horizontal gene transfer with a betabaculovirus ancestor. Phylogenetic inference with core gene amino acid sequence alignments placed SpexNPV-244.1 in a lineage containing alphabaculoviruses of Spodoptera frugiperda and Spodopotera exigua which in turn is part of a larger group of alphabaculoviruses from the subfamily Noctuinae in the lepidopteran family Noctuidae. Kimura-2-parameter pairwise nucleotide distances indicated that SpexNPV-244.1 represented a different and previously unlisted species in the genus Alphabaculovirus. Gene parity plots indicated that the gene order of SpexNPV-244. I was extensively collinear with that of Spodoptera exigua NPV (SeMNPV). These plots also revealed a group of 17 core genes whose order was conserved in other alpha-and betabaculoviruses. DOI PubMed
882. Fan, JT; Willdorf-Cohen, S; Schibli, EM; Paula, Z; Li, W; Skalski, TJG; Sergeenko, AT; Hohenadel, A; Frisken, BJ; Magliocca, E; Mustain, WE; Diesendruck, CE; Dekel, DR; Holdcroft, S.Poly(bis-arylimidazoliums) possessing high hydroxide ion exchange capacity and high alkaline stability.Nat. Commun., 2019, 10 Poly(bis-arylimidazoliums) possessing high hydroxide ion exchange capacity and high alkaline stability
Solid polymer electrolyte electrochemical energy conversion devices that operate under highly alkaline conditions afford faster reaction kinetics and the deployment of inexpensive electrocatalysts compared with their acidic counterparts. The hydroxide anion exchange polymer is a key component of any solid polymer electrolyte device that operates under alkaline conditions. However, durable hydroxide-conducting polymer electrolytes in highly caustic media have proved elusive, because polymers bearing cations are inherently unstable under highly caustic conditions. Here we report a systematic investigation of novel arylimidazolium and bis-arylimidazolium compounds that lead to the rationale design of robust, sterically protected poly(arylimidazolium) hydroxide anion exchange polymers that possess a combination of high ion-exchange capacity and exceptional stability. DOI PubMed
881. Gomes, LMF; Mahammed, A; Prosser, KE; Smith, JR; Silverman, MA; Walsby, CJ; Gross, Z; Storr, T.A catalytic antioxidant for limiting amyloid-beta peptide aggregation and reactive oxygen species generation.Chem. Sci., 2019, 10 A catalytic antioxidant for limiting amyloid-beta peptide aggregation and reactive oxygen species generation
Alzheimer's disease (AD) is a multifaceted disease that is characterized by increased oxidative stress, metal-ion dysregulation, and the formation of intracellular neurofibrillary tangles and extracellular amyloid-beta (A beta) aggregates. In this work we report the large affinity binding of the iron(III) 2,17-bis-sulfonato-5,10,15-tris(pentafluorophenyl)corrole complex FeL1 to the A beta peptide (K-d similar to 10(-7)) and the ability of the bound FeL1 to act as a catalytic antioxidant in both the presence and absence of Cu(II) ions. Specific findings are that: (a) an A beta histidine residue binds axially to FeL1; (b) that the resulting adduct is an efficient catalase; (c) this interaction restricts the formation of high molecular weight peptide aggregates. UV-Vis and electron paramagnetic resonance (EPR) studies show that although the binding of FeL1 does not influence the A beta-Cu(II) interaction (K-d similar to 10(-10)), bound FeL1 still acts as an antioxidant thereby significantly limiting reactive oxygen species (ROS) generation from A beta-Cu. Overall, FeL1 is shown to bind to the A beta peptide, and modulate peptide aggregation. In addition, FeL1 forms a ternary species with A beta-Cu(II) and impedes ROS generation, thus showing the promise of discrete metal complexes to limit the toxicity pathways of the A beta peptide. DOI PubMed
879. Gutiérrez-Cabrera, A.E., W.F. Zandberg, E.Zenteno, M.H. Rodríguez, B. Espinoza and C. Lowenberger.Glycosylation on proteins of the intestine and perimicrovillar membrane of Triatoma (Meccus) pallidipennis, under different feeding conditions.Insect Science, 2019, 26: 796-808 Glycosylation on proteins of the intestine and perimicrovillar membrane of Triatoma (Meccus) pallidipennis, under different feeding conditions.
feeding conditions; glycoproteins; lectins; perimicrovillar membrane; triatomine; vector-parasite interactions
Trypanosoma cruzi, the causative agent of Chagas disease, interacts with molecules in the midgut of its insect vector to multiply and reach the infective stage. Many studies suggest that the parasite binds to midgut-specific glycans. We identified several glycoproteins expressed in the intestine and perimicrovillar membrane (PMM) of Triatoma (Meccus) pallidipennis under different feeding conditions. In order to assess changes in protein-linked glycans, we performed lectin and immunoblot analyses on glycoprotein extracts from these intestinal tissues using well-characterized lectins, and an antibody, which collectively recognize a wide range of different glycans epitopes. We observed that the amount and composition of proteins and glycoproteins associated with different glycans structures changed over time in the intestines and PMM under different physiological conditions. PMM extracts contained a wide variety of glycoproteins with different sugar residues, including abundant high-mannose and complex sialylated glycans. We propose that these molecules could be involved in the process of parasite-vector interactions. DOI PubMed
878. Hall, ET; Hoesing, E; Sinkovics, E; Verheyen, EM.Actomyosin contractility modulates Wnt signaling through adherens junction stability.Mol. Biol. Cell, 2019, 30 Actomyosin contractility modulates Wnt signaling through adherens junction stability
Actomyosin contractility can influence the canonical Wnt signaling pathway in processes like mesoderm differentiation and tissue stiffness during tumorigenesis. We identified that increased nonmuscle myosin II activation and cellular contraction inhibited Wnt target gene transcription in developing Drosophila imaginal disks. Genetic interactions studies were used to show that this effect was due to myosin-induced accumulation of cortical F-actin resulting in clustering and accumulation of E-cadherin to the adherens junctions. This results in E-cadherin titrating any available beta-catenin, the Wnt pathway transcriptional coactivator, to the adherens junctions in order to maintain cell-cell adhesion under contraction. We show that decreased levels of cytoplasmic beta-catenin result in insufficient nuclear translocation for full Wnt target gene transcription. Previous studies have identified some of these interactions, but we present a thorough analysis using the wing disk epithelium to show the consequences of modulating myosin phosphatase. Our work elucidates a mechanism in which the dynamic promotion of actomyosin contractility refines patterning of Wnt transcription during development and maintenance of epithelial tissue in organisms. DOI PubMed
876. Hodgson, EE; Halpern, BS.Investigating cumulative effects across ecological scales.Conserv. Biol., 2019, 33 Investigating cumulative effects across ecological scales
cumulative effects assessment; meta-analysis; multispecies modeling; population modeling; qualitative modeling; review
Species, habitats, and ecosystems are increasingly exposed to multiple anthropogenic stressors, fueling a rapidly expanding research program to understand the cumulative impacts of these environmental modifications. Since the 1970s, a growing set of methods has been developed through two parallel, sometimes connected, streams of research within the applied and academic realms to assess cumulative effects. Past reviews of cumulative effects assessment (CEA) methods focused on approaches used by practitioners. Academic research has developed several distinct and novel approaches to conducting CEA. Understanding the suite of methods that exist will help practitioners and academics better address various ecological foci (physiological responses, population impacts, ecosystem impacts) and ecological complexities (synergistic effects, impacts across space and time). We reviewed 6 categories of methods (experimental, meta-analysis, single-species modeling, mapping, qualitative modeling, and multispecies modeling) and examined the ability of those methods to address different levels of complexity. We focused on research gaps and emerging priorities. We found that no single method assessed impacts across the 4 ecological foci and 6 ecological complexities considered. We propose that methods can be used in combination to improve understanding such that multimodel inference can provide a suite of comparable outputs, mapping methods can help prioritize localized models or experimental gaps, and future experiments can be paired from the outset with models they will inform. DOI PubMed
875. Horswill, C; Kindsvater, HK; Juan-Jorda, MJ; Dulvy, NK; Mangel, M; Matthiopoulos, J.Global reconstruction of life-history strategies: A case study using tunas.J. Appl. Ecol., 2019, 56: 855-865 Global reconstruction of life-history strategies: A case study using tunas
Bayesian imputation; data limited; demography; fecundity; life-history theory; missing data; principal market tuna; Scombridae
Measuring the demographic parameters of exploited populations is central to predicting their vulnerability and extinction risk. However, current rates of population decline and species loss greatly outpace our ability to empirically monitor all populations that are potentially threatened. The scale of this problem cannot be addressed through additional data collection alone, and therefore it is a common practice to conduct population assessments based on surrogate data collected from similar species. However, this approach introduces biases and imprecisions that are difficult to quantify. Recent developments in hierarchical modelling have enabled missing values to be reconstructed based on the correlations between available life-history data, linking similar species based on phylogeny and environmental conditions. However, these methods cannot resolve life-history variability among populations or species that are closely placed spatially or taxonomically. Here, theoretically motivated constraints that align with life-history theory offer a new avenue for addressing this problem. We describe a Bayesian hierarchical approach that combines fragmented, multispecies and multi-population data with established life-history theory, in order to objectively determine similarity between populations based on trait correlations (life-history trade-offs) obtained from model fitting. We reconstruct 59 unobserved life-history parameters for 23 populations of tuna that sustain some of the world's most valuable fisheries. Testing by cross-validation across different scenarios indicated that life-histories were accurately reconstructed when information was available for other populations of the same species. The reconstruction of several traits was also accurate for species represented by a single population, although credible intervals increased dramatically.Synthesis and applications. The described Bayesian hierarchical method provides access to life-history traits that are difficult to measure directly and reconstructs missing life-history information useful for assessing populations and species that are directly or indirectly affected by human exploitation of natural resources. The method is particularly useful for examining populations that are spatially or taxonomically similar, and the reconstructed life-history strategies described for the principal market tunas have immediate application to the world-wide management of these fisheries. The described Bayesian hierarchical method provides access to life-history traits that are difficult to measure directly and reconstructs missing life-history information useful for assessing populations and species that are directly or indirectly affected by human exploitation of natural resources. The method is particularly useful for examining populations that are spatially or taxonomically similar, and the reconstructed life-history strategies described for the principal market tunas have immediate application to the world-wide management of these fisheries. DOI PubMed
874. Hutter, H.Formation of longitudinal axon pathways in Caenorhabditis elegans.Semin. Cell Dev. Biol., 2019, 85 Formation of longitudinal axon pathways in Caenorhabditis elegans
Axon guidance; Growth cone; Ventral nerve cord; Pioneer; Follower
The small number of neurons and the simple architecture of the Caenorhabditis elegans (C. elegans) nervous system enables researchers to study axonal pathfinding at the level of individually identified axons. Axons in C. elegans extend predominantly along one of the two major body axes, the anterior-posterior axis and the dorso-ventral axis. This review will focus on axon navigation along the anterior-posterior axis, leading to the establishment of the longitudinal axon tracts, with a focus on the largest longitudinal axon tract, the ventral nerve cord (VNC). In the VNC, axons grow out in a stereotypic order, with early outgrowing axons (pioneers) playing an important role in guiding later outgrowing (follower) axons. Genetic screens have identified a number of genes specifically affecting the formation of longitudinal axon tracts. These genes include secreted proteins, putative receptors and adhesion molecules, as well as intracellular proteins regulating the cell's response to guidance cues. In contrast to dorso-ventral navigation, no major general guidance cues required for the establishment of longitudinal pathways have been identified so far. The limited penetrance of defects found in many mutants affecting longitudinal navigation suggests that guidance cues act redundantly in this process. The majority of the axon guidance genes identified in C. elegans are evolutionary conserved, i.e. have homologs in other animals, including vertebrates. For a number of these genes, a role in axon guidance has not been described outside C. elegans. Taken together, studies in C. elegans contribute to a fundamental understanding of the molecular basis of axonal navigation that can be extended to other animals, including vertebrates and probably humans as well. (C) 2017 Elsevier Ltd. All rights reserved. DOI PubMed
873. Kharouba, HM; Lewthwaite, JMM; Guralnick, R; Kerr, JT; Vellend, M.Using insect natural history collections to study global change impacts: challenges and opportunities.Philos. Trans. R. Soc. B-Biol. Sci., 2019, 374 Using insect natural history collections to study global change impacts: challenges and opportunities
specimens; museum; range shifts; climate change; seasonal timing
Over the past two decades, natural history collections (NHCs) have played an increasingly prominent role in global change research, but they have still greater potential, especially for the most diverse group of animals on Earth: insects. Here, we review the role of NHCs in advancing our understanding of the ecological and evolutionary responses of insects to recent global changes. Insect NHCs have helped document changes in insects' geographical distributions, phenology, phenotypic and genotypic traits over time periods up to a century. Recent work demonstrates the enormous potential of NHCs data for examining insect responses at multiple temporal, spatial and phylogenetic scales. Moving forward, insect NHCs offer unique opportunities to examine the morphological, chemical and genomic information in each specimen, thus advancing our understanding of the processes underlying species' ecological and evolutionary responses to rapid, widespread global changes. This article is part of the theme issue 'Biological collections for understanding biodiversity in the anthropocene'. DOI PubMed
872. Korecki, AJ; Hickmott, JW; Lam, SL; Dreolini, L; Mathelier, A; Baker, O; Kuehne, C; Bonaguro, RJ; Smith, J; Tan, CV; Zhou, M; Goldowitz, D; Deussing, JM; Stewart, AF; Wasserman, WW; Holt, RA; Simpson, EM.Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain, Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele.Genetics, 2019, 211 Twenty-Seven Tamoxifen-Inducible iCre-Driver Mouse Strains for Eye and Brain, Including Seventeen Carrying a New Inducible-First Constitutive-Ready Allele
gene; expression; retina; cornea; brain; inducible; constitutive; promoter; transgenic mice; Hprt locus; targeted mutation; bacterial artificial chromosome
To understand gene function, the cre/loxP conditional system is the most powerful available for temporal and spatial control of expression in mouse. However, the research community requires more cre recombinase expressing transgenic mouse strains (cre-drivers) that restrict expression to specific cell types. To address these problems, a high-throughput method for large-scale production that produces high-quality results is necessary. Further, endogenous promoters need to be chosen that drive cell type specific expression, or we need to further focus the expression by manipulating the promoter. Here we test the suitability of using knock-ins at the docking site 5 ' of Hprt for rapid development of numerous cre-driver strains focused on expression in adulthood, using an improved cre tamoxifen inducible allele (icre/ERT2), and testing a novel inducible-first, constitutive-ready allele (icre/f3/ERT2/f3). In addition, we test two types of promoters either to capture an endogenous expression pattern (MaxiPromoters), or to restrict expression further using minimal promoter element(s) designed for expression in restricted cell types (MiniPromoters). We provide new cre-driver mouse strains with applicability for brain and eye research. In addition, we demonstrate the feasibility and applicability of using the locus 5 ' of Hprt for the rapid generation of substantial numbers of cre-driver strains. We also provide a new inducible-first constitutive-ready allele to further speed cre-driver generation. Finally, all these strains are available to the research community through The Jackson Laboratory. DOI PubMed
871. Macfarland, L; Mahony, NA; Harrison, M; Green, D.Habitat-mediated breeding performance of Lewis's Woodpeckers (Melanerpes lewis) in British Columbia.PLoS One, 2019, 14 Habitat-mediated breeding performance of Lewis's Woodpeckers (Melanerpes lewis) in British Columbia
Tree cavities provide a critical resource for cavity-nesting animals, and high quality cavities can be difficult for animals to acquire in habitats where competition is high. We investigated the breeding performance of Lewis's Woodpeckers in three habitat types in British Columbia, Canada in 2013 and 2014. We also assessed whether the number of nest competitors and cavity availability influenced the habitat specific breeding performance of this threatened cavity nesting species. We found that daily nest survival rate was lower in burned habitat (0.15 +/- 0.08 (0.05-0.37)) than in live pine (0.72 +/- 0.10 (0.51-0.87)) or cottonwood (0.69 +/- 0.09 (0.51-0.83)) habitats. However, hatching success (the proportion of eggs that hatch) was lower in live pine habitat (0.59 +/- 0.09 95% CI) than burned (0.77 +/- 0.19 95% CI) or cottonwood (0.80 +/- 0.07 95% CI) habitat, and the fledging success of successful nests in live pine and burned habitat (1.86 +/- 0.31 and 1.88 +/- 0.59 95% CI, respectively) was slightly lower than in cottonwood habitat (2.61 +/- 0.45 95% CI). Consequently, Lewis's Woodpeckers in cottonwood habitat produced more fledglings per nesting attempt (2.05 +/- 0.49 95% CI) than in live pine (1.53 +/- 0.35 95% CI) or burned (0.79 +/- 0.49 95% CI) habitat. Habitats differed in the number of nesting competitors and the number of suitable cavities surrounding active Lewis's Woodpecker nests. Our results showed that cavity density best explained breeding performance differences although the mechanisms remain unclear. There was no evidence that the number of heterospecific nest competitors, including the invasive European Starling (Sturnus vulgaris), explained or influenced Lewis's Woodpecker breeding performance. Cavity density influenced the productivity of successful nests but did not explain habitat differences in hatching success or daily nest survival. Further work is required to understand the mechanistic basis for the habitat specific breeding performance of Lewis's Woodpeckers. Habitat differences in breeding performance in British Columbia are not consistent with those in other regions, highlighting the importance of regionally-specific demographic data for managing species at risk. DOI PubMed
870. Marushka, L; Kenny, TA; Batal, M; Cheung, WWL; Fediuk, K; Golden, CD; Salomon, AK; Sadik, T; Weatherdon, LV; Chan, HM.Potential impacts of climate-related decline of seafood harvest on nutritional status of coastal First Nations in British Columbia, Canada.PLoS One, 2019, 14 Potential impacts of climate-related decline of seafood harvest on nutritional status of coastal First Nations in British Columbia, Canada
Background Traditional food systems are under pressure from various stressors, including climate change which is projected to negatively alter the abundance of marine species harvested by coastal First Nations (FNs) in British Columbia (BC). Objective To model the potential impacts of the climate-related declines in seafood production on the nutritional status of coastal BC FNs. In addition, we projected potential changes in nutrient intakes, under different scenarios of substitution where traditional seafood is replaced with alternative non-traditional foods. Methods The study design is a mixed-method approach that combines two datasets: projected scenarios of climate-related change on seafood catch potential for coastal BC FNs and data derived from the cross-sectional First Nations Food, Nutrition, and Environment Study. The consumption of seafood was estimated using a food frequency questionnaire among 356 FNs. The contribution of seafood consumption to protein, eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), vitamins (A, B12, D, niacin), and minerals (zinc, selenium and iron) requirements was assessed using Dietary Reference Intakes (DRIs). Results Traditional seafood consumption provided daily recommendations of EPA+DHA (74-184%) and vitamin B12 (84-152%) and substantial levels of niacin (28-55%), selenium (29-55%), vitamin D (15-30%) and protein (14-30%). Projected climate change was estimated to reduce the intakes of essential nutrients by 21% and 31% under 'strong mitigation' (Representative Concentration Pathway, RCP2.6) and 'business-as-usual' (RCP8.5) climate change scenarios, respectively, by the year 2050 relative to 2000. The hypothetical substitution of seafood with selected alternative non-traditional foods does not provide adequate amounts of nutrients. Conclusion Traditionally-harvested seafood remains fundamental to the contemporary diet and health of coastal BC FNs. Potential dietary shifts aggravated by climate-related declines in seafood consumption may have significant nutritional and health implications for BC FN. Strategies to improve access to seafood harvest potential in coastal communities are needed to ensure nutritional health and overall well-being and to promote food security and food sovereignty in coastal FNs. DOI PubMed
868. McAlpine, JB; Chen, SN; Kutateladze, A; MacMillan, JB; Appendino, G; Barison, A; Beniddir, MA; Biavatti, MW; Bluml, S; Boufridi, A; Butler, MS; Capon, RJ; Choi, YH; Coppage, D; Crews, P; Crimmins, MT; Csete, M; Dewapriya, P; Egan, JM; Garson, MJ; Genta-Jouve, G; Gerwick, WH; Gross, H; Harper, MK; Hermanto, P; Hook, JM; Hunter, L; Jeannerat, D; Ji, NY; Johnson, TA; Kingston, DGI; Koshino, H; Lee, HW; Lewin, G; Li, J; Linington, RG; Liu, MM; McPhail, KL; Molinski, TF; Moore, BS; Nam, JW; Neupane, RP; Niemitz, M; Nuzillard, JM; Oberlies, NH; Ocampos, FMM; Pan, G; Quinn, RJ; Reddy, DS; Renault, JH; Rivera-Chavez, J; Robien, W; Saunders, CM; Schmidt, TJ; Seger, C; Shen, B; Steinbeck, C; Stuppner, H; Sturm, S; Taglialatela-Scafati, O; Tantillo, DJ; Verpoorte, R; Wang, BG; Williams, CM; Williams, PG; Wist, J; Yue, JM; Zhang, C; Xu, ZR; Simmler, C; Lankin, DC; Bisson, J; Pauli, GF.The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.Nat. Prod. Rep., 2019, 36: 35-107 The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research
With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields. DOI
867. Mergny, JL; Sen, D.DNA Quadruple Helices in Nanotechnology.Chem. Rev., 2019, 119: 6290-6325 DNA Quadruple Helices in Nanotechnology
DNA has played an early and powerful role in the development of bottom up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases. DOI PubMed
866. Miller, JJ; Blanchet, A; Orvain, C; Nouchikian, L; Reviriot, Y; Clarke, RM; Martelino, D; Wilson, D; Gaiddon, C; Storr, T.Bifunctional ligand design for modulating mutant p53 aggregation in cancer.Chem. Sci., 2019, 10: 10802-10814 Bifunctional ligand design for modulating mutant p53 aggregation in cancer
Protein misfolding and aggregation contributes to the development of a wide range of diseases. In cancer, over 50% of diagnoses are attributed to p53 malfunction due to missense mutations, many of which result in protein misfolding and accelerated aggregation. p53 mutations also frequently result in alteration or loss of zinc at the DNA-binding site, which increases aggregation via nucleation with zinc-bound p53. Herein, we designed two novel bifunctional ligands, L-I and L-H, to modulate mutant p53 aggregation and restore zinc binding using a metallochaperone approach. Interestingly, only the incorporation of iodine function in L-I resulted in modulation of mutant p53 aggregation, both in recombinant and cellular environments. Native mass spectrometry shows a protein-ligand interaction for L-I, as opposed to L-H, which is hypothesized to lead to the distinct difference in the p53 aggregation profile for the two ligands. Incorporation of a di-2-picolylamine binding unit into the ligand design provided efficient intracellular zinc uptake, resulting in metallochaperone capability for both L-I and L-H. The ability of L-I to reduce mutant p53 aggregation results in increased restoration of p53 transcriptional function and mediates both caspase-dependent and -independent cell death pathways. We further demonstrate that L-I exhibits minimal toxicity in non-cancerous organoids, and that it is well tolerated in mice. These results demonstrate that iodination of our ligand framework restores p53 function by interacting with and inhibiting mutant p53 aggregation and highlights L-I as a suitable candidate for comprehensive in vivo anticancer preclinical evaluations. DOI PubMed
863. Nugent, CM; Leong, JS; Christensen, KA; Rondeau, EB; Brachmann, MK; Easton, AA; Ouellet-Fagg, CL; Crown, MTT; Davidson, WS; Koop, B; Danzmann, RG; Ferguson, MM.Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus).PLoS One, 2019, 14 Design and characterization of an 87k SNP genotyping array for Arctic charr (Salvelinus alpinus)
We have generated a high-density, high-throughput genotyping array for characterizing genome-wide variation in Arctic charr (Salvelinus alpinus). Novel single nucleotide polymorphisms (SNPs) were identified in charr from the Fraser, Nauyuk and Tree River aquaculture strains, which originated from northern Canada and fish from Iceland using high coverage sequencing, reduced representation sequencing and RNA-seq datasets. The array was designed to capture genome-wide variation from a diverse suite of Arctic charr populations. Cross validation of SNPs from various sources and comparison with previously published Arctic charr SNP data provided a set of candidate SNPs that generalize across populations. Further candidate SNPs were identified based on minor allele frequency, association with RNA transcripts, even spacing across intergenic regions and association with the sex determining (sdY) gene. The performance of the 86,503 SNP array was assessed by genotyping Fraser, Nauyuk and Tree River strain individuals, as well as wild Icelandic Arctic charr. Overall, 63,060 of the SNPs were polymorphic within at least one group and 36.8% were unique to one of the four groups, suggesting that the array design allows for characterization of both within and across population genetic diversity. The concordance between sdY markers and known phenotypic sex indicated that the array can accurately determine the sex of individuals based on genotype alone. The Salp87k genotyping array provides researchers and breeders the opportunity to analyze genetic variation in Arctic charr at a more detailed level than previously possible. DOI PubMed
861. Omondi, FH; Chandrarathna, S; Mujib, S; Brumme, CJ; Jin, SW; Sudderuddin, H; Miller, RL; Rehimi, A; Laeyendecker, O; Bonner, P; Yue, FY; Benko, E; Kovacs, CM; Brockman, MA; Ostrowski, M; Brumme, ZL.HIV Subtype and Nef-Mediated Immune Evasion Function Correlate with Viral Reservoir Size in Early-Treated Individuals.J. Virol., 2019, 93 HIV Subtype and Nef-Mediated Immune Evasion Function Correlate with Viral Reservoir Size in Early-Treated Individuals
CD4 downregulation; HIV reservoir; HIV-1; HLA downregulation; Nef; viral pathogenesis
The HIV accessory protein Nef modulates key immune evasion and pathogenic functions, and its encoding gene region exhibits high sequence diversity. Given the recent identification of early HIV-specific adaptive immune responses as novel correlates of HIV reservoir size, we hypothesized that viral factors that facilitate the evasion of such responses-namely, Nef genetic and functional diversity-might also influence reservoir establishment and/or persistence. We isolated baseline plasma HIV RNA-derived nef clones from 30 acute/early-infected individuals who participated in a clinical trial of early combination antiretroviral therapy (cART) (<6 months following infection) and assessed each Nef clone's ability to downregulate CD4 and human leukocyte antigen (HLA) class I in vitro. We then explored the relationships between baseline clinical, immunological, and virological characteristics and the HIV reservoir size measured 48 weeks following initiation of suppressive cART (where the reservoir size was quantified in terms of the proviral DNA loads as well as the levels of replication-competent HIV in CD4(+) T cells). Maximal within-host Nef-mediated downregulation of HLA, but not CD4, correlated positively with postcART proviral DNA levels (Spearman's R = 0.61, P = 0.0004) and replicationcompetent reservoir sizes (Spearman's R = 0.36, P = 0.056) in univariable analyses. Furthermore, the Nef-mediated HLA downregulation function was retained in final multivariable models adjusting for established clinical and immunological correlates of reservoir size. Finally, HIV subtype B-infected persons (n = 25) harbored significantly larger viral reservoirs than non-subtype B-infected persons (2 infected with subtype CRF01_AE and 3 infected with subtype G). Our results highlight a potentially important role of viral factors-in particular, HIV subtype and accessory protein function-in modulating viral reservoir establishment and persistence. IMPORTANCE While combination antiretroviral therapies (cART) have transformed HIV infection into a chronic manageable condition, they do not act upon the latent HIV reservoir and are therefore not curative. As HIV cure or remission should be more readily achievable in individuals with smaller HIV reservoirs, achieving a deeper understanding of the clinical, immunological, and virological determinants of reservoir size is critical to eradication efforts. We performed a post hoc analysis of 30 participants of a clinical trial of early cART who had previously been assessed in detail for their clinical, immunological, and reservoir size characteristics. We observed that the HIV subtype and autologous Nef-mediated HLA downregulation function correlated with the viral reservoir size measured approximately 1 year post-cART initiation. Our findings highlight virological characteristics-both genetic and functional-as possible novel determinants of HIV reservoir establishment and persistence. DOI PubMed
860. Ponisio, LC; de Valpine, P; M'Gonigle, LK; Kremen, C.Proximity of restored hedgerows interacts with local floral diversity and species' traits to shape long-term pollinator metacommunity dynamics.Ecology Letters, 2019, 22: 1048-1060 Proximity of restored hedgerows interacts with local floral diversity and species' traits to shape long-term pollinator metacommunity dynamics
Agriculture; graph; hedgerow; metapopulation; network; restoration; wild bee
Disconnected habitat fragments are poor at supporting population and community persistence; restoration ecologists, therefore, advocate for the establishment of habitat networks across landscapes. Few empirical studies, however, have considered how networks of restored habitat patches affect metacommunity dynamics. Here, using a 10-year study on restored hedgerows and unrestored field margins within an intensive agricultural landscape, we integrate occupancy modelling with network theory to examine the interaction between local and landscape characteristics, habitat selection and dispersal in shaping pollinator metacommunity dynamics. We show that surrounding hedgerows and remnant habitat patches interact with the local floral diversity, bee diet breadth and bee body size to influence site occupancy, via colonisation and persistence dynamics. Florally diverse sites and generalist, small-bodied species are most important for maintaining metacommunity connectivity. By providing the first in-depth assessment of how a network of restored habitat influences long-term population dynamics, we confirm the conservation benefit of hedgerows for pollinator populations and demonstrate the importance of restoring and maintaining habitat networks within an inhospitable matrix. DOI PubMed
859. Salcedo-Porras, N; Guarneri, A; Oliveira, PL; Lowenberger, C.Rhodnius prolixus: Identification of missing components of the IMD immune signaling pathway and functional characterization of its role in eliminating bacteria.PLoS One, 2019, 14 Rhodnius prolixus: Identification of missing components of the IMD immune signaling pathway and functional characterization of its role in eliminating bacteria
The innate immune system in insects is regulated by specific signalling pathways. Most immune related pathways were identified and characterized in holometabolous insects such as Drosophila melanogaster, and it was assumed they would be highly conserved in all insects. The hemimetabolous insect, Rhodnius prolixus, has served as a model to study basic insect physiology, but also is a major vector of the human parasite, Trypanosome cruzi, that causes 10,000 deaths annually. The publication of the R. prolixus genome revealed that one of the main immune pathways, the Immune-deficiency pathway (IMD), was incomplete and probably non-functional, an observation shared with other hemimetabolous insects including the pea aphid (Acyrthosiphon pisum) and the bedbug (Cimex lectularius). It was proposed that the IMD pathway is inactive in R. prolixus as an adaptation to prevent eliminating beneficial symbiont gut bacteria. We used bioinformatic analyses based on reciprocal BLAST and HMM-profile searches to find orthologs for most of the "missing" elements of the IMD pathway and provide data that these are regulated in response to infection with Gram-negative bacteria. We used RNAi strategies to demonstrate the role of the IMD pathway in regulating the expression of specific antimicrobial peptides (AMPs) in the fat body of R. prolixus. The data indicate that the IMD pathway is present and active in R. prolixus, which opens up new avenues of research on R. prolixus-T. cruzi interactions. DOI PubMed
858. Sathiyaseelan, P; Rothe, K; Yang, KC; Xu, J; Chow, NS; Bortnik, S; Choutka, C; Ho, C; Jiang, XY; Gorski, SM.Diverse mechanisms of autophagy dysregulation and their therapeutic implications: does the shoe fit?Autophagy, 2019, 15 Diverse mechanisms of autophagy dysregulation and their therapeutic implications: does the shoe fit?
Autophagy; beclin1; BNIP3; cancer; hydroxychloroquine; LV320; mitophagy; neurodegeneration; polyQ; proteinopathies
In its third edition, the Vancouver Autophagy Symposium presented a platform for vibrant discussion on the differential roles of macroautophagy/autophagy in disease. This one-day symposium was held at the BC Cancer Research Centre in Vancouver, BC, bringing together experts in cell biology, protein biochemistry and medicinal chemistry across several different disease models and model organisms. The Vancouver Autophagy Symposium featured 2 keynote speakers that are well known for their seminal contributions to autophagy research, Dr. David Rubinsztein (Cambridge Institute for Medical Research) and Dr. Kay F. Macleod (University of Chicago). Key discussions included the context-dependent roles and mechanisms of dysregulation of autophagy in diseases and the corresponding need to consider context-dependent autophagy modulation strategies. Additional highlights included the differential roles of bulk autophagy versus selective autophagy, novel autophagy regulators, and emerging chemical tools to study autophagy inhibition. Interdisciplinary discussions focused on addressing questions such as which stage of disease to target, which type of autophagy to target and which component to target for autophagy modulation. DOI PubMed
857. Service, CN; Bateman, AW; Adams, MS; Artelle, KA; Reimchen, TE; Paquet, PC; Darimont, CT.Salmonid species diversity predicts salmon consumption by terrestrial wildlife.J. Anim. Ecol., 2019, 88: 392-404 Salmonid species diversity predicts salmon consumption by terrestrial wildlife
black bear; competition; foraging; grizzly bear; resource waves; salmon; stable isotope analysis; Ursus
Resource waves-spatial variation in resource phenology that extends feeding opportunities for mobile consumers-can affect the behaviour and productivity of recipient populations. Interspecific diversity among Pacific salmon species (Oncorhynchus spp.) creates staggered spawning events across space and time, thereby prolonging availability to terrestrial wildlife. We sought to understand how such variation might influence consumption by terrestrial predators compared with resource abundance and intra- and interspecific competition. Using stable isotope analysis, we investigated how the proportion of salmon in the annual diet of male black bears (Ursus americanus; n = 405) varies with species diversity and density of spawning salmon biomass, while also accounting for competition with sympatric black and grizzly bears (U. arctos horribilis), in coastal British Columbia, Canada. We found that the proportion of salmon in the annual diet of black bears was approximate to 40% higher in the absence of grizzly bears, but detected little effect of relative black bear density and salmon biomass density. Rather, salmon diversity had the largest positive effect on consumption. On average, increasing diversity from one salmon species to similar to four (with equal biomass contributions) approximately triples the proportion of salmon in diet. Given the importance of salmon to bear life histories, this work provides early empirical support for how resource waves may increase the productivity of consumers at population and landscape scales. Accordingly, terrestrial wildlife management might consider maintaining not only salmon abundance but also diversity. DOI PubMed
856. Shafaattalab, S; Li, AY; Lin, E; Stevens, CM; Dewar, LJ; Lynn, FC; Sanatani, S; Laksman, Z; Morin, RD; van Petegem, F; Hove-Madsen, L; Tieleman, DP; Davis, JP; Tibbits, GF.In vitro analyses of suspected arrhythmogenic thin filament variants as a cause of sudden cardiac death in infants.Proc. Natl. Acad. Sci. U. S. A., 2019, 116 In vitro analyses of suspected arrhythmogenic thin filament variants as a cause of sudden cardiac death in infants
cardiac troponin; thin filament; hiPSC-CM; sudden cardiac death; arrhythmia
Sudden unexpected death of an infant (SUDI) is a devastating occurrence for families. To investigate the genetic pathogenesis of SUDI, we sequenced >70 genes from 191 autopsy-negative SUDI victims. Ten infants sharing a previously unknown variant in troponin I (TnI) were identified. The mutation (TNNI1 R37C(+/-)) is in the fetal/neonatal paralog of TnI, a gene thought to be expressed in the heart up to the first 24 months of life. Using phylogenetic analysis and molecular dynamics simulations, it was determined that arginine at residue 37 in TNNI1 may play a critical functional role, suggesting that the variant may be pathogenic. We investigated the biophysical properties of the TNNI1 R37C mutation in human reconstituted thin filaments (RTFs) using fluorometry. RTFs reconstituted with the mutant R37C Tnl exhibited reduced Ca2+-binding sensitivity due to an increased Ca(2+)off-rate constant. Furthermore, we generated TNNI1 R37C(+/-)mutants in human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) using CRISPR-Cas9. In monolayers of hiPSC-CMs, we simultaneously monitored voltage and Ca2+ transients through optical mapping and compared them to their isogenic controls. We observed normal intrinsic beating patterns under control conditions in TNNI1 R37C(+/-)at stimulation frequencies of 55 beats/min (bpm), but these cells showed no restitution with increased stimulation frequency to 65 bpm and exhibited alternans at >75 bpm. The WT hiPSC-CMs did not exhibit any sign of arrhythmogenicity even at stimulation frequencies of 120 bpm. The approach used in this study provides critical physiological and mechanistic bases to investigate sarcomeric mutations in the pathogenesis of SUDI. DOI PubMed
855. Smith, NS; Côté, IM.Multiple drivers of contrasting diversity-invasibility relationships at fine spatial grains.Ecology, 2019, 100 Multiple drivers of contrasting diversity-invasibility relationships at fine spatial grains
biotic resistance; diversity-invasibility hypothesis; invasibility metrics; invasion paradox; invasion susceptibility; meta-analysis; spatial scale; systematic review
The diversity-invasibility hypothesis and ecological theory predict that high-diversity communities should be less easily invaded than species-poor communities, but empirical evidence does not consistently support this prediction. While fine-scale experiments tend to yield the predicted negative association between diversity and invasibility, broad-scale observational surveys generally report a positive correlation. This conflicting pattern between experiments and observational studies is referred to as the invasion paradox and is thought to arise because different processes control species composition at different spatial scales. Here, we test empirically the extent to which the strength and direction of published diversity-invasibility relationships depend on spatial scale and on the metrics used to measure invasibility. Using a meta-analytic framework, we explicitly separate the two components of spatial scale: grain and extent, by focusing on fine-grain studies that vary in extent. We find evidence of multiple drivers of the paradox. When we consider only fine-grain studies, we still observe conflicting patterns between experiments and observational studies. In contrast, when we examine studies that are conducted at both a fine grain and fine extent, there is broad overlap in effect sizes between experiments and observation, suggesting that comparing studies with similar extents resolves the paradox at local scales. However, we uncover systematic differences in the metrics used to measure invasibility between experiments, which use predominantly invader performance, and observational studies, which use mainly invader richness. When we consider studies with the same metric (i.e., invader performance), the contrasting associations between study types also disappear. It is not possible, at present, to fully disentangle the effect of spatial extent and metric on the paradox because both variables are systematically associated in different directions with study type. There is therefore an urgent need to conduct experiments and observational studies that incorporate the full range of variability in spatial extent and invasibility metric. DOI PubMed
854. Tafoya, S; Large, SJ; Liu, SX; Bustamante, C; Sivak, DA.Using a system's equilibrium behavior to reduce its energy dissipation in nonequilibrium processes.Proc. Natl. Acad. Sci. U. S. A., 2019, 116 Using a system's equilibrium behavior to reduce its energy dissipation in nonequilibrium processes
single molecule; nonequilibrium; dissipation; DNA hairpins; energetic efficiency
Cells must operate far from equilibrium, utilizing and dissipating energy continuously to maintain their organization and to avoid stasis and death. However, they must also avoid unnecessary waste of energy. Recent studies have revealed that molecular machines are extremely efficient thermodynamically compared with their macroscopic counterparts. However, the principles governing the efficient out-of-equilibrium operation of molecular machines remain a mystery. A theoretical framework has been recently formulated in which a generalized friction coefficient quantifies the energetic efficiency in nonequilibrium processes. Moreover, it posits that, to minimize energy dissipation, external control should drive the system along the reaction coordinate with a speed inversely proportional to the square root of that friction coefficient. Here, we demonstrate the utility of this theory for designing and understanding energetically efficient nonequilibrium processes through the unfolding and folding of single DNA hairpins. DOI PubMed
852. Taylor, J; Hutter, H.Multiple Pathways Act Together To Establish Asymmetry of the Ventral Nerve Cord in Caenorhabditis elegans.Genetics, 2019, 211 Multiple Pathways Act Together To Establish Asymmetry of the Ventral Nerve Cord in Caenorhabditis elegans
asymmetry; central nervous system; ventral nerve cord; axon guidance
The central nervous system of most animals is bilaterally symmetrical. Closer observation often reveals some functional or anatomical left-right asymmetries. In the nematode Caenorhabditis elegans, the most obvious asymmetry in the nervous system is found in the ventral nerve cord (VNC), where most axons are in the right axon tract. The asymmetry is established when axons entering the VNC from the brain switch from the left to the right side at the anterior end of the VNC. In genetic screens we identified several mutations compromising VNC asymmetry. This includes alleles of (encoding a transmembrane collagen), /perlecan and (encoding the actin modulator Enabled/Vasodilator-stimulated phosphoproteins). In addition, we evaluated mutants in known axon guidance pathways for asymmetry defects and used genetic interaction studies to place the genes into genetic pathways. In total we identified four different pathways contributing to the establishment of VNC asymmetry, represented by /netrin, SAX-3/Robo, , and /laminin. The combined inactivation of these pathways in triple and quadruple mutants leads to highly penetrant VNC asymmetry defects, suggesting these pathways are important contributors to the establishment of VNC asymmetry in C. elegans. DOI PubMed
851. Thompson, TQ; Bellinger, MR; O'Rourke, SM; Prince, DJ; Stevenson, AE; Rodrigues, AT; Sloat, MR; Speller, CF; Yang, DY; Butler, VL; Banks, MA; Miller, MR.Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.Proc. Natl. Acad. Sci. U. S. A., 2019, 116 Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations
conservation; evolution; genetics; biodiversity; salmon
Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost. DOI PubMed
850. Tiusanen, M; Huotari, T; Hebert, PDN; Andersson, T; Asmus, A; Bety, J; Davis, E; Gale, J; Hardwick, B; Hik, D; Korner, C; Lanctot, RB; Loonen, MJJE; Partanen, R; Reischke, K; Saalfeld, ST; Senez-Gagnon, F; Smith, PA; Sulavik, J; Syvanpera, I; Urbanowicz, C; Williams, S; Woodard, P; Zaika, Y; Roslin, T.Flower-visitor communities of an arcto-alpine plant-Global patterns in species richness, phylogenetic diversity and ecological functioning.Mol. Ecol., 2019, 28 Flower-visitor communities of an arcto-alpine plant-Global patterns in species richness, phylogenetic diversity and ecological functioning
arctic ecology; DNA barcoding; Dryas; ecosystem functioning; flower visitor; pollination
Pollination is an ecosystem function of global importance. Yet, who visits the flower of specific plants, how the composition of these visitors varies in space and time and how such variation translates into pollination services are hard to establish. The use of DNA barcodes allows us to address ecological patterns involving thousands of taxa that are difficult to identify. To clarify the regional variation in the visitor community of a widespread flower resource, we compared the composition of the arthropod community visiting species in the genus Dryas (mountain avens, family Rosaceae), throughout Arctic and high-alpine areas. At each of 15 sites, we sampled Dryas visitors with 100 sticky flower mimics and identified specimens to Barcode Index Numbers (BINs) using a partial sequence of the mitochondrial COI gene. As a measure of ecosystem functioning, we quantified variation in the seed set of Dryas. To test for an association between phylogenetic and functional diversity, we characterized the structure of local visitor communities with both taxonomic and phylogenetic descriptors. In total, we detected 1,360 different BINs, dominated by Diptera and Hymenoptera. The richness of visitors at each site appeared to be driven by local temperature and precipitation. Phylogeographic structure seemed reflective of geological history and mirrored trans-Arctic patterns detected in plants. Seed set success varied widely among sites, with little variation attributable to pollinator species richness. This pattern suggests idiosyncratic associations, with function dominated by few and potentially different taxa at each site. Taken together, our findings illustrate the role of post-glacial history in the assembly of flower-visitor communities in the Arctic and offer insights for understanding how diversity translates into ecosystem functioning. DOI PubMed
849. Trachman, RJ; Autour, A; Jeng, SCY; Abdolahzadeh, A; Andreoni, A; Cojocaru, R; Garipov, R; Dolgosheina, EV; Knutson, JR; Ryckelynck, M; Unrau, PJ; Ferre-D'Amare, AR.Structure and functional reselection of the Mango-III fluorogenic RNA aptamer.Nat. Chem. Biol., 2019, 15: 472-+ Structure and functional reselection of the Mango-III fluorogenic RNA aptamer
Several turn-on RNA aptamers that activate small-molecule fluorophores have been selected in vitro. Among these, the similar to 30 nucleotide Mango-III is notable because it binds the thiazole orange derivative TO1-Biotin with high affinity and fluoresces brightly (quantum yield 0.55). Uniquely among related aptamers, Mango-III exhibits biphasic thermal melting, characteristic of molecules with tertiary structure. We report crystal structures of TO1-Biotin complexes of Mango-III, a structure-guided mutant Mango-III(A1OU), and a functionally reselected mutant iMango-III. The structures reveal a globular architecture arising from an unprecedented pseudoknot-like connectivity between a G-quadruplex and an embedded non-canonical duplex. The fluorophore is restrained into a planar conformation by the G-quadruplex, a lone, long-range trans Watson-Crick pair (whose A1OU mutation increases quantum yield to 0.66), and a pyrimidine perpendicular to the nucleobase planes of those motifs. The improved iMango-III and Mango-III(A1OU) fluoresce similar to 50% brighter than enhanced green fluorescent protein, making them suitable tags for live cell RNA visualization. DOI PubMed
848. Tuck, ME; Kench, PS; Ford, MR; Masselink, G.Physical modelling of the response of reef islands to sea-level rise.Geology, 2019, 47: 803-806 Physical modelling of the response of reef islands to sea-level rise
Sea-level rise and increased storminess are expected to destabilize low-lying reef islands formed on coral reef platforms, and increased flooding is expected to render them uninhabitable within the coming decades. Such projections are founded on the assumption that islands are geologically static landforms that will simply drown as sea-level rises. Here, we present evidence from physical model experiments of a reef island that demonstrates islands have the capability to morphodynamically respond to rising sea level through island accretion. Challenging outputs from existing models based on the assumption that islands are geomorphologically inert, results demonstrate that islands not only move laterally on reef platforms, but overwash processes provide a mechanism to build and maintain the freeboard of islands above sea level. Implications of island building are profound, as it will offset existing scenarios of dramatic increases in island flooding. Future predictive models must include the morphodynamic behavior of islands to better resolve flood impacts and future island vulnerability. DOI
847. Venugopal, S; Moune, S; Williams-Jones, G; Druitt, T; Vigouroux, N; Wilson, A; Russell, JK.Two distinct mantle sources beneath the Garibaldi Volcanic Belt: Insight from olivine-hosted melt inclusions.Chem. Geol., 2019, 532, 119346 Two distinct mantle sources beneath the Garibaldi Volcanic Belt: Insight from olivine-hosted melt inclusions
Melt inclusions; Garibaldi Volcanic Belt; Cascades; Trace elements; Two mantle sources
The nature of the magmatic source beneath the Garibaldi Volcanic Belt (GVB) in NW Washington (USA) and SW British Columbia (Canada) has been debated both due to its classification as the northern equivalent of the High Cascades and the alkaline nature of northern basalts. Whole rock studies have shown that the GVB does not share the same magmatic source as the High Cascades (Mullen and Weis, 2013, 2015). Nonetheless, the presence of alkaline basalts in this arc raises questions about the exact source of mantle enrichment and whether it is related to the young age of the downgoing Juan de Fuca Plate ( < 10 Ma) or the presence of a slab tear at the northern end of the arc. To gain insight into the source that underlies the GVB, we sampled olivine-hosted melt inclusions from each volcanic centre along the arc. Major, volatile and trace element data reveal a northward compositional trend from arc-typical calc-alkaline magma in the south to OIB-like melts in the north near the slab tear. Furthermore, contributions from the subducting slab are relatively high beneath the southern end of the arc (Cl/Nb > 80) but rapidly decreases to the north (Cl/Nb < 50). Finally, the significant differences in Zr/Nb from south to north (80 and 9, respectively) suggest two distinct mantle sources since one source cannot produce melts with such different ratios. As such, we propose the GVB should be segmented into the Northern and Southern groups, each having its own mantle source. Based on the geographic proximity, the enriched nature of the Northern group melt inclusions is likely controlled by the slab tear at the northern termination of the subducting Juan de Fuca Plate. Melt modelling results show that 3-7 % partial melting of the primitive mantle with a garnet lherzolite residue can reproduce the composition of the Northern group. Melt inclusions from the Southern group, on the other hand, imply a depleted MORB mantle that has been modified by fluids derived from the downgoing slab. Variability within the Southern group itself reflects the amount of hydrous fluids supplied beneath each centre and is correlated with slab age and subsequent degree of dehydration. This study addresses the compositional diversity along the arc and provides evidence that the age of the downgoing plate and the presence of a slab tear exert a strong compositional control over eruptive products within one arc.PDF DOI
846. Wagner, MA; Reynolds, JD.Salmon increase forest bird abundance and diversity.PLoS One, 2019, 14 Salmon increase forest bird abundance and diversity
Resource subsidies across ecosystems can have strong and unforeseen ecological impacts. Marine-derived nutrients from Pacific salmon (Onchorhycus spp.) can be transferred to streams and riparian forests through diverse food web pathways, fertilizing forests and increasing invertebrate abundance, which may in turn affect breeding birds. We quantified the influence of salmon on the abundance and composition of songbird communities across a wide range of salmon-spawning biomass on 14 streams along a remote coastal region of British Columbia, Canada. Point-count data spanning two years were combined with salmon biomass and 13 environmental covariates in riparian forests to test for correlates with bird abundance, foraging guilds, individual species, and avian diversity. We show that bird abundance and diversity increase with salmon biomass and that watershed size and forest composition are less important predictors. This work provides new evidence for the importance of salmon to terrestrial ecosystems and information that can inform ecosystem-based management. DOI PubMed
845. Wang, JH; Zhang, LS; Li, XC; Zhang, XL; Yu, HZ.From kirigami to three-dimensional paper-based micro-analytical device: cut-and-paste fabrication and mobile app quantitation.RSC Adv., 2019, 9: 23267-23275 From kirigami to three-dimensional paper-based micro-analytical device: cut-and-paste fabrication and mobile app quantitation
Nowadays quantitative chemical analysis is usually costly, instrument-dependent, and time-consuming, which limits its implementation for remote locations and resource-limited regions. Inspired by the ancient papercutting art (kirigami), we herein introduce a novel cut-and-paste protocol to fabricate 3D microfluidic paper-based analytical devices (mu PADs) that are suitable for on-site quantitative assay applications. The preparation of the device is fast, simple, and independent of any lithographic devices or masks. Particularly designed reaction "channels" were pre-cut from a piece of filter paper, then assembled back to the silanized, superhydrophobic paper pads. The different layers of the device were assembled using a chemically-inert adhesive spray. The fabricated device has high efficiency of liquid handling (up to 60 times faster than conventional methods) and it is particularly inexpensive. Beyond the benchtop fabrication advantage, in conjunction with a custom mobile app developed for colorimetric analysis, we were able to quantify representative environmental contaminants (i.e., the amount of Cr(vi) and nitrite ions) in various water samples with the cut-and-paste mu PADs (namely kPADs). Their detection limits (0.7 mu g mL(-1) for Cr(vi) and 0.4 mu g mL(-1) for nitrite ions, respectively) are comparable with conventional spectrophotometric methods, which confirm the potential of kPADs for on-site environmental/sanitary monitoring and food toxin pre-screening. DOI
844. Wong, JD; Selinger, JC; Donelan, JM.Is natural variability in gait sufficient to initiate spontaneous energy optimization in human walking?J. Neurophysiol., 2019, 121: 1848-1855 Is natural variability in gait sufficient to initiate spontaneous energy optimization in human walking?
locomotion; energy optimization; gait; locomotion; motor learning; variability
In new walking contexts, the nervous system can adapt preferred gaits to minimize energetic cost. During treadmill walking, this optimization is not usually spontaneous but instead requires experience with the new energetic cost landscape. Experimenters can provide subjects with the needed experience by prescribing new gaits or instructing them to explore new gaits. Yet in familiar walking contexts, people naturally prefer energetically optimal gaits: the nervous system can optimize cost without an experimenter's guidance. Here we test the hypothesis that the natural gait variability of overground walking provides the nervous system with sufficient experience with new cost landscapes to initiate spontaneous minimization of energetic cost. We had subjects walk over paths of varying terrain while wearing knee exoskeletons that penalized walking as a function of step frequency. The exoskeletons created cost landscapes with minima that were, on average, 8% lower than the energetic cost at the initially preferred gaits and achieved at walking speeds and step frequencies that were 4% lower than the initially preferred values. We found that our overground walking trials amplified gait variability by 3.7-fold compared with treadmill walking, resulting in subjects gaining greater experience with new cost landscapes, including frequent experience with gaits at the new energetic minima. However, after 20 min and 2.0 km of walking in the new cost landscapes, we observed no consistent optimization of gait, suggesting that natural gait variability during overground walking is not always sufficient to initiate energetic optimization over the time periods and distances tested in this study. NEW & NOTEWORTHY While the nervous system can continuously optimize gait to minimize energetic cost, what initiates this optimization process during every day walking is unknown. Here we tested the hypothesis that the nervous system leverages the natural variability in gait experienced during overground walking to converge on new energetically optimal gaits created using exoskeletons. Contrary to our hypothesis, we found that participants did not adapt toward optimal gaits: natural variability is not always sufficient to initiate spontaneous energy optimization. DOI PubMed
843. Zhang, XJ; Yuan, JB; Sun, YM; Li, SH; Gao, Y; Yu, Y; Liu, CZ; Wang, QC; Lv, XJ; Zhang, XX; Ma, KY; Wang, XB; Lin, WC; Wang, L; Zhu, XL; Zhang, CS; Zhang, JQ; Jin, SJ; Yu, KJ; Kong, J; Xu, P; Chen, J; Zhang, HB; Sorgeloos, P; Sagi, A; Alcivar-Warren, A; Liu, ZJ; Wang, L; Ruan, J; Chu, KH; Liu, B; Li, FH; Xiang, JH.Penaeid shrimp genome provides insights into benthic adaptation and frequent molting.Nat. Commun., 2019, 10 Penaeid shrimp genome provides insights into benthic adaptation and frequent molting
Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering similar to 1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture. DOI PubMed
842. Alderman, SL; Lin, F; Gillis, TE; Farrell, AP; Kennedy, CJ.Developmental and latent effects of diluted bitumen exposure on early life stages of sockeye salmon (Oncorhynchus nerka).Aquat. Toxicol., 2018, 202 Developmental and latent effects of diluted bitumen exposure on early life stages of sockeye salmon (Oncorhynchus nerka)
Bitumen; Crude oil; Fish; Development; Toxicity; Morphogenesis
The early life stages of Pacific salmon are at risk of environmental exposure to diluted bitumen (dilbit) as Canada's oil sands industry continues to expand. The toxicity and latent effects of dilbit exposure were assessed in sockeye salmon (Oncorhynchus nerka) exposed to water-soluble fractions of dilbit (WSFd) from fertilization to the swim-up stage, and then reared in clean water for 8 months. Mortality was significantly higher in WSFd-exposed embryos, with cumulative mortality up to 4.6-fold higher in exposed relative to unexposed embryos. The sublethal effects of WSFd exposure included transcriptional up-regulation of cypla, a concentration-dependent delay in the onset and progression of hatching, as well as increased prevalence of developmental deformities at total polycyclic aromatic hydrocarbon (TPAH) concentrations >= 35 mu g L-1. Growth and body composition were negatively affected by WSFd exposure, including a concentration-specific decrease in soluble protein concentration and increases in total body lipid and triglyceride concentrations. Mortality continued during the first 2 months after transferring fish to clean water, reaching 53% in fish exposed to 100 mu g L-1 TPAH; but there was no latent impact on swimming performance, heart mass, or heart morphology in surviving fish after 8 months. A latent effect of WSFd exposure on brain morphology was observed, with fish exposed to 4 mu g L-1 TPAH having significantly larger brains compared to other treatment groups after 8 months in clean water. This study provides comprehensive data on the acute, sub-chronic, and latent impacts of dilbit exposure in early life stage sockeye, information that is critical for a proper risk analysis of the impact of a dilbit spill on this socioeconomically important fish species. DOI PubMed
841. Anderson, LS; Flowers, GE; Jarosch, AH; Adalgeirsdottir, GT; Geirsdottir, A; Miller, GH; Harning, DJ; Thorsteinsson, T; Magnusson, E; Palsson, F.Holocene glacier and climate variations in Vestfiroir, Iceland, from the modeling of Drangajokull ice cap.Quat. Sci. Rev., 2018, 190: 39-56 Holocene glacier and climate variations in Vestfiroir, Iceland, from the modeling of Drangajokull ice cap
Holocene; Glaciation; Glaciology; North Atlantic; Geomorphology; Glacial inception; Modelling; Little ice age; Holocene Thermal Maximum; Deglaciation
Drangajokull is a maritime ice cap located in northwest (Vestfiroir) Iceland. Drangajokull's evolution is therefore closely linked to atmospheric and ocean variability. In order to better constrain the Holocene climate and glacier history of Vestfiroir we model the past evolution of Drangajokull ice cap. Simulations from 10 ka to present are forced by general circulation model output, ice-core-based temperature reconstructions, and sea-surface temperature reconstructions. Based on these 10-thousand year simulations, Drangajokull did not persist through the Holocene. We estimate that air temperatures were 2.5-3.0 degrees C higher during the Holocene Thermal Maximum than the local 1960-1990 average. Simulations support Drangajokull's late Holocene inception between 2 and 1 ka, though intermittent ice likely occupied cirques as early as 2.6 ka. Drangajokull is primarily a Little Ice Age ice cap: it expanded between 1300 and 1750 CE, with the most rapid growth occurring between 1600 and 1750 CE. The maximum Holocene extent of Drangajokull occurred between 1700 and 1925 CE, despite the lowest late Holocene temperatures, occurring between 1650 and 1720 CE. Between 1700 and 1925 CE temperatures were likely 0.6-0.8 degrees C lower than the 1950-2015 reference temperature. The modern equilibrium line altitude (ELA) is bracketed by topographic thresholds: a 1 degrees C temperature increase from the modern ELA would eliminate the ice cap's accumulation area, while a reduction of 0.5 degrees C would lead to the rapid expansion of the ice cap across Vestfiroir. The proximity of Drangajokull to topographic thresholds may explain its late inception and rapid expansion during the Little Ice Age. (C) 2018 Elsevier Ltd. All rights reserved. DOI
840. Archibald, SB; Rasnitsyn, AP; Brothers, DJ; Mathewes, RW.Modernisation of the Hymenoptera: ants, bees, wasps, and sawflies of the early Eocene Okanagan Highlands of western North America.Can. Entomol., 2018, 150: 205-257 Modernisation of the Hymenoptera: ants, bees, wasps, and sawflies of the early Eocene Okanagan Highlands of western North America
Trigonalidae
Most major modern families of Hymenoptera were established in the Mesozoic, but the diversifications within ecologically key trophic guilds and lineages that significantly influence the character of modern terrestrial ecosystems - bees (Apiformes), ants (Formicidae), social Vespidae, parasitoids (Ichneumonidae), and phytophagous Tenthredinoidea - were previously known to occur mostly in the middle to late Eocene. We find these changes earlier, seen here in the early Eocene Okanagan Highlands fossil deposits of western North America. Some of these may have occurred even earlier, but have been obscured by taphonomic processes. We provide an overview of the Okanagan Highlands Hymenoptera to family level and in some cases below that, with a minimum of 25 named families and at least 30 when those tentatively assigned or distinct at family level, but not named are included. Some are poorly known as fossils (Trigonalidae, Siricidae, Peradeniidae, Monomachidae), and some represent the oldest confirmed occurrences (Trigonalidae, Pompilidae, Sphecidae sensu stricto, Peradeniidae, Monomachidae, and possibly Halictidae). Some taxa previously thought to be relictual or extinct by the end of the Cretaceous (Angarosphecidae, Archaeoscoliinae, some Diapriidae) are present and sometimes abundant in the early Eocene. Living relatives of some taxa are now present in different climate regimes or on different continents. DOI
839. Arthur, SE; Jiang, A; Grande, BM; Alcaide, M; Cojocaru, R; Rushton, CK; Mottok, A; Hilton, LK; Lat, PK; Zhao, EY; Culibrk, L; Ennishi, D; Jessa, S; Chong, L; Thomas, N; Pararajalingam, P; Meissner, B; Boyle, M; Davidson, J; Bushell, KR; Lai, D; Farinha, P; Slack, GW; Morin, GB; Shah, S; Sen, D; Jones, SJM; Mungall, AJ; Gascoyne, RD; Audas, TE; Unrau, P; Marra, MA; Connors, JM; Steidl, C; Scott, DW; Morin, RD.Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma.Nat. Commun., 2018, 9 Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma
Diffuse large B-cell lymphoma (DLBCL) is an aggressive cancer originating from mature B-cells. Prognosis is strongly associated with molecular subgroup, although the driver mutations that distinguish the two main subgroups remain poorly defined. Through an integrative analysis of whole genomes, exomes, and transcriptomes, we have uncovered genes and non-coding loci that are commonly mutated in DLBCL. Our analysis has identified novel cis-regulatory sites, and implicates recurrent mutations in the 3' UTR of NFKBIZ as a novel mechanism of oncogene deregulation and NF-kappa B pathway activation in the activated B-cell (ABC) subgroup. Small amplifications associated with over-expression of FCGR2B (the Fc gamma receptor protein IIB), primarily in the germinal centre B-cell (GCB) subgroup, correlate with poor patient outcomes suggestive of a novel oncogene. These results expand the list of subgroup driver mutations that may facilitate implementation of improved diagnostic assays and could offer new avenues for the development of targeted therapeutics. DOI PubMed
838. Autour, A; Jeng, SCY; Cawte, AD; Abdolahzadeh, A; Galli, A; Panchapakesan, SSS; Rueda, D; Ryckelynck, M; Unrau, PJ.Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells.Nat. Commun., 2018, 9 Fluorogenic RNA Mango aptamers for imaging small non-coding RNAs in mammalian cells
Despite having many key roles in cellular biology, directly imaging biologically important RNAs has been hindered by a lack of fluorescent tools equivalent to the fluorescent proteins available to study cellular proteins. Ideal RNA labelling systems must preserve biological function, have photophysical properties similar to existing fluorescent proteins, and be compatible with established live and fixed cell protein labelling strategies. Here, we report a microfluidics-based selection of three new high-affinity RNA Mango fluorogenic aptamers. Two of these are as bright or brighter than enhanced GFP when bound to TO1-Biotin. Furthermore, we show that the new Mangos can accurately image the subcellular localization of three small non-coding RNAs (5S, U6, and a box C/D scaRNA) in fixed and live mammalian cells. These new aptamers have many potential applications to study RNA function and dynamics both in vitro and in mammalian cells. DOI PubMed
837. Barrio, IC; Hik, DS; Thorsson, J; Svavarsdottir, K; Marteinsdottir, B; Jonsdottir, IS.The sheep in wolf's clothing? Recognizing threats for land degradation in Iceland using state-and-transition models.Land Degrad. Dev., 2018, 29: 1714-1725 The sheep in wolf's clothing? Recognizing threats for land degradation in Iceland using state-and-transition models
adaptive monitoring; land management; rangeland; sheep grazing
Land degradation and extensive soil erosion are serious environmental concerns in Iceland. Natural processes associated with a harsh climate and frequent volcanic activity have shaped Icelandic landscapes. However, following human settlement and the introduction of livestock in the ninth century, the extent of soil erosion rapidly escalated. Despite increased restoration and afforestation efforts and a considerable reduction in sheep numbers during the late 20th century, many Icelandic rangelands remain in poor condition. A deeper understanding of the ecology of these dynamic landscapes is needed, and state-and-transition models (STMs) can provide a useful conceptual framework. STMs have been developed for ecosystems worldwide to guide research, monitoring, and management but have been used at relatively small spatial scales and have not been extensively applied to high-latitude rangelands. Integrating the best available knowledge, we develop STMs for rangelands in Iceland, where sheep grazing is often regarded as a main driver of degradation. We use STMs at a countrywide scale for 3 time periods with different historical human influence, from presettlement to present days. We also apply our general STM to a case-study in the central highlands of Iceland to illustrate the potential application of these models at scales relevant to management. Our STMs identify the set of possible states, transitions and thresholds in these ecosystems, and their changes over time and suggest increasing complexity in recent times. This approach can help identify important knowledge gaps and inform management efforts and monitoring programmes, by identifying realistic and achievable conservation and restoration goals. DOI
836. Beetham, E; Kench, PS.Predicting wave overtopping thresholds on coral reef-island shorelines with future sea-level rise.Nat. Commun., 2018, 9 Predicting wave overtopping thresholds on coral reef-island shorelines with future sea-level rise
Wave-driven flooding is a serious hazard on coral reef-fringed coastlines that will be exacerbated by global sea-level rise. Despite the global awareness of atoll island vulnerability, little is known about the physical processes that control wave induced flooding on reef environments. To resolve the primary controls on wave-driven flooding at present and future sea levels, we present a globally applicable method for calculating wave overtopping thresholds on reef coastlines. A unique dataset of 60,000 fully nonlinear wave transformation simulations representing a wide range of wave energy, morphology and sea levels conditions was analysed to develop a tool for exploring the future trajectory of atoll island vulnerability to sea-level rise. The proposed reef-island overtopping threshold (RIOT) provides a widely applicable first-order assessment of reef-coast vulnerability to wave hazards with sea-level. Future overtopping thresholds identified for different atoll islands reveal marked spatial variability and highlight distinct morphological characteristics that enhance coastal resilience. DOI PubMed
835. Bigman, JS; Pardo, SA; Prinzing, TS; Dando, M; Wegner, NC; Dulvy, NK.Ecological lifestyles and the scaling of shark gill surface area.J. Morphol., 2018, 279 Ecological lifestyles and the scaling of shark gill surface area
allometry; ecomorphology; gill surface area; metabolism; scaling
Fish gill surface area varies across species and with respect to ecological lifestyles. The majority of previous studies only qualitatively describe gill surface area in relation to ecology and focus primarily on teleosts. Here, we quantitatively examined the relationship of gill surface area with respect to specific ecological lifestyle traits in elasmobranchs, which offer an independent evaluation of observed patterns in teleosts. As gill surface area increases ontogenetically with body mass, examination of how gill surface area varies with ecological lifestyle traits must be assessed in the context of its allometry (scaling). Thus, we examined how the relationship of gill surface area and body mass across 11 shark species from the literature and one species for which we made measurements, the Gray Smoothhound Mustelus californicus, varied with three ecological lifestyle traits: activity level, habitat, and maximum body size. Relative gill surface area (gill surface area at a specified body mass; here we used 5,000g, termed the 'standardized intercept') ranged from 4,724.98 to 35,694.39 cm(2) (mean and standard error: 17,796.65 +/- 2,948.61 cm(2)) and varied across species and the ecological lifestyle traits examined. Specifically, larger-bodied, active, oceanic species had greater relative gill surface area than smaller-bodied, less active, coastal species. In contrast, the rate at which gill surface area scaled with body mass (slope) was generally consistent across species (0.85 +/- 0.02) and did not differ statistically with activity level, habitat, or maximum body size. Our results suggest that ecology may influence relative gill surface area, rather than the rate at which gill surface area scales with body mass. Future comparisons of gill surface area and ecological lifestyle traits using the quantitative techniques applied in this study can provide further insight into patterns dictating the relationship between gill surface area, metabolism, and ecological lifestyle traits. DOI PubMed
834. Bird, CS; Verissimo, A; Magozzi, S; Abrantes, KG; Aguilar, A; Al-Reasi, H; Barnett, A; Bethea, DM; Biais, G; Borrell, A; Bouchoucha, M; Boyle, M; Brooks, EJ; Brunnschweiler, J; Bustamante, P; Carlisle, A; Catarino, D; Caut, S; Cherel, Y; Chouvelon, T; Churchill, D; Ciancio, J; Claes, J; Colaco, A; Courtney, DL; Cresson, P; Daly, R; de Necker, L; Endo, T; Figueiredo, I; Frisch, AJ; Hansen, JH; Heithaus, M; Hussey, NE; Iitembu, J; Juanes, F; Kinney, MJ; Kiszka, JJ; Klarian, SA; Kopp, D; Leaf, R; Li, YK; Lorrain, A; Madigan, DJ; Maljkovic, A; Malpica-Cruz, L; Matich, P; Meekan, MG; Menard, F; Menezes, GM; Munroe, SEM; Newman, MC; Papastamatiou, YP; Pethybridge, H; Plumlee, JD; Polo-Silva, C; Quaeck-Davies, K; Raoult, V; Reum, J; Torres-Rojas, YE; Shiffman, DS; Shipley, ON; Speed, CW; Staudinger, MD; Teffer, AK; Tilley, A; Valls, M; Vaudo, JJ; Wai, TC; Wells, RJD; Wyatt, ASJ; Yool, A; Trueman, CN.A global perspective on the trophic geography of sharks.Nat. Ecol. Evol., 2018, 2 A global perspective on the trophic geography of sharks
Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30 degrees and 50 degrees of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches. DOI PubMed
833. Bjorkman, AD; Myers-Smith, IH; Elmendorf, SC; Normand, S; Ruger, N; Beck, PSA; Blach-Overgaard, A; Blok, D; Cornelissen, JHC; Forbes, BC; Georges, D; Goetz, SJ; Guay, KC; Henry, GHR; HilleRisLambers, J; Hollister, RD; Karger, DN; Kattge, J; Manning, P; Prevey, JS; Rixen, C; Schaepman-Strub, G; Thomas, HJD; Vellend, M; Wilmking, M; Wipf, S; Carbognani, M; Hermanutz, L; Levesque, E; Molau, U; Petraglia, A; Soudzilovskaia, NA; Spasojevic, MJ; Tomaselli, M; Vowles, T; Alatalo, JM; Alexander, HD; Anadon-Rosell, A; Angers-Blondin, S; te Beest, M; Berner, L; Bjork, RG; Buchwal, A; Buras, A; Christie, K; Cooper, EJ; Dullinger, S; Elberling, B; Eskelinen, A; Frei, ER; Grau, O; Grogan, P; Hallinger, M; Harper, KA; Heijmans, MMPD; Hudson, J; Hulber, K; Iturrate-Garcia, M; Iversen, CM; Jaroszynska, F; Johnstone, JF; Jorgensen, RH; Kaarlejarvi, E; Klady, R; Kuleza, S; Kulonen, A; Lamarque, LJ; Lantz, T; Little, CJ; Speed, JDM; Michelsen, A; Milbau, A; Nabe-Nielsen, J; Nielsen, SS; Ninot, JM; Oberbauer, SF; Olofsson, J; Onipchenko, VG; Rumpf, SB; Semenchuk, P; Shetti, R; Collier, LS; Street, LE; Suding, KN; Tape, KD; Trant, A; Treier, UA; Tremblay, JP; Tremblay, M; Venn, S; Weijers, S; Zamin, T; Boulanger-Lapointe, N; Gould, WA; Hik, DS; Hofgaard, A; Jonsdottir, IS; Jorgenson, J; Klein, J; Magnusson, B; Tweedie, C; Wookey, PA; Bahn, M; Blonder, B; van Bodegom, PM; Bond-Lamberty, B; Campetella, G; Cerabolini, BEL; Chapin, FS; Cornwell, WK; Craine, J; Dainese, M; de Vries, FT; Diaz, S; Enquist, BJ; Green, W; Milla, R; Niinemets, U; Onoda, Y; Ordonez, JC; Ozinga, WA; Penuelas, J; Poorter, H; Poschlod, P; Reich, PB; Sande, B; Schamp, B; Sheremetev, S; Weiher, E.Plant functional trait change across a warming tundra biome.Nature, 2018, 562 Plant functional trait change across a warming tundra biome
The tundra is warming more rapidly than any other biome on Earth, and the potential ramifications are far-reaching because of global feedback effects between vegetation and climate. A better understanding of how environmental factors shape plant structure and function is crucial for predicting the consequences of environmental change for ecosystem functioning. Here we explore the biome-wide relationships between temperature, moisture and seven key plant functional traits both across space and over three decades of warming at 117 tundra locations. Spatial temperature-trait relationships were generally strong but soil moisture had a marked influence on the strength and direction of these relationships, highlighting the potentially important influence of changes in water availability on future trait shifts in tundra plant communities. Community height increased with warming across all sites over the past three decades, but other traits lagged far behind predicted rates of change. Our findings highlight the challenge of using space-for-time substitution to predict the functional consequences of future warming and suggest that functions that are tied closely to plant height will experience the most rapid change. They also reveal the strength with which environmental factors shape biotic communities at the coldest extremes of the planet and will help to improve projections of functional changes in tundra ecosystems with climate warming. DOI PubMed
832. Bonnefoy, S; Watson, CM; Kernohan, KD; Lemos, M; Hutchinson, S; Poulter, JA; Crinnion, LA; Berry, I; Simmonds, J; Vasudevan, P; O'Callaghan, C; Hirst, RA; Rutman, A; Huang, LJ; Hartley, T; Grynspan, D; Moya, E; Li, CM; Carr, IM; Bonthron, DT; Leroux, M; Boycott, KM; Bastin, P; Sheridan, EG.Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects.Am. J. Hum. Genet., 2018, 103 Biallelic Mutations in LRRC56, Encoding a Protein Associated with Intraflagellar Transport, Cause Mucociliary Clearance and Laterality Defects
Primary defects in motile cilia result in dysfunction of the apparatus responsible for generating fluid flows. Defects in these mechanisms underlie disorders characterized by poor mucus clearance, resulting in susceptibility to chronic recurrent respiratory infections, often associated with infertility; laterality defects occur in about 50% of such individuals. Here we report biallelic variants in LRRC56 (known as oda8 in Chlamydomonas) identified in three unrelated families. The phenotype comprises laterality defects and chronic pulmonary infections. High-speed video microscopy of cultured epithelial cells from an affected individual showed severely dyskinetic cilia but no obvious ultra-structural abnormalities on routine transmission electron microscopy (TEM). Further investigation revealed that LRRC56 interacts with the intraflagellar transport (IFT) protein IFT88. The link with IFT was interrogated in Trypanosoma brucei. In this protist, LRRC56 is recruited to the cilium during axoneme construction, where it co-localizes with IFT trains and is required for the addition of dynein arms to the distal end of the flagellum. In T. brucei carrying LRRC56-null mutations, or a variant resulting in the p. Leu259Pro substitution corresponding to the p. Leu140Pro variant seen in one of the affected families, we observed abnormal ciliary beat patterns and an absence of outer dynein arms restricted to the distal portion of the axoneme. Together, our findings confirm that deleterious variants in LRRC56 result in a human disease and suggest that this protein has a likely role in dynein transport during cilia assembly that is evolutionarily important for cilia motility. DOI PubMed
831. Boratynski, Z; Koskela, E; Mappes, T; Mills, SC; Mokkonen, M.Maintenance costs of male dominance and sexually antagonistic selection in the wild.Funct. Ecol., 2018, 32 Maintenance costs of male dominance and sexually antagonistic selection in the wild
antagonistic selection; basal metabolic rate; dominance behaviour; energetics; sexual conflict; testosterone
Variation in dominance status determines male mating and reproductive success, but natural selection for male dominance can be detrimental or antagonistic for female performance, and ultimately their fitness. Attaining and maintaining a high dominance status in a population of competing individuals is physiologically costly for males. But how male dominance status is mediated by maintenance energetics is currently not well understood, nor are the corresponding effects of male energetics on his sisters recognized. We conducted laboratory and field experiments on rodent populations to test whether selective breeding for male dominance status (dominant vs. subordinate breeding lines) antagonistically affected basal metabolic rate (BMR) and fitness of females under wild conditions. Our results showed elevated BMR in females, but not in males, from the dominant breeding line. However, phenotypically dominant males from the subordinate breeding line had the highest BMR. Males from the dominant line with low BMR sired the most litters and offspring in the field. Similarly, females from the dominant selection line tended to have more offspring if they had lower BMR, while the opposite trend was found in females from the subordinate selection line. Females with high and low BMR reproduced most often, as indicated by a significant quadratic selection gradient. The increased female BMR resulting from selection for male dominance suggests genetic incompatibility between sexes in metabolism inheritance. Elevated BMR in behaviourally dominant males, but not in males from the dominant breeding line, suggests physiological costs in males not genetically suited for dominance. Fitness costs of elevated maintenance costs (measured as BMR) shown here support the energetic compensation hypothesis where high BMR is selected against as it would trade off energy required for other important life-history attributes. A is available for this article. DOI
830. Bordeleau, X; Hatcher, BG; Denny, S; Fast, MD; Whoriskey, FG; Patterson, DA; Crossin, GT.Consequences of captive breeding: Fitness implications for wild-origin, hatchery-spawned Atlantic salmon kelts upon their return to the wild.Biol. Conserv., 2018, 225 Consequences of captive breeding: Fitness implications for wild-origin, hatchery-spawned Atlantic salmon kelts upon their return to the wild
Acoustic telemetry; Captivity stress; Carryover effect; Estuarine survival; Freshwater survival; Ocean Tracking Network
Broodstock collection and enhancement programs are a widely-used management practice within the Atlantic salmon's (Salmo solar) native range. Wild-origin adult salmon captured as part of these programs experience multiple stressors during their time in hatcheries. However, no studies have assessed the potential consequences of hatchery practices on the physiology (stress and immune states), migratory behaviour, and long-term survival of hatchery-spawned kelts that are subsequently released back to their natal river. To address these knowledge gaps, we obtained blood samples from, and acoustically tagged 30 hatchery-spawned kelts and 31 wild-spawned kelts, originating from endangered populations native to a UNESCO Biosphere Reserve in Canada during the autumns of 2014 and 2015. We then tracked individuals for up to two years through their downstream river migration, estuarine residence, ocean entry, and subsequent return as repeat-spawners. Our results indicated that hatchery-spawned kelts showed significantly higher stress levels (elevated plasma cortisol and glucose), as well as potentially altered immune states (increased circulating prostaglandin E-2) in comparison to wild spawned individuals. Behaviourally, hatchery-spawned kelts exited freshwater prematurely (similar to 66 days earlier on average) compared to wild-spawned counterparts, which was associated with a marked increase in estuarine mortality. Furthermore, survival to repeat-spawning was 0% (0/30) for hatchery-spawned kelts and 6.5% (2/31) for wild-spawned. Given that female repeat-spawners are generally larger and have increased fecundity, our findings suggest that a reduction in the fitness of post-spawners and likelihood of repeat-spawning as a result of hatchery stressors could have population-level consequences. Such impacts should be considered in conservation and management planning. DOI
829. Brandl, SJ; Goatley, CHR; Bellwood, DR; Tornabene, L.The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs.Biol. Rev., 2018, 93 The hidden half: ecology and evolution of cryptobenthic fishes on coral reefs
coral reef fish; small body size; microhabitat partitioning; speciation; trophic dynamics; functional role; biogeography; taxonomy; Gobiidae; Blennioidei
Teleost fishes are the most diverse group of vertebrates on Earth. On tropical coral reefs, their species richness exceeds 6000 species; one tenth of total vertebrate biodiversity. A large proportion of this diversity is composed of cryptobenthic reef fishes (CRFs): bottom-dwelling, morphologically or behaviourally cryptic species typically less than 50 mm in length. Yet, despite their diversity and abundance, these fishes are both poorly defined and understood. Herein we provide a new quantitative definition and synthesise current knowledge on the diversity, distribution and life history of CRFs. First, we use size distributions within families to define 17 core CRF families as characterised by the high prevalence (>10%) of small-bodied species (<50 mm). This stands in strong contrast to 42 families of large reef fishes, in which virtually no small-bodied species have evolved. We posit that small body size has allowed CRFs to diversify at extremely high rates, primarily by allowing for fine partitioning of microhabitats and facilitation of allopatric reproductive isolation; yet, we are far from understanding and documenting the biodiversity of CRFs. Using rates of description since 1758, we predict that approximately 30 new species of cryptobenthic species will be described per year until 2050 (approximately twice the annual rate compared to large fishes). Furthermore, we predict that by the year 2031, more than half of the described coral reef fish biodiversity will consist of CRFs. These fishes are the 'hidden half' of vertebrate biodiversity on coral reefs. Notably, global geographic coverage and spatial resolution of quantitative data on CRF communities is uniformly poor, which further emphasises the remarkable reservoir of biodiversity that is yet to be discovered. Although small body size may have enabled extensive diversification within CRF families, small size also comes with a suite of ecological challenges that affect fishes' capacities to feed, survive and reproduce; we identify a range of life-history adaptations that have enabled CRFs to overcome these limitations. In turn, these adaptations bestow a unique socio-ecological role on CRFs, which includes a key role in coral reef trophodynamics by cycling trophic energy provided by microscopic prey to larger consumers. Although small in body size, the ecology and evolutionary history of CRFs may make them a critical component of coral-reef food webs; yet our review also shows that these fishes are highly susceptible to a variety of anthropogenic disturbances. Understanding the consequences of these changes for CRFs and coral reef ecosystems will require us to shed more light on this frequently overlooked but highly diverse and abundant guild of coral reef fishes. DOI PubMed
828. Brumme, ZL; Kinloch, NN; Sanche, S; Wong, A; Martin, E; Cobarrubias, KD; Sandstrom, P; Levett, PN; Harrigan, PR; Joy, JB.Extensive host immune adaptation in a concentrated North American HIV epidemic.Aids, 2018, 32 Extensive host immune adaptation in a concentrated North American HIV epidemic
adaptation; clustering; epidemic; HIV; human leukocyte antigen; immune escape; phylogenetics; RT-I135X; Saskatchewan
Objective: HIV incidence in the Canadian province of Saskatchewan, where Indigenous persons make up 80% of those infected, are among the highest on the continent. Reports of accelerated HIV progression, associated with carriage of certain human leukocyte antigen (HLA) alleles (including the typically protective HLA-B*51) have also emerged from the region. Given that acquisition of HIV preadapted to host HLA negatively impacts clinical outcome, we hypothesized that HIV-host adaptation may be elevated in Saskatchewan. Design: Comparative analysis of population-level HIV sequence datasets from Saskatchewan and elsewhere in Canada/USA. Methods: We analyzed 1144 HIV subtype B Pol sequences collected in Saskatchewan between 2000 and 2016, comprising similar to 65% of cumulative provincial HIV cases, for the presence of 70 HLA-associated Pol mutations. Sequences from British Columbia (N = 6525) and elsewhere in Canada/USA (N = 6517) were used for comparison. HIV adaptation levels to 34 HLA alleles were also computed. Putative HIV transmission clusters were identified, and the prevalence of HLA-associated adaptations within and outside these clusters was investigated. Results: Analyses confirmed significantly elevated and temporally increasing levels of HIV adaptation to commonly expressed HLA alleles, in particular B*51. Notably, HLA-adapted HIV strains were significantly enriched among phylogenetic clusters in Saskatchewan. Conclusion: Extensive circulating HIV adaptation to HLA in Saskatchewan provides a plausible explanation for accelerated progression, while enrichment of adapted variants in phylogenetic clusters suggests they are being widely transmitted. Results highlight the utility of Pol sequences, routinely collected for drug resistance monitoring, for surveillance of HIV-host adaptation, and underscore the urgent need to expand HIV prevention and treatment programmes in Saskatchewan. Copyright (C) 2018 The Author(s). Published by Wolters Kluwer Health, Inc. DOI PubMed
827. Burt, JM; Tinker, MT; Okamoto, DK; Demes, KW; Holmes, K; Salomon, AK.Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts.Proc. R. Soc. B-Biol. Sci., 2018, 285 Sudden collapse of a mesopredator reveals its complementary role in mediating rocky reef regime shifts
regime shift; predator diversity; trophic cascade; kelp forests; sea otter; sea star wasting disease
While changes in the abundance of keystone predators can have cascading effects resulting in regime shifts, the role of mesopredators in these processes remains underexplored. We conducted annual surveys of rocky reef communities that varied in the recovery of a keystone predator (sea otter, Enhydra lutris) and the mass mortality of a mesopredator (sunflower sea star, Pycnopodia helianthoides) due to an infectious wasting disease. By fitting a population model to empirical data, we show that sea otters had the greatest impact on the mortality of large sea urchins, but that Pycnopodia decline corresponded to a 311% increase in medium urchins and a 30% decline in kelp densities. Our results reveal that predator complementarity in size-selective prey consumption strengthens top-down control on urchins, affecting the resilience of alternative reef states by reinforcing the resilience of kelp forests and eroding the resilience of urchin barrens. We reveal previously underappreciated species interactions within a 'classic' trophic cascade and regime shift, highlighting the critical role of middle-level predators in mediating rocky reef state transitions. DOI PubMed
824. Chaudhary, A; Pourfaraj, V; Mooers, AO.Projecting global land use-driven evolutionary history loss.Divers. Distrib., 2018, 24: 158-167 Projecting global land use-driven evolutionary history loss
biodiversity; evolutionary history; habitat loss; land use; phylogenetic diversity; species extinctions
Aim: Recent studies have mapped the global hotspots hosting high phylogenetic diversity (PD), but not the regions where this diversity is under threat due to human land use. This is because, to date, it is not clear how much PD is lost as species of a given taxon go extinct. The aim of this study was to identify the global regions projected to suffer the highest PD loss due to human land use in the near future. Location: Global. Methods: We demonstrate a novel approach combining countryside species-area relationship, species-specific evolutionary distinctiveness (ED) scores and a newly derived strong linear relationship between the cumulative ED loss and PD loss through pruning simulations on global evolutionary trees of mammals, birds, and amphibians under random species loss, to project global land use-driven phylogenetic diversity loss in 804 terrestrial ecoregions and 175 countries. We also allocate the total projected PD loss to different land use types (agriculture, forestry, grazing or urbanization) in each region to pinpoint the major drivers. Results: For the three taxa combined, we project a total loss of 9,472 million years (MY) of evolutionary history due to all land uses in all countries: 1,541 MY of mammal PD is at stake, 3,336 MY of bird PD and 4,595 MY of amphibian PD. Agriculture is responsible for loss of 1,579 MY; pasture 1990 MY, forestry 5,381 and urbanization 522. Land use in Indonesia, Colombia, India, Papua New Guinea, Madagascar and Philippines is projected to cause the most loss of PD. Main conclusions: Through the integrated approach, we can now project PD loss associated with species extinctions under alternative land conversion scenarios in a region. Overall, the results on hotspots and land use drivers may inform individual nations in designing regional strategies to achieve the international biodiversity and sustainability targets. DOI
823. Christensen, KA; Rondeau, EB; Minkley, DR; Leong, JS; Nugent, CM; Danzmann, RG; Ferguson, MM; Stadnik, A; Devlin, RH; Muzzerall, R; Edwards, M; Davidson, WS; Koop, BF.The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly.PLoS One, 2018, 13 The Arctic charr (Salvelinus alpinus) genome and transcriptome assembly
Arctic charr have a circumpolar distribution, persevere under extreme environmental conditions, and reach ages unknown to most other salmonids. The Salvelinus genus is primarily composed of species with genomes that are structured more like the ancestral salmonid genome than most Oncorhynchus and Salmo species of sister genera. It is thought that this aspect of the genome may be important for local adaptation (due to increased recombination) and anadromy (the migration of fish from saltwater to freshwater). In this study, we describe the generation of a new genetic map, the sequencing and assembly of the Arctic charr genome (GenBank accession: GCF_002910315.2) using the newly created genetic map and a previous genetic map, and present several analyses of the Arctic charr genes and genome assembly. The newly generated genetic map consists of 8,574 unique genetic markers and is similar to previous genetic maps with the exception of three major structural differences. The N50, identified BUSCOs, repetitive DNA content, and total size of the Arctic charr assembled genome are all comparable to other assembled salmonid genomes. An analysis to identify orthologous genes revealed that a large number of orthologs could be identified between salmonids and many appear to have highly conserved gene expression profiles between species. Comparing orthologous gene expression profiles may give us a better insight into which genes are more likely to influence species specific phenotypes. DOI PubMed
821. Clarke, RM; Jeen, T; Rigo, S; Thompson, JR; Kaake, LG; Thomas, F; Storr, T.Exploiting exciton coupling of ligand radical intervalence charge transfer transitions to tune NIR absorption.Chem. Sci., 2018, 9: 1610-1620 Exploiting exciton coupling of ligand radical intervalence charge transfer transitions to tune NIR absorption
We detail the rational design of a series of bimetallic bis-ligand radical Ni salen complexes in which the relative orientation of the ligand radical chromophores provides a mechanism to tune the energy of intense intervalence charge transfer (IVCT) bands in the near infrared (NIR) region. Through a suite of experimental (electrochemistry, electron paramagnetic resonance spectroscopy, UV-vis-NIR spectroscopy) and theoretical (density functional theory) techniques, we demonstrate that bimetallic Ni salen complexes form bis-ligand radicals upon two-electron oxidation, whose NIR absorption energies depend on the geometry imposed in the bis-ligand radical complex. Relative to the oxidized monomer [1(.)](+) (E = 4500 cm (1), epsilon = 27 700 M (1) cm (1)), oxidation of the cofacially constrained analogue 2 to [2(..)](2+) results in a blue-shifted NIR band (E = 4830 cm(-1), epsilon = 42 900 M-1 cm(-1)), while oxidation of 5 to [5(..)](2+), with parallel arrangement of chromophores, results in a red-shifted NIR band (E = 4150 cm(-1), epsilon = 46 600 M-1 cm(-1)); the NIR bands exhibit double the intensity in comparison to the monomer. Oxidation of the intermediate orientations results in band splitting for [3(..)](2+) (E - 4890 and 4200 cm(-1); epsilon -26 500 and 21 100 M-1 cm(-1)), and a red-shift for [4(..)](2+) using ortho-and meta-phenylene linkers, respectively. This study demonstrates for the first time, the applicability of exciton coupling to ligand radical systems absorbing in the NIR region and shows that by simple geometry changes, it is possible to tune the energy of intense low energy absorption by nearly 400 nm. DOI PubMed
820. Coatsworth, H; Caicedo, PA; Van Rossum, T; Ocampo, CB; Lowenberger, C.The Composition of Midgut Bacteria in Aedes aegypti (Diptera: Culicidae) That Are Naturally Susceptible or Refractory to Dengue Viruses.J Insect Sci., 2018, 18 The Composition of Midgut Bacteria in Aedes aegypti (Diptera: Culicidae) That Are Naturally Susceptible or Refractory to Dengue Viruses
vector competence; microbiome; midgut infection barrier
The composition, abundance, and diversity of midgut bacteria in mosquitoes can influence pathogen transmission. We used 16S rRNA microbiome profiling to survey midgut microbial diversity in pooled samples of laboratory colonized dengue-refractory, Cali-MIB, and dengue-susceptible, Cali-S Aedes aegypti (Linnaeus). The 16S rRNA sequences from the sugar-fed midguts of adult females clustered to 63 amplicon sequence variants (ASVs), primarily from Proteobacteria, Firmicutes, Flavobacteria, and Actinobacteria. An average of five ASVs dominated the midguts, and most ASVs were present in both Cali-MIB and Cali-S midguts. No differences in abundance were noted at any phylogenetic level (Phylum, Class, Order, Family, Genus) by analysis of composition of microbiome (w=0). No community diversity metrics were significantly different between refractory and susceptible mosquitoes. These data suggest that phenotypic differences in the susceptibility to dengue virus between Cali-MIB and Cali-S are not likely due to major differences in midgut bacterial communities. DOI PubMed
819. Cornell, R; Antonny, B.CCT alpha Commands Phospholipid Homeostasis from the Nucleus.Dev. Cell, 2018, 45 CCT alpha Commands Phospholipid Homeostasis from the Nucleus
Enzyme control by their products facilitates cellular homeostasis, but for phospholipids, feedback mechanisms also arise from changes in membrane physical properties. In this issue of Developmental Cell, Haider et al. (2018) show that in many actively growing cells, an enzyme of phosphatidylcholine synthesis senses lipid packing in the nuclear membrane. DOI PubMed
818. Crespi, B; Read, S; Hurd, P.The SETDB2 locus: evidence for a genetic link between handedness and atopic disease.Heredity, 2018, 120: 77-82 The SETDB2 locus: evidence for a genetic link between handedness and atopic disease
The gene SETDB2, which mediates aspects of laterality in animal model systems, has recently been linked with human handedness as measured continuously on a scale from strong left to strong right. By contrast, it was marginally associated with a left-right dichotomous measure, and it showed no evidence of association with absolute handedness strength independent of direction. We genotyped the SETDB2 handedness-associated single nucleotide polymorphism, rs4942830, in a large healthy population likewise phenotyped for continuous, absolute, and dichotomous handedness variables. Our results demonstrated significant effects of rs4942830 genotype on continuous handedness, and weaker, marginal effects on dichotomous handedness, but no effects on absolute handedness. These results help to establish the locus marked by the SNP rs4942830 as a strong candidate for mediating human handedness. Intriguingly, rs4942830 is also in complete linkage disequilibrium with rs386770867, a polymorphism recently shown to affect human serum levels of IgE production and other atopic phenotypes. These findings implicate this locus in the longstanding links of handedness with asthma and other atopic diseases. DOI
815. Davison, KM; Holloway, C; Gondara, L; Hatcher, AS.Independent associations and effect modification between lifetime substance use and recent mood disorder diagnosis with household food insecurity.PLoS One, 2018, 13 Independent associations and effect modification between lifetime substance use and recent mood disorder diagnosis with household food insecurity
Poor mental health and substance use are associated with food insecurity, however, their potential combined effects have not been studied. This study explored independent associations and effect modification between lifetime substance use and mood disorder in relation to food insecurity. Poisson regression analysis of data from British Columbia respondents (n = 13,450; 12 years+) in the 2007/08 Canadian Community Health Survey was conducted. Measures included The Household Food Security Survey Module (7.3% food insecure), recent diagnosis of a mood disorder (self-reported; 9.5%), lifetime use of cannabis, cocaine/crack, ecstasy, hallucinogens, and speed, any lifetime substance use, sociodemographic covariates, and the interaction terms of mood disorder by substance. For those with recent diagnosis of a mood disorder the prevalence of lifetime substance use ranged between 1.2 to 5.7% and were significantly higher than those without recent mood disorder diagnosis or lifetime use of substances (p's < 0.05). For respondents with a recent mood disorder diagnosis or who used cannabis, food insecurity prevalence was higher compared to the general sample (p < 0.001); prevalence was lower for cocaine/crack use (p < 0.05). Significant effect modification was found between mood disorder with cannabis, ecstasy, hallucinogen and any substance use over the lifetime (PRs 0.51 to 0.64, p's 0.022 to 0.001). Independent associations were found for cocaine/crack and speed use (PRs 1.68, p's < 0.001) and mood disorder (PRs 2.02, p's < 0.001). Based on these findings and the existing literature, future study about coping and resilience in the context of substance use, mental health, and food insecurity may lead to the development of relevant interventions aimed at mental well-being and food security. DOI PubMed
814. de Fuentes-Vicente, JA; Gutierrez-Cabrera, AE; Flores-Villegas, AL; Lowenberger, C; Benelli, G; Salazar-Schettino, PM; Cordoba-Aguilar, A.What makes an effective Chagas disease vector? Factors underlying Trypanosoma cruzi-triatomine interactions.Acta Trop., 2018, 183 What makes an effective Chagas disease vector? Factors underlying Trypanosoma cruzi-triatomine interactions
Chagas disease; Evolution; Host-parasite interaction; Meccus pallidipennis; Rhodnius prolixus; Triatoma barberi; Triatoma infestans; Triatoma dimidiata; Triatominae; Trypanosoma cruzi
The Chagas disease is caused by the parasite Trypanosoma cruzi, which infect blood-feeding triatomine bugs to finally reach mammal hosts. Chagas disease is endemic in Latin America, and is ranked among the 13 neglected tropical diseases worldwide. Currently, an estimate of 7 million people is infected by T. cruzi, leading to about 22000 deaths per year throughout the Americas. As occurs with other vectors, a major question towards control programs is what makes a susceptible bug. In this review, we focus on findings linked to insect gut structure and microbiota, immunity, genetics, blood sources, abiotic factors (with special reference to ambient temperature and altitude) to understand the interactions occurring between T. cruzi and triatomine bugs, under a co-evolutionary scenario. These factors lead to varying fitness benefits and costs for bugs, explaining why infection in the insect takes place and how it varies in time and space. Our analysis highlights that major factors are gut components and microbiota, blood sources and temperature. Although their close interaction has never been clarified, knowledge reviewed here may help to boost the success of triatomine control programs, reducing the use of insecticides. DOI PubMed
813. Del Bel, LM; Griffiths, N; Wilk, R; Wei, HC; Blagoveshchenskaya, A; Burgess, J; Polevoy, G; Price, JV; Mayinger, P; Brill, JA.The phosphoinositide phosphatase Sac1 regulates cell shape and microtubule stability in the developing Drosophila eye.Development, 2018, 145 The phosphoinositide phosphatase Sac1 regulates cell shape and microtubule stability in the developing Drosophila eye
Phosphatidylinositol 4-phosphate; PtdIns(4)P; Exocyst; IRM protein; Sac1; PI4KII; Drosophila
Epithelial patterning in the developing Drosophila melanogaster eye requires the Neph1 homolog Roughest (Rst), an immunoglobulin family cell surface adhesion molecule expressed in interommatidial cells (IOCs). Here, using a novel temperature-sensitive (ts) allele, we show that the phosphoinositide phosphatase Sac1 is also required for IOC patterning. Sac1(ts) mutants have rough eyes and retinal patterning defects that resemble rst mutants. Sac1(ts) retinas exhibit elevated levels of phosphatidylinositol 4-phosphate (PI4P), consistent with the role of Sac1 as a PI4P phosphatase. Indeed, genetic rescue and interaction experiments reveal that restriction of PI4P levels by Sac1 is crucial for normal eye development. Rst is delivered to the cell surface in Sac1(ts) mutants. However, Sac1(ts) mutant IOCs exhibit severe defects in microtubule organization, associated with accumulation of Rst and the exocyst subunit Sec8 in enlarged intracellular vesicles upon cold fixation ex vivo. Together, our data reveal a novel requirement for Sac1 in promoting microtubule stability and suggest that Rst trafficking occurs in a microtubule-and exocyst-dependent manner. DOI PubMed
812. Dhanda, AS; Vogl, AW; Albraiki, SE; Otey, CA; Beck, MR; Guttman, JA.Palladin Compensates for the Arp2/3 Complex and Supports Actin Structures during Listeria Infections.mBio, 2018, 9 Palladin Compensates for the Arp2/3 Complex and Supports Actin Structures during Listeria Infections
actin nucleation; actin polymerization; Listeria monocytogenes
Palladin is an important component of motile actin-rich structures and nucleates branched actin filament arrays in vitro. Here we examine the role of palladin during Listeria monocytogenes infections in order to tease out novel functions of palladin. We show that palladin is co-opted by L. monocytogenes during its cellular entry and intracellular motility. Depletion of palladin resulted in shorter and misshapen comet tails, and when actin-or VASP-binding mutants of palladin were overexpressed in cells, comet tails disintegrated or became thinner. Comet tail thinning resulted in parallel actin bundles within the structures. To determine whether palladin could compensate for the Arp2/3 complex, we overexpressed palladin in cells treated with the Arp2/3 inhibitor CK-666. In treated cells, bacterial motility could be initiated and maintained when levels of palladin were increased. To confirm these findings, we utilized a cell line depleted of multiple Arp2/3 complex subunits. Within these cells, L. monocytogenes failed to generate comet tails. When palladin was overexpressed in this Arp2/3 functionally null cell line, the ability of L. monocytogenes to generate comet tails was restored. Using purified protein components, we demonstrate that L. monocytogenes actin clouds and comet tails can be generated ( in a cell-free system) by palladin in the absence of the Arp2/3 complex. Collectively, our results demonstrate that palladin can functionally replace the Arp2/3 complex during bacterial actin-based motility. IMPORTANCE Structures containing branched actin filaments require the Arp2/3 complex. One of the most commonly used systems to study intracellular movement generated by Arp2/3-based actin motility exploits actin-rich comet tails made by Listeria. Using these infections together with live imaging and cell-free protein reconstitution experiments, we show that another protein, palladin, can be used in place of Arp2/3 to form actin-rich structures. Additionally, we show that palladin is needed for the structural integrity of comet tails as its depletion or mutation of critical regions causes dramatic changes to comet tail organization. These findings are the first to identify a protein that can functionally replace the Arp2/3 complex and have implications for all actin-based structures thought to exclusively use that complex. DOI PubMed
811. Dias, GM; Ramogida, CF; Rousseau, J; Zacchia, NA; Hoehr, C; Schaffer, P; Lin, VS; Benard, F.Zr-89 for antibody labeling and in vivo studies - A comparison between liquid and solid target production.Nucl. Med. Biol., 2018, 58 Zr-89 for antibody labeling and in vivo studies - A comparison between liquid and solid target production
Zirconium-89; Liquid target; Radioimmunoimaging; Positron emission tomography
Introduction: Zirconium-89 (Zr-89, t(1/2) = 78.4 h) liquid target (LT) production offers an approach to introduce this positron-emitting isotope to cyclotron centres without the need for a separate solid target (ST) production set up. We compared the production, purification, and antibody radiolabeling yields of Zr-89-(LT) and Zr-89-(ST), and assessed the feasibility of Zr-89-(LT) for preclinical PET/CT. Methods: Zr-89-(ST) production was performed with an Y-89 foil on a TR 19 cyclotron at 13.8 MeV. For LT production; an aqueous solution of yttrium nitrate (Y(NO3)(3) center dot 6H(2)O) was irradiated on a TR 13 cyclotron at 12 MeV. Zr-89 was purified from the ST or LT material with hydroxamate resin, and used to radiolabel p-SCN-Bn-Deferoxamine (DFO)-conjugated Trastuzumab. MicroPET-CT imaging was performed at 1, 3 and 5 days post-injection of Zr-89-DFO-Trastuzumab from ST or LT with biodistribution analysis on day 5. Results: Irradiation of the ST yielded 2.88 +/- 1.07 GBq/mu A with a beam current of 14.0 +/- 3.8 mu A and irradiation time of 137 +/- 48 min at end of bombardment while LT yielded 0.27 0.05 GBq/mu A with a beam current of 9.9 +/- 22 mu A and irradiation time of 221 +/- 29 min. Radiolabeling of DFO-Trastuzumab with Zr-89-(ST) or Zr-89-(LT) was successful with purity > 97% and specific activity > 0.12 MBq/mu g (of antibody). MicroPET-CT imaging and biodistribution profiles showed similar uptake of Zr-89-(ST)-DFO-Trastuzumab and Zr-89-(LT)-DFO-Trastuzumab in tumor and all organs of interest. Conclusion: Zr-89-(LT) was effectively used to prepare antibody bioconjugates with specific activities suitable for small animal imaging. PET imaging and biodistribution revealed similar behaviours between bioconjugates labeled with Zr-89 produced from the two target systems. (C) 2017 Published by Elsevier Inc. DOI PubMed
810. Flowers, GE.Hydrology and the future of the Greenland Ice Sheet.Nat. Commun., 2018, 9 Hydrology and the future of the Greenland Ice Sheet
Detection, attribution and projection of mass loss from the Greenland Ice Sheet has been a central focus of the glaciological community, with surface meltwater thought to play a key role in feedbacks that could accelerate sea-level rise. While the prospect of runaway sliding has faded, much remains uncertain when it comes to the role of surface runoff and subglacial discharge in Greenland's future. DOI PubMed
809. Fowler, MA; Paquet, M; Legault, V; Cohen, AA; Williams, TD.Physiological predictors of reproductive performance in the European Starling (Sturnus vulgaris).Front. Zool., 2018, 15 Physiological predictors of reproductive performance in the European Starling (Sturnus vulgaris)
Dysregulation; European starling; Physiological complexity; Physiological state; Principal components analysis; Reproductive fitness; Statistical distance; Sturnus vulgaris
Background: It is widely assumed that variation in fitness components has a physiological basis that might underlie selection on trade-offs, but the mechanisms driving decreased survival and future fecundity remain elusive. Here, we assessed whether physiological variables are related to workload ability or immediate fitness consequences and if they mediate future survival or reproductive success. We used data on 13 physiological variables measured in 93 female European starlings (Sturnus vulgaris) at two breeding stages (incubation, chick-rearing), for first-and second-broods over two years (152 observations). Results: There was little co-variation among the physiological variables, either in incubating or chick-rearing birds, but some systematic physiological differences between the two stages. Chick-rearing birds had lower hematocrit and plasma creatine kinase but higher hemoglobin, triglyceride and uric acid levels. Only plasma corticosterone was repeatable between incubation and chick-rearing. We assessed relationships between incubation or chick-rearing physiology and measures of workload, current productivity, future fecundity or survival in a univariate manner, and found very few significant relationships. Thus, we next explored the utility of multivariate analysis (principal components analysis, Mahalanobis distance) to account for potentially complex physiological integration, but still found no clear associations. Conclusions: This implies either that a) birds maintained physiological variables within a homeostatic range that did not affect their performance, b) there are relatively few links between physiology and performance, or, more likely, c) that the complexity of these relationships exceeds our ability to measure it. Variability in ecological context may complicate the relationship between physiology and behavior. We thus urge caution regarding the over-interpretation of isolated significant findings, based on single traits in single years, in the literature. DOI PubMed
807. Gill, EE; Chan, LS; Winsor, GL; Dobson, N; Lo, R; Sui, SJH; Dhillon, BK; Taylor, PK; Shrestha, R; Spencer, C; Hancock, REW; Unrau, PJ; Brinkman, FSL.High-throughput detection of RNA processing in bacteria.BMC Genomics, 2018, 19 High-throughput detection of RNA processing in bacteria
RNA processing; Nucleases; Transcription; RNA-Seq; Gene expression; Gene regulation; dRNA-Seq; pRNA-Seq; Pseudomonas aeruginosa
Background: Understanding the RNA processing of an organism's transcriptome is an essential but challenging step in understanding its biology. Here we investigate with unprecedented detail the transcriptome of Pseudomonas aeruginosa PAO1, a medically important and innately multi-drug resistant bacterium. We systematically mapped RNA cleavage and dephosphorylation sites that result in 5'-monophosphate terminated RNA (pRNA) using monophosphate RNA-Seq (pRNA-Seq). Transcriptional start sites (TSS) were also mapped using differential RNA-Seq (dRNA-Seq) and both datasets were compared to conventional RNA-Seq performed in a variety of growth conditions. Results: The pRNA-Seq library revealed known tRNA, rRNA and transfer-messenger RNA (tmRNA) processing sites, together with previously uncharacterized RNA cleavage events that were found disproportionately near the 5' ends of transcripts associated with basic bacterial functions such as oxidative phosphorylation and purine metabolism. The majority (97%) of the processed mRNAs were cleaved at precise codon positions within defined sequence motifs indicative of distinct endonucleolytic activities. The most abundant of these motifs corresponded closely to an E. coli RNase E site previously established in vitro. Using the dRNA-Seq library, we performed an operon analysis and predicted 3159 potential TSS. A correlation analysis uncovered 105 antiparallel pairs of TSS that were separated by 18 bp from each other and were centered on single palindromic TAT(A/T) ATA motifs (likely - 10 promoter elements), suggesting that, consistent with previous in vitro experimentation, these sites can initiate transcription bi-directionally and may thus provide a novel form of transcriptional regulation. TSS and RNA-Seq analysis allowed us to confirm expression of small non-coding RNAs (ncRNAs), many of which are differentially expressed in swarming and biofilm formation conditions. Conclusions: This study uses pRNA-Seq, a method that provides a genome-wide survey of RNA processing, to study the bacterium Pseudomonas aeruginosa and discover extensive transcript processing not previously appreciated. We have also gained novel insight into RNA maturation and turnover as well as a potential novel form of transcription regulation. NOTE: All sequence data has been submitted to the NCBI sequence read archive. Accession numbers are as follows: [NCBI sequence read archive: SRX156386, SRX157659, SRX157660, SRX157661, SRX157683 and SRX158075]. The sequence data is viewable using Jbrowse on www. pseudomonas. com. DOI PubMed
806. Greenberg, DA; Palen, WJ; Chan, KC; Jetz, W; Mooers, AO.Evolutionarily distinct amphibians are disproportionately lost from human-modified ecosystems.Ecology Letters, 2018, 21 Evolutionarily distinct amphibians are disproportionately lost from human-modified ecosystems
diversification; extinction risk; forests; global change; grasslands; habitat loss; land conversion; phylogenetic diversity
Humans continue to alter terrestrial ecosystems, but our understanding of how biodiversity responds is still limited. Anthropogenic habitat conversion has been associated with the loss of evolutionarily distinct bird species at local scales, but whether this evolutionary pattern holds across other clades is unknown. We collate a global dataset on amphibian assemblages in intact forests and nearby human-modified sites to assess whether evolutionary history influences susceptibility to land conversion. We found that evolutionarily distinct amphibian species are disproportionately lost when forested habitats are converted to alternative land-uses. We tested the hypothesis that grassland-associated amphibian lineages have both higher diversification and are pre-adapted to human landscapes, but found only weak evidence supporting this. The loss of evolutionarily distinct amphibians with land conversion suggests that preserving remnant forests will be vital if we aim to preserve the amphibian tree of life in the face of mounting anthropogenic pressures. DOI PubMed
805. Hennin, HL; Dey, CJ; Bety, J; Gilchrist, HG; Legagneux, P; Williams, TD; Love, OP.Higher rates of prebreeding condition gain positively impacts clutch size: A mechanistic test of the condition-dependent individual optimization model.Funct. Ecol., 2018, 32 Higher rates of prebreeding condition gain positively impacts clutch size: A mechanistic test of the condition-dependent individual optimization model
clutch size; common eider; condition gain; fattening rate; individual optimization; laying date; path analysis; triglyceride
1. A combination of timing of and body condition (i.e., mass) at arrival on the breeding grounds interact to influence the optimal combination of the timing of reproduction and clutch size in migratory species. This relationship has been formalized by Rowe et al. in a condition-dependent individual optimization model (American Naturalist, 1994, 143, 689-722), which has been empirically tested and validated in avian species with a capital-based breeding strategy. 2. This model makes a key, but currently untested prediction; that variation in the rate of body condition gain will shift the optimal combination of laying date and clutch size. This prediction is essential because it implies that individuals can compensate for the challenges associated with late timing of arrival or poor body condition at arrival on the breeding grounds through adjustment of their life history investment decisions, in an attempt to maximize fitness. 3. Using an 11-year data set in arctic-nesting common eiders (Somateria mollissima), quantification of fattening rates using plasma triglycerides (an energetic metabolite), and a path analysis approach, we test this prediction of this optimization model; controlling for arrival date and body condition, females that fatten more quickly will adjust the optimal combination of lay date and clutch size, in favour of a larger clutch size. 4. As predicted, females fattening at higher rates initiated clutches earlier and produced larger clutch sizes, indicating that fattening rate is an important factor in addition to arrival date and body condition in predicting individual variation in reproductive investment. However, there was no direct effect of fattening rate on clutch size (i.e., birds laying on the same date had similar clutch sizes, independent of their fattening rate). Instead, fattening rate indirectly affected clutch size via earlier lay dates, thus not supporting the original predictions of the optimization model. 5. Our results demonstrate that variation in the rate of condition gain allows individuals to shift flexibly along the seasonal decline in clutch size to presumably optimize the combination of laying date and clutch size. DOI
804. Hoover, B; Alcaide, M; Jennings, S; Sin, SYW; Edwards, SV; Nevitt, GA.Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa).Mol. Ecol., 2018, 27 Ecology can inform genetics: Disassortative mating contributes to MHC polymorphism in Leach's storm-petrels (Oceanodroma leucorhoa)
heterozygosity; major histocompatibility complex; mate choice; seabirds; sexual selection
Studies of MHC-based mate choice in wild populations often test hypotheses on species exhibiting female choice and male-male competition, which reflects the general prevalence of females as the choosy sex in natural systems. Here, we examined mutual mate-choice patterns in a small burrow-nesting seabird, the Leach's storm-petrel (Oceanodroma leucorhoa), using the major histocompatibility complex (MHC). The life history and ecology of this species are extreme: both partners work together to fledge a single chick during the breeding season, a task that requires regularly travelling hundreds of kilometres to and from foraging grounds over a 6- to 8-week provisioning period. Using a 5-year data set unprecedented for this species (n=1078 adults and 925 chicks), we found a positive relationship between variation in the likelihood of female reproductive success and heterozygosity at Ocle-DAB2, a MHC class IIB locus. Contrary to previous reports rejecting disassortative mating as a mechanism for maintaining genetic polymorphism in this species, here we show that males make significant disassortative mate-choice decisions. Variability in female reproductive success suggests that the most common homozygous females (Ocle-DAB2*01/Ocle-DAB2*01) may be physiologically disadvantaged and, therefore, less preferred as lifelong partners for choosy males. The results from this study support the role of mate choice in maintaining high levels of MHC variability in a wild seabird species and highlight the need to incorporate a broader ecological framework and sufficient sample sizes into studies of MHC-based mating patterns in wild populations in general. DOI PubMed
803. Iacona, GD; Sutherland, WJ; Mappin, B; Adams, VM; Armsworth, PR; Coleshaw, T; Cook, C; Craigie, I; Dicks, LV; Fitzsimons, JA; McGowan, J; Plumptre, AJ; Polak, T; Pullin, AS; Ringma, J; Rushworth, I; Santangeli, A; Stewart, A; Tulloch, A; Walsh, JC; Possingham, HP.Standardized reporting of the costs of management interventions for biodiversity conservation.Conserv. Biol., 2018, 32 Standardized reporting of the costs of management interventions for biodiversity conservation
conservation accountancy; conservation evidence; cost-benefit; effectiveness; return-on-investment
Effective conservation management interventions must combat threats and deliver benefits at costs that can be achieved within limited budgets. Considerable effort has focused on measuring the potential benefits of conservation interventions, but explicit quantification of the financial costs of implementation is rare. Even when costs have been quantified, haphazard and inconsistent reporting means published values are difficult to interpret. This reporting deficiency hinders progress toward a collective understanding of the financial costs of management interventions across projects and thus limits the ability to identify efficient solutions to conservation problems or attract adequate funding. We devised a standardized approach to describing financial costs reported for conservation interventions. The standards call for researchers and practitioners to describe the objective and outcome, context and methods, and scale of costed interventions, and to state which categories of costs are included and the currency and date for reported costs. These standards aim to provide enough contextual information that readers and future users can interpret the cost data appropriately. We suggest these standards be adopted by major conservation organizations, conservation science institutions, and journals so that cost reporting is comparable among studies. This would support shared learning and enhance the ability to identify and perform cost-effective conservation. Normalizacion de los Informes de Costos de Intervenciones de Manejo para la Conservacion de la Biodiversidad. Las intervenciones efectivas de manejo para la conservacion deben combatir amenazas y proporcionar beneficios con costos que se pueden obtener con presupuestos limitados. Se han enfocado esfuerzos considerables para medir los beneficios potenciales de las intervenciones de conservacion, pero es rara la cuantificacion explicita de los costos financieros de la implementacion. Aun cuando se han cuantificado los costos, los informes aleatorios e inconsistentes significa que los valores publicados son dificiles de entender. Esta deficiencia en los informes limita el progreso hacia un entendimiento colectivo de los costos financieros de las intervenciones de manejo y por lo tanto limita la habilidad de identificar soluciones eficientes a los problemas de conservacion o de atraer financiamiento adecuado. Disenamos un metodo estandarizado para describir los costos financieros reportados para las intervenciones para la conservacion. Los estandares requieren que los investigadores y practicantes describan el objetivo y resultados, el contexto y los metodos y la escala de las intervenciones presupuestadas y que citen las categorias de costos incluidas y la divisa y fecha de los costos reportados. Estos estandares tratan de proporcionar suficiente informacion contextual para que los lectores y futuros usuarios puedan interpretar los datos de costos apropiadamente. Sugerimos que estos estandares sean adoptados por las principales organizaciones de conservacion, las instituciones cientificas y las revistas para que los informes de costos sean comparables entre estudios. Esto daria soporte al aprendizaje compartido y incrementar la habilidad para identificar y realizar conservacion rentable. Resumen ?? ??????????????????????, ?????????????????????????????????, ???????????????????????????, ??????????????????????????????????????????????????????????????, ????????????????????????????????, ??????????????????????????, ????????????????????????????????, ???????????????????????????????????????????, ???????????????????????????????????????????????????, ???????????????????????????, ??????????????????????: ???; ??: ???? Article impact statement: Standardized reporting of conservation costs means data in published studies can be transferable and interpretable for improved conservation. DOI PubMed
802. Irwin, DE; Mila, B; Toews, DPL; Brelsford, A; Kenyon, HL; Porter, AN; Grossen, C; Delmore, KE; Alcaide, M; Irwin, JH.A comparison of genomic islands of differentiation across three young avian species pairs.Mol. Ecol., 2018, 27 A comparison of genomic islands of differentiation across three young avian species pairs
genomic differentiation; hybridization; islands of differentiation; Parulidae; speciation; warbler
Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in F-ST), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in F-ST, suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (pi(Within)) are almost as large as levels of between-group nucleotide distance (pi(Between)) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the F-ST peaks having low pi(Between) suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations. DOI PubMed
801. Jabado, RW; Kyne, PM; Pollom, RA; Ebert, DA; Simpfendorfer, CA; Ralph, GM; Al Dhaheri, SS; Akhilesh, KV; Ali, K; Ali, MH; Al Mamari, TMS; Bineesh, KK; El Hassan, IS; Fernando, D; Grandcourt, EM; Khan, MM; Moore, ABM; Owfi, F; Robinson, DP; Romanov, E; Soares, AL; Spaet, JLY; Tesfamichael, D; Valinassab, T; Dulvy, NK.Troubled waters: Threats and extinction risk of the sharks, rays and chimaeras of the Arabian Sea and adjacent waters.Fish. Fish., 2018, 19 Troubled waters: Threats and extinction risk of the sharks, rays and chimaeras of the Arabian Sea and adjacent waters
chondrichthyans; extinction risk; fisheries; IUCN Red List; population decline; species diversity
The extinction risk of sharks, rays and chimaeras is higher than that for most other vertebrates due to low intrinsic population growth rates of many species and the fishing intensity they face. The Arabian Sea and adjacent waters border some of the most important chondrichthyan fishing and trading nations globally, yet there has been no previous attempt to assess the conservation status of species occurring here. Using IUCN Red List of Threatened Species Categories and Criteria and their guidelines for application at the regional level, we present the first assessment of extinction risk for 153 species of sharks, rays and chimaeras. Results indicate that this region, home to 15% of described chondrichthyans including 30 endemic species, has some of the most threatened chondrichthyan populations in the world. Seventy-eight species (50.9%) were assessed as threatened (Critically Endangered, Endangered or Vulnerable), and 27 species (17.6%) as Near Threatened. Twenty-nine species (19%) were Data Deficient with insufficient information to assess their status. Chondrichthyan populations have significantly declined due to largely uncontrolled and unregulated fisheries combined with habitat degradation. Further, there is limited political will and national and regional capacities to assess, manage, conserve or rebuild stocks. Outside the few deepsea locations that are lightly exploited, the prognosis for the recovery of most species is poor in the near-absence of management. Concerted national and regional management measures are urgently needed to ensure extinctions are avoided, the sustainability of more productive species is secured, and to avoid the continued thinning of the regional food security portfolio. DOI
800. Jensen, VL; Lambacher, NJ; Li, CM; Mohan, S; Williams, CL; Inglis, PN; Yoder, BK; Blacque, OE; Leroux, MR.Role for intraflagellar transport in building a functional transition zone.EMBO Rep., 2018, 19 Role for intraflagellar transport in building a functional transition zone
C. elegans; cilia; dynein; IFT; transition zone
Synopsis Genetic disorders caused by cilia dysfunction, termed ciliopathies, frequently involve the intraflagellar transport (IFT) system. Mutations in IFT subunits-including IFT-dynein motor DYNC2H1-impair ciliary structures and Hedgehog signalling, typically leading to "skeletal" ciliopathies such as Jeune asphyxiating thoracic dystrophy. Intriguingly, IFT gene mutations also cause eye, kidney and brain ciliopathies often linked to defects in the transition zone (TZ), a ciliary gate implicated in Hedgehog signalling. Here, we identify a C. elegans temperature-sensitive (ts) IFT-dynein mutant (che-3; human DYNC2H1) and use it to show a role for retrograde IFT in anterograde transport and ciliary maintenance. Unexpectedly, correct TZ assembly and gating function for periciliary proteins also require IFT-dynein. Using the reversibility of the novel ts-IFT-dynein, we show that restoring IFT in adults (post-developmentally) reverses defects in ciliary structure, TZ protein localisation and ciliary gating. Notably, this ability to reverse TZ defects declines as animals age. Together, our findings reveal a previously unknown role for IFT in TZ assembly in metazoans, providing new insights into the pathomechanism and potential phenotypic overlap between IFT- and TZ-associated ciliopathies. DOI PubMed
799. Jha, S; Read, S; Hurd, P; Crespi, B.Segregating polymorphism in the NMDA receptor gene GRIN2A, schizotypy, and mental rotation among healthy individuals.Neuropsychologia, 2018, 117 Segregating polymorphism in the NMDA receptor gene GRIN2A, schizotypy, and mental rotation among healthy individuals
Schizotypy; Mental rotation; GRIN2A; NMDA receptor; Imagery
Common alleles associated with psychiatric disorders are often regarded as deleterious genes that influence vulnerability to disease, but they may also be considered as mediators of variation in adaptively structured cognitive phenotypes among healthy individuals. The schizophrenia-associated gene GRIN2A (glutamate ionotropic receptor NMDA type subunit 2a) codes for a protein subunit of the NMDA (N-methyl-D-aspartate) receptor that underlies central aspects of human cognition. Pharmacological NMDA blockage recapitulates the major features of schizophrenia in human subjects, and represents a key model for the neurological basis of this disorder. We genotyped two functional GRIN2A polymorphisms in a large population of healthy individuals who were scored for schizotypy and mental imagery/manipulation (the mental rotation test). Rare-allele homozygosity of the promoter microsatellite rs3219790 was associated with high total schizotypy (after adjustment for multiple comparisons) and with enhanced mental rotation ability (nominally, but not after adjustment for multiple comparisons), among males. These findings provide preliminary evidence regarding a genetic basis to previous reports of enhanced mental imagery in schizophrenia and schizotypy. The results also suggest that some schizophrenia-related alleles may be subject to cognitive tradeoffs involving both positive and negative effects on psychological phenotypes, which may help to explain the maintenance of psychiatric-disorder risk alleles in human populations. DOI PubMed
798. Juan-Jorda, MJ; Murua, H; Arrizabalaga, H; Dulvy, NK; Restrepo, V.Report card on ecosystem-based fisheries management in tuna regional fisheries management organizations.Fish. Fish., 2018, 19 Report card on ecosystem-based fisheries management in tuna regional fisheries management organizations
bycatch; ecosystem impacts; ecosystem-based fisheries management; RFMO; sharks; tunas
International instruments of fisheries governance have set the core principles for the management of highly migratory fishes. We evaluated the progress of tuna Regional Fisheries Management Organizations (tRFMOs) in implementing the ecological component of ecosystem-based fisheries management (EBFM). We first developed a best case tRFMO for EBFM implementation. Second, we developed criteria to evaluate progress in applying EBFM against this best case tRFMO. We assessed progress of the following four ecological components: target species, bycatch species, ecosystem properties and trophic relationships, and habitats. We found that many of the elements necessary for an operational EBFM are already present, yet they have been implemented in an ad hoc way, without a long-term vision and a formalized plan. Overall, tRFMOs have made considerable progress monitoring the impacts of fisheries on target species, moderate progress for bycatch species, and little progress for ecosystem properties and trophic relationships and habitats. The tRFMOs appear to be halfway towards implementing the ecological component of EBFM, yet it is clear that the low-hanging fruit has been plucked and the more difficult, but surmountable, issues remain, notably the sustainable management of bycatch. All tRFMOs share the same challenge of developing a formal mechanism to better integrate ecosystem science and advice into management decisions. We hope to further discussion across the tRFMOs to inform the development of operational EBFM plans. DOI
797. Kazmiruk, TN; Kazmiruk, VD; Bendell, LI.Abundance and distribution of microplastics within surface sediments of a key shellfish growing region of Canada.PLoS One, 2018, 13 Abundance and distribution of microplastics within surface sediments of a key shellfish growing region of Canada
The abundance and distribution of microplastics within 5 sediment size classes (>5000 mu m, 1000-5000 mu m, 250-1000 mu m, 250-0.63 mu m and <0.63 mu m) were determined for 16 sites within Lambert Channel and Baynes Sound, British Columbia, Canada. This region is Canada's premier growing area for the Pacific oyster (Crassostrea gigas). Microplastics were found at all sampling locations indicating widespread contamination of this region with these particles. Three types of microplastics were recovered: microbeads, which occurred in the greatest number (up to 25000/kg dry sediment) and microfibers and microfragments, which were much less in number compared with microbeads and occurred in similar amounts (100-300/kg dry sediment). Microbeads were recovered primarily in the <0.63 mu m and 250-0.63 mu m sediment size class, whereas microfragments and microfibers were generally identified in all 5 sediment size classes. Abundance and distribution of the three types of microplastics were spatially dependent with principal component analysis (PCA) indicating that 84 percent of the variation in abundance and distribution was due to the presence of high numbers of microbeads at three locations within the study region. At these sites, microbeads expressed as a percent component of the sediment by weight was similar to key geochemical components that govern trace metal behavior and availability to benthic organisms. Microbeads have been shown to accumulate metals from the aquatic environment, hence in addition to the traditional geochemical components such as silt and organic matter, microplastics also need to be considered as a sediment component that can influence trace metal geochemistry. Our findings have shown that BC's premier oyster growing region is highly contaminated with microplastics, notably microbeads. It would be prudent to assess the degree to which oysters from this region are ingesting microplastics. If so, it would have direct implications for Canada's oyster farming industry with respect to the health of the oyster and the quality of product that is being farmed and sets an example for other shellfish growing regions of the world. DOI PubMed
796. Kench, PS; Ford, MR; Owen, SD.Patterns of island change and persistence offer alternate adaptation pathways for atoll nations.Nat. Commun., 2018, 9 Patterns of island change and persistence offer alternate adaptation pathways for atoll nations
Sea-level rise and climatic change threaten the existence of atoll nations. Inundation and erosion are expected to render islands uninhabitable over the next century, forcing human migration. Here we present analysis of shoreline change in all 101 islands in the Pacific atoll nation of Tuvalu. Using remotely sensed data, change is analysed over the past four decades, a period when local sea level has risen at twice the global average (similar to 3.90 +/- 0.4 mm. yr(-1)). Results highlight a net increase in land area in Tuvalu of 73.5 ha (2.9%), despite sea-level rise, and land area increase in eight of nine atolls. Island change has lacked uniformity with 74% increasing and 27% decreasing in size. Results challenge perceptions of island loss, showing islands are dynamic features that will persist as sites for habitation over the next century, presenting alternate opportunities for adaptation that embrace the heterogeneity of island types and their dynamics. DOI
795. Keyvanloo, A; Shaghaghi, M; Zuckermann, MJ; Thewalt, JL.The Phase Behavior and Organization of Sphingomyelin/Cholesterol Membranes: A Deuterium NMR Study.Biophys. J., 2018, 114 The Phase Behavior and Organization of Sphingomyelin/Cholesterol Membranes: A Deuterium NMR Study
We have studied the dependence of the phase and domain characteristics of sphingomyelin (SM)/cholesterol model membranes on sterol content and temperature using deuterium nuclear magnetic resonance. NMR spectra of N-palmitoyl(D31)-D-erythro-sphingosylphosphorylcholine (PSM-d31) were taken for temperatures from 25 to 70 degrees C and cholesterol concentrations of 0-40%. Analogous experiments were performed using 1-palmitoyl, 2-palmitoyl(D31)-sn-glycero-3-phosphocholine (DPPC-d31)/cholesterol membranes to carefully compare the data obtained using palmitoyl chains that have similar "kinked" conformations. The constructed phase diagrams exhibit both solid-ordered (so) + liquid-ordered (lo) and liquid-disordered (ld) + lo phase-coexistence regions with a clear three-phase line. Macroscopic (micron-sized) coexistence of ld and lo phases was not observed; instead, line-broadening in the ld+lo region was characterized by intermediate exchange of lipids between the two types of domains. The length scales associated with the domains were estimated to be 75-150 nm for PSM-d31/cholesterol and DPPC-d31/cholesterol model membranes. DOI PubMed
794. Kindsvater, HK; Dulvy, NK; Horswill, C; Juan-Jorda, MJ; Mangel, M; Matthiopoulos, J.Overcoming the Data Crisis in Biodiversity Conservation.Trends Ecol. Evol., 2018, 33 Overcoming the Data Crisis in Biodiversity Conservation
How can we track population trends when monitoring data are sparse? Population declines can go undetected, despite ongoing threats. For example, only one of every 200 harvested species are monitored. This gapleads to uncertaintyabout the seriousness of declines and hampers effective conservation. Collecting more data is important, but we can also make better use of existing information. Prior knowledge of physiology, life history, and community ecology can be used to inform population models. Additionally, in multispecies models, information can be shared among taxa based on phylogenetic, spatial, or temporal proximity. By exploiting generalities across species that share evolutionary or ecological characteristics within Bayesian hierarchical models, we can fill crucial gaps in the assessment of species' status with unparalleled quantitative rigor. DOI PubMed
793. Kirkness, MWH; Forde, NR.Single-Molecule Assay for Proteolytic Susceptibility: Force-Induced Collagen Destabilization.Biophys. J., 2018, 114 Single-Molecule Assay for Proteolytic Susceptibility: Force-Induced Collagen Destabilization
Force plays a key role in regulating dynamics of biomolecular structure and interactions, yet techniques are lacking to manipulate and continuously read out this response with high throughput. We present an enzymatic assay for force-dependent accessibility of structure that makes use of a wireless mini-radio centrifuge force microscope to provide a real-time readout of kinetics. The microscope is designed for ease of use, fits in a standard centrifuge bucket, and offers high-throughput, video-rate readout of individual proteolytic cleavage events. Proteolysis measurements on thousands of tethered collagen molecules show a load-enhanced trypsin sensitivity, indicating destabilization of the triple helix. DOI PubMed
791. Knight, SM; Bradley, DW; Clark, RG; Gow, EA; Belisle, M; Berzins, LL; Blake, T; Bridge, ES; Burke, L; Dawson, RD; Dunn, PO; Garant, D; Holroyd, GL; Hussell, DJT; Lansdorp, O; Laughlin, AJ; Leonard, ML; Pelletier, F; Shutler, D; Siefferman, L; Taylor, CM; Trefry, HE; Vleck, CM; Vleck, D; Winkler, DW; Whittingham, LA; Norris, DR.Constructing and evaluating a continent-wide migratory songbird network across the annual cycle.Ecol. Monogr., 2018, 88 Constructing and evaluating a continent-wide migratory songbird network across the annual cycle
flyway; geolocator; migration; migratory connectivity; network theory; Tree Swallow
Determining how migratory animals are spatially connected between breeding and non-breeding periods is essential for predicting the effects of environmental change and for developing optimal conservation strategies. Yet, despite recent advances in tracking technology, we lack comprehensive information on the spatial structure of migratory networks across a species' range, particularly for small-bodied, long-distance migratory animals. We constructed a migratory network for a songbird and used network-based metrics to characterize the spatial structure and prioritize regions for conservation. The network was constructed using year-round movements derived from 133 archival light-level geolocators attached to Tree Swallows (Tachycineta bicolor) originating from 12 breeding sites across their North American breeding range. From these breeding sites, we identified 10 autumn stopover nodes (regions) in North America, 13 non-breeding nodes located around the Gulf of Mexico, Mexico, Florida, and the Caribbean, and 136 unique edges (migratory routes) connecting nodes. We found strong migratory connectivity between breeding and autumn stopover sites and moderate migratory connectivity between the breeding and non-breeding sites. We identified three distinct "communities" of nodes that corresponded to western, central, and eastern North American flyways. Several regions were important for maintaining network connectivity, with South Florida and Louisiana as the top ranked non-breeding nodes and the Midwest as the top ranked stopover node. We show that migratory songbird networks can have both a high degree of mixing between seasons yet still show regionally distinct migratory flyways. Such information will be crucial for accurately predicting factors that limit and regulate migratory songbirds throughout the annual cycle. Our study highlights how network-based metrics can be valuable for identifying overall network structure and prioritizing specific regions within a network for conserving a wide variety of migratory animals. DOI
790. Krogstad, MJ; Gehring, PM; Rosenkranz, S; Osborn, R; Ye, F; Liu, Y; Ruff, JPC; Chen, W; Wozniak, JM; Luo, H; Chmaissem, O; Ye, ZG; Phelan, D.The relation of local order to material properties in relaxor ferroelectrics.Nat. Mater., 2018, 17: 718-+ The relation of local order to material properties in relaxor ferroelectrics
Correlating electromechanical and dielectric properties with nanometre-scale order is the defining challenge for the development of piezoelectric oxides. Current lead (Pb)-based relaxor ferroelectrics can serve as model systems with which to unravel these correlations, but the nature of the local order and its relation to material properties remains controversial. Here we employ recent advances in diffuse scattering instrumentation to investigate crystals that span the phase diagram of PbMg1/3Nb2/3O3-xPbTiO(3) (PMN-xPT) and identify four forms of local order. From the compositional dependence, we resolve the coupling of each form to the dielectric and electromechanical properties observed. We show that relaxor behaviour does not correlate simply with ferroic diffuse scattering; instead, it results from a competition between local antiferroelectric correlations, seeded by chemical short-range order, and local ferroic order. The ferroic diffuse scattering is strongest where piezoelectricity is maximal and displays previously unrecognized modulations caused by anion displacements. Our observations provide new guidelines for evaluating displacive models and hence the piezoelectric properties of environmentally friendly next-generation materials. DOI PubMed
789. Lat, PK; Sen, D.(C(2)G(4))(n) repeat expansion sequences from the C9orf72 gene form an unusual DNA higher-order structure in the pH range of 5-6.PLoS One, 2018, 13 (C(2)G(4))(n) repeat expansion sequences from the C9orf72 gene form an unusual DNA higher-order structure in the pH range of 5-6
Massive expansion of a DNA hexanucleotide sequence repeat (C(2)G(4)) within the human C9orf72 gene has been linked to a number of neurodegenerative diseases. In sodium or potassium salt solutions, single-stranded d(C(2)G(4))(n) DNAs fold to form G-quadruplexes. We have found that in magnesium or lithium salt solutions, especially under slightly acidic conditions, d(C(2)G(4))(n) oligonucleotides fold to form a distinctive higher order structure whose most striking feature is an "inverted" circular dichroism spectrum, which is distinguishable from the spectrum of the left handed DNA double-helix, Z-DNA. On the basis of CD spectroscopy, gel mobility as well as chemical protection analysis, we propose that this structure, which we call "iCD-DNA", may be a left-handed Hoogsteen base-paired duplex, an unorthodox G-quadruplex/i-motif composite, or a non-canonical, "braided" DNA triplex. Given that iCD-DNA forms under slightly acidic solution conditions, we do not know at this point in time whether or not it forms within living cells. DOI PubMed
788. Leeney, RH; Mana, RR; Dulvy, NK.Fishers' ecological knowledge of sawfishes in the Sepik and Ramu rivers, northern Papua New Guinea.Endanger. Species Res., 2018, 36 Fishers' ecological knowledge of sawfishes in the Sepik and Ramu rivers, northern Papua New Guinea
Pristidae; Extinction risk; Anoxypristis cuspidata; Pristis pristis; Narrow sawfish; Largetooth sawfish; Interview surveys; Bycatch
Papua New Guinea (PNG) is geographically close to northern Australia, a key region tor 4 sawfish species. However, detailed data on sawtish presence in PNG are limited, particularly from the north coast. We conducted a short study to assess whether sawfishes are still present in 2 adjacent rivers - the Sepik and Ramu - in northern PNG. Interviews were conducted with fishers from villages along the Sepik River between Chambri Lake and the river mouth, as well as along the Keram River (a tributary of the Sepik) and the Ramu River. Landings by gillnet fishers at the mouth of the Sepik River were observed. At least 2 species, the narrow sawfish Anoxypristis cuspidata and the largetooth sawfish Pristis pristis, were present at the mouth of the Sepik River and were caught in gillnets used to target sharks and croakers (Sciaenidae). Largetooth sawfish aie still captured by fishers in the freshwater reaches of the Sepik, Ramu, and Keram rivers. The fins of sawfishes and other elasmobranchs provide a source of income, and sawfish meat is eaten locally or sold. The Sepik River and surrounding coastline remains important habitat for sawfishes; however, most interviewees reported a decline in sawfish catches over the course of their lifetimes. These findings corroborate existing evidence suggesting that PNG remains a global stronghold for sawfishes. Immediate collaboration with fishing communities and PNG's fisheries and conservation authorities is needed to ensure that any sawfish catches and habitats are appropriately managed so that populations do not decline further. DOI
787. Leistenschneider, E; Reiter, MP; San Andres, SA; Kootte, B; Holt, JD; Navratil, P; Babcock, C; Barbieri, C; Barquest, BR; Bergmann, J; Bollig, J; Brunner, T; Dunling, E; Finlay, A; Geissel, H; Graham, L; Greiner, F; Hergert, H; Hornung, C; Jesch, C; Klawitter, R; Lan, Y; Lascar, D; Leach, KG; Lippert, W; McKay, JE; Paul, SF; Schwenk, A; Short, D; Simonis, J; Soma, V; Steinbrugge, R; Stroberg, SR; Thompson, R; Wieser, ME; Will, C; Yavor, M; Andreoiu, C; Dickel, T; Dillmann, I; Gwinner, G; Plass, WR; Scheidenberger, C; Kwiatkowski, AA; Dilling, J.Dawning of the N=32 Shell Closure Seen through Precision Mass Measurements of Neutron-Rich Titanium Isotopes.Phys. Rev. Lett., 2018, 120 Dawning of the N=32 Shell Closure Seen through Precision Mass Measurements of Neutron-Rich Titanium Isotopes
A precision mass investigation of the neutron-rich titanium isotopes Ti51-55 was performed at TRIUMF's Ion Trap for Atomic and Nuclear science (TITAN). The range of the measurements covers the N = 32 shell closure, and the overall uncertainties of the Ti52-55 mass values were significantly reduced. Our results conclusively establish the existence of the weak shell effect at N = 32, narrowing down the abrupt onset of this shell closure. Our data were compared with state-of-the-art ab initio shell model calculations which, despite very successfully describing where the N = 32 shell gap is strong, overpredict its strength and extent in titanium and heavier isotones. These measurements also represent the first scientific results of TITAN using the newly commissioned multiple-reflection time-of-flight mass spectrometer, substantiated by independent measurements from TITAN's Penning trap mass spectrometer. DOI PubMed
786. Lewthwaite, JMM; Angert, AL; Kembel, SW; Goring, SJ; Davies, TJ; Mooers, AO; Sperling, FAH; Vamosi, SM; Vamosi, JC; Kerr, JT.Canadian butterfly climate debt is significant and correlated with range size.Ecography, 2018, 41 Canadian butterfly climate debt is significant and correlated with range size
climate debt; butterflies; global climate change; Canada; phylogenetics; life history; dispersal; range shifts; host plant
Climate change is causing rapid shifts in species' range limits, leading to poleward expansions and range losses toward the equator. However, 'climate debt', the gap between required and realized range shifts under changing climates, can accumulate when species are unable to track shifting conditions sufficiently rapidly to keep pace with climate changes. Currently, we do not know the rate at which species will keep pace via dispersal to track their climate envelopes, yet understanding potential differences in climate debt is central to estimating how climate change will influence extinction risk. Here, we use historical observations of 155 butterfly species found in Canada to construct climate-based environmental niche models for each species and then compare projections with observed modern distributions to quantify climate debts. This approach suggests that high levels of climate debt are accumulating within the vast majority of these species. Such failure to track changing climates may arise from some combination of interspecific interactions such as particular food availability for specialists, abiotic barriers such as mountain ranges, or species' intrinsic dispersal capacities. Our linear models relating climate debt to a variety of biological predictors suggest that the debts we documented are accumulating independently of dispersal ability, diet breadth, and phylogeny. A proxy for range size is the only significant predictor of climate debt, with species with narrower ranges accumulating more debt: this suggests that species with narrow ranges may be at risk from both a reduction of suitable habitat in their current range and the failure to colonize newly available habitat. Identifying the factors, whether intrinsic or imposed by local environmental conditions, that limit species' capacities to colonize areas beyond their historical limits is vital to conservation planning. DOI
785. Lindo, J; Rogers, M; Mallott, EK; Petzelt, B; Mitchell, J; Archer, D; Cybulski, JS; Malhi, RS; DeGiorgio, M.Patterns of Genetic Coding Variation in a Native American Population before and after European Contact.Am. J. Hum. Genet., 2018, 102 Patterns of Genetic Coding Variation in a Native American Population before and after European Contact
The effects of European colonization on the genomes of Native Americans may have produced excesses of potentially deleterious features, mainly due to the severe reductions in population size and corresponding losses of genetic diversity. This assumption, however, neither considers actual genomic patterns that existed before colonization nor does it adequately capture the effects of admixture. In this study, we analyze the whole-exome sequences of modern and ancient individuals from a Northwest Coast First Nation, with a demographic history similar to other indigenous populations from the Americas. We show that in approximately ten generations from initial European contact, the modern individuals exhibit reduced levels of novel and low-frequency variants, a lower proportion of potentially deleterious alleles, and decreased heterozygosity when compared to their ancestors. This pattern can be explained by a dramatic population decline, resulting in the loss of potentially damaging low-frequency variants, and subsequent admixture. We also find evidence that the indigenous population was on a steady decline in effective population size for several thousand years before contact, which emphasizes regional demography over the common conception of a uniform expansion after entry into the Americas. This study examines the genomic consequences of colonialism on an indigenous group and describes the continuing role of gene flow among modern populations. DOI PubMed
784. Martin, MP; Naranbhai, V; Shea, PR; Qi, Y; Ramsuran, V; Vince, N; Gao, XJ; Thomas, R; Brumme, ZL; Carlson, JM; Wolinsky, SM; Goedert, JJ; Walker, BD; Segal, FP; Deeks, SG; Haas, DW; Migueles, SA; Connors, M; Michael, N; Fellay, J; Gostick, E; Llewellyn-Lacey, S; Price, DA; Lafont, BA; Pymm, P; Saunders, PM; Widjaja, J; Wong, SC; Vivian, JP; Rossjohn, J; Brooks, AG; Carrington, M.Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1.J. Clin. Invest., 2018, 128 Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1
HLA-B*57 control of HIV involves enhanced CD8(+) T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57(+) individuals. Using whole-genome sequencing of untreated B*57(+) HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease. DOI PubMed
783. Mazel, F; Pennell, MW; Cadotte, MW; Diaz, S; Dalla Riva, GV; Grenyer, R; Leprieur, F; Mooers, AO; Mouillot, D; Tucker, CM; Pearse, WD.Prioritizing phylogenetic diversity captures functional diversity unreliably.Nat. Commun., 2018, 9 Prioritizing phylogenetic diversity captures functional diversity unreliably
In the face of the biodiversity crisis, it is argued that we should prioritize species in order to capture high functional diversity (FD). Because species traits often reflect shared evolutionary history, many researchers have assumed that maximizing phylogenetic diversity (PD) should indirectly capture FD, a hypothesis that we name the "phylogenetic gambit". Here, we empirically test this gambit using data on ecologically relevant traits from >15,000 vertebrate species. Specifically, we estimate a measure of surrogacy of PD for FD. We find that maximizing PD results in an average gain of 18% of FD relative to random choice. However, this average gain obscures the fact that in over one-third of the comparisons, maximum PD sets contain less FD than randomly chosen sets of species. These results suggest that, while maximizing PD protection can help to protect FD, it represents a risky conservation strategy. DOI PubMed
782. McPherson, JM; Yeager, LA; Baum, JK.A simulation tool to scrutinise the behaviour of functional diversity metrics.Methods Ecol. Evol., 2018, 9: 200-206 A simulation tool to scrutinise the behaviour of functional diversity metrics
abundance distributions; artificial ecological communities; functional diversity; functional redundancy; index reliability; R code; simulations; site-by-species abundance matrix; trait distributions; traits matrix
Many indices have been proposed to measure functional diversity and its four distinct dimensions: functional richness, evenness, divergence and redundancy. Identifying indices that reliably measure the functional diversity dimension(s) of interest requires careful testing of how each index responds to species' traits and abundance distributions. In the absence of a convenient simulation tool, tests with artificial data have to date explored only a limited number of scenarios or have altered trait and abundance distributions only indirectly based on principles of evolution and community assembly. We provide simul.comms, an R function that allows users to test the efficacy of functional diversity indices by easily creating artificial species communities with user-specified abundance and trait distributions for continuous, ordinal and categorical traits. To illustrate the function's utility, we examine the performance of R, a recently published abundance-sensitive index for functional redundancy. We use two approaches to designing simulation tests for this example analysis. The first uses simul.comms to create six separate sets of artificial communities to qualitatively assess how R responds to predictable changes in functional redundancy. The second uses simul.comms to independently alter seven community composition parameters, whose influence on R is then examined quantitatively via effect sizes in linear regression. Our analyses indicate that R broadly mirrors expected changes in functional redundancy and predictably responds to changes in community composition parameters. R appears, however, to primarily reflect trait distributions, responding minimally to variance in abundance and counter-intuitively to abundance range. Further refinement of tools to measure functional redundancy may therefore be desirable. The R tool we provide should assist with refining functional diversity measures, a critical step towards improving our ability to understand and mitigate the impacts of biodiversity loss on ecosystem functioning. Because simul.comms simply produces two linked matrices, a species-by-traits matrix and a site-by-species abundance matrix, it may be equally valuable in exploring questions and analytical approaches in other areas of community ecology. DOI
781. Meanwell, M; Adluri, BS; Yuan, ZL; Newton, J; Prevost, P; Nodwell, MB; Friesen, CM; Schaffer, P; Martin, RE; Britton, R.Direct heterobenzylic fluorination, difluorination and trifluoromethylthiolation with dibenzenesulfonamide derivatives.Chem. Sci., 2018, 9: 5608-5613 Direct heterobenzylic fluorination, difluorination and trifluoromethylthiolation with dibenzenesulfonamide derivatives
Functionalization of heterocyclic scaffolds with mono-or difluoroalkyl groups provides unique opportunities to modulate drug pK(a), influence potency and membrane permeability, and attenuate metabolism. While advances in the addition of fluoroalkyl radicals to heterocycles have been made, direct C(sp(3))-H heterobenzylic fluorination is comparatively unexplored. Here we demonstrate both mono-and difluorination of a range of alkyl heterocycles using a convenient process that relies on transient sulfonylation by the electrophilic fluorinating agent N-fluorobenzenesulfonimide. We also report heterobenzylic trifluoromethylthiolation and F-18-fluorination, providing a suite of reactions for late-stage C(sp(3))-H functionalization of drug leads and radiotracer discovery. DOI PubMed
779. Mokkonen, M; Koskela, E; Procyshyn, T; Crespi, B.Socio-reproductive Conflicts and the Father's Curse Dilemma.Am. Nat., 2018, 192 Socio-reproductive Conflicts and the Father's Curse Dilemma
genomic conflict; sexual conflict; parent-offspring conflict; testosterone; oxytocin; bank vole
Evolutionary conflicts between males and females can manifest over sexually antagonistic interactions at loci or over sexually antagonistic interests within a locus. The latter form of conflict, intralocus sexual conflict, arises from sexually antagonistic selection and constrains the fitness of individuals through a phenotypic compromise. These conflicts, and socio-reproductive interactions in general, are commonly mediated by hormones, and thus predictive insights can be gained from studying their mediating effects. Here, we integrate several lines of evidence to describe a novel, hormonally mediated reproductive dilemma that we call the father's curse, which results from an intralocus conflict between mating and parental efforts. Essentially, a genetic locus exerts pleiotropic and antagonistic effects on the mating effort of one individual and the parental effort of a related individual who is the primary provider of parental care. We outline the criteria for operation of the father's curse dilemma, provide evidence of the phenomenon, and discuss the predictions and outcomes arising from its dynamics. By integrating the effects of hormones into socio-reproductive conflicts and socio-reproductive effort, clearer links between genotypes, phenotypes, and fitness can be established. DOI PubMed
778. Molday, LL; Wahl, D; Sarunic, MV; Molday, RS.Localization and functional characterization of the p.Asn965Ser (N965S) ABCA4 variant in mice reveal pathogenic mechanisms underlying Stargardt macular degeneration.Hum. Mol. Genet., 2018, 27 Localization and functional characterization of the p.Asn965Ser (N965S) ABCA4 variant in mice reveal pathogenic mechanisms underlying Stargardt macular degeneration
ABCA4 is a member of the superfamily of ATP-binding cassette (ABC) proteins that transports N-retinylidene-phosphatidylethanolamine (N-Ret-PE) across outer segment disc membranes thereby facilitating the removal of potentially toxic retinoid compounds from photoreceptor cells. Mutations in the gene encoding ABCA4 are responsible for Stargardt disease (STGD1), an autosomal recessive retinal degenerative disease that causes severe vision loss. To define the molecular basis for STGD1 associated with the p.Asn965Ser (N965S) mutation in the Walker A motif of nucleotide binding domain 1 (NBD1), we generated a p.Asn965Ser knockin mouse and compared the subcellular localization and molecular properties of the disease variant with wild-type (WT) ABCA4. Here, we show that the p.Asn965Ser ABCA4 variant expresses at half the level of WT ABCA4, partially mislocalizes to the endoplasmic reticulum (ER) of photoreceptors, is devoid of N-Ret-PE activated ATPase activity, and causes an increase in autofluorescence and the bisretinoid A2E associated with lipofuscin deposits in retinal pigment epithelial cells as found in Stargardt patients and Abca4 knockout mice. We also show for the first time that a significant fraction of WT ABCA4 is retained in the inner segment of photoreceptors. On the basis of these studies we conclude that loss in substrate-dependent ATPase activity and protein misfolding are mechanisms underlying STGD1 associated with the p.Asn965Ser mutation in ABCA4. Functional and molecular modeling studies further suggest that similar pathogenic mechanisms are responsible for Tangiers disease associated with the p.Asn935Ser (N935S) mutation in the NBD1 Walker A motif of ABCA1. DOI PubMed
775. Moreno-Mayar, JV; Vinner, L; Damgaard, PD; de la Fuente, C; Chan, J; Spence, JP; Allentoft, ME; Vimala, T; Racimo, F; Pinotti, T; Rasmussen, S; Margaryan, A; Orbegozo, MI; Mylopotamitaki, D; Wooller, M; Bataille, C; Becerra-Valdivia, L; Chivall, D; Comeskey, D; Deviese, T; Grayson, DK; George, L; Harry, H; Alexandersen, V; Primeau, C; Erlandson, J; Rodrigues-Carvalho, C; Reis, S; Bastos, MQR; Cybulski, J; Vullo, C; Morello, F; Vilar, M; Wells, S; Gregersen, K; Hansen, KL; Lynnerup, N; Lahr, MM; Kjaer, K; Strauss, A; Alfonso-Durruty, M; Salas, A; Schroeder, H; Higham, T; Malhi, RS; Rasic, JT; Souza, L; Santos, FR; Malaspinas, AS; Sikora, M; Nielsen, R; Song, YS; Meltzer, DJ; Willerslev, E.Early human dispersals within the Americas.Science, 2018, 362 Early human dispersals within the Americas
Studies of the peopling of the Americas have focused on the timing and number of initial migrations. Less attention has been paid to the subsequent spread of people within the Americas. We sequenced 15 ancient human genomes spanning from Alaska to Patagonia; six are >= 10,000 years old (up to similar to 18x coverage). All are most closely related to Native Americans, including those from an Ancient Beringian individual and two morphologically distinct "Paleoamericans." We found evidence of rapid dispersal and early diversification that included previously unknown groups as people moved south. This resulted in multiple independent, geographically uneven migrations, including one that provides clues of a Late Pleistocene Australasian genetic signal, as well as a later Mesoamerican-related expansion. These led to complex and dynamic population histories from North to South America. DOI PubMed
774. Munier, B; Bendell, LI.Macro and micro plastics sorb and desorb metals and act as a point source of trace metals to coastal ecosystems.PLoS One, 2018, 13 Macro and micro plastics sorb and desorb metals and act as a point source of trace metals to coastal ecosystems
Nine urban intertidal regions in Burrard Inlet, Vancouver, British Columbia, Canada, were sampled for plastic debris. Debris included macro and micro plastics and originated from a wide diversity of uses ranging from personal hygiene to solar cells. Debris was characterized for its polymer through standard physiochemical characteristics, then subject to a weak acid extraction to remove the metals, zinc, copper, cadmium and lead from the polymer. Recently manufactured low density polyethylene (LDPE), nylon, polyethylene terephthalate (PET), polypropylene (PP), polystyrene (PS) and polyvinyl chloride (PVC) were subject to the same extraction. Data was statistically analyzed by appropriate parametric and non-parametric tests when needed with significance set at P < 0.05. Polymers identified in field samples in order of abundance were; PVC (39), LDPE (28), PS (18), polyethylene (PE, 9), PP (8), nylon (8), high density polyethylene (HDPE, 7), polycarbonate (PC, 6), PET (6), polyurethane (PUR, 3) and polyoxymethylene (POM, 2). PVC and LDPE accounted for 46% of all samples. Field samples of PVC, HDPE and LDPE had significantly greater amounts of acid extracted copper and HDPE, LDPE and PUR significantly greater amounts of acid extracted zinc. PVC and LDPE had significantly greater amounts of acid extracted cadmium and PVC tended to have greater levels of acid extracted lead, significantly so for HDPE. Five of the collected items demonstrated extreme levels of acid extracted metal; greatest concentrations were 188, 6667, 698,000 and 930 mu gg(-1) of copper, zinc, lead and cadmium respectively recovered from an unidentified object comprised of PVC. Comparison of recently manufactured versus field samples indicated that recently manufactured samples had significantly greater amounts of acid extracted cadmium and zinc and field samples significantly greater amounts of acid extracted copper and lead which was primarily attributed to metal extracted from field samples of PVC. Plastic debris will affect metals within coastal ecosystems by; 1) providing a sorption site (copper and lead), notably for PVC 2) desorption from the plastic i.e., the "inherent" load (cadmium and zinc) and 3) serving as a point source of acute trace metal exposure to coastal ecosystems. All three mechanisms will put coastal ecosystems at risk to the toxic effects of these metals. DOI PubMed
773. Mwimanzi, F; Toyoda, M; Mahiti, M; Mann, JK; Martin, JN; Bangsberg, D; Brockman, MA; Goulder, P; Kirchhoff, F; Brumme, ZL; Ndung'u, T; Ueno, T.Resistance of Major Histocompatibility Complex Class B (MHC-B) to Nef-Mediated Downregulation Relative to that of MHC-A Is Conserved among Primate Lentiviruses and Influences Antiviral T Cell Responses in HIV-1-Infected Individuals.J. Virol., 2018, 92 Resistance of Major Histocompatibility Complex Class B (MHC-B) to Nef-Mediated Downregulation Relative to that of MHC-A Is Conserved among Primate Lentiviruses and Influences Antiviral T Cell Responses in HIV-1-Infected Individuals
HLA; Nef; human immunodeficiency virus; immune evasion; lentiviruses
Patient-derived HIV-1 subtype B Nef clones downregulate HLA-A more efficiently than HLA-B. However, it remains unknown whether this property is common to Nef proteins across primate lentiviruses and how antiviral immune responses may be affected. We examined 263 Nef clones from diverse primate lentiviruses including different pandemic HIV-1 group M subtypes for their ability to downregulate major histocompatibility complex class A (MHC-A) and MHC-B from the cell surface. Though lentiviral Nef proteins differed markedly in their absolute MHC-A and MHC-B downregulation abilities, all lentiviral Nef lineages downregulated MHC-A, on average, 11 to 32% more efficiently than MHC-B. Nef genotype/phenotype analyses in a cohort of HIV-1 subtype C-infected patients (n = 168), together with site-directed mutagenesis, revealed Nef position 9 as a subtype-specific determinant of differential HLA-A versus HLA-B downregulation activity. Nef clones harboring nonconsensus variants at codon 9 downregulated HLA-B (though not HLA-A) significantly better than those harboring the consensus sequence at this site, resulting in reduced recognition of infected target cells by HIV-1-specific CD8(+) effector cells in vitro. Among persons expressing protective HLA class I alleles, carriage of Nef codon 9 variants was also associated with reduced ex vivo HIV-specific T cell responses. Our results demonstrate that Nef's inferior ability to downregulate MHC-B compared to that of MHC-A is conserved across primate lentiviruses and suggest that this property influences antiviral cellular immune responses. IMPORTANCE Primate lentiviruses encode the Nef protein that plays an essential role in establishing persistent infection in their respective host species. Nef interacts with the cytoplasmic region of MHC-A and MHC-B molecules and downregulates them from the infected cell surface to escape recognition by host cellular immunity. Using a panel of Nef alleles isolated from diverse primate lentiviruses including pandemic HIV-1 group M subtypes, we demonstrate that Nef proteins across all lentivi- DOI PubMed
772. Myers-Smith, IH; Hik, DS.Climate warming as a driver of tundra shrubline advance.J. Ecol., 2018, 106: 547-560 Climate warming as a driver of tundra shrubline advance
age distributions; alpine; climate; high-latitude; range expansion; recruitment; shrub; tundra; willow (Salix); Yukon
1. Climate warming is predicted to alter ecological boundaries in high-latitude ecosystems including the elevational or latitudinal extent of tall shrubs in Arctic and alpine tundra. Over 60 studies from 128 locations around the tundra biome have investigated shrub expansion in tundra ecosystems; however, only six studies test whether shrublines are actually advancing up hill-slopes or northward into tundra where tall shrubs are currently absent. 2. We test the hypothesis that willow shrublines have expanded to higher elevations in relation to climate across a 50 x 50 km area in the Kluane Region of the southwest Yukon Territory, Canada by surveying of 379 shrubs at 14 sites and sampling of 297 of the surveyed shrubs at 10 sites. We compared growth and recruitment to climate variables to test the climate sensitivity of shrub increase using annual radial growth analysis, age distributions and repeat field surveys to estimate the current rate of shrubline advance. 3. We found consistent and increasing rates of recruitment of alpine willows, with estimates of faster advancing shrublines on shallower hill-slopes. Mortality was extremely low across the elevation gradient. Aspect, elevation and species identity did not explain variation in recruitment patterns, suggesting a regional factor, such as climate, as the driver of the observed shrubline advance. 4. Annual radial growth of willows was best explained by variation in summer temperatures, and recruitment pulses by winter temperatures. Measured recruitment rates are similar to 20 +/- 5 individuals per hectare per decade (M +/- SE) and measured rates of increased shrub cover of similar to 5 +/- 1% per decade (M +/- SE) measured at the Pika Camp site between field surveys in 2009 and 2013. Our results suggest that shrubline will continue to advance over the next 50 years, if growing conditions remain suitable. However, if future conditions differ between summer and winter seasons, this could lead to contrasting trajectories for recruitment vs. growth, and influence the vegetation change observed on the landscape. 5. Synthesis. Our findings in the context of a review of the existing literature indicate that elevational and latitudinal shrublines, like treelines, are advancing in response to climate warming; however, the trajectories of change will depend on the climate drivers controlling recruitment vs. growth. DOI
771. Nelson-Flower, MJ; Wiley, EM; Flower, TP; Ridley, AR.Individual dispersal delays in a cooperative breeder: Ecological constraints, the benefits of philopatry and the social queue for dominance.J. Anim. Ecol., 2018, 87 Individual dispersal delays in a cooperative breeder: Ecological constraints, the benefits of philopatry and the social queue for dominance
benefits of philopatry; cooperative breeding; delayed dispersal; dual benefits; ecological constraints; family living; social queue; southern pied babbler
Delayed dispersal is a key step in the evolution of familial animal societies and cooperative breeding. However, no consensus has been reached on the ecological and social circumstances driving delayed dispersal. Here, we test predictions from the ecological constraints and benefits of philopatry hypotheses as well as the recently proposed dual benefits hypothesis to better understand the evolution of group-living and cooperative breeding. Furthermore, we consider how individual social circumstances within groups affect dispersal decisions. We examine 11years of life-history information on a wild population of cooperatively breeding southern pied babblers Turdoides bicolor. We investigate the effects of ecological conditions, natal-group membership and individual social context on male and female dispersal delays, disperser survival and acquisition of dominance. Female dispersal decisions are generally unconstrained by ecological or social circumstances. In contrast, males disperse in response to relaxed ecological constraints, decreases in nepotistic tolerance or when low social rank in the queue for dominance decreases their likelihood of gaining a dominant breeding position. Early dispersal by end-of-queue males often leads to a head-of-queue subordinate position in a non-natal group, thereby increasing access to dominant breeding positions. However, males and females remaining in natal groups gain benefits of philopatry via increased survival and, for head-of-queue males, very high likelihood of acquisition of a breeding position. Overall, predictions from the dual benefits hypothesis best describe these results, while some predictions from each of the ecological constraints and benefits of philopatry hypotheses were supported. The benefits of living and working together (collective action benefits) in large stable groups are of central importance in shaping dispersal delays in southern pied babbler societies. In addition, position in the subordinate social queue for dominance is the key in determining access to reproduction, particularly for males. This research highlights the importance of considering the costs and benefits of individual social circumstances in dispersal decisions and illustrates how the dual benefits hypothesis offers new perspectives in understanding delayed dispersal. DOI
770. Nosil, P; Villoutreix, R; de Carvalho, CF; Farkas, TE; Soria-Carrasco, V; Feder, JL; Crespi, BJ; Gompert, Z.Natural selection and the predictability of evolution in Timema stick insects.Science, 2018, 359: 765-770 Natural selection and the predictability of evolution in Timema stick insects
Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time (r(2) = 0.14) and driven by complex selective regimes and yearly fluctuations in climate. In contrast, temporal changes in pattern-morph frequencies are highly predictable due to negative frequency-dependent selection (r(2) = 0.86). For both traits, however, natural selection drives evolution around a dynamic equilibrium, providing some predictability to the process. DOI PubMed
769. Ogunshola, F; Anmole, G; Miller, RL; Goering, E; Nkosi, T; Muema, D; Mann, J; Ismail, N; Chopera, D; Ndung'u, T; Brockman, MA; Ndhlovu, ZM.Dual HLA B(star)42 and B(star)81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants.Nat. Commun., 2018, 9 Dual HLA B(star)42 and B(star)81-reactive T cell receptors recognize more diverse HIV-1 Gag escape variants
Some closely related human leukocyte antigen (HLA) alleles are associated with variable clinical outcomes following HIV-1 infection despite presenting the same viral epitopes. Mechanisms underlying these differences remain unclear but may be due to intrinsic characteristics of the HLA alleles or responding T cell repertoires. Here we examine CD8(+) T cell responses against the immunodominant HIV-1 Gag epitope TL9 (TPQDLNTML(180-188)) in the context of the protective allele B(star)81:01 and the less protective allele B(star)42:01. We observe a population of dual-reactive T cells that recognize TL9 presented by both B(star)81:01 and B(star)42:01 in individuals lacking one allele. The presence of dual-reactive T cells is associated with lower plasma viremia, suggesting a clinical benefit. In B(star)42:01 expressing individuals, the dual-reactive phenotype defines public T cell receptor (TCR) clones that recognize a wider range of TL9 escape variants, consistent with enhanced control of viral infection through containment of HIV-1 sequence adaptation. DOI PubMed
768. Ojwach, DBA; MacMillan, D; Reddy, T; Novitsky, V; Brumme, ZL; Brockman, MA; Ndung'u, T; Mann, JK.Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection.J. Virol., 2018, 92 Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection
replication capacity; HIV-1 subtype C; HLA polymorphisms
CD8(+) T cell-mediated escape mutations in Gag can reduce HIV-1 replication capacity (RC) and alter disease progression, but less is known about immunemediated attenuation in other HIV-1 proteins. We generated 487 recombinant viruses encoding RT-integrase from individuals with chronic (n = 406) and recent (n = 81) HIV-1 subtype C infection and measured their in vitro RC using a green fluorescent protein (GFP) reporter T cell assay. In recently infected individuals, reverse transcriptase (RT)-integrase-driven RC correlated significantly with viral load set point (r = 0.25; P = 0.03) and CD4(+) T cell decline (P = 0.013). Moreover, significant associations between RT integrase-driven RC and viral load (r = 0.28; P = 0.0001) and CD4(+) T cell count (r = -0.29; P < 0.0001) remained in chronic infection. In early HIV infection, host expression of the protective HLA-B*81 allele was associated with lower RC (P = 0.05), as was expression of HLA-B*07 (P = 0.02), suggesting early immune-driven attenuation of RT-integrase by these alleles. In chronic infection, HLA-A*30:09 (in linkage disequilibrium with HLA-B*81) was significantly associated with lower RC (P = 0.05), and all 6 HLA-B alleles with the lowest RC measurements represented protective alleles, consistent with long-term effects of host immune pressures on lowering RT-integrase RC. The polymorphisms V241I, I257V, P272K, and E297K in reverse transcriptase and I201V in integrase, all relatively uncommon polymorphisms occurring in or adjacent to optimally described HLA-restricted cytotoxic T-lymphocyte epitopes, were associated with reduced RC. Together, our data suggest that RT-integrase-driven RC is clinically relevant and provide evidence that immune-driven selection of mutations in RT-integrase can compromise RC. IMPORTANCE Identification of viral mutations that compromise HIV's ability to replicate may aid rational vaccine design. However, while certain escape mutations in Gag have been shown to reduce HIV replication and influence clinical progression, less is known about the consequences of mutations that naturally arise in other HIV proteins. Pol is a highly conserved protein, but the impact of Pol function on HIV disease progression is not well defined. Here, we generated recombinant viruses using the RT-integrase region of Pol derived from HIV-1C-infected individuals with recent and chronic infection and measured their ability to replicate in vitro. We demonstrate that RT-integrase-driven replication ability significantly impacts HIV disease progression. We further show evidence of immune-mediated attenuation in RT-integrase and identify specific polymorphisms in RT-integrase that significantly decrease HIV-1 replication ability, suggesting which Pol epitopes could be explored in vaccine development. DOI PubMed
766. Palomo, A; Pedersen, AG; Fowler, SJ; Dechesne, A; Sicheritz-Ponten, T; Smets, BF.Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira.ISME J., 2018, 12: 1779-1793 Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira
The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical beta-proteobacterial ammonia oxidizing bacteria (beta-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources. By contrast, compared to canonical Nitrospira, comammox Nitrospira harbor a higher diversity of urea transporters and copper homeostasis genes and lack cyanate hydratase genes. Additionally, the two comammox clades differ in their ammonium uptake systems. Contrary to beta-AOB, comammox Nitrospira genomes have single copies of the two central ammonia oxidation pathway operons. Similar to ammonia oxidizing archaea and some oligotrophic AOB strains, they lack genes involved in nitric oxide reduction. Furthermore, comammox Nitrospira genomes encode genes that might allow efficient growth at low oxygen concentrations. Regarding the evolutionary history of comammox Nitrospira, our analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from beta-AOB to comammox Nitrospira. We postulate that the absence of comammox genes in other sublineage II Nitrospira genomes is the result of subsequent loss. DOI PubMed
765. Pardo, SA; Cooper, AB; Reynolds, JD; Dulvy, NK.Quantifying the known unknowns: estimating maximum intrinsic rate of population increase in the face of uncertainty.ICES J. Mar. Sci., 2018, 75 Quantifying the known unknowns: estimating maximum intrinsic rate of population increase in the face of uncertainty
bycatch; Carcharhinus; Chondrichthyes; demography; Elasmobranchii; reference points; risk assessment
Sensitivity to overfishing is often estimated using simple models that depend upon life history parameters, especially for species lacking detailed biological information. Yet, there has been little exploration of how uncertainty in life history parameters can influence demographic parameter estimates and therefore fisheries management options. We estimate the maximum intrinsic rate of population increase (rmax) for ten coastal carcharhiniform shark populations using an unstructured life history model that explicitly accounts for uncertainty in life history parameters. We evaluate how the two directly estimated parameters, age at maturity amat and annual reproductive output b, most influenced rmax estimates. Uncertainty in age at maturity values was low, but resulted in moderate uncertainty in rmax estimates. The model was sensitive to uncertainty in annual reproductive output for the least fecund species with fewer than 5 female offspring per year, which is not unusual for large elasmobranchs, marine mammals, and seabirds. Managers and policy makers should be careful to restrict mortality on species with very low annual reproductive output< 2 females per year. We recommend elasmobranch biologists to measure frequency distributions of litter sizes (rather than just a range) as well as improving estimates of natural mortality of data-poor elasmobranchs. DOI
764. Perry, CT; Alvarez-Filip, L; Graham, NAJ; Mumby, PJ; Wilson, SK; Kench, PS; Manzello, DP; Morgan, KM; Slangen, ABA; Thomson, DP; Januchowski-Hartley, F; Smithers, SG; Steneck, RS; Carlton, R; Edinger, EN; Enochs, IC; Estrada-Saldivar, N; Haywood, MDE; Kolodziej, G; Murphy, GN; Perez-Cervantes, E; Suchley, A; Valentino, L; Boenish, R; Wilson, M; Macdonald, C.Loss of coral reef growth capacity to track future increases in sea level.Nature, 2018, 558: 396 Loss of coral reef growth capacity to track future increases in sea level
Sea-level rise (SLR) is predicted to elevate water depths above coral reefs and to increase coastal wave exposure as ecological degradation limits vertical reef growth, but projections lack data on interactions between local rates of reef growth and sea level rise. Here we calculate the vertical growth potential of more than 200 tropical western Atlantic and Indian Ocean reefs, and compare these against recent and projected rates of SLR under different Representative Concentration Pathway (RCP) scenarios. Although many reefs retain accretion rates close to recent SLR trends, few will have the capacity to track SLR projections under RCP4.5 scenarios without sustained ecological recovery, and under RCP8.5 scenarios most reefs are predicted to experience mean water depth increases of more than 0.5 m by 2100. Coral cover strongly predicts reef capacity to track SLR, but threshold cover levels that will be necessary to prevent submergence are well above those observed on most reefs. Urgent action is thus needed to mitigate climate, sea-level and future ecological changes in order to limit the magnitude of future reef submergence. DOI
763. Petrache, CM; Lv, BF; Astier, A; Dupont, E; Wang, YK; Zhang, SQ; Zhao, PW; Ren, ZX; Meng, J; Greenlees, PT; Badran, H; Cox, DM; Grahn, T; Julin, R; Juutinen, S; Konki, J; Pakarinen, J; Papadakis, P; Partanen, J; Rahkila, P; Sandzelius, M; Saren, J; Scholey, C; Sorri, J; Stolze, S; Uusitalo, J; Cederwall, B; Aktas, O; Ertoprak, A; Liu, H; Matta, S; Subramaniam, P; Guo, S; Liu, ML; Zhou, XH; Wang, KL; Kuti, I; Timar, J; Tucholski, A; Srebrny, J; Andreoiu, C.Evidence of chiral bands in even-even nuclei.Phys. Rev. C, 2018, 97 Evidence of chiral bands in even-even nuclei
Evidence for chiral doublet bands has been observed for the first time in the even-even nucleus Nd-136. One chiral band was firmly established. Four other candidates for chiral bands were also identified, which can contribute to the realization of the multiple pairs of chiral doublet bands (M.D) phenomenon. The observed bands are investigated by the constrained and tilted axis cranking covariant density functional theory (TAC-CDFT). Possible configurations have been explored. The experimental energy spectra, angular momenta, andB(M1)/B(E2) values for the assigned configurations are globally reproduced by TAC-CDFT. Calculated results support the chiral interpretation of the observed bands, which correspond to shapes with maximum triaxiality induced by different multiquasiparticle configurations in Nd-136. DOI
762. Quon, E; Sere, YY; Chauhan, N; Johansen, J; Sullivan, DP; Dittman, JS; Rice, WJ; Chan, RB; Di Paolo, G; Beh, CT; Menon, AK.Endoplasmic reticulum-plasma membrane contact sites integrate sterol and phospholipid regulation.PLoS. Biol., 2018, 16 Endoplasmic reticulum-plasma membrane contact sites integrate sterol and phospholipid regulation
Tether proteins attach the endoplasmic reticulum (ER) to other cellular membranes, thereby creating contact sites that are proposed to form platforms for regulating lipid homeostasis and facilitating non-vesicular lipid exchange. Sterols are synthesized in the ER and transported by non-vesicular mechanisms to the plasma membrane (PM), where they represent almost half of all PM lipids and contribute critically to the barrier function of the PM. To determine whether contact sites are important for both sterol exchange between the ER and PM and intermembrane regulation of lipid metabolism, we generated Delta-super-tether (Delta-s-tether) yeast cells that lack six previously identified tethering proteins (yeast extended synatotagmin [E-Syt], vesicle-associated membrane protein [VAMP]-associated protein [VAP], and TMEM16-anoctamin homologues) as well as the presumptive tether Ice2. Despite the lack of ER-PM contacts in these cells, ER-PM sterol exchange is robust, indicating that the sterol transport machinery is either absent from or not uniquely located at contact sites. Unexpectedly, we found that the transport of exogenously supplied sterol to the ER occurs more slowly in Delta-s-tether cells than in wild-type (WT) cells. We pinpointed this defect to changes in sterol organization and transbilayer movement within the PM bilayer caused by phospholipid dysregulation, evinced by changes in the abundance and organization of PM lipids. Indeed, deletion of either OSH4, which encodes a sterol/phosphatidylinositol-4-phosphate (PI4P) exchange protein, or SAC1, which encodes a PI4P phosphatase, caused synthetic lethality in Delta-s-tether cells due to disruptions in redundant PI4P and phospholipid regulatory pathways. The growth defect of Delta-s-tether cells was rescued with an artificial "ER-PM staple," a tether assembled from unrelated non-yeast protein domains, indicating that endogenous tether proteins have nonspecific bridging functions. Finally, we discovered that sterols play a role in regulating ER-PM contact site formation. In sterol-depleted cells, levels of the yeast E-Syt tether Tcb3 were induced and ER-PM contact increased dramatically. These results support a model in which ER-PM contact sites provide a nexus for coordinating the complex interrelationship between sterois, sphingolipids, and phospholipids that maintain PM composition and integrity. DOI PubMed
760. Ramezanpour, M; Lee, J; Taneva, SG; Tieleman, DP; Cornell, RB.An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair.J. Biol. Chem., 2018, 293 An auto-inhibitory helix in CTP:phosphocholine cytidylyltransferase hijacks the catalytic residue and constrains a pliable, domain-bridging helix pair
protein dynamic; molecular dynamics; allosteric regulation; lipid-protein interaction; protein cross-linking; CTP:phosphocholine cytidylyltransferase; regulation of catalysis; membrane activation; auto-inhibition; protein-membrane interaction; nucleotide transferase
The activity of CTP:phosphocholine cytidylyltransferase (CCT), a key enzyme in phosphatidylcholine synthesis, is regulated by reversible interactions of a lipid-inducible amphipathic helix (domain M) with membrane phospholipids. When dissociated from membranes, a portion of the M domain functions as an auto-inhibitory (AI) element to suppress catalysis. The AI helix from each subunit binds to a pair of helices (E) that extend from the base of the catalytic dimer to create a four-helix bundle. The bound AI helices make intimate contact with loop L2, housing a key catalytic residue, Lys(122). The impacts of the AI helix on active-site dynamics and positioning of Lys(122) are unknown. Extensive MD simulations with and without the AI helix revealed that backbone carbonyl oxygens at the point of contact between the AI helix and loop L2 can entrap the Lys(122) side chain, effectively competing with the substrate, CTP. In silico, removal of the AI helices dramatically increased E dynamics at a predicted break in the middle of these helices, enabling them to splay apart and forge new contacts with loop L2. In vitro cross-linking confirmed the reorganization of the E element upon membrane binding of the AI helix. Moreover, when E bending was prevented by disulfide engineering, CCT activation by membrane binding was thwarted. These findings suggest a novel two-part auto-inhibitory mechanism for CCT involving capture of Lys(122) and restraint of the pliable E helices. We propose that membrane binding enables bending of the E helices, bringing the active site closer to the membrane surface. DOI PubMed
759. Ren, W; Pengelly, R; Farren-Dai, M; Abadi, SSK; Oehler, V; Akintola, O; Draper, J; Meanwell, M; Chakladar, S; Swiderek, K; Moliner, V; Britton, R; Gloster, TM; Bennet, AJ.Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.Nat. Commun., 2018, 9 Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level
Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate's structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based a-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an a-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (H-2(3)) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (H-2(3)) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties. DOI PubMed
757. Roberts, NJ; Barendregt, RW; Clague, JJ.Pliocene and Pleistocene chronostratigraphy of continental sediments underlying the Altiplano at La Paz, Bolivia.Quat. Sci. Rev., 2018, 189: 105-126 Pliocene and Pleistocene chronostratigraphy of continental sediments underlying the Altiplano at La Paz, Bolivia
Plio-Pleistocene transition; mid-Piacenzian warm period; Glaciation; Tropical paleo-ice sheets; South America; Central Andes; Magnetostratigraphy; Paleoenvironmental change; Altiplano incision; Great American Biotic Interchange
Continental sediments underlying the Altiplano plateau provide insight into the late Cenozoic evolution of the Central Andes. We characterize the magnetostratigraphy and lithostratigraphy of the upper part of this fill sequence along a transect extending southwestward from the Cordillera Real at La Paz, Bolivia, where it is best exposed. Multiple polarity reversals and the locally extensive, 2.74-Ma Chijini Tuff enable correlation between our six sections and three previously reported sections. The tuff ties the composite polarity sequence to the geomagnetic polarity time scale, demonstrating that the stratigraphic record extends from the latest Gilbert Chron (ca. 3.8 Ma) to the late Olduvai subchron (ca. 1.8 Ma), or possibly Jaramillo subchron (ca. 1.0 Ma). The sequence provides Earth's longest known record of low-latitude glaciation and the only record of Pliocene tropical glaciation. It includes evidence for 16 late Pliocene and Early Pleistocene glaciations, separated by interglacials of sufficient length (>10(3)-10(4) a) to produce mature soil profiles. Successively larger ice caps formed directly before, during, and after the globally warm mid-Piacenzian (3.265-3.025 Ma), and throughout Plio-Pleistocene climate deterioration. The late Pliocene glacial units predate the onset of widespread Northern Hemisphere continental glaciation and in most cases unambiguously correspond to specific cool peaks of the astronomically tuned, benthic oxygen isotope (8180) record, including marine isotope stages MG2, M2, KM2, and G10. The glacial events broadly coincide with those nearer both poles, suggesting inter-hemispheric climate linkages. The early formation and subsequent expansion of ice caps beyond glacier margins of the Last Glacial Maximum suggest that the Cordillera Real likely attained its modern height before ca. 3.4 Ma. The number and timing of glaciations, and long-term sediment accumulation and incision rates suggest that the local Altiplano surface formed by ca. 1.8 Ma, after which headwaters of the Amazon River system breached the Cordillera Real and began to incise the fill sequence. The sequence spans at least 2 Ma before and during the first main pulses of the Great American Biotic Interchange, providing an important record of faunal migration. The arrival of savanna-adapted North American mammals in the Central Andes during this period points to the influence of glaciation on faunal migration in the southern tropics, similar to influences proposed in North and Central America. (C) 2018 Elsevier Ltd. All rights reserved. DOI
756. Rogers, LA; Salomon, AK; Connors, B; Krkosek, M.Collapse, Tipping Points, and Spatial Demographic Structure Arising from the Adopted Migrant Life History.Am. Nat., 2018, 192 Collapse, Tipping Points, and Spatial Demographic Structure Arising from the Adopted Migrant Life History
Allee effect; dispersal; recruitment; migration; learned behavior; spatial structure
The roles of dispersal and recruitment have long been a focal point in ecology and conservation. The adopted migrant hypothesis proposes a life history in which social learning transmits migratory knowledge between generations of iteroparous fish. Specifically, juveniles disperse from the parental spawning site, encounter and recruit to a local adult population, and learn migration routes between spawning and foraging habitats by following older, experienced fish. Although the adopted migrant life history may apply to many species of pelagic marine fishes, there is scant theoretical or empirical work on the consequent population dynamics. We developed and analyzed a mathematical model of this life history in which the recruitment of juveniles depends on the relative abundance of the local populations and recruitment overlap, which measures the ease with which juveniles are recruited by a nonparental population. We demonstrate that the adopted migrant life history can maintain spatial demographic structure among local populations, that it can also predispose local populations to collapse when a tipping point is crossed, and that recovery after collapse is impaired by reduced recruitment at small local population sizes. DOI PubMed
755. Rolland, J; Silvestro, D; Litsios, G; Faye, L; Salamin, N.Clownfishes evolution below and above the species level.Proc. R. Soc. B-Biol. Sci., 2018, 285 Clownfishes evolution below and above the species level
macroevolution; microevolution; intraspecific; interspecific; positive selection; RH1
The difference between rapid morphological evolutionary changes observed in populations and the long periods of stasis detected in the fossil record has raised a decade-long debate about the exact role played by intraspecific mechanisms at the interspecific level. Although they represent different scales of the same evolutionary process, micro-and macroevolution are rarely studied together and few empirical studies have compared the rates of evolution and the selective pressures between both scales. Here, we analyse morphological, genetic and ecological traits in clownfishes at different evolutionary scales and demonstrate that the tempo of molecular and morphological evolution at the species level can be, to some extent, predicted from parameters estimated below the species level, such as the effective population size or the rate of evolution within populations. We also show that similar codons in the gene of the rhodopsin RH1, a light-sensitive receptor protein, are under positive selection at the intra and interspecific scales, suggesting that similar selective pressures are acting at both levels. DOI PubMed
753. Shugar, DH; Clague, JJ; McSaveney, MJ.Late Holocene activity of Sherman and Sheridan glaciers, Prince William Sound, Alaska.Quat. Sci. Rev., 2018, 194: 116-127 Late Holocene activity of Sherman and Sheridan glaciers, Prince William Sound, Alaska
Sherman Glacier; Sheridan Glacier; Alaska; Climate change; Radiocarbon dating; Glacier-dammed lake; Holocene; Glaciation; Glacial geomorphology; Sedimentology
Two adjacent glaciers in the Chugach Mountains of south-central Alaska have markedly different histories on decadal to perhaps centennial timescales. Sheridan Glacier has advanced and retreated hundreds of metres during the latest Holocene. Its recent fluctuations have markedly altered local base level of Sherman River, which drains Sherman Glacier and flows into Sheridan Lake. Sheridan Glacier advanced to its greatest extent during the Little Ice Age, raising base level of Sherman River and inducing aggradation there of up to 17 m of sediment. Retreat of Sheridan Glacier formed a series of lakes that have coalesced. As lower lake outlets have become available, base level of Sherman River has dropped, resulting in the evacuation of substantial volumes of sediment from Sherman River valley. In about 2000, the terminus of Sheridan Glacier began to disintegrate; retreat accelerated dramatically in 2010. By 2016, the glacier had retreated an average of 600 m from its 2010 terminus, although some areas retreated up to 1.9 km and others did not retreat at all. Meanwhile, Sherman Glacier continued a slow advance initiated by a rock avalanche that blanketed much of its ablation area in the 1964 Alaska earthquake. (C) 2018 Elsevier Ltd. All rights reserved. DOI
752. Silva, AT; Lucas, MC; Castro-Santos, T; Katopodis, C; Baumgartner, LJ; Thiem, JD; Aarestrup, K; Pompeu, PS; O'Brien, GC; Braun, DC; Burnett, NJ; Zhu, DZ; Fjeldstad, HP; Forseth, T; Rajaratnam, N; Williams, JG; Cooke, SJ.The future of fish passage science, engineering, and practice.Fish. Fish., 2018, 19 The future of fish passage science, engineering, and practice
dams; ecohydraulics; fish conservation; fish migration; fishway; standardization
Much effort has been devoted to developing, constructing and refining fish passage facilities to enable target species to pass barriers on fluvial systems, and yet, fishway science, engineering and practice remain imperfect. In this review, 17 experts from different fish passage research fields (i.e., biology, ecology, physiology, ecohydraulics, engineering) and from different continents (i.e., North and South America, Europe, Africa, Australia) identified knowledge gaps and provided a roadmap for research priorities and technical developments. Once dominated by an engineering-focused approach, fishway science today involves a wide range of disciplines from fish behaviour to socioeconomics to complex modelling of passage prioritization options in river networks. River barrier impacts on fish migration and dispersal are currently better understood than historically, but basic ecological knowledge underpinning the need for effective fish passage in many regions of the world, including in biodiversity hotspots (e.g., equatorial Africa, South-East Asia), remains largely unknown. Designing efficient fishways, with minimal passage delay and post-passage impacts, requires adaptive management and continued innovation. While the use of fishways in river restoration demands a transition towards fish passage at the community scale, advances in selective fishways are also needed to manage invasive fish colonization. Because of the erroneous view in some literature and communities of practice that fish passage is largely a proven technology, improved international collaboration, information sharing, method standardization and multidisciplinary training are needed. Further development of regional expertise is needed in South America, Asia and Africa where hydropower dams are currently being planned and constructed. DOI
751. Stains, M; Harshman, J; Barker, MK; Chasteen, SV; Cole, R; DeChenne-Peters, SE; Eagan, MK; Esson, JM; Knight, JK; Laski, FA; Levis-Fitzgerald, M; Lee, CJ; Lo, SM; McDonnell, LM; Mckay, TA; Michelotti, N; Musgrove, A; Palmer, MS; Plank, KM; Rodela, TM; Sanders, ER; Schimpf, NG; Schulte, PM; Smith, MK; Stetzer, M; Van Valkenburgh, B; Vinson, E; Weir, LK; Wendel, PJ; Wheeler, LB; Young, AM.Anatomy of STEM teaching in North American universities Lecture is prominent, but practices vary.Science, 2018, 359: 1468-1470 Anatomy of STEM teaching in North American universities Lecture is prominent, but practices vary
DOI PubMed
750. Stein, RW; Mull, CG; Kuhn, TS; Aschliman, NC; Davidson, LNK; Joy, JB; Smith, GJ; Dulvy, NK; Mooers, AO.Global priorities for conserving the evolutionary history of sharks, rays and chimaeras.Nat. Ecol. Evol., 2018, 2 Global priorities for conserving the evolutionary history of sharks, rays and chimaeras
In an era of accelerated biodiversity loss and limited conservation resources, systematic prioritization of species and places is essential. In terrestrial vertebrates, evolutionary distinctness has been used to identify species and locations that embody the greatest share of evolutionary history. We estimate evolutionary distinctness for a large marine vertebrate radiation on a dated taxon-complete tree for all 1,192 chondrichthyan fishes (sharks, rays and chimaeras) by augmenting a new 610-species molecular phylogeny using taxonomic constraints. Chondrichthyans are by far the most evolutionarily distinct of all major radiations of jawed vertebrates-the average species embodies 26 million years of unique evolutionary history. With this metric, we identify 21 countries with the highest richness, endemism and evolutionary distinctness of threatened species as targets for conservation prioritization. On average, threatened chondrichthyans are more evolutionarily distinct-further motivating improved conservation, fisheries management and trade regulation to avoid significant pruning of the chondrichthyan tree of life. DOI PubMed
749. Stephenson, RL; Paul, S; Wiber, M; Angel, E; Benson, AJ; Charles, A; Chouinard, O; Clemens, M; Edwards, D; Foley, P; Jennings, L; Jones, O; Lane, D; McIsaac, J; Mussells, C; Neis, B; Nordstrom, B; Parlee, C; Pinkerton, E; Saunders, M; Squires, K; Sumaila, UR.Evaluating and implementing social-ecological systems: A comprehensive approach to sustainable fisheries.Fish. Fish., 2018, 19 Evaluating and implementing social-ecological systems: A comprehensive approach to sustainable fisheries
Canadian Fisheries Research Network; comprehensive fisheries evaluation; decision support frameworks; human dimensions; social-ecological systems; sustainable fisheries
Fisheries sustainability is recognized to have four pillars: ecological, economic, social (including cultural) and institutional (or governance). Although international agreements, and legislation in many jurisdictions, call for implementation of all four pillars of sustainability, the social, economic and institutional aspects (i.e., the human dimensions) have not been comprehensively and collectively addressed to date. This study describes a framework for comprehensive fisheries evaluation developed by the Canadian Fisheries Research Network (CFRN) that articulates the full spectrum of ecological, economic, social and institutional objectives required under international agreements, together with candidate performance indicators for sustainable fisheries. The CFRN framework is aimed at practical fisheries evaluation and management and has a relatively balanced distribution of elements across the four pillars of sustainability relative to 10 alternative management decision support tools and indicator scorecards, which are heavily focused on ecological and economic aspects. The CFRN framework has five immediate uses: (a) It can serve as a logic frame for defining management objectives; (b) it can be used to define alternate management options to achieve given objectives; (c) it can serve as a tool for comparing management scenarios/options in decision support frameworks; (d) it can be employed to create a report card for comprehensive fisheries management evaluation; and (e) it is a tool for practical implementation of an integrated social-ecological system approach. DOI
748. Taylor, J; Unsoeld, T; Hutter, H.The transmembrane collagen COL-99 guides longitudinally extending axons in C-elegans.Mol. Cell. Neurosci., 2018, 89 The transmembrane collagen COL-99 guides longitudinally extending axons in C-elegans
We have identified the transmembrane collagen, COL-99, in a genetic screen for novel genes involved in axon guidance in the nematode C. deguns. COL-99 is similar to transmembrane collagens type XIII, XXIII and XXV in vertebrates. col-99 mutants exhibit guidance defects in axons extending along the major longitudinal axon tracts, most prominently the left ventral nerve cord (VNC). COL-99 is expressed in the hypodermis during the time of axon outgrowth. We provide evidence that a furin cleavage site in COL-99 is essential for function, suggesting that COL-99 is released from the cells producing it. Vertebrate homologs of COL-99 have been shown to be expressed in mammalian nervous systems and linked to various neurological disease but have not been associated with guidance of extending neurons. col-99 acts genetically with the discoidin domain receptors ddr-1 and ddr-2, which are expressed by neurons affected in col-99 mutants. Discoidin domain receptors are activated by collagens in vertebrates. DDR-1 and DDR-2 may function as receptors for COL-99. Our results establish a novel role for a transmembrane collagen in axonal guidance and asymmetry establishment of the VNC. DOI PubMed
746. Thomsen, SK; Mazurkiewicz, DM; Stanley, TR; Green, DJ.El Nino/Southern Oscillation-driven rainfall pulse amplifies predation by owls on seabirds via apparent competition with mice.Proc. R. Soc. B-Biol. Sci., 2018, 285 El Nino/Southern Oscillation-driven rainfall pulse amplifies predation by owls on seabirds via apparent competition with mice
El Nino/Southern Oscillation; predator-mediated apparent competition; predation; marine-terrestrial links; rainfall; mathematical model
Most approaches for assessing species vulnerability to climate change have focused on direct impacts via abiotic changes rather than indirect impacts mediated by changes in species interactions. Changes in rainfall regimes may influence species interactions from the bottom-up by increasing primary productivity in arid environments, but subsequently lead to less predictable top-down effects. Our study demonstrates how the effects of an EL Nino/Southern Oscillation (ENSO)-driven rainfall pulse ricochets along a chain of interactions between marine and terrestrial food webs, leading to enhanced predation of a vulnerable marine predator on its island breeding grounds. On Santa Barbara Island, barn owls (Tyto alba) are the main predator of a nocturnal seabird, the Scripps's murrelet (Synthliboramphus scrippsi), as well as an endemic deer mouse. We followed the links between rainfall, normalized difference vegetation index and subsequent peaks in mouse and owl abundance. After the mouse population declined steeply, there was approximately 15-fold increase in the number of murrelets killed by owls. We also simulated these dynamics with a mathematical model and demonstrate that bottom-up resource pulses can lead to subsequent declines in alternative prey. Our study highlights the need for understanding how species interactions will change with shifting rainfall patterns through the effects of ENSO under global change. DOI PubMed
745. Toor, A; Culibrk, L; Singhera, GK; Moon, KM; Prudova, A; Foster, LJ; Moore, MM; Dorscheid, DR; Tebbutt, SJ.Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium.PLoS One, 2018, 13 Transcriptomic and proteomic host response to Aspergillus fumigatus conidia in an air-liquid interface model of human bronchial epithelium
Aspergillus fumigatus (A. fumigatus) is a wide-spread fungus that is a potent allergen in hypersensitive individuals but also an opportunistic pathogen in immunocompromised patients. It reproduces asexually by releasing airborne conidiospores (conidia). Upon inhalation, fungal conidia are capable of reaching the airway epithelial cells (AECs) in bronchial and alveolar tissues. Previous studies have predominantly used submerged monolayer cultures for studying this host-pathogen interaction; however, these cultures do not recapitulate the mucocililary differentiation phenotype of the in vivo epithelium in the respiratory tract. Thus, the aim of this study was to use well-differentiated primary human bronchial epithelial cells (HBECs) grown at the air-liquid interface (ALI) to determine their transcriptomic and proteomic responses following interaction with A. fumigatus conidia. We visualized conidial interaction with HBECs using confocal laser scanning microscopy (CLSM), and applied NanoString nCounter and shotgun proteomics to assess gene expression changes in the human cells upon interaction with A. fumigatus conidia. Western blot analysis was used to assess the expression of top three differentially expressed proteins, CALR, SET and NUCB2. CLSM showed that, unlike submerged monolayer cultures, well-differentiated ALI cultures of primary HBECs were estimated to internalize less than 1% of bound conidia. Nevertheless, transcriptomic and proteomic analyses revealed numerous differentially expressed host genes; these were enriched for pathways including apoptosis/autophagy, translation, unfolded protein response and cell cycle (up-regulated); complement and coagulation pathways, iron homeostasis, nonsense mediated decay and rRNA binding (down-regulated). CALR and SET were confirmed to be up-regulated in ALI cultures of primary HBECs upon exposure to A. fumigatus via western blot analysis. Therefore, using transcriptomics and proteomics approaches, ALI models recapitulating the bronchial epithelial barrier in the conductive zone of the respiratory tract can provide novel insights to the molecular response of bronchial epithelial cells upon exposure to A. fumigatus conidia. DOI PubMed
744. Tricola, GM; Simons, MJP; Atema, E; Boughton, RK; Brown, JL; Dearborn, DC; Divoky, G; Eimes, JA; Huntington, CE; Kitaysky, AS; Juola, FA; Lank, DB; Litwa, HP; Mulder, EGA; Nisbet, ICT; Okanoya, K; Safran, RJ; Schoech, SJ; Schreiber, EA; Thompson, PM; Verhulst, S; Wheelwright, NT; Winkler, DW; Young, R; Vleck, CM; Haussmann, MF.The rate of telomere loss is related to maximum lifespan in birds.Philos. Trans. R. Soc. B-Biol. Sci., 2018, 373 The rate of telomere loss is related to maximum lifespan in birds
telomeres; bird; lifespan; ageing; senescence; comparative analysis
Telomeres are highly conserved regions of DNA that protect the ends of linear chromosomes. The loss of telomeres can signal an irreversible change to a cell's state, including cellular senescence. Senescent cells no longer divide and can damage nearby healthy cells, thus potentially placing them at the crossroads of cancer and ageing. While the epidemiology, cellular and molecular biology of telomeres are well studied, a newer field exploring telomere biology in the context of ecology and evolution is just emerging. With work to date focusing on how telomere shortening relates to individual mortality, less is known about how telomeres relate to ageing rates across species. Here, we investigated telomere length in cross-sectional samples from 19 bird species to determine how rates of telomere loss relate to interspecific variation in maximum lifespan. We found that bird species with longer lifespans lose fewer telomeric repeats each year compared with species with shorter lifespans. In addition, phylogenetic analysis revealed that the rate of telomere loss is evolutionarily conserved within bird families. This suggests that the physiological causes of telomere shortening, or the ability to maintain telomeres, are features that may be responsible for, or co-evolved with, different lifespans observed across species. This article is part of the theme issue 'Understanding diversity in telomere dynamics'. DOI
743. Uryu, O; Ou, QX; Komura-Kawa, T; Kamiyama, T; Iga, M; Syrzycka, M; Hirota, K; Kataoka, H; Honda, BM; King-Jones, K; Niwa, R.Cooperative Control of Ecdysone Biosynthesis in Drosophila by Transcription Factors Seance, Ouija Board, and Molting Defective.Genetics, 2018, 208: 605-622 Cooperative Control of Ecdysone Biosynthesis in Drosophila by Transcription Factors Seance, Ouija Board, and Molting Defective
Drosophila; ecdysone; heterochromatin; steroid hormone biosynthesis; transcription; zinc finger
Ecdysteroids are steroid hormones that control many aspects of development and physiology. During larval development, ecdysone is synthesized in an endocrine organ called the prothoracic gland through a series of ecdysteroidogenic enzymes encoded by the Halloween genes. The expression of the Halloween genes is highly restricted and dynamic, indicating that their spatiotemporal regulation is mediated by their tight transcriptional control. In this study, we report that three zinc finger-associated domain (ZAD)-C2H2 zinc finger transcription factorsSeance (Sean), Ouija board (Ouib), and Molting defective (Mld)cooperatively control ecdysone biosynthesis in the fruit fly Drosophila melanogaster. Sean and Ouib act in cooperation with Mld to positively regulate the transcription of neverland and spookier, respectively, two Halloween genes. Remarkably, loss-of-function mutations in sean, ouib, or mld can be rescued by the expression of neverland, spookier, or both, respectively. These results suggest that the three transcription factors have distinct roles in coordinating the expression of just two genes in Drosophila. Given that neverland and spookier are located in constitutive heterochromatin, Sean, Ouib, and Mld represent the first example of a transcription factor subset that regulates genes located in constitutive heterochromatin. DOI
742. van den Top, GG; Reynolds, JD; Prins, HHT; Mattsson, J; Green, DJ; Ydenberg, RC.From salmon to salmonberry: The effects of salmon-derived nutrients on the stomatal density of leaves of the nitriphilic shrub Rubus spectabilis.Funct. Ecol., 2018, 32 From salmon to salmonberry: The effects of salmon-derived nutrients on the stomatal density of leaves of the nitriphilic shrub Rubus spectabilis
Great Bear Rainforest; nutrient subsidy; Rubus spectabilis; salmonberry; salmon-derived nutrients; stomata; stomatal density
Nutrients derived from the carcasses of Pacific salmon have been shown to have wide-ranging effects on riparian systems. These include changes in community species composition and an increase in leaf nitrogen concentration, with the latter effect pronounced in the nitriphilic shrub Rubus spectabilis (salmonberry). Experimental work with other species has shown that leaf stomatal density increases in response to nitrogen fertilization. We predicted that the stomatal density of salmonberry leaves would vary directly with the density of spawning salmon in salmonberry leaves collected from 16 streams in the vicinity of Bella Bella, on British Columbia's central coast. We estimated the stomatal density along each stream, and quantified stream characteristics, including the number of spawning salmon (Oncorhynchus spp.), canopy cover, stem density and soil moisture. We found that salmon have both direct and indirect effects on stomatal density, the latter mediated by canopy cover and stem density. Salmonberry stomatal density increased by 1.12 stomata per mm(2) (similar to 0.5%) for every kg of salmon per metre of stream. Over the range of salmon densities observed (1.8-49.0 kg per metre of stream), stomatal density increased by almost 45 mm(-2), or more than 20%. These data confirm that the stomatal density in salmonberry responds positively to the opportunity for greater productivity provided by salmon carcasses. The data provide insight into the physiological and morphological processes supporting nitrogen uptake, which in turn influences plant community composition. A is available for this article. DOI
741. Vuong, AM; Braun, JM; Webster, GM; Zoeller, RT; Hoofnagle, AN; Sjodin, A; Yolton, K; Lanphear, BP; Chen, AM.Polybrominated diphenyl ether (PBDE) exposures and thyroid hormones in children at age 3 years.Environ. Int., 2018, 117 Polybrominated diphenyl ether (PBDE) exposures and thyroid hormones in children at age 3 years
Polybrominated diphenyl ethers (PBDEs); Thyroid hormones; Epidemiology; Thyroid function; Brominated flame retardants; Endocrine disruption
Background: Polybrominated diphenyl ethers (PBDEs) reduce serum thyroid hormone concentrations in animal studies, but few studies have examined the impact of early-life PBDE exposures on thyroid hormone disruption in childhood. Methods: We used data from 162 mother-child pairs from the Health Outcomes and Measures of the Environment Study (2003-2006, Cincinnati, OH). We measured PBDEs in maternal serum at 16 +/- 3 weeks gestation and in child serum at 1-3 years. Thyroid hormones were measured in serum at 3 years. We used multiple informant models to investigate associations between prenatal and early-life PBDE exposures and thyroid hormone levels at age 3 years. Results: Prenatal PBDEs were associated with decreased thyroid stimulating hormone (TSH) levels at age 3 years. A 10-fold increase in prenatal SPBDEs (BDE-28, -47, -99, -100, and -153) was associated with a 27.6% decrease (95% CI -40.8%, -11.3%) in TSH. A ten-fold increase in prenatal SPBDEs was associated with a 0.25 pg/mL (0.07, 0.43) increase in free triiodothyronine (FT3). Child sex modified associations between prenatal PBDEs and thyroid hormones, with significant decrements in TSH among females and decreased free T4 (FT4) in males. Prenatal SPBDEs were not associated with TT4, FT4, or total T3. Conclusions: These findings suggest an inverse relationship between prenatal SPBDEs and TSH at 3 years. Associations may be sexually dimorphic, with an inverse relationship between prenatal BDE-47 and -99 and TSH in females and null associations among males. DOI PubMed
740. Walsh, JC; Minto, C; Jardim, E; Anderson, SC; Jensen, OP; Afflerbach, J; Dickey-Collas, M; Kleisner, KM; Longo, C; Osio, GC; Selig, ER; Thorson, JT; Rudd, MB; Papacostas, KJ; Kittinger, JN; Rosenberg, AA; Cooper, AB.Trade-offs for data-limited fisheries when using harvest strategies based on catch-only models.Fish. Fish., 2018, 19 Trade-offs for data-limited fisheries when using harvest strategies based on catch-only models
catch-only model; data-limited; data-poor; harvest control rule; management strategy evaluation; superensemble
Many of the world's fisheries are unassessed, with little information about population status or risk of overfishing. Unassessed fisheries are particularly predominant in developing countries and in small-scale fisheries, where they are important for food security. Several catch-only methods based on time series of fishery catch and commonly available life-history traits have been developed to estimate stock status (defined as biomass relative to biomass at maximum sustainable yield: B/B-MSY). While their stock status performance has been extensively studied, performance of catch-only models as a management tool is unknown. We evaluated the extent to which a superensemble of three prominent catch-only models can provide a reliable basis for fisheries management and how performance compares across management strategies that control catch or fishing effort. We used a management strategy evaluation framework to determine whether a superensemble of catch-only models can reliably inform harvest control rules (HCRs). Across five simulated fish life histories and two harvest-dynamic types, catch-only models and HCR combinations reduced the risk of overfishing and increased the proportion of stocks above B-MSY compared to business as usual, though often resulted in poor yields. Precautionary HCRs based on fishing effort were robust and insensitive to error in catch-only models, while catch-based HCRs caused high probabilities of overfishing and more overfished populations. Catch-only methods tended to overestimate B/B-MSY for our simulated data sets. The catch-only superensemble combined with precautionary effort-based HCRs could be part of a stepping stone approach for managing some data-limited stocks while working towards more data-moderate assessment methods. DOI
739. Williamson, SN; Anslow, FS; Clarke, GKC; Gamon, JA; Jarosch, AH; Hik, DS.Spring warming in Yukon mountains is not amplified by the snow albedo feedback.Sci Rep, 2018, 8 Spring warming in Yukon mountains is not amplified by the snow albedo feedback
alpine
Decreasing spring snow cover may amplify Arctic warming through the snow albedo feedback. To examine the impact of snowmelt on increasing temperature we used a 5,000 m elevation gradient in Yukon, Canada, extending from valley-bottom conifer forests, through middle elevation tundra, to high elevation icefields, to compare validated downscaled reanalysis air temperature patterns across elevational bands characterized by different patterns of spring snowmelt. From 2000 to 2014 we observed surface warming of 0.01 degrees C/a.1,000 m in May (0.14 degrees C/a at 1,000 m to 0.19 degrees C/a at 5,000 m), and uniform cooling of 0.09 degrees C/a in June at all elevations. May temperature trends across elevationally dependent land cover types were highly correlated with each other despite large variations in albedo and snow cover trends. Furthermore, a clear dependency of infrared skin temperature on snow cover mediated albedo decline was observed in tundra, but this was insufficient to influence average diurnal air temperature. We observed negative June temperature trends which we attribute to increasing daytime cloud cover because albedo and snow cover trends were unchanging. We conclude that 8-day and monthly averaged Spring air temperature trends are responding to a synoptic external forcing that is much stronger than the snow albedo feedback in sub-Arctic mountains. DOI
738. Xu, J; Camfield, R; Gorski, SM.The interplay between exosomes and autophagy - partners in crime.J. Cell Sci., 2018, 131 The interplay between exosomes and autophagy - partners in crime
Autophagy; Exosome; Lysosome; Extracellular vesicle
The eukaryotic endomembrane system is a complex series of interconnected membranous organelles that play important roles in responding to stress and maintaining cell homeostasis during health and disease. Two components of this system, exosome biogenesis and autophagy, are linked by the endolysosomal pathway. Exosomes are cargo-laden extracellular vesicles that arise from endosome-derived multivesicular bodies, and autophagy is a lysosomal-dependent degradation and recycling pathway. Recent studies have revealed shared molecular machinery between exosome biogenesis and autophagy, as well as substantial crosstalk between these two processes. In this Review, we first describe the classic view of exosome biogenesis and autophagy, including their links to the endolysosomal pathway. We then present the evidence for autophagy-related proteins in exosome biogenesis, the emerging roles of amphisomes and the evolving models of exosome-autophagy pathway interactions. Finally, we discuss the implications of exosome and autophagy interplay in the context of neurodegeneration and cancer. DOI PubMed
737. Young, OR; Webster, DG; Cox, ME; Raakjaer, J; Blaxekjaer, LO; Einarsson, N; Virginia, RA; Acheson, J; Bromley, D; Cardwell, E; Carothers, C; Eythorsson, E; Howarth, RB; Jentoft, S; McCay, BJ; McCormack, F; Osherenko, G; Pinkerton, E; van Ginkel, R; Wilson, JA; Rivers, L; Wilson, RS.Moving beyond panaceas in fisheries governance.Proc. Natl. Acad. Sci. U. S. A., 2018, 115 Moving beyond panaceas in fisheries governance
governance; fisheries; panacea mindset; individual transferable quotas; institutional diagnostics
In fisheries management as in environmental governance more generally regulatory arrangements that are thought to be helpful in some contexts frequently become panaceas or, in other words, simple formulaic policy prescriptions believed to solve a given problem in a wide range of contexts, regardless of their actual consequences. When this happens, management is likely to fail, and negative side effects are common. We focus on the case of individual transferable quotas to explore the panacea mindset, a set of factors that promote the spread and persistence of panaceas. These include conceptual narratives that make easy answers like panaceas seem plausible, power disconnects that create vested interests in panaceas, and heuristics and biases that prevent people from accurately assessing panaceas. Analysts have suggested many approaches to avoiding panaceas, but most fail to conquer the underlying panacea mindset. Here, we suggest the codevelopment of an institutional diagnostics toolkit to distill the vast amount of information on fisheries governance into an easily accessible, open, on-line database of checklists, case studies, and related resources. Toolkits like this could be used in many governance settings to challenge users' understandings of a policy's impacts and help them develop solutions better tailored to their particular context. They would not replace the more comprehensive approaches found in the literature but would rather be an intermediate step away from the problem of panaceas. DOI PubMed
736. Yu, SC; Zheng, CR; Zhou, F; Baillie, DL; Rose, AM; Deng, ZX; Chu, JSC.Genomic identification and functional analysis of essential genes in Caenorhabditis elegans.BMC Genomics, 2018, 19 Genomic identification and functional analysis of essential genes in Caenorhabditis elegans
Essential gene; Lethal; Genetic balancer; Whole genome sequencing (WGS); Functional characterization
BackgroundEssential genes are required for an organism's viability and their functions can vary greatly, spreading across many pathways. Due to the importance of essential genes, large scale efforts have been undertaken to identify the complete set of essential genes and to understand their function. Studies of genome architecture and organization have found that genes are not randomly disturbed in the genome.ResultsUsing combined genetic mapping, Illumina sequencing, and bioinformatics analyses, we successfully identified 44 essential genes with 130 lethal mutations in genomic regions of C. elegans of around 7.3Mb from Chromosome I (left). Of the 44 essential genes, six of which were genes not characterized previously by mutant alleles, let-633/let-638 (B0261.1), let-128 (C53H9.2), let-511 (W09C3.4), let-162 (Y47G6A.18), let-510 (Y47G6A.19), and let-131 (Y71G12B.6). Examine essential genes with Hi-C data shows that essential genes tend to cluster within TAD units rather near TAD boundaries. We have also shown that essential genes in the left half of chromosome I in C. elegans function in enzyme and nucleic acid binding activities during fundamental processes, such as DNA replication, transcription, and translation. From protein-protein interaction networks, essential genes exhibit more protein connectivity than non-essential genes in the genome. Also, many of the essential genes show strong expression in embryos or early larvae stages, indicating that they are important to early development.ConclusionsOur results confirmed that this work provided a more comprehensive picture of the essential gene and their functional characterization. These genetic resources will offer important tools for further heath and disease research. DOI PubMed
734. Zhang, YJ; Pitchiaya, S; Cieslik, M; Niknafs, YS; Tien, JCY; Hosono, Y; Iyer, MK; Yazdani, S; Subramaniam, S; Shukla, SK; Jiang, X; Wang, LS; Liu, TY; Uhl, M; Gawronski, AR; Qiao, YY; Xiao, LB; Dhanasekaran, SM; Juckette, KM; Kunju, LP; Cao, XH; Patel, U; Batish, M; Shukla, GC; Paulsen, MT; Ljungman, M; Jiang, H; Mehra, R; Backofen, R; Sahinalp, CS; Freier, SM; Watt, AT; Guo, SL; Wei, JT; Feng, FY; Malik, R; Chinnaiyan, AM.Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.Nature Genet., 2018, 50 Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression
The androgen receptor (AR) plays a critical role in the development of the normal prostate as well as prostate cancer. Using an integrative transcriptomic analysis of prostate cancer cell lines and tissues, we identified ARLNC1 (AR-regulated long noncoding RNA 1) as an important long noncoding RNA that is strongly associated with AR signaling in prostate cancer progression. Not only was ARLNC1 induced by the AR protein, but ARLNC1 stabilized the AR transcript via RNA-RNA interaction. ARLNC1 knockdown suppressed AR expression, global AR signaling and prostate cancer growth in vitro and in vivo. Taken together, these data support a role for ARLNC1 in maintaining a positive feedback loop that potentiates AR signaling during prostate cancer progression and identify ARLNC1 as a novel therapeutic target. DOI PubMed
733. Alsahafi, N; Richard, J; Prevost, J; Coutu, M; Brassard, N; Parsons, MS; Kaufmann, DE; Brockman, M; Finzi, A.Impaired Downregulation of NKG2D Ligands by Nef Proteins from Elite Controllers Sensitizes HIV-1-Infected Cells to Antibody-Dependent Cellular Cytotoxicity.J. Virol., 2017, 91 Impaired Downregulation of NKG2D Ligands by Nef Proteins from Elite Controllers Sensitizes HIV-1-Infected Cells to Antibody-Dependent Cellular Cytotoxicity
HIV-1; Nef; elite controllers; ADCC; NKG2D; gp120; CD4
HIV-1 Nef clones isolated from a rare subset of HIV-1-infected elite controllers (EC), with the ability to suppress viral load to undetectable levels in the absence of antiretroviral therapy, are unable to fully downregulate CD4 from the plasma membrane of CD4(+) T cells. Residual CD4 left at the plasma membrane allows Env-CD4 interaction, which leads to increased exposure of Env CD4-induced epitopes and increases susceptibility of infected cells to antibody-dependent cellular cytotoxicity (ADCC). ADCC is mediated largely by natural killer (NK) cells, which control their activation status through the cumulative signals received through activating and inhibitory receptors. Recently, the activating NKG2D receptor was demonstrated to positively influence ADCC responses. Since HIV-1 Nef has been reported to reduce the expression of NKG2D ligands, we evaluated the relative abilities of Nef from EC and progressors to downmodulate NKG2D ligands. Furthermore, we assessed the impact of EC and progressor Nef on the ADCC susceptibility of HIV-1infected cells. We observed a significantly increased expression of NKG2D ligands on cells infected with viruses coding for Nef from EC. Importantly, NKG2D ligand expression levels correlated with enhanced susceptibility of HIV-1-infected cells to ADCC. The biological significance of this correlation was corroborated by the demonstration that antibody-mediated blockade of NKG2D significantly reduced ADCC of cells infected with viruses carrying Nef from EC. These results suggest the involvement of NKG2D-NKG2D ligand interactions in the enhanced susceptibility of EC HIV1-infected cells to ADCC responses. IMPORTANCE Attenuated Nef functions have been reported in HIV-1 isolated from EC. The inability of elite controller Nef to fully remove CD4 from the surface of infected cells enhanced their susceptibility to elimination by ADCC. We now show that downregulation of NKG2D ligands by HIV-1 Nef from EC is inefficient and leaves infected cells susceptible to ADCC. These data suggest a critical role for NKG2D ligands in anti-HIV-1 ADCC responses. DOI
732. Anderson, SC; Branch, TA; Cooper, AB; Dulvy, NK.Black-swan events in animal populations.Proceedings of the National Academy of Sciences of the United States of America, 2017, 114: 3252-3257 Black-swan events in animal populations
mass mortality; ecological surprises; population dynamics; die-offs; ecological risk
Black swans are improbable events that nonetheless occur-often with profound consequences. Such events drive important transitions in social systems (e.g., banking collapses) and physical systems (e.g., earthquakes), and yet it remains unclear the extent to which ecological population numbers buffer or suffer from such extremes. Here, we estimate the prevalence and direction of black-swan events (heavy-tailed process noise) in 609 animal populations after accounting for population dynamics (productivity, density dependence, and typical stochasticity). We find strong evidence for black-swan events in similar to 4% of populations. These events occur most frequently for birds (7%), mammals (5%), and insects (3%) and are not explained by any life-history covariates but tend to be driven by external perturbations such as climate, severe winters, predators, parasites, or the combined effect of multiple factors. Black-swan events manifest primarily as population die-offs and crashes (86%) rather than unexpected increases, and ignoring heavy-tailed process noise leads to an underestimate in the magnitude of population crashes. We suggest modelers consider heavy-tailed, downward-skewed probability distributions, such as the skewed Student t used here, when making forecasts of population abundance. Our results demonstrate the importance of both modeling heavy-tailed downward events in populations, and developing conservation strategies that are robust to ecological surprises. DOI
730. Bazzicalupo, AL; Buyck, B; Saar, I; Vauras, J; Carmean, D; Berbee, ML.Troubles with mycorrhizal mushroom identification where morphological differentiation lags behind barcode sequence divergence.Taxon, 2017, 66: 791-810 Troubles with mycorrhizal mushroom identification where morphological differentiation lags behind barcode sequence divergence
barcode; Benjamin Woo; ITS2; Pacific Northwest; Russula; species delimitation; type specimens
Species of Russula (Russulaceae), a large, cosmopolitan, ectomycorrhizal fungal genus are notoriously difficult to identify. To delimit species and to evaluate their morphology, we sequenced the similar to 400 bp ITS2 ribosomal DNA region from 713 Pacific Northwest Russula specimens from Benjamin Woo's exceptional collection. As a topological constraint for analysis of the ITS2, we sequenced and inferred a phylogeny from the ITS, LSU, RPB2 and EF1-alpha regions from 50 European and North American specimens of major clades in Russula. We delimited 72 candidate species from Woo's collection's ITS2 sequences using ABGD, GMYC, PTP, and mothur software. To guide application of names, we sequenced a similar to 200 bp portion of the ITS from 18 American type specimens. Of the 72 delimited species, 28 matched a type or a currently barcoded European species. Among the remaining 44 are poorly known or undescribed species. We tested the congruence of morphology with delimitations for 23 species represented by 10 or more specimens each. No morphological character alone was consistently diagnostic across all specimens of any of the 23 candidate species. Ordination of combined field characters followed by pairwise multivariate analysis of variance showed that centroids were significantly different in 221 of 253 species pair comparisons. Ordination also showed that specimens from the same species were widely dispersed, overlapping with specimens from other species. This explains why only 48.5% of specimens were correctly assigned to their species in a canonical variates analysis of combined field and spore characters. Based on sequence comparisons, we contribute to correcting the broad and confusing misapplications of European names that have long obscured patterns of Russula's geographical distribution and diversification. Our evidence suggests that morphology in Russula diverges slowly, and that phenotypic plasticity, convergence, or retention of ancestral polymorphisms blur the distinctions among recently derived species.Website DOI
729. Blanchard, JL; Watson, RA; Fulton, EA; Cottrell, RS; Nash, KL; Bryndum-Buchholz, A; Buchner, M; Carozza, DA; Cheung, WWL; Elliott, J; Davidson, LNK; Dulvy, NK; Dunne, JP; Eddy, TD; Galbraith, E; Lotze, HK; Maury, O; Muller, C; Tittensor, DP; Jennings, S.Linked sustainability challenges and trade-offs among fisheries, aquaculture and agriculture.Nature Ecology & Evolution, 2017, 1: 1240-1249 Linked sustainability challenges and trade-offs among fisheries, aquaculture and agriculture
Fisheries and aquaculture make a crucial contribution to global food security, nutrition and livelihoods. However, the UN Sustainable Development Goals separate marine and terrestrial food production sectors and ecosystems. To sustainably meet increasing global demands for fish, the interlinkages among goals within and across fisheries, aquaculture and agriculture sectors must be recognized and addressed along with their changing nature. Here, we assess and highlight development challenges for fisheries-dependent countries based on analyses of interactions and trade-offs between goals focusing on food, biodiversity and climate change. We demonstrate that some countries are likely to face double jeopardies in both fisheries and agriculture sectors under climate change. The strategies to mitigate these risks will be context-dependent, and will need to directly address the trade-offs among Sustainable Development Goals, such as halting biodiversity loss and reducing poverty. Countries with low adaptive capacity but increasing demand for food require greater support and capacity building to transition towards reconciling trade-offs. Necessary actions are context-dependent and include effective governance, improved management and conservation, maximizing societal and environmental benefits from trade, increased equitability of distribution and innovation in food production, including continued development of low input and low impact aquaculture. DOI
728. Bruel, AL; Franco, B; Duffourd, Y; Thevenon, J; Jego, L; Lopez, E; Deleuze, JF; Doummar, D; Giles, RH; Johnson, CA; Huynen, MA; Chevrier, V; Burglen, L; Morleo, M; Desguerres, I; Pierquin, G; Doray, B; Gilbert-Dussardier, B; Reversade, B; Steichen-Gersdorf, E; Baumann, C; Panigrahi, I; Fargeot-Espaliat, A; Dieux, A; David, A; Goldenberg, A; Bongers, E; Gaillard, D; Argente, J; Aral, B; Gigot, N; St-Onge, J; Birnbaum, D; Phadke, SR; Cormier-Daire, V; Eguether, T; Pazour, GJ; Herranz-Perez, V; Goldstein, JS; Pasquier, L; Loget, P; Saunier, S; Megarbane, A; Rosnet, O; Leroux, MR; Wallingford, JB; Blacque, OE; Nachury, MV; Attie-Bitach, T; Riviere, JB; Faivre, L; Thauvin-Robinet, C.Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes.J. Med. Genet., 2017, 54: 371-380 Fifteen years of research on oral-facial-digital syndromes: from 1 to 16 causal genes
Oral-facial-digital syndromes (OFDS) gather rare genetic disorders characterised by facial, oral and digital abnormalities associated with a wide range of additional features (polycystic kidney disease, cerebral malformations and several others) to delineate a growing list of OFDS subtypes. The most frequent, OFD type I, is caused by a heterozygous mutation in the OFD1 gene encoding a centrosomal protein. The wide clinical heterogeneity of OFDS suggests the involvement of other ciliary genes. For 15 years, we have aimed to identify the molecular bases of OFDS. This effort has been greatly helped by the recent development of whole-exome sequencing (WES). Here, we present all our published and unpublished results for WES in 24 cases with OFDS. We identified causal variants in five new genes (C2CD3, TMEM107, INTU, KIAA0753 and IFT57) and related the clinical spectrum of four genes in other ciliopathies (C5orf42, TMEM138, TMEM231 and WDPCP) to OFDS. Mutations were also detected in two genes previously implicated in OFDS. Functional studies revealed the involvement of centriole elongation, transition zone and intraflagellar transport defects in OFDS, thus characterising three ciliary protein modules: the complex KIAA0753-FOPNL-OFD1, a regulator of centriole elongation; the Meckel-Gruber syndrome module, a major component of the transition zone; and the CPLANE complex necessary for IFT-A assembly. OFDS now appear to be a distinct subgroup of ciliopathies with wide heterogeneity, which makes the initial classification obsolete. A clinical classification restricted to the three frequent/well-delineated subtypes could be proposed, and for patients who do not fit one of these three main subtypes, a further classification could be based on the genotype. DOI
727. Caicedo, JC; Cooper, S; Heigwer, F; Warchal, S; Qiu, P; Molnar, C; Vasilevich, AS; Barry, JD; Bansal, HS; Kraus, O; Wawer, M; Paavolainen, L; Herrmann, MD; Rohban, M; Hung, J; Hennig, H; Concannon, J; Smith, I; Clemons, PA; Singh, S; Rees, P; Horvath, P; Linington, RG; Carpenter, AE.Data-analysis strategies for image-based cell profiling.Nat. Methods, 2017, 14: 849-863 Data-analysis strategies for image-based cell profiling
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences. DOI PubMed
726. Carroll, CS; Grieve, CL; Murugathasan, I; Bennet, AJ; Czekster, CM; Liu, HT; Naismith, J; Moore, MM.The rhizoferrin biosynthetic gene in the fungal pathogen Rhizopus delemar is a novel member of the NIS gene family.Int. J. Biochem. Cell Biol., 2017, 89: 136-146 The rhizoferrin biosynthetic gene in the fungal pathogen Rhizopus delemar is a novel member of the NIS gene family
Mucormycosis; Rhizopus delemar; Siderophore biosynthesis; NRPS-independent siderophore (NIS)
Iron is essential for growth and in low iron environments such as serum many bacteria and fungi secrete ferric iron-chelating molecules called siderophores. All fungi produce hydroxamate siderophores with the exception of Mucorales fungi, which secrete rhizoferrin, a polycarboxylate siderophore. Here we investigated the biosynthesis of rhizoferrin by the opportunistic human pathogen, Rhizopus delemar. We searched the genome of R. delemar 99-880 for a homologue of the bacterial NRPS-independent siderophore (NIS) protein, SfnaD, that is involved in biosynthesis of staphyloferrin A in Staphylococcus aureus. A protein was identified in R. delemar with 22% identity and 37% similarity with SfnaD, containing an N-terminal IucA/IucC family domain, and a C-terminal conserved ferric iron reductase FhuF-like transporter domain. Expression of the putative fungal rhizoferrin synthetase (ifs) gene was repressed by iron. The rfs gene was cloned and expressed in E.coli and siderophore biosynthesis from citrate and diaminobutane was confirmed using high resolution LC-MS. Substrate specificity was investigated showing that Rfs produced AMP when oxaloacetic acid, tricarballylic acid, omithine, hydroxylamine, diaminopentane and diaminopropane were employed as substrates. Based on the production of AMP and the presence of a mono-substituted rhizoferrin, we suggest that Rfs is a member of the superfamily of adenylating enzymes. We used site-directed mutagenesis to mutate selected conserved residues predicted to be in the Rfs active site. These studies revealed that H484 is essential for Rfs activity and L544 may play a role in amine recognition by the enzyme. This study on Rfs is the first characterization of a fungal NIS enzyme. Future work will determine if rhizoferrin biosynthesis is required for virulence in Mucorales fungi. DOI
725. Casasanta, MA; Yoo, CC; Smith, HB; Duncan, AJ; Cochrane, K; Varano, AC; Allen-Vercoe, E; Slade, DJ.A chemical and biological toolbox for Type Vd secretion: Characterization of the phospholipase A1 autotransporter FplA from Fusobacterium nucleatum.J. Biol. Chem., 2017, 292: 20240-20254 A chemical and biological toolbox for Type Vd secretion: Characterization of the phospholipase A1 autotransporter FplA from Fusobacterium nucleatum
chemical biology; colorectal cancer; host-pathogen interaction; phospholipase A; protein secretion; Fusobacterium; autotransporter
Fusobacterium nucleatum is an oral pathogen that is linked to multiple human infections and colorectal cancer. Strikingly, F. nucleatum achieves virulence in the absence of large, multiprotein secretion systems (Types I, II, III, IV, and VI), which are widely used by Gram-negative bacteria for pathogenesis. By contrast, F. nucleatum strains contain genomic expansions of Type V secreted effectors (autotransporters) that are critical for host cell adherence, invasion, and biofilm formation. Here, we present the first characterization of an F. nucleatum Type Vd phospholipase class A1 autotransporter (strain ATCC 25586, gene FN1704) that we hereby rename Fusobacterium phospholipase autotransporter (FplA). Biochemical analysis of multiple Fusobacterium strains revealed that FplA is expressed as a full-length 85-kDa outer membrane-embedded protein or as a truncated phospholipase domain that remains associated with the outer membrane. Whereas the role of Type Vd secretion in bacteria remains unidentified, we show that FplA binds with high affinity to host phosphoinositide-signaling lipids, revealing a potential role for this enzyme in establishing an F. nucleatum intracellular niche. To further analyze the role of FplA, we developed an fplA gene knock-out strain, which will guide future in vivo studies to determine its potential role in F. nucleatum pathogenesis. In summary, using recombinant FplA constructs, we have identified a biochemical toolbox that includes lipid substrates for enzymatic assays, potent inhibitors, and chemical probes to detect, track, and characterize the role of Type Vd secreted phospholipases in Gram-negative bacteria. DOI
723. Chin, EH; Schmidt, KL; Martel, KM; Wong, CK; Hamden, JE; Gibson, WT; Soma, KK; Christians, JK.A maternal high-fat, high-sucrose diet has sexspecific effects on fetal glucocorticoids with little consequence for offspring metabolism and voluntary locomotor activity in mice.PLoS One, 2017, 12 A maternal high-fat, high-sucrose diet has sexspecific effects on fetal glucocorticoids with little consequence for offspring metabolism and voluntary locomotor activity in mice
Maternal overnutrition and obesity during pregnancy can have long-term effects on offspring physiology and behaviour. These developmental programming effects may be mediated by fetal exposure to glucocorticoids, which is regulated in part by placental 11 beta-hydroxysteroid dehydrogenase (11 beta-HSD) type 1 and 2. We tested whether a maternal high-fat, high-sucrose diet would alter expression of placental 11 beta-HSD1 and 2, thereby increasing fetal exposure to maternal glucocorticoids, with downstream effects on offspring physiology and behaviour. C57BL/6J mice were fed a high-fat, high-sucrose (HFHS) diet or a nutrient-matched low-fat, no-sucrose control diet prior to and during pregnancy and lactation. At day 17 of gestation, HFHS dams had similar to 20% lower circulating corticosterone levels than controls. Furthermore, there was a significant interaction between maternal diet and fetal sex for circulating corticosterone levels in the fetuses, whereby HFHS males tended to have higher corticosterone than control males, with no effect in female fetuses. However, placental 11 beta-HSD1 or 11 beta-HSD2 expression did not differ between diets or show an interaction between diet and sex. To assess potential long-term consequences of this sex-specific effect on fetal corticosterone, we studied locomotor activity and metabolic traits in adult offspring. Despite a sex-specific effect of maternal diet on fetal glucocorticoids, there was little evidence of sex-specific effects on offspring physiology or behaviour, although HFHS offspring of both sexes had higher circulating corticosterone at 9 weeks of age. Our results suggest the existence of as yet unknown mechanisms that mitigate the effects of altered glucocorticoid exposure early in development, making offspring resilient to the potentially negative effects of a HFHS maternal diet. DOI
722. Choutka, C; DeVorkin, L; Go, NE; Hou, YCC; Moradian, A; Morin, GB; Gorski, SM.Hsp83 loss suppresses proteasomal activity resulting in an upregulation of caspase-dependent compensatory autophagy.Autophagy, 2017, 13: 1573-1589 Hsp83 loss suppresses proteasomal activity resulting in an upregulation of caspase-dependent compensatory autophagy
apoptosis; caspase; compensatory autophagy; Dcp-1; Drosophila; heat-shock protein; Hsp83; ubiquitin-proteasome system
The 2 main degradative pathways that contribute to proteostasis are the ubiquitin-proteasome system and autophagy but how they are molecularly coordinated is not well understood. Here, we demonstrate an essential role for an effector caspase in the activation of compensatory autophagy when proteasomal activity is compromised. Functional loss of Hsp83, the Drosophila ortholog of human HSP90 (heat shock protein 90), resulted in reduced proteasomal activity and elevated levels of the effector caspase Dcp-1. Surprisingly, genetic analyses showed that the caspase was not required for cell death in this context, but instead was essential for the ensuing compensatory autophagy, female fertility, and organism viability. The zymogen pro-Dcp-1 was found to interact with Hsp83 and undergo proteasomal regulation in an Hsp83-dependent manner. Our work not only reveals unappreciated roles for Hsp83 in proteasomal activity and regulation of Dcp-1, but identifies an effector caspase as a key regulatory factor for sustaining adaptation to cell stress in vivo. DOI
721. Christensen, KA; Davidson, WS.Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar).PLoS One, 2017, 12 Autopolyploidy genome duplication preserves other ancient genome duplications in Atlantic salmon (Salmo salar)
Salmonids (e.g. Atlantic salmon, Pacific salmon, and trouts) have a long legacy of genome duplication. In addition to three ancient genome duplications that all teleosts are thought to share, salmonids have had one additional genome duplication. We explored a methodology for untangling these duplications from each other to better understand them in Atlantic salmon. In this methodology, homeologous regions (paralogous/duplicated genomic regions originating from a whole genome duplication) from the most recent genome duplication were assumed to have duplicated genes at greater density and have greater sequence similarity. This assumption was used to differentiate duplicated gene pairs in Atlantic salmon that are either from the most recent genome duplication or from earlier duplications. From a comparison with multiple vertebrate species, it is clear that Atlantic salmon have retained more duplicated genes from ancient genome duplications than other vertebrates-often at higher density in the genome and containing fewer synonymous mutations. It may be that polysomic inheritance is the mechanism responsible for maintaining ancient gene duplicates in salmonids. Polysomic inheritance (when multiple chromosomes pair during meiosis) is thought to be relatively common in salmonids compared to other vertebrate species. These findings illuminate how genome duplications may not only increase the number of duplicated genes, but may also be involved in the maintenance of them from previous genome duplications as well. DOI
719. Cornell, A; Gibson, KF; Williams, TD.Physiological maturity at a critical life-history transition and flight ability at fledging.Functional Ecology, 2017, 31: 662-670 Physiological maturity at a critical life-history transition and flight ability at fledging
developmental maturity; fledging; flight ability; haemoglobin; life-history transition; physiology
<ol start="1" class="">
<li>Developmental maturity (e.g. body condition, body mass) at major life-history transitions is known to affect fitness across a wide range of taxa.</li>
<li>Fledging (leaving the nest), a major life-history transition in birds, is associated with high post-fledging mortality and is widely assumed to be related to poor initial flight ability of fledglings, which, in turn, might be related to developmental maturity at fledging.</li>
<li>We investigated individual variation in developmental maturity of both somatic and physiological traits at this critical life-history transition in different ecological contexts (year, first or second broods) to determine the importance of physiological traits related to oxygen-carrying capacity (haematocrit, haemoglobin) for individual variation in initial flight ability at fledging.</li>
<li>Haemoglobin concentration and haematocrit at fledging had much higher variance than somatic traits and were more variable across ecological contexts. Furthermore, fledgling haemoglobin concentration was the least developmentally mature of all traits (on average, only 78% of adult concentration).</li>
<li>Fledglings from second broods, which are known to have lower post-fledging survival, were less developmentally mature than fledglings from first broods for all traits (except tarsus), with haematocrit and haemoglobin concentration being the most developmentally immature traits (in first vs. second broods, haematocrit: 47·1% vs. 40·9%; haemoglobin: 13·3 vs. 11·6 g dL<sup>−1</sup>).</li>
<li>Models predicting individual variation in two aspects of initial flight ability (total energy gain, take-off angle) were significantly improved when physiological traits (in particular haemoglobin) were incorporated into models based on somatic traits.</li>
</ol> DOI
717. Crespi, BJ; Procyshyn, TL.Williams syndrome deletions and duplications: Genetic windows to understanding anxiety, sociality, autism, and schizophrenia.Neurosci. Biobehav. Rev., 2017, 79: 14-26 Williams syndrome deletions and duplications: Genetic windows to understanding anxiety, sociality, autism, and schizophrenia
Williams syndrome; Prosociality; Anxiety; Oxytocin; Autism; Schizophrenia
We describe and evaluate an integrative hypothesis for helping to explain the major neurocognitive features of individuals with Williams syndrome region deletions and duplications. First, we demonstrate how the cognitive differences between Williams syndrome individuals, individuals with duplications of this region, and healthy individuals parallel the differences between individuals subject to effects of increased or decreased oxytocin. Second, we synthesize evidence showing that variation in expression of the gene GTF2I (General Transcription Factor II-I) underlies the primary social phenotypes of Williams syndrome and that common genetic variation in GTF2I mediates oxytocin reactivity, and its correlates, in healthy populations. Third, we describe findings relevant to the hypothesis that the GTF2I gene is subject to parent of origin effects whose behavioral expression fits with predictions from the kinship theory of genomic imprinting. Fourth, we describe how Williams syndrome can be considered, in part, as an autistic syndrome of Lorna Wing's 'active-but-odd' autism subtype, in contrast to associations of duplications with both schizophrenia and autism. DOI
716. D'Aloia, CC; Daigle, RM; Côté, IM; Curtis, JMR; Guichard, F; Fortin, MJ.A multiple-species framework for integrating movement processes across life stages into the design of marine protected areas.Biol. Conserv., 2017, 216: 93-100 A multiple-species framework for integrating movement processes across life stages into the design of marine protected areas
Pelagic larval duration; Home range; Marxan; MPA; Movement; Larval dispersal
A major objective of marine protected area (MPA) network design is to ensure the persistence of species with diverse life histories and functional traits. Considering how species differ in their propensity to move within and between MPAs is therefore a key consideration for multi-species MPA network design. Here, we propose a conceptual framework to incorporate ecological processes that affect movement at multiple life stages into the MPA network design process. We illustrate how our framework can be implemented using a set of hypothetical species that represent regional trait diversity in coastal British Columbia, Canada. We focused on two ecological processes: (1) dispersal during the larval phase and (2) daily home range movement during the adult phase. To identify functional connectivity patterns, we used a biophysical model to simulate larval dispersal, and then prioritized highly-connected patches using a reserve selection algorithm. To ensure that individual reserves were commensurate with home ranges, we also imposed reserve size constraints. Candidate areas for protection were identified based on multi-species connectivity patterns and home range size constraints. Collectively, this conceptual framework offers a flexible approach to multi-species, cross-life stage conservation planning, which can be further adapted to address complex life histories. As marine conservation efforts around the globe aim to design ecologically connected networks of protected areas, the integration of movement and connectivity data throughout ontogeny will be a key component of effective multi-species MPA network design. DOI
715. Daigle, RM; Archambault, P; Halpern, BS; Lowndes, JSS; Côté, IM.Incorporating public priorities in the Ocean Health Index: Canada as a case study.PLoS One, 2017, 12 Incorporating public priorities in the Ocean Health Index: Canada as a case study
The Ocean Health Index (OHI) is a framework to assess ocean health by considering many benefits (called 'goals') provided by the ocean provides to humans, such as food provision, tourism opportunities, and coastal protection. The OHI framework can be used to assess marine areas at global or regional scales, but how various OHI goals should be weighted to reflect priorities at those scales remains unclear. In this study, we adapted the framework in two ways for application to Canada as a case study. First, we customized the OHI goals to create a national Canadian Ocean Health Index (COHI). In particular, we altered the list of iconic species assessed, added methane clathrates and subsea permafrost as carbon storage habitats, and developed a new goal, 'Aboriginal Needs', to measure access of Aboriginal people to traditional marine hunting and fishing grounds. Second, we evaluated various goal weighting schemes based on preferences elicited from the general public in online surveys. We quantified these public preferences in three ways: using Likert scores, simple ranks from a best-worst choice experiment, and model coefficients from the analysis of elicited choice experiment. The latter provided the clearest statistical discrimination among goals, and we recommend their use because they can more accurately reflect both public opinion and the trade-offs faced by policy-makers. This initial iteration of the COHI can be used as a baseline against which future COHI scores can be compared, and could potentially be used as a management tool to prioritise actions on a national scale and predict public support for these actions given that the goal weights are based on public priorities. DOI
714. Davidson, LNK; Dulvy, NK.Global marine protected areas to prevent extinctions.Nature Ecology & Evolution, 2017, 1 Global marine protected areas to prevent extinctions
One goal of global marine protected areas (MPAs) is to ensure they represent a breadth of taxonomic biodiversity. Ensuring representation of species in MPAs, however, would require protecting vast areas of the global oceans and does not explicitly prioritize species of conservation concern. When threatened species are considered, a recent study found that only a small fraction of their geographic ranges are within the global MPA network. Which global marine areas, and what conservation actions beyond MPAs could be prioritized to prevent marine extinctions (Convention on Biological Diversity Aichi Target 12), remains unknown. Here, we use systematic conservation planning approaches to prioritize conservation actions for sharks, rays and chimaeras (class Chondrichthyes). We use chondrichthyans as they have the highest proportion of threatened species of any marine class. We find that expanding the MPA network by 3% in 70 nations would cover half of the geographic range of 99 imperilled endemic chondrichthyans. Our hotspot analysis reveals that just 12 nations harbour more than half (53) of the imperilled endemics. Four of these hotspot nations are within the top ten chondrichthyan fishing nations in the world, but are yet to implement basic chondrichthyan fisheries management. Given their geopolitical realities, conservation action for some countries will require relief and reorganization to enable sustainable fisheries and species protection. DOI
712. Dulvy, NK; Simpfendorfer, CA; Davidson, LNK; Fordham, SV; Brautigam, A; Sant, G; Welch, DJ.Challenges and Priorities in Shark and Ray Conservation.Curr. Biol., 2017, 27: R565-R572 Challenges and Priorities in Shark and Ray Conservation
Sharks, rays, and chimaeras (Class Chondrichthyes; herein 'sharks') are the earliest extant jawed vertebrates and exhibit some of the greatest functional diversity of all vertebrates. Ecologically, they influence energy transfer vertically through trophic levels and sometimes trophic cascades via direct consumption and predation risk. Through movements and migrations, they connect horizontally and temporally across habitats and ecosystems, integrating energy flows at large spatial scales and across time. This connectivity flows from ontogenetic growth in size and spatial movements, which in turn underpins their relatively low reproductive rates compared with other exploited ocean fishes. Sharks are also ecologically and demographically diverse and are taken in a wide variety of fisheries for multiple products (e.g. meat, fins, teeth, and gills). Consequently, a range of fisheries management measures are generally preferable to 'silver bullet' and 'one size fits all' conservation actions. Some species with extremely low annual reproductive output can easily become endangered and hence require strict protections to minimize mortality. Other, more prolific species can withstand fishing over the long term if catches are subject to effective catch limits throughout the species' range. We identify, based on the IUCN Red List status, 64 endangered species in particular need of new or stricter protections and 514 species in need of improvements to fisheries management. We designate priority countries for such actions, recognizing the widely differing fishing pressures and conservation capacity. We hope that this analysis assists efforts to ensure this group of ecologically important and evolutionarily distinct animals can support both ocean ecosystems and human activities in the future. DOI
711. Dura, T; Horton, BP; Cisternas, M; Ely, LL; Hong, I; Nelson, AR; Wesson, RL; Pilarczyk, JE; Parnell, AC; Nikitina, D.Subduction zone slip variability during the last millennium, south-central Chile.Quat. Sci. Rev., 2017, 175: 112-137 Subduction zone slip variability during the last millennium, south-central Chile
Prehistoric earthquakes; Subduction zone segmentation; Tsunami deposits; Diatom paleoecology; Coastal paleoseismology; Coastal hazards
The Arauco Peninsula (37 degrees-38 degrees S) in south-central Chile has been proposed as a possible barrier to the along-strike propagation of megathrust ruptures, separating historical earthquakes to the south (1960 AD 1837, 1737, and 1575) and north (2010 AD, 1835, 1751, 1657, and 1570) of the peninsula. However, the 2010 (Mw 8.8) earthquake propagated into the Arauco Peninsula, re-rupturing part of the megathrust that had ruptured only 50 years earlier during the largest subduction zone earthquake in the instrumental record (M-w 9.5). To better understand long-term slip variability in the Arauco Peninsula region, we analyzed four coastal sedimentary sections from two sites (Tirua, 38.3 degrees S and Quidico, 38.1 degrees S) located within the overlap of the 2010 and 1960 ruptures to reconstruct a similar to 600-year record of coseismic land-level change and tsunami inundation. Stratigraphic, lithologic, and diatom results show variable coseismic land-level change coincident with tsunami inundation of the Tirua and Quidico marshes that is consistent with regional historical accounts of coseismic subsidence during earthquakes along the Valdivia portion of the subduction zone (1960 AD and 1575) and coseismic uplift during earthquakes along the Maule portion of the subduction zone (2010 AD, 1835, 1751). In addition, we document variable coseismic land-level change associated with three new prehistoric earthquakes and accompanying tsunamis in 1470-1570 AD, 1425-1455, and 270-410. The mixed record of coseismic subsidence and uplift that we document illustrates the variability of down-dip and lateral slip distribution at the overlap of the 2010 and 1960 ruptures, showing that ruptures have repeatedly propagated into, but not through the Arauco Peninsula and suggesting the area has persisted as a long-term impediment to slip through at least seven of the last megathrust earthquakes (similar to 600 years). (C) 2017 Elsevier Ltd. All rights reserved. DOI
710. Eichorn, C; Hrabar, M; Van Ryn, EC; Brodie, BS; Blake, AJ; Gries, G.How flies are flirting on the fly.BMC Biology, 2017, 15 How flies are flirting on the fly
Lucilia sericata; Mate location; Visual mate signals; Wing flashes; Flicker fusion frequency
Background: Flies have some of the most elaborate visual systems in the Insecta, often featuring large, sexually dimorphic eyes with specialized "bright zones" that may have a functional role during mate-seeking behavior. The fast visual system of flies is considered to be an adaptation in support of their advanced flight abilities. Here, we show that the immense processing speed of the flies' photoreceptors plays a crucial role in mate recognition. Results: Video-recording wing movements of abdomen-mounted common green bottle flies, Lucilia sericata, under direct light at 15,000 frames per second revealed that wing movements produce a single, reflected light flash per wing beat. Such light flashes were not evident when we video-recorded wing movements under diffuse light. Males of L. sericata are strongly attracted to wing flash frequencies of 178 Hz, which are characteristic of free-flying young females (prospective mates), significantly more than to 212, 235, or 266 Hz, characteristic of young males, old females, and old males, respectively. In the absence of phenotypic traits of female flies, and when given a choice between light emitting diodes that emitted either constant light or light pulsed at a frequency of 110, 178, 250, or 290 Hz, males show a strong preference for the 178-Hz pulsed light, which most closely approximates the wing beat frequency of prospective mates. Conclusions: We describe a previously unrecognized visual mate recognition system in L. sericata. The system depends upon the sex- and age-specific frequencies of light flashes reflecting off moving wings, and the ability of male flies to distinguish between the frequency of light flashes produced by rival males and prospective mates. Our findings imply that insect photoreceptors with fast processing speed may not only support agile flight with advanced maneuverability but may also play a supreme role in mate recognition. The low mating propensity of L. sericata males on cloudy days, when light flashes from the wings of flying females are absent, seems to indicate that these flies synchronize sexual communication with environmental conditions that optimize the conspicuousness of their communication signals, as predicted by sensory drive theory. DOI
709. Eng, ML; Bishop, CA; Crump, D; Jones, SP; Williams, TD; Drouillard, KG; Elliott, JE.Catbirds are the New Chickens: High Sensitivity to a Dioxin-like Compound in a Wildlife Species.Environ. Sci. Technol., 2017, 51: 5252-5258 Catbirds are the New Chickens: High Sensitivity to a Dioxin-like Compound in a Wildlife Species
Dioxins and dioxin-like compounds (DLCs) are highly toxic and persistent global pollutants with extremely large differences in sensitivity across taxonomic groups. The chicken has long been considered uniquely sensitive to DLCs among avian species; but DLC toxicity in nondomesticated birds is largely untested, and the relevance of the chicken as an ecological model is uncertain. New approaches that use genotyping of the AHR1 ligand binding domain to screen for DLC sensitivity among avian species predicted that the gray catbird, a relevant wildlife species, is also highly sensitive. We tested this prediction using egg injections of a dioxin-like PCB (PCB-126) and found that the catbird is at least as sensitive as the chicken to DLCs, based on both embryotoxicity and mRNA induction of phase I metabolizing enzymes (CYP1A4/5). This study is the first to confirm that there are wildlife species as sensitive as the chicken and demonstrates how using predictive genotyping methods and targeted bioassays can focus toxicity assessments on ecologically relevant species. DOI
708. Fernandes, PG; Ralph, GM; Nieto, A; Criado, MG; Vasilakopoulos, P; Maravelias, CD; Cook, RM; Pollom, RA; Kovacic, M; Pollard, D; Farrell, ED; Florin, AB; Polidoro, BA; Lawson, JM; Lorance, P; Uiblein, F; Craig, M; Allen, DJ; Fowler, SL; Walls, RHL; Comeros-Raynal, MT; Harvey, MS; Dureuil, M; Biscoito, M; Pollock, C; Phillips, SRM; Ellis, JR; Papaconstantinou, C; Soldo, A; Keskin, C; Knudsen, SW; de Sola, LG; Serena, F; Collette, BB; Nedreaas, K; Stump, E; Russell, BC; Garcia, S; Afonso, P; Jung, ABJ; Alvarez, H; Delgado, J; Dulvy, NK; Carpenter, KE.Coherent assessments of Europe's marine fishes show regional divergence and megafauna loss.Nature Ecology & Evolution, 2017, 1 Coherent assessments of Europe's marine fishes show regional divergence and megafauna loss
Europe has a long tradition of exploiting marine fishes and is promoting marine economic activity through its Blue Growth strategy. This increase in anthropogenic pressure, along with climate change, threatens the biodiversity of fishes and food security. Here, we examine the conservation status of 1,020 species of European marine fishes and identify factors that contribute to their extinction risk. Large fish species (greater than 1.5 m total length) are most at risk; half of these are threatened with extinction, predominantly sharks, rays and sturgeons. This analysis was based on the latest International Union for Conservation of Nature (IUCN) European regional Red List of marine fishes, which was coherent with assessments of the status of fish stocks carried out independently by fisheries management agencies: no species classified by IUCN as threatened were considered sustainable by these agencies. A remarkable geographic divergence in stock status was also evident: in northern Europe, most stocks were not overfished, whereas in the Mediterranean Sea, almost all stocks were overfished. As Europe proceeds with its sustainable Blue Growth agenda, two main issues stand out as needing priority actions in relation to its marine fishes: the conservation of marine fish megafauna and the sustainability of Mediterranean fish stocks. DOI
707. Flamarique, IN.A vertebrate retina with segregated colour and polarization sensitivity.Proceedings of the Royal Society B-Biological Sciences, 2017, 284 A vertebrate retina with segregated colour and polarization sensitivity
anchovy; optic nerve; cone photoreceptor; axial dichroism
Besides colour and intensity, some invertebrates are able to independently detect the polarization of light. Among vertebrates, such separation of visual modalities has only been hypothesized for some species of anchovies whose cone photoreceptors have unusual ultrastructure that varies with retinal location. Here, I tested this hypothesis by performing physiological experiments of colour and polarization discrimination using the northern anchovy, Engraulis mordax. Optic nerve recordings showed that the ventro-temporal (VT), but not the ventro-nasal (VN), retina was polarization sensitive, and this coincided with the exclusive presence of polarization-sensitive photoreceptors in the VT retina. Spectral (colour) sensitivity recordings from the VN retina indicated the contribution of two spectral cone mechanisms to the optic nerve response, whereas only one contributed to the VT retina. This was supported by the presence of only one visual pigment in the VT retina and two in the VN retina, suggesting that only the VN retina was associated with colour sensitivity. Behavioural tests further demonstrated that anchovies could discriminate colour and the polarization of light using the ventral retina. Thus, in analogy with the visual system of some invertebrates, the northern anchovy has a retina with segregated retinal pathways for colour and polarization vision. DOI
706. Fowler, MA; Williams, TD.A Physiological Signature of the Cost of Reproduction Associated with Parental Care.Am. Nat., 2017, 190: 762-773 A Physiological Signature of the Cost of Reproduction Associated with Parental Care
physiological cost of reproduction; workload; parental care; oxygen-carrying capacity; oxidative stress; energy
Costs of reproduction are an integral and long-standing component of life-history theory, but we still know relatively little about the specific physiological mechanisms underlying these trade-offs. We experimentally manipulated workload during parental care in female European starlings (Sturnus vulgaris) using attachment of radios and/or wing clipping and assessed measures of workload, current breeding productivity, future fecundity, and survival (local return rate) in relation to treatment. Females with wing clipping and radio attachment paid a clear cost of reproduction compared with all other treatment groups: they had lower future fecundity and lower return rates despite having lower current breeding productivity. We then measured 13 physiological traits, including measures of aerobic/metabolic capacity, oxidative stress and muscle damage, intermediary metabolism and energy supply, and immune function. Our results show that the cost of reproduction in females with wing clipping and radio attachment was associated with lower oxygen-carrying capacity (lower hematocrit and hemoglobin levels), lower energy reserves (plasma nonesterified fatty acid and triglyceride levels), decreased immune function (lower haptoglobin levels), and elevated levels of oxidative stress (higher levels of dROMs [reactive oxygen metabolites] and lower levels of the endogenous antioxidant uric acid). Our study provides evidence that costs of reproduction involve a widespread decline in physiological function across multiple physiological systems consistent with long-standing ideas of cumulative wear and tear and allostatic load. DOI
705. Friesen, OJ; Dashtgard, SE; Miller, J; Schmitt, L; Baldwin, C.Permeability heterogeneity in bioturbated sediments and implications for waterflooding of tight-oil reservoirs, Cardium Formation, Pembina Field, Alberta, Canada.Mar. Pet. Geol., 2017, 82: 371-387 Permeability heterogeneity in bioturbated sediments and implications for waterflooding of tight-oil reservoirs, Cardium Formation, Pembina Field, Alberta, Canada
Pembina Field; Cardium Formation; Ichnology; Permeability; Bioturbation; Stratigraphy
Bioturbated sediments recording distal expressions of paralic depositional environments are increasingly being exploited for hydrocarbons in the super-giant Pembina Field (Cardium Formation), Alberta, Canada. These strata were previously considered unproductive due to limited vertical and horizontal connectivity between permeable beds. In these "tight oil" plays (0.1-10 mD), pressure decay profile permeametry (micropermeability) data indicate that sand-filled burrows provide vertical permeable pathways between bioturbated and parallel-laminated sandstone beds in the central, northeast and northwest parts of the field. This relationship enables the economic exploitation of hydrocarbons via horizontal drilling and multi-stage hydraulic fracturing. As the exploitation of bioturbated strata progresses in the Pembina Field, additional primary targets are being sought out, and horizontal waterflooding is being considered in areas where horizontal wells exist. Proximal to historical produced conventional targets, reservoir analyses indicate that areas where the bioturbated facies average permeability lies between 035 mD and 0.85 mD and sandstone isopach thicknesses are between 0.25 m and 2.5 m should be targeted in east central Pembina. Micropermeability values enable correlation of bulk permeability from plugs and full-diameter samples to the heterogeneous permeability distributions in intensely bioturbated strata. Bulk and micro permeability data are graphically compared, and permeability distributions are mapped across the field. Using isopach thickness of bioturbated facies, production data, and permeability data, "sweet spots" are identified for placement of effective waterfioods. Production information for recently drilled horizontal wells in the Pembina Field demonstrate that bioturbated muddy sandstones and sandy mudstones in paralic environments can be economically exploited when sand-filled burrows provide connectivity between sand beds. However, well performance within these poorly understood unconventional tight oil plays can better be predicted with an in-depth characterization of their fades and complex permeability heterogeneities. Based on our results, it is clear that micropermeability analysis can be effectively employed to differentiate between economic and sub-economic plays, identify areas with high effective permeability, and high-grade areas for enhanced oil recovery schemes. (C) 2017 Elsevier Ltd. All rights reserved. DOI
704. Frishkof, LO; de Valpine, P; M'Gonigle, LK.Phylogenetic occupancy models integrate imperfect detection and phylogenetic signal to analyze community structure.Ecology, 2017, 98: 198-210 Phylogenetic occupancy models integrate imperfect detection and phylogenetic signal to analyze community structure
detectability; environmental gradient; hierarchical model; JAGS; phylogenetic generalized linear mixed effect model; phylogenetic diversity; phylogenetic occupancy model; trait-based
Biological communities are structured phylogenetically-closely related species are typically more likely to be found at the same sites. This may be, in part, because they respond similarly to environmental gradients. Accurately surveying biological communities is, however, made difficult by the fact that detection of species is not perfect. In recent years, numerous statistical methods have been developed that aim to overcome deficiencies in the species detection process. However, these methods do not allow investigators to assess phylogenetic community structure. Here, we introduce the phylogenetic occupancy model (POM), which accounts for imperfect species detection while assessing phylogenetic patterns in community structure. Using simulated data sets we show that the POM grants less biased estimates of phylogenetic structure than models without imperfect detection, and can correctly ascertain the effects of species traits on community composition while accounting for evolutionary non-independence of taxa. Integrating phylogenetic methods into widely used occupancy models will help clarify how evolutionary history influences modern day communities. DOI
703. Green, SJ; Demes, K; Arbeider, M; Palen, WJ; Salomon, AK; Sisk, TD; Webster, M; Ryan, ME.Oil sands and the marine environment: current knowledge and future challenges.Frontiers in Ecology and the Environment, 2017, 15: 74-83 Oil sands and the marine environment: current knowledge and future challenges
The environmental consequences of bitumen extraction from oil sands deposits are at the center of North American natural resource and energy policy debate, yet impacts on ocean environments have received little attention. Using a quantitative framework, we identify knowledge gaps and research needs related to the effects of oil sands development on marine biota. Fifteen sources of stress and disturbance - varying greatly in spatial and temporal scale - are generated via two pathways: (1) the coastal storage and oceanic transport of bitumen products, and (2) the contribution of industry-derived greenhouse gases to climate change in the ocean. Of highest research priority are the fate, behavior, and biological effects of bitumen in the ocean. By contrast, climate-change impacts are scientifically well established but not considered in key regulatory processes. Most stressors co-occur and are generated by other industries, yet cumulative effects are so far unaccounted for in decision making associated with new projects. Our synthesis highlights priority research needed to inform future energy development decisions, and opportunities for policy processes to acknowledge the full scope of potential and realized environmental consequences. DOI
702. Greenberg, DA; Palen, WJ; Mooers, AO.Amphibian species traits, evolutionary history and environment predict Batrachochytrium dendrobatidis infection patterns, but not extinction risk.Evol. Appl., 2017, 10: 1130-1145 Amphibian species traits, evolutionary history and environment predict Batrachochytrium dendrobatidis infection patterns, but not extinction risk
amphibian; Batrachochytrium dendrobatidis; chytridiomycosis; extinction; phylogeny; resistance; tolerance; traits
The fungal pathogen Batrachochytrium dendrobatidis (B.dendrobatidis) has emerged as a major agent of amphibian extinction, requiring conservation intervention for many susceptible species. Identifying susceptible species is challenging, but many aspects of species biology are predicted to influence the evolution of host resistance, tolerance, or avoidance strategies towards disease. In turn, we may expect species exhibiting these distinct strategies to differ in their ability to survive epizootic disease outbreaks. Here, we test for phylogenetic and trait-based patterns of B.dendrobatidis infection risk and infection intensity among 302 amphibian species by compiling a global data set of B.dendrobatidis infection surveys across 95 sites. We then use best-fit models that associate traits, taxonomy and environment with B.dendrobatidis infection risk and intensity to predict host disease mitigation strategies (tolerance, resistance, avoidance) for 122 Neotropical amphibian species that experienced epizootic B.dendrobatidis outbreaks, and noted species persistence or extinction from these events. Aspects of amphibian species life history, habitat use and climatic niche were consistently linked to variation in B.dendrobatidis infection patterns across sites around the world. However, predicted B.dendrobatidis infection risk and intensity based on site environment and species traits did not reveal a consistent pattern between the predicted host disease mitigation strategy and extinction outcome. This suggests that either tolerant or resistant species may have no advantage in ameliorating disease during epizootic events, or that other factors drive the persistence of amphibian populations during chytridiomycosis outbreaks. These results suggest that using a trait-based approach may allow us to identify species with resistance or tolerance to endemic B.dendrobatidis infections, but that this approach may be insufficient to ultimately identify species at risk of extinction from epizootics. DOI
701. Guenin, S; Hardouin, J; Paynel, F; Muller, K; Mongelard, G; Driouich, A; Lerouge, P; Kermode, AR; Lehner, A; Mollet, JC; Pelloux, J; Gutierrez, L; Mareck, A.AtPME3, a ubiquitous cell wall pectin methylesterase of Arabidopsis thaliana, alters the metabolism of cruciferin seed storage proteins during post-germinative growth of seedlings.Journal of Experimental Botany, 2017, 68: 1083-1095 AtPME3, a ubiquitous cell wall pectin methylesterase of Arabidopsis thaliana, alters the metabolism of cruciferin seed storage proteins during post-germinative growth of seedlings
Arabidopsis; AtPME3; CRUCIFERIN; etiolated hypocotyl; pectin methylesterase; seed germination; transcriptomic analyses
AtPME3 (At3g14310) is a ubiquitous cell wall pectin methylesterase. Atpme3-1 loss-of-function mutants exhibited distinct phenotypes from the wild type (WT), and were characterized by earlier germination and reduction of root hair production. These phenotypical traits were correlated with the accumulation of a 21.5-kDa protein in the different organs of 4-day-old Atpme3-1 seedlings grown in the dark, as well as in 6-week-old mutant plants. Microarray analysis showed significant down-regulation of the genes encoding several pectin-degrading enzymes and enzymes involved in lipid and protein metabolism in the hypocotyl of 4-day-old dark grown mutant seedlings. Accordingly, there was a decrease in proteolytic activity of the mutant as compared with the WT. Among the genes specifying seed storage proteins, two encoding CRUCIFERINS were up-regulated. Additional analysis by RT-qPCR showed an overexpression of four CRUCIFERIN genes in the mutant Atpme3-1, in which precursors of the alpha- and beta-subunits of CRUCIFERIN accumulated. Together, these results provide evidence for a link between AtPME3, present in the cell wall, and CRUCIFERIN metabolism that occurs in vacuoles. DOI
700. Hart, MW; Guerra, V.Finding genes and lineages under selection in speciation.Mol. Ecol., 2017, 26: 3587-3590 Finding genes and lineages under selection in speciation
echinoderm fertilization; positive selection; RNAseq; speciation
What are the genes and traits that respond to selection and cause prezygotic reproductive isolation between species? This question has been hard to answer because genomes are large, the targets of selection may be scattered across the genome (Sabeti et al., 2007) and different genes may respond to the same selective pressure in different populations (Scheinfeldt et al., 2012). In this issue of Molecular Ecology, Weber et al. (2017) use a clever comparative approach and leading-edge transcriptomic methods to identify the species and genes under positive selection for divergence between brittle stars (the echinoderm class Ophiuroidea) in the Ophioderma longicauda species complex. They found convincing evidence of positive or diversifying selection acting on two genes encoding ion channels that form part of the signal transduction cascade within the sperm in response to pheromones. Evidence for selection was concentrated in genes from one species (called C5, with internal fertilization and female parental care of brooded juveniles and not in the other species (called C3, with more conventional broadcast spawning and planktonic development of embryos and larvae). That analysis greatly extends the range of taxa, life history traits and molecules that are associated with positive selection in speciation. It also illustrates some of the current limitations on the application of RNAseq methods in the search for the targets of selection in nonmodel organisms like brittle stars. From both points of view, the new work by Weber et al. (2017) has important implications for our understanding of speciation in the ocean. DOI
699. Hussey, NE; DiBattista, JD; Moore, JW; Ward, EJ; Fisk, AT; Kessel, S; Guttridge, TL; Feldheim, KA; Franks, BR; Gruber, SH; Weideli, OC; Chapman, DD.Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions.Proceedings of the Royal Society B-Biological Sciences, 2017, 284 Risky business for a juvenile marine predator? Testing the influence of foraging strategies on size and growth rate under natural conditions
food web; lemon shark; life history; natural selection; predation risk; stable isotopes
Mechanisms driving selection of body size and growth rate in wild marine vertebrates are poorly understood, thus limiting knowledge of their fitness costs at ecological, physiological and genetic scales. Here, we indirectly tested whether selection for size-related traits of juvenile sharks that inhabit a nursery hosting two dichotomous habitats, protected mangroves (low predation risk) and exposed seagrass beds (high predation risk), is influenced by their foraging behaviour. Juvenile sharks displayed a continuum of foraging strategies between mangrove and seagrass areas, with some individuals preferentially feeding in one habitat over another. Foraging habitat was correlated with growth rate, whereby slower growing, smaller individuals fed predominantly in sheltered mangroves, whereas larger, faster growing animals fed over exposed seagrass. Concomitantly, tracked juveniles undertook variable movement behaviours across both the low and high predation risk habitat. These data provide supporting evidence for the hypothesis that directional selection favouring smaller size and slower growth rate, both heritable traits in this shark population, may be driven by variability in foraging behaviour and predation risk. Such evolutionary pathways may be critical to adaptation within predator-driven marine ecosystems. DOI
698. Hutchinson, I; Clague, J.Were they all giants? Perspectives on late Holocene plate-boundary earthquakes at the northern end of the Cascadia subduction zone.Quat. Sci. Rev., 2017, 169: 29-49 Were they all giants? Perspectives on late Holocene plate-boundary earthquakes at the northern end of the Cascadia subduction zone
Holocene; North America; Cascadia; Vancouver Island; Paleoseismology; Tsunamis; Radioogenic isotopes
The relative magnitude of plate-boundary earthquakes at the northern end of the Cascadia subduction zone was assessed from the temporal concordance between the ages of coseismically buried late Holocene soils in southwest Washington, their counterparts in central and southern Cascadia, offshore turbidites, and paleoseismic deposits on the west coast of Vancouver Island. Only three of the seven buried soils in southwest Washington that can be reliably traced as buried soils or paleotsunami deposits in the coastal lowlands of south-central and southern Cascadia have well-dated counterparts in northern Cascadia. The three wide-ranging events date from Cascadia earthquakes Y (similar to 250 cal BP), U (similar to 1260 cal BP), and N (similar to 2520 cal BP). All three likely ruptured the entire plate margin, and therefore potentially qualify as "giants" (M-w >= 9). Deposits that may derive from tsunamis generated by earthquakes S (similar to 1570 cal BP), L (similar to 2870 cal BP) and J (similar to 3360 cal BP) can also be found in northern Cascadia, but the ages of these deposits are not yet well-enough constrained to determine whether they are coeval with their southern counterparts. Earthquake W (similar to 850 cal BP), appears to be present in the northern Cascadia paleoseismic record, but yields considerably older ages than in central Cascadia, and may be missing from southernmost Cascadia. The onshore record of an offshore turbidite (12) displays a similar spatiotemporal pattern to that of earthquake W. (C) 2017 Elsevier Ltd. All rights reserved. DOI
697. Jensen, VL; Leroux, MR.Gates for soluble and membrane proteins, and two trafficking systems (IFT and LIFT), establish a dynamic ciliary signaling compartment.Curr. Opin. Cell Biol., 2017, 47: 83-91 Gates for soluble and membrane proteins, and two trafficking systems (IFT and LIFT), establish a dynamic ciliary signaling compartment
Primary cilia are microtubule-based organelles found on most mammalian cell surfaces. They possess a soluble matrix and membrane contiguous with the cell body cytosol and plasma membrane, and yet, have distinct compositions that can be modulated to enable dynamic signal transduction. Here, we discuss how specialized ciliary compartments are established using a coordinated network of gating, trafficking and targeting activities. Cilium homeostasis is maintained by a size-selective molecular mesh that limits soluble protein entry, and by a membrane diffusion barrier localized at the transition zone. Bidirectional protein shuttling between the cell body and cilium uses IntraFlagellar Transport (IFT), and prenylated ciliary protein delivery is achieved through Lipidated protein IntraFlagellar Targeting (LIFT). Elucidating how these gates and transport systems function will help reveal the roles that cilia play in ciliary signaling and the growing spectrum of disorders termed ciliopathies. DOI
696. Jones, MR; Mathieu, E; Dyrager, C; Faissner, S; Vaillancourt, Z; Korshavn, KJ; Lim, MH; Ramamoorthy, A; Yong, VW; Tsutsui, S; Stys, PK; Storr, T.Multi-target-directed phenol-triazole ligands as therapeutic agents for Alzheimer's disease.Chem. Sci., 2017, 8: 5636-5643 Multi-target-directed phenol-triazole ligands as therapeutic agents for Alzheimer's disease
Alzheimer's disease (AD) is a multifactorial disease that is characterized by the formation of intracellular neurofibrillary tangles and extracellular amyloid-beta (A beta) plaque deposits. Increased oxidative stress, metal ion dysregulation, and the formation of toxic A beta peptide oligomers are all considered to contribute to the etiology of AD. In this work we have developed a series of ligands that are multi-target-directed in order to address several disease properties. 2-(1-(3-Hydroxypropyl)-1H-1,2,3-triazol-4-yl) phenol (POH), 2-(1-(2-morpholinoethyl)-1H-1,2,3-triazol-4-yl) phenol (PMorph), and 2-(1-(2-thiomorpholinoethyl)-1H-1,2,3-triazol-4-yl) phenol (PTMorph) have been synthesized and screened for their antioxidant capacity, Cu-binding affinity, interaction with the A beta peptide and modulation of A beta peptide aggregation, and the ability to limit A beta(1-42)-induced neurotoxicity in human neuronal culture. The synthetic protocol and structural variance incorporated via click chemistry, highlights the influence of R-group modification on ligand-A beta interactions and neuroprotective effects. Overall, this study demonstrates that the phenoltriazole ligand scaffold can target multiple factors associated with AD, thus warranting further therapeutic development. DOI PubMed
694. Kiguoya, MW; Mann, JK; Chopera, D; Gounder, K; Lee, GQ; Hunt, PW; Martin, JN; Ball, TB; Kimani, J; Brumme, ZL; Brockman, MA; Ndung'u, T.Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression.J. Virol., 2017, 91 Subtype-Specific Differences in Gag-Protease-Driven Replication Capacity Are Consistent with Intersubtype Differences in HIV-1 Disease Progression
HIV-1 subtype; Gag-protease; viral replication capacity
There are marked differences in the spread and prevalence of HIV-1 subtypes worldwide, and differences in clinical progression have been reported. However, the biological reasons underlying these differences are unknown. Gag-protease is essential for HIV-1 replication, and Gag-protease-driven replication capacity has previously been correlated with disease progression. We show that Gag-protease replication capacity correlates significantly with that of whole isolates (r = 0.51; P = 0.04), indicating that Gag-protease is a significant contributor to viral replication capacity. Furthermore, we investigated subtype-specific differences in Gag-protease driven replication capacity using large well-characterized cohorts in Africa and the Americas. Patient-derived Gag-protease sequences were inserted into an HIV-1 NL4-3 backbone, and the replication capacities of the resulting recombinant viruses were measured in an HIV-1-inducible reporter T cell line by flow cytometry. Recombinant viruses expressing subtype C Gag-proteases exhibited substantially lower replication capacities than those expressing subtype B Gag-proteases (P < 0.0001); this observation remained consistent when representative Gag-protease sequences were engineered into an HIV-1 subtype C backbone. We identified Gag residues 483 and 484, located within the Alix-binding motif involved in virus budding, as major contributors to subtype-specific replicative differences. In East African cohorts, we observed a hierarchy of Gag-protease-driven replication capacities, i.e., subtypes A/C < D < intersubtype recombinants (P < 0.0029), which is consistent with reported intersubtype differences in disease progression. We thus hypothesize that the lower Gag protease-driven replication capacity of subtypes A and C slows disease progression in individuals infected with these subtypes, which in turn leads to greater opportunity for transmission and thus increased prevalence of these subtypes. IMPORTANCE HIV-1 subtypes are unevenly distributed globally, and there are reported differences in their rates of disease progression and epidemic spread. The biological determinants underlying these differences have not been fully elucidated. Here, we show that HIV-1 Gag-protease-driven replication capacity correlates with the replication capacity of whole virus isolates. We further show that subtype B displays a significantly higher Gag-protease-mediated replication capacity than does subtype C, and we identify a major genetic determinant of these differences. Moreover, in two independent East African cohorts we demonstrate a reproducible hierarchy of Gag-protease-driven replicative capacity, whereby recombinants exhibit the greatest replication, followed by subtype D, followed by subtypes A and C. Our data identify Gag-protease as a major determinant of subtype differences in disease progression among HIV-1 subtypes; furthermore, we propose that the poorer viral replicative capacity of subtypes A and C may paradoxically contribute to their more efficient spread in sub-Saharan Africa. DOI
693. Kindsvater, HK; Reynolds, JD; de Mitcheson, YS; Mangel, M.Selectivity matters: Rules of thumb for management of plate-sized, sex-changing fish in the live reef food fish trade.Fish. Fish., 2017, 18: 821-836 Selectivity matters: Rules of thumb for management of plate-sized, sex-changing fish in the live reef food fish trade
capture-based aquaculture; egg limitation; fishery selectivity; live reef food fish; protogynous hermaphrodite; spawning potential ratio
Effective management of fisheries depends on the selectivity of different fishing methods, control of fishing effort and the life history and mating system of the target species. For sex-changing species, it is unclear how the truncation of age-structure or selection of specific size or age classes (by fishing for specific markets) affects population dynamics. We specifically address the consequences of plate-sized selectivity, whereby submature, plate-sized fish are preferred in the live reef food fish trade. We use an age-structured model to investigate the decline and recovery of populations fished with three different selectivity scenarios (asymptotic, dome-shaped and plate-sized) applied to two sexual systems (female-first hermaphroditism and gonochorism). We parameterized our model with life-history data from Brown-marbled grouper (Epinephelus fuscoguttatus) and Napoleon fish (Cheilinus undulatus). Plate-sized selectivity had the greatest negative effect on population trajectories, assuming accumulated fishing effort across ages was equal, while the relative effect of fishing on biomass was greatest with low natural mortality. Fishing such sex-changing species before maturation decreased egg production (and the spawning potential ratio) in two ways: average individual size decreased and, assuming plasticity, females became males at a smaller size. Somatic growth rate affected biomass if selectivity was based on size at age because in slow growers, a smaller proportion of total biomass was vulnerable to fishing. We recommend fisheries avoid taking individuals near their maturation age, regardless of mating system, unless catch is tightly controlled. We also discuss the implications of fishing post-settlement individuals on population dynamics and offer practical management recommendations. DOI
692. Lambinet, V; Hayden, ME; Reigl, K; Gomis, S; Gries, G.Linking magnetite in the abdomen of honey bees to a magnetoreceptive function.Proceedings of the Royal Society B-Biological Sciences, 2017, 284 Linking magnetite in the abdomen of honey bees to a magnetoreceptive function
honey bees; magnetoreception; magnetic sense; magnetite; hysteresis loop; magnetic remanence
Previous studies of magnetoreception in honey bees, Apis mellifera, focused on the identification of magnetic material, its formation, the location of the receptor and potential underlying sensory mechanisms, but never directly linked magnetic material to a magnetoreceptive function. In our study, we demonstrate that ferromagnetic material consistent with magnetite plays an integral role in the bees' magnetoreceptor. Subjecting lyophilized and pelletized bee tagmata to analyses by a superconducting quantum interference device generated a distinct hysteresis loop for the abdomen but not for the thorax or the head of bees, indicating the presence of ferromagnetic material in the bee abdomen. Magnetic remanence of abdomen pellets produced from bees that were, or were not, exposed to the 2.2-kOe field of a magnet while alive differed, indicating that magnet exposure altered the magnetization of this magnetite in live bees. In behavioural two-choice field experiments, bees briefly exposed to the same magnet, but not sham-treated control bees, failed to sense a custom-generated magnetic anomaly, indicating that magnet exposure had rendered the bees' magnetoreceptor dysfunctional. Our data support the conclusion that honey bees possess a magnetite-based magnetoreceptor located in the abdomen. DOI
691. Lascar, D; Klawitter, R; Babcock, C; Leistenschneider, E; Stroberg, SR; Barquest, BR; Finlay, A; Foster, M; Gallant, AT; Hunt, P; Kelly, J; Kootte, B; Lan, Y; Paul, SF; Phan, ML; Reiter, MP; Schultz, B; Short, D; Simonis, J; Andreoiu, C; Brodeur, M; Dillmann, I; Gwinner, G; Holt, JD; Kwiatkowski, AA; Leach, KG; Dilling, J.Precision mass measurements of Cd125-127 isotopes and isomers approaching the N=82 closed shell.Phys. Rev. C, 2017, 96 Precision mass measurements of Cd125-127 isotopes and isomers approaching the N=82 closed shell
We present the results of precision mass measurements of neutron-rich cadmium isotopes. These nuclei approach the N = 82 closed neutron shell and are important to nuclear structure as they lie near doubly magic Sn-132 on the chart of nuclides. Of particular note is the clear identification of the ground-state mass in Cd-127 along with the isomeric state. We show that the ground state identified in a previous mass measurement which dominates the mass value in the Atomic Mass Evaluation is an isomeric state. In addition to Cd-127/m, we present other cadmium masses measured (Cd-125/m and Cd-126) in a recent TITAN experiment at TRIUMF. Finally, we compare our measurements to new ab initio shell-model calculations and comment on the state of the field in the N = 82 region. DOI
690. Lawson, JM; Fordham, SV; O'Malley, MP; Davidson, LNK; Walls, RHL; Heupel, MR; Stevens, G; Fernando, D; Budziak, A; Simpfendorfer, CA; Ender, I; Francis, MP; di Sciara, GN; Dulvy, NK.Sympathy for the devil: a conservation strategy for devil and manta rays.PeerJ, 2017, 5 Sympathy for the devil: a conservation strategy for devil and manta rays
Elasmobranch; Conservation planning; Convention on the International Trade in Endangered Species (CITES); Convention on the Conservation of Migratory Species of Wild Animals (CMS); Extinction risk International Union for the Conservation of Nature (IUCN); Multilateral Environmental Agreements (MEAs); Tourism; Wildlife trade; Charismatic species
Background. International trade for luxury products, medicines, and tonics poses a threat to both terrestrial and marine wildlife. The demand for and consumption of gill plates (known as Peng Yu Sai, "Fish Gill of Mobulid Ray") from devil and manta rays (subfamily Mobulinae, collectively referred to as mobulids) poses a significant threat to these marine fishes because of their extremely low productivity. The demand for these gill plates has driven an international trade supplied by largely unmonitored and unregulated catches from target, and incidental fisheries around the world. Scientific research, conservation campaigns, and legal protections for devil rays have lagged behind those for manta rays despite similar threats across all mobufids. Methods. To investigate the difference in attention given to devil rays and manta rays, we examined trends in the scientific literature and updated species distribution maps for all mobufids. Using available information on target and incidental fisheries, and gathering information on fishing and trade regulations (at international, national, and territorial levels), we examined how threats and protective measures overlap with species distribution. We then used a species conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the knowledge and protection of both devil and manta rays. Results and Discussion. Our literature review revealed that there had been nearly 2.5-times more "manta"-titled publications, than "mobula" or "devil ray"-titled publications over the Past 4.5 years (January 2012 June 2016). The majority of these recent publications were reports on occurrence of mobulid species. These publications contributed to updated Area of Occupancy and Extent of Occurrence maps which showed expanded distributions for most mobulid species and overlap between the two genera. While several international protections have recently expanded to include all mobulids, there remains a greater number of national, state, and territory-level protections for manta rays compared to devil rays. We hypothesize that there are fewer scientific publications and regulatory protections for devil rays due primarily to perceptions of charisma that favour manta rays. We suggest that the well-established species conservation framework used here offers an objective solution to close this gap. To advance the goals of the conservation strategy we highlight opportunities for parity in protection and suggest solutions to help reduce target and by catch fisheries. DOI
689. Leung, B; Greenberg, DA; Green, DM.Trends in mean growth and stability in temperate vertebrate populations.Divers. Distrib., 2017, 23: 1372-1380 Trends in mean growth and stability in temperate vertebrate populations
amphibian declines; biodiversity crisis; ecological instability; population trends; temperate biodiversity; vertebrate conservation
Aim: Considerable controversy exists over the nature of the "Biodiversity Crisis." While some studies suggest declining diversity, others suggest no loss on average. Population declines necessarily precede species loss and may therefore be a more sensitive metric. We examine trends in abundances to test the hypotheses: (1) losses are experienced disproportionately by some taxa, in particular amphibians; (2) positive trends in alien or unexploited species mask declines in native or exploited species, respectively; (3) populations are becoming more unstable, and variances of within-population growth rates are increasing. Location: Freshwater and terrestrial habitats in North America and Europe. Methods: We analysed abundances of 4,343 population time series of 983 species of temperate amphibians, birds, bony fishes, reptiles and mammals from 1970 to 2014. Population mean trends were estimated using a state-space model to account for observation error, and then, linear mixed-effects models were used to test mean differences among groups. As a measure of instability, trends over time in variance of population growth rates were analysed using a Breusch-Pagan test for heteroscedacity, and integrated across populations using meta-analysis. Results: Mean trends for amphibians suggested a systematic decline, whereas birds, reptiles and mammals were increasing, on average, and freshwater fishes showed no net change in general. Origin and exploitation status did not explain the mean patterns. Large-bodied birds and range-restricted mammals exhibited stronger increases compared to their counterparts. For all taxonomic groups, population fluctuations have been increasing overall. Main conclusions: Addressing amphibian declines should be a priority in temperate regions. Comparatively, the lack of broad declines in the other vertebrate classes is promising and not attributable to increases in alien or non-exploited species. Yet, caution remains warranted given that patterns of increasing variance suggested that populations are generally becoming more unstable, even in temperate, developed nations, with arguably the strongest environmental regulations. DOI
688. Lewthwaite, JMM; Debinski, DM; Kerr, JT.High community turnover and dispersal limitation relative to rapid climate change.Global Ecology and Biogeography, 2017, 26: 459-471 High community turnover and dispersal limitation relative to rapid climate change
Beta diversity; Canada; climate change; community composition; conservation; dispersal; macroecology; species turnover; temperature
Aim Many competing hypotheses seek to identify the mechanisms behind species richness gradients. Yet, the determinants of species turnover over broad scales are uncertain. We test whether environmental dissimilarity predicts biotic turnover spatially and temporally across an array of environmental variables and spatial scales using recently observed climate changes as a pseudo-experimental opportunity. Location Canada. Methods We used an extensive database of observation records of 282 Canadian butterfly species collected between 1900 and 2010 to characterize spatial and temporal turnover based on Jaccard indices. We compare relationships between spatial turnover and differences in an array of relevant environmental conditions, including aspects of temperature, precipitation, elevation, primary productivity and land cover. Measurements were taken within 100-, 200- and 400-km grid cells, respectively. We tested the relative importance of each variable in predicting spatial turnover using bootstrap analysis. Finally, we tested for effects of temperature and precipitation change on temporal turnover, including distinctly accounting for turnover under individual species' potential dispersal limitations. Results Temperature differences between areas correlate with spatial turnover in butterfly assemblages, independently of distance, sampling differences or the spatial resolution of the analysis. Increasing temperatures are positively related to biotic turnover within quadrats through time. Limitations on species dispersal may cause observed biotic turnover to be lower than expected given the magnitude of temperature changes through time. Main conclusions Temperature differences can account for spatial trends in biotic dissimilarity and turnover through time in areas where climate is changing. Butterfly communities are changing quickly in some areas, probably reflecting the dispersal capacities of individual species. However, turnover is lower through time than expected in many areas, suggesting that further work is needed to understand the factors that limit dispersal across broad regions. Our results illustrate the large-scale effects of climate change on biodiversity in areas with strong environmental gradients. DOI
687. Lichtenberg, EM; Kennedy, CM; Kremen, C; Batary, P; Berendse, F; Bommarco, R; Bosque-Perez, NA; Carvalheiro, LG; Snyder, WE; Williams, NM; Winfree, R; Klatt, BK; Astrom, S; Benjamin, F; Brittain, C; Chaplin-Kramer, R; Clough, Y; Danforth, B; Diekotter, T; Eigenbrode, SD; Ekroos, J; Elle, E; Freitas, BM; Fukuda, Y; Gaines-Day, HR; Grab, H; Gratton, C; Holzschuh, A; Isaacs, R; Isaia, M; Jha, S; Jonason, D; Jones, VP; Klein, AM; Krauss, J; Letourneau, DK; Macfadyen, S; Mallinger, RE; Martin, EA; Martinez, E; Memmott, J; Morandin, L; Neame, L; Otieno, M; Park, MG; Pfiffner, L; Pocock, MJO; Ponce, C; Potts, SG; Poveda, K; Ramos, M; Rosenheim, JA; Rundlof, M; Sardinas, H; Saunders, ME; Schon, NL; Sciligo, AR; Sidhu, CS; Steffan-Dewenter, I; Tscharntke, T; Vesely, M; Weisser, WW; Wilson, JK; Crowder, DW.A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes.Global Change Biology, 2017, 23: 4946-4957 A global synthesis of the effects of diversified farming systems on arthropod diversity within fields and across agricultural landscapes
agricultural management schemes; arthropod diversity; biodiversity; evenness; functional groups; landscape complexity; meta-analysis; organic farming; plant diversity
Agricultural intensification is a leading cause of global biodiversity loss, which can reduce the provisioning of ecosystem services in managed ecosystems. Organic farming and plant diversification are farm management schemes that may mitigate potential ecological harm by increasing species richness and boosting related ecosystem services to agroecosystems. What remains unclear is the extent to which farm management schemes affect biodiversity components other than species richness, and whether impacts differ across spatial scales and landscape contexts. Using a global metadataset, we quantified the effects of organic farming and plant diversification on abundance, local diversity (communities within fields), and regional diversity (communities across fields) of arthropod pollinators, predators, herbivores, and detritivores. Both organic farming and higher in-field plant diversity enhanced arthropod abundance, particularly for rare taxa. This resulted in increased richness but decreased evenness. While these responses were stronger at local relative to regional scales, richness and abundance increased at both scales, and richness on farms embedded in complex relative to simple landscapes. Overall, both organic farming and in-field plant diversification exerted the strongest effects on pollinators and predators, suggesting these management schemes can facilitate ecosystem service providers without augmenting herbivore (pest) populations. Our results suggest that organic farming and plant diversification promote diverse arthropod metacommunities that may provide temporal and spatial stability of ecosystem service provisioning. Conserving diverse plant and arthropod communities in farming systems therefore requires sustainable practices that operate both within fields and across landscapes. DOI
686. Lonn, E; Koskela, E; Mappes, T; Mokkonen, M; Sims, AM; Watts, PC.Balancing selection maintains polymorphisms at neurogenetic loci in field experiments.Proc. Natl. Acad. Sci. U. S. A., 2017, 114: 3690-3695 Balancing selection maintains polymorphisms at neurogenetic loci in field experiments
Avpr1a; Oxtr; sexual conflict; density-dependent selection; Myodes glareolus
Most variation in behavior has a genetic basis, but the processes determining the level of diversity at behavioral loci are largely unknown for natural populations. Expression of arginine vasopressin receptor 1a (Avpr1a) and oxytocin receptor (Oxtr) in specific regions of the brain regulates diverse social and reproductive behaviors in mammals, including humans. That these genes have important fitness consequences and that natural populations contain extensive diversity at these loci implies the action of balancing selection. In Myodes glareolus, Avpr1a and Oxtr each contain a polymorphic microsatellite locus located in their 5' regulatory region (the regulatory region-associated microsatellite, RRAM) that likely regulates gene expression. To test the hypothesis that balancing selection maintains diversity at behavioral loci, we released artificially bred females and males with different RRAM allele lengths into field enclosures that differed in population density. The length of Avpr1a and Oxtr RRAMs was associated with reproductive success, but population density and the sex interacted to determine the optimal genotype. In general, longer Avpr1a RRAMs were more beneficial for males, and shorter RRAMs were more beneficial for females; the opposite was true for Oxtr RRAMs. Moreover, Avpr1a RRAM allele length is correlated with the reproductive success of the sexes during different phases of reproduction; for males, RRAM length correlated with the numbers of newborn offspring, but for females selection was evident on the number of weaned offspring. This report of density- dependence and sexual antagonism acting on loci within the arginine vasopressin- oxytocin pathway explains how genetic diversity at Avpr1a and Oxtr could be maintained in natural populations. DOI
685. Macdonald, C; Gallagher, AJ; Barnett, A; Brunnschweiler, J; Shiffman, DS; Hammerschlag, N.Conservation potential of apex predator tourism.Biol. Conserv., 2017, 215: 132-141 Conservation potential of apex predator tourism
Predator; Ecotourism; Wildlife; Tourism; Conservation tools; Carnivores; Sharks; Crocodiles; Big cats
In recent decades, public interest in apex predators has led to the creation and expansion of predator-focused wildlife tourism. As wildlife tourism has become an increasing topic of study for both social and biological scientists, researchers have debated whether these activities serve conservation goals by providing non-consumptive values for wildlife. Discussion of predator tourism requires additional recognition of predator-specific biological and ecological characteristics, consideration of human safety concerns, and mitigation of human wildlife conflict. By reviewing tourism activities centered on both aquatic and terrestrial predators from diverse taxa (sharks, crocodiles, and big cats), we evaluate the potential benefits and conservation challenges associated with predator tourism. Our review suggests that positive conservation outcomes are possible, but not assured given historical, cultural, and ecological complexities. We explore some of the factors which determine whether tourism contributes to conservation outcomes, including (1) effective protection of animals and habitats, (2) avoidance and mitigation of human-wildlife conflict, (3) quality of associated educational interpretation and outreach, (4) collaboration with local stakeholders, and (5) use of generated funds to advance conservation goals. Our findings suggest tourism is most likely to support predator conservation and/or recovery when the industry has both public and political support and under conditions of effective regulation focused on management, monitoring and enforcement by local, national, and international bodies. DOI
684. Macqueen, DJ; Primmer, CR; Houston, RD; Nowak, BF; Bernatchez, L; Bergseth, S; Davidson, WS; Gallardo-Escarate, C; Goldammer, T; Guiguen, Y; Iturra, P; Kijas, JW; Koop, BF; Lien, S; Maass, A; Martin, SAM; McGinnity, P; Montecino, M; Naish, KA; Nichols, KM; Olafsson, K; Omholt, SW; Palti, Y; Plastow, GS; Rexroad, CE; Rise, ML; Ritchie, RJ; Sandve, SR; Schulte, PM; Tello, A; Vidal, R; Vik, JO; Wargelius, A; Yanez, JM.Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture.BMC Genomics, 2017, 18 Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture
Salmonid fish; Genome biology; Functional annotation; Comparative biology; Standardized data and metadata; Data sharing; Aquaculture; Whole genome duplication; Evolution; Phenotyping
We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic variation. The outcomes of FAASG will have diverse applications, ranging from improved understanding of genome evolution, to improving the efficiency and sustainability of aquaculture production, supporting the future of fundamental and applied research in an iconic fish lineage of major societal importance. DOI
682. Mazel, F; Mooers, AO; Dalla Riva, GV; Pennell, MW.Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity.Syst. Biol., 2017, 66: 1019-1027 Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity
Conservation; evolutionary diversity; functional diversity; species prioritization; trait evolution
For decades, academic biologists have advocated for making conservation decisions in light of evolutionary history. Specifically, they suggest that policy makers should prioritize conserving phylogenetically diverse assemblages. The most prominent argument is that conserving phylogenetic diversity (PD) will also conserve diversity in traits and features (functional diversity [FD]), which may be valuable for a number of reasons. The claim that PD-maximized ("maxPD") sets of taxa will also have high FD is often taken at face value and in cases where researchers have actually tested it, they have done so by measuring the phylogenetic signal in ecologically important functional traits. The rationale is that if traits closely mirror phylogeny, then saving the maxPD set of taxa will tend to maximize FD and if traits do not have phylogenetic structure, then saving the maxPD set of taxa will be no better at capturing FD than criteria that ignore PD. Here, we suggest that measuring the phylogenetic signal in traits is uninformative for evaluating the effectiveness of using PD in conservation. We evolve traits under several different models and, for the first time, directly compare the FD of a set of taxa that maximize PD to the FD of a random set of the same size. Under many common models of trait evolution and tree shapes, conserving the maxPD set of taxa will conserve more FD than conserving a random set of the same size. However, this result cannot be generalized to other classes of models. We find that under biologically plausible scenarios, using PD to select species can actually lead to less FD compared with a random set. Critically, this can occur even when there is phylogenetic signal in the traits. Predicting exactly when we expect using PD to be a good strategy for conserving FD is challenging, as it depends on complex interactions between tree shape and the assumptions of the evolutionary model. Nonetheless, if our goal is to maintain trait diversity, the fact that conserving taxa based on PD will not reliably conserve at least as much FD as choosing randomly raises serious concerns about the general utility of PD in conservation. DOI
681. Menounos, B; Goehring, BM; Osborn, G; Margold, M; Ward, B; Bond, J; Clarke, GKC; Clague, JJ; Lakeman, T; Koch, J; Caffee, MW; Gosse, J; Stroeven, AP; Seguinot, J; Heyman, J.Cordilleran Ice Sheet mass loss preceded climate reversals near the Pleistocene Termination.Science, 2017, 358: 781-784 Cordilleran Ice Sheet mass loss preceded climate reversals near the Pleistocene Termination
The Cordilleran Ice Sheet (CIS) once covered an area comparable to that of Greenland. Previous geologic evidence and numerical models indicate that the ice sheet covered much of westernmost Canada as late as 12.5 thousand years ago (ka). New data indicate that substantial areas throughout westernmost Canada were ice free prior to 12.5 ka and some as early as 14.0 ka, with implications for climate dynamics and the timing of meltwater discharge to the Pacific and Arctic oceans. Early Bolling-Allerod warmth halved the mass of the CIS in as little as 500 years, causing 2.5 to 3.0 meters of sea-level rise. Dozens of cirque and valley glaciers, along with the southern margin of the CIS, advanced into recently deglaciated regions during the Bolling-Allerod and Younger Dryas. DOI PubMed
680. Moeller, DA; Runquist, RDB; Moe, AM; Geber, MA; Goodwillie, C; Cheptou, PO; Eckert, CG; Elle, E; Johnston, MO; Kalisz, S; Ree, RH; Sargent, RD; Vallejo-Marin, M; Winn, AA.Global biogeography of mating system variation in seed plants.Ecology Letters, 2017, 20: 375-384 Global biogeography of mating system variation in seed plants
Biotic interactions; breeding system; floral evolution; latitudinal gradient; life history; outcrossing; plant-pollinator interaction; pollination; self-fertilisation; sexual system
Latitudinal gradients in biotic interactions have been suggested as causes of global patterns of biodiversity and phenotypic variation. Plant biologists have long speculated that outcrossing mating systems are more common at low than high latitudes owing to a greater predictability of plant-pollinator interactions in the tropics; however, these ideas have not previously been tested. Here, we present the first global biogeographic analysis of plant mating systems based on 624 published studies from 492 taxa. We found a weak decline in outcrossing rate towards higher latitudes and among some biomes, but no biogeographic patterns in the frequency of self-incompatibility. Incorporating life history and growth form into biogeographic analyses reduced or eliminated the importance of latitude and biome in predicting outcrossing or self-incompatibility. Our results suggest that biogeographic patterns in mating system are more likely a reflection of the frequency of life forms across latitudes rather than the strength of plant-pollinator interactions. DOI
679. Monroe, MJ; Bokma, F.Does density-dependent diversification mirror ecological competitive exclusion?PLoS One, 2017, 12 Does density-dependent diversification mirror ecological competitive exclusion?
Density-dependence is a term used in ecology to describe processes such as birth and death rates that are regulated by the number of individuals in a population. Evolutionary biologists have borrowed the term to describe decreasing rates of species accumulation, suggesting that speciation and extinction rates depend on the total number of species in a clade. If this analogy with ecological density-dependence holds, diversification of clades is restricted because species compete for limited resources. We hypothesize that such competition should not only affect numbers of species, but also prevent species from being phenotypically similar. Here, we present a method to detect whether competitive interactions between species have ordered phenotypic traits on a phylogeny, assuming that competition prevents related species from having identical trait values. We use the method to analyze clades of birds and mammals, with body size as the phenotypic trait. We find no sign that competition has prevented species from having the same body size. Thus, since body size is a key ecological trait and competition does not seem to be responsible for differences in body size between species, we conclude that the diversification slowdown that is prevalent in these clades is unlikely due to the ecological interference implied by the term density dependence. DOI
677. Morrissy, AS; Cavalli, FMG; Remke, M; Ramaswamy, V; Shih, DJH; Holgado, BL; Farooq, H; Donovan, LK; Garzia, L; Agnihotri, S; Kiehna, EN; Mercier, E; Mayoh, C; Papillon-Cavanagh, S; Nikbakht, H; Gayden, T; Torchia, J; Picard, D; Merino, DM; Vladoiu, M; Luu, B; Wu, X; Daniels, C; Horswell, S; Thompson, YY; Hovestadt, V; Northcott, PA; Jones, DTW; Peacock, J; Wang, X; Mack, SC; Reimand, J; Albrecht, S; Fontebasso, AM; Thiessen, N; Li, Y; Schein, JE; Lee, D; Carlsen, R; Mayo, M; Tse, K; Tam, A; Dhalla, N; Ally, A; Chuah, E; Cheng, Y; Plettner, P; Li, HI; Corbett, RD; Wong, T; Long, W; Loukides, J; Buczkowicz, P; Hawkins, CE; Tabori, U; Rood, BR; Myseros, JS; Packer, RJ; Korshunov, A; Lichter, P; Kool, M; Pfister, SM; Schuller, U; Dirks, P; Huang, A; Bouffet, E; Rutka, JT; Bader, GD; Swanton, C; Ma, Y; Moore, RA; Mungall, AJ; Majewski, J; Jones, SJM; Das, S; Malkin, D; Jabado, N; Marra, MA; Taylor, MD.Spatial heterogeneity in medulloblastoma.Nature Genet., 2017, 49: 780-+ Spatial heterogeneity in medulloblastoma
Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy. Conversely, somatic mutations that affect genes suitable for targeted therapeutics demonstrated high levels of spatial heterogeneity in MB, malignant glioma, and renal cell carcinoma (RCC). Actionable targets found in a single MB biopsy were seldom clonal across the entire tumor, which brings the efficacy of monotherapies against a single target into question. Clinical trials of targeted therapies for MB should first ensure the spatially ubiquitous nature of the target mutation. DOI
676. O'Rourke, N; Heisel, MJ; Canham, SL; Sixsmith, A.Predictors of suicide ideation among older adults with bipolar disorder.PLoS One, 2017, 12 Predictors of suicide ideation among older adults with bipolar disorder
Objectives Bipolar disorder (BD) carries the greatest risk of death by suicide of all psychiatric conditions as 25%-50% of those with BD will make one or more suicide attempt, and about 15% will intentionally end their lives. Among young adults with BD, substance misuse, medication non-adherence, age at onset, and comorbid psychiatric conditions each predict self-harm. It is currently unclear if these same factors or others predict suicide ideation among older adults with BD. Methods We recruited a global sample of 220 older adults with BD over 19 days using socio-demographically targeted, social media advertising and online data collection (Mean = 58.50, SD = 5.42; range 50 to 81 years). Path analyses allowed us to identify direct and indirect predictors of suicide ideation among older adults with BD. Results Cognitive failures (perception, memory, and motor function), depressive symptoms, alcohol misuse, and dissatisfaction with life as direct predictors of suicide ideation; duration of BD symptoms and medication non-adherence emerged as indirect predictors. Of note, the significant impact of sleep on suicide ideation is indirect via depressive symptoms, cognitive failures, medication non-adherence and life dissatisfaction. Conclusions As with young adults with BD, alcohol misuse and medication non-adherence emerged as significant predictors of suicide ideation. In addition, cognitive failures directly and indirectly predict suicide ideation in this sample of older adults with BD. Population aging and treatment efficacy are leading to ever growing numbers of older adults with BD. Both direct and indirect predictors of suicide ideation need to be considered in future BD research and treatment planning. DOI
675. Ottenburghs, J; Megens, HJ; Kraus, RHS; van Hooft, P; van Wieren, SE; Crooijmans, RPMA; Ydenberg, RC; Groenen, MAM; Prins, HHT.A history of hybrids? Genomic patterns of introgression in the True Geese.BMC Evol. Biol., 2017, 17 A history of hybrids? Genomic patterns of introgression in the True Geese
Hybridization; Phylogenetic Networks; D-statistic; PSMC; Phylogenomics
Background: The impacts of hybridization on the process of speciation are manifold, leading to distinct patterns across the genome. Genetic differentiation accumulates in certain genomic regions, while divergence is hampered in other regions by homogenizing gene flow, resulting in a heterogeneous genomic landscape. A consequence of this heterogeneity is that genomes are mosaics of different gene histories that can be compared to unravel complex speciation and hybridization events. However, incomplete lineage sorting (often the outcome of rapid speciation) can result in similar patterns. New statistical techniques, such as the D-statistic and hybridization networks, can be applied to disentangle the contributions of hybridization and incomplete lineage sorting. We unravel patterns of hybridization and incomplete lineage sorting during and after the diversification of the True Geese (family Anatidae, tribe Anserini, genera Anser and Branta) using an exon-based hybridization network approach and taking advantage of discordant gene tree histories by re-sequencing all taxa of this clade. In addition, we determine the timing of introgression and reconstruct historical effective population sizes for all goose species to infer which demographic or biogeographic factors might explain the observed patterns of introgression. Results: We find indications for ancient interspecific gene flow during the diversification of the True Geese and were able to pinpoint several putative hybridization events. Specifically, in the genus Branta, both the ancestor of the White-cheeked Geese (Hawaiian Goose, Canada Goose, Cackling Goose and Barnacle Goose) and the ancestor of the Brent Goose hybridized with Red-breasted Goose. One hybridization network suggests a hybrid origin for the Red-breasted Goose, but this scenario seems unlikely and it not supported by the D-statistic analysis. The complex, highly reticulated evolutionary history of the genus Anser hampered the estimation of ancient hybridization events by means of hybridization networks. The reconstruction of historical effective population sizes shows that most species showed a steady increase during the Pliocene and Pleistocene. These large effective population sizes might have facilitated contact between diverging goose species, resulting in the establishment of hybrid zones and consequent gene flow. Conclusions: Our analyses suggest that the evolutionary history of the True Geese is influenced by introgressive hybridization. The approach that we have used, based on genome-wide phylogenetic incongruence and network analyses, will be a useful procedure to reconstruct the complex evolutionary histories of many naturally hybridizing species groups. DOI
674. Panchapakesan, SSS; Ferguson, ML; Hayden, EJ; Chen, X; Hoskins, AA; Unrau, PJ.Ribonucleoprotein purification and characterization using RNA Mango.RNA, 2017, 23: 1592-1599 Ribonucleoprotein purification and characterization using RNA Mango
RNA; Mango; fluorophore; desthiobiotin; purification; RNP pull-down; TO1; TO3
The characterization of RNA-protein complexes (RNPs) is a difficult but increasingly important problem in modern biology. By combining the compact RNA Mango aptamer with a fluorogenic thiazole orange desthiobiotin (TO1-Dtb or TO3-Dtb) ligand, we have created an RNA tagging system that simplifies the purification and subsequent characterization of endogenous RNPs. Mango-tagged RNP complexes can be immobilized on a streptavidin solid support and recovered in their native state by the addition of free biotin. Furthermore, Mango-based RNP purification can be adapted to different scales of RNP isolation ranging from pull-down assays to the isolation of large amounts of biochemically defined cellular RNPs. We have incorporated the Mango aptamer into the S. cerevisiae U1 small nuclear RNA (snRNA), shown that the Mango-snRNA is functional in cells, and used the aptamer to pull down a U1 snRNA-associated protein. To demonstrate large-scale isolation of RNPs, we purified and characterized bacterial RNA polymerase holoenzyme (HE) in complex with a Mango-containing 6S RNA. We were able to use the combination of a red-shifted TO3-Dtb ligand and eGFP-tagged HE to follow the binding and release of the 6S RNA by two-color native gel analysis as well as by single-molecule fluorescence cross-correlation spectroscopy. Together these experiments demonstrate how the Mango aptamer in conjunction with simple derivatives of its flurophore ligands enables the purification and characterization of endogenous cellular RNPs in vitro. DOI
672. Panmanee, W; Charoenlap, N; Atichartpongkul, S; Mahavihakanont, A; Whiteside, MD; Winsor, G; Brinkman, FSL; Mongkolsuk, S; Hassett, DJ.The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate: pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide.PLoS One, 2017, 12 The OxyR-regulated phnW gene encoding 2-aminoethylphosphonate: pyruvate aminotransferase helps protect Pseudomonas aeruginosa from tert-butyl hydroperoxide
The LysR member of bacterial transactivators, OxyR, governs transcription of genes involved in the response to H2O2 and organic (alkyl) hydroperoxides (AHP) in the Gram-negative pathogen, Pseudomonas aeruginosa. We have previously shown that organisms lacking OxyR are rapidly killed by < 2 or 500 mM H2O2 in planktonic and biofilm bacteria, respectively. In this study, we first employed a bioinformatic approach to elucidate the potential regulatory breadth of OxyR by scanning the entire P. aeruginosa PAO1 genome for canonical OxyR promoter recognition sequences (ATAG-N-7-CTAT-N-7-ATAG-N-7-CTAT). Of > 100 potential OxyR-controlled genes, 40 were strategically selected that were not predicted to be involved in the direct response to oxidative stress (e.g., catalase, peroxidase, etc.) and screened such genes by RT-PCR analysis for potentially positive or negative control by OxyR. Differences were found in 7 of 40 genes when comparing an oxyR mutant vs. PAO1 expression that was confirmed by beta-galactosidase reporter assays. Among these, phnW, encoding 2-aminoethylphosphonate: pyruvate aminotransferase, exhibited reduced expression in the oxyR mutant compared to wild-type bacteria. Electrophoretic mobility shift assays indicated binding of OxyR to the phnW promoter and DNase I footprinting analysis also revealed the sequences to which OxyR bound. Interestingly, a phnW mutant was more susceptible to t-butyl-hydroperoxide (t-BOOH) treatment than wild-type bacteria. Although we were unable to define the direct mechanism underlying this phenomenon, we believe that this may be due to a reduced efficiency for this strain to degrade t-BOOH relative to wild-type organisms because of modulation of AHP gene transcription in the phnW mutant. DOI
671. Pantophlet, R; Trattnig, N; Murrell, S; Lu, NM; Chau, D; Rempel, C; Wilson, IA; Kosma, P.Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity.Nature Communications, 2017, 8 Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity
Oligomannose-type glycans are among the major targets on the gp120 component of the HIV envelope protein (Env) for broadly neutralizing antibodies (bnAbs). However, attempts to elicit oligomannose-specific nAbs by immunizing with natural or synthetic oligomannose have so far not been successful, possibly due to B cell tolerance checkpoints. Here we design and synthesize oligomannose mimetics, based on the unique chemical structure of a recently identified bacterial lipooligosaccharide, to appear foreign to the immune system. One of these mimetics is bound avidly by members of a family of oligomannose-specific bnAbs and their putative common germline precursor when presented as a glycoconjugate. The crystal structure of one of the mimetics bound to a member of this bnAb family confirms the antigenic resemblance. Lastly, immunization of human-antibody transgenic animals with a lead mimetic evokes nAbs with specificities approaching those of existing bnAbs. These results provide evidence for utilizing antigenic mimicry to elicit oligomannose-specific bnAbs to HIV-1. DOI
669. Pesudo, V; Borge, MJG; Moro, AM; Lay, JA; Nacher, E; Gomez-Camacho, J; Tengblad, O; Acosta, L; Alcorta, M; Alvarez, MAG; Andreoiu, C; Bender, PC; Braid, R; Cubero, M; Di Pietro, A; Fernandez-Garcia, JP; Figuera, P; Fisichella, M; Fulton, BR; Garnsworthy, AB; Hackman, G; Hager, U; Kirsebom, OS; Kuhn, K; Lattuada, M; Marquinez-Duran, G; Martel, I; Miller, D; Moukaddam, M; O'Malley, PD; Perea, A; Rajabali, MM; Sanchez-Benitez, AM; Sarazin, F; Scuderi, V; Svensson, CE; Unsworth, C; Wang, ZM.Scattering of the Halo Nucleus Be-11 on Au-197 at Energies around the Coulomb Barrier.Phys. Rev. Lett., 2017, 118 Scattering of the Halo Nucleus Be-11 on Au-197 at Energies around the Coulomb Barrier
Angular distributions of the elastic, inelastic, and breakup cross sections of the halo nucleus Be-11 on Au-197 were measured at energies below (E-lab = 31.9 MeV) and around (39.6 MeV) the Coulomb barrier. These three channels were unambiguously separated for the first time for reactions of Be-11 on a high-Z target at low energies. The experiment was performed at TRIUMF (Vancouver, Canada). The differential cross sections were compared with three different calculations: semiclassical, inert-core continuum-coupled-channels and continuum-coupled-channels ones with including core deformation. These results show conclusively that the elastic and inelastic differential cross sections can only be accounted for if core-excited admixtures are taken into account. The cross sections for these channels strongly depend on the B(E1) distribution in Be-11, and the reaction mechanism is sensitive to the entanglement of core and halo degrees of freedom in Be-11. DOI PubMed
668. Pierce, OM; McNair, GR; He, X; Kajiura, H; Fujiyama, K; Kermode, AR.N-glycan structures and downstream mannose-phosphorylation of plant recombinant human alpha-l-iduronidase: toward development of enzyme replacement therapy for mucopolysaccharidosis I.Plant Mol.Biol., 2017, 95: 593-606 N-glycan structures and downstream mannose-phosphorylation of plant recombinant human alpha-l-iduronidase: toward development of enzyme replacement therapy for mucopolysaccharidosis I
Lysosomal storage diseases; Mucopolysaccharidosis I; Enzyme replacement therapy; Mannose-6-phosphate tag; Lysosomal targeting; Alpha-L-iduronidase
Arabidopsis N-glycan processing mutants provide the basis for tailoring recombinant enzymes for use as replacement therapeutics to treat lysosomal storage diseases, including N-glycan mannose phosphorylation to ensure lysosomal trafficking and efficacy. Functional recombinant human alpha-l-iduronidase (IDUA; EC 3.2.1.76) enzymes were generated in seeds of the Arabidopsis thaliana complex-glycan-deficient (cgl) C5 background, which is deficient in the activity of N-acetylglucosaminyl transferase I, and in seeds of the Arabidopsis gm1 mutant, which lacks Golgi alpha-mannosidase I (GM1) activity. Both strategies effectively prevented N-glycan maturation and the resultant N-glycan structures on the consensus sites for N-glycosylation of the human enzyme revealed high-mannose N-glycans of predominantly Man(5) (cgl-IDUA) or Man(6-8) (gm1-IDUA) structures. Both forms of IDUA were equivalent with respect to their kinetic parameters characterized by cleavage of the artificial substrate 4-methylumbelliferyl-iduronide. Because recombinant lysosomal enzymes produced in plants require the addition of mannose-6-phosphate (M6P) in order to be suitable for lysosomal delivery in human cells, we characterized the two IDUA proteins for their amenability to downstream in vitro mannose phosphorylation mediated by a soluble form of the human phosphotransferase (UDP-GlcNAc: lysosomal enzyme N-acetylglucosamine [GlcNAc]-1-phosphotransferase). Gm1-IDUA exhibited a slight advantage over the cgl-IDUA in the in vitro M6P-tagging process, with respect to having a better affinity (i.e. lower K (m)) for the soluble phosphotransferase. This may be due to the greater number of mannose residues comprising the high-mannose N-glycans of gm1-IDUA. Our elite cgl- line produces IDUA at > 5.7% TSP (total soluble protein); screening of the gm1 lines showed a maximum yield of 1.5% TSP. Overall our findings demonstrate the relative advantages and disadvantages associated with the two platforms to create enzyme replacement therapeutics for lysosomal storage diseases. DOI
664. Reiter, JF; Leroux, MR.Genes and molecular pathways underpinning ciliopathies.Nat. Rev. Mol. Cell Biol., 2017, 18: 533-547 Genes and molecular pathways underpinning ciliopathies
Motile and non-motile (primary) cilia are nearly ubiquitous cellular organelles. The dysfunction of cilia causes diseases known as ciliopathies. The number of reported ciliopathies (currently 35) is increasing, as is the number of established (187) and candidate (241) ciliopathy-associated genes. The characterization of ciliopathy-associated proteins and phenotypes has improved our knowledge of ciliary functions. In particular, investigating ciliopathies has helped us to understand the molecular mechanisms by which the cilium-associated basal body functions in early ciliogenesis, as well as how the transition zone functions in ciliary gating, and how intraflagellar transport enables cargo trafficking and signalling. Both basic biological and clinical studies are uncovering novel ciliopathies and the ciliary proteins involved. The assignment of these proteins to different ciliary structures, processes and ciliopathy subclasses (first order and second order) provides insights into how this versatile organelle is built, compartmentalized and functions in diverse ways that are essential for human health. DOI
663. Riesch, R; Muschick, M; Lindtke, D; Villoutreix, R; Comeault, AA; Farkas, TE; Lucek, K; Hellen, E; Soria-Carrasco, V; Dennis, SR; de Carvalho, CF; Safran, RJ; Sandoval, CP; Feder, J; Gries, R; Crespi, BJ; Gries, G; Gompert, Z; Nosil, P.Transitions between phases of genomic differentiation during stick-insect speciation.Nature Ecology & Evolution, 2017, 1 Transitions between phases of genomic differentiation during stick-insect speciation
Speciation can involve a transition from a few genetic loci that are resistant to gene flow to genome-wide differentiation. However, only limited data exist concerning this transition and the factors promoting it. Here, we study phases of speciation using data from >100 populations of 11 species of Timema stick insects. Consistent with early phases of genie speciation, adaptive colour-pattern loci reside in localized genetic regions of accentuated differentiation between populations experiencing gene flow. Transitions to genome-wide differentiation are also observed with gene flow, in association with differentiation in polygenic chemical traits affecting mate choice. Thus, intermediate phases of speciation are associated with genome-wide differentiation and mate choice, but not growth of a few genomic islands. We also find a gap in genomic differentiation between sympatric taxa that still exchange genes and those that do not, highlighting the association between differentiation and complete reproductive isolation. Our results suggest that substantial progress towards speciation may involve the alignment of multi-faceted aspects of differentiation. DOI
662. Robinson, JPW; Williams, ID; Edwards, AM; McPherson, J; Yeager, L; Vigliola, L; Brainard, RE; Baum, JK.Fishing degrades size structure of coral reef fish communities.Global Change Biology, 2017, 23: 1009-1022 Fishing degrades size structure of coral reef fish communities
body size; community structure; coral reef fish; exploitation; fisheries; macroecology; overfishing; size spectra; size-based approaches
Fishing pressure on coral reef ecosystems has been frequently linked to reductions of large fishes and reef fish biomass. Associated impacts on overall community structure are, however, less clear. In size-structured aquatic ecosystems, fishing impacts are commonly quantified using size spectra, which describe the distribution of individual body sizes within a community. We examined the size spectra and biomass of coral reef fish communities at 38 US-affiliated Pacific islands that ranged in human presence from near pristine to human population centers. Size spectra 'steepened' steadily with increasing human population and proximity to market due to a reduction in the relative biomass of large fishes and an increase in the dominance of small fishes. Reef fish biomass was substantially lower on inhabited islands than uninhabited ones, even at inhabited islands with the lowest levels of human presence. We found that on populated islands size spectra exponents decreased (analogous to size spectra steepening) linearly with declining biomass, whereas on uninhabited islands there was no relationship. Size spectra were steeper in regions of low sea surface temperature but were insensitive to variation in other environmental and geomorphic covariates. In contrast, reef fish biomass was highly sensitive to oceanographic conditions, being influenced by both oceanic productivity and sea surface temperature. Our results suggest that community size structure may be a more robust indicator than fish biomass to increasing human presence and that size spectra are reliable indicators of exploitation impacts across regions of different fish community compositions, environmental drivers, and fisheries types. Size-based approaches that link directly to functional properties of fish communities, and are relatively insensitive to abiotic variation across biogeographic regions, offer great potential for developing our understanding of fishing impacts in coral reef ecosystems. DOI
661. Roslin, T; Hardwick, B; Novotny, V; Petry, WK; Andrew, NR; Asmus, A; Barrio, IC; Basset, Y; Boesing, AL; Bonebrake, TC; Cameron, EK; Dattilo, W; Donoso, DA; Drozd, P; Gray, CL; Hik, DS; Hill, SJ; Hopkins, T; Huang, S; Koane, B; Laird-Hopkins, B; Laukkanen, L; Lewis, OT; Milne, S; Mwesige, I; Nakamura, A; Nell, CS; Nichols, E; Prokurat, A; Sam, K; Schmidt, NM; Slade, A; Slade, V; Suchankova, A; Teder, T; van Nouhuys, S; Vandvik, V; Weissflog, A; Zhukovich, V; Slade, EM.Higher predation risk for insect prey at low latitudes and elevations.Science, 2017, 356: 742-744 Higher predation risk for insect prey at low latitudes and elevations
Biotic interactions underlie ecosystem structure and function, but predicting interaction outcomes is difficult. We tested the hypothesis that biotic interaction strength increases toward the equator, using a global experiment with model caterpillars to measure predation risk. Across an 11,660-kilometer latitudinal gradient spanning six continents, we found increasing predation toward the equator, with a parallel pattern of increasing predation toward lower elevations. Patterns across both latitude and elevation were driven by arthropod predators, with no systematic trend in attack rates by birds or mammals. These matching gradients at global and regional scales suggest consistent drivers of biotic interaction strength, a finding that needs to be integrated into general theories of herbivory, community organization, and life-history evolution. DOI
660. Rubin, CM; Horton, BP; Sieh, K; Pilarczyk, JE; Daly, P; Ismail, N; Parnell, AC.Highly variable recurrence of tsunamis in the 7,400 years before the 2004 Indian Ocean tsunami.Nat. Commun., 2017, 8 Highly variable recurrence of tsunamis in the 7,400 years before the 2004 Indian Ocean tsunami
The devastating 2004 Indian Ocean tsunami caught millions of coastal residents and the scientific community off-guard. Subsequent research in the Indian Ocean basin has identified prehistoric tsunamis, but the timing and recurrence intervals of such events are uncertain. Here we present an extraordinary 7,400 year stratigraphic sequence of prehistoric tsunami deposits from a coastal cave in Aceh, Indonesia. This record demonstrates that at least 11 prehistoric tsunamis struck the Aceh coast between 7,400 and 2,900 years ago. The average time period between tsunamis is about 450 years with intervals ranging from a long, dormant period of over 2,000 years, to multiple tsunamis within the span of a century. Although there is evidence that the likelihood of another tsunamigenic earthquake in Aceh province is high, these variable recurrence intervals suggest that long dormant periods may follow Sunda megathrust ruptures as large as that of the 2004 Indian Ocean tsunami. DOI PubMed
659. Sandkam, BA; Joy, JB; Watson, CT; Breden, F.Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection.Genome Biol. Evol., 2017, 9: 3100-3107 Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection
opsin; gene conversion; Poeciliidae; vision; LWS
Many models of evolution by sexual selection predict a coevolution of sensory systems and mate preferences, but the genomic architecture (number and arrangement of contributing loci) underlying these characters could constrain this coevolution. Here, we examine how the genomic organization and evolution of the opsin genes (responsible for tuning color vision) can influence the evolutionary trajectory of sexually selected traits across 15 species in the family Poeciliidae, which includes classic systems for studies of color-mediated sexual selection such as guppies, swordtails, and mollies. Although male coloration patterns and the importance of this coloration in female mate choice vary widely within and among genera, sequencing revealed low variability at amino acid sites that tune Long Wavelength-Sensitive (LWS) opsins in this speciose family. Although most opsin genes in these species appear to have evolved along traditional mutation-selection dynamics, we identified high rates of gene conversion between two of the LWS loci (LWS-1 and LWS-3), likely due to the inverted tandem repeat nature of these genes. Yet members of the subgenus Lebistes appear to resist LWS gene conversion. The LWS opsins are responsible for detecting and discriminating red and orange coloration-akey sexually selected trait inmembers of the subgenus Lebistes. Takent together these results suggest selection is acting against the homogenizing effects of gene conversion to maintain LWS-1/LWS-3 differences within this subgenus. DOI
658. Serrato, IM; Caicedo, PA; Orobio, Y; Lowenberger, C; Ocampo, CB.Vector competence and innate immune responses to dengue virus infection in selected laboratory and field-collected Stegomyia aegypti (= Aedes aegypti).Med. Vet. Entomol., 2017, 31: 312-319 Vector competence and innate immune responses to dengue virus infection in selected laboratory and field-collected Stegomyia aegypti (= Aedes aegypti)
Apoptosis; caspases; dengue virus; innate immunity; vector competence
Control of dengue virus (DenV) transmission, primarily based on strategies to reduce populations of the principle vector Stegomya aegypti (= Aedes aegypti) (Diptera: Culicidae), is difficult to sustain over time. Other potential strategies aim to manipulate characteristics such as vector competence (VC), the innate capacity of the vector to transmit the virus. Previous studies have identified genetic factors, including differential expression of apoptosis-related genes, associated with the refractory and susceptible phenotypes in selected strains of S. aegypti from Cali, Colombia. The present study was designed to evaluate the variability of VC in selected strains against different DenV serotypes and to determine whether field-collected mosquitoes respond similarly to selected laboratory strains in terms of enhanced or reduced expression of apoptosis-related genes. Vector competence differed between strains, but did not differ in response to different DenV serotypes. Differences in VC were observed among mosquitoes collected from different localities in Cali. The overexpression of the pro-apoptosis genes, caspase 16 and Aedronc, was conserved in field-collected refractory mosquitoes and the selected laboratory refractory strain. The results suggest that the apoptosis response is conserved among all refractory mosquitoes to inhibit the development of all DenV serotypes. DOI
656. Stevens, CM; Rayani, K; Singh, G; Lotfalisalmasi, B; Tieleman, DP; Tibbits, GF.Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca2+-sensitizing mutations.J. Biol. Chem., 2017, 292: 11915-11926 Changes in the dynamics of the cardiac troponin C molecule explain the effects of Ca2+-sensitizing mutations
Cardiac troponin C (cTnC) is the regulatory protein that initiates cardiac contraction in response to Ca2+. TnC binding Ca2+ initiates a cascade of protein-protein interactions that begins with the opening of the N-terminal domain of cTnC, followed by cTnC binding the troponin I switch peptide (TnI(SW)). We have evaluated, through isothermal titration calorimetry and molecular-dynamics simulation, the effect of several clinically relevant mutations (A8V, L29Q, A31S, L48Q, Q50R, and C84Y) on the Ca2+ affinity, structural dynamics, and calculated interaction strengths between cTnC and each of Ca2+ and TnI(SW). Surprisingly the Ca2+ affinity measured by isothermal titration calorimetry was only significantly affected by half of these mutations including L48Q, which had a 10-fold higher affinity than WT, and the Q50R and C84Y mutants, each of which had affinities 3-fold higher than wild type. This suggests that Ca2+ affinity of the N-terminal domain of cTnC in isolation is insufficient to explain the pathogenicity of these mutations. Molecular-dynamics simulation was used to evaluate the effects of these mutations on Ca2+ binding, structural dynamics, and TnI interaction independently. Many of the mutations had a pronounced effect on the balance between the open and closed conformations of the TnC molecule, which provides an indirect mechanism for their pathogenic properties. Our data demonstrate that the structural dynamics of the cTnC molecule are key in determining myofilament Ca2+ sensitivity. Our data further suggest that modulation of the structural dynamics is the underlying molecular mechanism for many disease mutations that are far from the regulatory Ca2+-binding site of cTnC. DOI
655. Sutherland, WJ; Barnard, P; Broad, S; Clout, M; Connor, B; Côté, IM; Dicks, LV; Doran, H; Entwistle, AC; Fleishman, E; Fox, M; Gaston, KJ; Gibbons, DW; Jiang, Z; Keim, B; Lickorish, FA; Markillie, P; Monk, KA; Pearce-Higgins, JW; Peck, LS; Pretty, J; Spalding, MD; Tonneijck, FH; Wintle, BC; Ockendon, N.A 2017 Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity.Trends in Ecology & Evolution, 2017, 32: 31-40 A 2017 Horizon Scan of Emerging Issues for Global Conservation and Biological Diversity
We present the results of our eighth annual horizon scan of emerging issues likely to affect global biological diversity, the environment, and conservation efforts in the future. The potential effects of these novel issues might not yet be fully recognized or understood by the global conservation community, and the issues can be regarded as both opportunities and risks. A diverse international team with collective expertise in horizon scanning, science communication, and conservation research, practice, and policy reviewed 100 potential issues and identified 15 that qualified as emerging, with potential substantial global effects. These issues include new developments in energy storage and fuel production, sand extraction, potential solutions to combat coral bleaching and invasive marine species, and blockchain technology. DOI
654. Tucker, CM; Cadotte, MW; Carvalho, SB; Davies, TJ; Ferrier, S; Fritz, SA; Grenyer, R; Helmus, MR; Jin, LS; Mooers, AO; Pavoine, S; Purschke, O; Redding, DW; Rosauer, DF; Winter, M; Mazel, F.A guide to phylogenetic metrics for conservation, community ecology and macroecology.Biol. Rev., 2017, 92: 698-715 A guide to phylogenetic metrics for conservation, community ecology and macroecology
biodiversity hotspots; biogeography; community assembly; conservation; diversity metrics; evolutionary history; phylogenetic diversity; prioritization; range size
The use of phylogenies in ecology is increasingly common and has broadened our understanding of biological diversity. Ecological sub-disciplines, particularly conservation, community ecology and macroecology, all recognize the value of evolutionary relationships but the resulting development of phylogenetic approaches has led to a proliferation of phylogenetic diversity metrics. The use of many metrics across the sub-disciplines hampers potential meta-analyses, syntheses, and generalizations of existing results. Further, there is no guide for selecting the appropriatemetric for a given question, and different metrics are frequently used to address similar questions. To improve the choice, application, and interpretation of phylo-diversity metrics, we organize existing metrics by expanding on a unifying framework for phylogenetic information. Generally, questions about phylogenetic relationships within or between assemblages tend to ask three types of question: how much; how different; or how regular? We show that these questions reflect three dimensions of a phylogenetic tree: richness, divergence, and regularity. We classify 70 existing phylo-diversity metrics based on their mathematical form within these three dimensions and identify 'anchor' representatives: for alpha-diversity metrics these are PD (Faith's phylogenetic diversity), MPD (mean pairwise distance), and VPD (variation of pairwise distances). By analysing mathematical formulae and using simulations, we use this framework to identify metrics that mix dimensions, and we provide a guide to choosing and using the most appropriate metrics. We show that metric choice requires connecting the research question with the correct dimension of the framework and that there are logical approaches to selecting and interpreting metrics. The guide outlined herein will help researchers navigate the current jungle of indices. DOI
653. Wade, J; Dyck, B; Palin, RM; Moore, JDP; Smye, AJ.The divergent fates of primitive hydrospheric water on Earth and Mars.Nature, 2017, 552: 391-+ The divergent fates of primitive hydrospheric water on Earth and Mars
Despite active transport into Earth's mantle, water has been present on our planet's surface for most of geological time(1,2). Yet water disappeared from the Martian surface soon after its formation. Although some of the water on Mars was lost to space via photolysis following the collapse of the planet's magnetic field(3-5), the widespread serpentinization of Martian crust(6,7) suggests that metamorphic hydration reactions played a critical part in the sequestration of the crust. Here we quantify the relative volumes of water that could be removed from each planet's surface via the burial and metamorphism of hydrated mafic crusts, and calculate mineral transition-induced bulk-density changes at conditions of elevated pressure and temperature for each. The metamorphic mineral assemblages in relatively FeO-rich Martian lavas can hold about 25 per cent more structurally bound water than those in metamorphosed terrestrial basalts, and can retain it at greater depths within Mars. Our calculations suggest that in excess of 9 per cent by volume of the Martian mantle may contain hydrous mineral species as a consequence of surface reactions, compared to about 4 per cent by volume of Earth's mantle. Furthermore, neither primitive nor evolved hydrated Martian crust show noticeably different bulk densities compared to their anhydrous equivalents, in contrast to hydrous mafic terrestrial crust, which transforms to denser eclogite upon dehydration. This would have allowed efficient overplating and burial of early Martian crust in a stagnant-lid tectonic regime, in which the lithosphere comprised a single tectonic plate, with only the warmer, lower crust involved in mantle convection. This provided an important sink for hydrospheric water and a mechanism for oxidizing the Martian mantle. Conversely, relatively buoyant mafic crust and hotter geothermal gradients on Earth reduced the potential for upper-mantle hydration early in its geological history, leading to water being retained close to its surface, and thus creating conditions conducive for the evolution of complex multicellular life. DOI PubMed
652. Waldron, A; Miller, DC; Redding, D; Mooers, A; Kuhn, TS; Nibbelink, N; Roberts, JT; Tobias, JA; Gittleman, JL.Reductions in global biodiversity loss predicted from conservation spending.Nature, 2017, 551: 364-+ Reductions in global biodiversity loss predicted from conservation spending
Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals(1,2), but success to date has been very limited(3-5). A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity(6-9); however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment(6-9). For greater effectiveness, we need an evidence-based model(10-12) that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment between 1996 and 2008 reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country. We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures)(13-18). Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds. DOI
651. Wang, FB; Coureuil, M; Osinski, T; Orlova, A; Altindal, T; Gesbert, G; Nassif, X; Egelman, EH; Craig, L.Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution.Structure, 2017, 25: 1423-+ Cryoelectron Microscopy Reconstructions of the Pseudomonas aeruginosa and Neisseria gonorrhoeae Type IV Pili at Sub-nanometer Resolution
We report here cryoelectron microscopy reconstructions of type IV pili (T4P) from two important human pathogens, Pseudomonas aeruginosa and Neisseria gonorrhoeae, at similar to 8 and 5 angstrom resolution, respectively. The two structures reveal distinct arrangements of the pilin globular domains on the pilus surfaces, which impart different helical parameters, but similar packing of the conserved N-terminal alpha helices, alpha 1, in the filament core. In contrast to the continuous alpha helix seen in the X-ray crystal structures of the P. aeruginosa and N. gonorrhoeae pilin subunits, alpha 1 in the pilus filaments has a melted segment located between conserved helix-breaking residues Gly14 and Pro22, as seen for the Neisseria meningitidis T4P. Using mutagenesis we show that Pro22 is critical for pilus assembly, as are Thr2 and Glu5, which are positioned to interact in the hydrophobic filament core. These structures provide a framework for understanding T4P assembly, function, and biophysical properties. DOI
650. Wang, M; Audas, TE; Lee, S.Disentangling a Bad Reputation: Changing Perceptions of Amyloids.Trends Cell Biol., 2017, 27: 465-467 Disentangling a Bad Reputation: Changing Perceptions of Amyloids
Historically, amyloids were perceived as toxic/irreversible protein aggregates associated with neurodegenerative disorders including Alzheimer's and Parkinson's diseases. Recent papers are challenging this perception by uncovering widespread cellular roles for physiological amyloidogenesis. These findings suggest that the amyloid-fold should be considered, alongside the native-fold and unfolded configurations, as a physiological and reversible protein organization. DOI
648. Watts, PC; Kallio, ER; Koskela, E; Lonn, E; Mappes, T; Mokkonen, M.Stabilizing selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci.Proceedings of the Royal Society B-Biological Sciences, 2017, 284 Stabilizing selection on microsatellite allele length at arginine vasopressin 1a receptor and oxytocin receptor loci
gene dynamics; reproductive behaviour; noncoding genome; VNTR
The loci arginine vasopressin receptor 1a (avpr1a) and oxytocin receptor (oxtr) have evolutionarily conserved roles in vertebrate social and sexual behaviour. Allelic variation at a microsatellite locus in the 50 regulatory region of these genes is associated with fitness in the bank vole Myodes glareolus. Given the low frequency of long and short alleles at these microsatellite loci in wild bank voles, we used breeding trials to determine whether selection acts against long and short alleles. Female bank voles with intermediate length avpr1a alleles had the highest probability of breeding, while male voles whose avpr1a alleles were very different in length had reduced probability of breeding. Moreover, there was a significant interaction between male and female oxtr genotypes, where potential breeding pairs with dissimilar length alleles had reduced probability of breeding. These data show how genetic variation at microsatellite loci associated with avpr1a and oxtr is associated with fitness, and highlight complex patterns of selection at these loci. More widely, these data show how stabilizing selection might act on allele length frequency distributions at gene-associated microsatellite loci. DOI
647. Williamson, SN; Hik, DS; Gamon, JA; Jarosch, AH; Anslow, FS; Clarke, GKC; Rupp, TS.Spring and summer monthly MODIS LST is inherently compared to air temperature in snow covered sub-Arctic mountains.Remote Sens. Environ., 2017, 189: 14-24 Spring and summer monthly MODIS LST is inherently compared to air temperature in snow covered sub-Arctic mountains
MODIS LST; Downscaled NARR; SNAP; Snow cover; Cloud cover; Cryosphere: alpine
Satellite-derived land surface temperature (skin temperature) provides invaluable information for data-sparse high elevation and Arctic regions. However, the relationship between satellite-derived clear-sky skin temperature and various downscaled air temperature products for snow covered sub-Arctic alpine regions remain poorly understood, such that trend analysis or air temperature product integration is difficult. We compared monthly average air temperatures from two independent downscaled temperature products to MODIS Land Surface Temperature (LST) and air temperature at nine meteorological stations situated above tree-line in the southwest Yukon, Canada, between May and August 2008 for a full range of snow cover fractions. We found that both down scaled products generally agreed with LST for the low elevation, snow-free, vegetation classes. However, a systematic cold bias in Average LST emerged for snow fractions greater than approximately 40%, and this bias increased in magnitude as snow cover increased. In these situations the downscaled air temperatures were 57 degrees C warmer than Average LST for snow fractions of >90%, and this pattern was largely independent of the number of measurements of LST within a month. Maximum LST was similar to average air temperatures for high snow fractions, but Minimum LST was colder by 10 degrees C or more for all snow fractions. Consequently, the average of Maximum and Minimum LST produces the cold bias, compared to air temperature, for high snow cover fractions. Air temperature measured at nine meteorological monitoring stations located between elevations of 1408-2690 m, on land cover classes Barren, Sparsely Vegetated or Permanent Snow and Ice, confirmed the cold bias results when incorporating Minimum LST in monthly averages. For snow fractions of <40% the RMSE for all of the temperature products was <2.5 degrees C when compared to station air temperature and all biases were positive and <2.0 degrees C. For snow fractions of >40%, the average LST bias became strongly negative at -4.5 degrees C, and the RMSE increased to 6.1 degrees C, whereas the downscaled products bias and RMSE were similar to those from snow fractions of <40%. A weak warm bias for all the temperature products occurred for small snow fractions over non-forested land cover classes. Downscaled air temperature fields show physically real differences from Average LST in spring and summer, caused by snow cover and the interplay of Maximum and Minimum LST. These findings indicate that the integration of MODIS 1ST with downscaled air temperature products or local air temperature requires the incorporation of snow cover. (C) 2016 Elsevier Inc. All rights reserved. DOI
646. Woodsworth, DJ; Holt, RA.Cell-Based Therapeutics: Making a Faustian Pact with Biology.Trends Mol. Med, 2017, 23: 104-115 Cell-Based Therapeutics: Making a Faustian Pact with Biology
The diversity and specialization found in biological molecules, pathways, and cells is staggering, and should be exploited for therapeutic use. Through evolution these biological systems have attained a level of functionality that would be impossible to recapitulate with de novo assembly. To adapt these systems for therapeutic applications it will be often necessary to re-engineer molecules and pathways to yield novel sensory, control, and effector modules for insertion into existing, specialized cellular chassis. However, these efforts will be greatly impeded and confounded by the noise, complexity, and context dependency inherent in biological systems. Thus, we argue that repurposing biology for cell-based therapeutics will be an arduous process, but one that will yield great benefit, and is superior to any alternative. DOI
645. Wright, AE; Darolti, I; Bloch, NI; Oostra, V; Sandkam, B; Buechel, SD; Kolm, N; Breden, F; Vicoso, B; Mank, JE.Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation.Nature Communications, 2017, 8 Convergent recombination suppression suggests role of sexual selection in guppy sex chromosome formation
Sex chromosomes evolve once recombination is halted between a homologous pair of chromosomes. The dominant model of sex chromosome evolution posits that recombination is suppressed between emerging X and Y chromosomes in order to resolve sexual conflict. Here we test this model using whole genome and transcriptome resequencing data in the guppy, a model for sexual selection with many Y-linked colour traits. We show that although the nascent Y chromosome encompasses nearly half of the linkage group, there has been no perceptible degradation of Y chromosome gene content or activity. Using replicate wild populations with differing levels of sexually antagonistic selection for colour, we also show that sexual selection leads to greater expansion of the non-recombining region and increased Y chromosome divergence. These results provide empirical support for longstanding models of sex chromosome catalysis, and suggest an important role for sexual selection and sexual conflict in genome evolution. DOI
644. Yeager, LA; Deith, MCM; McPherson, JM; Williams, ID; Baum, JK.Scale dependence of environmental controls on the functional diversity of coral reef fish communities.Global Ecology and Biogeography, 2017, 26: 1177-1189 Scale dependence of environmental controls on the functional diversity of coral reef fish communities
climate; ecosystem function; environmental gradient; functional evenness; functional redundancy; functional richness; habitat complexity; macroecology; species richness
AimThe functional composition of local assemblages is hypothesized to be controlled by hierarchical environmental filters, whereby the importance of different abiotic and biotic factors varies across both spatial scales and the different dimensions of functional diversity. We examine scale dependence in functional diversity-environment relationships with the ultimate aim of advancing models that predict the response of functional diversity to global change. LocationCoral reefs surrounding 23 minimally disturbed central-western Pacific islands. Time period2010-2015. Major taxa studiedCoral reef fishes. MethodsWe surveyed 1,423 reef sites using a standardized monitoring protocol and classified the 547 taxa encountered based on traits related to resource use, body size and behaviour. For each fish community, we calculated species richness and three metrics of functional diversity: functional richness, functional redundancy and functional evenness. We then built nested models at three spatial scales to evaluate the predictive power of environmental conditions over each component of functional diversity. ResultsClimatic variables (e.g., primary productivity) and geomorphic context (e.g., bathymetric slope) were more important in predicting functional diversity at coarse spatial scales. In contrast, local measures of habitat quality, including benthic complexity, depth and hard coral cover, were generally most important at finer scales. All diversity metrics were better predicted at coarser scales, but which predictors were important varied among metrics. Main conclusionsThe observed scale dependence in environmental predictors of functional diversity generally matches models of hierarchical filters on functional community assembly. Contrary to expectation, however, functional evenness and functional redundancy, which incorporate information on biomass distributions, were not better predicted at finer spatial scales. Instead, broad-scale variation in environmental variables was most important in predicting all components of functional diversity. Furthermore, the distinct responses of each functional diversity metric to environmental variation indicate that each measures a unique dimension of reef-fish diversity, and environmental change may affect each differently. DOI
643. Zhang, L; Liu, M; Ren, W; Zhou, ZY; Dong, GH; Zhang, YJ; Peng, B; Hao, XH; Wang, CY; Jiang, ZD; Jing, WX; Ye, ZG.ALD preparation of high-k HfO2 thin films with enhanced energy density and efficient electrostatic energy storage.RSC Adv., 2017, 7: 8388-8393 ALD preparation of high-k HfO2 thin films with enhanced energy density and efficient electrostatic energy storage
High-k dielectric HfO2 thin films with a predominant monoclinic phase were prepared by atomic layer deposition (ALD). The annealed HfO2 films exhibited a large dielectric constant, of up to epsilon(r) = 26 with a high breakdown field of over 4000 kV cm(-1). The best performance with a maximum recoverable energy density of 21.3 J cm(-3) and energy efficiency of 75% was obtained with the 63 nm HfO2 films. In addition, a well-defined temperature dependence of the energy storage properties from room temperature to 150 degrees C was demonstrated, indicating a stable energy density variation between 11.0 and 13.0 J cm(-3) with a high energy efficiency of about 80%. These achievements provide a platform for synthesizing high-k dielectric thin films with enhanced energy densities and efficiencies. DOI
642. Alsahafi, N; Ding, SL; Richard, J; Markle, T; Brassard, N; Walker, B; Lewis, GK; Kaufmann, DE; Brockman, MA; Finzi, A.Nef Proteins from HIV-1 Elite Controllers Are Inefficient at Preventing Antibody-Dependent Cellular Cytotoxicity.Journal of Virology, 2016, 90: 2993-3002 Nef Proteins from HIV-1 Elite Controllers Are Inefficient at Preventing Antibody-Dependent Cellular Cytotoxicity
Impairment of Nef function, including reduced CD4 downregulation, was described in a subset of HIV-1-infected individuals that control viral replication without antiretroviral treatment (elite controllers [EC]). Elimination of HIV-1-infected cells by antibody-dependent cellular cytotoxicity (ADCC) requires the presence of envelope glycoproteins (Env) in the CD4-bound conformation, raising the possibility that accumulating CD4 at the surface of virus-infected cells in EC could interact with Env and thereby sensitize these cells to ADCC. We observed a significant increase in the exposure of Env epitopes targeted by ADCC-mediating antibodies at the surface of cells expressing Nef isolates from EC; this correlated with enhanced susceptibility to ADCC. Altogether, our results suggest that enhanced susceptibility of HIV-1-infected cells to ADCC may contribute to the EC phenotype. DOI
641. Arthington, AH; Dulvy, NK; Gladstone, W; Winfield, IJ.Fish conservation in freshwater and marine realms: status, threats and management.Aquatic Conservation-Marine and Freshwater Ecosystems, 2016, 26: 838-857 Fish conservation in freshwater and marine realms: status, threats and management
extinction risk; threats; correlates of risk; conservation reserves; restoration; recovery plans; fisheries management; climate change
1. Despite the disparities in size and volume of marine and freshwater realms, a strikingly similar number of species is found in each - with 15 150 Actinopterygian fishes in fresh water and 14 740 in the marine realm. Their ecological and societal values are widely recognized yet many marine and freshwater fishes increasingly risk local, regional or global extinction. 2. The prevailing threats in aquatic systems are habitat loss and degradation, invasive species, pollution, over-exploitation and climate change. Unpredictable synergies with climate change greatly complicate the impacts of other stressors that threaten many marine and freshwater fishes. 3. Isolated and fragmented habitats typically present the most challenging environments for small, specialized freshwater and marine fishes, whereas overfishing is by far the greatest threat to larger marine and freshwater species. Species that migrate within or between freshwater and marine realms may face high catchability in predictable migration bottlenecks, and degradation of breeding habitat, feeding habitat or the intervening migration corridors. 4. Conservation reserves are vital to protect species-rich habitats, important radiations, and threatened endemic species. Integration of processes that connect terrestrial, freshwater and marine protected areas promises more effective conservation outcomes than disconnected reserves. Diadromous species in particular require more attention in aquatic restoration and conservation planning across disparate government agencies. 5. Human activities and stressors that increasingly threaten freshwater and marine fishes must be curbed to avoid a wave of extinctions. Freshwater recovery programmes range from plans for individual species to recovery of entire basin faunas. Reducing risks to threatened marine species in coastal habitats also requires conservation actions at multiple scales. Most of the world's larger economically important fisheries are relatively well-monitored and well-managed but there are urgent needs to curb fishing mortality and minimize catch of the most endangered species in both realms. Copyright (C) 2016 John Wiley & Sons, Ltd. DOI
640. Audas, TE; Audas, DE; Jacob, MD; Ho, JJD; Khacho, M; Wang, ML; Perera, JK; Gardiner, C; Bennett, CA; Head, T; Kryvenko, ON; Jorda, M; Daunert, S; Malhotra, A; Trinkle-Mulcahy, L; Gonzalgo, ML; Lee, S.Adaptation to stressors by Systemic Protein Amyloidogenesis.Developmental Cell, 2016, 39: 155-168 Adaptation to stressors by Systemic Protein Amyloidogenesis
The amyloid state of protein organization is typically associated with debilitating human neuropathies and is seldom observed in physiology. Here, we uncover a systemic program that leverages the amyloidogenic propensity of proteins to regulate cell adaptation to stressors. On stimulus, cells assemble the amyloid bodies (A-bodies), nuclear foci containing heterogeneous proteins with amyloid-like biophysical properties. A discrete peptidic sequence, termed the amyloid-converting motif (ACM), is capable of targeting proteins to the A-bodies by interacting with ribosomal intergenic noncoding RNA (rIGSRNA). The pathological beta-amyloid peptide, involved in Alzheimer's disease, displays ACM-like activity and undergoes stimuli-mediated amyloidogenesis in vivo. Upon signal termination, elements of the heat-shock chaperone pathway disaggregate the A-bodies. Physiological amyloidogenesis enables cells to store large quantities of proteins and enter a dormant state in response to stressors. We suggest that cells have evolved a post-translational pathway that rapidly and reversibly converts native-fold proteins to an amyloid-like solid phase. DOI
639. Ayranci, K; Dashtgard, SE.Asymmetrical deltas below wave base: Insights from the Fraser River Delta, Canada.Sedimentology, 2016, 63: 761-779 Asymmetrical deltas below wave base: Insights from the Fraser River Delta, Canada
Asymmetrical delta; Fraser River Delta; ichnology; neoichnology; sedimentology; tides
The Fraser River Delta exhibits distinct asymmetry in the sedimentological and neoichnological characteristics of the updrift (south) and downdrift (north) sides of the main distributary channel in water depths below storm-wave base. The asymmetry is the result of net northward tidal flow. Tides erode sediments across the updrift delta front, whereas the downdrift delta front is an area of net deposition. A submarine channel prevents sand eroded from the updrift delta front from reaching the downdrift delta. The updrift delta front and updrift upper prodelta are composed of sand or heterolithic sand and mud that show a low density of burrowing (Bioturbation Index 0 to 3) and are dominated by simple traces. The downdrift delta front and prodelta, and the updrift lower prodelta are composed of homogeneous muds with significantly higher bioturbation intensities (Bioturbation Index 3 to 6), and a more diverse suite of traces akin to Cruziana Ichnofacies. Using the Fraser River Delta as an archetype and comparing the Fraser to the Amazon River Delta, a preliminary model for deep-water (below storm-wave base: ca 20 m) asymmetrical deltas is proposed. Firstly, deep-water asymmetrical deltas are recognized from sediments deposited below storm-wave base. At these depths, tidal and ocean currents are more likely to impact sediment transport, but wave processes are less effective as a sediment transport mechanism. Sediments deposited below storm-wave base in deep-water asymmetrical deltas will display the following: (i) the updrift delta front will be coarser-grained (for example, sand-dominated or heterolithic sand and mud), than the downdrift delta front (for example, mud-dominated); and (ii) the updrift delta front should show low-diversity suites of simple burrows. Depending on sedimentation rates, the downdrift delta front and prodelta may show either high diversity suites of traces that are dominated by both complex and simple burrows (low sedimentation rates) or low density and diversity suites akin to the updrift delta front (high sedimentation rates). DOI
638. Barrio, IC; Bueno, CG; Gartzia, M; Soininen, EM; Christie, KS; Speed, JDM; Ravolainen, VT; Forbes, BC; Gauthier, G; Horstkotte, T; Hoset, KS; Hoye, TT; Jonsdottir, IS; Levesque, E; Morsdorf, MA; Olofsson, J; Wookey, PA; Hik, DS.Biotic interactions mediate patterns of herbivore diversity in the Arctic.Glob. Ecol. Biogeogr., 2016, 25: 1108-1118 Biotic interactions mediate patterns of herbivore diversity in the Arctic
Biodiversity; biotic interactions; predator-prey; species richness; trophic interactions; tundra
AimUnderstanding the forces shaping biodiversity patterns, particularly for groups of organisms with key functional roles, will help predict the responses of ecosystems to environmental changes. Our aim was to evaluate the relative role of different drivers in shaping the diversity patterns of vertebrate herbivores, a group of organisms exerting a strong trophic influence in terrestrial Arctic ecosystems. This biome, traditionally perceived as homogeneous and low in biodiversity, includes wide variation in biotic and physical conditions and is currently undergoing major environmental change. LocationThe Arctic (including the High Arctic, Low Arctic and Subarctic) MethodsWe compiled available data on vertebrate (birds and mammals) herbivore distribution at a pan-Arctic scale, and used eight variables that represent the most relevant hypotheses for explaining patterns of species richness. We used range maps rasterized on a 100kmx100km equal-area grid to analyse richness patterns of all vertebrate herbivore species combined, and birds and mammalian herbivores separately. ResultsOverall, patterns of herbivore species richness in the Arctic were positively related to plant productivity (measured using the normalized difference vegetation index) and to the species richness of predators. Greater species richness of herbivores was also linked to areas with a higher mean annual temperature. Species richness of avian and mammalian herbivores were related to the distance from the coast, with the highest avian richness in coastal areas and mammalian richness peaking further inland. Main conclusionsHerbivore richness in the Arctic is most strongly linked to primary productivity and the species richness of predators. Our results suggest that biotic interactions, with either higher or lower trophic levels or both, can drive patterns of species richness at a biome-wide scale. Rapid ongoing environmental changes in the Arctic are likely to affect herbivore diversity through impacts on both primary productivity and changes in predator communities via range expansion of predators from lower latitudes. DOI
636. Begin, C; Schelten, CK; Nugues, MM; Hawkins, J; Roberts, C; Côté, IM.Effects of Protection and Sediment Stress on Coral Reefs in Saint Lucia.PLoS One, 2016, 11 Effects of Protection and Sediment Stress on Coral Reefs in Saint Lucia
The extent to which Marine Protected Areas (MPAs) benefit corals is contentious. On one hand, MPAs could enhance coral growth and survival through increases in herbivory within their borders; on the other, they are unlikely to prevent disturbances, such as terrestrial runoff, that originate outside their boundaries. We examined the effect of spatial protection and terrestrial sediment on the benthic composition of coral reefs in Saint Lucia. In 2011 (10 to 16 years after MPAs were created), we resurveyed 21 reefs that had been surveyed in 2001 and analyzed current benthic assemblages as well as changes in benthic cover over that decade in relation to protection status, terrestrial sediment influence (measured as the proportion of terrigenous material in reef-associated sediment) and depth. The cover of all benthic biotic components has changed significantly over the decade, including a decline in coral and increase in macroalgae. Protection status was not a significant predictor of either current benthic composition or changes in composition, but current cover and change in cover of several components were related to terrigenous content of sediment deposited recently. Sites with a higher proportion of terrigenous sediment had lower current coral cover, higher macroalgal cover and greater coral declines. Our results suggest that terrestrial sediment is an important factor in the recent degradation of coral reefs in Saint Lucia and that the current MPA network should be complemented by measures to reduce runoff from land. DOI
635. Bhat, JM; Hutter, H.Pioneer Axon Navigation Is Controlled by AEX-3, a Guanine Nucleotide Exchange Factor for RAB-3 in Caenorhabditis elegans.Genetics, 2016, 203: 1235-1247 Pioneer Axon Navigation Is Controlled by AEX-3, a Guanine Nucleotide Exchange Factor for RAB-3 in Caenorhabditis elegans
nervous system; axon guidance; pioneer; GEF; vesicle trafficking
Precise and accurate axon tract formation is an essential aspect of brain development. This is achieved by the migration of early outgrowing axons (pioneers) allowing later outgrowing axons (followers) to extend toward their targets in the embryo. In Caenorhabditis elegans the AVG neuron pioneers the right axon tract of the ventral nerve cord, the major longitudinal axon tract. AVG is essential for the guidance of follower axons and hence organization of the ventral nerve cord. In an enhancer screen for AVG axon guidance defects in a nid-1/Nidogen mutant background, we isolated an allele of aex-3. aex-3 mutant animals show highly penetrant AVG axon navigation defects. These defects are dependent on a mutation in nid-1/Nidogen, a basement membrane component. Our data suggest that AEX-3 activates RAB-3 in the context of AVG axon navigation. aex-3 genetically acts together with known players of vesicular exocytosis: unc-64/Syntaxin, unc-31/CAPS, and ida-1/IA-2. Furthermore our genetic interaction data suggest that AEX-3 and the UNC-6/Netrin receptor UNC-5 act in the same pathway, suggesting AEX-3 might regulate the trafficking and/or insertion of UNC-5 at the growth cone to mediate the proper guidance of the AVG axon. DOI
634. Braun, DC; Moore, JW; Candy, J; Bailey, RE.Population diversity in salmon: linkages among response, genetic and life history diversity.Ecography, 2016, 39: 317-328 Population diversity in salmon: linkages among response, genetic and life history diversity
Response diversity and asynchrony are important for stability and resilience of meta-populations, however little is known about the mechanisms that might drive such processes. In salmon populations, response diversity and asynchrony have been linked to the stability of their meta-populations and the fisheries that integrate across them. We examined how population diversity influenced response diversity and asynchrony in 42 populations of Chinook salmon from the Fraser River, British Columbia. We examined diversity in the survival responses to large-scale ocean climate variables for populations that differed in life history. Different life-histories responded differently to ocean environmental conditions. For instance, an increase of offshore temperature was associated with decreased survival for a population with ocean rearing juveniles but increased survival for a population with stream rearing juveniles. In a second analysis, we examined asynchrony in abundance between populations, which we then correlated with life history, spatial, and genetic diversity. Populations that were more genetically distant had the most different population dynamics. Collectively, these results suggest that fine-scale population diversity can contribute to the asynchrony and response diversity that underpins the stability of fisheries or metapopulation dynamics, and emphasize the need to manage and conserve this scale of population diversity. DOI
633. Bueno, CG; Williamson, SN; Barrio, IC; Helgadottir, A; Hik, DS.Moss Mediates the Influence of Shrub Species on Soil Properties and Processes in Alpine Tundra.PLoS One, 2016, 11 Moss Mediates the Influence of Shrub Species on Soil Properties and Processes in Alpine Tundra
alpine plants
In tundra ecosystems, bryophytes influence soil processes directly and indirectly through interactions with overstory shrub species. We experimentally manipulated moss cover and measured seasonal soil properties and processes under two species of deciduous shrubs with contrasting canopy structures, Salix planifolia pulchra and Betula glandulosa-nana complex. Soil properties (seasonal temperature, moisture and C:N ratios) and processes (seasonal litter decomposition and soil respiration) were measured over twelve months. Shrub species identity had the largest influence on summer soil temperatures and soil respiration rates, which were higher under Salix canopies. Mosses were associated with lower soil moisture irrespective of shrub identity, but modulated the effects of shrubs on winter soil temperatures and soil C:N ratios so that moss cover reduced differences in soil winter temperatures between shrub species and reduced C:N ratios under Betula but not under Salix canopies. Our results suggest a central role of mosses in mediating soil properties and processes, with their influence depending on shrub species identity. Such species-dependent effects need to be accounted for when forecasting vegetation dynamics under ongoing environmental changes. DOI
632. Bulla, M; Valcu, M; Dokter, AM; Dondua, AG; Kosztolanyi, A; Rutten, AL; Helm, B; Sandercock, BK; Casler, B; Ens, BJ; Spiegel, CS; Hassell, CJ; Kupper, C; Minton, C; Burgas, D; Lank, DB; Payer, DC; Loktionov, EY; Nol, E; Kwon, E; Smith, F; Gates, HR; Vitnerova, H; Pruter, H; Johnson, JA; St Clair, JJH; Lamarre, JF; Rausch, J; Reneerkens, J; Conklin, JR; Burger, J; Liebezeit, J; Bety, J; Coleman, JT; Figuerola, J; Hooijmeijer, JCEW; Alves, JA; Smith, JAM; Weidinger, K; Koivula, K; Gosbell, K; Exo, KM; Niles, L; Koloski, L; McKinnon, L; Praus, L; Klaassen, M; Giroux, MA; Sladecek, M; Boldenow, ML; Goldstein, MI; Salek, M; Senner, N; Ronka, N; Lecomte, N; Gilg, O; Vincze, O; Johnson, OW; Smith, PA; Woodard, PF; Tomkovich, PS; Battley, PF; Bentzen, R; Lanctot, RB; Porter, R; Saalfeld, ST; Freeman, S; Brown, SC; Yezerinac, S; Szekely, T; Montalvo, T; Piersma, T; Loverti, V; Pakanen, VM; Tijsen, W; Kempenaers, B.Unexpected diversity in socially synchronized rhythms of shorebirds.Nature, 2016, 540: 109-+ Unexpected diversity in socially synchronized rhythms of shorebirds
The behavioural rhythms of organisms are thought to be under strong selection, influenced by the rhythmicity of the environment(1-4). Such behavioural rhythms are well studied in isolated individuals under laboratory conditions(1,5), but free-living individuals have to temporally synchronize their activities with those of others, including potential mates, competitors, prey and predators(6-10). Individuals can temporally segregate their daily activities (for example, prey avoiding predators, subordinates avoiding dominants) or synchronize their activities (for example, group foraging, communal defence, pairs reproducing or caring for offspring)(6-9,11). The behavioural rhythms that emerge from such social synchronization and the underlying evolutionary and ecological drivers that shape them remain poorly understood(5-7,9). Here we investigate these rhythms in the context of biparental care, a particularly sensitive phase of social synchronization(12) where pair members potentially compromise their individual rhythms. Using data from 729 nests of 91 populations of 32 biparentally incubating shorebird species, where parents synchronize to achieve continuous coverage of developing eggs, we report remarkable within-and between-species diversity in incubation rhythms. Between species, the median length of one parent's incubation bout varied from 1-19 h, whereas period length-the time in which a parent's probability to incubate cycles once between its highest and lowest value-varied from 6-43 h. The length of incubation bouts was unrelated to variables reflecting energetic demands, but species relying on crypsis (the ability to avoid detection by other animals) had longer incubation bouts than those that are readily visible or who actively protect their nest against predators. Rhythms entrainable to the 24-h light-dark cycle were less prevalent at high latitudes and absent in 18 species. Our results indicate that even under similar environmental conditions and despite 24-h environmental cues, social synchronization can generate far more diverse behavioural rhythms than expected from studies of individuals in captivity(5-7,9). The risk of predation, not the risk of starvation, may be a key factor underlying the diversity in these rhythms. DOI
631. Carroll, CS; Amankwa, LN; Pinto, LJ; Fuller, JD; Moore, MM.Detection of a Serum Siderophore by LC-MS/MS as a Potential Biomarker of Invasive Aspergillosis.PLoS One, 2016, 11 Detection of a Serum Siderophore by LC-MS/MS as a Potential Biomarker of Invasive Aspergillosis
Invasive aspergillosis (IA) is a life-threatening systemic mycosis caused primarily by Aspergillus fumigatus. Early diagnosis of IA is based, in part, on an immunoassay for circulating fungal cell wall carbohydrate, galactomannan (GM). However, a wide range of sensitivity and specificity rates have been reported for the GM test across various patient populations. To obtain iron in vivo, A. fumigatus secretes the siderophore, N, N', N ''-triacetylfusarinine C (TAFC) and we hypothesize that TAFC may represent a possible biomarker for early detection of IA. We developed an ultra performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) method for TAFC analysis from serum, and measured TAFC in serum samples collected from patients at risk for IA. The method showed lower and upper limits of quantitation (LOQ) of 5 ng/ml and 750 ng/ml, respectively, and complete TAFC recovery from spiked serum. As proof of concept, we evaluated 76 serum samples from 58 patients with suspected IA that were investigated for the presence of GM. Fourteen serum samples obtained from 11 patients diagnosed with probable or proven IA were also analyzed for the presence of TAFC. Control sera (n = 16) were analyzed to establish a TAFC cut-off value (>= 6 ng/ml). Of the 36 GM-positive samples (>= 0.5 GM index) from suspected IA patients, TAFC was considered positive in 25 (69%). TAFC was also found in 28 additional GM-negative samples. TAFC was detected in 4 of the 14 samples (28%) from patients with proven/probable aspergillosis. Log-transformed TAFC and GM values from patients with proven/probable IA, healthy individuals and SLE patients showed a significant correlation with a Pearson r value of 0.77. In summary, we have developed a method for the detection of TAFC in serum that revealed this fungal product in the sera of patients at risk for invasive aspergillosis. A prospective study is warranted to determine whether this method provides improved early detection of IA. DOI
629. Cekic, N; Heinonen, JE; Stubbs, KA; Roth, C; He, Y; Bennet, AJ; McEachern, EJ; Davies, GJ; Vocadlo, DJ.Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by human O-GlcNAcase.Chemical Science, 2016, 7: 3742-3750 Analysis of transition state mimicry by tight binding aminothiazoline inhibitors provides insight into catalysis by human O-GlcNAcase
The modification of nucleocytoplasmic proteins with O-linked N-acetylglucosamine (O-GlcNAc) plays diverse roles in multicellular organisms. Inhibitors of O-GlcNAc hydrolase (OGA), the enzyme that removes O-GlcNAc from proteins, lead to increased O-GlcNAc levels in cells and are seeing widespread adoption in the field as a research tool used in cells and in vivo. Here we synthesize and study a series of tight binding carbohydrate-based inhibitors of human OGA (hOGA). The most potent of these 2'-aminothiazolines binds with a sub-nanomolar K-i value to hOGA (510 +/- 50 pM) and the most selective has greater than 1 800 000-fold selectivity for hOGA over mechanistically related human lysosomal beta-hexosaminidase. Structural data of inhibitors in complex with an hOGA homologue reveals the basis for variation in binding among these compounds. Using linear free energy analyses, we show binding of these 2'-aminothiazoline inhibitors depends on the pK(a) of the aminothiazoline ring system, revealing the protonation state of the inhibitor is a key driver of binding. Using series of inhibitors and synthetic substrates, we show that 2'-aminothiazoline inhibitors are transition state analogues of hOGA that bind to the enzyme up to 1-million fold more tightly than the substrate. These collective data support an oxazoline, rather than a protonated oxazolinium ion, intermediate being formed along the reaction pathway. Inhibitors from this series will prove generally useful tools for the study of O-GlcNAc. The new insights gained here, into the catalytic mechanism of hOGA and the fundamental drivers of potency and selectivity of OGA inhibitors, should enable tuning of hOGA inhibitors with desirable properties. DOI
628. Chisholm, AD; Hutter, H; Jin, YS; Wadsworth, WG.The Genetics of Axon Guidance and Axon Regeneration in Caenorhabditis elegans.Genetics, 2016, 204: 849-882 The Genetics of Axon Guidance and Axon Regeneration in Caenorhabditis elegans
netrin; semaphorin; ephrin; Wnt; Slit; Robo; fasciculation; DLK; growth cone; actin; microtubule; WormBook
The correct wiring of neuronal circuits depends on outgrowth and guidance of neuronal processes during development. In the past two decades, great progress has been made in understanding the molecular basis of axon outgrowth and guidance. Genetic analysis in Caenorhabditis elegans has played a key role in elucidating conserved pathways regulating axon guidance, including Netrin signaling, the slit Slit/Robo pathway, Wnt signaling, and others. Axon guidance factors were first identified by screens for mutations affecting animal behavior, and by direct visual screens for axon guidance defects. Genetic analysis of these pathways has revealed the complex and combinatorial nature of guidance cues, and has delineated how cues guide growth cones via receptor activity and cytoskeletal rearrangement. Several axon guidance pathways also affect directed migrations of non-neuronal cells in C. elegans, with implications for normal and pathological cell migrations in situations such as tumor metastasis. The small number of neurons and highly stereotyped axonal architecture of the C. elegans nervous system allow analysis of axon guidance at the level of single identified axons, and permit in vivo tests of prevailing models of axon guidance. C. elegans axons also have a robust capacity to undergo regenerative regrowth after precise laser injury (axotomy). Although such axon regrowth shares some similarities with developmental axon outgrowth, screens for regrowth mutants have revealed regeneration-specific pathways and factors that were not identified in developmental screens. Several areas remain poorly understood, including how major axon tracts are formed in the embryo, and the function of axon regeneration in the natural environment. DOI
626. Collen, B; Dulvy, NK; Gaston, KJ; Gardenfors, U; Keith, DA; Punt, AE; Regan, HM; Bohm, M; Hedges, S; Seddon, M; Butchart, SHM; Hilton-Taylor, C; Hoffmann, M; Bachman, SP; Akcakaya, HR.Clarifying misconceptions of extinction risk assessment with the IUCN Red List.Biology Letters, 2016, 12 Clarifying misconceptions of extinction risk assessment with the IUCN Red List
climate change; geographical range; population decline; rarity; spatial autocorrelation; uncertainty
The identification of species at risk of extinction is a central goal of conservation. As the use of data compiled for IUCN Red List assessments expands, a number of misconceptions regarding the purpose, application and use of the IUCN Red List categories and criteria have arisen. We outline five such classes of misconception; the most consequential drive proposals for adapted versions of the criteria, rendering assessments among species incomparable. A key challenge for the future will be to recognize the point where understanding has developed so markedly that it is time for the next generation of the Red List criteria. We do not believe we are there yet but, recognizing the need for scrutiny and continued development of Red Listing, conclude by suggesting areas where additional research could be valuable in improving the understanding of extinction risk among species. DOI
624. Côté, IM; Darling, ES; Brown, CJ.Interactions among ecosystem stressors and their importance in conservation.Proceedings of the Royal Society B-Biological Sciences, 2016, 283 Interactions among ecosystem stressors and their importance in conservation
ecological surprises; non-additive effects; global change; ecological experiments
Interactions between multiple ecosystem stressors are expected to jeopardize biological processes, functions and biodiversity. The scientific community has declared stressor interactions-notably synergies-a key issue for conservation and management. Here, we review ecological literature over the past four decades to evaluate trends in the reporting of ecological interactions (synergies, antagonisms and additive effects) and highlight the implications and importance to conservation. Despite increasing popularity, and ever-finer terminologies, we find that synergies are (still) not the most prevalent type of interaction, and that conservation practitioners need to appreciate and manage for all interaction outcomes, including antagonistic and additive effects. However, it will not be possible to identify the effect of every interaction on every organism's physiology and every ecosystem function because the number of stressors, and their potential interactions, are growing rapidly. Predicting the type of interactions may be possible in the near-future, using meta-analyses, conservation-oriented experiments and adaptive monitoring. Pending a general framework for predicting interactions, conservation management should enact interventions that are robust to uncertainty in interaction type and that continue to bolster biological resilience in a stressful world. DOI
623. Crespi, BJ.Oxytocin, testosterone, and human social cognition.Biological Reviews, 2016, 91: 390-408 Oxytocin, testosterone, and human social cognition
oxytocin; testosterone; social cognition; autism; schizophrenia; depression
I describe an integrative social-evolutionary model for the adaptive significance of the human oxytocinergic system. The model is based on a role for this hormone in the generation and maintenance of social familiarity and affiliation across five homologous, functionally similar, and sequentially co-opted contexts: mothers with offspring, female and male mates, kin groups, individuals with reciprocity partners, and individuals within cooperating and competing social groups defined by culture. In each situation, oxytocin motivates, mediates and rewards the cognitive and behavioural processes that underlie the formation and dynamics of a more or less stable social group, and promotes a relationship between two or more individuals. Such relationships may be positive (eliciting neurological reward, reducing anxiety and thus indicating fitness-enhancing effects), or negative (increasing anxiety and distress, and thus motivating attempts to alleviate a problematic, fitness-reducing social situation). I also present evidence that testosterone exhibits opposite effects from oxytocin on diverse aspects of cognition and behaviour, most generally by favouring self-oriented, asocial and antisocial behaviours. I apply this model for effects of oxytocin and testosterone to understanding human psychological disorders centrally involving social behaviour. Reduced oxytocin and higher testosterone levels have been associated with under-developed social cognition, especially in autism. By contrast, some combination of oxytocin increased above normal levels, and lower testosterone, has been reported in a notable number of studies of schizophrenia, bipolar disorder and depression, and, in some cases, higher oxytocin involves maladaptively 'hyper-developed' social cognition in these conditions. This pattern of findings suggests that human social cognition and behaviour are structured, in part, by joint and opposing effects of oxytocin and testosterone, and that extremes of such joint effects partially mediate risks and phenotypes of autism and psychotic-affective conditions. These considerations have direct implications for the development of therapies for alleviating disorders of social cognition, and for understanding how such disorders are associated with the evolution of human cognitive-affective architecture. DOI
622. Crespi, BJ.The convergent and divergent evolution of social-behavioral economics.Behavioral and Brain Sciences, 2016, 39 The convergent and divergent evolution of social-behavioral economics
Human hunter-gatherers share a suite of traits with social insects, which demonstrates convergent social evolution of these taxa prior to agriculture. Humans differ from social insects in that their divisions of labor are more competitive than cooperative. Resulting higher within-group competition in humans has been alleviated by religion and culturally imposed monogamy, both of which also find parallels among social insects. DOI
621. Croll, DA; Dewar, H; Dulvy, NK; Fernando, D; Francis, MP; Galvan-Magana, F; Hall, M; Heinrichs, S; Marshall, A; Mccauley, D; Newton, KM; Notarbartolo-Di-Sciara, G; O'Malley, M; O'Sullivan, J; Poortvliet, M; Roman, M; Stevens, G; Tershy, BR; White, WT.Vulnerabilities and fisheries impacts: the uncertain future of manta and devil rays.Aquatic Conservation-Marine and Freshwater Ecosystems, 2016, 26: 562-575 Vulnerabilities and fisheries impacts: the uncertain future of manta and devil rays
coastal; ocean; conservation evaluation; endangered species; fish; fishing
1. Manta and devil rays of the subfamily Mobulinae (mobulids) are rarely studied, large, pelagic elasmobranchs, with all eight of well-evaluated species listed on the IUCN Red List as threatened or near threatened. 2. Mobulids have life history characteristics (matrotrophic reproduction, extremely low fecundity, and delayed age of first reproduction) that make them exceptionally susceptible to overexploitation. 3. Targeted and bycatch mortality from fisheries is a globally important and increasing threat, and targeted fisheries are incentivized by the high value of the global trade in mobulid gill plates. 4. Fisheries bycatch of mobulids is substantial in tuna purse seine fisheries. 5. Thirteen fisheries in 12 countries specifically targeting mobulids, and 30 fisheries in 23 countries with mobulid bycatch were identified. 6. Aside from a few recently enacted national restrictions on capture, there is no comprehensive monitoring, assessment or control of mobulid fisheries or bycatch. Recent listing through the Convention on the International Trade in Endangered Species (CITES) may benefit mobulids of the genus Manta (manta rays), but none of the mobulids in the genus Mobula (devil rays) are protected. 7. The relative economic costs of catch mitigation are minimal, particularly compared with a broad range of other, more complicated, marine conservation issues. Copyright (C) 2015 John Wiley & Sons, Ltd. DOI
620. Crossin, GT; Love, OP; Cooke, SJ; Williams, TD.Glucocorticoid manipulations in free-living animals: considerations of dose delivery, life-history context and reproductive state.Functional Ecology, 2016, 30: 116-125 Glucocorticoid manipulations in free-living animals: considerations of dose delivery, life-history context and reproductive state
baseline levels; corticosterone; cortisol; fitness; glucocorticoids; implants
1. Experimental glucocorticoid (GC) manipulations can be useful for identifying the mechanisms that drive life-history and fitness variation in free-living animals, but predicting the effects of GC treatment can be complicated. Much of the uncertainty stems from the multifaceted role of GCs in organismal metabolism, and their variable influence with respect to life-history stage, ecological context, age, sex and individual variation. 2. Glucocorticoid hormones have been implicated in the regulation of parental care in many vertebrate taxa but in two seemingly contradictory ways, which sets up a potential GC-induced 'reproductive conflict'. Circulating GCs mediate adaptive physiological and behavioural responses to stressful events, and elevated levels can lead to trade offs between reproductive effort and survival (e.g. the current reproduction vs. survival hypothesis). The majority of studies examining the fitness effects of GC manipulations extend from this hypothesis. However, when animals are not stressed (likely most of the time) baseline GCs act as key metabolic regulators of daily energy balance, homoeostasis, osmoregulation and food acquisition, with pleiotropic effects on locomotor activity or foraging behaviour. Slight increases in circulating baseline levels can then have positive effects on reproductive effort (e.g. the 'cort' fitness/adaptation hypotheses), but comparatively few GC manipulation studies have targeted these small, non-stress induced increases. 3. We review studies of GC manipulations and examine the specific hypotheses used to predict the effects of manipulations in wild, breeding vertebrates. We argue that given the dichotomous function of GCs the current 'reproduction vs. survival' paradigm is unnecessarily restrictive and predicts only deleterious GC effects on fitness. Therefore, a broader set of hypotheses should be considered when testing the fitness effects of GC manipulations. 4. When framing experimental manipulation studies, we urge researchers to consider three key points: life-history context (e.g. long vs. short lived, semelparous vs. iteroparous, etc.), ecological context and dose delivery. DOI
619. Dashtgard, SE; MacEachern, JA.Unburrowed mudstones may record only slightly lowered oxygen conditions in warm, shallow basins.Geology, 2016, 44: 371-374 Unburrowed mudstones may record only slightly lowered oxygen conditions in warm, shallow basins
Unbioturbated mudstones and highly bioturbated silty and sandy mudstones from the late Albian of Alberta, Canada, are characterized by their ichnological, foraminiferal, and geochemical signatures. A comparison of these data sets is undertaken to isolate the dissolved oxygen (DO) conditions that led to the preservation of unbioturbated mudstones versus highly bioturbated silty and sandy mudstones. Highly diverse and abundant benthic foraminiferal assemblages, coupled with conclusive geochemical signatures, indicate that unbioturbated mudstones were deposited under oxic bottom waters. The paucity of bioturbation in these rocks is attributed to the persistence of low-oxic conditions (5 > DO > 2 mg L-1) at the seafloor, comparable to the present-day Gulf of Mexico. We assert that unbioturbated mudstone should not automatically be attributed to oxygen deficiency (< 2 mg L-1). Instead, it may reflect oxygenation sufficient to support benthic microfauna (foraminifera) but insufficient to sustain a diverse ecosystem of macrofauna (burrowing fauna). Moreover, we propose that the distribution of unburrowed mudstones deposited below low-oxic waters is predictable. A paucity of bioturbation is normal in shallow marine (below fair-weather wave base to similar to 200 m water depth) deposits of subtropical to tropical ocean basins and/or semienclosed seaways. DOI
618. Davidson, LNK; Krawchuk, MA; Dulvy, NK.Why have global shark and ray landings declined: improved management or overfishing?Fish and Fisheries, 2016, 17: 438-458 Why have global shark and ray landings declined: improved management or overfishing?
Conservation; Convention on International Trade in Endangered Species; elasmobranch; fin trade; fishing mortality; National Plans of Action
Global chondrichthyan (shark, ray, skate and chimaera) landings, reported to the United Nations Food and Agriculture Organization (FAO), peaked in 2003 and in the decade since have declined by almost 20%. In the FAO's 2012 'State of the World's Fisheries and Aquaculture' report, the authors 'hoped' the reductions in landings were partially due to management implementation rather than population decline. Here, we tested their hypothesis. Post-peak chondrichthyan landings trajectories from 126 countries were modelled against seven indirect and direct fishing pressure measures and eleven measures of fisheries management performance, while accounting for ecosystem attributes. We found the recent improvement in international or national fisheries management was not yet strong enough to account for the recent decline in chondrichthyan landings. Instead, the landings declines were more closely related to fishing pressure and ecosystem attribute measures. Countries with the greatest declines had high human coastal population sizes or high shark and ray meat exports such as Pakistan, Sri Lanka and Thailand. While important progress had been made, country-level fisheries management measures did not yet have the strength or coverage to halt overfishing and avert population declines of chondrichthyans. Increased implementation of legally binding operational fisheries management and species-specific reporting is urgently required to avoid declines and ensure fisheries sustainability and food security. DOI
616. Dulvy, NK; Davidson, LNK; Kyne, PM; Simpfendorfer, CA; Harrison, LR; Carlson, JK; Fordham, SV.Ghosts of the coast: global extinction risk and conservation of sawfishes.Aquatic Conservation-Marine and Freshwater Ecosystems, 2016, 26: 134-153 Ghosts of the coast: global extinction risk and conservation of sawfishes
estuary; functional redundancy; habitat degradation and loss; mangrove; range contraction
1. Sawfish are arguably the world's most imperilled marine fishes. All five species are classified as highly threatened with extinction: three are Critically Endangered (smalltooth sawfish Pristis pectinata, largetooth sawfish Pristis pristis, and green sawfish Pristis zijsron); two are Endangered (narrow sawfish Anoxypristis cuspidata, and dwarf sawfish Pristis clavata). 2. Sawfishes are threatened primarily due to a combination of their low intrinsic rates of population increase, high catchability in fisheries, and high value. Sawfishes are among the world's largest marine fishes, and they are caught by a wide range of fishing gears owing to their tooth-studded rostra being easily entangled. Sawfish fins are some of the most valuable for shark fin soup, and their rostra have long been traded as curios. In addition, they inhabit shallow coastal waters, estuaries, and rivers of the tropics and subtropics, down to a maximum depth rarely exceeding 100 m and are associated with threatened mangrove and seagrass habitats. 3. Historically, sawfishes were distributed in the coastal waters of 90 countries and territories. Over the past century, their geographic distribution has been greatly diminished. For example, the smalltooth sawfish is now found in <20% of its former range. Globally, sawfishes are now entirely absent from 20 countries; 43 countries have lost at least one species. 4. Sawfishes are legally protected, to some degree, in 16 of the 90 range states. These safeguards encompass, on average, 81% of their Extant distribution; however, the quality and breadth of protection varies dramatically across countries and species. Smalltooth sawfish currently has the least amount of such coverage of only half (49%) of Extant distribution. 5. he global conservation strategy specifies actions to protect sawfish and their habitats. Such actions are urgently warranted to avoid global extinction and to restore robust populations for the benefit of coastal ecosystem function and biodiversity. (c) 2014 The Authors. Aquatic Conservation: Marine and Freshwater Ecosystems published by John Wiley & Sons, Ltd. DOI
615. Dunn, JC; Buchanan, GM; Stein, RW; Whittingham, MJ; McGowan, PJK.Optimising different types of biodiversity coverage of protected areas with a case study using Himalayan Galliformes.Biological Conservation, 2016, 196: 22-30 Optimising different types of biodiversity coverage of protected areas with a case study using Himalayan Galliformes
Species distribution modelling; Conservation priority-setting; Maxent; Degazettement
International targets have committed governments to expanding the global protected area (PA) network to 17% of the terrestrial surface by 2020. Optimising PA placement in the landscape is challenging due to a poor knowledge of biodiversity distribution and multiple definitions of conservation value. We explore these two issues using a case study of a highly threatened bird Order in a region of conservation concern where PA network effectiveness for biodiversity has not been formally explored previously. To determine if the existing PA network protects the most important areas for 24 species of Himalayan Galliformes, we use a novel method to compare the current network placement to results produced from Zonation prioritisation software and modelled species distributions. Specifically, we identify areas of high species richness and then weight maps by three different species specific conservation values. The current PA network captures ranges poorly. We found statistically significantly poorer fits between the optimal and the existing placement of the Himalayan PA network for Zonation results that were: (i) unweighted; (ii) weighted by Red List score; and (iii) weighted by endemism to the Himalaya. Across these and two other Zonation results, the placement of the optimal PA network covered 58% more of Galliformes distributions than the existing network. We advocate some refinements to the existing PA network to maximise Galliformes coverage and suggest that our method could be used to model the optimal PA network for a wide range of species and/or regions, something which will support the assessment and attainment of CBD targets. Crown Copyright (C) 2016 Published by Elsevier Ltd. DOI
614. Flamarique, IN.Diminished foraging performance of a mutant zebrafish with reduced population of ultraviolet cones.Proceedings of the Royal Society B-Biological Sciences, 2016, 283 Diminished foraging performance of a mutant zebrafish with reduced population of ultraviolet cones
ultraviolet cone; retina; foraging; zebrafish
Ultraviolet (UV) cones are photoreceptors that sense light in the range 300-450 nm and are found in the retinas of non-mammalian vertebrates and small mammals. Despite their widespread presence across taxa, the functions that these cones exert in the lives of animals remain largely unknown. In this study, I used the zebrafish for (lots of rods) mutant, characterized by a diminished UV cone population compared to that of wild-type zebrafish, to test whether its foraging performance differed from that of the wild-type (control). The mean location distance and angle (variables that are reliable indicators of foraging performance) at which control fish detected zooplankton prey were, on average, 24 and 90% greater than corresponding measures for for fish. Such inferior foraging performance of the mutant could be explained by reduced contrast perception of the prey, resulting from the diminished population of UV cones and associated sensitivity. Thus, UV cones enhance the foraging performance of zebrafish, a crucial ecological function that may explain why small zooplanktivorous fishes retain UV cones throughout their lives. DOI
613. Frishkoff, LO; Karp, DS; Flanders, JR; Zook, J; Hadly, EA; Daily, GC; M'Gonigle, LK.Climate change and habitat conversion favour the same species.Ecology Letters, 2016, 19: 1081-1090 Climate change and habitat conversion favour the same species
Anthropocene; bird; climate niche; countryside biogeography; deforestation; habitat conversion; homogenisation
Land-use change and climate change are driving a global biodiversity crisis. Yet, how species' responses to climate change are correlated with their responses to land-use change is poorly understood. Here, we assess the linkages between climate and land-use change on birds in Neotropical forest and agriculture. Across > 300 species, we show that affiliation with drier climates is associated with an ability to persist in and colonise agriculture. Further, species shift their habitat use along a precipitation gradient: species prefer forest in drier regions, but use agriculture more in wetter zones. Finally, forest-dependent species that avoid agriculture are most likely to experience decreases in habitable range size if current drying trends in the Neotropics continue as predicted. This linkage suggests a synergy between the primary drivers of biodiversity loss. Because they favour the same species, climate and land-use change will likely homogenise biodiversity more severely than otherwise anticipated. DOI
612. Genge, CE; Stevens, CM; Davidson, WS; Singh, G; Tieleman, DP; Tibbits, GF.Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC.Genome Biology and Evolution, 2016, 8: 994-1011 Functional Divergence in Teleost Cardiac Troponin Paralogs Guides Variation in the Interaction of TnI Switch Region with TnC
molecular coevolution; protein interaction; functional divergence; structural subfunctionalization; regulatory subfunctionalization; troponin
Gene duplication results in extra copies of genes that must coevolve with their interacting partners in multimeric protein complexes. The cardiac troponin (Tn) complex, containing TnC, Tnl, and TnT, forms a distinct functional unit critical for the regulation of cardiac muscle contraction. In teleost fish, the function of the Tn complex is modified by the consequences of differential expression of paralogs in response to environmental thermal challenges. In this article, we focus on the interaction between TnI and TnC, coded for by genes that have independent evolutionary origins, but the co-operation of their protein products has necessitated coevolution. In this study, we characterize functional divergence of TnC and TnI paralogs, specifically the interrelated roles of regulatory subfunctionalization and structural subfunctionalization. We determined that differential paralog transcript expression in response to temperature acclimation results in three combinations of TnC and TnI in the zebrafish heart: TnC TnC1b/Tn11.1, and TnCla/Tn11.5. Phylogenetic analysis of these highly conserved proteins identified functionally divergent residues in TnI and TnC. The structural and functional effect of these Tn combinations was modeled with molecular dynamics simulation to link divergent sites to changes in interaction strength. Functional divergence in TnI and TnC were not limited to the residues involved with TnC/TnI switch interaction, which emphasizes the complex nature of Tn function. Patterns in domain-specific divergent selection and interaction energies suggest that substitutions in the TnI switch region are crucial to modifying TnI/TnC function to maintain cardiac contraction with temperature changes. This integrative approach introduces Tn as a model of functional divergence that guides the coevolution of interacting proteins. DOI
611. Gibbs, J; Elle, E; Bobiwash, K; Haapalainen, T; Isaacs, R.Contrasting Pollinators and Pollination in Native and Non-Native Regions of Highbush Blueberry Production.PLoS One, 2016, 11 Contrasting Pollinators and Pollination in Native and Non-Native Regions of Highbush Blueberry Production
Highbush blueberry yields are dependent on pollination by bees, and introduction of managed honey bees is the primary strategy used for pollination of this crop. Complementary pollination services are also provided by wild bees, yet highbush blueberry is increasingly grown in regions outside its native range where wild bee communities may be less adapted to the crop and growers may still be testing appropriate honey bee stocking densities. To contrast crop pollination in native and non-native production regions, we sampled commercial 'Bluecrop' blueberry fields in British Columbia and Michigan with grower-selected honey bee stocking rates (0-39.5 hives per ha) to compare bee visitors to blueberry flowers, pollination and yield deficits, and how those vary with local-and landscape-scale factors. Observed and Chao-1 estimated species richness, as well as Shannon diversity of wild bees visiting blueberries were significantly higher in Michigan where the crop is within its native range. The regional bee communities were also significantly different, with Michigan farms having greater dissimilarity than British Columbia. Blueberry fields in British Columbia had fewer visits by honey bees than those in Michigan, irrespective of stocking rate, and they also had lower berry weights and a significant pollination deficit. In British Columbia, pollination service increased with abundance of wild bumble bees, whereas in Michigan the abundance of honey bees was the primary predictor of pollination. The proportion of seminatural habitat at local and landscape scales was positively correlated with wild bee abundance in both regions. Wild bee abundance declined significantly with distance from natural borders in Michigan, but not in British Columbia where large-bodied bumble bees dominated the wild bee community. Our results highlight the varying dependence of crop production on different types of bees and reveal that strategies for pollination improvement in the same crop can vary greatly across production regions. DOI
610. Groner, ML; Rogers, LA; Bateman, AW; Connors, BM; Frazer, LN; Godwin, SC; Krkosek, M; Lewis, MA; Peacock, SJ; Rees, EE; Revie, CW; Schlagel, UE.Lessons from sea louse and salmon epidemiology.Philosophical Transactions of the Royal Society B-Biological Sciences, 2016, 371 Lessons from sea louse and salmon epidemiology
Atlantic salmon; ecological modelling; emerging infectious disease; fish farm; marine disease; Pacific salmon
Effective disease management can benefit from mathematical models that identify drivers of epidemiological change and guide decision-making. This is well illustrated in the host-parasite system of sea lice and salmon, which has been modelled extensively due to the economic costs associated with sea louse infections on salmon farms and the conservation concerns associated with sea louse infections on wild salmon. Consequently, a rich modelling literature devoted to sea louse and salmon epidemiology has been developed. We provide a synthesis of the mathematical and statistical models that have been used to study the epidemiology of sea lice and salmon. These studies span both conceptual and tactical models to quantify the effects of infections on host populations and communities, describe and predict patterns of transmission and dispersal, and guide evidence-based management of wild and farmed salmon. As aquaculture production continues to increase, advances made in modelling sea louse and salmon epidemiology should inform the sustainable management of marine resources. DOI
609. Gutierrez-Cabrera, AE; Cordoba-Aguilar, A; Zenteno, E; Lowenberger, C; Espinoza, B.Origin, evolution and function of the hemipteran perimicrovillar membrane with emphasis on Reduviidae that transmit Chagas disease.Bulletin of Entomological Research, 2016, 106: 279-291 Origin, evolution and function of the hemipteran perimicrovillar membrane with emphasis on Reduviidae that transmit Chagas disease
evolution; perimicrovillar membrane; insects; triatomines
The peritrophic matrix is a chitin-protein structure that envelops the food bolus in the midgut of the majority of insects, but is absent in some groups which have, instead, an unusual extra-cellular lipoprotein membrane named the perimicrovillar membrane. The presence of the perimicrovillar membrane (PMM) allows these insects to exploit restricted ecological niches during all life stages. It is found only in some members of the superorder Paraneoptera and many of these species are of medical and economic importance. In this review we present an overview of the midgut and the digestive system of insects with an emphasis on the order Paraneoptera and differences found across phylogenetic groups. We discuss the importance of the PMM in Hemiptera and the apparent conservation of this structure among hemipteran groups, suggesting that the basic mechanism of PMM production is the same for different hemipteran species. We propose that the PMM is intimately involved in the interaction with parasites and as such should be a target for biological and chemical control of hemipteran insects of economic and medical importance. DOI
607. Hanson, MA; Clague, JJ.Record of glacial Lake Missoula floods in glacial Lake Columbia, Washington.Quat. Sci. Rev., 2016, 133: 62-76 Record of glacial Lake Missoula floods in glacial Lake Columbia, Washington
Glacial Lake Missoula; Glacial Lake Columbia; Outburst floods; Stratigraphy; Sedimentology
During the last glaciation (marine oxygen isotope stage 2), outburst floods from glacial Lake Missoula deposited diagnostic sediments within glacial Lake Columbia. Two dominant outburst flood lithofacies are present within glacial Lake Columbia deposits: a flood expansion bar facies and a finer-grained hyperpycnite facies. We conclude that the flood sediments have a glacial Lake Missoula source because: (1) current indicators indicate westward flow through the lake, and upvalley flow followed by downvalley flow in tributary valleys; (2) no flood sediments are found north of a certain point; (3) there is a dominance of Belt-Purcell Supergroup clasts in a flood expansion bar; and (4) some of the finer grained beds have a pink colour, reflective of glacial Lake Missoula lake-bottom sediments. A new radiocarbon age of 13,400 +/- 100 C-14 BP on plant detritus found below 37 flood beds helps constrain the timing of outburst flooding from glacial Lake Missoula. (C) 2015 Elsevier Ltd. All rights reserved. DOI
606. Harden, N; Wang, SJH; Krieger, C.Making the connection - shared molecular machinery and evolutionary links underlie the formation and plasticity of occluding junctions and synapses.Journal of Cell Science, 2016, 129: 3067-3076 Making the connection - shared molecular machinery and evolutionary links underlie the formation and plasticity of occluding junctions and synapses
Epithelial plasticity; Paranodal junction; Septate junction; Synapse; Synaptic plasticity; Tight junction
The pleated septate junction (pSJ), an ancient structure for cell-cell contact in invertebrate epithelia, has protein components that are found in three more-recent junctional structures, the neuronal synapse, the paranodal region of the myelinated axon and the vertebrate epithelial tight junction. These more-recent structures appear to have evolved through alterations of the ancestral septate junction. During its formation in the developing animal, the pSJ exhibits plasticity, although the final structure is extremely robust. Similar to the immature pSJ, the synapse and tight junctions both exhibit plasticity, and we consider evidence that this plasticity comes at least in part from the interaction of members of the immunoglobulin cell adhesion molecule superfamily with highly regulated membrane-associated guanylate kinases. This plasticity regulation probably arose in order to modulate the ancestral pSJ and is maintained in the derived structures; we suggest that it would be beneficial when studying plasticity of one of these structures to consider the literature on the others. Finally, looking beyond the junctions, we highlight parallels between epithelial and synaptic membranes, which both show a polarized distribution of many of the same proteins - evidence that determinants of apicobasal polarity in epithelia also participate in patterning of the synapse. DOI
605. Hennin, HL; Bety, J; Legagneux, P; Gilchrist, HG; Williams, TD; Love, OP.Energetic Physiology Mediates Individual Optimization of Breeding Phenology in a Migratory Arctic Seabird.American Naturalist, 2016, 188: 434-445 Energetic Physiology Mediates Individual Optimization of Breeding Phenology in a Migratory Arctic Seabird
individual optimization; breeding phenology; fattening rate; energetic management; triglycerides; glucocorticoids
The influence of variation in individual state on key reproductive decisions impacting fitness is well appreciated in evolutionary ecology. Rowe et al. (1994) developed a condition-dependent individual optimization model predicting that three key factors impact the ability of migratory female birds to individually optimize breeding phenology to maximize fitness in seasonal environments: arrival condition, arrival date, and ability to gain in condition on the breeding grounds. While empirical studies have confirmed that greater arrival body mass and earlier arrival dates result in earlier laying, no study has assessed whether individual variation in energetic management of condition gain effects this key fitness-related decision. Using an 8-year data set from over 350 prebreeding female Arctic common eiders (Somateria mollissima), we tested this component of the model by examining whether individual variation in two physiological traits influencing energetic management (plasma triglycerides: physiological fattening rate; baseline corticosterone: energetic demand) predicted individual variation in breeding phenology after controlling for arrival date and body mass. As predicted by the optimization model, individuals with higher fattening rates and lower energetic demand had the earliest breeding phenology (shortest delays between arrival and laying; earliest laying dates). Our results are the first to empirically determine that individual flexibility in prebreeding energetic management influences key fitness-related reproductive decisions, suggesting that individuals have the capacity to optimally manage reproductive investment. DOI
604. Holding, S; Allen, DM; Foster, S; Hsieh, A; Larocque, I; Klassen, J; Van Pelt, SC.Groundwater vulnerability on small islands.Nat. Clim. Chang., 2016, 6: 1100-+ Groundwater vulnerability on small islands
The majority of naturally occurring freshwater on small islands is groundwater, which is primarily recharged by precipitation(1). Recharge rates are therefore likely to be impacted by climate change(2). Freshwater resources on small islands are particularly vulnerable to climate change because they are limited in size and easily compromised(3-5). Here we have compiled available aquifer system characteristics and water-use data for 43 small island developing states distributed worldwide, based on local expert knowledge, publications and regional data sets. Current vulnerability was assessed by evaluating the recharge volume per capita. For future vulnerability, climate change projections were used to estimate changes in aquifer recharge. We find that 44% of islands are in a state of water stress, and while recharge is projected to increase by as much as 117% on 12 islands situated in the western Pacific and Indian Ocean, recharge is projected to decrease by up to 58% on the remaining 31 islands. Of great concern is the lack of enacted groundwater protection legislation for many of the small island developing states identified as highly vulnerable to current and future conditions. Recharge indicators, shown alongside the state of legal groundwater protections, provide a global picture of groundwater supply vulnerability under current and future climate change conditions. DOI
603. Hurteau, LA; Mooers, AO; Reynolds, JD; Hocking, MD.Salmon nutrients are associated with the phylogenetic dispersion of riparian flowering-plant assemblages.Ecology, 2016, 97: 450-460 Salmon nutrients are associated with the phylogenetic dispersion of riparian flowering-plant assemblages
angiosperms; community assembly; flowering plants; marine nutrient subsidy; mean nearest taxon distance; Oncorhynchus; phylogenetic community structure; salmon
A signature of nonrandom phylogenetic community structure has been interpreted as indicating community assembly processes. Significant clustering within the phylogenetic structure of a community can be caused by habitat filtering due to low nutrient availability. Nutrient limitation in temperate Pacific coastal rainforests can be alleviated to some extent by marine nutrient subsidies introduced by migrating salmon, which leave a quantitative signature on the makeup of plant communities near spawning streams. Thus, nutrient-mediated habitat filtering could be reduced by salmon nutrients. Here, we ask how salmon abundance affects the phylogenetic structure of riparian flowering plant assemblages across 50 watersheds in the Great Bear Rainforest of British Columbia, Canada. Based on a regional pool of 60 plant species, we found that assemblages become more phylogenetically dispersed and species poor adjacent to streams with higher salmon spawning density. In contrast, increased phylogenetic clumping and species richness was seen in sites with low salmon density, with steeper slopes, further from the stream edge, and within smaller watersheds. These observations are all consistent with abiotic habitat filtering and biotic competitive exclusion acting together across local and landscape-scale gradients in nutrient availability to structure assembly of riparian flowering plants. In this case, rich salmon nutrients appear to release riparian flowering-plant assemblages from the confines of a low-nutrient habitat filter that drives phylogenetic clustering. DOI
602. Irwin, DE; Alcaide, M; Delmore, KE; Irwin, JH; Owens, GL.Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species.Molecular Ecology, 2016, 25: 4488-4507 Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species
genomic differentiation; greenish warbler; linked selection; Phylloscopus trochiloides; selective sweep; speciation
Recent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this 'sweep-before-differentiation' model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions. DOI
601. Iworima, DG; Pasqualotto, BA; Rintoul, GL.Kif5 regulates mitochondrial movement, morphology, function and neuronal survival.Molecular and Cellular Neuroscience, 2016, 72: 22-33 Kif5 regulates mitochondrial movement, morphology, function and neuronal survival
kif5; Mitochondrial dynamics; Mitochondrial remodelling excitotoxicity; Mitochondrial trafficking; ro-GFP; ATeam
Due to the unique architecture of neurons, trafficking of mitochondria throughout processes to regions of high energetic demand is critical to sustain neuronal health. It has been suggested that compromised mitochondrial trafficking may play a role in neurodegenerative diseases. We evaluated the consequences of disrupted kif5c-mediated mitochondrial trafficking on mitochondrial form and function in primary rat cortical neurons. Morphological changes in mitochondria appeared to be due to remodelling, a phenomenon distinct from mitochondrial fission, which resulted in punctate-shaped mitochondria. We also demonstrated that neurons displaying punctate mitochondria exhibited relatively decreased ROS and increased cellular ATP levels using ROS-sensitive GFP and ATP FRET probes, respectively. Somewhat unexpectedly, neurons overexpressing the dominant negative form of kif5c exhibited enhanced survival following excitotoxicity, suggesting that the impairment of mitochondrial trafficking conferred some form of neuroprotection. However, when neurons were exposed to H2O2, disruption of kif5c exacerbated cell death indicating that the effect on cell viability was dependent on the mode of toxicity. Our results suggest a novel role of kif5c. In addition to mediating mitochondrial transport, kif5c plays a role in the mechanism of regulating mitochondrial morphology. Our results also suggest that kif5c mediated mitochondrial dynamics may play an important role in regulating mitochondrial function and in turn cellular health. Moreover, our studies demonstrate an interesting interplay between the regulation of mitochondrial motility and morphology. (C) 2016 Elsevier Inc. All rights reserved. DOI
600. Jackson, M; Belton, P; McMahon, S; Hart, M; McCann, S; Azevedo, D; Hurteau, L.The First Record of Aedes (Hulecoeteomyia) japonicus (Diptera: Culicidae) and Its Establishment in Western Canada.Journal of Medical Entomology, 2016, 53: 241-244 The First Record of Aedes (Hulecoeteomyia) japonicus (Diptera: Culicidae) and Its Establishment in Western Canada
invasive species; virus vector; distribution; overwintering
The potential disease-carrying mosquito, Aedes japonicus (Theobald) (Diptera: Culicidae), was identified among larvae collected in suburban Vancouver, BC, in July 2014, and over 200 were found at the same site in February 2015 where it presumably had overwintered in the egg stage. In late May 2015, a female was captured taking a bloodmeal 13km east of the larval site. This population and those in the Washington and Oregon states are clearly disjunct from those in eastern North America, and their origin, probably from one or more different introductions from Asia, is discussed. Key characters of those in British Columbia are examined and match the description of subspecies japonicus, presumably like the others in North America.Website DOI
599. Jeng, SCY; Chan, HHY; Booy, EP; Mckenna, SA; Unrau, PJ.Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers.RNA, 2016, 22: 1884-1892 Fluorophore ligand binding and complex stabilization of the RNA Mango and RNA Spinach aptamers
aptamer; fluorophore; RNA Mango; RNA Spinach; concerted binding; G-quadruplex
The effective tracking and purification of biological RNAs and RNA protein complexes is currently challenging. One promising strategy to simultaneously address both of these problems is to develop high-affinity RNA aptamers against taggable small molecule fluorophores. RNA Mango is a 39-nucleotide, parallel-stranded G-quadruplex RNA aptamer motif that binds with nanomolar affinity to a set of thiazole orange (TO1) derivatives while simultaneously inducing a 10(3)-fold increase in fluorescence. We find that RNA Mango has a large increase in its thermal stability upon the addition of its TO1-Biotin ligand. Consistent with this thermal stabilization, RNA Mango can effectively discriminate TO1-Biotin from a broad range of small molecule fluorophores. In contrast, RNA Spinach, which is known to have a substantially more rigid G-quadruplex structure, was found to bind to this set of fluorophores, often with higher affinity than to its native ligand, 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI), and did not exhibit thermal stabilization in the presence of the TO1-Biotin fluorophore. Our data suggest that RNA Mango is likely to use a concerted ligand-binding mechanism that allows it to simultaneously bind and recognize its TO1-Biotin ligand, whereas RNA Spinach appears to lack such a mechanism. The high binding affinity and fluorescent efficiency of RNA Mango provides a compelling alternative to RNA Spinach as an RNA reporter system and paves the way for the future development of small fluorophore RNA reporter systems. DOI
598. Johansen, J; Alfaro, G; Beh, CT.Polarized Exocytosis Induces Compensatory Endocytosis by Sec4p-Regulated Cortical Actin Polymerization.PLoS Biology, 2016, 14 Polarized Exocytosis Induces Compensatory Endocytosis by Sec4p-Regulated Cortical Actin Polymerization
Polarized growth ismaintained by both polarized exocytosis, which transports membrane components to specific locations on the cell cortex, and endocytosis, which retrieves these components before they can diffuse away. Despite functional links between these two transport pathways, they are generally considered to be separate events. Using live cell imaging, in vivo and in vitro protein binding assays, and in vitro pyrene-actin polymerization assays, we show that the yeast Rab GTPase Sec4p couples polarized exocytosis with cortical actin polymerization, which induces endocytosis. After polarized exocytosis to the plasma membrane, Sec4p binds Las17/Bee1p (yeastWiskott-Aldrich Syndrome protein [WASp]) in a complex with Sla1p and Sla2p during actin patch assembly. Mutations that inactivate Sec4p, or its guanine nucleotide exchange factor (GEF) Sec2p, inhibit actin patch formation, whereas the activating sec4-Q79L mutation accelerates patch assembly. In vitro assays of Arp2/3-dependent actin polymerization established that GTP.S-Sec4p overrides Sla1p inhibition of Las17p-dependent actin nucleation. These results support a model in which Sec4p relocates along the plasma membrane frompolarized sites of exocytic vesicle fusion to nascent sites of endocytosis. Activated Sec4p then promotes actin polymerization and triggers compensatory endocytosis, which controls surface expansion and kinetically refines cell polarization. DOI
597. Karp, DS; Moses, R; Gennet, S; Jones, MS; Joseph, S; M'Gonigle, LK; Ponisio, LC; Snyder, WE; Kremen, C.Agricultural practices for food safety threaten pest control services for fresh produce.Journal of Applied Ecology, 2016, 53: 1402-1412 Agricultural practices for food safety threaten pest control services for fresh produce
agriculture; agro-ecology; biological control; co-management; compost; food safety; foodborne disease; natural enemies; pest control; produce
1. Over the past decade, several foodborne disease outbreaks provoked widespread reforms to the fresh produce industry. Subsequent concerns about wildlife vectors and contaminated manures created pressure on growers to discontinue use of manure-based composts and remove nearby semi-natural vegetation. Despite widespread adoption, impacts of these practices on ecosystem services such as pest control have not been assessed. 2. We used a landscape-scale field experiment to quantify associations between compost applications, semi-natural vegetation, pest control services and lettuce yields on organic farms throughout California's Central Coast, a region experiencing food safety reforms. 3. We found that farms with surrounding semi-natural vegetation supported a diverse arthropod assemblage, whereas a herbivore-dominated assemblage occupied farms in simplified landscapes. Moreover, predatory arthropods consumed more herbivores at sites with more surrounding non-crop vegetation and reduced aphid pest infestations in lettuce. 4. Compost improved lettuce yields by increasing soil nutrients and organic matter, but affected neither pest control nor Escherichia coli prevalence. 5. Synthesis and applications. Food safety concerns are prompting practices that simplify farms and landscapes. Our results demonstrate that two practices elimination of manure based composts and removal of non-crop vegetation are likely having negative impacts on arthropod biodiversity, pest control and soil quality. Critically, our findings and previous research suggest that compost can be applied safely and that habitat removal is likely ineffective at mitigating food safety risk. There is thus scope for co-managing fresh produce fields for food safety, ecosystem services, and biodiversity through applying appropriately treated composts and stopping habitat removal. DOI
596. Keeling, CI; Li, M; Sandhu, HK; Henderson, H; Saint Yuen, MM; Bohlmann, J.Quantitative metabolome, proteome and transcriptome analysis of midgut and fat body tissues in the mountain pine beetle, Dendroctonus ponderosae Hopkins, and insights into pheromone biosynthesis.Insect Biochemistry and Molecular Biology, 2016, 70: 170-183 Quantitative metabolome, proteome and transcriptome analysis of midgut and fat body tissues in the mountain pine beetle, Dendroctonus ponderosae Hopkins, and insights into pheromone biosynthesis
Cytochrome P450; Mevalonate pathway; Midgut; Fat bodies
Bark beetles (Coleoptera: Scolytinae) are pests of many forests around the world. The mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins, is a significant pest of western North American pine forests. The MPB is able to overcome the defences of pine trees through pheromone-assisted aggregation that results in a mass attack of host trees. These pheromones, both male and female produced, are believed to be biosynthesized in the midgut and/or fat bodies of these insects. We used metabolite analysis, quantitative proteomics (iTRAQ) and transcriptomics (RNA-seq) to identify proteins and transcripts differentially expressed between sexes and between tissues when treated with juvenile hormone III. Juvenile hormone III induced frontalin biosynthesis in males and trans-verbenol biosynthesis in females, as well as affected the expression of many proteins and transcripts in sex- and tissue-specific ways. Based on these analyses, we identified candidate genes involved in the biosynthesis of frontalin, exo-brevicomin, and trans-verbenol pheromones. (C) 2016 Elsevier Ltd. All rights reserved. DOI
595. Kindsvater, HK; Braun, DC; Otto, SP; Reynolds, JD.Costs of reproduction can explain the correlated evolution of semelparity and egg size: theory and a test with salmon.Ecology Letters, 2016, 19: 687-696 Costs of reproduction can explain the correlated evolution of semelparity and egg size: theory and a test with salmon
Costs of reproduction; demography; iteroparity; life history theory; offspring size; salmon; semelparity
Species' life history traits, including maturation age, number of reproductive bouts, offspring size and number, reflect adaptations to diverse biotic and abiotic selection pressures. A striking example of divergent life histories is the evolution of either iteroparity (breeding multiple times) or semelparity (breed once and die). We analysed published data on salmonid fishes and found that semelparous species produce larger eggs, that egg size and number increase with salmonid body size among populations and species and that migratory behaviour and parity interact. We developed three hypotheses that might explain the patterns in our data and evaluated them in a stage-structured modelling framework accounting for different growth and survival scenarios. Our models predict the observation of small eggs in iteroparous species when egg size is costly to maternal survival or egg number is constrained. By exploring trait co-variation in salmonids, we generate new hypotheses for the evolution of trade-offs among life history traits. DOI
594. Kindsvater, HK; Mangel, M; Reynolds, JD; Dulvy, NK.Ten principles from evolutionary ecology essential for effective marine conservation.Ecology and Evolution, 2016, 6: 2125-2138 Ten principles from evolutionary ecology essential for effective marine conservation
Conservation; demography; extinction risk; fish; life-history theory; management; reference points; sustainability
Sustainably managing marine species is crucial for the future health of the human population. Yet there are diverse perspectives concerning which species can be exploited sustainably, and how best to do so. Motivated by recent debates in the published literature over marine conservation challenges, we review ten principles connecting life-history traits, population growth rate, and density-dependent population regulation. We introduce a framework for categorizing life histories, POSE (Precocial-Opportunistic-Survivor-Episodic), which illustrates how a species' life-history traits determine a population's compensatory capacity. We show why considering the evolutionary context that has shaped life histories is crucial to sustainable management. We then review recent work that connects our framework to specific opportunities where the life-history traits of marine species can be used to improve current conservation practices. DOI
592. Knight, R; Marlatt, VL; Baker, JA; Lo, BP; Debruyn, AMH; Elphick, JR; Martyniuk, CJ.Dietary selenium disrupts hepatic triglyceride stores and transcriptional networks associated with growth and Notch signaling in juvenile rainbow trout.Aquatic Toxicology, 2016, 180: 103-114 Dietary selenium disrupts hepatic triglyceride stores and transcriptional networks associated with growth and Notch signaling in juvenile rainbow trout
Dietary; Growth; Transcriptomics; Metabolites; Lipid peroxidation; Oxidative stress
Dietary Se has been shown to adversely affect adult fish by altering growth rates and metabolism. To determine the underlying mechanisms associated with these observations, we measured biochemical and transcriptomic endpoints in rainbow trout following dietary Se exposures. Treatment groups of juvenile rainbow trout were fed either control Lumbriculus variegatus worms or worms cultured on selenized yeast. Selenized yeast was cultured at four nominal doses of 5, 10, 20 or 40 mg/kg Se dry weight (measured dose in the worms of 7.1, 10.7, 19.5, and 31.8 mg/kg Se dw respectively) and fish were fed for 60 days. At 60 d, hepatic triglycerides, glycogen, total glutathione, 8-isoprostane and the transcriptome response in the liver (n = 8/group) were measured. Fish fed the nominal dose of 20 and 40 mg/kg Se dry weight had lower body weight and a shorter length, as well as lower triglyceride in the liver compared to controls. Evidence was lacking for an oxidative stress response and there was no change in total glutathione, 8-isoprostane levels, nor relative mRNA levels for glutathione peroxidase isoforms among groups. Microarray analysis revealed that molecular networks for long-chain fatty acid transport, lipid transport, and low density lipid oxidation were increased in the liver of fish fed 40 mg/kg, and this is hypothesized to be associated with the lower triglyceride levels in these fish. In addition, up-regulated gene networks in the liver of 40 mg/kg Se treated fish included epidermal growth factor receptor signaling, growth hormone receptor, and insulin growth factor receptor 1 signaling pathways. These molecular changes are hypothesized to be compensatory and related to impaired growth. A gene network related to Notch signaling, which is involved in cell-cell communication and gene transcription regulation, was also increased in the liver following dietary treatments with both 20 and 40 mg/kg Se. Transcriptomic data support the hypothesis that dietary Se increases the expression of networks for growth-related signaling cascades in addition to those related to fatty acid synthesis and metabolism. We propose that the disruption of metabolites related to triglyceride processing and storage, as well as gene networks for epidermal growth factor and Notch signaling in the liver, represent key molecular initiating events for adverse outcomes related to growth and Se toxicity in fish. (C) 2016 Elsevier B.V. All rights reserved. DOI
591. Kolappan, S; Coureuil, M; Yu, X; Nassif, X; Egelman, EH; Craig, L.Structure of the Neisseria meningitidis Type IV pilus.Nature Communications, 2016, 7 Structure of the Neisseria meningitidis Type IV pilus
Neisseria meningitidis use Type IV pili (T4P) to adhere to endothelial cells and breach the blood brain barrier, causing cause fatal meningitis. T4P are multifunctional polymers of the major pilin protein, which share a conserved hydrophobic N terminus that is a curved extended alpha-helix, alpha 1, in X-ray crystal structures. Here we report a 1.44 angstrom crystal structure of the N. meningitidis major pilin PilE and a similar to 6 angstrom cryo-electron microscopy reconstruction of the intact pilus, from which we built an atomic model for the filament. This structure reveals the molecular arrangement of the N-terminal alpha-helices in the filament core, including a melted central portion of alpha 1 and a bridge of electron density consistent with a predicted salt bridge necessary for pilus assembly. This structure has important implications for understanding pilus biology. DOI
590. Krieger, C; Wang, SJH; Yoo, SH; Harden, N.Adducin at the Neuromuscular Junction in Amyotrophic Lateral Sclerosis: Hanging on for Dear Life.Frontiers in Cellular Neuroscience, 2016, 10 Adducin at the Neuromuscular Junction in Amyotrophic Lateral Sclerosis: Hanging on for Dear Life
amyotrophic lateral sclerosis; neuromuscular junction; adducin; Hu-li tai shao; Discs large; neural cell adhesion molecule
The neurological dysfunction in amyotrophic lateral sclerosis (ALS)/motor neurone disease (MND) is associated with defective nerve -muscle contacts early in the disease suggesting that perturbations of cell adhesion molecules (CAMs) linking the pre-and post-synaptic components of the neuromuscular junction (NMJ) are involved. To search for candidate proteins implicated in this degenerative process, researchers have studied the Drosophila larval NMJ and find that the cytoskeleton-associated protein, adducin, is ideally placed to regulate synaptic contacts. By controlling the levels of synaptic proteins, adducin can de-stabilize synaptic contacts. Interestingly, elevated levels of phosphorylated adducin have been reported in ALS patients and in a mouse model of the disease. Adducin is regulated by phosphorylation through protein kinase C (PKC), some isoforms of which exhibit Ca2+ -dependence, raising the possibility that changes in intracellular Ca2+ might alter PKC activation and secondarily influence adducin phosphorylation. Furthermore, adducin has interactions with the alpha subunit of the Na+/K+ -ATPase. Thus, the phosphorylation of adducin may secondarily influence synaptic stability at the NMJ and so influence pre-and post-synaptic integrity at the NMJ in ALS. DOI
589. Kupper, C; Stocks, M; Risse, JE; dos Remedios, N; Farrell, LL; Mcrae, SB; Morgan, TC; Karlionova, N; Pinchuk, P; Verkuil, YI; Kitaysky, AS; Wingfield, JC; Piersma, T; Zeng, K; Slate, J; Blaxter, M; Lank, DB; Burke, T.A supergene determines highly divergent male reproductive morphs in the ruff.Nature Genetics, 2016, 48: 79-+ A supergene determines highly divergent male reproductive morphs in the ruff
Three strikingly different alternative male mating morphs (aggressive 'independents', semicooperative 'satellites' and female-mimic 'faeders') coexist as a balanced polymorphism in the ruff, Philomachus pugnax, a lek-breeding wading bird(1-3). Major differences in body size, ornamentation, and aggressive and mating behaviors are inherited as an autosomal polymorphism(4,5). We show that development into satellites and faeders is determined by a supergene(6-8) consisting of divergent alternative, dominant and non-recombining haplotypes of an inversion on chromosome 11, which contains 125 predicted genes. Independents are homozygous for the ancestral sequence. One breakpoint of the inversion disrupts the essential CENP-N gene (encoding centromere protein N), and pedigree analysis confirms the lethality of homozygosity for the inversion. We describe new differences in behavior, testis size and steroid metabolism among morphs and identify polymorphic genes within the inversion that are likely to contribute to the differences among morphs in reproductive traits. DOI
587. Leung, A; Hua, K; Ramachandran, P; Hingwing, K; Wu, M; Koh, PL; Hawkins, N.C-elegans HAM-1 functions in the nucleus to regulate asymmetric neuroblast division.Developmental Biology, 2016, 410: 56-69 C-elegans HAM-1 functions in the nucleus to regulate asymmetric neuroblast division
ham-1; Asymmetric cell division; Neuroblast; Nuclear localization; C. elegans
All 302 neurons in the C. elegans hermaphrodite arise through asymmetric division of neuroblasts. During embryogenesis, the C elegans ham-1 gene is required for several asymmetric neuroblast divisions in lineages that generate both neural and apoptotic cells. By antibody staining, endogenous HAM-1 is found exclusively at the cell cortex in many cells during embryogenesis and is asymmetrically localized in dividing cells. Here we show that in transgenic embryos expressing a functional GFP::HAM-1 fusion protein, GFP expression is also detected in the nucleus, in addition to the cell cortex. Consistent with the nuclear localization is the presence of a putative DNA binding winged-helix domain within the N-terminus of HAM-1. Through a deletion analysis we determined that the C-terminus of the protein is required for nuclear localization and we identified two nuclear localization sequences (NLSs). A subcellular fractionation experiment from wild type embryos, followed by Western blotting, revealed that endogenous HAM-1 is primarily found in the nucleus. Our analysis also showed that the N-terminus is necessary for cortical localization. While ham-1 function is essential for asymmetric division in the lineage that generates the PLM mechanosensory neuron, we showed that cortical localization may not required. Thus, our results suggest that there is a nuclear function for HAM-1 in regulating asymmetric neuroblast division and that the requirement for cortical localization may be lineage dependent. (C) 2015 Elsevier Inc. All rights reserved. DOI
586. Li, CM; Jensen, VL; Park, K; Kennedy, J; Garcia-Gonzalo, FR; Romani, M; De Mori, R; Bruel, AL; Gaillard, D; Doray, B; Lopez, E; Riviere, JB; Faivre, L; Thauvin-Robinet, C; Reiter, JF; Blacque, OE; Valente, EM; Leroux, MR.MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Transition Zone.PLoS Biology, 2016, 14 MKS5 and CEP290 Dependent Assembly Pathway of the Ciliary Transition Zone
Cilia have a unique diffusion barrier ("gate") within their proximal region, termed transition zone (TZ), that compartmentalises signalling proteins within the organelle. The TZ is known to harbour two functional modules/complexes (Meckel syndrome [MKS] and Nephro-nophthisis [NPHP]) defined by genetic interaction, interdependent protein localisation (hierarchy), and proteomic studies. However, the composition and molecular organisation of these modules and their links to human ciliary disease are not completely understood. Here, we reveal Caenorhabditis elegans CEP-290 (mammalian Cep290/Mks4/Nphp6 orthologue) as a central assembly factor that is specific for established MKS module components and depends on the coiled coil region of MKS-5 (Rpgrip1L/Rpgrip1) for TZ localisation. Consistent with a critical role in ciliary gate function, CEP-290 prevents inappropriate entry of membrane-associated proteins into cilia and keeps ARL-13 (Arl13b) from leaking out of cilia via the TZ. We identify a novel MKS module component, TMEM-218 (Tmem218), that requires CEP-290 and other MKS module components for TZ localisation and functions together with the NPHP module to facilitate ciliogenesis. We show that TZ localisation of TMEM-138 (Tmem138) and CDKL-1 (Cdkl1/Cdkl2/Cdkl3/Cdlk4 related), not previously linked to a specific TZ module, similarly depends on CEP-290; surprisingly, neither TMEM-138 or CDKL-1 exhibit interdependent localisation or genetic interactions with core MKS or NPHP module components, suggesting they are part of a distinct, CEP-290-associated module. Lastly, we show that families presenting with Oral-Facial-Digital syndrome type 6 OFD6) have likely pathogenic mutations in CEP-290-dependent TZ proteins, namely Tmem17, Tmem138, and Tmem231. Notably, patient fibroblasts harbouring mutated Tmem17, a protein not yet ciliopathy-associated, display ciliogenesis defects. Together, our findings expand the repertoire of MKS module-associated proteins-including the previously uncharacterised mammalian Tmem80-and suggest an MKS-5 and CEP-290-dependent assembly pathway for building a functional TZ. DOI
585. Li, F; Zhang, SJ; Yang, TN; Xu, Z; Zhang, N; Liu, G; Wang, JJ; Wang, JL; Cheng, ZX; Ye, ZG; Luo, J; Shrout, TR; Chen, LQ.The origin of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution crystals.Nat. Commun., 2016, 7 The origin of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution crystals
The discovery of ultrahigh piezoelectricity in relaxor-ferroelectric solid solution single crystals is a breakthrough in ferroelectric materials. A key signature of relaxor-ferroelectric solid solutions is the existence of polar nanoregions, a nanoscale inhomogeneity, that coexist with normal ferroelectric domains. Despite two decades of extensive studies, the contribution of polar nanoregions to the underlying piezoelectric properties of relaxor ferroelectrics has yet to be established. Here we quantitatively characterize the contribution of polar nanoregions to the dielectric/piezoelectric responses of relaxor-ferroelectric crystals using a combination of cryogenic experiments and phase-field simulations. The contribution of polar nanoregions to the room-temperature dielectric and piezoelectric properties is in the range of 50-80%. A mesoscale mechanism is proposed to reveal the origin of the high piezoelectricity in relaxor ferroelectrics, where the polar nanoregions aligned in a ferroelectric matrix can facilitate polarization rotation. This mechanism emphasizes the critical role of local structure on the macroscopic properties of ferroelectric materials. DOI PubMed
584. Lien, S; Koop, BF; Sandve, SR; Miller, JR; Kent, MP; Nome, T; Hvidsten, TR; Leong, JS; Minkley, DR; Zimin, A; Grammes, F; Grove, H; Gjuvsland, A; Walenz, B; Hermansen, RA; von Schalburg, K; Rondeau, EB; Di Genova, A; Samy, JKA; Vik, JO; Vigeland, MD; Caler, L; Grimholt, U; Jentoft, S; Vage, DI; de Jong, P; Moen, T; Baranski, M; Palti, Y; Smith, DR; Yorke, JA; Nederbragt, AJ; Tooming-Klunderud, A; Jakobsen, KS; Jiang, XT; Fan, DD; Liberles, DA; Vidal, R; Iturra, P; Jones, SJM; Jonassen, I; Maass, A; Omholt, SW; Davidson, WS.The Atlantic salmon genome provides insights into rediploidization.Nature, 2016, 533: 200-+ The Atlantic salmon genome provides insights into rediploidization
The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes. DOI
583. Loucks, CM; Bialas, NJ; Dekkers, MPJ; Walker, DS; Grundy, LJ; Li, CM; Inglis, PN; Kida, K; Schafer, WR; Blacque, OE; Jansen, G; Leroux, MR.PACRG, a protein linked to ciliary motility, mediates cellular signaling.Molecular Biology of the Cell, 2016, 27: 2133-2144 PACRG, a protein linked to ciliary motility, mediates cellular signaling
Cilia are microtubule-based organelles that project from nearly all mammalian cell types. Motile cilia generate fluid flow, whereas nonmotile (primary) cilia are required for sensory physiology and modulate various signal transduction pathways. Here we investigate the nonmotile ciliary signaling roles of parkin coregulated gene (PACRG), a protein linked to ciliary motility. PACRG is associated with the protofilament ribbon, a structure believed to dictate the regular arrangement of motility-associated ciliary components. Roles for protofilament ribbon-associated proteins in nonmotile cilia and cellular signaling have not been investigated. We show that PACRG localizes to a small subset of nonmotile cilia in Caenorhabditis elegans, suggesting an evolutionary adaptation for mediating specific sensory/signaling functions. We find that it influences a learning behavior known as gustatory plasticity, in which it is functionally coupled to heterotrimeric G-protein signaling. We also demonstrate that PACRG promotes longevity in C. elegans by acting upstream of the lifespan-promoting FOXO transcription factor DAF-16 and likely upstream of insulin/IGF signaling. Our findings establish previously unrecognized sensory/signaling functions for PACRG and point to a role for this protein in promoting longevity. Furthermore, our work suggests additional ciliary motility-signaling connections, since EFHC1 (EF-hand containing 1), a potential PACRG interaction partner similarly associated with the protofilament ribbon and ciliary motility, also positively regulates lifespan. DOI
582. MacQueen, P; Zurek, J; Williams-Jones, G.Connected magma plumbing system between Cerro Negro and El Hoyo Complex, Nicaragua revealed by gravity survey.Journal of Volcanology and Geothermal Research, 2016, 327: 375-384 Connected magma plumbing system between Cerro Negro and El Hoyo Complex, Nicaragua revealed by gravity survey
Gravity; Nicaragua; Cerro Negro; El Hoyo; Structure; Magmatic plumbing
Cerro Negro, near Leon, Nicaragua is a young, relatively small basaltic cinder cone volcano that has been unusually active during its short lifespan. Multiple explosive eruptions have deposited significant amounts of ash on Leon and the surrounding rural communities. While a number of studies investigate the geo-chemistry and stress regime of the volcano, subsurface structures have only been studied by diffuse soil gas surveys. These studies have raised several questions as to the proper classification of Cerro Negro and its relation to neighboring volcanic features. To address these questions, we collected 119 gravity measurements around Cerro Negro volcano in an attempt to delineate deep structures at the volcano. The resulting complete Bouguer anomaly map revealed local positive gravity anomalies (wavelength 0.5 to 2 km, magnitude +4 mGal) and regional positive (10 km wavelength, magnitudes +10 and +8 mGal) and negative (12 and 6 km wavelength, magnitudes 18 and 13 mGal) Bouguer anomalies. Further analysis of these gravity data through inversion has revealed both local and regional density anomalies that we interpret as intrusive complexes at Cerro Negro and in the Nicaraguan Volcanic Arc. The local density anomalies at Cerro Negro have a density of 2700 kg m(-3) (basalt) and are located between -250 and -2000 m above sea level. The distribution of recovered density anomalies suggests that eruptions at Cerro Negro may be tapping an interconnected magma plumbing system beneath El Hoyo, Cerro La Mula, and Cerro Negro, and more than seven other proximal volcanic features, implying that Cerro Negro should be considered the newest cone of a Cerro Negro-El Hoyo volcanic complex. (C) 2016 Elsevier B.V. All rights reserved.PDF DOI
581. Madin, EMP; Dill, LM; Ridlon, AD; Heithaus, MR; Warner, RR.Human activities change marine ecosystems by altering predation risk.Global Change Biology, 2016, 22: 44-60 Human activities change marine ecosystems by altering predation risk
behaviour; fishing; human impacts; indirect effects; marine ecosystem; nonconsumptive effects; nonlethal effects; predation risk; Predator-prey interactions; risk effects; trophic cascades
In ocean ecosystems, many of the changes in predation risk - both increases and decreases - are human-induced. These changes are occurring at scales ranging from global to local and across variable temporal scales. Indirect, risk-based effects of human activity are known to be important in structuring some terrestrial ecosystems, but these impacts have largely been neglected in oceans. Here, we synthesize existing literature and data to explore multiple lines of evidence that collectively suggest diverse human activities are changing marine ecosystems, including carbon storage capacity, in myriad ways by altering predation risk. We provide novel, compelling evidence that at least one key human activity, overfishing, can lead to distinct, cascading risk effects in natural ecosystems whose magnitude exceeds that of presumed lethal effects and may account for previously unexplained findings. We further discuss the conservation implications of human-caused indirect risk effects. Finally, we provide a predictive framework for when human alterations of risk in oceans should lead to cascading effects and outline a prospectus for future research. Given the speed and extent with which human activities are altering marine risk landscapes, it is crucial that conservation and management policy considers the indirect effects of these activities in order to increase the likelihood of success and avoid unfortunate surprises. DOI
580. Marlatt, VL; Sherrard, R; Kennedy, CJ; Elphick, JR; Martyniuk, CJ.Application of molecular endpoints in early life stage salmonid environmental biomonitoring.Aquatic Toxicology, 2016, 173: 178-191 Application of molecular endpoints in early life stage salmonid environmental biomonitoring
Environmental monitoring; Gene expression; Metals; PAH; Salmonid; Development
Molecular endpoints can enhance existing whole animal bioassays by more fully characterizing the biological impacts of aquatic pollutants. Laboratory and field studies were used to examine the utility of adopting molecular endpoints for a well-developed in situ early life stage (eyed embryo to onset of swim-up fry) salmonid bioassay to improve diagnostic assessments of water quality in the field. Coastal cutthroat trout (Oncorhynchus clarki clarki) were exposed in the laboratory to the model metal (zinc, 40 mu g/L) and the polycyclic aromatic hydrocarbon (pyrene, 100 mu g/L) in water to examine the resulting early life stage salmonid responses. In situ field exposures and bioassays were conducted in parallel to evaluate the water quality of three urban streams in British Columbia (two sites with anthropogenic inputs and one reference site). The endpoints measured in swim-up fry included survival, deformities, growth (weight and length), vitellogenin (vtg) and metallothionein (Mt) protein levels, and hepatic gene expression (e.g., metallothioneins [mta and mtb], endocrine biomarkers [vtg and estrogen receptors, esr] and xenobiotic-metabolizing enzymes [cytochrome P4501A3, cyp1a3 and glutathione transferases, gstk]). No effects were observed in the zinc treatment, however exposure of swim-up fry to pyrene resulted in decreased survival, deformities and increased estrogen receptor alpha (er1) mRNA levels. In the field exposures, xenobiotic-metabolizing enzymes (cyp1a3, gstk) and zinc transporter (zntBigM103) mRNA were significantly increased in swim-up fry deployed at the sites with more anthropogenic inputs compared to the reference site. Cluster analysis revealed that gene expression profiles in individuals from the streams receiving anthropogenic inputs were more similar to each other than to the reference site. Collectively, the results obtained in this study suggest that molecular endpoints may be useful, and potentially more sensitive, indicators of site-specific contamination in real-world, complex exposure scenarios in addition to whole body morphometric and physiological measures. (C) 2016 Elsevier B.V. All rights reserved. DOI
579. Martin, SD; Brown, SD; Wick, DA; Nielsen, JS; Kroeger, DR; Twumasi-Boateng, K; Holt, RA; Nelson, BH.Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines.PLoS One, 2016, 11 Low Mutation Burden in Ovarian Cancer May Limit the Utility of Neoantigen-Targeted Vaccines
Due to advances in sequencing technology, somatically mutated cancer antigens, or neoantigens, are now readily identifiable and have become compelling targets for immunotherapy. In particular, neoantigen-targeted vaccines have shown promise in several pre-clinical and clinical studies. However, to date, neoantigen-targeted vaccine studies have involved tumors with exceptionally high mutation burdens. It remains unclear whether neoantigen-targeted vaccines will be broadly applicable to cancers with intermediate to low mutation burdens, such as ovarian cancer. To address this, we assessed whether a derivative of the murine ovarian tumor model ID8 could be targeted with neoantigen vaccines. We performed whole exome and transcriptome sequencing on ID8-G7 cells. We identified 92 somatic mutations, 39 of which were transcribed, missense mutations. For the 17 top predicted MHC class I binding mutations, we immunized mice subcutaneously with synthetic long peptide vaccines encoding the relevant mutation. Seven of 17 vaccines induced robust mutation-specific CD4 and/or CD8 T cell responses. However, none of the vaccines prolonged survival of tumor-bearing mice in either the prophylactic or therapeutic setting. Moreover, none of the neoantigen-specific T cell lines recognized ID8-G7 tumor cells in vitro, indicating that the corresponding mutations did not give rise to bonafide MHC-presented epitopes. Additionally, bioinformatic analysis of The Cancer Genome Atlas data revealed that only 12% (26/220) of HGSC cases had a >= 90% likelihood of harboring at least one authentic, naturally processed and presented neoantigen versus 51% (80/158) of lung cancers. Our findings highlight the limitations of applying neoantigen-targeted vaccines to tumor types with intermediate/low mutation burdens. DOI
578. McAuley, EM; Bertram, SM.Field Crickets Compensate for Unattractive Static Long-Distance Call Components by Increasing Dynamic Signalling Effort.PLoS One, 2016, 11 Field Crickets Compensate for Unattractive Static Long-Distance Call Components by Increasing Dynamic Signalling Effort
The evolution of multiple sexual signals presents a dilemma since individuals selecting a mate should pay attention to the most honest signal and ignore the rest; however, multiple signals may evolve if, together, they provide more information to the receiver than either one would alone. Static and dynamic signals, for instance, can act as multiple messages, providing information on different aspects of signaller quality that reflect condition at different time scales. While the nature of static signals makes them difficult or impossible for individuals to augment, dynamic signals are much more susceptible to temporary fluctuations in effort. We investigated whether male Texas field crickets, Gryllus texensis, that produce unattractive static signals compensate by dynamically increasing their calling effort. Our findings lend partial support to the compensation hypothesis, as males that called at unattractive carrier frequencies (a static trait) spent more time calling each night (a dynamic trait). Interestingly, this finding was most pronounced in males that called with attractive pulse characteristics (static traits) but did not occur in males that called with unattractive pulse characteristics. Males that signalled with unattractive pulse characteristics (duration and pause) spent less time calling through the night. Our correlative findings on wild caught males suggest that only males that signal with attractive pulse characteristics may be able to afford to pay the costs of both trait exaggeration and increased calling effort to compensate for poor carrier frequencies. DOI
577. McClenachan, L; Cooper, AB; Dulvy, NK.Rethinking Trade-Driven Extinction Risk in Marine and Terrestrial Megafauna.Current Biology, 2016, 26: 1640-1646 Rethinking Trade-Driven Extinction Risk in Marine and Terrestrial Megafauna
Large animals hunted for the high value of their parts (e.g., elephant ivory and shark fins) are at risk of extinction due to both intensive international trade pressure and intrinsic biological sensitivity. However, the relative role of trade, particularly in non-perishable products, and biological factors in driving extinction risk is not well understood [1-4]. Here we identify a taxonomically diverse group of >100 marine and terrestrial megafauna targeted for international luxury markets; estimate their value across three points of sale; test relationships among extinction risk, high value, and body size; and quantify the effects of two mitigating factors: poaching fines and geographic range size. We find that body size is the principal driver of risk for lower value species, but that this biological pattern is eliminated above a value threshold, meaning that the most valuable species face a high extinction risk regardless of size. For example, once mean product values exceed US$12,557 kg(-1), body size no longer drives risk. Total value scales with size for marine animals more strongly than for terrestrial animals, incentivizing the hunting of large marine individuals and species. Poaching fines currently have little effect on extinction risk; fines would need to be increased 10- to 100-fold to be effective. Large geographic ranges reduce risk for terrestrial, but not marine, species, whose ranges are ten times greater. Our results underscore both the evolutionary and ecosystem consequences of targeting large marine animals and the need to geographically scale up and prioritize conservation of high-value marine species to avoid extinction. DOI
576. McDonnell, L; Barker, MK; Wieman, C.Concepts First, Jargon Second Improves Student Articulation of Understanding.Biochem. Mol. Biol. Educ., 2016, 44: 12-19 Concepts First, Jargon Second Improves Student Articulation of Understanding
vocabulary; learning; concept; introductory biology
In this experiment, students in a large undergraduate biology course were first exposed to the concepts without new technical vocabulary ("jargon") in a pre-class reading assignment. Their learning of the concepts and jargon was compared with that of an equivalent group of students in another section of the same course, whose pre-class reading presented both the jargon and concepts together in the traditional manner. Both groups had the same active-learning classes with the same instructor, and then completed the same post-test. Although the two groups performed the same on the multiple choice questions of the post-test, the group exposed to concepts first and jargon second included 1.5 times and 2.5 times more correct arguments on two free-response questions about the concepts. The correct use of jargon between the two groups was similar, with the exception of one jargon term that the control group used more often. These results suggest that modest instructional changes whereby new concepts are introduced in a concepts-first, jargon-second manner can increase student learning, as demonstrated by their ability to articulate their understanding of new concepts. (C) 2015 by The International Union of Biochemistry and Molecular Biology, DOI PubMed
575. Miller, CA; Williams-Jones, G.Internal structure and volcanic hazard potential of Mt Tongariro, New Zealand, from 3D gravity and magnetic models.Journal of Volcanology and Geothermal Research, 2016, 319: 12-28 Internal structure and volcanic hazard potential of Mt Tongariro, New Zealand, from 3D gravity and magnetic models
Gravity; Magnetic; 3D modelling; Volcanic hazard; Hydrothermal system; Volcanic structure
A new 3D geophysical model of the Mt Tongariro Volcanic Massif (TgVM), New Zealand, provides a high resolution view of the volcano's internal structure and hydrothermal system, from which we derive implications for volcanic hazards. Geologically constrained 3D inversions of potential field data provides a greater level of insight into the volcanic structure than is possible from unconstrained models. A complex region of gravity highs and lows (+/- 6 mGal) is set within a broader, similar to 20 mGal gravity low. A magnetic high (1300 nT) is associated with Mt Ngauruhoe, while a substantial, thick, demagnetised area occurs to the north, coincident with a gravity low and interpreted as representing the hydrothermal system. The hydrothermal system is constrained to the west by major faults, interpreted as an impermeable barrier to fluid migration and extends to basement depth. These faults are considered low probability areas for future eruption sites, as there is little to indicate they have acted as magmatic pathways. Where the hydrothermal system coincides with steep topographic slopes, an increased likelihood of landslides is present and the newly delineated hydrothermal system maps the area most likely to have phreatic eruptions. Such eruptions, while small on a global scale, are important hazards at the TgVM as it is a popular hiking area with hundreds of visitors per day in close proximity to eruption sites. The model shows that the volume of volcanic material erupted over the lifespan of the TgVM is five to six times greater than previous estimates, suggesting a higher rate of magma supply, in line with global rates of andesite production. We suggest that our model of physical property distribution can be used to provide constraints for other models of dynamic geophysical processes occurring at the TgVM. (C) 2016 Elsevier B.V. All rights reserved. DOI
574. Mokkonen, M; Lindstedt, C.The evolutionary ecology of deception.Biological Reviews, 2016, 91: 1020-1035 The evolutionary ecology of deception
information; mimicry; sexual conflict; co-evolution; evolutionary ecology; communication
Through. dishonest signals or actions, individuals often misinfbrm others to their own benefit. We review recent literature to explore the evolutionary and ecological conditions for deception to be more likely to evolve and he maintained. We identify four conditions: (1) high misinformation potential through perceptual constraints of perceiver; (2) costs and benefits of responding to deception; (3) asymmetric power relationships between individuals and (4) exploitation of common goods. We discuss behavioural and physiological mechanisms that form a deception continuum from secrecy to overt signals. Deceptive tactics usually succeed by being rare and are often evolving under co -evolutionary arms races, sometimes leading to the evolution of polymorphism. The degree of deception can also vary depending on the environmental conditions. Finally, we suggest a conceptual framework for studying deception and highlight important questions for future studies.
573. Morrissy, AS; Garzia, L; Shih, DJH; Zuyderduyn, S; Huang, X; Skowron, P; Remke, M; Cavalli, FMG; Ramaswamy, V; Lindsay, PE; Jelveh, S; Donovan, LK; Wang, X; Luu, B; Zayne, K; Li, YS; Mayoh, C; Thiessen, N; Mercier, E; Mungall, KL; Ma, Y; Tse, K; Zeng, T; Shumansky, K; Roth, AJL; Shah, S; Farooq, H; Kijima, N; Holgado, BL; Lee, JJY; Matan-Lithwick, S; Liu, J; Mack, SC; Manno, A; Michealraj, KA; Nor, C; Peacock, J; Qin, L; Reimand, J; Rolider, A; Thompson, YY; Wu, XC; Pugh, T; Ally, A; Bilenky, M; Butterfield, YSN; Carlsen, R; Cheng, Y; Chuah, E; Corbett, RD; Dhalla, N; He, A; Lee, D; Li, HYI; Long, W; Mayo, M; Plettner, P; Qian, JQ; Schein, JE; Tam, A; Wong, T; Birol, I; Zhao, YJ; Faria, CC; Pimentel, J; Nunes, S; Shalaby, T; Grotzer, M; Pollack, IF; Hamilton, RL; Li, XN; Bendel, AE; Fults, DW; Walter, AW; Kumabe, T; Tominaga, T; Collins, VP; Cho, YJ; Hoffman, C; Lyden, D; Wisoff, JH; Garvin, JH; Stearns, DS; Massimi, L; Schuller, U; Sterba, J; Zitterbart, K; Puget, S; Ayrault, O; Dunn, SE; Tirapelli, DPC; Carlotti, CG; Wheeler, H; Hallahan, AR; Ingram, W; MacDonald, TJ; Olson, JJ; Van Meir, EG; Lee, JY; Wang, KC; Kim, SK; Cho, BK; Pietsch, T; Fleischhack, G; Tippelt, S; Ra, YS; Bailey, S; Lindsey, JC; Clifford, SC; Eberhart, CG; Cooper, MK; Packer, RJ; Massimino, M; Garre, ML; Bartels, U; Tabori, U; Hawkins, CE; Dirks, P; Bouffet, E; Rutka, JT; Wechsler-Reya, RJ; Weiss, WA; Collier, LS; Dupuy, AJ; Korshunov, A; Jones, DTW; Kool, M; Northcott, PA; Pfister, SM; Largaespada, DA; Mungall, AJ; Moore, RA; Jabado, N; Bader, GD; Jones, SJM; Malkin, D; Marra, MA; Taylor, MD.Divergent clonal selection dominates medulloblastoma at recurrence.Nature, 2016, 529: 351-+ Divergent clonal selection dominates medulloblastoma at recurrence
The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon-driven, functional genomic mouse model of medulloblastoma with 'humanized' in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (<5%). Whole-genome sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (<12% diagnostic events were retained at recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. DOI
572. Mwimanzi, P; Tietjen, I; Miller, SC; Shahid, A; Cobarrubias, K; Kinloch, NN; Baraki, B; Richard, J; Finzi, A; Fedida, D; Brumme, ZL; Brockman, MA.Novel Acylguanidine-Based Inhibitor of HIV-1.Journal of Virology, 2016, 90: 9495-9508 Novel Acylguanidine-Based Inhibitor of HIV-1
The emergence of transmissible HIV-1 strains with resistance to antiretroviral drugs highlights a continual need for new therapies. Here we describe a novel acylguanidine-containing compound, 1-(2-(azepan-1-yl)nicotinoyl)guanidine (or SM111), that inhibits in vitro replication of HIV-1, including strains resistant to licensed protease, reverse transcriptase, and integrase inhibitors, without major cellular toxicity. At inhibitory concentrations, intracellular p24(Gag) production was unaffected, but virion release (measured as extracellular p24(Gag)) was reduced and virion infectivity was substantially impaired, suggesting that SM111 acts at a late stage of viral replication. SM111-mediated inhibition of HIV-1 was partially overcome by a Vpu I17R mutation alone or a Vpu W22* truncation in combination with Env N136Y. These mutations enhanced virion infectivity and Env expression on the surface of infected cells in the absence and presence of SM111 but also impaired Vpu's ability to downregulate CD4 and BST2/tetherin. Taken together, our results support acylguanidines as a class of HIV-1 inhibitors with a distinct mechanism of action compared to that of licensed antiretrovirals. Further research on SM111 and similar compounds may help to elucidate knowledge gaps related to Vpu's role in promoting viral egress and infectivity. IMPORTANCE New inhibitors of HIV-1 replication may be useful as therapeutics to counteract drug resistance and as reagents to perform more detailed studies of viral pathogenesis. SM111 is a small molecule that blocks the replication of wild-type and drug-resistant HIV-1 strains by impairing viral release and substantially reducing virion infectivity, most likely through its ability to prevent Env expression at the infected cell surface. Partial resistance to SM111 is mediated by mutations in Vpu and/or Env, suggesting that the compound affects host/viral protein interactions that are important during viral egress. Further characterization of SM111 and similar compounds may allow more detailed pharmacological studies of HIV-1 egress and provide opportunities to develop new treatments for HIV-1. DOI
571. Myers, JH; Cory, JS.Ecology and evolution of pathogens in natural populations of Lepidoptera.Evolutionary Applications, 2016, 9: 231-247 Ecology and evolution of pathogens in natural populations of Lepidoptera
disease ecology; disease transmission; forest Lepidoptera; insect pathogens; migration; population regulation; tritrophic interactions; virulence
Pathogens are ubiquitous in insect populations and yet few studies examine their dynamics and impacts on host populations. We discuss four lepidopteran systems and explore their contributions to disease ecology and evolution. More specifically, we elucidate the role of pathogens in insect population dynamics. For three species, western tent caterpillars, African armyworm and introduced populations of gypsy moth, infection by nucleopolyhedrovirus (NPV) clearly regulates host populations or reduces their outbreaks. Transmission of NPV is largely horizontal although low levels of vertical transmission occur, and high levels of covert infection in some cases suggest that the virus can persist in a nonsymptomatic form. The prevalence of a mostly vertically transmitted protozoan parasite, Ophryocystis elektroscirrha, in monarch butterflies is intimately related to their migratory behaviour that culls highly infected individuals. Virulence and transmission are positively related among genotypes of this parasite. These systems clearly demonstrate that the interactions between insects and pathogens are highly context dependent. Not only is the outcome a consequence of changes in density and genetic diversity: environmental factors, particularly diet, can have strong impacts on virulence, transmission and host resistance or tolerance. What maintains the high level of host and pathogen diversity in these systems, however, remains a question. DOI
570. Nesbitt, HK; Moore, JW.Species and population diversity in Pacific salmon fisheries underpin indigenous food security.Journal of Applied Ecology, 2016, 53: 1489-1499 Species and population diversity in Pacific salmon fisheries underpin indigenous food security
aboriginal; biodiversity; diversity-stability; First Nations; portfolio effect; rights and title; small-scale fisheries; subsistence; traditional; watershed management
1. Indigenous people arc considered to be among the most vulnerable to food insecurity and biodiversity loss. Biodiversity is cited as a key component of indigenous food security; however, quantitative examples of this linkage are limited. 2. We examined how species and population diversity influence the food security of indigenous fisheries for Pacific salmon (Oncorhynchus species). We compared two dimensions of food security- catch stability (interannual variability) and access (season length)- across a salmon diversity gradient for 21 fisheries on the Fraser River, Canada, over 30 years, using linear regression models. We used population diversity proxies derived from a range of existing measures because population-specific data were unavailable. 3. While both population and species diversity were generally associated with higher catch stability and temporal access, population diversity had a stronger signal. Fisheries with access to high species diversity had up to 1.4 times more stable catch than predicted by the portfolio effect and up to 1.2 times longer fishing seasons than fisheries with access to fewer species. Fisheries with access to high population diversity had up to 3.8 times more stable catch and three times longer seasons than fisheries with access to fewer populations. 4. Catch stability of Chinook Oncorhynchus tshawytschct and sockeye Oncorhynchus nerka fisheries was best explained by the number of populations and conservation units, respectively, that migrate past a fishery en route to spawning grounds. Similar population diversity metrics were important explanatory variables for season length of sockeye, pink Oncorhynchus god) uscha, coho Oncorhynchus kisutch and churn Oncorhynchus keta fisheries. 5. Synthesis and applications. We show an empirical example of how multiple scales of biodiversity support food security across a large watershed and suggest that protecting fine-scale salmon diversity will help promote food security for indigenous people. The scales of environmental assessments need to match the scales of the socio-ecological processes that will be affected by development. We illustrate that upstream projects that damage salmon habitat could degrade the food security of downstream indigenous fisheries, with implications to Canadian indigenous people and to watersheds around the world where migratory fishes support local fisheries. DOI
569. Ng, D; Harn, T; Altindal, T; Kolappan, S; Marles, JM; Lala, R; Spielman, I; Gao, Y; Hauke, CA; Kovacikova, G; Verjee, Z; Taylor, RK; Biais, N; Craig, L.The Vibrio cholerae Minor Pilin TcpB Initiates Assembly and Retraction of the Toxin-Coregulated Pilus.PLoS Pathogens, 2016, 12 The Vibrio cholerae Minor Pilin TcpB Initiates Assembly and Retraction of the Toxin-Coregulated Pilus
Type IV pilus (T4P) systems are complex molecular machines that polymerize major pilin proteins into thin filaments displayed on bacterial surfaces. Pilus functions require rapid extension and depolymerization of the pilus, powered by the assembly and retraction ATPases, respectively. A set of low abundance minor pilins influences pilus dynamics by unknown mechanisms. The Vibrio cholerae toxin-coregulated pilus (TCP) is among the simplest of the T4P systems, having a single minor pilin TcpB and lacking a retraction ATPase. Here we show that TcpB, like its homolog CofB, initiates pilus assembly. TcpB co-localizes with the pili but at extremely low levels, equivalent to one subunit per pilus. We used a micro-pillars assay to demonstrate that TCP are retractile despite the absence of a retraction ATPase, and that retraction relies on TcpB, as a V. cholerae tcpB Glu5Val mutant is fully piliated but does not induce micropillars movements. This mutant is impaired in TCP-mediated autoagglutination and TcpF secretion, consistent with retraction being required for these functions. We propose that TcpB initiates pilus retraction by incorporating into the growing pilus in a Glu5-dependent manner, which stalls assembly and triggers processive disassembly. These results provide a framework for understanding filament dynamics in more complex T4P systems and the closely related Type II secretion system. DOI
568. Noble, JW; Hunter, DV; Roskelley, CD; Chan, EKL; Mills, J.Loukoumasomes Are Distinct Subcellular Structures from Rods and Rings and Are Structurally Associated with MAP2 and the Nuclear Envelope in Retinal Cells.PLoS One, 2016, 11 Loukoumasomes Are Distinct Subcellular Structures from Rods and Rings and Are Structurally Associated with MAP2 and the Nuclear Envelope in Retinal Cells
"Rods and rings " (RR) and loukoumasomes are similarly shaped, subcellular macromolecular structures with as yet unknown function. RR, so named because of their shape, are formed in response to inhibition in the GTP or CTP synthetic pathways and are highly enriched in the two key enzymes of the nucleotide synthetic pathway. Loukoumasomes also occur as linear and toroidal bodies and were initially inferred to be the same as RR, largely due to their shared shape and size and the fact that it was unclear if they shared the same subcomponents. In human retinoblastoma tissue and cells we have observed toroidal, perinuclear, macromolecular structures of similar size and antigenicity to those previously reported in neurons (neuronal-loukoumasomes). To further characterize the subcomponents of the retinal-loukoumasomes, confocal analysis following immunocytochemical staining for alpha-tubulin, beta-III tubulin and detyrosinated tubulin was performed. These studies indicate that retinal-loukoumasomes are enriched for beta-III tubulin and other tubulins associated with microtubules. Immunofluorescence together with the in situ proximity ligation assay (PLA), confirmed that beta-III tubulin colocalized with detyrosinated tubulin within loukoumasomes. Our results indicate that these tissues contain only loukoumasomes because these macromolecular structures are immunoreactive with an anti-tubulin antibody but are not recognized by the prototype anti-RR/inosine monophosphate dehydrogenase (IMPDH) antibody (It2006). To further compare the RR and retinal-loukoumasomes, retinoblastoma cells were exposed to the IMPDH-inhibitor ribavirin, a drug known to induce the formation of RR. In contrast to RR, the production of retinal-loukoumasomes was unaffected. Coimmunostaining of Y79 cells for beta-III tubulin and IMPDH indicate that these cells, when treated with ribavirin, can contain both retinal-loukoumasomes and RR and that these structures are antigenically distinct. Subcellular fractionation studies indicate that ribavirin increased the RR subcomponent, IMPDH, in the nuclear fraction of Y79 cells from 21.3 +/- 5.8% (0 mM ribavirin) to 122.8 +/- 7.9% (1 mM ribavirin) while the subcellular localization of the retinal-loukoumasome subcomponent tubulin went unaltered. Further characterization of retinal-loukoumasomes in retinoblastoma cells reveals that they are intimately associated with lamin folds within the nuclear envelope. Using immunofluorescence and the in situ PLA in this cell type, we have observed colocalization of beta-III tubulin with MAP2. As MAP2 is a microtubule-associated protein implicated in microtubule crosslinking, this supports a role for microtubule crosslinkers in the formation of retinal-loukoumasomes. Together, these results suggest that loukoumasomes and RR are distinct subcellular macromolecular structures, formed by different cellular processes and that there are other loukoumasome-like structures within retinal tissues and cells. DOI
567. Nunes, RD; Ventura-Martins, G; Moretti, DM; Medeiros-Castro, P; Rocha-Santos, C; Daumas, CRD; Bittencourt-Cunha, PRB; Martins-Cardoso, K; Cudischevitch, CO; Menna-Barreto, RFS; Oliveira, JHM; Gusmao, DS; Lemos, FJA; Alviano, DS; Oliveira, PL; Lowenberger, C; Majerowicz, D; Oliveira, RM; Mesquita, RD; Atella, GC; Silva-Neto, MAC.Polyphenol-Rich Diets Exacerbate AMPK-Mediated Autophagy, Decreasing Proliferation of Mosquito Midgut Microbiota, and Extending Vector Lifespan.PLoS Neglected Tropical Diseases, 2016, 10 Polyphenol-Rich Diets Exacerbate AMPK-Mediated Autophagy, Decreasing Proliferation of Mosquito Midgut Microbiota, and Extending Vector Lifespan
Background Mosquitoes feed on plant-derived fluids such as nectar and sap and are exposed to bioactive molecules found in this dietary source. However, the role of such molecules on mosquito vectorial capacity is unknown. Weather has been recognized as a major determinant of the spread of dengue, and plants under abiotic stress increase their production of polyphenols. Results Here, we show that including polyphenols in mosquito meals promoted the activation of AMP-dependent protein kinase (AMPK). AMPK positively regulated midgut autophagy leading to a decrease in bacterial proliferation and an increase in vector lifespan. Suppression of AMPK activity resulted in a 6-fold increase in midgut microbiota. Similarly, inhibition of polyphenol-induced autophagy induced an 8-fold increase in bacterial proliferation. Mosquitoes maintained on the polyphenol diet were readily infected by dengue virus. Conclusion The present findings uncover a new direct route by which exacerbation of autophagy through activation of the AMPK pathway leads to a more efficient control of mosquito midgut microbiota and increases the average mosquito lifespan. Our results suggest for the first time that the polyphenol content and availability of the surrounding vegetation may increase the population of mosquitoes prone to infection with arboviruses. DOI
566. Ottenburghs, J; van Hooft, P; van Wieren, SE; Ydenberg, RC; Prins, HHT.Hybridization in geese: a review.Frontiers in Zoology, 2016, 13 Hybridization in geese: a review
Hybridization; Introgression; Behaviour; Nest parasitism; Extra-pair copulations; Fertility; Anatidae; Captivity
The high incidence of hybridization in waterfowl (ducks, geese and swans) makes this bird group an excellent study system to answer questions related to the evolution and maintenance of species boundaries. However, knowledge on waterfowl hybridization is biased towards ducks, with a large knowledge gap in geese. In this review, we assemble the available information on hybrid geese by focusing on three main themes: (1) incidence and frequency, (2) behavioural mechanisms leading to hybridization, and (3) hybrid fertility. Hybridization in geese is common on a species-level, but rare on a per-individual level. An overview of the different behavioural mechanisms indicates that forced extra-pair copulations and interspecific nest parasisitm can both lead to hybridization. Other sources of hybrids include hybridization in captivity and vagrant geese, which may both lead to a scarcity of conspecifics. The different mechanisms are not mutually exclusive and it is currently not possible to discriminate between the different mechanisms without quantitative data. Most hybrid geese are fertile; only in crosses between distantly related species do female hybrids become sterile. This fertility pattern, which is in line with Haldane's Rule, may facilitate interspecific gene flow between closely related species. The knowledge on hybrid geese should be used, in combination with the information available on hybridization in ducks, to study the process of avian speciation. DOI
565. Palomo, A; Fowler, SJ; Gulay, A; Rasmussen, S; Sicheritz-Ponten, T; Smets, BF.Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.ISME J., 2016, 10: 2569-2581 Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.
Rapid gravity sand filtration is a drinking water production technology widely used around the world. Microbially catalyzed processes dominate the oxidative transformation of ammonia, reduced manganese and iron, methane and hydrogen sulfide, which may all be present at millimolar concentrations when groundwater is the source water. In this study, six metagenomes from various locations within a groundwater-fed rapid sand filter (RSF) were analyzed. The community gene catalog contained most genes of the nitrogen cycle, with particular abundance in genes of the nitrification pathway. Genes involved in different carbon fixation pathways were also abundant, with the reverse tricarboxylic acid cycle pathway most abundant, consistent with an observed Nitrospira dominance. From the metagenomic data set, 14 near-complete genomes were reconstructed and functionally characterized. On the basis of their genetic content, a metabolic and geochemical model was proposed. The organisms represented by draft genomes had the capability to oxidize ammonium, nitrite, hydrogen sulfide, methane, potentially iron and manganese as well as to assimilate organic compounds. A composite Nitrospira genome was recovered, and amo-containing Nitrospira genome contigs were identified. This finding, together with the high Nitrospira abundance, and the abundance of atypical amo and hao genes, suggests the potential for complete ammonium oxidation by Nitrospira, and a major role of Nitrospira in the investigated RSFs and potentially other nitrifying environments. DOI PubMed
564. Pardo, SA; Kindsvater, HK; Cuevas-Zimbron, E; Sosa-Nishizaki, O; Perez-Jimenez, JC; Dulvy, NK.Growth, productivity, and relative extinction risk of a data-sparse devil ray.Scientific Reports, 2016, 6 Growth, productivity, and relative extinction risk of a data-sparse devil ray
Devil rays (Mobula spp.) face intensifying fishing pressure to meet the ongoing international demand for gill plates. The paucity of information on growth, mortality, and fishing effort for devil rays make quantifying population growth rates and extinction risk challenging. Furthermore, unlike manta rays (Manta spp.), devil rays have not been listed on CITES. Here, we use a published size-at-age dataset for the Spinetail Devil Ray (Mobula japanica), to estimate somatic growth rates, age at maturity, maximum age, and natural and fishing mortality. We then estimate a plausible distribution of the maximum intrinsic population growth rate (r(max)) and compare it to 95 other chondrichthyans. We find evidence that larger devil ray species have low somatic growth rate, low annual reproductive output, and low maximum population growth rates, suggesting they have low productivity. Fishing rates of a small-scale artisanal Mexican fishery were comparable to our estimate of r(max), and therefore probably unsustainable. Devil ray r(max) is very similar to that of manta rays, indicating devil rays can potentially be driven to local extinction at low levels of fishing mortality and that a similar degree of protection for both groups is warranted. DOI
563. Pardo, SA; Kindsvater, HK; Reynolds, JD; Dulvy, NK.Maximum intrinsic rate of population increase in sharks, rays, and chimaeras: the importance of survival to maturity.Canadian Journal of Fisheries and Aquatic Sciences, 2016, 73: 1159-1163 Maximum intrinsic rate of population increase in sharks, rays, and chimaeras: the importance of survival to maturity
The maximum intrinsic rate of population increase (r(max)) is a commonly estimated demographic parameter used in assessments of extinction risk. In teleosts, r(max) can be calculated using an estimate of spawners per spawner, but for chondrichthyans, most studies have used annual reproductive output (b) instead. This is problematic as it effectively assumes all juveniles survive to maturity. Here, we propose an updated r(max) equation that uses a simple mortality estimator that also accounts for survival to maturity: the reciprocal of average life-span. For 94 chondrichthyans, we now estimate that r(max) values are on average 10% lower than previously published. Our updated r(max) estimates are lower than previously published for species that mature later relative to maximum age and those with high annual fecundity. The most extreme discrepancies in r(max) values occur in species with low age at maturity and low annual reproductive output. Our results indicate that chondrichthyans that mature relatively later in life, and to a lesser extent those that are highly fecund, are less resilient to fishing than previously thought. DOI
562. Patino, S; Keever, CC; Sunday, JM; Popovic, I; Byrne, M; Hart, MW.Sperm Bindin Divergence under Sexual Selection and Concerted Evolution in Sea Stars.Molecular Biology and Evolution, 2016, 33: 1988-2001 Sperm Bindin Divergence under Sexual Selection and Concerted Evolution in Sea Stars
sexual selection; positive selection; gamete recognition; fertilization; speciation
Selection associated with competition among males or sexual conflict between mates can create positive selection for high rates of molecular evolution of gamete recognition genes and lead to reproductive isolation between species. We analyzed coding sequence and repetitive domain variation in the gene encoding the sperm acrosomal protein bindin in 13 diverse sea star species. We found that bindin has a conserved coding sequence domain structure in all 13 species, with several repeated motifs in a large central region that is similar among all sea stars in organization but highly divergent among genera in nucleotide and predicted amino acid sequence. More bindin codons and lineages showed positive selection for high relative rates of amino acid substitution in genera with gonochoric outcrossing adults (and greater expected strength of sexual selection) than in selfing hermaphrodites. That difference is consistent with the expectation that selfing (a highly derivedmating system) maymoderate the strength of sexual selection and limit the accumulation of bindin amino acid differences. The results implicate both positive selection on single codons and concerted evolution within the repetitive region in bindin divergence, and suggest that both single amino acid differences and repeat differences may affect sperm-egg binding and reproductive compatibility. DOI
561. Ponisio, LC; M'Gonigle, LK; Kremen, C.On-farm habitat restoration counters biotic homogenization in intensively managed agriculture.Global Change Biology, 2016, 22: 704-715 On-farm habitat restoration counters biotic homogenization in intensively managed agriculture
-diversity; bees (Hymenoptera: Apoidea); community assembly; ecological filter; pollinators; trait diversity
To slow the rate of global species loss, it is imperative to understand how to restore and maintain native biodiversity in agricultural landscapes. Currently, agriculture is associated with lower spatial heterogeneity and turnover in community composition (-diversity). While some techniques are known to enhance -diversity, it is unclear whether habitat restoration can re-establish -diversity. Using a long-term pollinator dataset, comprising approximate to 9,800 specimens collected from the intensively managed agricultural landscape of the Central Valley of California, we show that on-farm habitat restoration in the form of native plant hedgerows', when replicated across a landscape, can boost -diversity by approximately 14% relative to unrestored field margins, to levels similar to some natural communities. Hedgerows restore -diversity by promoting the assembly of phenotypically diverse communities. Intensively managed agriculture imposes a strong ecological filter that negatively affects several important dimensions of community trait diversity, distribution, and uniqueness. However, by helping to restore phenotypically diverse pollinator communities, small-scale restorations such as hedgerows provide a valuable tool for conserving biodiversity and promoting ecosystem services. DOI
560. Ponisio, LC; Wilkin, K; M'Gonigle, LK; Kulhanek, K; Cook, L; Thorp, R; Griswold, T; Kremen, C.Pyrodiversity begets plant-pollinator community diversity.Global Change Biology, 2016, 22: 1794-1808 Pyrodiversity begets plant-pollinator community diversity
bees (Hymenoptera: Apoidea); community assembly; drought; environmental heterogeneity; fire regime; fire severity
Fire has a major impact on the structure and function of many ecosystems globally. Pyrodiversity, the diversity of fires within a region (where diversity is based on fire characteristics such as extent, severity, and frequency), has been hypothesized to promote biodiversity, but changing climate and land management practices have eroded pyrodiversity. To assess whether changes in pyrodiversity will have impacts on ecological communities, we must first understand the mechanisms that might enable pyrodiversity to sustain biodiversity, and how such changes might interact with other disturbances such as drought. Focusing on plant-pollinator communities in mixed-conifer forest with frequent fire in Yosemite National Park, California, we examine how pyrodiversity, combined with drought intensity, influences those communities. We find that pyrodiversity is positively related to the richness of the pollinators, flowering plants, and plant-pollinator interactions. On average, a 5% increase in pyrodiversity led to the gain of approximately one pollinator and one flowering plant species and nearly two interactions. We also find that a diversity of fire characteristics contributes to the spatial heterogeneity (-diversity) of plant and pollinator communities. Lastly, we find evidence that fire diversity buffers pollinator communities against the effects of drought-induced floral resource scarcity. Fire diversity is thus important for the maintenance of flowering plant and pollinator diversity and predicted shifts in fire regimes to include less pyrodiversity compounded with increasing drought occurrence will negatively influence the richness of these communities in this and other forested ecosystems. In addition, lower heterogeneity of fire severity may act to reduce spatial turnover of plant-pollinator communities. The heterogeneity of community composition is a primary determinant of the total species diversity present in a landscape, and thus, lower pyrodiversity may negatively affect the richness of plant-pollinator communities across large spatial scales. DOI
559. Popescu, VD; Artelle, KA; Pop, MI; Manolache, S; Rozylowicz, L.Assessing biological realism of wildlife population estimates in data-poor systems.Journal of Applied Ecology, 2016, 53: 1248-1259 Assessing biological realism of wildlife population estimates in data-poor systems
abundance estimates; biological plausibility; brown bear; Eurasian lynx; large carnivores; monitoring; population growth; Romania; trophy hunting; wolf
Large carnivore management is often contentious, particularly in jurisdictions where hunting and conservation efforts collide. Regulated hunting is a common management tool, yet relevant decisions are commonly taken in the absence of reliable population data and are driven by factors other than biological considerations. We used European large carnivore (brown bear Ursus arctos, wolf Canis lupus and Eurasian lynx Lynx lynx) management to evaluate the biological plausibility of reported population estimates used in hunting decisions. We used Romania as a test case as this region is not only data-poor, but the public and private game managers are beneficiaries of revenue from hunting activities. We assessed the following: (i) how population growth rates calculated from reported abundances between 2005 and 2012 compared to published growth rates empirically derived from European and North American populations; (ii) whether biological unrealism compounded through time by testing whether reported estimates fell within the bounds of biologically plausible trajectories; and (iii) the relationship between the occurrence of biologically unrealistic estimates and financial incentives (amount of hunting). For U. arctos, which generates high revenue, estimated annual population growth rates were frequently greater than maximum published growth rates (up to 1<bold></bold>5 for reported versus 1<bold></bold>136 in the literature). Reported estimates were greater than maximum simulated populations in 32% of cases, and the difference was positively correlated with hunting (r(s)=0<bold></bold>576). Population growth rates for C. lupus overshot the maximum published growth rate (1<bold></bold>35) less frequently, reported estimates were within the bounds of biologically plausible estimates (91% of cases), and there was a weak correlation between hunting and biologically unrealistic estimates (r(s)=0<bold></bold>182).L. lynx population growth rates derived from reported estimates were lower than minimum simulated populations (60% of cases), and there was a weak correlation between hunting and biologically unrealistic estimates (r(s)=0<bold></bold>164).Synthesis and applications. Our study suggests that comparing population estimates used by management agencies to demographic data obtained through rigorous peer-reviewed studies is a useful approach for evaluating the biological plausibility of wildlife data in data-poor systems, especially when management decisions might be influenced by non-scientific incentives. DOI
557. Redman, EM; Wilson, K; Cory, JS.Trade-offs and mixed infections in an obligate-killing insect pathogen.Journal of Animal Ecology, 2016, 85: 1200-1209 Trade-offs and mixed infections in an obligate-killing insect pathogen
dose-response; entomopathogen; infection diversity; mortality rate; polymorphism; transmission potential; virulence
1. Natural populations of pathogens are frequently composed of numerous interacting strains. Understanding what maintains this diversity remains a key focus of research in disease ecology. In addition, within-host pathogen dynamics can have a strong impact on both infection outcome and the evolution of pathogen virulence, and thus, understanding the impact of pathogen diversity is important for disease management. 2. We compared eight genetically distinguishable variants from Spodoptera exempta nucleopolyhedrovirus (SpexNPV) isolated from the African armyworm, Spodoptera exempta. NPVs are obligate killers, and the vast majority of transmission stages are not released until after the host has died. 3. The NPV variants differed significantly in their virulence and could be clustered into two groups based on their dose-response curves. They also differed in their speed of kill and productivity (transmission potential) for S. exempta. The mixed-genotype wild-type (WT) SpexNPV, from which each variant was isolated, was significantly more virulent than any individual variant and its mean mortality rate was within the fastest group of individual variants. However, the WT virus produced fewer new infectious stages than any single variant, which might reflect competition among the variants. 4. A survival analysis, combining the mortality and speed of kill data, confirmed the superiority of the genetically mixed WT virus over any single variant. Spodoptera exempta larvae infected with WT SpexNPV were predicted to die 2.7 and 1.9 times faster than insects infected with isolates from either of the two clusters of genotypes. 5. Theory suggests that there are likely to be trade-offs between pathogen fitness traits. Across all larvae, there was a negative linear relationship between virus yield and speed of kill, such that more rapid host death carried the cost of producing fewer transmission stages. We also found a near-significant relationship for the same trend at the intervariant level. However, there was no evidence for a significant relationship between the induced level of mortality and transmission potential (virus yield) or speed of kill. DOI
556. Robinson, BJ; Stanisavljevic, B; Silverman, MA; Scalettar, BA.Stochastic Subcellular Organization of Dense-Core Vesicles Revealed by Point Pattern Analysis.Biophysical Journal, 2016, 111: 852-863 Stochastic Subcellular Organization of Dense-Core Vesicles Revealed by Point Pattern Analysis
Dense-core vesicles (DCVs) are regulated secretory organelles found in many types of neurons. In neurons of the hippocampus, their cargo includes proteins that mediate several pivotal processes, including differentiation and synaptic plasticity. Motivated by interest in DCV distribution and its impact on cargo action, we have used fluorescence microscopy and statistical analysis to develop a quantitative model of the subcellular organization of DCVs in hippocampal neurons that are spontaneously active (their most prevalent state). We also have tested the functionally motivated hypothesis that these organelles are synaptically enriched. Variance-to-mean ratio, frequency distribution, and Moran's autocorrelation analyses reveal that DCV distribution along shafts, and within synapses, follows Poisson statistics, establishing that stochastically dictated organization sustains cargo function. Occupancy in boutons exceeds that at nearby extrasynaptic axonal sites by approximately threefold, revealing significant local presynaptic enrichment. Widespread stochastic organization is consistent with the emerging functional importance of synaptically and extrasynaptically localized DCVs. Presynaptic enrichment is consistent with the established importance of protecting presynaptic sites from depletion of DCV cargo. These results enhance understanding of the link between DCV organization and mechanisms of cargo action, and they reinforce the emerging theme that randomness is a prevalent aspect of synaptic organization and composition. DOI
555. Robinson, KJ; Hurd, PL; Read, S; Crespi, BJ.The PCSK6 gene is associated with handedness, the autism spectrum, and magical ideation in a non-clinical population.Neuropsychologia, 2016, 84: 205-212 The PCSK6 gene is associated with handedness, the autism spectrum, and magical ideation in a non-clinical population
Handedness; Lateralization; PCSK6 gene; VNTR; Autism; Schizotypy
Common polymorphisms in the gene PCSK6, whose protein product mediates the development of brain and body asymmetry through the NODAL pathway, have recently been associated with handedness in three studies, making it a key candidate gene for understanding the developmental and expression of human lateralization. We tested the hypothesis that the PCSK6 VNTR polymorphism rs1053972 influences the expression of handedness and aspects of dimensional schizotypy and autism. For a sample of 709 healthy individuals, rs1053972 genotype was significantly associated with categorical measures of handedness, and with dimensional handedness in subsets of the population with high schizotypy and magical ideation or a lack of strong right-handedness. Both findings showed evidence of stronger or exclusive effects among females, compared to males. Genotypes of PCSK6 also showed significant sex limited associations with magical ideation, a component of positive schizotypal cognition measured using the Schizotypal Personality Questionnaire, and total autism score, measured using the Autism Spectrum Quotient. These results partially replicate previous studies on effects of PCSK6 rs1053972 genetic variation on handedness phenotypes, link the PCSK6 gene with the dimensional expression of neurodevelopmental conditions in healthy individuals, and show that associations of this gene with handedness and psychological phenotypes exhibit evidence of sex-limited effects. (C) 2016 Elsevier Ltd. All rights reserved. DOI PubMed
553. Shayegan, M; Altindal, T; Kiefl, E; Forde, NR.Intact Telopeptides Enhance Interactions between Collagens.Biophysical Journal, 2016, 111: 2404-2416 Intact Telopeptides Enhance Interactions between Collagens
Collagen is the fundamental structural component of a wide range of connective tissues and of the extracellular matrix. It undergoes self-assembly from individual triple-helical proteins into well-ordered fibrils, a process that is key to tissue development and homeostasis, and to processes such as wound healing. Nucleation of this assembly is known to be slowed considerably by pepsin removal of short nonhelical regions that flank collagen's triple helix, known as telopeptides. Using optical tweezers to perform microrheology measurements, we explored the changes in viscoelasticity of solutions of collagen with and without intact telopeptides. Our experiments reveal that intact telopeptides contribute a significant frequency-dependent enhancement of the complex shear modulus. An analytical model of polymers associating to establish chemical equilibrium among higher-order species shows trends in G' and G '' consistent with our experimental observations, including a concentration-dependent crossover in G ''/c around 300 Hz. This work suggests that telopeptides facilitate transient intermolecular interactions between collagen proteins, even in the acidic conditions used here. DOI
552. Stang, JB; Barker, M; Perez, S; Ives, J; Roll, I.Active learning in pre-class assignments: exploring the use of interactive simulations to enhance reading assignments.2016 Physics Education Research Conference, 2016, : 332-335 Active learning in pre-class assignments: exploring the use of interactive simulations to enhance reading assignments
Pre-class reading assignments help prepare students for active classes by providing a first exposure to the terms and concepts to be used during class. We investigate if the use of inquiry-oriented PhET-based activities in conjunction with pre-class reading assignments can improve both the preparation of students for in-class learning and student attitudes towards and engagement with pre-class assignments. Over three course modules covering different topics, students were assigned randomly to complete either a textbook-only pre-class assignment or both a textbook pre-class assignment and a PhET-based activity. The assignments helped prepare students for class, as measured by performance on the pre-class quiz relative to a beginning-of-semester pretest, but no evidence for increased learning due the PhET activity was observed. Students rated the assignments which included PhET as more enjoyable and, for the topic latest in the semester, reported spending more time on the assignments when PhET was included. DOI
551. Stevens, CM; Rayani, K; Genge, CE; Singh, G; Liang, B; Roller, JM; Li, C; Li, AY; Tieleman, DP; van Petegem, F; Tibbits, GF.Characterization of Zebrafish Cardiac and Slow Skeletal Troponin C Paralogs by MD Simulation and ITC.Biophysical Journal, 2016, 111: 38-49 Characterization of Zebrafish Cardiac and Slow Skeletal Troponin C Paralogs by MD Simulation and ITC
Zebrafish, as a model for teleost fish, have two paralogous troponin C (TnC) genes that are expressed in the heart differentially in response to temperature acclimation. Upon Ca2+ binding, TnC changes conformation and exposes a hydrophobic patch that interacts with troponin I and initiates cardiac muscle contraction. Teleost-specific TnC paralogs have not yet been functionally characterized. In this study we have modeled the structures of the paralogs using molecular dynamics simulations at 18 degrees C and 28 degrees C and calculated the different Ca2+-binding properties between the teleost cardiac (cTnC or TnC1a) and slow-skeletal (ssTnC or TnC1b) paralogs through potential-of-mean-force calculations. These values are compared with thermodynamic binding properties obtained through isothermal titration calorimetry (ITC). The modeled structures of each of the paralogs are similar at each temperature, with the exception of helix C, which flanks the Ca2+ binding site; this region is also home to paralog-specific sequence substitutions that we predict have an influence on protein function. The short timescale of the potential-of-mean-force calculation precludes the inclusion of the conformational change on the Delta G of Ca2+ interaction, whereas the ITC analysis includes the Ca2+ binding and conformational change of the TnC molecule. ITC analysis has revealed that ssTnC has higher Ca2+ affinity than cTnC for Ca2+ overall, whereas each of the paralogs has increased affinity at 28 degrees C compared to 18 degrees C. Microsecond-timescale simulations have calculated that the cTnC paralog transitions from the closed to the open state more readily than the ssTnC paralog, an unfavorable transition that would decrease the ITC-derived Ca2+ affinity while simultaneously increasing the Ca2+ sensitivity of the myofilament. We propose that the preferential expression of cTnC at lower temperatures increases myofilament Ca2+ sensitivity by this mechanism, despite the lower Ca2+ affinity that we have measured by ITC. DOI
550. Suraci, JP; Clinchy, M; Dill, LM; Roberts, D; Zanette, LY.Fear of large carnivores causes a trophic cascade.Nature Communications, 2016, 7 Fear of large carnivores causes a trophic cascade
The fear large carnivores inspire, independent of their direct killing of prey, may itself cause cascading effects down food webs potentially critical for conserving ecosystem function, particularly by affecting large herbivores and mesocarnivores. However, the evidence of this has been repeatedly challenged because it remains experimentally untested. Here we show that experimentally manipulating fear itself in free-living mesocarnivore (raccoon) populations using month-long playbacks of large carnivore vocalizations caused just such cascading effects, reducing mesocarnivore foraging to the benefit of the mesocarnivore's prey, which in turn affected a competitor and prey of the mesocarnivore's prey. We further report that by experimentally restoring the fear of large carnivores in our study system, where most large carnivores have been extirpated, we succeeded in reversing this mesocarnivore's impacts. We suggest that our results reinforce the need to conserve large carnivores given the significant "ecosystem service'' the fear of them provides. DOI
549. Swan, KD; McPherson, JM; Seddon, PJ; Moehrenschlager, A.Managing Marine Biodiversity: The Rising Diversity and Prevalence of Marine Conservation Translocations.Conservation Letters, 2016, 9: 239-251 Managing Marine Biodiversity: The Rising Diversity and Prevalence of Marine Conservation Translocations
Assisted colonization; conservation translocation; ecological replacement; ecosystem recovery; oceans; marine; reinforcement; reintroduction; species recovery
Translocations, the human-mediated movement and free-release of living organisms, are increasingly used as conservation tools in imperiled terrestrial ecosystems. Marine ecosystems, too, are increasingly threatened, and marine restoration efforts are escalating. But the methods and motivations for marine restoration are varied, so the extent to which they involve conservation-motivated translocations is unclear. Because translocations involve considerable risks, building on previous experience to establish and implement best practice guidelines for policy application is imperative. We conducted a global literature review to determine what marine conservation translocation experience exists. Our review indicates marine conservation translocations are widespread and increasingly common. Reinforcements and reintroductions predominate, but precedent for assisted colonizations and ecological replacements also exists. In 39 years, 487 translocation projects were conducted to conserve over 242 marine species or their ecosystems. Most projects involved coastal invertebrates (44%) or plants (30%). Few species were of conservation concern according to the IUCN Red List, likely reflecting the leading objective for most (60%) marine conservation translocations, which was ecosystem rather than species recovery. With currently no standard metrics for evaluating translocation success or ecosystem function, we recommend future projects follow the relevant IUCN guidelines and identify specific targets to measure the efficacy of translocations. DOI
548. Thomsen, SK; Green, DJ.Cascading effects of predation risk determine how marine predators become terrestrial prey on an oceanic island.Ecology, 2016, 97: 3530-3537 Cascading effects of predation risk determine how marine predators become terrestrial prey on an oceanic island
apex predators; barn owls; deer mice; giving up densities; indirect interactions; mesopredators; murrelets; predation; risk effects; seabirds; trophic cascade
Apex predators can suppress the foraging activity of mesopredators, which may then result in cascading benefits for the prey of those mesopredators. We studied the interactions between a top predator, the Barn Owl (Tyto alba), and their primary prey, an island endemic deer mouse (Peromyscus maniculatus elusus), which in turn consumes the eggs of seabirds nesting on Santa Barbara Island in California. Scripps's Murrelets (Synthliboramphus scrippsi), a threatened nocturnal seabird, arrive annually to breed on this island, and whose first egg is particularly vulnerable to predation by mice. We took advantage of naturally occurring extreme variations in the density of mice and owls on the island over 3 years and predicted that (1) mouse foraging would decrease with increasing predation risk from owls and moonlight and (2) these decreases in foraging would reduce predation on murrelet eggs. We measured the giving up densities of mice with experimental foraging stations and found that mice were sensitive to predation risk and foraged less when owls were more abundant and less during the full moon compared to the new moon. We also monitored the fates of 151 murrelet eggs, and found that murrelet egg predation declined as owl abundance increased, and was lower during the full moon compared to the new moon. Moreover, high owl abundance suppressed egg predation even when mice were extremely abundant. We conclude that there is a behaviorally mediated cascade such that owls on the island had a positive indirect effect on murrelet egg survival. Our study adds to the wider recognition of the strength of risk effects to structure food webs, as well as highlighting the complex ways that marine and terrestrial food webs can intersect. DOI
547. Trebilcou, R; Dulvy, NK; Anderson, SC; Salomon, AK.The paradox of inverted biomass pyramids in kelp forest fish communities.Proceedings of the Royal Society B-Biological Sciences, 2016, 283 The paradox of inverted biomass pyramids in kelp forest fish communities
ecosystem baseline; fractionation; habitat complexity; species interaction; size spectra; stable isotope analysis
Theory predicts that bottom-heavy biomass pyramids or 'stacks' should predominate in real-world communities if trophic-level increases with body size (mean predator-to-prey mass ratio (PPMR) more than 1). However, recent research suggests that inverted biomass pyramids (IBPs) characterize relatively pristine reef fish communities. Here, we estimated the slope of a kelp forest fish community biomass spectrum from underwater visual surveys. The observed biomass spectrum slope is strongly positive, reflecting an IBP. This is incongruous with theory because this steep positive slope would only be expected if trophic position decreased with increasing body size (consumer-to-resource mass ratio, less than 1). We then used delta N-15 signatures of fish muscle tissue to quantify the relationship between trophic position and body size and instead detected strong evidence for the opposite, with PPMR 1650 (50% credible interval 280-12 000). The natural history of kelp forest reef fishes suggests that this paradox could arise from energetic subsidies in the form of movement of mobile consumers across habitats, and from seasonally pulsed production inputs at small body sizes. There were four to five times more biomass at large body sizes (1-2 kg) than would be expected in a closed steady-state community providing a measure of the magnitude of subsidies. DOI
546. Voisin, E; Williams, VE.Side-chain shuffling: regioselective synthesis of mixed tail discotic mesogens.RSC Adv., 2016, 6: 11262-11265 Side-chain shuffling: regioselective synthesis of mixed tail discotic mesogens
A procedure for the regioselective synthesis of discotic mesogens bearingmultiple side chains of different lengths is reported. A series of isomeric dibenzoquinoxaline mesogens obtained by this route showed phase behaviour that was highly sensitive to chain location. DOI
545. Volik, S; Alcaide, M; Morin, RD; Collins, C.Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies.Molecular Cancer Research, 2016, 14: 898-908 Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies
Precision oncology is predicated upon the ability to detect specific actionable genomic alterations and to monitor their adaptive evolution during treatment to counter resistance. Because of spatial and temporal heterogeneity and comorbidities associated with obtaining tumor tissues, especially in the case of metastatic disease, traditional methods for tumor sampling are impractical for this application. Known to be present in the blood of cancer patients for decades, cell-free DNA(cfDNA) is beginning to inform on tumor genetics, tumor burden, and mechanisms of progression and drug resistance. This substrate is amenable for inexpensive noninvasive testing and thus presents a viable approach to serial sampling for screening and monitoring tumor progression. The fragmentation, low yield, and variable admixture of normal DNA present formidable technical challenges for realization of this potential. This review summarizes the history of cfDNA discovery, its biological properties, and explores emerging technologies for clinically relevant sequence-based analysis of cfDNA in cancer patients. Molecular barcoding (or Unique Molecular Identifier, UMI)-based methods currently appear to offer an optimal balance between sensitivity, flexibility, and cost and constitute a promising approach for clinically relevant assays for near real-time monitoring of treatment-induced mutational adaptations to guide evidence-based precision oncology. DOI
544. Weir, LK; Kindsvater, HK; Young, KA; Reynolds, JD.Sneaker Males Affect Fighter Male Body Size and Sexual Size Dimorphism in Salmon.American Naturalist, 2016, 188: 264-271 Sneaker Males Affect Fighter Male Body Size and Sexual Size Dimorphism in Salmon
alternative mating strategies; competition; latitudinal clines; salmonids; sexual selection
Large male body size is typically favored by directional sexual selection through competition for mates. However, alternative male life-history phenotypes, such as "sneakers," should decrease the strength of sexual selection acting on body size of large "fighter" males. We tested this prediction with salmon species; in southern populations, where sneakers are common, fighter males should be smaller than in northern populations, where sneakers are rare, leading to geographical clines in sexual size dimorphism (SSD). Consistent with our prediction, fighter male body size and SSD (fighter male: female size) increase with latitude in species with sneaker males (Atlantic salmon Salmo salar and masu salmon Oncorhynchus masou) but not in species without sneakers (chum salmon Oncorhynchus keta and pink salmon Oncorhynchus gorbuscha). This is the first evidence that sneaker males affect SSD across populations and species, and it suggests that alternative male mating strategies may shape the evolution of body size. DOI
543. Williamson, SN; Barrio, IC; Hik, DS; Gamon, JA.Phenology and species determine growing-season albedo increase at the altitudinal limit of shrub growth in the sub-Arctic.Glob. Change Biol., 2016, 22: 3621-3631 Phenology and species determine growing-season albedo increase at the altitudinal limit of shrub growth in the sub-Arctic
albedo; alpine tundra; Betula; growing season; phenology; Salix
Arctic warming is resulting in reduced snow cover and increased shrub growth, both of which have been associated with altered land surface-atmospheric feedback processes involving sensible heat flux, ground heat flux and biogeochemical cycling. Using field measurements, we show that two common Arctic shrub species (Betula glandulosa and Salix pulchra), which are largely responsible for shrub encroachment in tundra, differed markedly in albedo and that albedo of both species increased as growing season progressed when measured at their altitudinal limit. A moveable apparatus was used to repeatedly measure albedo at six precise spots during the summer of 2012, and resampled in 2013. Contrary to the generally accepted view of shrub-covered areas having low albedo in tundra, full-canopy prostrate B. glandulosa had almost the highest albedo of all surfaces measured during the peak of the growing season. The higher midsummer albedo is also evident in localized MODIS albedo aggregated from 2000 to 2013, which displays a similar increase in growing-season albedo. Using our field measurements, we show the ensemble summer increase in tundra albedo counteracts the generalized effect of earlier spring snow melt on surface energy balance by approximately 40%. This summer increase in albedo, when viewed in absolute values, is as large as the difference between the forest and tundra transition. These results indicate that near future (<50 years) changes in growing-season albedo related to Arctic vegetation change are unlikely to be particularly large and might constitute a negative feedback to climate warming in certain circumstances. Future efforts to calculate energy budgets and a sensible heating feedback in the Arctic will require more detailed information about the relative abundance of different ground cover types, particularly shrub species and their respective growth forms and phenology. DOI
542. Alvarez-Filip, L; Paddack, MJ; Ben Collen; Robertson, DR; Côté, IM.Simplification of Caribbean Reef-Fish Assemblages over Decades of Coral Reef Degradation.PLoS One, 2015, 10 Simplification of Caribbean Reef-Fish Assemblages over Decades of Coral Reef Degradation
Caribbean coral reefs are becoming structurally simpler, largely due to human impacts. The consequences of this trend for reef-associated communities are currently unclear, but expected to be profound. Here, we assess whether changes in fish assemblages have been non-random over several decades of declining reef structure. More specifically, we predicted that species that depend exclusively on coral reef habitat (i.e., habitat specialists) should be at a disadvantage compared to those that use a broader array of habitats (i.e., habitat generalists). Analysing 3727 abundance trends of 161 Caribbean reef-fishes, surveyed between 1980 and 2006, we found that the trends of habitat-generalists and habitat-specialists differed markedly. The abundance of specialists started to decline in the mid-1980s, reaching a low of similar to 60% of the 1980 baseline by the mid-1990s. Both the average and the variation in abundance of specialists have increased since the early 2000s, although the average is still well below the baseline level of 1980. This modest recovery occurred despite no clear evidence of a regional recovery in coral reef habitat quality in the Caribbean during the 2000s. In contrast, the abundance of generalist fishes remained relatively stable over the same three decades. Few specialist species are fished, thus their population declines are most likely linked to habitat degradation. These results mirror the observed trends of replacement of specialists by generalists, observed in terrestrial taxa across the globe. A significant challenge that arises from our findings is now to investigate if, and how, such community-level changes in fish populations affect ecosystem function. DOI PubMed
541. Anderson, SC; Moore, JW; McClure, MM; Dulvy, NK; Cooper, AB.Portfolio conservation of metapopulations under climate change.Ecological Applications, 2015, 25: 559-572 Portfolio conservation of metapopulations under climate change
biocomplexity; diversity-stability ecosystem-based management; Oncorhynchus spp; Pacific salmon; portfolio effect; prioritization; range contraction; response diversity; risk assessment; stochastic simulation
Climate change is likely to lead to increasing population variability and extinction risk. Theoretically, greater population diversity should buffer against rising climate variability, and this theory is often invoked as a reason for greater conservation. However, this has rarely been quantified. Here we show how a portfolio approach to managing population diversity can inform metapopulation conservation priorities in a changing world. We develop a salmon metapopulation model in which productivity is driven by spatially distributed thermal tolerance and patterns of short- and long-term climate change. We then implement spatial conservation scenarios that control population carrying capacities and evaluate the metapopulation portfolios as a financial manager might: along axes of conservation risk and return. We show that preserving a diversity of thermal tolerances minimizes risk, given environmental stochasticity, and ensures persistence, given long-term environmental change. When the thermal tolerances of populations are unknown, doubling the number of populations conserved may nearly halve expected metapopulation variability. However, this reduction in variability can come at the expense of long-term persistence if climate change increasingly restricts available habitat, forcing ecological managers to balance society's desire for short-term stability and long-term viability. Our findings suggest the importance of conserving the processes that promote thermal-tolerance diversity, such as genetic diversity, habitat heterogeneity, and natural disturbance regimes, and demonstrate that diverse natural portfolios may be critical for metapopulation conservation in the face of increasing climate variability and change. DOI
539. Arbuthnott, D; Crespi, BJ; Schwander, T.Female Stick Insects Mate Multiply to Find Compatible Mates.American Naturalist, 2015, 186: 519-530 Female Stick Insects Mate Multiply to Find Compatible Mates
polyandry; mate choice; genetic compatibility; sexual selection; phasmid
Why females of many species mate multiply in the absence of direct benefits remains an open question in evolutionary ecology. Interacting and mating with multiple males can be costly to females in terms of time, resources, predation risk, and disease transmission. A number of indirect genetic benefits have been proposed to explain such behaviors, but the relative importance of these mechanisms in natural systems remains unclear. We tested for several direct and indirect benefits of polyandry in the walking stick Timema cristinae. We found no evidence of direct benefits with respect to longevity or fecundity. However, male x female genotypic interactions affected egg-hatching success and offspring production independent of relatedness, suggesting that mating with certain males benefits females and that the best male may differ for each female. Furthermore, multiply mated females biased paternity toward one or few males, and the extent of this bias was positively correlated to egg-hatching success. Our data, therefore, provide evidence for indirect benefits through compatibility effects in this species. By mating multiply, females may improve their chances of mating with a compatible male if compatibility cannot be assessed before mating. Such compatibility effects can explain the evolution and maintenance of polyandry in Timema and many other species. DOI
538. Arnal, A; Ujvari, B; Crespi, B; Gatenby, RA; Tissot, T; Vittecoq, M; Ewald, PW; Casali, A; Ducasse, H; Jacqueline, C; Misse, D; Renaud, F; Roche, B; Thomas, F.Evolutionary perspective of cancer: myth, metaphors, and reality.Evolutionary Applications, 2015, 8: 541-544 Evolutionary perspective of cancer: myth, metaphors, and reality
adaptationism; cancer; evolutionary processes
The evolutionary perspective of cancer (which origins and dynamics result from evolutionary processes) has gained significant international recognition over the past decade and generated a wave of enthusiasm among researchers. In this context, several authors proposed that insights into evolutionary and adaptation dynamics of cancers can be gained by studying the evolutionary strategies of organisms. Although this reasoning is fundamentally correct, in our opinion, it contains a potential risk of excessive adaptationism, potentially leading to the suggestion of complex adaptations that are unlikely to evolve among cancerous cells. For example, the ability of recognizing related conspecifics and adjusting accordingly behaviors as in certain free-living species appears unlikely in cancer. Indeed, despite their rapid evolutionary rate, malignant cells are under selective pressures for their altered lifestyle for only few decades. In addition, even though cancer cells can theoretically display highly sophisticated adaptive responses, it would be crucial to determine the frequency of their occurrence in patients with cancer, before therapeutic applications can be considered. Scientists who try to explain oncogenesis will need in the future to critically evaluate the metaphorical comparison of selective processes affecting cancerous cells with those affecting organisms. This approach seems essential for the applications of evolutionary biology to understand the origin of cancers, with prophylactic and therapeutic applications. DOI
537. Arrowsmith, CH; Audia, JE; Austin, C; Baell, J; Bennett, J; Blagg, J; Bountra, C; Brennan, PE; Brown, PJ; Bunnage, ME; Buser-Doepner, C; Campbell, RM; Carter, AJ; Cohen, P; Copeland, RA; Cravatt, B; Dahlin, JL; Dhanak, D; Edwards, AM; Frye, SV; Gray, N; Grimshaw, CE; Hepworth, D; Howe, T; Huber, KVM; Jin, J; Knapp, S; Kotz, JD; Kruger, RG; Lowe, D; Mader, MM; Marsden, B; Mueller-Fahrnow, A; Muller, S; O'Hagan, RC; Overington, JP; Owen, DR; Rosenberg, SH; Roth, B; Ross, R; Schapira, M; Schreiber, SL; Shoichet, B; Sundstrom, M; Superti-Furga, G; Taunton, J; Toledo-Sherman, L; Walpole, C; Walters, MA; Willson, TM; Workman, P; Young, RN; Zuercher, WJ.The promise and peril of chemical probes.Nat. Chem. Biol., 2015, 11: 536-541 The promise and peril of chemical probes
Chemical probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these shortcomings, we will create a community-driven wiki resource to improve quality and convey current best practice. DOI PubMed
536. Avidor-Reiss, T; Leroux, MR.Shared and Distinct Mechanisms of Compartmentalized and Cytosolic Ciliogenesis.Current Biology, 2015, 25: R1143-R1150 Shared and Distinct Mechanisms of Compartmentalized and Cytosolic Ciliogenesis
Most motile and all non-motile (also known as primary) eukaryotic cilia possess microtubule-based axonemes that are assembled at the cell surface to form hair-like or more elaborate compartments endowed with motility and/or signaling functions. Such compartmentalized ciliogenesis depends on the core intraflagellar transport (IFT) machinery and the associated Bardet-Biedl syndrome complex (BBSome) for dynamic delivery of ciliary components. The transition zone (TZ), an ultrastructurally complex barrier or 'gate' at the base of cilia, also contributes to the formation of compartmentalized cilia. Yet, some ciliated protists do not have IFT components and, like some metazoan spermatozoa, use IFT-independent mechanisms to build axonemes exposed to the cytosol. Moreover, various ciliated protists lack TZ components, whereas Drosophila sperm surprisingly requires the activity of dynamically localized TZ proteins for cytosolic ciliogenesis. Here, we discuss the various ways eukaryotes use IFT and/or TZ proteins to generate the wide assortment of compartmentalized and cytosolic cilia observed in nature. Consideration of the different ciliogenesis pathways allows us to propose how three types of cytosol-exposed cilia (primary, secondary and tertiary), including cilia found in the human sperm proximal segment, are likely generated by evolutionary derivations of compartmentalized ciliogenesis. DOI
535. Boddy, AM; Kokko, H; Breden, F; Wilkinson, GS; Aktipis, CA.Cancer susceptibility and reproductive trade-offs: a model of the evolution of cancer defences.Philosophical Transactions of the Royal Society B-Biological Sciences, 2015, 370 Cancer susceptibility and reproductive trade-offs: a model of the evolution of cancer defences
cancer defences; life-history trade-offs; reproductive competition; sexual selection; comparative oncology
The factors influencing cancer susceptibility and why it varies across species are major open questions in the field of cancer biology. One underexplored source of variation in cancer susceptibility may arise from trade-offs between reproductive competitiveness (e.g. sexually selected traits, earlier reproduction and higher fertility) and cancer defence. We build a model that contrasts the probabilistic onset of cancer with other, extrinsic causes of mortality and use it to predict that intense reproductive competition will lower cancer defences and increase cancer incidence. We explore the trade-off between cancer defences and intraspecific competition across different extrinsic mortality conditions and different levels of trade-off intensity, and find the largest effect of competition on cancer in species where low extrinsic mortality combines with strong trade-offs. In such species, selection to delay cancer and selection to outcompete conspecifics are both strong, and the latter conflicts with the former. We discuss evidence for the assumed trade-off between reproductive competitiveness and cancer susceptibility. Sexually selected traits such as ornaments or large body size require high levels of cell proliferation and appear to be associated with greater cancer susceptibility. Similar associations exist for female traits such as continuous egg-laying in domestic hens and earlier reproductive maturity. Trade-offs between reproduction and cancer defences may be instantiated by a variety of mechanisms, including higher levels of growth factors and hormones, less efficient cell-cycle control and less DNA repair, or simply a larger number of cell divisions (relevant when reproductive success requires large body size or rapid reproductive cycles). These mechanisms can affect intra-and interspecific variation in cancer susceptibility arising from rapid cell proliferation during reproductive maturation, intrasexual competition and reproduction. DOI
534. Brodie, BS; Smith, MA; Lawrence, J; Gries, G.Effects of Floral Scent, Color and Pollen on Foraging Decisions and Oocyte Development of Common Green Bottle Flies.PLoS One, 2015, 10 Effects of Floral Scent, Color and Pollen on Foraging Decisions and Oocyte Development of Common Green Bottle Flies
The common green bottle fly Lucilia sericata (Meigen) and other filth flies frequently visit pollen-rich composite flowers such as the Oxeye daisy, Leucanthemum vulgare Lam. In laboratory experiments with L. sericata, we investigated the effect of generic floral scent and color cues, and of Oxeye daisy-specific cues, on foraging decisions by recently eclosed flies. We also tested the effect of a floral pollen diet with 0-35% moisture content on the ability of females to mature their oocytes. Our data indicate that (1) young flies in the presence of generic floral scent respond more strongly to a uniformly yellow cue than to any other uniform color cue (green, white, black, blue, red) except for ultraviolet (UV); (2) the floral scent of Oxeye daisies enhances the attractiveness of a yellow cue; and (3) moisture-rich pollen provides nutrients that facilitate ovary maturation of flies. With evidence that L. sericata exploits floral cues during foraging, and that pollen can be an alternate protein source to animal feces and carrion, Pollen apparently plays a major role in the foraging ecology of L. sericata and possibly other filth flies. These flies, in turn, may play a significant role as pollinators, as supported by a recently published study. DOI
533. Cavolo, SL; Zhou, CM; Ketcham, SA; Suzuki, MM; Ukalovic, K; Silverman, MA; Schroer, TA; Levitan, ES.Mycalolide B dissociates dynactin and abolishes retrograde axonal transport of dense-core vesicles.Molecular Biology of the Cell, 2015, 26: 2664-2672 Mycalolide B dissociates dynactin and abolishes retrograde axonal transport of dense-core vesicles
Axonal transport is critical for maintaining synaptic transmission. Of interest, anterograde and retrograde axonal transport appear to be interdependent, as perturbing one directional motor often impairs movement in the opposite direction. Here live imaging of Drosophila and hippocampal neuron dense-core vesicles (DCVs) containing a neuropeptide or brain-derived neurotrophic factor shows that the F-actin depolymerizing macrolide toxin mycalolide B (MB) rapidly and selectively abolishes retrograde, but not anterograde, transport in the axon and the nerve terminal. Latrunculin A does not mimic MB, demonstrating that F-actin depolymerization is not responsible for unidirectional transport inhibition. Given that dynactin initiates retrograde transport and that amino acid sequences implicated in macrolide toxin binding are found in the dynactin component actin-related protein 1, we examined dynactin integrity. Remarkably, cell extract and purified protein experiments show that MB induces disassembly of the dynactin complex. Thus imaging selective retrograde transport inhibition led to the discovery of a small-molecule dynactin disruptor. The rapid unidirectional inhibition by MB suggests that dynactin is absolutely required for retrograde DCV transport but does not directly facilitate ongoing anterograde DCV transport in the axon or nerve terminal. More generally, MB's effects bolster the conclusion that anterograde and retrograde axonal transport are not necessarily interdependent. DOI
531. Cornes, E; Porta-de-la-Riva, M; Aristizabal-Corrales, D; Brokate-Llanos, AM; Garcia-Rodriguez, FJ; Ertl, I; Diaz, M; Fontrodona, L; Reis, K; Johnsen, R; Baillie, D; Munoz, MJ; Sarov, M; Dupuy, D; Ceron, J.Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans.RNA, 2015, 21: 1544-1553 Cytoplasmic LSM-1 protein regulates stress responses through the insulin/IGF-1 signaling pathway in Caenorhabditis elegans
Caenorhabditis elegans; stress response; LSM; daf-16; P bodies; stress granules
Genes coding for members of the Sm-like (LSm) protein family are conserved through evolution from prokaryotes to humans. These proteins have been described as forming homo-or heterocomplexes implicated in a broad range of RNA-related functions. To date, the nuclear LSm2-8 and the cytoplasmic LSm1-7 heteroheptamers are the best characterized complexes in eukaryotes. Through a comprehensive functional study of the LSm family members, we found that lsm-1 and lsm-3 are not essential for C. elegans viability, but their perturbation, by RNAi or mutations, produces defects in development, reproduction, and motility. We further investigated the function of lsm-1, which encodes the distinctive protein of the cytoplasmic complex. RNA-seq analysis of lsm-1 mutants suggests that they have impaired Insulin/IGF-1 signaling (IIS), which is conserved in metazoans and involved in the response to various types of stress through the action of the FOXO transcription factor DAF-16. Further analysis using a DAF-16:: GFP reporter indicated that heat stress-induced translocation of DAF-16 to the nuclei is dependent on lsm-1. Consistent with this, we observed that lsm-1 mutants display heightened sensitivity to thermal stress and starvation, while overexpression of lsm-1 has the opposite effect. We also observed that under stress, cytoplasmic LSm proteins aggregate into granules in an LSM-1-dependent manner. Moreover, we found that lsm-1 and lsm-3 are required for other processes regulated by the IIS pathway, such as aging and pathogen resistance. DOI
530. Correa, K; Lhorente, JP; Lopez, ME; Bassini, L; Naswa, S; Deeb, N; Di Genova, A; Maass, A; Davidson, WS; Yanez, JM.Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes.BMC Genomics, 2015, 16 Genome-wide association analysis reveals loci associated with resistance against Piscirickettsia salmonis in two Atlantic salmon (Salmo salar L.) chromosomes
Salmon Rickettsial Syndrome; Genome Wide Association Analysis; Pathogen resistance; Atlantic salmon; Single Nucleotide Polymorphism
Background: Pisciricketssia salmonis is the causal agent of Salmon Rickettsial Syndrome (SRS), which affects salmon species and causes severe economic losses. Selective breeding for disease resistance represents one approach for controlling SRS in farmed Atlantic salmon. Knowledge concerning the architecture of the resistance trait is needed before deciding on the most appropriate approach to enhance artificial selection for P. salmonis resistance in Atlantic salmon. The purpose of the study was to dissect the genetic variation in the resistance to this pathogen in Atlantic salmon. Methods: 2,601 Atlantic salmon smolts were experimentally challenged against P. salmonis by means of intra-peritoneal injection. These smolts were the progeny of 40 sires and 118 dams from a Chilean breeding population. Mortalities were recorded daily and the experiment ended at day 40 post-inoculation. Fish were genotyped using a 50K Affymetrix (R) Axiom (R) myDesign (TM) Single Nucleotide Polymorphism (SNP) Genotyping Array. A Genome Wide Association Analysis was performed on data from the challenged fish. Linear regression and logistic regression models were tested. Results: Genome Wide Association Analysis indicated that resistance to P. salmonis is a moderately polygenic trait. There were five SNPs in chromosomes Ssa01 and Ssa17 significantly associated with the traits analysed. The proportion of the phenotypic variance explained by each marker is small, ranging from 0.007 to 0.045. Candidate genes including interleukin receptors and fucosyltransferase have been found to be physically linked with these genetic markers and may play an important role in the differential immune response against this pathogen. Conclusions: Due to the small amount of variance explained by each significant marker we conclude that genetic resistance to this pathogen can be more efficiently improved with the implementation of genetic evaluations incorporating genotype information from a dense SNP array. DOI
529. Crespi, BJ.Cognitive trade-offs and the costs of resilience.Behavioral and Brain Sciences, 2015, 38 Cognitive trade-offs and the costs of resilience
Genetic, endocrinological, and psychological evidence demonstrates that resilience commonly trades off with sensitivity. The existence of such trade-offs indicates that resilience bears costs as well as benefits, and that some disorders can best be conceptualized in terms of extremes of trade-offs rather than expression of deficits. Testing for cognitive trade-offs should be a priority for psychiatry, psychology, neuroscience, and genetics. DOI
528. d'Eon-Eggertson, F; Dulvy, NK; Peterman, RM.Reliable Identification of Declining Populations in an Uncertain World.Conservation Letters, 2015, 8: 86-96 Reliable Identification of Declining Populations in an Uncertain World
Decline indicators; error rates; IUCN; Monte Carlo simulation; extinction-risk assessment; process variation; observation error
Assessments of extinction risk based on population declines are widely used, yet scientists have little quantitative understanding of their reliability. Incorrectly classifying whether a population is declining or not can lead to inappropriate conservation actions or management measures, with potentially profound societal costs. Here we evaluate key causes of misclassification of decline status and assess the reliability of 20 decline metrics using a stochastic model to simulate time series of population abundance of sockeye salmon (Oncorhynchus nerka). We show that between-year variability in population productivity (process variation) and, to a lesser extent, variability in abundance estimates (observation error) are important causes of unreliable identification of population status. We found that using all available data, rather than just the most recent three generations, consistently improved the reliability of risk assessments. The approach outlined here can improve understanding of the reliability of risk assessments, thereby reducing concerns that may impede their use for exploited taxa such as marine fishes. DOI
527. Dembo, M; Matzke, NJ; Mooers, AO; Collard, M.Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships.Proceedings of the Royal Society B-Biological Sciences, 2015, 282: 133-141 Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships
human origins; phylogeny; Bayesian morphological analysis
The phylogenetic relationships of several hominin species remain controversial. Two methodological issues contribute to the uncertainty use of partial, inconsistent datasets and reliance on phylogenetic methods that are ill-suited to testing competing hypotheses. Here, we report a study designed to overcome these issues. We first compiled a supermatrix of craniodental characters for all widely accepted hominin species. We then took advantage of recently developed Bayesian methods for building trees of serially sampled tips to test among hypotheses that have been put forward in three of the most important current debates in hominin phylogenetics the relationship between Australopithecus sediba and Homo, the taxonomic status of the Dmanisi hominins, and the place of the so-called hobbit fossils from Flores, Indonesia, in the hominin tree. Based on our results, several published hypotheses can be statistically rejected. For example, the data do not support the claim that Dmanisi hominins and all other early Homo specimens represent a single species, nor that the hobbit fossils are the remains of small-bodied modern humans, one of whom had Down syndrome. More broadly, our study provides a new baseline dataset for future work on hominin phylogeny and illustrates the promise of Bayesian approaches for understanding hominin phylogenetic relationships. DOI
525. Dong, LL; Liu, HF; Zhang, JC; Yang, SJ; Kong, GY; Chu, JSC; Chen, NS; Wang, DW.Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research.BMC Genomics, 2015, 16 Single-molecule real-time transcript sequencing facilitates common wheat genome annotation and grain transcriptome research
SMRT sequencing; PacBio RSII; Genome annotation; Transcriptome; Grain development; Common wheat
Background: The large and complex hexaploid genome has greatly hindered genomics studies of common wheat (Triticum aestivum, AABBDD). Here, we investigated transcripts in common wheat developing caryopses using the emerging single-molecule real-time (SMRT) sequencing technology PacBio RSII, and assessed the resultant data for improving common wheat genome annotation and grain transcriptome research. Results: We obtained 197,709 full-length non-chimeric (FLNC) reads, 74.6 % of which were estimated to carry complete open reading frame. A total of 91,881 high-quality FLNC reads were identified and mapped to 16,188 chromosomal loci, corresponding to 13,162 known genes and 3026 new genes not annotated previously. Although some FLNC reads could not be unambiguously mapped to the current draft genome sequence, many of them are likely useful for studying highly similar homoeologous or paralogous loci or for improving chromosomal contig assembly in further research. The 91,881 high-quality FLNC reads represented 22,768 unique transcripts, 9591 of which were newly discovered. We found 180 transcripts each spanning two or three previously annotated adjacent loci, suggesting that they should be merged to form correct gene models. Finally, our data facilitated the identification of 6030 genes differentially regulated during caryopsis development, and full-length transcripts for 72 transcribed gluten gene members that are important for the end-use quality control of common wheat. Conclusions: Our work demonstrated the value of PacBio transcript sequencing for improving common wheat genome annotation through uncovering the loci and full-length transcripts not discovered previously. The resource obtained may aid further structural genomics and grain transcriptome studies of common wheat. DOI
524. Dulvy, NK; Kindsvater, HK.Recovering the potential of coral reefs.Nature, 2015, 520: 304-305 Recovering the potential of coral reefs
An analysis of fish declines in coral reefs shows that simple fishing limits and implementation of marine protected areas can be enough to support recovery of coral ecosystem resilience. PubMed
523. Dura, T; Cisternas, M; Horton, BP; Ely, LL; Nelson, AR; Wesson, RL; Pilarczyk, JE.Coastal evidence for Holocene subduction-zone earthquakes and tsunamis in central Chile.Quat. Sci. Rev., 2015, 113: 93-111 Coastal evidence for Holocene subduction-zone earthquakes and tsunamis in central Chile
Prehistoric earthquakes; Tsunami deposits; Diatom paleoecology; Coastal paleoseismology; Coastal hazards
The similar to 500-year historical record of seismicity along the central Chile coast (30-34 degrees S) is characterized by a series of similar to M 8.0-8.5 earthquakes followed by low tsunamis (<4 m) occurring on the megathrust about every 80 years. One exception is the AD 1730 great earthquake (M 9.0-9.5) and high tsunami (>10 m), but the frequency of such large events is unknown. We extend the seismic history of central Chile through a study of a lowland stratigraphic sequence along the metropolitan coast north of Valparaiso (33 degrees S). At this site, higher relative sea level during the mid Holocene created a tidal marsh and the accommodation space necessary for sediment that preserves earthquake and tsunami evidence. Within this 2600-yr-long sequence, we traced six laterally continuous sand beds probably deposited by high tsunamis. Plant remains that underlie the sand beds were radiocarbon dated to 6200, 5600, 5000, 4400, 3800, and 3700 cal yr BP. Sediment properties and diatom assemblages of the sand beds for example, anomalous marine planktonic diatoms and upward fining of silt-sized diatom valves point to a marine sediment source and high-energy deposition. Grain-size analysis shows a strong similarity between inferred tsunami deposits and modern coastal sediment. Upward fining sequences characteristic of suspension deposition are present in five of the six sand beds. Despite the lack of significant lithologic changes between the sedimentary units under- and overlying tsunami deposits, we infer that the increase in freshwater siliceous microfossils in overlying units records coseismic uplift concurrent with the deposition of five of the sand beds. During our mid-Holocene window of evidence preservation, the mean recurrence interval of earthquakes and tsunamis is similar to 500 years. Our findings imply that the frequency of historical earthquakes in central Chile is not representative of the greatest earthquakes and tsunamis that the central Chilean subduction zone has produced. (C) 2014 Elsevier Ltd. All rights reserved. DOI
522. Elliot, MG; Crespi, BJ.Genetic recapitulation of human pre-eclampsia risk during convergent evolution of reduced placental invasiveness in eutherian mammals.Philosophical Transactions of the Royal Society B-Biological Sciences, 2015, 370 Genetic recapitulation of human pre-eclampsia risk during convergent evolution of reduced placental invasiveness in eutherian mammals
placentation; pre-eclampsia; positive selection; candidate genes; Darwinian medicine
The relationship between phenotypic variation arising through individual development and phenotypic variation arising through diversification of species has long been a central question in evolutionary biology. Among humans, reduced placental invasion into endometrial tissues is associated with diseases of pregnancy, especially pre-eclampsia, and reduced placental invasiveness has also evolved, convergently, in at least 10 lineages of eutherian mammals. We tested the hypothesis that a common genetic basis underlies both reduced placental invasion arising through a developmental process in human placental disease and reduced placental invasion found as a derived trait in the diversification of Euarchontoglires (rodents, lagomorphs, tree shrews, colugos and primates). Based on whole-genome analyses across 18 taxa, we identified 1254 genes as having evolved adaptively across all three lineages exhibiting independent evolutionary transitions towards reduced placental invasion. These genes showed strong evidence of enrichment for associations with pre-eclampsia, based on genetic-association studies, gene-expression analyses and gene ontology. We further used in silico prediction to identify a subset of 199 genes that are likely targets of natural selection during transitions in placental invasiveness and which are predicted to also underlie human placental disorders. Our results indicate that abnormal ontogenies can recapitulate major phylogenetic shifts in mammalian evolution, identify new candidate genes for involvement in pre-eclampsia, imply that study of species with less-invasive placentation will provide useful insights into the regulation of placental invasion and pre-eclampsia, and recommend a novel comparative functional-evolutionary approach to the study of genetically based human disease and mammalian diversification. DOI PubMed
521. Felt, W; Selinger, JC; Donelan, JM; Remy, CD."Body-In-The-Loop": Optimizing Device Parameters Using Measures of Instantaneous Energetic Cost.PLoS One, 2015, 10 "Body-In-The-Loop": Optimizing Device Parameters Using Measures of Instantaneous Energetic Cost
locomotion;
This paper demonstrates methods for the online optimization of assistive robotic devices such as powered prostheses, orthoses and exoskeletons. Our algorithms estimate the value of a physiological objective in real-time (with a body "in-the-loop") and use this information to identify optimal device parameters. To handle sensor data that are noisy and dynamically delayed, we rely on a combination of dynamic estimation and response surface identification. We evaluated three algorithms (Steady-State Cost Mapping, Instantaneous Cost Mapping, and Instantaneous Cost Gradient Search) with eight healthy human subjects. Steady-State Cost Mapping is an established technique that fits a cubic polynomial to averages of steady-state measures at different parameter settings. The optimal parameter value is determined from the polynomial fit. Using a continuous sweep over a range of parameters and taking into account measurement dynamics, Instantaneous Cost Mapping identifies a cubic polynomial more quickly. Instantaneous Cost Gradient Search uses a similar technique to iteratively approach the optimal parameter value using estimates of the local gradient. To evaluate these methods in a simple and repeatable way, we prescribed step frequency via a metronome and optimized this frequency to minimize metabolic energetic cost. This use of step frequency allows a comparison of our results to established techniques and enables others to replicate our methods. Our results show that all three methods achieve similar accuracy in estimating optimal step frequency. For all methods, the average error between the predicted minima and the subjects' preferred step frequencies was less than 1% with a standard deviation between 4% and 5%. Using Instantaneous Cost Mapping, we were able to reduce subject walking-time from over an hour to less than 10 minutes. While, for a single parameter, the Instantaneous Cost Gradient Search is not much faster than Steady-State Cost Mapping, the Instantaneous Cost Gradient Search extends favorably to multi-dimensional parameter spaces. DOI PubMed
520. Fernandes, VM; Pradhan-Sundd, T; Blaquiere, JA; Verheyen, EM.Ras/MEK/MAPK-mediated regulation of heparin sulphate proteoglycans promotes retinal fate in the Drosophila eye-antennal disc.Developmental Biology, 2015, 402: 109-118 Ras/MEK/MAPK-mediated regulation of heparin sulphate proteoglycans promotes retinal fate in the Drosophila eye-antennal disc
Ras/MEK/MAPK; Regional-fate; Selector factors; Wingless; JAK/STAT; Unpaired
Generating cellular heterogeneity is crucial to the development of complex organs. Organ-fate selector genes and signalling pathways generate cellular diversity by subdividing and patterning naive tissues to assign them regional identities. The Drosophila eye-antennal imaginal disc is a well-characterised system in which to study regional specification; it is first divided into antennal and eye fates and subsequently retinal differentiation occurs within only the eye field. During development, signalling pathways and selector genes compete with and mutually antagonise each other to subdivide the tissue. Wingless (Wg) signalling is the main inhibitor of retinal differentiation; it does so by promoting antennal/head-fate via selector factors and by antagonising Hedgehog (Hh), the principal differentiation-initiating signal. Wg signalling must be suppressed by JAK/STAT at the disc posterior in order to initiate retinal differentiation. Ras/MEK/MAPK signalling has also been implicated in initiating retinal differentiation but its mode of action is not known. We find that compromising Ras/MEK/MAPK signalling in the early larval disc results in expanded antennal/head cuticle at the expense of the compound eye. These phenotypes correspond both to perturbations in selector factor expression, and to de-repressed wg. Indeed, STAT activity is reduced due to decreased mobility of the ligand Unpaired (Upd) along with a corresponding loss in Dally-like protein (Dlp), a heparan sulphate proteoglycan (HSPG) that aids Upd diffusion. Strikingly, blocking HSPG biogenesis phenocopies compromised Ras/MEK/MAPK, while restoring HSPG expression rescues the adult phenotype significantly. This study identifies a novel mode by which the Ras/MEK/MAPK pathway regulates regional-fate specification via HSPGs during development. (C) 2015 Elsevier Inc. All rights reserved. DOI
519. Garside, VC; Cullum, R; Alder, O; Lu, DY; Werff, RV; Bilenky, M; Zhao, Y; Jones, SJM; Marra, MA; Underhill, TM; Hoodless, PA.SOX9 modulates the expression of key transcription factors required for heart valve development.Development, 2015, 142: 4340-4350 SOX9 modulates the expression of key transcription factors required for heart valve development
Transcriptional networks; SOX9; Heart valves; Proliferation; Transcription factor; Limb; ChIP-Seq; Genome; Mouse; Embryogenesis; RNA-Seq
Heart valve formation initiates when endothelial cells of the heart transform into mesenchyme and populate the cardiac cushions. The transcription factor SOX9 is highly expressed in the cardiac cushion mesenchyme, and is essential for heart valve development. Loss of Sox9 in mouse cardiac cushion mesenchyme alters cell proliferation, embryonic survival, and valve formation. Despite this important role, little is known about how SOX9 regulates heart valve formation or its transcriptional targets. Therefore, we mapped putative SOX9 binding sites by ChIP-Seq in E12.5 heart valves, a stage at which the valve mesenchyme is actively proliferating and initiating differentiation. Embryonic heart valves have been shown to express a high number of genes that are associated with chondrogenesis, including several extracellular matrix proteins and transcription factors that regulate chondrogenesis. Therefore, we compared regions of putative SOX9 DNA binding between E12.5 heart valves and E12.5 limb buds. We identified context-dependent and context-independent SOX9-interacting regions throughout the genome. Analysis of context-independent SOX9 binding suggests an extensive role for SOX9 across tissues in regulating proliferation-associated genes including key components of the AP-1 complex. Integrative analysis of tissue-specific SOX9-interacting regions and gene expression profiles on Sox9-deficient heart valves demonstrated that SOX9 controls the expression of several transcription factors with previously identified roles in heart valve development, including Twist1, Sox4, Mecom and Pitx2. Together, our data identify SOX9-coordinated transcriptional hierarchies that control cell proliferation and differentiation during valve formation. DOI
518. Gazel, E; Hayes, JL; Hoernle, K; Kelemen, P; Everson, E; Holbrook, WS; Hauff, F; van den Bogaard, P; Vance, EA; Chu, SY; Calvert, AJ; Carr, MJ; Yogodzinski, GM.Continental crust generated in oceanic arcs.Nat. Geosci., 2015, 8: 321-327 Continental crust generated in oceanic arcs
Thin oceanic crust is formed by decompression melting of the upper mantle at mid-ocean ridges, but the origin of the thick and buoyant continental crust is enigmatic. Juvenile continental crust may form from magmas erupted above intra-oceanic subduction zones, where oceanic lithosphere subducts beneath other oceanic lithosphere. However, it is unclear why the subduction of dominantly basaltic oceanic crust would result in the formation of andesitic continental crust at the surface. Here we use geochemical and geophysical data to reconstruct the evolution of the Central American land bridge, which formed above an intra-oceanic subduction system over the past 70Myr. We find that the geochemical signature of erupted lavas evolved from basaltic to andesitic about 10Myr ago-coincident with the onset of subduction of more oceanic crust that originally formed above the Galapagos mantle plume. We also find that seismic P-waves travel through the crust at velocities intermediate between those typically observed for oceanic and continental crust. We develop a continentality index to quantitatively correlate geochemical composition with the average P-wave velocity of arc crust globally. We conclude that although the formation and evolution of continents may involve many processes, melting enriched oceanic crust within a subduction zone-a process probably more common in the Archaean-can produce juvenile continental crust. DOI
517. Gesell, A; Blaukopf, M; Madilao, L; Yuen, MMS; Withers, SG; Mattsson, J; Russell, JH; Bohlmann, J.The Gymnosperm Cytochrome P450 CYP750B1 Catalyzes Stereospecific Monoterpene Hydroxylation of (+)-Sabinene in Thujone Biosynthesis in Western Redcedar.Plant Physiology, 2015, 168: 94-U776 The Gymnosperm Cytochrome P450 CYP750B1 Catalyzes Stereospecific Monoterpene Hydroxylation of (+)-Sabinene in Thujone Biosynthesis in Western Redcedar
Western redcedar (WRC; Thuja plicata) produces high amounts of oxygenated thujone monoterpenoids associated with resistance against herbivore feeding, particularly ungulate browsing. Thujones and other monoterpenoids accumulate in glandular structures in the foliage of WRC. Thujones are produced from (+)-sabinene by sabinol and sabinone. Using metabolite analysis, enzyme assays with WRC tissue extracts, cloning, and functional characterization of cytochrome P450 monooxygenases, we established that transsabin- 3-ol but not cis-sabin-3-ol is the intermediate in thujone biosynthesis in WRC. Based on transcriptome analysis, full-length complementary DNA cloning, and characterization of expressed P450 proteins, we identified CYP750B1 and CYP76AA25 as the enzymes that catalyze the hydroxylation of (+)-sabinene to trans-sabin-3-ol. Gene-specific transcript analysis in contrasting WRC genotypes producing high and low amounts of monoterpenoids, including a glandless low-terpenoid clone, as well as assays for substrate specificity supported a biological role of CYP750B1 in alpha- and beta-thujone biosynthesis. This P450 belongs to the apparently gymnosperm-specific CYP750 family and is, to our knowledge, the first member of this family to be functionally characterized. In contrast, CYP76AA25 has a broader substrate spectrum, also converting the sesquiterpene farnesene and the herbicide isoproturon, and its transcript profiles are not well correlated with thujone accumulation.Website DOI
516. Godwin, SC; Dill, LM; Reynolds, JD; Krkosek, M.Sea lice, sockeye salmon, and foraging competition: lousy fish are lousy competitors.Canadian Journal of Fisheries and Aquatic Sciences, 2015, 72: 1113-1120 Sea lice, sockeye salmon, and foraging competition: lousy fish are lousy competitors
Pathogens threaten wildlife globally, but these impacts are not restricted to direct mortality from disease. For fish, which experience periods of extremely high mortality during their early life history, infections may primarily influence population dynamics and conservation through indirect effects on ecological processes such as competition and predation. We conducted a competitive foraging experiment using outmigrating juvenile Fraser River sockeye salmon (Oncorhynchus nerka) to determine whether fish with high abundances of parasitic sea lice (Caligus clemensi and Lepeophtheirus salmonis) have reduced competitive abilities when foraging. Highly infected sockeye were 20% less successful at consuming food, on average, than lightly infected fish. Competitive ability also increased with fish body size. Our results provide the first evidence that parasite exposure may have negative indirect effects on the fitness of juvenile sockeye salmon and suggest that indirect effects of pathogens may be of key importance for the conservation of marine fish. DOI
514. Gutierrez, AP; Yanez, JM; Fukui, S; Swift, B; Davidson, WS.Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar).PLoS One, 2015, 10(3): e0119730 Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)
Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype similar to 480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program. DOI PubMed
513. Hall, ET; Verheyen, EM.Ras-activated Dsor1 promotes Wnt signaling in Drosophila development.Journal of Cell Science, 2015, 128: 4499-4511 Ras-activated Dsor1 promotes Wnt signaling in Drosophila development
Wnt; Wingless; MAPK; Dsor1; MEK; InR; EGFR
Wnt/Wingless (Wg) and Ras-MAPK signaling both play fundamental roles in growth and cell fate determination, and when dysregulated, can lead to tumorigenesis. Several conflicting modes of interaction between Ras-MAPK and Wnt signaling have been identified in specific cellular contexts, causing synergistic or antagonistic effects on target genes. We find novel evidence that the Drosophila homolog of the dual specificity kinases MEK1/2 (also known as MAP2K1/2), Downstream of Raf1 (Dsor1), is required for Wnt signaling. Knockdown of Dsor1 results in loss of Wg target gene expression, as well as reductions in stabilized Armadillo (Arm; Drosophila beta-catenin). We identify a close physical interaction between Dsor1 and Arm, and find that catalytically inactive Dsor1 causes a reduction in active Arm. These results suggest that Dsor1 normally counteracts the Axin-mediated destruction of Arm. We find that Ras-Dsor1 activity is independent of upstream activation by EGFR, and instead it appears to be activated by the insulin-like growth factor receptor to promote Wg signaling. Taken together, our results suggest that there is a new crosstalk pathway between insulin and Wg signaling that is mediated by Dsor1. DOI
512. Harding, JMS; Segal, MR; Reynolds, JD.Location Is Everything: Evaluating the Effects of Terrestrial and Marine Resource Subsidies on an Estuarine Bivalve.PLoS One, 2015, 10 Location Is Everything: Evaluating the Effects of Terrestrial and Marine Resource Subsidies on an Estuarine Bivalve
Estuaries are amongst the world's most productive ecosystems, lying at the intersection between terrestrial and marine environments. They receive substantial inputs from adjacent landscapes but the importance of resource subsidies is not well understood. Here, we test hypotheses for the effects of both terrestrial- and salmon-derived resource subsidies on the diet (inferred from stable isotopes of muscle tissue), size and percent nitrogen of the soft-shell clam (Mya arenaria), a sedentary estuarine consumer. We examine how these relationships shift across natural gradients among 14 estuaries that vary in upstream watershed size and salmon density on the central coast of British Columbia, Canada. We also test how assimilation and response to subsidies vary at smaller spatial scales within estuaries. The depletion and enrichment of stable isotope ratios in soft-shell clam muscle tissue correlated with increasing upstream watershed size and salmon density, respectively. The effects of terrestrial- and salmon-derived subsidies were also strongest at locations near stream outlets. When we controlled for age of individual clams, there were larger individuals with higher percent nitrogen content in estuaries below larger watersheds, though this effect was limited to the depositional zones below river mouths. Pink salmon exhibited a stronger effect on isotope ratios of clams than chum salmon, which could reflect increased habitat overlap as spawning pink salmon concentrate in lower stream reaches, closer to intertidal clam beds. However, there were smaller clams in estuaries that had higher upstream pink salmon densities, possibly due to differences in habitat requirements. Our study highlights the importance of upstream resource subsidies to this bivalve species, but that individual responses to subsidies can vary at smaller scales within estuaries. DOI
511. Heideman, M; Menounos, B; Clague, JJ.An 825-year long varve record from Lillooet Lake, British Columbia, and its potential as a flood proxy.Quat. Sci. Rev., 2015, 126: 158-174 An 825-year long varve record from Lillooet Lake, British Columbia, and its potential as a flood proxy
Varves; Floods; Natural hazards; Lillooet River valley; British Columbia
Lillooet River in southwest British Columbia has produced damaging floods many times during the past century. The floods are recorded in Lillooet Lake, into which the river flows, as anomalously thick clastic varves. in order to determine whether an 825-year long varve record obtained from 12 percussion and vibracores can be used as flood proxy, we compare river discharge records dating back to 1914 to the thickness of the varves deposited during the same time period. Correlations between varve thickness and a variety of historical discharge measures are low to moderate for the periods 1914-2004 (r(2) = 0.37) and 1914-1945 (r(2) = 0.40), but higher for the period 1946-2004 (r(2) = 0.55). The best correlation (r(2) = 0.55) is between maximum fall discharge and varve thickness during the most recent period (1946-2004). Varve thickness for the earlier period of hydrometric data (1914-1946), which is a time of rapid glacier retreat and warmer temperatures in British Columbia, is best explained with a discharge proxy combining nival runoff, glacier runoff, and maximum fall discharge. Landslides, glacier fluctuations, river dyking, artificial lowering of Lillooet Lake, as well as lag effects of storms are responsible for the considerable unexplained variance in the relation between discharge measures and varve thickness over the historic period. The cores contain many anomalously thick varves, some of which we attribute to previously dated prehistoric landslides in the watershed or to local landslides into the lake. We conclude that many historic and prehistoric floods are faithfully recorded as anomalously thick clastic varves, but that other processes operating in the watershed preclude using this record as a reliable paleo-flood proxy. (C) 2015 Elsevier Ltd. All rights reserved. DOI
510. Hench, J; Henriksson, J; Abou-Zied, AM; Luppert, M; Dethlefsen, J; Mukherjee, K; Tong, YG; Tang, L; Gangishetti, U; Baillie, DL; Burglin, TR.The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis.PLoS One, 2015, 10 The Homeobox Genes of Caenorhabditis elegans and Insights into Their Spatio-Temporal Expression Dynamics during Embryogenesis
Homeobox genes play crucial roles for the development of multicellular eukaryotes. We have generated a revised list of all homeobox genes for Caenorhabditis elegans and provide a nomenclature for the previously unnamed ones. We show that, out of 103 homeobox genes, 70 are co-orthologous to human homeobox genes. 14 are highly divergent, lacking an obvious ortholog even in other Caenorhabditis species. One of these homeobox genes encodes 12 homeodomains, while three other highly divergent homeobox genes encode a novel type of double homeodomain, termed HOCHOB. To understand how transcription factors regulate cell fate during development, precise spatio-temporal expression data need to be obtained. Using a new imaging framework that we developed, Endrov, we have generated spatio-temporal expression profiles during embryogenesis of over 60 homeobox genes, as well as a number of other developmental control genes using GFP reporters. We used dynamic feedback during recording to automatically adjust the camera exposure time in order to increase the dynamic range beyond the limitations of the camera. We have applied the new framework to examine homeobox gene expression patterns and provide an analysis of these patterns. The methods we developed to analyze and quantify expression data are not only suitable for C. elegans, but can be applied to other model systems or even to tissue culture systems. DOI
509. Hutter, H; Moerman, D.Big Data in Caenorhabditis elegans: quo vadis?Molecular Biology of the Cell, 2015, 26: 3909-3914 Big Data in Caenorhabditis elegans: quo vadis?
A clear definition of what constitutes "Big Data" is difficult to identify, but we find it most useful to define Big Data as a data collection that is complete. By this criterion, researchers on Caenorhabditis elegans have a long history of collecting Big Data, since the organism was selected with the idea of obtaining a complete biological description and understanding of development. The complete wiring diagram of the nervous system, the complete cell lineage, and the complete genome sequence provide a framework to phrase and test hypotheses. Given this history, it might be surprising that the number of "complete" data sets for this organism is actually rather small-not because of lack of effort, but because most types of biological experiments are not currently amenable to complete large-scale data collection. Many are also not inherently limited, so that it becomes difficult to even define completeness. At present, we only have partial data on mutated genes and their phenotypes, gene expression, and protein-protein interaction-important data for many biological questions. Big Data can point toward unexpected correlations, and these unexpected correlations can lead to novel investigations; however, Big Data cannot establish causation. As a result, there is much excitement about Big Data, but there is also a discussion on just what Big Data contributes to solving a biological problem. Because of its relative simplicity, C. elegans is an ideal test bed to explore this issue and at the same time determine what is necessary to build a multicellular organism from a single cell. DOI
508. Javadi, A; Najjar, Z; Bahadori, S; Vatanpour, V; Malek, A; Abouzari-Lotf, E; Shockravi, A.High refractive index and low-birefringence polyamides containing thiazole and naphthalene units.RSC Adv., 2015, 5: 91670-91682 High refractive index and low-birefringence polyamides containing thiazole and naphthalene units
Highly refractive and solution processable polyamides (PAs) were synthesized by the introduction of thiazole rings, naphthalene groups, and thioether linkages. These PAs were synthesized by the polycondensation of a new diamine monomer, 5,5'-thiobis(2-amino-4-(2-naphthyl) thiazole) (DA), with various aromatic diacids. The bulky pendant naphthyl units endowed the resulting PAs with non-coplanar structures and excellent solubilities in organic solvents. The obtained PAs showed high thermal stability, with 10% weight loss temperatures exceeding 478 degrees C under nitrogen and 431 degrees C in air atmosphere, while their glass transition temperatures were in the range of 194-229 degrees C. The synergic effects of the thiazole groups, naphthyl substituents, and thioether linkages provided PAs with very high refractive indices of up to 1.7701 at 632.8 nm, along with small birefringences (<0.0076) and high Abbe's numbers. The structure-property relationships of these PAs due to the presence of naphthyl substituents were also studied in detail by comparing the results with the previously reported analogous PAs. DOI
506. Juan-Jorda, MJ; Mosqueira, I; Freire, J; Dulvy, NK.Population declines of tuna and relatives depend on their speed of life.Proceedings of the Royal Society B-Biological Sciences, 2015, 282 Population declines of tuna and relatives depend on their speed of life
vulnerability; declines; life histories; fishes; fishing mortality; scombrids
Larger-bodied species in a wide range of taxonomic groups including mammals, fishes and birds tend to decline more steeply and are at greater risk of extinction. Yet, the diversity in life histories is governed not only by body size, but also by time-related traits. A key question is whether this size-dependency of vulnerability also holds, not just locally, but globally across a wider range of environments. We test the relative importance of size-and time-related life-history traits and fishing mortality in determining population declines and current exploitation status in tunas and their relatives. We use high-quality datasets of half a century of population trajectories combined with population-level fishing mortalities and life-history traits. Time-related traits (e.g. growth rate), rather than size-related traits (e.g. maximum size), better explain the extent and rate of declines and current exploitation status across tuna assemblages, after controlling for fishing mortality. Consequently, there is strong geographical patterning in population declines, such that populations with slower life histories (found at higher cooler latitudes) have declined most and more steeply and have a higher probability of being overfished than populations with faster life histories (found at tropical latitudes). Hence, the strong, temperature-driven, latitudinal gradients in life-history traits may underlie the global patterning of population declines, fisheries collapses and local extinctions. DOI
505. Keith, D; Akcakaya, HR; Butchart, SHM; Collen, B; Dulvy, NK; Holmes, EE; Hutchings, JA; Keinath, D; Schwartz, MK; Shelton, AO; Waples, RS.Temporal correlations in population trends: Conservation implications from time-series analysis of diverse animal taxa.Biological Conservation, 2015, 192: 247-257 Temporal correlations in population trends: Conservation implications from time-series analysis of diverse animal taxa
Population growth rate; Population trend; Endangered species; Time series; Vertebrates
Population trends play a large role in species risk assessments and conservation planning, and species are often considered threatened if their recent rate of decline meets certain thresholds, regardless how large the population is. But how reliable an indicator of extinction risk is a single estimate of population trend? Given the integral role this decline-based approach has played in setting conservation priorities, it is surprising that it has undergone little empirical scrutiny. We compile an extensive global dataset of time series of abundance data for over 1300 vertebrate populations to provide the first major test of the predictability of population growth rates in nature. We divided each time series into assessment and response periods and examined the correlation between growth rates in the two time periods. In birds, population declines tended to be followed by further declines, but mammals, salmon, and other bony fishes showed the opposite pattern: past declines were associated with subsequent population increases, and vice versa. Furthermore, in these taxa subsequent growth rates were higher when initial declines were more severe. These patterns agreed with data simulated under a null model for a dynamically stable population experiencing density dependence. However, this type of result could also occur if conservation actions positively affected the population following initial declines a scenario that our data were too limited to rigorously evaluate. This ambiguity emphasizes the importance of understanding the underlying causes of population trajectories in drawing inferences about rates of decline in abundance. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). DOI
503. Kleijn, D; Winfree, R; Bartomeus, I; Carvalheiro, LG; Henry, M; Isaacs, R; Klein, AM; Kremen, C; M'Gonigle, LK; Rader, R; Ricketts, TH; Williams, NM; Adamson, NL; Ascher, JS; Baldi, A; Batary, P; Benjamin, F; Biesmeijer, JC; Blitzer, EJ; Bommarco, R; Brand, MR; Bretagnolle, V; Button, L; Cariveau, DP; Chifflet, R; Colville, JF; Danforth, BN; Elle, E; Garratt, MPD; Herzog, F; Holzschuh, A; Howlett, BG; Jauker, F; Jha, S; Knop, E; Krewenka, KM; Le Feon, V; Mandelik, Y; May, EA; Park, MG; Pisanty, G; Reemer, M; Riedinger, V; Rollin, O; Rundlof, M; Sardinas, HS; Scheper, J; Sciligo, AR; Smith, HG; Steffan-Dewenter, I; Thorp, R; Tscharntke, T; Verhulst, J; Viana, BF; Vaissiere, BE; Veldtman, R; Westphal, C; Potts, SG.Delivery of crop pollination services is an insufficient argument for wild pollinator conservation.Nature Communications, 2015, 6 Delivery of crop pollination services is an insufficient argument for wild pollinator conservation
There is compelling evidence that more diverse ecosystems deliver greater benefits to people, and these ecosystem services have become a key argument for biodiversity conservation. However, it is unclear how much biodiversity is needed to deliver ecosystem services in a cost- effective way. Here we show that, while the contribution of wild bees to crop production is significant, service delivery is restricted to a limited subset of all known bee species. Across crops, years and biogeographical regions, crop-visiting wild bee communities are dominated by a small number of common species, and threatened species are rarely observed on crops. Dominant crop pollinators persist under agricultural expansion and many are easily enhanced by simple conservation measures, suggesting that cost- effective management strategies to promote crop pollination should target a different set of species than management strategies to promote threatened bees. Conserving the biological diversity of bees therefore requires more than just ecosystem-service-based arguments. DOI
502. Kolappan, S; Ng, D; Yang, GX; Harn, T; Craig, L.Crystal Structure of the Minor Pilin CofB, the Initiator of CFA/III Pilus Assembly in Enterotoxigenic Escherichia coli.Journal of Biological Chemistry, 2015, 290: 25805-25818 Crystal Structure of the Minor Pilin CofB, the Initiator of CFA/III Pilus Assembly in Enterotoxigenic Escherichia coli
Type IV pili are extracellular polymers of the major pilin subunit. These subunits are held together in the pilus filament by hydrophobic interactions among their N-terminal alpha-helices, which also anchor the pilin subunits in the inner membrane prior to pilus assembly. Type IV pilus assembly involves a conserved group of proteins that span the envelope of Gram-negative bacteria. Among these is a set of minor pilins, so named because they share their hydrophobic N-terminal polymerization/membrane anchor segment with the major pilins but are much less abundant. Minor pilins influence pilus assembly and retraction, but their precise functions are not well defined. The Type IV pilus systems of enterotoxigenic Escherichia coli and Vibrio cholerae are among the simplest of Type IV pilus systems and possess only a single minor pilin. Here we show that the enterotoxigenic E. coli minor pilins CofB and LngB are required for assembly of their respective Type IV pili, CFA/III and Longus. Low levels of the minor pilins are optimal for pilus assembly, and CofB can be detected in the pilus fraction. We solved the 2.0 angstrom crystal structure of N-terminally truncated CofB, revealing a pilin-like protein with an extended C-terminal region composed of two discrete domains connected by flexible linkers. The C-terminal region is required for CofB to initiate pilus assembly. We propose a model for CofB-initiated pilus assembly with implications for understanding filament growth in more complex Type IV pilus systems as well as the related Type II secretion system. DOI
501. Kremen, C; M'Gonigle, LK.Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollinator species.Journal of Applied Ecology, 2015, 52: 602-610 Small-scale restoration in intensive agricultural landscapes supports more specialized and less mobile pollinator species
Apoidea; bee; before-after control-impact; conservation; hedgerow; land-use change; pollination service; response traits; syrphid fly
Agriculture now constitutes 40-50% of terrestrial land use globally. By enhancing habitat suitability and connectivity, restoration within agricultural landscapes could have a major influence on biodiversity conservation. However, habitat management within intensive agricultural landscapes may primarily boost abundances of common, highly mobile generalists, rather than vulnerable or endangered species. We studied pollinator community response to small-scale habitat restoration in the intensively farmed Central Valley of California to determine whether restoration could also promote more specialized, less common and/or less mobile species. Composition of pollinator communities was assessed in five experimental and 10 control (unrestored) sites before and after restoration of native plant hedgerows over an 8-year period, using a before-after control-impact design. We characterized bee and fly species based on functional response traits [floral specialization, habitat specialization, abundance, body size and sociality (bees only)] known to influence the response to habitat change. We modelled how species occurrences changed with habitat restoration over time as modulated by their response traits. We found that hedgerows not only significantly enhanced occurrences of native bee and syrphid fly species, but that as hedgerows matured, they had a greater positive effect on species that were more specialized in floral and nesting resources and smaller (less mobile). Synthesis and applications. Unlike previous studies that suggest habitat restoration in agricultural landscapes only benefits mobile, generalist species, our results suggest that small-scale habitat restoration can promote species whose traits likely render them particularly vulnerable to habitat degradation. Thus, even within highly intensive agricultural landscapes, small-scale habitat restoration can be a conservation management tool. However, tailoring habitat enhancements to promote certain species or guilds may be critical for their success as a conservation intervention in agricultural landscapes. Unlike previous studies that suggest habitat restoration in agricultural landscapes only benefits mobile, generalist species, our results suggest that small-scale habitat restoration can promote species whose traits likely render them particularly vulnerable to habitat degradation. Thus, even within highly intensive agricultural landscapes, small-scale habitat restoration can be a conservation management tool. However, tailoring habitat enhancements to promote certain species or guilds may be critical for their success as a conservation intervention in agricultural landscapes. DOI
500. La Croix, AD; Dashtgard, SE.A synthesis of depositional trends in intertidal and upper subtidal sediments across the tidal-fluvial-transition: Fraser River, Canada.J. Sediment. Res., 2015, 85: 683-698 A synthesis of depositional trends in intertidal and upper subtidal sediments across the tidal-fluvial-transition: Fraser River, Canada
Sedimentological, neoichnological, palynological, and geochemical trends from upper subtidal and intertidal positions on channel bars in the lower Fraser River, Canada are synthesized into a single, coherent framework. From these data we define criteria for determining depositional position in shallow water depths in tide-influenced rivers. Three sedimentological trends are observed from the river mouth, through the locus of mud deposition (within the turbidity maximum zone (TMZ)), and into the freshwater-tidal zone. (1) The recurrence (per meter) and thickness of mud beds increase towards the TMZ and tapers in both the landward and seaward directions. (2) Muddy current ripples and graded current ripples are most abundant in the TMZ; they are less common with decreasing brackish-water influence and are absent in the freshwater river reach. (3) Heterolithic bedding (i.e., flaser, wavy, and lenticular) is common in the TMZ, less common seaward, and absent from the freshwater realm. In addition to the sedimentological trends, four ichnological trends parallel decreasing water salinity. With decreasing salinity, there is: (1) a decrease in bioturbation intensity from BI 2-3 to BI 0-1; (2) a decrease in the abundance of bioturbated beds; (3) a marked decrease in the diversity of traces from 5-6 forms to 1-2 forms; and, (4) a decrease in the diameter and length of traces. Traces are rare to absent in the tidal freshwater zone. Palynological and geochemical trends generally follow ichnological trends but are less obvious. Neither dinocyst abundance nor geochemical signature can be used to determine relative position in a tide-influenced river channel, although dinocyst abundances greater than 1% indicate significant marine influence, and 0-1% marine dinocysts indicate tidal influence. Although it is not feasible to determine exact depositional position within the tidal-fluvial transition, our results suggest that it is possible to determine where sediments were deposited relative to the TMZ. In turn, predicting relative depositional position can assist in unraveling stratigraphy and in recognizing nested channels in architecturally complex sedimentary successions. DOI
498. Lebovitz, CB; DeVorkin, L; Bosc, D; Rothe, K; Singh, J; Bally, M; Jiang, XY; Young, RN; Lum, JJ; Gorski, SM.Precision autophagy: Will the next wave of selective autophagy markers and specific autophagy inhibitors feed clinical pipelines?Autophagy, 2015, 11: 1949-1952 Precision autophagy: Will the next wave of selective autophagy markers and specific autophagy inhibitors feed clinical pipelines?
autophagy; biomarker; cancer; hydroxychloroquine; LC3; neurodegeneration; pancreatic cancer; selective autophagy; SQSTM1; TRIM
Research presented at the Vancouver Autophagy Symposium (VAS) 2014 suggests that autophagy's influence on health and disease depends on tight regulation and precision targeting of substrates. Discussions recognized a pressing need for robust biomarkers that accurately assess the clinical utility of modulating autophagy in disease contexts. Biomarker discovery could flow from investigations of context-dependent triggers, sensors, and adaptors that tailor the autophagy machinery to achieve target specificity. In his keynote address, Dr. Vojo Deretic (University of New Mexico) described the discovery of a cargo receptor family that utilizes peptide motif-based cargo recognition, a mechanism that may be more precise than generic substrate tagging. The keynote by Dr. Alec Kimmelman (Harvard Medical School) emphasized that unbiased screens for novel selective autophagy factors may accelerate the development of autophagy-based therapies. Using a quantitative proteomics screen for de novo identification of autophagosome substrates in pancreatic cancer, Kimmelman's group discovered a new type of selective autophagy that regulates bioavailable iron. Additional presentations revealed novel autophagy regulators and receptors in metabolic diseases, proteinopathies, and cancer, and outlined the development of specific autophagy inhibitors and treatment regimens that combine autophagy modulation with anticancer therapies. VAS 2014 stimulated interdisciplinary discussions focused on the development of biomarkers, drugs, and preclinical models to facilitate clinical translation of key autophagy discoveries. DOI
497. Lebovitz, CB; Robertson, AG; Goya, R; Jones, SJ; Morin, RD; Marra, MA; Gorski, SM.Cross-cancer profiling of molecular alterations within the human autophagy interaction network.Autophagy, 2015, 11: 1668-1687 Cross-cancer profiling of molecular alterations within the human autophagy interaction network
AML; autophagy; cancer; gene expression; LAPTM4B; mutation; SNV; SQSTM1; TCGA; tumor
Aberrant activation or disruption of autophagy promotes tumorigenesis in various preclinical models of cancer, but whether the autophagy pathway is a target for recurrent molecular alteration in human cancer patient samples is unknown. To address this outstanding question, we surveyed 211 human autophagy-associated genes for tumor-related alterations to DNA sequence and RNA expression levels and examined their association with patient survival outcomes in multiple cancer types with sequence data from The Cancer Genome Atlas consortium. We found 3 (RB1CC1/FIP200, ULK4, WDR45/WIPI4) and one (ATG7) core autophagy genes to be under positive selection for somatic mutations in endometrial carcinoma and clear cell renal carcinoma, respectively, while 29 autophagy regulators and pathway interactors, including previously identified KEAP1, NFE2L2, and MTOR, were significantly mutated in 6 of the 11 cancer types examined. Gene expression analyses revealed that GABARAPL1 and MAP1LC3C/LC3C transcripts were less abundant in breast cancer and non-small cell lung cancers than in matched normal tissue controls; ATG4D transcripts were increased in lung squamous cell carcinoma, as were ATG16L2 transcripts in kidney cancer. Unsupervised clustering of autophagy-associated mRNA levels in tumors stratified patient overall survival in 3 of 9 cancer types (acute myeloid leukemia, clear cell renal carcinoma, and head and neck cancer). These analyses provide the first comprehensive resource of recurrently altered autophagy-associated genes in human tumors, and highlight cancer types and subtypes where perturbed autophagy may be relevant to patient overall survival. DOI
496. Lee, SY; Ryan, ME; Hamlet, AF; Palen, WJ; Lawler, JJ; Halabisky, M.Projecting the Hydrologic Impacts of Climate Change on Montane Wetlands.PLoS One, 2015, 10 Projecting the Hydrologic Impacts of Climate Change on Montane Wetlands
Wetlands are globally important ecosystems that provide critical services for natural communities and human society. Montane wetland ecosystems are expected to be among the most sensitive to changing climate, as their persistence depends on factors directly influenced by climate (e.g. precipitation, snowpack, evaporation). Despite their importance and climate sensitivity, wetlands tend to be understudied due to a lack of tools and data relative to what is available for other ecosystem types. Here, we develop and demonstrate a new method for projecting climate-induced hydrologic changes in montane wetlands. Using observed wetland water levels and soil moisture simulated by the physically based Variable Infiltration Capacity (VIC) hydrologic model, we developed site-specific regression models relating soil moisture to observed wetland water levels to simulate the hydrologic behavior of four types of montane wetlands (ephemeral, intermediate, perennial, permanent wetlands) in the U.S. Pacific Northwest. The hybrid models captured observed wetland dynamics in many cases, though were less robust in others. We then used these models to a) hindcast historical wetland behavior in response to observed climate variability (1916-2010 or later) and classify wetland types, and b) project the impacts of climate change on montane wetlands using global climate model scenarios for the 2040s and 2080s (A1B emissions scenario). These future projections show that climate-induced changes to key driving variables (reduced snowpack, higher evapotranspiration, extended summer drought) will result in earlier and faster drawdown in Pacific Northwest montane wetlands, leading to systematic reductions in water levels, shortened wetland hydroperiods, and increased probability of drying. Intermediate hydroperiod wetlands are projected to experience the greatest changes. For the 2080s scenario, widespread conversion of intermediate wetlands to fastdrying ephemeral wetlands will likely reduce wetland habitat availability for many species. DOI
495. Lindholm, AK; Sandkam, B; Pohl, K; Breden, F.Poecilia picta, a Close Relative to the Guppy, Exhibits Red Male Coloration Polymorphism: A System for Phylogenetic Comparisons.PLoS One, 2015, 10 Poecilia picta, a Close Relative to the Guppy, Exhibits Red Male Coloration Polymorphism: A System for Phylogenetic Comparisons
Studies on the evolution of female preference and male color polymorphism frequently focus on single species since traits and preferences are thought to co-evolve. The guppy, Poecilia reticulata, has long been a premier model for such studies because female preferences and orange coloration are well known to covary, especially in upstream/downstream pairs of populations. However, focused single species studies lack the explanatory power of the comparative method, which requires detailed knowledge of multiple species with known evolutionary relationships. Here we describe a red color polymorphism in Poecilia picta, a close relative to guppies. We show that this polymorphism is restricted to males and is maintained in natural populations of mainland South America. Using tests of female preference we show female P. picta are not more attracted to red males, despite preferences for red/orange in closely related species, such as P. reticulata and P. parae. Male color patterns in these closely related species are different from P. picta in that they occur in discrete patches and are frequently Y chromosome-linked. P. reticulata have an almost infinite number of male patterns, while P. parae males occur in discrete morphs. We show the red male polymorphism in P. picta extends continuously throughout the body and is not a Y-linked trait despite the theoretical prediction that sexually-selected characters should often be linked to the heterogametic sex chromosome. The presence/absence of red male coloration of P. picta described here makes this an ideal system for phylogenetic comparisons that could reveal the evolutionary forces maintaining mate choice and color polymorphisms in this speciose group. DOI
494. Liu, Y; Muller, K; El-Kassaby, YA; Kermode, AR.Changes in hormone flux and signaling in white spruce (Picea glauca) seeds during the transition from dormancy to germination in response to temperature cues.BMC Plant Biology, 2015, 15 Changes in hormone flux and signaling in white spruce (Picea glauca) seeds during the transition from dormancy to germination in response to temperature cues
Seed dormancy; Auxin; ABA; GAs; Moist-chilling; Seed germination; White spruce
Background: Seeds use environmental cues such as temperature to coordinate the timing of their germination, allowing plants to synchronize their life history with the seasons. Winter chilling is of central importance to alleviate seed dormancy, but very little is known of how chilling responses are regulated in conifer seeds. White spruce (Picea glauca) is an important conifer species of boreal forests in the North American taiga. The recent sequencing and assembly of the white spruce genome allows for comparative gene expression studies toward elucidating the molecular mechanisms governing dormancy alleviation by moist chilling. Here we focused on hormone metabolite profiling and analyses of genes encoding components of hormone signal transduction pathways, to elucidate changes during dormancy alleviation and to help address how germination cues such as temperature and light trigger radicle emergence. Results: ABA, GA, and auxin underwent considerable changes as seeds underwent moist chilling and during subsequent germination; likewise, transcripts encoding hormone-signaling components (e.g. ABI3, ARF4 and Aux/IAA) were differentially regulated during these critical stages. During moist chilling, active IAA was maintained at constant levels, but IAA conjugates (IAA-Asp and IAA-Glu) were substantially accumulated. ABA concentrations decreased during germination of previously moist-chilled seeds, while the precursor of bioactive GA1 (GA53) accumulated. We contend that seed dormancy and germination may be partly mediated through the changing hormone concentrations and a modulation of interactions between central auxin-signaling pathway components (TIR1/AFB, Aux/IAA and ARF4). In response to germination cues, namely exposure to light and to increased temperature: the transfer of seeds from moist-chilling to 30 degrees C, significant changes in gene transcripts and protein expression occurred during the first six hours, substantiating a very swift reaction to germination-promoting conditions after seeds had received sufficient exposure to the chilling stimulus. Conclusions: The dormancy to germination transition in white spruce seeds was correlated with changes in auxin conjugation, auxin signaling components, and potential interactions between auxin-ABA signaling cascades (e.g. the transcription factor ARF4 and ABI3). Auxin flux adds a new dimension to the ABA: GA balance mechanism that underlies both dormancy alleviation by chilling, and subsequent radicle emergence to complete germination by warm temperature and light stimuli. DOI
492. M'Gonigle, LK; Ponisio, LC; Cutler, K; Kremen, C.Habitat restoration promotes pollinator persistence and colonization in intensively managed agriculture.Ecological Applications, 2015, 25: 1557-1565 Habitat restoration promotes pollinator persistence and colonization in intensively managed agriculture
agro-ecosystem; habitat restoration; hedgerows; occupancy; persistence; pollinators
Widespread evidence of pollinator declines has led to policies supporting habitat restoration including in agricultural landscapes. Yet, little is yet known about the effectiveness of these restoration techniques for promoting stable populations and communities of pollinators, especially in intensively managed agricultural landscapes. Introducing floral resources, such as flowering hedgerows, to enhance intensively cultivated agricultural landscapes is known to increase the abundances of native insect pollinators in and around restored areas. Whether this is a result of local short-term concentration at flowers or indicative of true increases in the persistence and species richness of these communities remains unclear. It is also unknown whether this practice supports species of conservation concern (e.g., those with more specialized dietary requirements). Analyzing occupancies of native bees and syrphid flies from 330 surveys across 15 sites over eight years, we found that hedgerow restoration promotes rates of between-season persistence and colonization as compared with unrestored field edges. Enhanced persistence and colonization, in turn, led to the formation of more species-rich communities. We also find that hedgerows benefit floral resource specialists more than generalists, emphasizing the value of this restoration technique for conservation in agricultural landscapes. DOI
491. Ma, N; Shan, YL; Liao, BJ; Kong, GY; Wang, C; Huang, K; Zhang, H; Cai, XJ; Chen, SB; Pei, DQ; Chen, NS; Pan, GJ.Factor-induced Reprogramming and Zinc Finger Nuclease-aided Gene Targeting Cause Different Genome Instability in -Thalassemia Induced Pluripotent Stem Cells (iPSCs).Journal of Biological Chemistry, 2015, 290: 12079-12089 Factor-induced Reprogramming and Zinc Finger Nuclease-aided Gene Targeting Cause Different Genome Instability in -Thalassemia Induced Pluripotent Stem Cells (iPSCs)
Gene Therapy; Genomic Instability; Genomics; Induced Pluripotent Stem Cell (iPS Cell) (iPSC); Reprogramming
Background: Genome alterations need to be investigated before clinical application of iPS cells. Results: Reprogramming and gene targeting can generate substantial but different genomic variations. Conclusion: Stringent genomic monitoring and selection are needed both at the time of iPSC derivation and after gene targeting. Significance: This study examined the genome instability during iPSC generation and subsequent gene correction and revealed different genome alterations at each step. The generation of personalized induced pluripotent stem cells (iPSCs) followed by targeted genome editing provides an opportunity for developing customized effective cellular therapies for genetic disorders. However, it is critical to ascertain whether edited iPSCs harbor unfavorable genomic variations before their clinical application. To examine the mutation status of the edited iPSC genome and trace the origin of possible mutations at different steps, we have generated virus-free iPSCs from amniotic cells carrying homozygous point mutations in -hemoglobin gene (HBB) that cause severe -thalassemia (-Thal), corrected the mutations in both HBB alleles by zinc finger nuclease-aided gene targeting, and obtained the final HBB gene-corrected iPSCs by excising the exogenous drug resistance gene with Cre recombinase. Through comparative genomic hybridization and whole-exome sequencing, we uncovered seven copy number variations, five small insertions/deletions, and 64 single nucleotide variations (SNVs) in -Thal iPSCs before the gene targeting step and found a single small copy number variation, 19 insertions/deletions, and 340 single nucleotide variations in the final gene-corrected -Thal iPSCs. Our data revealed that substantial but different genomic variations occurred at factor-induced somatic cell reprogramming and zinc finger nuclease-aided gene targeting steps, suggesting that stringent genomic monitoring and selection are needed both at the time of iPSC derivation and after gene targeting. DOI
490. Marliere, NP; Latorre-Estivalis, JM; Lorenzo, MG; Carrasco, D; Alves-Silva, J; Rodrigues, JD; Ferreira, LD; Lara, LD; Lowenberger, C; Guarneri, AA.Trypanosomes Modify the Behavior of Their Insect Hosts: Effects on Locomotion and on the Expression of a Related Gene.PLoS Neglected Tropical Diseases, 2015, 9 Trypanosomes Modify the Behavior of Their Insect Hosts: Effects on Locomotion and on the Expression of a Related Gene
Background As a result of evolution, the biology of triatomines must have been significantly adapted to accommodate trypanosome infection in a complex network of vector-vertebrate-parasite interactions. Arthropod-borne parasites have probably developed mechanisms, largely still unknown, to exploit the vector-vertebrate host interactions to ensure their transmission to suitable hosts. Triatomines exhibit a strong negative phototaxis and nocturnal activity, believed to be important for insect survival against its predators. Methodology/Principal Findings In this study we quantified phototaxis and locomotion in starved fifth instar nymphs of Rhodnius prolixus infected with Trypanosoma cruzi or Trypanosoma rangeli. T. cruzi infection did not alter insect phototaxis, but induced an overall 20% decrease in the number of bug locomotory events. Furthermore, the significant differences induced by this parasite were concentrated at the beginning of the scotophase. Conversely, T. rangeli modified both behaviors, as it significantly decreased bug negative phototaxis, while it induced a 23% increase in the number of locomotory events in infected bugs. In this case, the significant effects were observed during the photophase. We also investigated the expression of Rpfor, the triatomine ortholog of the foraging gene known to modulate locomotion in other insects, and found a 4.8 fold increase for T. rangeli infected insects. Conclusions/Significance We demonstrated for the first time that trypanosome infection modulates the locomotory activity of the invertebrate host. T. rangeli infection seems to be more broadly effective, as besides affecting the intensity of locomotion this parasite also diminished negative phototaxis and the expression of a behavior-associated gene in the triatomine vector. DOI
489. Mesquita, RD; Vionette-Amaral, RJ; Lowenberger, C; Rivera-Pomar, R; Monteiro, FA; Minx, P; Spieth, J; Carvalho, AB; Panzera, F; Lawson, D; Torres, AQ; Ribeiro, JMC; Sorgine, MHF; Waterhouse, RM; Montague, MJ; Abad-Franch, F; Alves-Bezerra, M; Amaral, LR; Araujo, HM; Araujo, RN; Aravind, L; Atella, GC; Azambuja, P; Berni, M; Bittencourt-Cunha, PR; Braz, GRC; Calderon-Fernandez, G; Carareto, CMA; Christensen, MB; Costa, IR; Costa, SG; Dansa, M; Daumas, CRO; De-Paula, IF; Dias, FA; Dimopoulos, G; Emrich, SJ; Esponda-Behrens, N; Fampa, P; Fernandez-Medina, RD; da Fonseca, RN; Fontenele, M; Fronick, C; Fulton, LA; Gandara, AC; Garcia, ES; Genta, FA; Giraldo-Calderon, GI; Gomes, B; Gondim, KC; Granzotto, A; Guarneri, AA; Guigo, R; Harry, M; Hughes, DST; Jablonka, W; Jacquin-Joly, E; Juarez, MP; Koerich, LB; Latorre-Estivalis, JM; Lavore, A; Lawrence, GG; Lazoski, C; Lazzari, CR; Lopes, RR; Lorenzo, MG; Lugon, MD; Majerowicz, D; Marcet, PL; Mariotti, M; Masuda, H; Megy, K; Melo, ACA; Missirlis, F; Mota, T; Noriega, FG; Nouzova, M; Nunes, RD; Oliveira, RLL; Oliveira-Silveira, G; Ons, S; Pagola, L; Paiva-Silva, GO; Pascual, A; Pavan, MG; Pedrini, N; Peixoto, AA; Pereira, MH; Pike, A; Polycarpo, C; Prosdocimi, F; Ribeiro-Rodrigues, R; Robertson, HM; Salerno, AP; Salmon, D; Santesmasses, D; Schama, R; Seabra, ES; Silva-Cardoso, L; Silva-Neto, MAC; Souza-Gomes, M; Sterkel, M; Taracena, ML; Tojo, M; Tu, ZJ; Tubio, JMC; Ursic-Bedoya, R; Venancio, TM; Walter-Nuno, AB; Wilson, D; Warren, WC; Wilson, RK; Huebner, E; Dotson, EM; Oliveira, PL.Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection.Proceedings of the National Academy of Sciences of the United States of America, 2015, 112: 14936-14941 Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection
Rhodnius prolixus; genome; hematophagy; immunity; Chagas disease
Rhodnius prolixus not only has served as a model organism for the study of insect physiology, but also is a major vector of Chagas disease, an illness that affects approximately seven million people worldwide. We sequenced the genome of R. prolixus, generated assembled sequences covering 95% of the genome (similar to 702 Mb), including 15,456 putative protein-coding genes, and completed comprehensive genomic analyses of this obligate blood-feeding insect. Although immune-deficiency (IMD)-mediated immune responses were observed, R. prolixus putatively lacks key components of the IMD pathway, suggesting a reorganization of the canonical immune signaling network. Although both Toll and IMD effectors controlled intestinal microbiota, neither affected Trypanosoma cruzi, the causal agent of Chagas disease, implying the existence of evasion or tolerance mechanisms. R. prolixus has experienced an extensive loss of selenoprotein genes, with its repertoire reduced to only two proteins, one of which is a selenocysteine-based glutathione peroxidase, the first found in insects. The genome contained actively transcribed, horizontally transferred genes from Wolbachia sp., which showed evidence of codon use evolution toward the insect use pattern. Comparative protein analyses revealed many lineage-specific expansions and putative gene absences in R. prolixus, including tandem expansions of genes related to chemoreception, feeding, and digestion that possibly contributed to the evolution of a blood-feeding lifestyle. The genome assembly and these associated analyses provide critical information on the physiology and evolution of this important vector species and should be instrumental for the development of innovative disease control methods. DOI
487. Moen, T; Torgersen, J; Santi, N; Davidson, WS; Baranski, M; Odegard, J; Kjoglum, S; Velle, B; Kent, M; Lubieniecki, KP; Isdal, E; Lien, S.Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon.Genetics, 2015, 200: 1313-+ Epithelial Cadherin Determines Resistance to Infectious Pancreatic Necrosis Virus in Atlantic Salmon
IPN; QTL; salmon; cadherin; disease resistance
Infectious pancreatic necrosis virus (IPNV) is the cause of one of the most prevalent diseases in farmed Atlantic salmon (Salmo salar). A quantitative trait locus (QTL) has been found to be responsible for most of the genetic variation in resistance to the virus. Here we describe how a linkage disequilibrium-based test for deducing the QTL allele was developed, and how it was used to produce IPN-resistant salmon, leading to a 75% decrease in the number of IPN outbreaks in the salmon farming industry. Furthermore, we describe how whole-genome sequencing of individuals with deduced QTL genotypes was used to map the QTL down to a region containing an epithelial cadherin (cdh1) gene. In a coimmunoprecipitation assay, the Cdh1 protein was found to bind to IPNV virions, strongly indicating that the protein is part of the machinery used by the virus for internalization. Immunofluorescence revealed that the virus colocalizes with IPNV in the endosomes of homozygous susceptible individuals but not in the endosomes of homozygous resistant individuals. A putative causal single nucleotide polymorphism was found within the full-length cdh1 gene, in phase with the QTL in all observed haplotypes except one; the absence of a single, all-explaining DNA polymorphism indicates that an additional causative polymorphism may contribute to the observed QTL genotype patterns. Cdh1 has earlier been shown to be necessary for the internalization of certain bacteria and fungi, but this is the first time the protein is implicated in internalization of a virus. DOI
486. Mokkonen, M; Crespi, BJ.Genomic conflicts and sexual antagonism in human health: insights from oxytocin and testosterone.Evolutionary Applications, 2015, 8: 307-325 Genomic conflicts and sexual antagonism in human health: insights from oxytocin and testosterone
genomic imprinting; kinship theory; parental antagonism; parent-offspring conflict; sexual antagonism; sexual conflict
We review the hypothesized and observed effects of two of the major forms of genomic conflicts, genomic imprinting and sexual antagonism, on human health. We focus on phenotypes mediated by peptide and steroid hormones (especially oxytocin and testosterone) because such hormones centrally mediate patterns of physical and behavioral resource allocation that underlie both forms of conflict. In early development, a suite of imprinted genes modulates the human oxytocinergic system as predicted from theory, with paternally inherited gene expression associated with higher oxytocin production, and increased solicitation to mothers by infants. This system is predicted to impact health through the incompatibility of paternal-gene and maternal-gene optima and increased vulnerability of imprinted gene systems to genetic and epigenetic changes. Early alterations to oxytocinergic systems have long-term negative impacts on human psychological health, especially through their effects on attachment and social behavior. In contrast to genomic imprinting, which generates maladaptation along an axis of mother-infant attachment, sexual antagonism is predicted from theory to generate maladaptation along an axis of sexual dimorphism, modulated by steroid and peptide hormones. We describe evidence of sexual antagonism from studies of humans and other animals, demonstrating that sexually antagonistic effects on sex-dimorphic phenotypes, including aspects of immunity, life history, psychology, and behavior, are commonly observed and lead to forms of maladaptation that are demonstrated, or expected, to impact human health. Recent epidemiological and psychiatric studies of schizophrenia in particular indicate that it is mediated, in part, by sexually antagonistic alleles. The primary implication of this review is that data collection focused on (i) effects of imprinted genes that modulate the oxytocin system, and (ii) effects of sexually antagonistic alleles on sex-dimorphic, disease-related phenotypes will lead to novel insights into both human health and the evolutionary dynamics of genomic conflicts. DOI PubMed
485. Moore, JW; Carr-Harris, C; Gottesfeld, AS; MacIntyre, D; Radies, D; Cleveland, M; Barnes, C; Joseph, W; Williams, G; Gordon, J; Shepert, B.Selling First Nations down the river.Science, 2015, 349: 596-596 Selling First Nations down the river
483. Orzechowski, EA; Lockwood, R; Byrnes, JEK; Anderson, SC; Finnegan, S; Finkel, ZV; Harnik, PG; Lindberg, DR; Liow, LH; Lotze, HK; McClain, CR; McGuire, JL; O'Dea, A; Pandolfi, JM; Simpson, C; Tittensor, DP.Marine extinction risk shaped by trait-environment interactions over 500 million years.Global Change Biology, 2015, 21: 3595-3607 Marine extinction risk shaped by trait-environment interactions over 500 million years
differential extinction risk; extinction selectivity; geographic range; life habit; mass extinction; mollusk; survivorship
Perhaps the most pressing issue in predicting biotic responses to present and future global change is understanding how environmental factors shape the relationship between ecological traits and extinction risk. The fossil record provides millions of years of insight into how extinction selectivity (i.e., differential extinction risk) is shaped by interactions between ecological traits and environmental conditions. Numerous paleontological studies have examined trait-based extinction selectivity; however, the extent to which these patterns are shaped by environmental conditions is poorly understood due to a lack of quantitative synthesis across studies. We conducted a meta-analysis of published studies on fossil marine bivalves and gastropods that span 458 million years to uncover how global environmental and geochemical changes covary with trait-based extinction selectivity. We focused on geographic range size and life habit (i.e., infaunal vs. epifaunal), two of the most important and commonly examined predictors of extinction selectivity. We used geochemical proxies related to global climate, as well as indicators of ocean acidification, to infer average global environmental conditions. Life-habit selectivity is weakly dependent on environmental conditions, with infaunal species relatively buffered from extinction during warmer climate states. In contrast, the odds of taxa with broad geographic ranges surviving an extinction (>2500km for genera, >500km for species) are on average three times greater than narrow-ranging taxa (estimate of odds ratio: 2.8, 95% confidence interval=2.3-3.5), regardless of the prevailing global environmental conditions. The environmental independence of geographic range size extinction selectivity emphasizes the critical role of geographic range size in setting conservation priorities. DOI
482. Patil, VP; Karels, TJ; Hik, DS.Ecological, Evolutionary and Social Constraints on Reproductive Effort: Are Hoary Marmots Really Biennial Breeders?PLoS One, 2015, 10 Ecological, Evolutionary and Social Constraints on Reproductive Effort: Are Hoary Marmots Really Biennial Breeders?
Biennial breeding is a rare life-history trait observed in animal species living in harsh, unproductive environments. This reproductive pattern is thought to occur in 10 of 14 species in the genus Marmota, making marmots useful model organisms for studying its ecological and evolutionary implications. Biennial breeding in marmots has been described as an obligate pattern which evolved as a mechanism to mitigate the energetic costs of reproduction (Evolved Constraint hypothesis). However, recent anecdotal evidence suggests that it is a facultative pattern controlled by annual variation in climate and food availability (Environmental Constraint hypothesis). Finally, in social animals like marmots, biennial breeding could result from reproductive competition between females within social groups (Social Constraint hypothesis). We evaluated these three hypotheses using mark-recapture data from an 8-year study of hoary marmot (Marmota caligata) population dynamics in the Yukon. Annual variation in breeding probability was modeled using multi-state markrecapture models, while other reproductive life-history traits were modeled with generalized linear mixed models. Hoary marmots were neither obligate nor facultative biennial breeders, and breeding probability was insensitive to evolved, environmental, or social factors. However, newly mature females were significantly less likely to breed than older individuals. Annual breeding did not result in increased mortality. Female survival and, to a lesser extent, average fecundity were correlated with winter climate, as indexed by the Pacific Decadal Oscillation. Hoary marmots are less conservative breeders than previously believed, and the evidence for biennial breeding throughout Marmota, and in other arctic/alpine/antarctic animals, should be re-examined. Prediction of future population dynamics requires an accurate understanding of life history strategies, and of how life history traits allow animals to cope with changes in weather and other demographic influences. DOI
481. Perry, CT; Steneck, RS; Murphy, GN; Kench, PS; Edinger, EN; Smithers, SG; Mumby, PJ.Regional-scale dominance of non-framework building corals on Caribbean reefs affects carbonate production and future reef growth.Glob. Change Biol., 2015, 21: 1153-1164 Regional-scale dominance of non-framework building corals on Caribbean reefs affects carbonate production and future reef growth
Acropora; carbonate budgets; caribbean; coral reefs; Orbicella; reef growth
Coral cover on Caribbean reefs has declined rapidly since the early 1980's. Diseases have been a major driver, decimating communities of framework building Acropora and Orbicella coral species, and reportedly leading to the emergence of novel coral assemblages often dominated by domed and plating species of the genera Agaricia, Porites and Siderastrea. These corals were not historically important Caribbean framework builders, and typically have much smaller stature and lower calcification rates, fuelling concerns over reef carbonate production and growth potential. Using data from 75 reefs from across the Caribbean we quantify: (i) the magnitude of non-framework building coral dominance throughout the region and (ii) the contribution of these corals to contemporary carbonate production. Our data show that live coral cover averages 18.2% across our sites and coral carbonate production 4.1kg CaCO(3)m(-2)yr(-1). However, non-framework building coral species dominate and are major carbonate producers at a high proportion of sites; they are more abundant than Acropora and Orbicella at 73% of sites; contribute an average 68% of the carbonate produced; and produce more than half the carbonate at 79% of sites. Coral cover and carbonate production rate are strongly correlated but, as relative abundance of non-framework building corals increases, average carbonate production rates decline. Consequently, the use of coral cover as a predictor of carbonate budget status, without species level production rate data, needs to be treated with caution. Our findings provide compelling evidence for the Caribbean-wide dominance of non-framework building coral taxa, and that these species are now major regional carbonate producers. However, because these species typically have lower calcification rates, continued transitions to states dominated by non-framework building coral species will further reduce carbonate production rates below predecline' levels, resulting in shifts towards negative carbonate budget states and reducing reef growth potential. DOI
480. Ponisio, LC; M'Gonigle, LK; Mace, KC; Palomino, J; de Valpine, P; Kremen, C.Diversification practices reduce organic to conventional yield gap.Proceedings of the Royal Society B-Biological Sciences, 2015, 282 Diversification practices reduce organic to conventional yield gap
organic yield; conventional yield; meta-analysis
Agriculture today places great strains on biodiversity, soils, water and the atmosphere, and these strains will be exacerbated if current trends in population growth, meat and energy consumption, and food waste continue. Thus, farming systems that are both highly productive and minimize environmental harms are critically needed. How organic agriculture may contribute to world food production has been subject to vigorous debate over the past decade. Here, we revisit this topic comparing organic and conventional yields with a new meta-dataset three times larger than previously used (115 studies containing more than 1000 observations) and a new hierarchical analytical framework that can better account for the heterogeneity and structure in the data. We find organic yields are only 19.2% (+/- 3.7%) lower than conventional yields, a smaller yield gap than previous estimates. More importantly, we find entirely different effects of crop types and management practices on the yield gap compared with previous studies. For example, we found no significant differences in yields for leguminous versus non-leguminous crops, perennials versus annuals or developed versus developing countries. Instead, we found the novel result that two agricultural diversification practices, multi-cropping and crop rotations, substantially reduce the yield gap (to 9 +/- 4% and 8 +/- 5%, respectively) when the methods were applied in only organic systems. These promising results, based on robust analysis of a larger meta-dataset, suggest that appropriate investment in agroecological research to improve organic management systems could greatly reduce or eliminate the yield gap for some crops or regions. DOI
479. Pradhan-Sundd, T; Verheyen, EM.The Myopic-Ubpy-Hrs nexus enables endosomal recycling of Frizzled.Molecular Biology of the Cell, 2015, 26: 3329-3342 The Myopic-Ubpy-Hrs nexus enables endosomal recycling of Frizzled
Endosomal trafficking of signaling proteins plays an essential role in cellular homeostasis. The seven-pass transmembrane protein Frizzled (Fz) is a critical component of Wnt signaling. Although Wnt signaling is proposed to be regulated by endosomal trafficking of Fz, the molecular events that enable this regulation are not completely understood. Here we show that the endosomal protein Myopic (Mop) regulates Fz trafficking in the Drosophila wing disk by inhibiting the ubiquitination and degradation of Hrs. Deletion of Mop or Hrs results in endosomal accumulation of Fz and therefore reduced Wnt signaling. The in situ proximity ligation assay revealed a strong association between Mop and Hrs in the Drosophila wing disk. Overexpression of Hrs rescues the trafficking defect caused by mop knockdown. Mop aids in the maintenance of Ubpy, which deubiquitinates (and thus stabilizes) Hrs. In the absence of the ubiquitin ligase Cbl, Mop is dispensable. These findings support a previously unknown role for Mop in endosomal trafficking of Fz in Wnt-receiving cells. DOI
478. Ramogida, CF; Pan, JH; Ferreira, CL; Patrick, BO; Rebullar, K; Yapp, DTT; Lin, KS; Adam, MJ; Orvig, C.Nitroimidazole-Containing H(2)dedpa and H(2)CHXdedpa Derivatives as Potential PET Imaging Agents of Hypoxia with Ga-68.Inorg. Chem., 2015, 54: 4953-4965 Nitroimidazole-Containing H(2)dedpa and H(2)CHXdedpa Derivatives as Potential PET Imaging Agents of Hypoxia with Ga-68
Ga-68 is an attractive radiometal for use in positron emission tomography (PET) imaging. The success of Ga-68-based agents is dependent on a chelator that exhibits rapid radiometal incorporation, and strong kinetic inertness to prevent transchelation of Ga-68 in vivo. The linear chelating agents H(2)dedpa (1,2-[[6-carboxypyridin-2-yl]methylamino]ethane) and H2CHXdedpa (CHX = cyclohexyl/cyclohexane) (N4O2) have recently been developed that bind Ga3+ quickly and under mild conditions, ideal properties to be incorporated into a Ga-68 PET imaging agent. Herein, nitroimidazole (NI) derivatives of H(2)dedpa and H(2)CHXdedpa to investigate specific targeting of hypoxic tumor cells are investigated, given that NI can be reduced and retained exclusively in hypoxic cells. Nine N,N'-bis-alkylated derivatives of H(2)dedpa and H2CHXdedpa have been synthesized; they have been screened for their ability to bind gallium, and cyclic voltammetry of nonradioactive complexes was performed to probe the redox cycling mechanism of NI. The compounds were radiolabeled with Ga-67 and Ga-68 and show promising radiolabeling efficiencies (>99%) when labeled at 10(-5) M for 10 min at room temperature. Moreover, stability studies (via apo-transferrin challenge, 37 degrees C) show that the Ga-67 complexes exhibit exceptional stability (86-99% intact) after 2 h. In vitro uptake studies under hypoxic (0.5% O-2) and normoxic (21% O-2) conditions in three cancerous cell lines [HT-29 (colon), LCC6HER-2 (breast), and CHO (Chinese hamster ovarian)] were performed. Of the four H(2)dedpa or H(2)CHXdedpa NI derivatives tested, all showed preferential uptake in hypoxic cells compared to normoxic cells with hypoxic/normoxic ratios as high as 7.9 +/- 2.7 after 120 min. The results suggest that these novel bis-alkylated NI-containing H(2)dedpa and H(2)CHXdedpa ligands would be ideal candidates for further testing in vivo for PET imaging of hypoxia with Ga-68. DOI PubMed
477. Rujas, E; Gulzar, N; Morante, K; Tsumoto, K; Scott, JK; Nieva, JL; Caaveiro, JMM.Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10.Journal of Virology, 2015, 89: 11975-11989 Structural and Thermodynamic Basis of Epitope Binding by Neutralizing and Nonneutralizing Forms of the Anti-HIV-1 Antibody 4E10
The 4E10 antibody recognizes the membrane-proximal external region (MPER) of the HIV-1 Env glycoprotein gp41 transmembrane subunit, exhibiting one of the broadest neutralizing activities known to date. The neutralizing activity of 4E10 requires solvent-exposed hydrophobic residues at the apex of the complementarity-determining region (CDR) H3 loop, but the molecular basis for this requirement has not been clarified. Here, we report the cocrystal structures and the energetic parameters of binding of a peptide bearing the 4E10-epitope sequence (4E10ep) to nonneutralizing versions of the 4E10 Fab. Nonneutralizing Fabs were obtained by shortening and decreasing the hydrophobicity of the CDR-H3 loop (termed Delta Loop) or by substituting the two tryptophan residues of the CDR-H3 apex with Asp residues (termed WDWD), which also decreases hydrophobicity but preserves the length of the loop. The analysis was complemented by the first crystal structure of the 4E10 Fab in its ligand-free state. Collectively, the data ruled out major conformational changes of CDR-H3 at any stage during the binding process (equilibrium or transition state). Although these mutations did not impact the affinity of wild-type Fab for the 4E10ep in solution, the two nonneutralizing versions of 4E10 were deficient in binding to MPER inserted in the plasma membrane (mimicking the environment faced by the antibody in vivo). The conclusions of our structure-function analysis strengthen the idea that to exert effective neutralization, the hydrophobic apex of the solvent-exposed CDR-H3 loop must recognize an antigenic structure more complex than just the linear alpha-helical epitope and likely constrained by the viral membrane lipids. IMPORTANCE The broadly neutralizing anti-HIV-1 4E10 antibody blocks infection caused by nearly all viral strains and isolates examined thus far. However, 4E10 (or 4E10-like) antibodies are rarely found in HIV-1-infected individuals or elicited through vaccination. Impediments to the design of successful 4E10 immunogens are partly attributed to an incomplete understanding of the structural and binding characteristics of this class of antibodies. Since the broadly neutralizing activity of 4E10 is abrogated by mutations of the tip of the CDR-H3, we investigated their impact on binding of the MPER-epitope at the atomic and energetic levels. We conclude that the difference between neutralizing and nonneutralizing antibodies of 4E10 is neither structural nor energetic but is related to the capacity to recognize the HIV-1 gp41 epitope inserted in biological membranes. Our findings strengthen the idea that to elicit similar neutralizing antibodies, the suitable MPER vaccine must be "delivered" in a membrane environment. DOI
476. Ryan, CP; Dawson, A; Sharp, PJ; Williams, TD.Uncoupling clutch size, prolactin, and luteinizing hormone using experimental egg removal.General and Comparative Endocrinology, 2015, 213: 1-8 Uncoupling clutch size, prolactin, and luteinizing hormone using experimental egg removal
Clutch size; Prolactin; Luteinizing hormone; Avian reproduction; Egg removal
Clutch size is a key avian fitness and life history trait. A physiological model for clutch size determination (CSD), involving an anti-gonadal effect of prolactin (PRL) via suppression of luteinizing hormone (LH), was proposed over 20 years ago, but has received scant experimental attention since. The few studies looking at a PRL-based mechanistic hypothesis for CSD have been equivocal, but recent experiments utilizing a pharmacological agent to manipulate PRL in the zebra finch (Taeniopygia guttata) found no support for a role of this hormone in clutch size determination. Here, we take a complementary approach by manipulating clutch size through egg removal, examining co-variation in PRL and LH between two breeding attempts, as well as through experimentally-extended laying. Clutch size increased for egg removal females, but not controls, but this was not correlated with changes in PRL. or LH. There were also no differences in PRL between egg removal females and controls, nor did PRL levels during early, mid- or late-laying of supra-normal clutches predict clutch size. By uncoupling PRL, LH and clutch size in our study, several key predictions of the PRL-based mechanistic model for CSD were not supported. However, a positive correlation between PRL levels late in laying and days relative to the last egg (clutch completion) provides an alternative explanation for the equivocal results surrounding the conventional PRL-based physiological model for CSD. We suggest that females coordinate PRL-mediated incubation onset with clutch completion to minimize hatching asynchrony and sibling hierarchy, a behavior that is amplified in females laying larger clutches. (C) 2015 Elsevier Inc. All rights reserved. DOI PubMed
475. Sandkam, B; Young, CM; Breden, F.Beauty in the eyes of the beholders: colour vision is tuned to mate preference in the Trinidadian guppy (Poecilia reticulata).Molecular Ecology, 2015, 24: 596-609 Beauty in the eyes of the beholders: colour vision is tuned to mate preference in the Trinidadian guppy (Poecilia reticulata)
animal mating; breeding; behaviour; social evolution; ecological genetics; evolutionary theory; population geneticsempirical; sexual selection
A broad range of animals use visual signals to assess potential mates, and the theory of sensory exploitation suggests variation in visual systems drives mate preference variation due to sensory bias. Trinidadian guppies (Poecilia reticulata), a classic system for studies of the evolution of female mate choice, provide a unique opportunity to test this theory by looking for covariation in visual tuning, light environment and mate preferences. Female preference co-evolves with male coloration, such that guppy females from low-predation' environments have stronger preferences for males with more orange/red coloration than do females from high-predation' environments. Here, we show that colour vision also varies across populations, with low'-predation guppies investing more of their colour vision to detect red/orange coloration. In independently colonized watersheds, guppies expressed higher levels of both LWS-1 and LWS-3 (the most abundant LWS opsins) in low-predation' populations than high-predation' populations at a time that corresponds to differences in cone cell abundance. We also observed that the frequency of a coding polymorphism differed between high- and low-predation populations. Together, this shows that the variation underlying preference could be explained by simple changes in expression and coding of opsins, providing important candidate genes to investigate the genetic basis of female preference variation in this model system. DOI PubMed
474. Sandkam, BA; Young, CM; Breden, FMW; Bourne, GR; Breden, F.Color vision varies more among populations than among species of live-bearing fish from South America.BMC Evolutionary Biology, 2015, 15 Color vision varies more among populations than among species of live-bearing fish from South America
Mate choice; Opsin; Guppy; Poeciliidae; Sensory bias; Population divergence
Background: Sensory Bias models for the evolution of mate preference place a great emphasis on the role of sensory system variation in mate preferences. However, the extent to which sensory systems vary across-versus within-species remains largely unknown. Here we assessed whether color vision varies in natural locations where guppies (Poecilia reticulata) and their two closest relatives, Poecilia parae and Poecilia picta, occur in extreme sympatry and school together. All three species base mate preferences on male coloration but differ in the colors preferred. Results: Measuring opsin gene expression, we found that within sympatric locations these species have similar color vision and that color vision differed more across populations of conspecifics. In addition, all three species differ across populations in the frequency of the same opsin coding polymorphism that influences visual tuning. Conclusions: Together, this shows sensory systems vary considerably across populations and supports the possibility that sensory system variation is involved in population divergence of mate preference. DOI
473. Schmouth, JF; Arenillas, D; Corso-Diaz, X; Xie, YY; Bohacec, S; Banks, KG; Bonaguro, RJ; Wong, SH; Jones, SJM; Marra, MA; Simpson, EM; Wasserman, WW.Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.BMC Genomics, 2015, 16 Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development
SAGE; Nuclear receptor; Nr2e1; Transcriptome; Neocortex; Transcription factor
Background: Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundreds of target genes, and bind more than 300 co-interacting proteins. However, recognition of the critical role of Nr2e1 in neural stem cells and neocortex development is relatively recent, thus the molecular mechanisms involved for this nuclear receptor are only beginning to be understood. Serial analysis of gene expression (SAGE), has given researchers both qualitative and quantitative information pertaining to biological processes. Thus, in this work, six LongSAGE mouse libraries were generated from laser microdissected tissue samples of dorsal VZ/SVZ (ventricular zone and subventricular zone) from the telencephalon of wild-type (Wt) and Nr2e1-null embryos at the critical development ages E13.5, E15.5, and E17.5. We then used a novel approach, implementing multiple computational methods followed by biological validation to further our understanding of Nr2e1 in neocortex development. Results: In this work, we have generated a list of 1279 genes that are differentially expressed in response to altered Nr2e1 expression during in vivo neocortex development. We have refined this list to 64 candidate direct-targets of NR2E1. Our data suggested distinct roles for Nr2e1 during different neocortex developmental stages. Most importantly, our results suggest a possible novel pathway by which Nr2e1 regulates neurogenesis, which includes Lhx2 as one of the candidate direct-target genes, and SOX9 as a co-interactor. Conclusions: In conclusion, we have provided new candidate interacting partners and numerous well-developed testable hypotheses for understanding the pathways by which Nr2e1 functions to regulate neocortex development. DOI
472. Selinger, JC; O'Connor, SM; Wong, JD; Donelan, JM.Humans Can Continuously Optimize Energetic Cost during Walking.Curr. Biol., 2015, 25: 2452-2456 Humans Can Continuously Optimize Energetic Cost during Walking
locomotion;
People prefer to move in ways that minimize their energetic cost [1-9]. For example, people tend to walk at a speed that minimizes energy use per unit distance [5-8] and, for that speed, they select a step frequency that makes walking less costly [3, 4, 6, 10-12]. Although aspects of this preference appear to be established over both evolutionary [9, 13-15] and developmental [16] timescales, it remains unclear whether people can also optimize energetic cost in real time. Here we show that during walking, people readily adapt established motor programs to minimize energy use. To accomplish this, we used robotic exoskeletons to shift people's energetically optimal step frequency to frequencies higher and lower than normally preferred. In response, we found that subjects adapted their step frequency to converge on the new energetic optima within minutes and in response to relatively small savings in cost (<5%). When transiently perturbed from their new optimal gait, subjects relied on an updated prediction to rapidly re-converge within seconds. Our collective findings indicate that energetic cost is not just an outcome of movement, but also plays a central role in continuously shaping it. DOI PubMed
471. Shahid, A; Olvera, A; Anmole, G; Kuang, XT; Cotton, LA; Plana, M; Brander, C; Brockman, MA; Brumme, ZL.Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function.Journal of Virology, 2015, 89: 11557-11571 Consequences of HLA-B*13-Associated Escape Mutations on HIV-1 Replication and Nef Function
HLA-B*13 is associated with superior in vivo HIV-1 viremia control. Protection is thought to be mediated by sustained targeting of key cytotoxic T lymphocyte (CTL) epitopes and viral fitness costs of CTL escape in Gag although additional factors may contribute. We assessed the impact of 10 published B*13-associated polymorphisms in Gag, Pol, and Nef, in 23 biologically relevant combinations, on HIV-1 replication capacity and Nef-mediated reduction of cell surface CD4 and HLA class I expression. Mutations were engineered into HIV-1(NL4.3), and replication capacity was measured using a green fluorescent protein (GFP) reporter T cell line. Nef-mediated CD4 and HLA-A*02 downregulation was assessed by flow cytometry, and T cell recognition of infected target cells was measured via coculture with an HIV-specific luciferase reporter cell line. When tested individually, only Gag-I147L and Gag-I437L incurred replicative costs (5% and 17%, respectively), consistent with prior reports. The Gag-I437L-mediated replication defect was rescued to wild-type levels by the adjacent K436R mutation. A novel B*13 epitope, comprising 8 residues and terminating at Gag(147), was identified in p24(Gag) (GQMVHQAI(Gag140-147)). No other single or combination Gag, Pol, or Nef mutant impaired viral replication. Single Nef mutations did not affect CD4 or HLA downregulation; however, the Nef double mutant E24Q-Q107R showed 40% impairment in HLA downregulation with no evidence of Nef stability defects. Moreover, target cells infected with HIV-1-Nef(E24Q-Q107R) were recognized better by HIV-specific T cells than those infected with HIV-1NL4.3 or single Nef mutants. Our results indicate that CTL escape in Gag and Nef can be functionally costly and suggest that these effects may contribute to long-term HIV-1 control by HLA-B*13. IMPORTANCE Protective effects of HLA-B*13 on HIV-1 disease progression are mediated in part by fitness costs of CTL escape mutations in conserved Gag epitopes, but other mechanisms remain incompletely known. We extend our knowledge of the impact of B*13-driven escape on HIV-1 replication by identifying Gag-K436R as a compensatory mutation for the fitness-costly Gag-I437L. We also identify Gag-I147L, the most rapidly and commonly selected B*13-driven substitution in HIV-1, as a putative C-terminal anchor residue mutation in a novel B*13 epitope. Most notably, we identify a novel escape-driven fitness defect: B*13-driven substitutions E24Q and Q107R in Nef, when present together, substantially impair this protein's ability to downregulate HLA class I. This, in turn, increases the visibility of infected cells to HIV-specific T cells. Our results suggest that B*13-associated escape mutations impair HIV-1 replication by two distinct mechanisms, that is, by reducing Gag fitness and dampening Nef immune evasion function. DOI
470. Shelton, AO; Hutchings, JA; Waples, RS; Keith, DM; Akcakaya, HR; Dulvy, NK.Maternal age effects on Atlantic cod recruitment and implications for future population trajectories.ICES Journal of Marine Science, 2015, 72: 1769-1778 Maternal age effects on Atlantic cod recruitment and implications for future population trajectories
age-structure; age truncation; maternal effects; recruitment; Ricker; productivity
Exploited fish populations frequently exhibit truncated age-structure. To address a basic question in fisheries science and conservation biology-how does age truncation affect population dynamics and productivity?-we explored the effect of age-structure on recruitment dynamics of ten stocks of Atlantic cod (Gadus morhua). Based on six alternative stock-recruitment relationships, we compared models that included and excluded maternal age-structure effects on recruitment. In all ten stocks, a recruitment model that included a maternal age-dependent effect was preferred over the standard Ricker model and in seven of the ten stocks, the preferred statistical model included a positive effect of either maternal age or mass on recruitment. Simulations comparing standard and maternal age dependent recruitment two decades into the future suggest that the inclusion of maternal age in recruitment models has little effect on projected biomasses. However, this similarity in biomass trajectory masked an increased sensitivity of populations with maternal age-dependent recruitment to stock age-structure. In particular, simulations with maternal age-dependent recruitment responded strongly to changes in fishing mortality on the oldest age classes, while simulations using standard recruitment models did not. Populations with maternal age-dependent recruitment can exhibit increased biomass catch even if fishing mortality on older individuals was reduced. Overall, simulations suggested that the influence of maternal age on population dynamics are more nuanced than suggested by previous research and indicate that careful consideration of the effects of age-structure on populations may lead to substantially different fisheries management reference points-particularly with respect to age-specific fishing mortality-than classical models. While these results suggest a link between maternal age and population productivity, future research requires the incorporation of biologically reasonable and empirically defensible mechanisms to clarify the effect of age on population dynamics. DOI
469. Shikano, I; Oak, MC; Halpert-Scanderbeg, O; Cory, JS.Trade-offs between transgenerational transfer of nutritional stress tolerance and immune priming.Functional Ecology, 2015, 29: 1156-1164 Trade-offs between transgenerational transfer of nutritional stress tolerance and immune priming
Bacillus thuringiensis; baculovirus; environmental context; fitness costs; food quality; host-parasite interaction; invertebrate immunity; maternal effect; pathogen resistance
Transgenerational effects are often assumed to have adaptive value as a driver of variation in offspring and parental fitness. Studies of transgenerational effects often focus on single environmental variables. However, in nature, it is unlikely for one factor to vary independently from others and there are likely to be trade-offs between different stressors. We altered the nutritional environment of both parents and offspring to examine how nutritional stress influences transgenerational immune priming (TGIP) with a sublethal challenge by the bacterial pathogen Bacillus thuringiensis, in the cabbage looper, Trichoplusia ni. Transgenerational immune priming was adaptive when offspring encountered the same pathogen experienced by their parents, such that offspring resistance to B.thuringiensis increased 15-fold and antibacterial activity in the haemolymph increased by as much as 4-fold. However, this was not a general increase in pathogen resistance as susceptibility to a second pathogen, the baculovirus, TnSNPV remained the same. Interestingly, nutritional stress in the parents both enhanced nutritional stress tolerance of offspring and heightened resistance to both B.thuringiensis and TnSNPV. Elevated pathogen resistance was linked to increased egg size. There was a significant trade-off between TGIP and the transfer of nutritional stress tolerance when parents encountered both stressors simultaneously, such that parents transferred resistance to pathogens but not nutritional stress tolerance. These results highlight the trade-offs that can modulate the occurrence and magnitude of transgenerational effects and illustrate the importance of assessing interactions between multiple environmental variables. At high population densities, disease risk increases and resour-ces become depleted. Thus, our findings could have significant implications for population dynamics. DOI
468. Sodi, VL; Khaku, S; Krutilina, R; Schwab, LP; Vocadlo, DJ; Seagroves, TN; Reginato, MJ.mTOR/MYC Axis Regulates O-GlcNAc Transferase Expression and O-GlcNAcylation in Breast Cancer.Molecular Cancer Research, 2015, 13: 923-933 mTOR/MYC Axis Regulates O-GlcNAc Transferase Expression and O-GlcNAcylation in Breast Cancer
Cancers exhibit altered metabolism characterized by increased glucose and glutamine uptake. The hexosamine biosynthetic pathway (HBP) uses glucose and glutamine, and directly contributes to O-linked-b-N-acetylglucosamine (O-GlcNAc) modifications on intracellular proteins. Multiple tumor types contain elevated total O-GlcNAcylation, in part, by increasing O-GlcNAc transferase (OGT) levels, the enzyme that catalyzes this modification. Although cancer cells require OGT for oncogenesis, it is not clear how tumor cells regulate OGT expression and O-GlcNAcylation. Here, it is shown that the PI3K-mTOR-MYC signaling pathway is required for elevation of OGT and O-GlcNAcylation in breast cancer cells. Treatment with PI3K and mTOR inhibitors reduced OGT protein expression and decreased levels of overall O-GlcNAcyla-tion. In addition, both AKT and mTOR activation is sufficient to elevate OGT/O-GlcNAcylation. Downstream of mTOR, the oncogenic transcription factor c-MYC is required and sufficient for increased OGT protein expression in an RNA-independent manner and c-MYC regulation of OGT mechanistically requires the expression of c-MYC transcriptional target HSP90A. Finally, mammary tumor epithelial cells derived from MMTV-c-myc transgenic mice contain elevated OGT and O-GlcNAcylation and OGT inhibition in this model induces apoptosis. Thus, OGT and O-GlcNAcylation levels are elevated via activation of an mTOR/MYC cascade. (C)2015 AACR. DOI
467. Sota, T, P. Belton, M. Tseng, H.S. Yong & M. Mogi.Phylogeography of the Coastal Mosquito Aedes togoi across Climatic Zones: Testing an Anthropogenic Dispersal Hypothesis.PLOS One, 2015, 10 (6) : e0131230 Phylogeography of the Coastal Mosquito Aedes togoi across Climatic Zones: Testing an Anthropogenic Dispersal Hypothesis
The coastal mosquito Aedes togoi occurs more or less continuously from subarctic to subtropic
zones along the coasts of the Japanese islands and the East Asian mainland. It
occurs also in tropical Southeast Asia and the North American Pacific coast, and the populations
there are thought to have been introduced from Japan by ship. To test this hypothesis,
the genetic divergence among geographic populations of A. togoi was studied using
one mitochondrial and three nuclear gene sequences. We detected 71 mitochondrial haplotypes
forming four lineages, with high nucleotide diversity around temperate Japan and
declining towards peripheral ranges. The major lineage (L1) comprised 57 haplotypes from
temperate and subarctic zones in Japan and Southeast Asia including southern China and
Taiwan. Two other lineages were found from subtropical islands (L3) and a subarctic area
(L4) of Japan. The Canadian population showed one unique haplotype (L2) diverged from
the other lineages. In the combined nuclear gene tree, individuals with mitochondrial L4
haplotypes diverged from those with the other mitochondrial haplotypes L1—L3; although
individuals with L1—L3 haplotypes showed shallow divergences in the nuclear gene
sequences, individuals from Southeast Asia and Canada each formed a monophyletic
group. Overall, the genetic composition of the Southeast Asian populations was closely
related to that of temperate Japanese populations, suggesting recent gene flow between
these regions. The Canadian population might have originated from anthropogenic introduction
from somewhere in Asia, but the possibility that it could have spread across the Beringian
land bridge cannot be ruled out. DOI
466. St Clair, CT; Baird, P; Ydenberg, R; Elner, R; Bendell, LI.Trace elements in pacific Dunlin (Calidris alpina pacifica): patterns of accumulation and concentrations in kidneys and feathers.Ecotoxicology, 2015, 24: 29-44 Trace elements in pacific Dunlin (Calidris alpina pacifica): patterns of accumulation and concentrations in kidneys and feathers
Cadmium; Dunlin; Habitat preference; Risk assessment; Selenium; Trace elements
Trace element concentrations were measured in Pacific Dunlin (Calidris alpina pacifica) to identify factors that influence accumulation and to assess toxicity risks. We report concentrations of cadmium, copper, and zinc in kidneys as well as copper, lead, mercury, selenium and zinc in feathers. Relationships between element concentrations and Dunlin age, sex, bill length, habitat preference, trophic level, and sample group were investigated with regression analyses. Stable isotope ratios of carbon and nitrogen in Dunlin muscle tissue were used to determine habitat preference and trophic level, respectively. Cadmium concentrations in kidneys were significantly related to habitat preference: [Cd] in estuarine foragers >[Cd] in terrestrial foragers. Cadmium accumulation was age-dependent as concentrations increased significantly within 10 months of hatch dates but not afterward. Concentrations of cadmium and zinc in kidneys as well as lead and mercury in feathers were below those known to cause deleterious effects in birds. In contrast, selenium concentrations in feathers (range: 2.1-14.0 A mu g/g) were often at levels associated with toxicity risks (> 5 A mu g/g). Toxicity thresholds are not available for copper in kidneys or copper and zinc in feathers; however, measured concentrations of these elements were within documented ranges for sandpipers. Future studies should assess potential impacts of selenium on embryonic development in Dunlin and other sandpipers. Risk assessments would yield more conclusive results for all elements if impacts under ecologically relevant stresses (e.g. development in the wild, migration, predation) were better understood. DOI PubMed
464. Sunday, JM; Pecl, GT; Frusher, S; Hobday, AJ; Hill, N; Holbrook, NJ; Edgar, GJ; Stuart-Smith, R; Barrett, N; Wernberg, T; Watson, RA; Smale, DA; Fulton, EA; Slawinski, D; Feng, M; Radford, BT; Thompson, PA; Bates, AE.Species traits and climate velocity explain geographic range shifts in an ocean-warming hotspot.Ecology Letters, 2015, 18: 944-953 Species traits and climate velocity explain geographic range shifts in an ocean-warming hotspot
Benthic invertebrates; climate change; climate response; fishes; functional traits; invasion; range expansion; range shifts; range size
Species' ranges are shifting globally in response to climate warming, with substantial variability among taxa, even within regions. Relationships between range dynamics and intrinsic species traits may be particularly apparent in the ocean, where temperature more directly shapes species' distributions. Here, we test for a role of species traits and climate velocity in driving range extensions in the ocean-warming hotspot of southeast Australia. Climate velocity explained some variation in range shifts, however, including species traits more than doubled the variation explained. Swimming ability, omnivory and latitudinal range size all had positive relationships with range extension rate, supporting hypotheses that increased dispersal capacity and ecological generalism promote extensions. We find independent support for the hypothesis that species with narrow latitudinal ranges are limited by factors other than climate. Our findings suggest that small-ranging species are in double jeopardy, with limited ability to escape warming and greater intrinsic vulnerability to stochastic disturbances. DOI
463. Swain, NR; Reynolds, JD.Effects of Salmon-Derived Nutrients and Habitat Characteristics on Population Densities of Stream-Resident Sculpins.PLoS One, 2015, 10 Effects of Salmon-Derived Nutrients and Habitat Characteristics on Population Densities of Stream-Resident Sculpins
Movement of nutrients across ecosystem boundaries can have important effects on food webs and population dynamics. An example from the North Pacific Rim is the connection between productive marine ecosystems and freshwaters driven by annual spawning migrations of Pacific salmon (Oncorhynchus spp). While a growing body of research has highlighted the importance of both pulsed nutrient subsidies and disturbance by spawning salmon, their effects on population densities of vertebrate consumers have rarely been tested, especially across streams spanning a wide range of natural variation in salmon densities and habitat characteristics. We studied resident freshwater prickly (Cottus asper), and coastrange sculpins (C. aleuticus) in coastal salmon spawning streams to test whether their population densities are affected by spawning densities of pink and chum salmon (O. gorbuscha and O. keta), as well as habitat characteristics. Coastrange sculpins occurred in the highest densities in streams with high densities of spawning pink and chum salmon. They also were more dense in streams with high pH, large watersheds, less area covered by pools, and lower gradients. In contrast, prickly sculpin densities were higher in streams with more large wood and pools, and less canopy cover, but their densities were not correlated with salmon. These results for coastrange sculpins provide evidence of a numerical population response by freshwater fish to increased availability of salmon subsidies in streams. These results demonstrate complex and context-dependent relationships between spawning Pacific salmon and coastal ecosystems and can inform an ecosystem-based approach to their management and conservation. DOI
462. Tamburello, N; Côté, IM; Dulvy, NK.Energy and the Scaling of Animal Space Use.American Naturalist, 2015, 186: 196-211 Energy and the Scaling of Animal Space Use
allometry; home range; metabolic theory; prey handling; prey size; spatial ecology
Daily animal movements are usually limited to a discrete home range area that scales allometrically with body size, suggesting that home-range size is shaped by metabolic rates and energy availability across species. However, there is little understanding of the relative importance of the various mechanisms proposed to influence home-range scaling (e.g., differences in realm productivity, thermoregulation, locomotion strategy, dimensionality, trophic guild, and prey size) and whether these extend beyond the commonly studied birds and mammals. We derive new home-range scaling relationships for fishes and reptiles and use a model-selection approach to evaluate the generality of home-range scaling mechanisms across 569 vertebrate species. We find no evidence that home-range allometry varies consistently between aquatic and terrestrial realms or thermoregulation strategies, but we find that locomotion strategy, foraging dimension, trophic guild, and prey size together explain 80% of the variation in home-range size across vertebrates when controlling for phylogeny and tracking method. Within carnivores, smaller relative prey size among gape-limited fishes contributes to shallower scaling relative to other predators. Our study reveals how simple morphological traits and prey-handling ability can profoundly influence individual space use, which underpins broader-scale patterns in the spatial ecology of vertebrates. DOI
461. Tan, B; Fowler, SJ; Abu Laban, N; Dong, XL; Sensen, CW; Foght, J; Gieg, LM.Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples.ISME J., 2015, 9: 2028-2045 Comparative analysis of metagenomes from three methanogenic hydrocarbon-degrading enrichment cultures with 41 environmental samples
Methanogenic hydrocarbon metabolism is a key process in subsurface oil reservoirs and hydrocarbon-contaminated environments and thus warrants greater understanding to improve current technologies for fossil fuel extraction and bioremediation. In this study, three hydrocarbon-degrading methanogenic cultures established from two geographically distinct environments and incubated with different hydrocarbon substrates (added as single hydrocarbons or as mixtures) were subjected to metagenomic and 16S rRNA gene pyrosequencing to test whether these differences affect the genetic potential and composition of the communities. Enrichment of different putative hydrocarbon-degrading bacteria in each culture appeared to be substrate dependent, though all cultures contained both acetate-and H-2-utilizing methanogens. Despite differing hydrocarbon substrates and inoculum sources, all three cultures harbored genes for hydrocarbon activation by fumarate addition (bssA, assA, nmsA) and carboxylation (abcA, ancA), along with those for associated downstream pathways (bbs, bcr, bam), though the cultures incubated with hydrocarbon mixtures contained a broader diversity of fumarate addition genes. A comparative metagenomic analysis of the three cultures showed that they were functionally redundant despite their enrichment backgrounds, sharing multiple features associated with syntrophic hydrocarbon conversion to methane. In addition, a comparative analysis of the culture metagenomes with those of 41 environmental samples (containing varying proportions of methanogens) showed that the three cultures were functionally most similar to each other but distinct from other environments, including hydrocarbon-impacted environments (for example, oil sands tailings ponds and oil-affected marine sediments). This study provides a basis for understanding key functions and environmental selection in methanogenic hydrocarbon-associated communities. DOI PubMed
460. Taracena, ML; Oliveira, PL; Almendares, O; Umana, C; Lowenberger, C; Dotson, EM; Paiva-Silva, GO; Pennington, PM.Genetically Modifying the Insect Gut Microbiota to Control Chagas Disease Vectors through Systemic RNAi.PLoS Neglected Tropical Diseases, 2015, 9 Genetically Modifying the Insect Gut Microbiota to Control Chagas Disease Vectors through Systemic RNAi
Technologies based on RNA interference may be used for insect control. Sustainable strategies are needed to control vectors of Chagas disease such as Rhodnius prolixus. The insect microbiota can be modified to deliver molecules to the gut. Here, Escherichia coli HT115(DE3) expressing dsRNA for the Rhodnius heme-binding protein (RHBP) and for catalase (CAT) were fed to nymphs and adult triatomine stages. RHBP is an egg protein and CAT is an antioxidant enzyme expressed in all tissues by all developmental stages. The RNA interference effect was systemic and temporal. Concentrations of E. coli HT115(DE3) above 3.35 x 10(7) CFU/mL produced a significant RHBP and CAT gene knockdown in nymphs and adults. RHBP expression in the fat body was reduced by 99% three days after feeding, returning to normal levels 10 days after feeding. CAT expression was reduced by 99% and 96% in the ovary and the posterior midgut, respectively, five days after ingestion. Mortality rates increased by 24-30% in first instars fed RHBP and CAT bacteria. Molting rates were reduced by 100% in first instars and 80% in third instars fed bacteria producing RHBP or CAT dsRNA. Oviposition was reduced by 43% (RHBP) and 84% (CAT). Embryogenesis was arrested in 16% (RHBP) and 20% (CAT) of laid eggs. Feeding females 105 CFU/mL of the natural symbiont, Rhodococcus rhodnii, transformed to express RHBP-specific hairpin RNA reduced RHBP expression by 89% and reduced oviposition. Modifying the insect microbiota to induce systemic RNAi in R. prolixus may result in a paratransgenic strategy for sustainable vector control. DOI
459. Trebilco, R; Dulvy, NK; Stewart, H; Salomon, AK.The role of habitat complexity in shaping the size structure of a temperate reef fish community.Marine Ecology Progress Series, 2015, 532: 197-211 The role of habitat complexity in shaping the size structure of a temperate reef fish community
Biomass size spectra; Community ecology; Coral reef; Ecosystem baseline; Energy flow; Foundation species
Understanding how habitat complexity shapes fish communities is necessary to predict the consequences of future habitat change. On temperate rocky reefs, the presence and characteristics of canopy-forming kelps and the architectural complexity, or rugosity, of the underlying rocky substratum are foundational elements of habitat complexity. However, it is not yet clear how these factors shape the size structure of rocky-reef-associated fish communities. Here, we use biomass spectrum models to evaluate how fish community size structure in high-latitude rocky-reef kelp forests is shaped by substratum rugosity and the degree of closure and density of the kelp canopy. We found that the presence of a closed kelp canopy was associated with an average 75% increase in overall fish biomass compared to open-canopy reefs. Furthermore, on the highest-rugosity reefs, the biomass of small fishes (32-64 g) was 800% higher than on the lowest-rugosity reefs, while large fish (1-2 kg) biomass was 60% lower. Consequently, biomass was more evenly distributed across body-size classes on high-rugosity reefs. By decomposing the biomass spectrum into total biomass and mean individual body mass, we found that higher kelp stipe densities also tended to be associated with larger fishes, but this effect was outweighed by the tendency for more small-bodied fishes with increasing rugosity. This study demonstrates how size-based analyses can give new insights into the ecology of temperate reef communities, and may be useful for tracking changes in kelp-associated assemblages in the coming decades with the maturation of marine protected areas, the recovery of sea otter populations, and changing climate. DOI
458. Watson, CT; Steinberg, KM; Graves, TA; Warren, RL; Malig, M; Schein, J; Wilson, RK; Holt, RA; Eichler, EE; Breden, F.Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity.Genes and Immunity, 2015, 16: 24-34 Sequencing of the human IG light chain loci from a hydatidiform mole BAC library reveals locus-specific signatures of genetic diversity
Germline variation at immunoglobulin (IG) loci is critical for pathogen-mediated immunity, but establishing complete haplotype sequences in these regions has been problematic because of complex sequence architecture and diploid source DNA. We sequenced BAC clones from the effectively haploid human hydatidiform mole cell line, CHMThtert, across the light chain IG loci, kappa (IGK) and lambda (IGL), creating single haplotype representations of these regions. The IGL haplotype generated here is 1.25 Mb of contiguous sequence, including four novel IGLV alleles, one novel IGLC allele, and an 11.9-kb insertion. The CH17 IGK haplotype consists of two 644 kb proximal and 466 kb distal contigs separated by a large gap of unknown size; these assemblies added 49 kb of unique sequence extending into this gap. Our analysis also resulted in the characterization of seven novel IGKV alleles and a 16.7-kb region exhibiting signatures of interlocus sequence exchange between distal and proximal IGKV gene clusters. Genetic diversity in IGK/IGL was compared with that of the IG heavy chain (IGH) locus within the same haploid genome, revealing threefold (IGK) and sixfold (IGL) higher diversity in the IGH locus, potentially associated with increased levels of segmental duplication and the telomeric location of IGH. DOI PubMed
457. Wilkinson, GS; Breden, F; Mank, JE; Ritchie, MG; Higginson, AD; Radwan, J; Jaquiery, J; Salzburger, W; Arriero, E; Barribeau, SM; Phillips, PC; Renn, SCP; Rowe, L.The locus of sexual selection: moving sexual selection studies into the post-genomics era.Journal of Evolutionary Biology, 2015, 28: 739-755 The locus of sexual selection: moving sexual selection studies into the post-genomics era
candidate gene; cis-regulation; forward genetics; genomewide association studies; resequencing; reverse genetics; transcriptome
Sexual selection drives fundamental evolutionary processes such as trait elaboration and speciation. Despite this importance, there are surprisingly few examples of genes unequivocally responsible for variation in sexually selected phenotypes. This lack of information inhibits our ability to predict phenotypic change due to universal behaviours, such as fighting over mates and mate choice. Here, we discuss reasons for this apparent gap and provide recommendations for how it can be overcome by adopting contemporary genomic methods, exploiting underutilized taxa that may be ideal for detecting the effects of sexual selection and adopting appropriate experimental paradigms. Identifying genes that determine variation in sexually selected traits has the potential to improve theoretical models and reveal whether the genetic changes underlying phenotypic novelty utilize common or unique molecular mechanisms. Such a genomic approach to sexual selection will help answer questions in the evolution of sexually selected phenotypes that were first asked by Darwin and can furthermore serve as a model for the application of genomics in all areas of evolutionary biology. DOI PubMed
456. Wray, JC; Elle, E.Flowering phenology and nesting resources influence pollinator community composition in a fragmented ecosystem.Landscape Ecology, 2015, 30: 261-272 Flowering phenology and nesting resources influence pollinator community composition in a fragmented ecosystem
Habitat fragmentation; Oak-savannah; Landscape matrix; Community composition; Flowering plants; Nesting resources
Habitat loss is the leading cause of extinctions on the planet. However, negative effects of habitat loss and fragmentation on biodiversity can be reduced if resources in urban or semi-natural areas in the surrounding matrix can be used by wildlife. We investigated the influence of floral and nesting resources in urban- and forest-associated oak-savannah fragments, surrounding urban and forest matrix, and urban areas spatially independent from oak-savannah habitat on pollinator community composition in a fragmented oak-savannah ecosystem. Both independent urban and urban matrix sites supported high abundance and richness of plants and pollinators relative to other fragment categories, especially towards the end of the season when plants and pollinators in oak-savannah fragments were scarce. A species of particular conservation concern in our region, Bombus occidentalis, was supported by late-flowering resources in our urban sites. Forest-associated oak-savannah fragments were missing late-season species while urban-associated fragments supported high abundance and richness of mid- to late-season pollinators, likely due to supplemental use of floral resources in the urban matrix. Female cavity-nesting and ground-nesting bees were not restricted by the availability of natural nesting resources we expected them to require (e.g. small cavities, bare soil). These results provide important information on native pollinators in a highly fragmented habitat, and suggest that we should consider matrix quality in conservation planning. DOI
455. Zhang, YJ; Li, D; Sun, BY.Do Housekeeping Genes Exist?PLoS One, 2015, 10 Do Housekeeping Genes Exist?
The searching of human housekeeping (HK) genes has been a long quest since the emergence of transcriptomics, and is instrumental for us to understand the structure of genome and the fundamentals of biological processes. The resolved genes are frequently used in evolution studies and as normalization standards in quantitative gene-expression analysis. Within the past 20 years, more than a dozen HK-gene studies have been conducted, yet none of them sampled human tissues completely. We believe an integration of these results will help remove false positive genes owing to the inadequate sampling. Surprisingly, we only find one common gene across 15 examined HK-gene datasets comprising 187 different tissue and cell types. Our subsequent analyses suggest that it might not be appropriate to rigidly define HK genes as expressed in all tissue types that have diverse developmental, physiological, and pathological states. It might be beneficial to use more robustly identified HK functions for filtering criteria, in which the representing genes can be a subset of genome. These genes are not necessarily the same, and perhaps need not to be the same, everywhere in our body. DOI
454. Atlas, WI; Palen, WJ.Prey Vulnerability Limits Top-Down Control and Alters Reciprocal Feedbacks in a Subsidized Model Food Web.PLOS One, 2014, 9 Prey Vulnerability Limits Top-Down Control and Alters Reciprocal Feedbacks in a Subsidized Model Food Web
Resource subsidies increase the productivity of recipient food webs and can affect ecosystem dynamics. Subsidies of prey often support elevated predator biomass which may intensify top-down control and reduce the flow of reciprocal subsidies into adjacent ecosystems. However, top-down control in subsidized food webs may be limited if primary consumers posses morphological or behavioral traits that limit vulnerability to predation. In forested streams, terrestrial prey support high predator biomass creating the potential for strong top-down control, however armored primary consumers often dominate the invertebrate assemblage. Using empirically based simulation models, we tested the response of stream food webs to variations in subsidy magnitude, prey vulnerability, and the presence of two top predators. While terrestrial prey inputs increased predator biomass (+12%), the presence of armored primary consumers inhibited top-down control, and diverted most aquatic energy (similar to 75%) into the riparian forest through aquatic insect emergence. Food webs without armored invertebrates experienced strong trophic cascades, resulting in higher algal (similar to 50%) and detrital (similar to 1600%) biomass, and reduced insect emergence (-90%). These results suggest prey vulnerability can mediate food web responses to subsidies, and that top-down control can be arrested even when predator-invulnerable consumers are uncommon (20%) regardless of the level of subsidy. DOI
453. Bates, AE; Pecl, GT; Frusher, S; Hobday, AJ; Wernberg, T; Smale, DA; Sunday, JM; Hill, NA; Dulvy, NK; Colwell, RK; Holbrook, NJ; Fulton, EA; Slawinski, D; Feng, M; Edgar, GJ; Radford, BT; Thompson, PA; Watson, RA.Defining and observing stages of climate-mediated range shifts in marine systems.Global Environmental Change-Human and Policy Dimensions, 2014, 26: 27-38 Defining and observing stages of climate-mediated range shifts in marine systems
Species redistribution; Attribution; Prediction; Biogeography; Warming; Abundance-occupancy relationship
Climate change is transforming the structure of biological communities through the geographic extension and contraction of species' ranges. Range edges are naturally dynamic, and shifts in the location of range edges occur at different rates and are driven by different mechanisms. This leads to challenges when seeking to generalize responses among taxa and across systems. We focus on warming-related range shifts in marine systems to describe extensions and contractions as stages. Range extensions occur as a sequence of (1) arrival, (2) population increase, and (3) persistence. By contrast, range contractions occur progressively as (1) performance decline, (2) population decrease and (3) local extinction. This stage-based framework can be broadly applied to geographic shifts in any species, life-history stage, or population subset. Ideally the probability of transitioning through progressive range shift stages could be estimated from empirical understanding of the various factors influencing range shift rates. Nevertheless, abundance and occupancy data at the spatial resolution required to quantify range shifts are often unavailable and we suggest the pragmatic solution of considering observations of range shifts within a confidence framework incorporating the type, amount and quality of data. We use case studies to illustrate how diverse evidence sources can be used to stage range extensions and contractions and assign confidence that an observed range shift stage has been reached. We then evaluate the utility of trait-based risk (invasion) and vulnerability (extinction) frameworks for application in a range shift context and find inadequacies, indicating an important area for development. We further consider factors that influence rates of extension and contraction of range edges in marine habitats. Finally, we suggest approaches required to increase our capacity to observe and predict geographic range shifts under climate change. (C) 2014 Elsevier Ltd. All rights reserved. DOI
452. Button, L; Elle, E.Wild bumble bees reduce pollination deficits in a crop mostly visited by managed honey bees.Agriculture Ecosystems & Environment, 2014, 197: 255-263 Wild bumble bees reduce pollination deficits in a crop mostly visited by managed honey bees
Pollination deficit; Edge effect; Mixed pollinator strategy; Apis mellifera; Bombus; Blueberry
We assessed the pollinator community of two cultivars of highbush blueberry (Vaccinium corymbosum, Duke and Bluecrop), and determined the importance of different pollinators to overall crop yield by measuring pollination deficits. The importance of distance to putative wild pollinator habitat (natural field edges) for pollinator abundance within fields and crop yield was also considered. Managed honey bees made 70% of flower visits (85% to Duke, 49% to Bluecrop). Wild bumble bees made half of the visits to Bluecrop. Though bumble bees were observed less frequently as distance from the natural edge increased, there was no effect of distance on levels of crop pollination. Pollination deficits were less pronounced in Duke than Bluecrop, with maximum (hand) pollination leading to a 12% (Duke) to 23% (Bluecrop) increase in yield. Exclusion of pollinators reduced yield by 50-80% compared to ambient pollination. For both cultivars, pollination deficits declined most strongly with either increasing bumble bee visits or increasing total visits (honey bees and bumble bees combined), and in no case were deficit levels significantly reduced by honey bees alone. This study supports a growing body of literature that suggests managed honey bees alone cannot reduce deficits, and that wild pollinators are needed to maximize yields in pollinator-dependent agricultural systems. (C) 2014 Elsevier B.V. All rights reserved. DOI
451. Chamberlain, S; Vazquez, DP; Carvalheiro, L; Elle, E; Vamosi, JC.Phylogenetic tree shape and the structure of mutualistic networks.Journal of Ecology, 2014, 102: 1234-1243 Phylogenetic tree shape and the structure of mutualistic networks
connectance; diversity; modularity; nestedness; network structure; phylogeny imbalance; plant population and community dynamics; plant-pollinator interactions
1. Species community composition is known to alter the network of interactions between two trophic levels, potentially affecting its functioning (e. g. plant pollination success) and the stability of communities. Phylogenies vary in shape with regard to the rate of evolutionary change across a tree (influencing tree balance) and variation in the timing of branching events (affecting the distribution of node ages in trees), both of which may influence the structure of species interaction networks. Because related species are likely to share many of the traits that regulate interactions, the shape of phylogenetic trees may provide some insights into the distribution of traits within communities, and hence the likelihood of interaction among species. However, little attention has been paid to the potential effects of changes in phylogenetic diversity (PD) on interaction networks. 2. Phylogenetic diversity is influenced by species diversity within a community, but also how distantly-related the constituent species are from one another. Here, we evaluate the relationship between two important measures of phylogenetic diversity (tree shape and age of nodes) and the structure of plant-pollinator interaction networks using empirical and simulated data. Whereas the former allows us to evaluate patterns in real communities, the latter allows us to evaluate more systematically the relationship between tree shape and network structure under three different models of trait evolution. 3. In empirical networks, less balanced plant phylogenies were associated with lower connectance in interaction networks indicating that communities with the descendants of recent radiations are more diverged and specialized in their partnerships. In simulations, tree balance and the distribution of nodes through time were included in the best models for modularity, and the second best models for connectance and nestedness. In models assuming random evolutionary change through time (i.e. Brownian motion), less balanced trees and trees with nodes near the tips exhibited greater modularity, whereas in models with an early burst of radiation followed by relative stasis (i.e. early-burst models) more balanced trees and trees with nodes near roots had greater modularity. 4. Synthesis. Overall, these results suggest that the shape of phylogenies can influence the structure of plant-pollinator interaction networks. However, the mismatch between simulations and empirical data indicate that no simple model of trait evolution mimics that observed in real communities. DOI
450. Chamberlain, SA; Cartar, RV; Worley, AC; Semmler, SJ; Gielens, G; Elwell, S; Evans, ME; Vamosi, JC; Elle, E.Traits and phylogenetic history contribute to network structure across Canadian plant-pollinator communities.Oecologia, 2014, 176: 545-556 Traits and phylogenetic history contribute to network structure across Canadian plant-pollinator communities
Mutualism; Interaction webs; Trophic levels; Morphological trait; Functional trait
Interaction webs, or networks, define how the members of two or more trophic levels interact. However, the traits that mediate network structure have not been widely investigated. Generally, the mechanism that determines plant-pollinator partnerships is thought to involve the matching of a suite of species traits (such as abundance, phenology, morphology) between trophic levels. These traits are often unknown or hard to measure, but may reflect phylogenetic history. We asked whether morphological traits or phylogenetic history were more important in mediating network structure in mutualistic plant-pollinator interaction networks from Western Canada. At the plant species level, sexual system, growth form, and flower symmetry were the most important traits. For example species with radially symmetrical flowers had more connections within their modules (a subset of species that interact more among one another than outside of the module) than species with bilaterally symmetrical flowers. At the pollinator species level, social species had more connections within and among modules. In addition, larger pollinators tended to be more specialized. As traits mediate interactions and have a phylogenetic signal, we found that phylogenetically close species tend to interact with a similar set of species. At the network level, patterns were weak, but we found increasing functional trait and phylogenetic diversity of plants associated with increased weighted nestedness. These results provide evidence that both specific traits and phylogenetic history can contribute to the nature of mutualistic interactions within networks, but they explain less variation between networks. DOI PubMed
449. Dulvy, NK; Fowler, SL; Musick, JA; Cavanagh, RD; Kyne, PM; Harrison, LR; Carlson, JK; Davidson, LNK; Fordham, SV; Francis, MP; Pollock, CM; Simpfendorfer, CA; Burgess, GH; Carpenter, KE; Compagno, LJV; Ebert, DA; Gibson, C; Heupel, MR; Livingstone, SR; Sanciangco, JC; Stevens, JD; Valenti, S; White, WT.Extinction risk and conservation of the world's sharks and rays.Elife, 2014, 3 Extinction risk and conservation of the world's sharks and rays
The rapid expansion of human activities threatens ocean-wide biodiversity. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally distributed lineage of 1,041 chondrichthyan fishes-sharks, rays, and chimaeras. We estimate that one-quarter are threatened according to IUCN Red List criteria due to overfishing (targeted and incidental). Large-bodied, shallow-water species are at greatest risk and five out of the seven most threatened families are rays. Overall chondrichthyan extinction risk is substantially higher than for most other vertebrates, and only one-third of species are considered safe. Population depletion has occurred throughout the world's ice-free waters, but is particularly prevalent in the Indo-Pacific Biodiversity Triangle and Mediterranean Sea. Improved management of fisheries and trade is urgently needed to avoid extinctions and promote population recovery. DOI
448. Dupuch, A; Bertolo, A; Magnan, P; Dill, LM.Indirect effects of asymmetrical competition among top predators determine spatial patterns of predation risk for prey.Aquatic Sciences, 2014, 76: 543-552 Indirect effects of asymmetrical competition among top predators determine spatial patterns of predation risk for prey
Brook trout; Competition; Trophic interactions; Spatial scale; Tethering experiment
Asymmetrical interspecific competition among top predators can indirectly affect the predation risk for their prey by altering the abundance, diet, and habitat use of inferior competitors. However, the indirect effects of such biological interactions are poorly known because of the difficulties in measuring predation risk in nature. We addressed this issue by assessing the effect of asymmetrical competition among brook trout (Salvelinus fontinalis) and two superior non-piscivorous competitors, creek chub (Semotilus atromaculatus) and white sucker (Catostomus commersonii), on the predation risk of a brook trout prey, northern redbelly dace (Chrosomus eos). We determined the spatio-temporal patterns of relative predation risk of dace with tethering experiments in 11 lakes containing either only brook trout and dace (n = 5), or brook trout, dace, chub, and sucker (n = 6). The diel pattern of the relative predation risk and the overall relative predation risk of dace were not significantly different in lakes with or without brook trout competitors. However, we observed a significant shift in the relative predation risk from the lower pelagic to the upper pelagic and littoral zones in the presence of brook trout competitors. This study highlights the fact that the outcome of interactions can vary in space and that care should be used when extrapolating the results of small-scale experiments or coarse-scale estimates to the whole ecosystem. DOI
447. Farhadian, N; Malek, K; Shariaty-Niassar, M; Maghari, A.Investigating the interactions of the enantiomers of phenylglycine with nanopores of ZSM-5 zeolite.J. Chem. Sci., 2014, 126: 569-578 Investigating the interactions of the enantiomers of phenylglycine with nanopores of ZSM-5 zeolite
Nanostructure; zeolite; chirality; amino acid; molecular dynamics simulation
In this study, molecular dynamics simulation has been used to investigate the interactions of both chiral forms of phenylglycine amino acid (R- and S-isomers) with micropores of ZSM5-zeolite. Calculated results show that phenylglycine molecules interact with zeolite surface by electrostatic interaction of their positively charged ammonium group and negatively charged carboxylic group. This leads to the formation of two hetero hydrogen bonds between amino groups and oxygen of zeolite framework and also one hydrogen bond between the carboxylic groups and the zeolite surface. Further analyses show that S-isomers have stronger interactions with zeolite surface in comparison to R-isomers. So, movement, radius of gyration and angle of orientation of S-isomers inside nanopores are decreased, while R-isomers interact more strongly with each other. However, both chiral forms have diffusive behaviour along the pores with the self diffusion coefficient of about two orders of magnitude less than that in free water. DOI
446. Farmer, RG; Leonard, ML; Flemming, JEM; Anderson, SC.Observer aging and long-term avian survey data quality.Ecology and Evolution, 2014, 4: 2563-2576 Observer aging and long-term avian survey data quality
Avian ecology; citizen science; observer error; point counts; population trend estimation
Long-term wildlife monitoring involves collecting time series data, often using the same observers over multiple years. Aging-related changes to these observers may be an important, under-recognized source of error that can bias management decisions. In this study, we used data from two large, independent bird surveys, the Atlas of the Breeding Birds of Ontario ("OBBA") and the North American Breeding Bird Survey ("BBS"), to test for age-related observer effects in long-term time series of avian presence and abundance. We then considered the effect of such aging phenomena on current population trend estimates. We found significantly fewer detections among older versus younger observers for 13 of 43 OBBA species, and declines in detection as an observer ages for 4 of 6 vocalization groups comprising 59 of 64 BBS species. Consistent with hearing loss influencing this pattern, we also found evidence for increasingly severe detection declines with increasing call frequency among nine high-pitched bird species (OBBA); however, there were also detection declines at other frequencies, suggesting important additional effects of aging, independent of hearing loss. We lastly found subtle, significant relationships between some species' published population trend estimates and (1) their corresponding vocalization frequency (n >= 22 species) and (2) their estimated declines in detectability among older observers (n = 9 high-frequency, monotone species), suggesting that observer aging can negatively bias long-term monitoring data for some species in part through hearing loss effects. We recommend that survey designers and modelers account for observer age where possible. DOI PubMed
445. Fowler, SJ; Gutierrez-Zamora, ML; Manefield, M; Gieg, LM.Identification of toluene degraders in a methanogenic enrichment culture.FEMS Microbiol. Ecol., 2014, 89: 625-636 Identification of toluene degraders in a methanogenic enrichment culture
stable isotope probing; RT-qPCR; anaerobic; methanogenesis; toluene; metabolism
Methanogenic biodegradation involves the cooperative metabolism of syntrophic bacteria that catalyse the initial attack and subsequent degradation of hydrocarbons, and methanogens that convert intermediates such as hydrogen and carbon dioxide, formate, and/or acetate to methane. The identity of syntrophic microbes and the nature of their interactions with other syntrophs and methanogens are not well understood. Furthermore, it is difficult to isolate the organisms responsible for the initial activation and subsequent degradation of hydrocarbon substrates under methanogenic conditions due to the thermodynamic relationships that exist among microbes in methanogenic communities. We used time-resolved RNA stable isotope probing and RT-qPCR to identify the organisms involved in the initial attack on toluene and subsequent degradation reactions in a highly enriched toluene-degrading methanogenic culture. Our results reveal the importance of a Desulfosporosinus sp. in anaerobic toluene activation in the culture. Other organisms that appear to play roles in toluene degradation include Syntrophaceae, Desulfovibrionales and Chloroflexi. The high bacterial diversity observed in this culture and the extensive labelling of different phylogenetic groups over the course of the stable isotope probing experiment highlight the complexity of the relationships that exist in methanogenic ecosystems. DOI PubMed
444. Frishkoff, LO; Karp, DS; M'Gonigle, LK; Mendenhall, CD; Zook, J; Kremen, C; Hadly, EA; Daily, GC.Loss of avian phylogenetic diversity in neotropical agricultural systems.Science, 2014, 345: 1343-1346 Loss of avian phylogenetic diversity in neotropical agricultural systems
Habitat conversion is the primary driver of biodiversity loss, yet little is known about how it is restructuring the tree of life by favoring some lineages over others. We combined a complete avian phylogeny with 12 years of Costa Rican bird surveys (118,127 detections across 487 species) sampled in three land uses: forest reserves, diversified agricultural systems, and intensive monocultures. Diversified agricultural systems supported 600 million more years of evolutionary history than intensive monocultures but 300 million fewer years than forests. Compared with species with many extant relatives, evolutionarily distinct species were extirpated at higher rates in both diversified and intensive agricultural systems. Forests are therefore essential for maintaining diversity across the tree of life, but diversified agricultural systems may help buffer against extreme loss of phylogenetic diversity. DOI
443. Gorman, KB; Williams, TD; Fraser, WR.Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis).PLOS One, 2014, 9 Ecological Sexual Dimorphism and Environmental Variability within a Community of Antarctic Penguins (Genus Pygoscelis)
Background: Sexual segregation in vertebrate foraging niche is often associated with sexual size dimorphism (SSD), i.e., ecological sexual dimorphism. Although foraging behavior of male and female seabirds can vary markedly, differences in isotopic (carbon, delta C-13 and nitrogen, delta N-15) foraging niche are generally more pronounced within sexually dimorphic species and during phases when competition for food is greater. We examined ecological sexual dimorphism among sympatric nesting Pygoscelis penguins asking whether environmental variability is associated with differences in male and female pre-breeding foraging niche. We predicted that all Pygoscelis species would forage sex-specifically, and that higher quality winter habitat, i.e., higher or lower sea ice coverage for a given species, would be associated with a more similar foraging niche among the sexes. Results: P2/P8 primers reliably amplified DNA of all species. On average, male Pygoscelis penguins are structurally larger than female conspecifics. However, chinstrap penguins were more sexually dimorphic in culmen and flipper features than Adelie and gentoo penguins. Adelies and gentoos were more sexually dimorphic in body mass than chinstraps. Only male and female chinstraps and gentoos occupied separate delta N-15 foraging niches. Strong year effects in delta N-15 signatures were documented for all three species, however, only for Adelies, did yearly variation in delta N-15 signatures tightly correlate with winter sea ice conditions. There was no evidence that variation in sex-specific foraging niche interacted with yearly winter habitat quality. Conclusion: Chinstraps were most sexually size dimorphic followed by gentoos and Adelies. Pre-breeding sex-specific foraging niche was associated with overall SSD indices across species; male chinstrap and gentoo penguins were enriched in delta N-15 relative to females. Our results highlight previously unknown trophic pathways that link Pygoscelis penguins with variation in Southern Ocean sea ice suggesting that each sex within a species should respond similarly in pre-breeding trophic foraging to changes in future winter habitat. DOI
442. Green, SJ; Dulvy, NK; Brooks, AML; Akins, JL; Cooper, AB; Miller, S; Côté, IM.Linking removal targets to the ecological effects of invaders: a predictive model and field test.Ecological Applications, 2014, 24: 1311-1322 Linking removal targets to the ecological effects of invaders: a predictive model and field test
ecological model; eradication; exotic species; lionfish; marine management; metabolic scaling theory; population control; predation; productivity; Pterois miles; Pterois volitans; size-based analysis
Species invasions have a range of negative effects on recipient ecosystems, and many occur at a scale and magnitude that preclude complete eradication. When complete extirpation is unlikely with available management resources, an effective strategy may be to suppress invasive populations below levels predicted to cause undesirable ecological change. We illustrated this approach by developing and testing targets for the control of invasive Indo-Pacific lionfish (Pterois volitans and P. miles) on Western Atlantic coral reefs. We first developed a size-structured simulation model of predation by lionfish on native fish communities, which we used to predict threshold densities of lionfish beyond which native fish biomass should decline. We then tested our predictions by experimentally manipulating lionfish densities above or below reef-specific thresholds, and monitoring the consequences for native fish populations on 24 Bahamian patch reefs over 18 months. We found that reducing lionfish below predicted threshold densities effectively protected native fish community biomass from predation-induced declines. Reductions in density of 25-92%, depending on the reef, were required to suppress lionfish below levels predicted to overconsume prey. On reefs where lionfish were kept below threshold densities, native prey fish biomass increased by 50-70%. Gains in small (<6 cm) size classes of native fishes translated into lagged increases in larger size classes over time. The biomass of larger individuals (>15 cm total length), including ecologically important grazers and economically important fisheries species, had increased by 10-65% by the end of the experiment. Crucially, similar gains in prey fish biomass were realized on reefs subjected to partial and full removal of lionfish, but partial removals took 30% less time to implement. By contrast, the biomass of small native fishes declined by >50% on all reefs with lionfish densities exceeding reef-specific thresholds. Large inter-reef variation in the biomass of prey fishes at the outset of the study, which influences the threshold density of lionfish, means that we could not identify a single rule of thumb for guiding control efforts. However, our model provides a method for setting reef-specific targets for population control using local monitoring data. Our work is the first to demonstrate that for ongoing invasions, suppressing invaders below densities that cause environmental harm can have a similar effect, in terms of protecting the native ecosystem on a local scale, to achieving complete eradication. DOI PubMed
441. Greenspoon, PB; M'Gonigle, LK.Host-parasite interactions and the evolution of nonrandom mating.Evolution, 2014, 68: 3570-3580 Host-parasite interactions and the evolution of nonrandom mating
Assortative mating; coevolution; disassortative mating; maternal effects; modifier model; parasites
Some species mate nonrandomly with respect to alleles underlying immunity. One hypothesis proposes that this is advantageous because nonrandom mating can lead to offspring with superior parasite resistance. We investigate this hypothesis, generalizing previous models in four ways: First, rather than only examining invasibility of modifiers of nonrandom mating, we identify evolutionarily stable strategies. Second, we study coevolution of both haploid and diploid hosts and parasites. Third, we allow for maternal parasite transmission. Fourth, we allow for many alleles at the interaction locus. We find that evolutionarily stable rates of assortative or disassortative mating are usually near zero or one. However, for one case, in which assumptions most closely match the major histocompatibility complex (MHC) system, intermediate rates of disassortative mating can evolve. Across all cases, with haploid hosts, evolution proceeds toward complete disassortative mating, whereas with diploid hosts either assortative or disassortative mating can evolve. Evolution of nonrandom mating is much less affected by the ploidy of parasites. For the MHC case, maternal transmission of parasites, because it creates an advantage to producing offspring that differ from their parents, leads to higher evolutionarily stable rates of disassortative mating. Lastly, with more alleles at the interaction locus, disassortative mating evolves to higher levels. DOI
440. Herdegen, M; Alexander, HJ; Babik, W; Mavarez, J; Breden, F; Radwan, J.Population structure of guppies in north-eastern Venezuela, the area of putative incipient speciation.BMC Evolutionary Biology, 2014, 14 Population structure of guppies in north-eastern Venezuela, the area of putative incipient speciation
Gene flow; Introgression; Reproductive barriers; Sexual selection; mtDNA; Microsatellites
Background: Geographic barriers to gene flow and divergence among populations in sexual traits are two important causes of genetic isolation which may lead to speciation. Genetic isolation may be facilitated if these two mechanisms act synergistically. The guppy from the Cumana region (within the Cariaco drainage) of eastern Venezuela has been previously described as a case of incipient speciation driven by sexual selection, significantly differentiated in sexual colouration and body shape from the common guppy, Poecilia reticulata. The latter occurs widely in northern Venezuela, including the south-eastern side of Cordillera de la Costa, where it inhabits streams belonging to the San Juan drainage. Here, we present molecular and morphological analyses of differentiation among guppy populations in the Cariaco and San Juan drainages. Our analyses are based on a 953 bp long mtDNA fragment, a set of 15 microsatellites (519 fish from 20 populations), and four phenotypic traits. Results: Both microsatellite and mtDNA data showed that guppies inhabiting the two drainages are characterised by a significant genetic differentiation, but a higher proportion of the genetic variance was distributed among populations within regions. Most guppies in the Cariaco drainage had mtDNA from a distinct lineage, but we also found evidence for widespread introgression of mtDNA from the San Juan drainage into the Cariaco drainage. Phenotypically, populations in the two regions differed significantly only in the number of black crescents. Phenotypic clustering did not support existence of two distinct groupings, but indicated a degree of distinctiveness of Central Cumana (CC) population. However, CC population showed little differentiation at the neutral markers from the proximate populations within the Cariaco drainage. Conclusions: Our findings are consistent with only partial genetic isolation between the two geographic regions and indicate that the geographic barrier of Cordillera de la Costa has not played an important role in strengthening the incomplete pre-zygotic reproductive barrier between Cumana and common guppy. Significant phenotypic differentiation between genetically similar (in terms of neutral variation) populations suggests that mate choice can maintain divergence at sexually selected traits despite gene flow. However, neither genetic nor phenotypic clustering supported delineation of two species within the region. DOI
439. Heupel, MR; Knip, DM; Simpfendorfer, CA; Dulvy, NK.Sizing up the ecological role of sharks as predators.Marine Ecology Progress Series, 2014, 495: 291-298 Sizing up the ecological role of sharks as predators
Top-down control; Predator-prey interactions; Predation risk; Home range; Ecology of fear
The decline of predators in a variety of ecosystems has transformed community structure through mesopredator release and trophic cascades. Elasmobranch fishes, one of the earth's most ubiquitous and diverse clade of predatory species, provide a model group for defining marine predator roles. We consider whether the ecological predatory role of sharks is adequately defined by terrestrial-derived notions of apex-and mesopredation. Indeterminate growth and ontogenetic diet shifts may mean species-level classification of predatory roles is inadequate. We propose that examining the trophic level and body size of species might be the most pragmatic and informative way to define the ecological roles of predators. DOI
438. Kissel, AM; Palen, WJ; Govindarajulu, P; Bishop, CA.Quantifying Ecological Life Support: The Biological Efficacy of Alternative Supplementation Strategies for Imperiled Amphibian Populations.Conservation Letters, 2014, 7: 441-450 Quantifying Ecological Life Support: The Biological Efficacy of Alternative Supplementation Strategies for Imperiled Amphibian Populations
Population supplementation; matrix models; captive breeding; head-start; amphibian conservation; species recovery
Global biodiversity loss has prompted diverse efforts to stem or reverse declines for many species. Such efforts are often implemented before the efficacy of alternative management actions is quantified. Here, we use matrix models to compare the effectiveness of two supplementation strategies, head-starting early life stages and captive breeding for reintroduction, at reducing extinction risk of declining amphibians. We use the imperiled Oregon spotted frog (Rana pretiosa) as a case study and find that when supplementation occurs after metamorphosis, captive breeding is more effective at reducing extinction risk than head-starting, but the difference declines with increasing supplementation effort. We also find that captive breeding with release as larvae yields similar reductions in extinction risk, and is two orders of magnitude more effective at reducing extinction probabilities than head-starting the same stage. Our results highlight that even basic demographic data can be leveraged to assess tradeoffs among alternative supplementation strategies. DOI
437. M Berbee, L Le Renard, D Carmean.Online access to the Kalgutkar and Jansonius database of fossil fungi.Palynology, 2014, 39: 103-109 Online access to the Kalgutkar and Jansonius database of fossil fungi
Ascomycota, calibration, conidia, database, fungal evolution, fungal fossils, geological time
An important compendium of fossil fungi is now publicly available through a searchable online database. The original compendium was the work of Kalgutkar and Jansonius, who combed through 238 references and collated and annotated published descriptions for 1783 taxa of fungal fossils. By translating these data to a FileMaker Pro database and to the Web, we increase options for searching, sorting, annotating and updating this information. Database search results provide lists of names, ages and thumbnail images of palynomorphs. An individual record from the results list can be expanded in a new browser window to show a complete description for a taxon. The database is timely because developments in molecular systematics are helping to place spore characters in a phylogenetic framework. Some of the previously ambiguous fossil fungi can now be placed into phylogenetic lineages. We anticipate that the Web version of the data will serve as a convenient entry point into the fungal fossil record, leading to integration of more information from fossils into fungal phylogenies.Website DOI
436. Margold, M; Stroeven, AP; Clague, JJ; Heyman, J.Timing of terminal Pleistocene deglaciation at high elevations in southern and central British Columbia constrained by Be-10 exposure dating.Quat. Sci. Rev., 2014, 99: 193-202 Timing of terminal Pleistocene deglaciation at high elevations in southern and central British Columbia constrained by Be-10 exposure dating
Cordilleran Ice Sheet; Be-10 exposure dating; Deglaciation
The Cordilleran Ice Sheet (CIS) covered most of British Columbia and southern Yukon Territory at the local Last Glacial Maximum (ILGM) during Marine Oxygen Isotope Stage 2. However, its subsequent demise is not well understood, particularly at high elevations east of its ocean-terminating margin. We present Be-10 exposure ages from two high-elevation sites in southern and central British Columbia that help constrain the time of initial deglaciation at these sites. We sampled granodiorite erratics at elevations of 2126-2230 m a.s.l. in the Marble Range and 1608-1785 m a.s.l. in the Telkwa Range at the western margin of the Interior Plateau. The erratics at both sites are near ice-marginal meltwater channels that delineate the local ice surface slope and thus the configuration of the ice sheet during deglaciation. The locations of the erratics and their relations to meltwater channels ensure that the resulting Be-10 ages date CIS deglaciation and not the retreat of local montane glaciers. Our sample sites emerged above the surface of the CIS as its divide migrated westward from the Interior Plateau to the axis of the Coast Mountains. Two of the four samples from the summit area of the Marble Range yielded apparent exposure ages of 14.0 +/- 0.7 and 15.2 +/- 0.8 ka. These ages are 1.8-3.0 ka younger than the well-established ILGM age of ca 17 ka for the Puget lobe of the CIS in Washington State; they are 1.7 ka younger than the ILGM age for the Puget lobe if a snow-shielding correction to their uncertainty-weighted mean age is applied. The other two samples yielded much older apparent exposure ages (20.6 +/- 1.4 and 33.0 +/- 1.5 ka), indicating the presence of inherited isotopes. Four samples collected from the summit area of the Telkwa Range in the Hazelton Mountains yielded well clustered apparent exposure ages of 10.1 +/- 0.6, 10.2 +/- 0.7, 10.4 +/- 0.5, and 11.5 +/- 1.1 ka. Significant present-day snow cover introduces a large uncertainty in the apparent exposure ages from this site. A snow-shielding correction based on present-day snow cover data increases the uncertainty-weighted mean exposure age of the Telkwa Range erratics to 12.4 +/- 0.7 ka, consistent with deglacial C-14 ages from areas near sea level to the west. Our exposure ages show a thinning of the southern portion of the CIS shortly after the ILGM and persistence of a remnant mountain ice cap in the central Coast Mountains into the Younger Dryas Chronozone. Our data also show that the summit area of the Marble Range was ice-covered during the ILGM. The presence of an ice body of considerable dimension in north-central British Columbia until, or possibly even after, the Younger Dryas highlights the need for geomorphological and geochronological studies of the ice dispersal centre over the Skeena Mountains in northwest British Columbia and the need for better understanding of the response of the CIS to Lateglacial climate fluctuations. (C) 2014 Elsevier Ltd. All rights reserved. DOI
434. McFarlane, HE; Watanabe, Y; Yang, WL; Huang, Y; Ohlrogge, J; Samuels, AL.Golgi- and Trans-Golgi Network-Mediated Vesicle Trafficking Is Required for Wax Secretion from Epidermal Cells.Plant Physiology, 2014, 164: 1250-1260 Golgi- and Trans-Golgi Network-Mediated Vesicle Trafficking Is Required for Wax Secretion from Epidermal Cells
Lipid secretion from epidermal cells to the plant surface is essential to create the protective plant cuticle. Cuticular waxes are unusual secretory products, consisting of a variety of highly hydrophobic compounds including saturated very-long-chain alkanes, ketones, and alcohols. These compounds are synthesized in the endoplasmic reticulum (ER) but must be trafficked to the plasma membrane for export by ATP-binding cassette transporters. To test the hypothesis that wax components are trafficked via the endomembrane system and packaged in Golgi-derived secretory vesicles, Arabidopsis (Arabidopsis thaliana) stem wax secretion was assayed in a series of vesicle-trafficking mutants, including gnom like1-1 (gnl1-1), transport particle protein subunit120-4, and echidna (ech). Wax secretion was dependent upon GNL1 and ECH. Independent of secretion phenotypes, mutants with altered ER morphology also had decreased wax biosynthesis phenotypes, implying that the biosynthetic capacity of the ER is closely related to its structure. These results provide genetic evidence that wax export requires GNL1- and ECH-dependent endomembrane vesicle trafficking to deliver cargo to plasma membrane-localized ATP-binding cassette transporters. DOI
433. O'Regan, SM; Palen, WJ; Anderson, SC.Climate warming mediates negative impacts of rapid pond drying for three amphibian species.Ecology, 2014, 95: 845-855 Climate warming mediates negative impacts of rapid pond drying for three amphibian species
Spea intermontana; global warming; wetland drying; metamorphosis; phenotypic plasticity; Rana aurora; Pseudacris regilla; life history
Anthropogenic climate change will present both opportunities and challenges for pool-breeding amphibians. Increased water temperature and accelerated drying may directly affect larval growth, development, and survival, yet the combined effects of these processes on larvae with future climate change remain poorly understood. Increased surface temperatures are projected to warm water and decrease water inputs, leading to earlier and faster wetland drying. So it is often assumed that larvae will experience negative synergistic impacts with combined warming and drying. However, an alternative hypothesis is that warming-induced increases in metabolic rate and aquatic resource availability might compensate for faster drying rates, generating antagonistic larval responses. We conducted a mesocosm experiment to test the individual and interactive effects of pool permanency (permanent vs. temporary) and water temperature (ambient vs. +similar to 3 degrees C) on three anurans with fast-to-slow larval development rates (Great Basin spadefoot [Spea intermontana], Pacific chorus frog [Pseudacris regilla], and northern red-legged frog [Rana aurora]). We found that although tadpoles in warmed pools reached metamorphosis 15-17 days earlier, they did so with little cost (<2 mm) to size, likely due to greater periphyton growth in warmed pools easing drying-induced resource competition. Warming and drying combined to act antagonistically on early growth (P = 0.06) and survival (P = 0.06), meaning the combined impact was less than the sum of the individual impacts. Warming and drying acted additively on time to and size at metamorphosis. These nonsynergistic impacts may result from cotolerance of larvae to warming and drying, as well as warming helping to offset negative impacts of drying. Our results indicate that combined pool warming and drying may not always be harmful for larval amphibians. However, they also demonstrate that antagonistic responses are difficult to predict, which poses a challenge to proactive conservation and management. Our study highlights the importance of considering the nature of multiple stressor interactions as amphibians are exposed to an increasing number of anthropogenic threats. DOI
432. Palen, WJ; Sisk, TD; Ryan, ME; Arvai, JL; Jaccard, M; Salomon, AK; Homer-Dixon, T; Lertzman, KP.Consider the global impacts of oil pipelines.Nature, 2014, 510: 465-467 Consider the global impacts of oil pipelines
PubMed
431. Perry, CT; Murphy, GN; Kench, PS; Edinger, EN; Smithers, SG; Steneck, RS; Mumby, PJ.Changing dynamics of Caribbean reef carbonate budgets: emergence of reef bioeroders as critical controls on present and future reef growth potential.Proc. R. Soc. B-Biol. Sci., 2014, 281 Changing dynamics of Caribbean reef carbonate budgets: emergence of reef bioeroders as critical controls on present and future reef growth potential
coral reefs; Caribbean; carbonate budgets; bioerosion; parrotfish; Diadema
Coral cover has declined rapidly on Caribbean reefs since the early 1980s, reducing carbonate production and reef growth. Using a cross-regional dataset, we show that widespread reductions in bioerosion rates-a key carbonate cycling process-have accompanied carbonate production declines. Bioerosion by parrotfish, urchins, endolithic sponges and microendoliths collectively averages 2 G (where G = kg CaCO3 m(-2) yr(-1)) (range 0.96-3.67 G). This rate is at least 75% lower than that reported from Caribbean reefs prior to their shift towards their present degraded state. Despite chronic overfishing, parrotfish are the dominant bioeroders, but erosion rates are reduced from averages of approximately 4 to 1.6 G. Urchin erosion rates have declined further and are functionally irrelevant to bioerosion on most reefs. These changes demonstrate a fundamental shift in Caribbean reef carbonate budget dynamics. To-date, reduced bioerosion rates have partially offset carbonate production declines, limiting the extent to which more widespread transitions to negative budget states have occurred. However, given the poor prognosis for coral recovery in the Caribbean and reported shifts to coral community states dominated by slower calcifying taxa, a continued transition from production to bioerosion-controlled budget states, which will increasingly threaten reef growth, is predicted. DOI
430. Schuetz, M; Benske, A; Smith, RA; Watanabe, Y; Tobimatsu, Y; Ralph, J; Demura, T; Ellis, B; Samuels, AL.Laccases Direct Lignification in the Discrete Secondary Cell Wall Domains of Protoxylem.Plant Physiology, 2014, 166: 798-U489 Laccases Direct Lignification in the Discrete Secondary Cell Wall Domains of Protoxylem
Plants precisely control lignin deposition in spiral or annular secondary cell wall domains during protoxylem tracheary element (TE) development. Because protoxylem TEs function to transport water within rapidly elongating tissues, it is important that lignin deposition is restricted to the secondary cell walls in order to preserve the plasticity of adjacent primary wall domains. The Arabidopsis (Arabidopsis thaliana) inducible VASCULAR NAC DOMAIN7 (VND7) protoxylem TE differentiation system permits the use of mutant backgrounds, fluorescent protein tagging, and high-resolution live-cell imaging of xylem cells during secondary cell wall development. Enzymes synthesizing monolignols, as well as putative monolignol transporters, showed a uniform distribution during protoxylem TE differentiation. By contrast, the oxidative enzymes LACCASE4 (LAC4) and LAC17 were spatially localized to secondary cell walls throughout protoxylem TE differentiation. These data support the hypothesis that precise delivery of oxidative enzymes determines the pattern of cell wall lignification. This view was supported by lac4lac17 mutant analysis demonstrating that laccases are necessary for protoxylem TE lignification. Overexpression studies showed that laccases are sufficient to catalyze ectopic lignin polymerization in primary cell walls when exogenous monolignols are supplied. Our data support a model of protoxylem TE lignification in which monolignols are highly mobile once exported to the cell wall, and in which precise targeting of laccases to secondary cell wall domains directs lignin deposition. DOI
429. Stroeven, AP; Fabel, D; Margold, M; Clague, JJ; Xu, S.Investigating absolute chronologies of glacial advances in the NW sector of the Cordilleran Ice Sheet with terrestrial in situ cosmogenic nuclides.Quat. Sci. Rev., 2014, 92: 429-443 Investigating absolute chronologies of glacial advances in the NW sector of the Cordilleran Ice Sheet with terrestrial in situ cosmogenic nuclides
Cordilleran Ice Sheet; Exposure dating; Yukon Territory; Pleistocene glaciations
Geologic mapping in Yukon Territory, Canada, over the past 100 years has revealed a consistent pattern of diminishing Cordilleran Ice Sheet (CIS) extent during successively younger glaciations. Although this pattern is generally accepted, there is still much uncertainty about the number of glaciations, their ages, and the dynamics of the different lobes that constituted the digitate ice sheet margin, their subglacial thermal regimes, and ice thicknesses. We address uncertainties in the timing of glaciation using cosmogenic nuclide exposure dating at key localities that straddle several major lobes of the CIS in west-central Yukon Territory. Differences in exposure duration within what are thought to be the same map units are perhaps due to inheritance (older than expected), but more likely result from postglacial shielding (younger than expected) or surface erosion. Despite a significant spread in exposure durations on moraines and within map units, and tending to rely on longest exposure durations on moraines due to postglacial degradation and shielding, our results indicate that the McConnell glacial advance occurred during Marine Oxygen Isotope Stage (MIS) 2, judging from oldest minimum apparent exposure ages of 15.7 +/- 1.5 and 17.7 +/- 1.6 ka, a Gladstone glacial advance occurred before 51.8 +/- 4.7 ka (MIS 4) and Reid glacial advances before 79.8 +/- 7.3 and 82.8 +/- 7.5 ka (consistent with MIS 6). Traces of even older glacial advances predate 100 ka (107.5 +/- 9.9-154.3 +/- 14.2 ka). (C) 2013 Elsevier Ltd. All rights reserved. DOI
428. Sunday, JM; Popovic, I; Palen, WJ; Foreman, MGG; Hart, MW.Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.Molecular Ecology, 2014, 23: 5036-5047 Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer
larval dispersal; marine connectivity; oceanographic circulation model; population genetics
Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks. DOI PubMed
427. Suraci, JP; Clinchy, M; Zanette, LY; Currie, CMA; Dill, LM.Mammalian mesopredators on islands directly impact both terrestrial and marine communities.Oecologia, 2014, 176: 1087-1100 Mammalian mesopredators on islands directly impact both terrestrial and marine communities
Predator-prey interactions; Marine food webs; Mesopredator release; Nest predation; Trophic cascades
Medium-sized mammalian predators (i.e. mesopredators) on islands are known to have devastating effects on the abundance and diversity of terrestrial vertebrates. Mesopredators are often highly omnivorous, and on islands, may have access not only to terrestrial prey, but to marine prey as well, though impacts of mammalian mesopredators on marine communities have rarely been considered. Large apex predators are likely to be extirpated or absent on islands, implying a lack of top-down control of mesopredators that, in combination with high food availability from terrestrial and marine sources, likely exacerbates their impacts on island prey. We exploited a natural experiment-the presence or absence of raccoons (Procyon lotor) on islands in the Gulf Islands, British Columbia, Canada-to investigate the impacts that this key mesopredator has on both terrestrial and marine prey in an island system from which all native apex predators have been extirpated. Long-term monitoring of song sparrow (Melospiza melodia) nests showed raccoons to be the predominant nest predator in the Gulf Islands. To identify their community-level impacts, we surveyed the distribution of raccoons across 44 Gulf Islands, and then compared terrestrial and marine prey abundances on six raccoon-present and six raccoon-absent islands. Our results demonstrate significant negative effects of raccoons on terrestrial, intertidal, and shallow subtidal prey abundance, and point to additional community-level effects through indirect interactions. Our findings show that mammalian mesopredators not only affect terrestrial prey, but that, on islands, their direct impacts extend to the surrounding marine community. DOI PubMed
426. Swain, NR; Hocking, MD; Harding, JN; Reynolds, JD.Effects of salmon on the diet and condition of stream-resident sculpins.Canadian Journal of Fisheries and Aquatic Sciences, 2014, 71: 521-532 Effects of salmon on the diet and condition of stream-resident sculpins
Pacific salmon (Oncorhynchus spp.) can subsidize freshwater food webs with marine-derived nutrients from their eggs, juveniles, and carcasses. However, trophic interactions between spawning salmon and freshwater fish across natural gradients in salmon subsidies remain unclear. We tested how salmon affected the diets and condition of two dominant freshwater consumers - prickly and coastrange sculpins (Cottus asper and Cottus aleuticus, respectively) - across a wide gradient of pink salmon (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) biomass from 33 streams in the Great Bear Rainforest of British Columbia, Canada. Sculpin diets shifted from invertebrates and juvenile salmonids to salmon eggs when salmon arrived in autumn, with salmon-derived nutrient contributions to diets and sculpin condition increasing with increasing biomass of spawning salmon among streams. Season, habitat, and individual sculpin body size and species also mediated the effects of salmon on sculpin diet as inferred from their carbon and nitrogen stable isotope signatures. This study shows the timing and pathways by which spawning salmon influence the diets and condition of freshwater consumers, and some of the individual and environmental factors that can regulate uptake of salmon nutrients in streams, thus informing ecosystem-based management. DOI
425. Tang, YT; Ge, BX; Sen, D; Yu, HZ.Functional DNA switches: rational design and electrochemical signaling.Chemical Society Reviews, 2014, 43: 518-529 Functional DNA switches: rational design and electrochemical signaling
Recent developments in nanoscience research have demonstrated that DNA switches (rationally designed DNA nanostructures) constitute a class of versatile building blocks for the fabrication and assembly of electronic devices and sensors at the nanoscale. Functional DNA sequences and structures such as aptamers, DNAzymes, G-quadruplexes, and i-motifs can be readily prepared in vitro, and subsequently adapted to an electrochemical platform by coupling with redox reporters. The conformational or conduction switching of such electrode-bound DNA modules in response to an external stimulus can then be monitored by conventional voltammetric measurements. In this review, we describe how we are able to design and examine functional DNA switches, particularly those systems that utilize electrochemical signaling. We also discuss different available options for labeling functional DNA with redox reporters, and comment on the function-oriented signaling pathways. DOI
424. Tissier, ML; Williams, TD; Criscuolo, F.Maternal Effects Underlie Ageing Costs of Growth in the Zebra Finch (Taeniopygia guttata).PLOS One, 2014, 9 Maternal Effects Underlie Ageing Costs of Growth in the Zebra Finch (Taeniopygia guttata)
Maternal effects provide a mechanism to adapt offspring phenotype and optimize the mother's fitness to current environmental conditions. Transferring steroids to the yolk is one way mothers can translate environmental information into potential adaptive signals for offspring. However, maternally-derived hormones might also have adverse effects for offspring. For example, recent data in zebra finch chicks suggested that ageing related-processes (i.e. oxidative stress and telomere loss) were increased after egg-injection of corticosterone (CORT). Still, we have few experimental data describing the effect of maternal effects on the growth-ageing trade-off in offspring. Here, we chronically treated pre-laying zebra finch females (Taeniopygia guttata) with 17-beta-estradiol (E-2) or CORT, and followed offspring growth and cellular ageing rates (oxidative stress and telomere loss). CORT treatment decreased growth rate in male chicks and increased rate of telomere loss in mothers and female offspring. E-2 increased body mass gain in male offspring, while reducing oxidative stress in both sexes but without affecting telomere loss. Since shorter telomeres were previously found to be a proxy of individual lifespan in zebra finches, maternal effects may, through pleiotropic effects, be important determinants of offspring life-expectancy by modulating ageing rate during embryo and post-natal growth. DOI
423. Tsui, MTK; Blum, JD; Finlay, JC; Balogh, SJ; Nollet, YH; Palen, WJ; Power, ME.Variation in Terrestrial and Aquatic Sources of Methylmercury in Stream Predators as Revealed by Stable Mercury Isotopes.Environmental Science & Technology, 2014, 48: 10128-10135 Variation in Terrestrial and Aquatic Sources of Methylmercury in Stream Predators as Revealed by Stable Mercury Isotopes
Mercury (Hg) is widely distributed in the environment, and its organic form, methylmercury (MeHg), can extensively bioaccumulate and biomagnify in aquatic and terrestrial food webs. Concentrations of MeHg in organisms are highly variable, and the sources in natural food webs are often not well understood. This study examined stable isotope ratios of MeHg (mass-dependent fractionation, as delta Hg-202(MeHg); and mass-independent fractionation, as Delta Hg-199(MeHg)) in benthic invertebrates, juvenile steelhead trout (Oncorhynchus mykiss), and water striders (Gerris remigis) along a stream productivity gradient, as well as carnivorous terrestrial invertebrates, in a forested watershed at the headwater of South Fork Eel River in northern California. Throughout the sampling sites, delta Hg-202(MeHg) (after correction due to the effect of MeHg photodegradation) was significantly different between benthic (median = -1.40 parts per thousand; range, -2.34 to -0.78 parts per thousand; total number of samples = 29) and terrestrial invertebrates (median = +0.51 parts per thousand; range, -0.37 to +1.40 parts per thousand; total number of samples = 9), but no major difference between these two groups was found for Delta Hg-199(MeHg). Steelhead trout (52 individual fishes) have MeHg of predominantly aquatic origins, with a few exceptions at the upstream locations (e.g., 1 fish collected in a tributary had a purely terrestrial MeHg source and 4 fishes had mixed aquatic and terrestrial MeHg sources). Water striders (seven pooled samples) derive MeHg largely from terrestrial sources throughout headwater sections. These data suggest that direct terrestrial subsidy (e.g., terrestrial invertebrates falling into water) can be important for some stream predators in headwater streams and could represent an important means of transfer of terrestrially derived MeHg (e.g., in situ methylation within forests, atmospheric sources) to aquatic ecosystems. Moreover, these findings show that terrestrial subsidies can enhance MeHg bioaccumulation of consumers in headwater streams where aqueous MeHg levels are very low. DOI PubMed
422. von Schalburg, KR; Gowen, BE; Messmer, AM; Davidson, WS; Koop, BF.Sex-specific expression and localization of aromatase and its regulators during embryonic and larval development of Atlantic salmon.Comparative Biochemistry and Physiology B-Biochemistry & Molecular Biology, 2014, 168: 33-44 Sex-specific expression and localization of aromatase and its regulators during embryonic and larval development of Atlantic salmon
Gonad; Gut; Kidney; Neural cord; Skeletal muscle
The products of dax1, foxl2a and mis have each been shown to have proliferative and/or differentiative activities during mammalian organogenesis. These factors also play a role in regulating the biosynthesis of estrogen, particularly by modulating the activity of aromatase cyp19a. We demonstrate the transcription and translation of these genes during salmon embryogenesis. We were able to track sex-specific differences in these processes through accurate determination of the sex of each embryo and larva examined from genotyped microsatellites. We detected sex- and stage-specific immunolabeling of the embryonic gut, kidney, gonads, neural cord and skeletal muscle by DAX-1, FOXL2A and MIS. These results indicate the potential of these factors to mediate proliferation and/or differentiation programs during development of these tissues. As well, immunolabeling of skeletal muscle by CYP19B1 throughout the study reveals probable neurogenic activity associated with peripheral radial glial cells and the growing embryonic musculature. (C) 2013 Elsevier Inc. All rights reserved. DOI
421. Yuzwa, SA; Vocadlo, DJ.O-GlcNAc and neurodegeneration: biochemical mechanisms and potential roles in Alzheimer's disease and beyond.Chem. Soc. Rev., 2014, 43: 6839-6858 O-GlcNAc and neurodegeneration: biochemical mechanisms and potential roles in Alzheimer's disease and beyond
Alzheimer disease (AD) is a growing problem for aging populations worldwide. Despite significant efforts, no therapeutics are available that stop or slow progression of AD, which has driven interest in the basic causes of AD and the search for new therapeutic strategies. Longitudinal studies have clarified that defects in glucose metabolism occur in patients exhibiting Mild Cognitive Impairment (MCI) and glucose hypometabolism is an early pathological change within AD brain. Further, type 2 diabetes mellitus (T2DM) is a strong risk factor for the development of AD. These findings have stimulated interest in the possibility that disrupted glucose regulated signaling within the brain could contribute to the progression of AD. One such process of interest is the addition of O-linked N-acetylglucosamine (O-GlcNAc) residues onto nuclear and cytoplasmic proteins within mammals. O-GlcNAc is notably abundant within brain and is present on hundreds of proteins including several, such as tau and the amyloid precursor protein, which are involved in the pathophysiology AD. The cellular levels of O-GlcNAc are coupled to nutrient availability through the action of just two enzymes. O-GlcNAc transferase (OGT) is the glycosyltransferase that acts to install O-GlcNAc onto proteins and O-GlcNAcase (OGA) is the glycoside hydrolase that acts to remove O-GlcNAc from proteins. Uridine 5'-diphosphate-N-acetylglucosamine (UDP-GlcNAc) is the donor sugar substrate for OGT and its levels vary with cellular glucose availability because it is generated from glucose through the hexosamine biosynthetic pathway (HBSP). Within the brains of AD patients O-GlcNAc levels have been found to be decreased and aggregates of tau appear to lack O-GlcNAc entirely. Accordingly, glucose hypometabolism within the brain may result in disruption of the normal functions of O-GlcNAc within the brain and thereby contribute to downstream neurodegeneration. While this hypothesis remains largely speculative, recent studies using different mouse models of AD have demonstrated the protective benefit of pharmacologically increased brain O-GlcNAc levels. In this review we summarize the state of knowledge in the area of O-GlcNAc as it pertains to AD while also addressing some of the basic biochemical roles of O-GlcNAc and how these might contribute to protecting against AD and other neurodegenerative diseases. DOI PubMed
420. Aloni, R; Foster, A; Mattsson, J.TRANSFUSION TRACHEIDS IN THE CONIFER LEAVES OF THUJA PLICATA (CUPRESSACEAE) ARE DERIVED FROM PARENCHYMA AND THEIR DIFFERENTIATION IS INDUCED BY AUXIN.American Journal of Botany, 2013, 100: 1949-1956 TRANSFUSION TRACHEIDS IN THE CONIFER LEAVES OF THUJA PLICATA (CUPRESSACEAE) ARE DERIVED FROM PARENCHYMA AND THEIR DIFFERENTIATION IS INDUCED BY AUXIN
VASCULAR DIFFERENTIATION; TRANSPORT INHIBITORS; LEAF VEIN; TISSUE; GIBBERELLIN; ARABIDOPSIS; FOLIAR; PHLOEM; PINUS
Premise of the study: Conifer leaves are characterized by the differentiation of transfusion tracheids either adjacent to the vascular bundle or away from bundles. Toward uncovering the mechanism regulating this differentiation, we tested the hypotheses that transfusion tracheids differentiate from parenchyma rather than from procambium and that auxin acts as an inducer of this process. Methods: Transfusion tracheids were studied at different developmental stages in both dissected and cleared juvenile and mature leaves. Auxin accumulation was induced by application of either auxin to juvenile leaves or of auxin transport inhibitors in lanolin to stems. Key results: Transfusion tracheids originate from parenchyma cells during late stages of leaf development, after the activity of the procambium has ceased. Transfusion tracheids differentiate also in the leaf tip, a region in which there are no procambial cells. Application of either auxin or auxin transport inhibitors resulted in a significant increase in transfusion tracheids in leaves. Disruption of the leaf vascular bundle combined with auxin application resulted in direct differentiation of transfusion tracheids from parenchyma cells; the regeneration of a vascular bundle around the disruption was polar and supports both hypotheses. Conclusions: The results provide experimental support for a parenchymatic origin of the transfusion tracheids in a conifer leaf and for auxin acting as an inducer of these cells. Our results suggest a new model in which auxin production in the leaf apex continues after primary tracheids and parenchyma cells have differentiated, and this late auxin flow induces transfusion tracheids from parenchyma cells. DOI
419. Anderson, SC; Cooper, AB; Dulvy, NK.Ecological prophets: quantifying metapopulation portfolio effects.Methods in Ecology and Evolution, 2013, 4: 971-981 Ecological prophets: quantifying metapopulation portfolio effects
TAYLORS POWER-LAW; DIVERSITY-STABILITY RELATIONSHIPS; STATISTICAL INEVITABILITY; TEMPORAL STABILITY; FISH POPULATIONS; TIME-SERIES; BIODIVERSITY; VARIABILITY; DYNAMICS; PRODUCTIVITY
1. A financial portfolio metaphor is often used to describe how population diversity can increase temporal stability of a group of populations. The portfolio effect (PE) refers to the stabilizing effect from a population acting as a group or portfolio' of diverse subpopulations instead of a single homogeneous population or asset'. A widely used measure of the PE (the average-CV PE) implicitly assumes that the slope (z) of a log-log plot of mean temporal abundance and variance (Taylor's power law) equals two. 2. Existing theory suggests an additional unexplored empirical PE that accounts for z, the mean-variance PE. We use a theoretical and empirical approach to explore the strength and drivers of the PE for metapopulations when we account for Taylor's power law compared with when we do not. Our empirical comparison uses data from 51 metapopulations and 1070 subpopulations across salmon, moths and reef fishes. 3. Ignoring Taylor's power law may overestimate the stabilizing effect of population diversity for metapopulations. The disparity between the metrics is greatest at low z values where the average-CV PE indicates a strong PE. Compared with the mean-variance method, the average-CV PE estimated a stronger PE in 84% of metapopulations by up to sevenfold. The divergence between the methods was strongest for reef fishes (1.0 < z < 1.7) followed by moths (1.5 < z < 1.9). The PEs were comparable for salmon where z approximate to 2. 4. We outline practical recommendations for estimating ecological PEs based on research questions, study systems and available data. Because most PEs were stabilizing and diversity can be slow to restore, our meta-analysis of metapopulations suggests that the safest management approach is to conserve biological complexity. DOI
418. Artelle, KA; Anderson, SC; Cooper, AB; Paquet, PC; Reynolds, JD; Darimont, CT.Confronting Uncertainty in Wildlife Management: Performance of Grizzly Bear Management.PLOS One, 2013, 8 Confronting Uncertainty in Wildlife Management: Performance of Grizzly Bear Management
DECISION-MAKING; CONSERVATION; FISHERIES; POPULATION; MORTALITY
Scientific management of wildlife requires confronting the complexities of natural and social systems. Uncertainty poses a central problem. Whereas the importance of considering uncertainty has been widely discussed, studies of the effects of unaddressed uncertainty on real management systems have been rare. We examined the effects of outcome uncertainty and components of biological uncertainty on hunt management performance, illustrated with grizzly bears (Ursus arctos horribilis) in British Columbia, Canada. We found that both forms of uncertainty can have serious impacts on management performance. Outcome uncertainty alone - discrepancy between expected and realized mortality levels - led to excess mortality in 19% of cases (population-years) examined. Accounting for uncertainty around estimated biological parameters (i.e., biological uncertainty) revealed that excess mortality might have occurred in up to 70% of cases. We offer a general method for identifying targets for exploited species that incorporates uncertainty and maintains the probability of exceeding mortality limits below specified thresholds. Setting targets in our focal system using this method at thresholds of 25% and 5% probability of overmortality would require average target mortality reductions of 47% and 81%, respectively. Application of our transparent and generalizable framework to this or other systems could improve management performance in the presence of uncertainty. DOI
417. Barker, MK; Rose, DR.Specificity of Processing alpha-Glucosidase I Is Guided by the Substrate Conformation CRYSTALLOGRAPHIC AND IN SILICO STUDIES.J. Biol. Chem., 2013, 288: 13563-13574 Specificity of Processing alpha-Glucosidase I Is Guided by the Substrate Conformation CRYSTALLOGRAPHIC AND IN SILICO STUDIES
Processing alpha-glucosidase I (GluI) is a key member of the eukaryotic N-glycosylation processing pathway, selectively catalyzing the first glycoprotein trimming step in the endoplasmic reticulum. Inhibition of GluI activity impacts the infectivity of enveloped viruses; however, despite interest in this protein from a structural, enzymatic, and therapeutic standpoint, little is known about its structure and enzymatic mechanism in catalysis of the unique glycan substrate Glc(3)Man(9)GlcNAc(2). The first structural model of eukaryotic GluI is here presented at 2-angstrom resolution. Two catalytic residues are proposed, mutations of which result in catalytically inactive, properly folded protein. Using Autodocking methods with the known substrate and inhibitors as ligands, including a novel inhibitor characterized in this work, the active site of GluI was mapped. From these results, a model of substrate binding has been formulated, which is most likely conserved in mammalian GluI. DOI PubMed
416. Baylis, T; Cierlik, I; Sundberg, E; Mattsson, J.SHORT INTERNODES/STYLISH genes, regulators of auxin biosynthesis, are involved in leaf vein development in Arabidopsis thaliana.New Phytologist, 2013, 197: 737-750 SHORT INTERNODES/STYLISH genes, regulators of auxin biosynthesis, are involved in leaf vein development in Arabidopsis thaliana
Arabidopsis; auxin; cotyledon; leaf; SHORT INTERNODES; STYLISH; vein
Leaves depend on highly developed venation systems to collect fixed carbon for transport and to distribute water. We hypothesized that local regulation of auxin biosynthesis plays a role in vein development. To this effect, we assessed the role of the SHORT INTERNODES/STYLISH (SHI/STY) gene family, zinc-finger transcription factors linked to regulation of auxin biosynthesis, in Arabidopsis thaliana leaf vein development. Gene functions were assessed by a combination of high-resolution spatio-temporal expression analysis of promoter-marker lines and phenotypic analysis of plants homozygous for single and multiple mutant combinations. The SHI/STY genes showed expression patterns with variations on a common theme of activity in incipient and developing cotyledon and leaf primordia, narrowing to apices and hydathode regions. Mutant analysis of single to quintuple mutant combinations revealed dose-dependent defects in vein patterning affecting multiple vein traits, most notably in cotyledons. Here we demonstrate that local regulation of auxin biosynthesis is an important aspect of leaf vein development. Our findings also support a model in which auxin synthesized at the periphery of primordia affects vein development. DOI
415. Burkholder, DA; Heithaus, MR; Fourqurean, JW; Wirsing, A; Dill, LM.Patterns of top-down control in a seagrass ecosystem: could a roving apex predator induce a behaviour-mediated trophic cascade?Journal of Animal Ecology, 2013, 82: 1192-1202 Patterns of top-down control in a seagrass ecosystem: could a roving apex predator induce a behaviour-mediated trophic cascade?
TURTLE CHELONIA-MYDAS; GREEN TURTLE; SEA-TURTLES; THALASSIA-TESTUDINUM; WESTERN-AUSTRALIA; SHARK BAY; SUBTROPICAL EMBAYMENT; PHOSPHORUS LIMITATION; COASTAL ECOSYSTEMS; GALEOCERDO-CUVIER
1. The loss of large-bodied herbivores and/or top predators has been associated with large-scale changes in ecosystems around the world, but there remain important questions regarding the contexts in which such changes are most likely and the mechanisms through which they occur, particularly in marine ecosystems. We used long-term exclusion cages to examine the effects of large grazers (sea cows, Dugong dugon; sea turtles Chelonia mydas) on seagrass community structure, biomass and nutrient dynamics. Experiments were conducted in habitats with high risk of predation (interior of shallow banks) and lower risk (edges of banks) to elucidate whether nonconsumptive (risk) effects of tiger sharks (Galeocerdo cuvier), a roving predator, structure herbivore impacts on seagrasses. In lower-risk habitats, excluding large herbivores resulted in increased leaf length for Cymodocea angustata and Halodule uninervis. C.angustata shoot densities nearly tripled when released from herbivory, while H.uninervis nearly disappeared from exclusion cages over the course of the study. We found no support for the hypothesis that grazing increases seagrass nutrient content. Instead, phosphorus content was higher in seagrasses within exclosures. This pattern is consistent with decreased light availability in the denser C.angustata canopies that formed in exclosures, and may indicate that competition for light led to the decrease in H.uninervis. Impacts of large grazers were consistent with a behaviour-mediated trophic cascade (BMTC) initiated by tiger sharks and mediated by risk-sensitive foraging by large grazers. Our results suggest that large-bodied grazers likely played important roles in seagrass ecosystem dynamics historically and that roving predators are capable of initiating a BMTC. Conservation efforts in coastal ecosystems must account for such interactions or risk unintended consequences. Video DOI
414. Caicedo, PA; Baron, OL; Perez, M; Alexander, N; Lowenberger, C; Ocampo, CB.Selection of Aedes aegypti (Diptera: Culicidae) strains that are susceptible or refractory to Dengue-2 virus.Canadian Entomologist, 2013, 145: 273-282 Selection of Aedes aegypti (Diptera: Culicidae) strains that are susceptible or refractory to Dengue-2 virus
QUANTITATIVE TRAIT LOCI; VECTOR COMPETENCE; GEOGRAPHIC STRAINS; ORAL INFECTION; TRANSMISSION; FECUNDITY; GENETICS
The vector competence (VC) of Aedes aegypti (Linnaeus) (Diptera: Culicidae) varies geographically and is affected by both genetic and environmental factors. Understanding the molecular mechanisms that influence VC may help develop novel control strategies. The selection of susceptible and refractory strains is the first step in this process. We collected immature A. aegypti in the field and established strains that were susceptible and refractory to Dengue-2 virus by isofamily selection through several generations. Infection was detected by immunofluorescence of head or midgut tissues to determine infection barriers and the % of VC by tissue. We selected three strains: Susceptible (Cali-S) (96.4% susceptible at F-19), Refractory with a midgut escape barrier (Cali-MEB) (44.1% refractory at F-15), and Refractory with a midgut infection barrier (Cali-MIB) (40% refractory at F-16). The effects of the infection were measured using Kaplan-Meier survival rates over the first seven generations. All selected strains showed a similar decrease in survival and in the number of eggs laid/female through the seven generations, suggesting that changes were a result of the selection process rather than the virus infection. The results of this study suggest that VC is associated with multiple genes, which have additive effects on susceptibility. DOI
412. Chung, IYW; Paetzel, M.Crystal Structures of Yellowtail Ascites Virus VP4 Protease TRAPPING AN INTERNAL CLEAVAGE SITE TRANS ACYL-ENZYME COMPLEX IN A NATIVE SER/LYS DYAD ACTIVE SITE.J. Biol. Chem., 2013, 288: 13068-13081 Crystal Structures of Yellowtail Ascites Virus VP4 Protease TRAPPING AN INTERNAL CLEAVAGE SITE TRANS ACYL-ENZYME COMPLEX IN A NATIVE SER/LYS DYAD ACTIVE SITE
Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala(716)) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser(633) as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water. DOI PubMed
411. Côté, IM.Inadvertent consequences of fishing: the case of the sex-changing shrimp.Journal of Animal Ecology, 2013, 82: 495-497 Inadvertent consequences of fishing: the case of the sex-changing shrimp
SELECTIVE HARVEST; CONSERVATION; POPULATIONS; CASCADES; DYNAMICS; ANIMALS; GROWTH; SIZE
The Hokkai shrimp Pandalus latirostris starts life as a male, but eventually turns into a female given the right size and social conditions. The traps used in the fishery targeting this species selectively retain the larger females, leaving a severely male-biased sex ratio in nature and social conditions that bear no resemblance to those that prompted (or prevented) sex change. Photo: Susumu Chiba Chiba, S., Yoshino, K., Kanaiwa, M., Kawajiri, T. & Goshima, S. (2013) Maladaptive sex ratio adjustment by a sex-changing shrimp in selective fishing environments. Journal of Animal Ecology, 82, 631640. Fishing can have many unintended consequences. In this issue, Chiba etal. () demonstrate that size-selective harvesting of a sex-changing shrimp effectively voids their normally adaptive adjustments to population sex ratio. The shrimp's decision' to change sex depends largely on the relative abundance of mature males and females in early summer, before fishing begins. However, fishing traps selectively retain females, leading to heavily male-biased sex ratios at the onset of autumn breeding that are different from the ratios that influenced sex-change decisions. Although this phenomenon is not yet expressed in catch trends, maladaptive sex-change decisions could ultimately affect population productivity and persistence. DOI
410. Côté, IM; Green, SJ; Hixon, MA.Predatory fish invaders: Insights from Indo-Pacific lionfish in the western Atlantic and Caribbean.Biological Conservation, 2013, 164: 50-61 Predatory fish invaders: Insights from Indo-Pacific lionfish in the western Atlantic and Caribbean
The invasion of western Atlantic marine habitats by two predatory Indo-Pacific lionfish, Pterois volitans and P. miles, has recently unfolded at an unprecedented rate, with ecological consequences anticipated to be largely negative. We take stock of recently accumulated knowledge about lionfish ecology and behaviour and examine how this information is contributing to our general understanding of the patterns and processes underpinning marine predator invasions, and to the specific issue of lionfish management. Lionfish were first reported off Florida in 1985. Since their establishment in The Bahamas in 2004, they have colonised 7.3 million km(2) of the western Atlantic and Caribbean region, and populations have grown exponentially at many locations. These dramatic increases potentially result from a combination of life-history characteristics of lionfish, including early maturation, early reproduction, anti-predatory defenses, unique predatory behaviour, and ecological versatility, as well as features of the recipient communities, including prey naivete, weak competitors, and native predators that are overfished and naive to lionfish. Lionfish have reduced the abundance of small native reef fishes by up to 95% at some invaded sites. Population models predict that culling can reduce lionfish abundance substantially, but removal rates must be high. Robust empirical estimates of the cost-effectiveness and effects of removal strategies are urgently needed because lionfish management will require a long-term, labour-intensive effort that may be possible only at local scales. The ultimate causes of the invasion were inadequate trade legislation and poor public awareness of the effects of exotic species on marine ecosystems. The lionfish invasion highlights the need for prevention, early detection, and rapid response to marine invaders. (C) 2013 Elsevier Ltd. All rights reserved. DOI
409. Crespi, B.Diametric gene-dosage effects as windows into neurogenetic architecture.Current Opinion in Neurobiology, 2013, 23: 143-151 Diametric gene-dosage effects as windows into neurogenetic architecture
17Q21.31 MICRODELETION SYNDROME; PRADER-WILLI-SYNDROME; BEHAVIORAL PHENOTYPES; BIPOLAR DISORDER; UP-REGULATION; KANSL1 CAUSE; AUTISM; SCHIZOPHRENIA; MICE; 16P11.2
Gene expression can be modulated in two opposite directions, towards higher or lower amounts of product. How do diametric changes in gene dosage influence neurological development and function? Recent studies of transgenic and knockout mouse models, genomic copy-number variants, imprinted-gene expression alterations, and sex-chromosome aneuploidies are revealing examples of 'mirror-extreme' brain and behavior phenotypes, which provide unique insights into neurodevelopmental architecture. These convergent studies quantitatively connect gene dosages with specific trajectories and outcomes, with important implications for the experimental dissection of normal neurological functions, the genetic analysis of psychiatric disorders, the development of pharmacological therapies, and mechanisms for the evolution of human brain and behavior. DOI
408. Crespi, B; Nosil, P.Conflictual speciation: species formation via genomic conflict.Trends in Ecology & Evolution, 2013, 28: 48-57 Conflictual speciation: species formation via genomic conflict
SELFISH GENETIC ELEMENTS; HYBRID MALE-STERILITY; FEMALE MEIOTIC DRIVE; REPRODUCTIVE ISOLATION; TRANSPOSABLE ELEMENTS; X-CHROMOSOME; DROSOPHILA-MELANOGASTER; ECOLOGICAL SPECIATION; SEXUAL-DIMORPHISM; FLOWERING PLANTS
A remarkable suite of forms of genomic conflict has recently been implicated in speciation. We propose that these diverse roles of genomic conflict in speciation processes can be unified using the concept of 'conflictual speciation'. Conflictual speciation centers on the evolution of reproductive isolation as a byproduct of antagonistic selection among genomic elements with divergent fitness interests. Intragenomic conflicts are expected to readily generate Dobzhansky-Muller incompatibilities, due to population-specific interactions between opposing elements, and thus they could be especially important in speciation. Moreover, selection from genomic conflicts should be relatively unrelenting across ecological and evolutionary time scales. We explain how intra-genomic conflicts can promote, or sometimes constrain, speciation, and describe evidence relating conflicts to the evolution of reproductive isolation. DOI
407. Crespi, EJ; Williams, TD; Jessop, TS; Delehanty, B.Life history and the ecology of stress: how do glucocorticoid hormones influence life-history variation in animals?Functional Ecology, 2013, 27: 93-106 Life history and the ecology of stress: how do glucocorticoid hormones influence life-history variation in animals?
PREDICT SURVIVAL PROBABILITIES; MARSUPIAL ANTECHINUS-STUARTII; PHASCOGALE-CALURA MARSUPIALIA; TROUT ONCORHYNCHUS-MYKISS; GALAPAGOS MARINE IGUANAS; RED-TAILED PHASCOGALE; LONG-LIVED SEABIRD; CORTICOSTERONE LEVELS; STEROID-HORMONES; PHYSIOLOGICAL STRESS
Glucocorticoids hormones (GCs) are intuitively important for mediation of age-dependent vertebrate life-history transitions through their effects on ontogeny alongside underpinning variation in life-history traits and trade-offs in vertebrates. These concepts largely derive from the ability of GCs to alter energy allocation, physiology and behaviour that influences key life-history traits involving age-specific life-history transitions, reproduction and survival. Studies across vertebrates have shown that the neuroendocrine stress axis plays a role in the developmental processes that lead up to age-specific early life-history transitions. While environmental sensitivity of the stress axis allows for it to modulate the timing of these transitions within species, little is known as to how variation in stress axis function has been adapted to produce interspecific variation in the timing of life-history transitions. Our assessment of the literature confirms that of previous reviews that there is only equivocal evidence for correlative or direct functional relationships between GCs and variation in reproduction and survival. We conclude that the relationships between GCs and life-history traits are complex and general patterns cannot be easily discerned with current research approaches and experimental designs. We identify several future research directions including: (i) integration of proximate and ultimate measures, including longitudinal studies that measure effects of GCs on more than one life-history trait or in multiple environmental contexts, to test explicit hypotheses about how GCs and life-history variation are related and (ii) the measurement of additional factors that modulate the effects of GCs on life-history traits (e.g. GC receptors and binding protein levels) to better infer neurendocrine stress axis actions. Conceptual models of HPA/I axis actions, such as allostatic load and reactive scope, to some extent explicitly predict the role of GCs in a life-history context, but are descriptive in nature. We propose that GC effects on life-history transitions, survival probabilities and fecundity can be modelled in existing quantitative demographic frameworks to improve our understanding of how GC variation influences life-history evolution and GC-mediated effects on population dynamics DOI
406. Crosley, EJ; Elliot, MG; Christians, JK; Crespi, BJ.Placental invasion, preeclampsia risk and adaptive molecular evolution at the origin of the great apes: Evidence from genome-wide analyses.Placenta, 2013, 34: 127-132 Placental invasion, preeclampsia risk and adaptive molecular evolution at the origin of the great apes: Evidence from genome-wide analyses
DEEP TROPHOBLAST INVASION; MATRIX-METALLOPROTEINASES; NONHUMAN-PRIMATES; INSULIN-RECEPTORS; LOWLAND GORILLA; GENE-EXPRESSION; CELL INVASION; ACTIVIN-A; PREGNANCY; INHIBIN
Introduction: Recent evidence from chimpanzees and gorillas has raised doubts that preeclampsia is a uniquely human disease. The deep extravillous trophoblast (EVT) invasion and spiral artery remodeling that characterizes our placenta (and is abnormal in preeclampsia) is shared within great apes, setting Homininae apart from Hylobatidae and Old World Monkeys, which show much shallower trophoblast invasion and limited spiral artery remodeling. We hypothesize that the evolution of a more invasive placenta in the lineage ancestral to the great apes involved positive selection on genes crucial to EVT invasion and spiral artery remodeling. Furthermore, identification of placentally-expressed genes under selection in this lineage may identify novel genes involved in placental development. Methods: We tested for positive selection in approximately 18,000 genes using the ratio of non-synonymous to synonymous amino acid substitution for protein-coding DNA. DAVID Bioinformatics Resources identified biological processes enriched in positively selected genes, including processes related to EVT invasion and spiral artery remodeling. Results: Analyses revealed 295 and 264 genes under significant positive selection on the branches ancestral to Hominidae (Human, Chimp, Gorilla, Orangutan) and Homininae (Human, Chimp, Gorilla), respectively. Gene ontology analysis of these gene sets demonstrated significant enrichments for several functional gene clusters relevant to preeclampsia risk, and sets of placentally-expressed genes that have been linked with preeclampsia and/or trophoblast invasion in other studies. Conclusion: Our study represents a novel approach to the identification of candidate genes and amino acid residues involved in placental pathologies by implicating them in the evolution of highly-invasive placenta. (C) 2012 Elsevier Ltd. All rights reserved. DOI
405. Crossin, GT; Phillips, RA; Lattin, CR; Romero, LM; Williams, TD.Corticosterone mediated costs of reproduction link current to future breeding.General and Comparative Endocrinology, 2013, 193: 112-120 Corticosterone mediated costs of reproduction link current to future breeding
GIANT PETRELS MACRONECTES; PIED FLYCATCHERS; ADRENOCORTICAL-RESPONSE; FORAGING BEHAVIOR; SEXUAL CONFLICT; FEATHER QUALITY; SOUTH GEORGIA; KING PENGUINS; PARENTAL CARE; LONG-TERM
Life-history theory predicts that costs are associated with reproduction. One possible mediator of costs involves the secretion of glucocorticoid hormones, which in birds can be measured in feathers grown during the breeding period. Glucocorticoids mediate physiological responses to unpredictable environmental or other stressors, but they can also function as metabolic regulators during more predictable events such as reproduction. Here we show that corticosterone ("Cort") in feathers grown during the breeding season reflects reproductive effort in two Antarctic seabird species (giant petrels, Macronectes spp.). In females of both species, but not males, feather Cort ("fCort") was nearly 1.5-fold higher in successful than failed breeders (those that lost their eggs/chicks), suggesting a cost of successful reproduction, i.e., high fCort levels in females reflect the elevated plasma Cort levels required to support high metabolic demands of chick-rearing. Successful breeding also led to delayed moult prior to winter migration. The fCort levels and pre-migration moult score that we measured at the end of current breeding were predictive of subsequent reproductive effort in the following year. Birds with high fCort and a delayed initiation of moult were much more likely to defer breeding in the following year. Cort levels and the timing of moult thus provide a potential mechanism for the tradeoff between current and future reproduction. Crown Copyright (C) 2013 Published by Elsevier Inc. All rights reserved. DOI
404. Darling, ES; McClanahan, TR; Côté, IM.Life histories predict coral community disassembly under multiple stressors.Global Change Biology, 2013, 19: 1930-1940 Life histories predict coral community disassembly under multiple stressors
MARINE PROTECTED AREAS; WESTERN INDIAN-OCEAN; REGION-WIDE DECLINES; CLIMATE-CHANGE; REEF CORALS; TEMPERATURE-VARIATION; GLOBAL ANALYSIS; KENYAN REEFS; COLONY SIZE; ECOSYSTEMS
Climate change is reshaping biological communities against a background of existing human pressure. Evaluating the impacts of multiple stressors on community dynamics can be particularly challenging in species-rich ecosystems, such as coral reefs. Here, we investigate whether life-history strategies and cotolerance to different stressors can predict community responses to fishing and temperature-driven bleaching using a 20-year time series of coral assemblages in Kenya. We found that the initial life-history composition of coral taxa largely determined the impacts of bleaching and coral loss. Prior to the 1998 bleaching event, coral assemblages within no-take marine reserves were composed of three distinct life histories competitive, stress-tolerant and weedy and exhibited strong declines following bleaching with limited subsequent recovery. In contrast, fished reefs had lower coral cover, fewer genera and were composed of stress-tolerant and weedy corals that were less affected by bleaching over the long term. Despite these general patterns, we found limited evidence for cotolerance as coral genera and life histories were variable in their sensitivities to fishing and bleaching. Overall, fishing and bleaching have reduced coral diversity and led to altered coral communities of survivor' species with stress-tolerant and weedy life histories. Our findings are consistent with expectations that climate change interacting with existing human pressure will result in the loss of coral diversity and critical reef habitat. DOI
403. Deheshi, S; Pasqualotto, BA; Rintoul, GL.Mitochondrial trafficking in neuropsychiatric diseases.Neurobiology of Disease, 2013, 51: 66-71 Mitochondrial trafficking in neuropsychiatric diseases
CULTURED HIPPOCAMPAL-NEURONS; CHILDHOOD-ONSET SCHIZOPHRENIA; IMPAIRED AXONAL-TRANSPORT; ALZHEIMERS-DISEASE; NEURODEGENERATIVE DISEASES; AMYLOID-BETA; CALCIUM UNIPORTER; MONOAMINE OXIDASE; FOREBRAIN NEURONS; CORTICAL-NEURONS
Mitochondria have numerous roles in healthy neuronal functioning and in neuronal injury mechanisms. They are quite dynamic organelles in that they fuse, divide and move throughout axons and dendrites. The mechanisms of mitochondrial motility have received much attention, however the significance of the dynamic nature of mitochondria in neurons is unclear. Nonetheless, deficits in mitochondrial trafficking have been implicated in numerous neurodegenerative disorders. The role of aberrant mitochondrial trafficking in neuropsychiatric disorders is not as well understood, but may involve similar mechanisms. In this review we examine the evidence which implicates changes in mitochondrial trafficking in the pathogenesis of neuropsychiatric disorders and hypothesize how defective mitochondrial transport may contribute to disease mechanisms. (C) 2012 Elsevier Inc. All rights reserved. DOI
402. Dinsdale, NL; Hurd, PL; Wakabayashi, A; Elliot, M; Crespi, BJ.How Are Autism and Schizotypy Related? Evidence from a Non-Clinical Population.PLOS One, 2013, 8 How Are Autism and Schizotypy Related? Evidence from a Non-Clinical Population
SPECTRUM QUOTIENT AQ; HIGH-FUNCTIONING AUTISM; GENERAL-POPULATION; MAGICAL IDEATION; MIXED-HANDEDNESS; HAND PREFERENCE; SEX-DIFFERENCES; SOCIAL BRAIN; SCHIZOPHRENIA; DISORDERS
Both autism spectrum conditions (ASCs) and schizophrenia spectrum conditions (SSCs) involve altered or impaired social and communicative functioning, but whether these shared features indicate overlapping or different etiological factors is unknown. We outline three hypotheses (overlapping, independent, and diametric) for the possible relationship between ASCs and SSCs, and compare their predictions for the expected relationships between autistic and schizotypal phenotypes using the Autism Spectrum Quotient and the Schizotypal Personality Questionnaire-Brief Revised from a large non-clinical sample of undergraduate students. Consistent with previous research, autistic features were positively associated with several schizotypal features, with the most overlap occurring between interpersonal schizotypy and autistic social and communication phenotypes. The first component of a principal components analysis (PCA) of subscale scores reflected these positive correlations, and suggested the presence of an axis (PC1) representing general social interest and aptitude. By contrast, the second principal component (PC2) exhibited a pattern of positive and negative loadings indicative of an axis from autism to positive schizotypy, such that positive schizotypal features loaded in the opposite direction to core autistic features. These overall PCA patterns were replicated in a second data set from a Japanese population. To evaluate the validity of our interpretation of the PCA results, we measured handedness and mental rotation ability, as these are established correlates of SSCs and ASCs, respectively. PC2 scores were significantly associated with hand preference, such that increasingly 'schizotypal' scores predicted reduced strength of handedness, which is consistent with previous research. PC1 scores were positively related to performance on the mental rotation task, suggesting trade-offs between social skills and visual-spatial ability. These results provide novel evidence for an autism-positive schizotypy axis, and highlight the importance of recognizing that psychological variation involving reduced social interest and functioning may have diverse causes. DOI
401. Dulvy, NK.Super-sized MPAs and the marginalization of species conservation.Aquatic Conservation-Marine and Freshwater Ecosystems, 2013, 23: 357-362 Super-sized MPAs and the marginalization of species conservation
EXTINCTION RISK; MARINE RESERVES; CLIMATE-CHANGE; POPULATIONS
DOI
400. Eens, M; Jaspers, VLB; Van den Steen, E; Bateson, M; Carere, C; Clergeau, P; Costantini, D; Dolenec, Z; Elliott, JE; Flux, J; Gwinner, H; Halbrook, RS; Heeb, P; Mazgajski, TD; Moksnes, A; Polo, V; Soler, JJ; Sinclair, R; Veiga, JP; Williams, TD; Covaci, A; Pinxten, R.Can starling eggs be useful as a biomonitoring tool to study organohalogenated contaminants on a worldwide scale?Environment International, 2013, 51: 141-149 Can starling eggs be useful as a biomonitoring tool to study organohalogenated contaminants on a worldwide scale?
BROMINATED FLAME RETARDANTS; POLYBROMINATED DIPHENYL ETHERS; PERSISTENT ORGANIC POLLUTANTS; ENDOCRINE-DISRUPTING CHEMICALS; STURNUS-VULGARIS; EUROPEAN STARLINGS; GREAT-LAKES; PARUS-MAJOR; ORGANOCHLORINE PESTICIDES; GLOBAL DISTRIBUTION
Large-scale international monitoring studies are important to assess emission patterns and environmental distributions of organohalogenated contaminants (OHCs) on a worldwide scale. In this study, the presence of OHCs was investigated on three continents (Europe, North America and Australasia), using eggs of starlings (Sturnus vulgaris and Sturnus unicolor) to assess their suitability for large-scale monitoring studies. To the best of our knowledge, this is the first study using bird eggs of the same species as a biomonitor for OHCs on an intercontinental scale. We found significant differences in OHC concentrations of the eggs among sampling locations, except for hexachlorocyclohexanes (HCHs). Mean concentrations of sum polychlorinated biphenyls (PCBs) in eggs ranged from 78 26 ng/g lipid weight (lw) in Australia to 2900 +/- 1300 ng/g lw in the United States. The PCB profile was dominated by CB 153 and CB 138 in all locations, except for New Zealand, where the contribution of CB 95, CB 101 and CB 149 was also high. The highest mean sum polybrominated diphenyl ether (PBDE) concentrations were found in Canada (4400 +/- 830 ng/g lw), while the lowest mean PBDE concentrations were measured in Spain (3.7 +/- 0.1 ng/g lw). The PBDE profile in starling eggs was dominated by BDE 47 and BDE 99 in all countries, but in Belgium, the higher brominated PBDEs had a higher contribution compared to other countries. For the organochlorine pesticides (OCPs), dichlorodiphenyltrichloroethanes (DDTs) ranged from 110 +/- 16 ng/g lw in France to 17,000 +/- 3400 ng/g lw in New Zealand, while HCHs and hexachlorobenzene were generally in low concentrations in all sampling locations. Chlordanes were remarkably high in eggs from the United States (2500 +/- 1300 ng/g lw). The OCP profile in all countries was largely dominated by p,p'-DDE. In general, the worldwide trends we observed in starling eggs were in accordance with the literature on human and environmental OHC data, which suggests that there is potential for using starling eggs as a biomonitoring tool on a large geographical scale. (C) 2012 Elsevier Ltd. All rights reserved. DOI
399. Eng, ML; Elliott, JE; Letcher, RJ; Williams, TD.Individual variation in body burden, lipid status, and reproductive investment is related to maternal transfer of a brominated diphenyl ether (BDE-99) to eggs in the zebra finch.Environmental Toxicology and Chemistry, 2013, 32: 345-352 Individual variation in body burden, lipid status, and reproductive investment is related to maternal transfer of a brominated diphenyl ether (BDE-99) to eggs in the zebra finch
YOLK PRECURSOR DYNAMICS; HERRING GULL EGGS; ORGANOCHLORINE COMPOUNDS; POLYCHLORINATED-BIPHENYLS; TAENIOPYGIA-GUTTATA; FLAME RETARDANTS; TEMPORAL TRENDS; DOMESTIC-FOWL; GREAT-LAKES; BIRDS
Avian eggs are exposed to hydrophobic contaminants through maternal transfer. How maternal transfer of contaminants within a species is influenced by individual variation in characteristics such as body burden, yolk precursor levels, or reproductive investment is not understood. The authors investigated sources of variation in the maternal transfer of 2,2',4,4',5-pentabromodiphenyl ether (BDE-99) in zebra finches (Taeniopygia guttata). The authors dosed adult female zebra finches with levels of BDE-99 relevant to exposure in wild birds (0, 33.7 or 173.8?ng/g body wt/d) for three weeks prior to pairing. Maternal BDE-99 and very-low-density lipoprotein (VLDL) in plasma were measured during egg formation and at clutch completion, and BDE-99 was measured in the corresponding egg. The lipid-normalized egg-to-maternal tissue BDE-99 relationship decreased with increasing maternal burden. Individual variation in maternal VLDL was related to BDE-99 transfer to the eggs when BDE-99 was at background levels in control birds, but not when BDE-99 was elevated in dosed birds. The decrease in maternal plasma BDE-99 over the laying period was only significant (p?<?0.05) in the high-dose birds. Finally, the decrease in BDE-99 in maternal plasma during egg-laying was significantly positively correlated with clutch mass in the high-dose group. These results suggest that the relationship between maternal and egg contaminant levels can be highly variable. This has significant implications for using eggs as indicators of adult or environmental concentrations. Environ. Toxicol. Chem. 2013;32:345352. (C) 2012 SETAC DOI
398. Eng, ML; Williams, TD; Elliott, JE.Developmental exposure to a brominated flame retardant: An assessment of effects on physiology, growth, and reproduction in a songbird, the zebra finch.Environmental Pollution, 2013, 178: 343-349 Developmental exposure to a brominated flame retardant: An assessment of effects on physiology, growth, and reproduction in a songbird, the zebra finch
POLYBROMINATED DIPHENYL ETHERS; KESTRELS FALCO-SPARVERIUS; AMERICAN KESTRELS; TAENIOPYGIA-GUTTATA; HALIAEETUS-LEUCOCEPHALUS; ANAS-PLATYRHYNCHOS; EMBRYONIC EXPOSURE; THYROID-HORMONES; OXIDATIVE STRESS; STURNUS-VULGARIS
Mixtures of polybrominated diphenyl ethers (PBDEs) have been widely used as additive flame retardants, and BDE-99 is one of the most predominant congeners found in the environment. BDE-99 has been reported in avian samples worldwide, yet knowledge of its toxicity to birds is minimal. We assessed the short- and long-term effects of nestling exposure to environmentally relevant levels of BDE-99 in a model passerine, the zebra finch. Early exposure to BDE-99 did not affect hematocrit, oxidative stress, or thyroid hormones in either the juvenile or adult stages, and there were no effects on chick growth or survival. BDE-99 exposure caused a dose-dependent delay in timing of reproduction, but there were no other effects on reproductive success. In zebra finches, endpoints related to reproductive behavior appear to be the most sensitive to BDE-99. However, passerines overall appear to be less sensitive than birds of prey or mammals to PBDE exposure. (c) 2013 Elsevier Ltd. All rights reserved. DOI
397. Feng, XY; Xiu, BS; Chen, K; Yang, XQ; Zhang, HT; Yue, J; Tan, YJ; Li, HM; Nicholson, RA; Tam, AW; Zhao, P; Zhang, L; Liu, J; Song, XG; Wang, GH; Zhang, HQ.Enhanced serodiagnostic utility of novel Mycobacterium tuberculosis polyproteins.Journal of Infection, 2013, 66: 366-375 Enhanced serodiagnostic utility of novel Mycobacterium tuberculosis polyproteins
PULMONARY TUBERCULOSIS; ACTIVE TUBERCULOSIS; ANTIBODY-RESPONSES; DIAGNOSIS; ANTIGENS; IDENTIFICATION; BIOMARKERS; PROTEINS; ASSAYS
Objectives: The detection of Mycobacterium tuberculosis specific antibodies in human sera has been a rapid and important diagnostic aid for tuberculosis (TB) control and prevention. However, any single antigen is not enough to be used to cover the antibody profiles of all TB patients. Methods: Seven single antigens (38 kDa, ESAT-6, CFP10, Mtb8.4, MPT64, TB16.3 and Mtb8) were evaluated serodiagnostically. Two novel M. tuberculosis polyproteins, 38kD-ESAT6-CFP10 (38F) and Mtb8.4-MPT64-TB16.3-Mtb8 (64F), were expressed and the novel 38F-64F indirect ELISA assay used to analyze antibody responses to polyproteins in serum samples. Results: The sensitivity of the novel 38F-64F indirect ELISA alone was much higher than that of the sputum culture test (86.91% vs. 50.62%) and that of the sputum smear test (78.64% vs. 47.57%). The novel 38F-64F indirect ELISA had a sensitivity of 74.16% with sera from extrapulmonary TB patients and a sensitivity of 37.14% with sera from LTBI. The specificity of the novel 38F-64F indirect ELISA was 90.36% with the sera from healthy blood donors and 94.15% with the sera from non-TB patients. Conclusions: The novel 38F-64F indirect ELISA assay had effective diagnostic performance and would make meaningful contribution to the diagnosis of TB disease in developing countries. (C) 2012 The British Infection Association. Published by Elsevier Ltd. All rights reserved. DOI
396. Flamarique, IN.Opsin switch reveals function of the ultraviolet cone in fish foraging.Proceedings of the Royal Society B-Biological Sciences, 2013, 280: Opsin switch reveals function of the ultraviolet cone in fish foraging
visual pigment; cone photoreceptor; retina; rainbow trout
Although several studies have shown that ultraviolet (UV) wavelengths are important in naturally occurring, visually guided behaviours of vertebrates, the function of the UV cone in such behaviours is unknown. Here, I used thyroid hormone to transform the UV cones of young rainbow trout into blue cones, a phenomenon that occurs naturally as the animal grows, to test whether the resulting loss of UV sensitivity affected the animal's foraging performance on Daphnia magna, a prey zooplankton. The distances and angles at which prey were located (variables that are known indicators of foraging performance) were significantly reduced for UV knock-out fish compared with controls. Optical measurements and photon-catch calculations revealed that the contrast of Daphnia was greater when perceived by the visual system of control versus that of thyroid-hormone-treated fish, demonstrating that the UV cone enhanced the foraging performance of young rainbow trout. Because most juvenile fishes have UV cones and feed on zooplankton, this finding has wide implications for understanding the visual ecology of fishes. The enhanced target contrast provided by UV cones could be used by other vertebrates in various behaviours, including foraging, mate selection and communication. DOI
395. Flamarique, IN; Bergstrom, C; Cheng, CL; Reimchen, TE.Role of the iridescent eye in stickleback female mate choice.Journal of Experimental Biology, 2013, 216: 2806-2812 Role of the iridescent eye in stickleback female mate choice
PREY-SEARCH BEHAVIOR; GASTEROSTEUS-ACULEATUS; THREESPINE STICKLEBACKS; NUPTIAL COLOR; 3-SPINED STICKLEBACKS; SPECTRAL SENSITIVITY; POLARIZED-LIGHT; VISUAL-SYSTEMS; ULTRAVIOLET; SIGNAL
Many vertebrates exhibit prominent body colours that are used in courtship and territorial communication. Some fishes also have an eye whose iris becomes iridescent during the mating season, as in the threespine stickleback. Behavioural studies in this species have focused on the redness of the throat/jaw as the primary determinant of female mate choice. Unlike the iridescent eye, however, the red throat/jaw is not present in all stickleback populations, suggesting that the colour of the eye may be equally important for female mate choice. Here, we used data on photoreceptors and environmental light to assess body conspicuousness and the colour contrast of courtship signals for stickleback populations living in a range of waters, from clear (mesotrophic) to red light shifted (dystrophic). This analysis indicated that the redness of the throat/jaw is expressed to enhance the contrast of the eye. To test the importance of eye colour as a courtship signal, we carried out mate choice experiments in which females were presented with identical videos of a courting male but for the colour of the eye and/or the throat/jaw. Females did not choose based on differences in throat/jaw redness between videos, but preferred males with the highest contrast between the eye and the throat/jaw. This result points to the blue iridescent eye as a primary courtship signal in stickleback female mate choice. DOI
394. Flamarique, IN; Cheng, CL; Bergstrom, C; Reimchen, TE.Pronounced heritable variation and limited phenotypic plasticity in visual pigments and opsin expression of threespine stickleback photoreceptors.Journal of Experimental Biology, 2013, 216: 656-667 Pronounced heritable variation and limited phenotypic plasticity in visual pigments and opsin expression of threespine stickleback photoreceptors
INNER NUCLEAR LAYER; SALMONID FISHES; GASTEROSTEUS-ACULEATUS; CONE PHOTORECEPTORS; BLUEFIN KILLIFISH; LUCANIA-GOODEI; NUPTIAL COLOR; SINGLE CONES; POLARIZED-LIGHT; GENE-EXPRESSION
Vertebrate colour vision is mediated by the differential expression of visual pigment proteins (opsins) in retinal cone photoreceptors. Many species alter opsin expression during life, either as part of development or as a result of changes in habitat. The latter, a result of phenotypic plasticity, appears common among fishes, but its cellular origin and ecological significance are unknown. Here, we used adult threespine stickleback fish from different photic regimes to investigate heritable variability and phenotypic plasticity in opsin expression. Fish from clear waters had double cones that expressed long (LWS) and middle (RH2) wavelength opsins, one per double cone member. In contrast, fish from red light-shifted lakes had double cones that were >95% LWS/LWS pairs. All fish had single cones that predominantly expressed a short wavelength (SWS2) opsin but ultraviolet cones, expressing a SWS1 opsin, were present throughout the retina. Fish from red light-shifted lakes, when transferred to clear waters, had a similar to 2% increase in RH2/LWS double cones, though double cone density remained constant. Comparison of visual pigment absorbance and light transmission in the environment indicated that the opsin complements of double cones maximized sensitivity to the background light, whereas single cones had visual pigments that were spectrally offset from the dominant background wavelengths. Our results indicate that phenotypic plasticity in opsin expression is minor in sticklebacks and of questionable functional significance. DOI
393. Foster, AJ; Hall, DE; Mortimer, L; Abercromby, S; Gries, R; Gries, G; Bohlmann, J; Russell, J; Mattsson, J.Identification of Genes in Thuja plicata Foliar Terpenoid Defenses.Plant Physiology, 2013, 161: 1993-2004 Identification of Genes in Thuja plicata Foliar Terpenoid Defenses
WHITE-PINE WEEVIL; HIGH-QUALITY RNA; CONIFER DEFENSE; SITKA SPRUCE; WESTERN REDCEDAR; FUNCTIONAL-CHARACTERIZATION; CHAMAECYPARIS-NOOTKATENSIS; BIOSYNTHESIS; METABOLISM; DEER cedar
Thuja plicata (western redcedar) is a long-lived conifer species whose foliage is rarely affected by disease or insect pests, but can be severely damaged by ungulate browsing. Deterrence to browsing correlates with high foliar levels of terpenoids, in particular the monoterpenoid a-thujone. Here, we set out to identify genes whose products may be involved in the production of a-thujone and other terpenoids in this species. First, we generated a foliar transcriptome database from which to draw candidate genes. Second, we mapped the storage of thujones and other terpenoids to foliar glands. Third, we used global expression profiling to identify more than 600 genes that are expressed at high levels in foliage with glands, but can either not be detected or are expressed at low levels in a natural variant lacking foliar glands. Fourth, we used in situ RNA hybridization to map the expression of a putative monoterpene synthase to the epithelium of glands and used enzyme assays with recombinant protein of the same gene to show that it produces sabinene, the monoterpene precursor of a-thujone. Finally, we identified candidate genes with predicted enzymatic functions for the conversion of sabinene to a-thujone. Taken together, this approach generated both general resources and detailed functional characterization in the identification of genes of foliar terpenoid biosynthesis in T. plicata.Website DOI
392. Frekers, D; Simon, MC; Andreoiu, C; Bale, JC; Brodeur, M; Brunner, T; Chaudhuri, A; Chowdhury, U; Lopez-Urrutia, JRC; Delheij, P; Ejiri, H; Ettenauer, S; Gallant, AT; Gavrin, V; Grossheim, A; Harakeh, MN; Jang, F; Kwiatkowski, AA; Lassen, J; Lennarz, A; Luichtl, M; Ma, T; Macdonald, TD; Mane, E; Robertson, D; Schultz, BE; Simon, VV; Teigelhofer, A; Dilling, J.Penning-trap Q-value determination of the Ga-71(v, e(-))Ge-71 reaction using threshold charge breeding of on-line produced isotopes.Physics Letters B, 2013, 722: 233-237 Penning-trap Q-value determination of the Ga-71(v, e(-))Ge-71 reaction using threshold charge breeding of on-line produced isotopes
Mass-measurement; Ion-traps; Highly-charged ions; Radioactive beams; Neutrino-induced reactions; Solar neutrinos
We present a first direct Q-value measurement of the Ga-71(v, e(-))Ge-71 reaction using the TITAN mass-measurement facility at ISAC/TRIUMF. The measurements were performed in a Penning trap on neon-like Ga-71(21+) and Ge-71(22+) using isobar separation of the on-line produced mother and daughter nuclei through threshold charge breeding in an electron-beam ion trap. In addition, isoionic samples of Ga-71(21+) and Ge-71(21+) were stored concurrently in the Penning trap and provided a separate Q-value measurement. Both independent measurements result in a combined Q-value of 233.5 +/- 1.2 keV, which is in agreement with the previously accepted Q-value for the v cross-section calculations. Together with a recent measurement of the v-response from the excited states in Ge-71, we conclude that there are no further uncertainties in the nuclear structure, which could remove the persistent discrepancy between the SAGE and GALLEX calibration measurements performed with neutrinos from reactor-produced Cr-51 and Ar-37 sources and the theoretical expectation. (c) 2013 Elsevier B.V. All rights reserved. DOI
391. Goring, S; Lacourse, T; Pellatt, MG; Mathewes, RW.Pollen assemblage richness does not reflect regional plant species richness: a cautionary tale.Journal of Ecology, 2013, 101: 1137-1145 Pollen assemblage richness does not reflect regional plant species richness: a cautionary tale
WESTERN NORTH-AMERICA; TEMPERATE RAIN-FOREST; PALYNOLOGICAL RICHNESS; FLORISTIC DIVERSITY; TAXONOMIC RICHNESS; BRITISH-COLUMBIA; BIODIVERSITY; CLIMATE; RESOLUTION; DYNAMICS
1. Palaeoecological records of species richness spanning time intervals over which climate variables have shifted relative to one another can help reduce issues of colinearity that might affect our understanding of patterns of species richness. 2. Fossil pollen assemblages have the potential to serve as a proxy for past plant richness because they record the presence of plant taxa. However, pollen assemblages are typically limited by low taxonomic resolution and taphonomic processes (pollen production, transport, deposition and preservation), which may degrade the degree to which pollen accurately represents vegetation communities. 3. We combined pollen assemblages from modern lake sediments (n=546; n=167 in British Columbia, Canada) in the Pacific Northwest, with a detailed data base (n=16071) of plant presence across the province and a published record of gamma richness to test the accuracy of pollen assemblages as a proxy for regional patterns of plant richness. 4. A generalized linear model using plant richness resolved at multiple taxonomic levels suggests taxonomic differences between plant and pollen taxa may reduce the ability of pollen richness to predict plant richness at the site level, but that this relationship is still recoverable, albeit with broad confidence intervals. 5. Spatially explicit analysis using a generalized additive model shows that predicted plant richness has no relationship with raw pollen assemblage richness at all taxonomic levels. 6. The taxonomic composition of the region (i.e. the ratio of wind-pollinated to insect-pollinated species) and/or the morphological specificity of the dominant pollen types in the region may play a role in limiting the reconstruction of plant richness from pollen richness. Nonetheless, we believe this study is the first to empirically test the relationship between plant and pollen richness, and fails to find a significant relationship. 7. Synthesis. Palynological richness in itself cannot be considered a universally reliable proxy for inferring plant richness; however, broad spatial and temporal patterns of change in richness have been reported in the literature. Our findings suggest that more work is needed to understand previously reported patterns of pollen assemblage richness through time and in space. We suggest the use of functional diversity or phylogenetically based analysis may help link pollen richness to plant community richness. DOI
390. Green, SJ; Tamburello, N; Miller, SE; Akins, JL; Côté, IM.Habitat complexity and fish size affect the detection of Indo-Pacific lionfish on invaded coral reefs.Coral Reefs, 2013, 32: 413-421 Habitat complexity and fish size affect the detection of Indo-Pacific lionfish on invaded coral reefs
UNDERWATER VISUAL-CENSUS; ABUNDANCE; INVASION; DENSITY; ASSEMBLAGES; POPULATIONS; ATLANTIC; BEHAVIOR
A standard approach to improving the accuracy of reef fish population estimates derived from underwater visual censuses (UVCs) is the application of species-specific correction factors, which assumes that a species' detectability is constant under all conditions. To test this assumption, we quantified detection rates for invasive Indo-Pacific lionfish (Pterois volitans and P. miles), which are now a primary threat to coral reef conservation throughout the Caribbean. Estimates of lionfish population density and distribution, which are essential for managing the invasion, are currently obtained through standard UVCs. Using two conventional UVC methods, the belt transect and stationary visual census (SVC), we assessed how lionfish detection rates vary with lionfish body size and habitat complexity (measured as rugosity) on invaded continuous and patch reefs off Cape Eleuthera, the Bahamas. Belt transect and SVC surveys performed equally poorly, with both methods failing to detect the presence of lionfish in > 50 % of surveys where thorough, lionfish-focussed searches yielded one or more individuals. Conventional methods underestimated lionfish biomass by similar to 200 %. Crucially, detection rate varied significantly with both lionfish size and reef rugosity, indicating that the application of a single correction factor across habitats and stages of invasion is unlikely to accurately characterize local populations. Applying variable correction factors that account for site-specific lionfish size and rugosity to conventional survey data increased estimates of lionfish biomass, but these remained significantly lower than actual biomass. To increase the accuracy and reliability of estimates of lionfish density and distribution, monitoring programs should use detailed area searches rather than standard visual survey methods. Our study highlights the importance of accounting for sources of spatial and temporal variation in detection to increase the accuracy of survey data from coral reef systems. DOI
389. Greenspoon, PB; M'Gonigle, LK.The evolution of mutation rate in an antagonistic coevolutionary model with maternal transmission of parasites.Proceedings of the Royal Society B-Biological Sciences, 2013, 280 The evolution of mutation rate in an antagonistic coevolutionary model with maternal transmission of parasites
mutation rate; parasites; coevolution; modifier model; maternal effects
By constantly selecting for novel genotypes, coevolution between hosts and parasites can favour elevated mutation rates. Models of this process typically assume random encounters. However, offspring are often more likely to encounter their mother's parasites. Because parents and offspring are genetically similar, they may be susceptible to the same parasite strains and thus, in hosts, maternal transmission should select for mechanisms that decrease intergenerational genetic similarity. In parasites, however, maternal transmission should select for genetic similarity. We develop and analyse a model of host and parasite mutation rate evolution when parasites are maternally inherited. In hosts, we find that maternal transmission has two opposing effects. First, it eliminates coevolutionary cycles that previous work shows select for higher mutation. Second, it independently selects for higher mutation rates, because offspring that differ from their mothers are more likely to avoid infection. In parasites, however, the two effects of maternal transmission act in the same direction. As for hosts, maternal transmission eliminates coevolutionary cycles, thereby reducing selection for increased mutation. Unlike for hosts, however, maternal transmission additionally selects against higher mutation by favouring parasite offspring that are the same as their mothers. DOI
387. Gudde, RM; Joy, JB; Mooers, AO.Imperilled phylogenetic endemism of Malagasy lemuriformes.Diversity and Distributions, 2013, 19: 664-675 Imperilled phylogenetic endemism of Malagasy lemuriformes
IUCN RED LIST; CONSERVATION PRIORITIES; EVOLUTIONARY HISTORY; SPECIES RICHNESS; BIODIVERSITY CONSERVATION; MADAGASCAR LEMURS; MIXED MODELS; DIVERSITY; EXTINCTION; HOTSPOTS
Aim To highlight where in Madagascar the phylogenetically and spatially rare lemur species at risk of extinction are concentrated. Location Madagascar. Methods Phylogenetic endemism (PE) is a combined measure for apportioning a phylogenetic tree across a landscape used to identify those geographical locations that contain spatially rare phylogenetic diversity (Rosauer etal., 2009). We present a simple extension (imperilled phylogenetic endemism) that scales this phylogenetic diversity by the probability of its loss to extinction. We apply these measures to a composite phylogeny of all confirmed Malagasy lemuriform species using International Union for Conservation of Nature (IUCN) extent of occurrence and threat status data. Results We find that, because nonimperilled species are scattered about the lemuriform tree, interior branches of the tree are still quite secure: this also means that areas of high phylogenetic endemism for Madagascar lemuriformes are often the same areas as those of high imperilled PE (IPE), as both are heavily weighted by branches nearer the tips. However, although the North of Madagascar holds the largest amount of spatially rare evolutionary history using both PE and IPE, there are additional pockets of imperilled history in the south and west. Main Conclusions Correlations of endemism and threat status with phylogenetic isolation are modest across lemurs and so are not substitutable conservation values. They might best be integrated on the landscape using IPE. As illustrated here, IPE successfully highlights areas containing species which are at once threatened with extinction and that are phylogenetically and spatially rare. DOI
386. Hackerott, S; Valdivia, A; Green, SJ; Côté, IM; Cox, CE; Akins, L; Layman, CA; Precht, WF; Bruno, JF.Native Predators Do Not Influence Invasion Success of Pacific Lionfish on Caribbean Reefs.PLOS One, 2013, 8 Native Predators Do Not Influence Invasion Success of Pacific Lionfish on Caribbean Reefs
EXOTIC PLANT INVASIONS; REGION-WIDE DECLINES; CORAL-REEF; COMMUNITIES; RECRUITMENT; ABUNDANCE; ATLANTIC; ECOLOGY
Biotic resistance, the process by which new colonists are excluded from a community by predation from and/or competition with resident species, can prevent or limit species invasions. We examined whether biotic resistance by native predators on Caribbean coral reefs has influenced the invasion success of red lionfishes (Pterois volitans and Pterois miles), piscivores from the Indo-Pacific. Specifically, we surveyed the abundance (density and biomass) of lionfish and native predatory fishes that could interact with lionfish (either through predation or competition) on 71 reefs in three biogeographic regions of the Caribbean. We recorded protection status of the reefs, and abiotic variables including depth, habitat type, and wind/wave exposure at each site. We found no relationship between the density or biomass of lionfish and that of native predators. However, lionfish densities were significantly lower on windward sites, potentially because of habitat preferences, and in marine protected areas, most likely because of ongoing removal efforts by reserve managers. Our results suggest that interactions with native predators do not influence the colonization or post-establishment population density of invasive lionfish on Caribbean reefs. DOI
385. Hart, MW.Structure and evolution of the sea star egg receptor for sperm bindin.Molecular Ecology, 2013, 22: 2143-2156 Structure and evolution of the sea star egg receptor for sperm bindin
POSITIVE DARWINIAN SELECTION; GAMETE-RECOGNITION; PHYLOGENETIC ANALYSIS; MAXIMUM-LIKELIHOOD; GENETIC ALGORITHM; NEXT-GENERATION; PROTEIN; URCHINS; LYSIN; POPULATION
Selection on coevolving sperm- and egg-recognition molecules is a potent engine of population divergence leading to reproductive isolation and speciation. The study of receptorligand pairs can reveal co-evolution of male- and female-expressed genes or differences between their evolution in response to selective factors such as sperm competition and sexual conflict. Phylogeographical studies of these patterns have been limited by targeted gene methods that favour short protein-coding sequences amplifiable by PCR. Here, I use high-throughput transcriptomic methods to characterize the structure and divergence of full-length coding sequences for the gene encoding the protein component of a large complex egg surface glycopeptide receptor for the sperm acrosomal protein bindin from the sea star Patiria miniata. I used a simple but effective method for resolving nucleotide polymorphisms into haplotypes for phylogeny-based analyses of selection. The protein domain organization of sea star egg bindin receptor (EBR1) was similar to sea urchins and included a pair of protein-recognition domains plus a series of tandem repeat domains of two types. Two populations separated by a well-characterized phylogeographical break included lineages of EBR1 alleles under positive selection at several codons (similar to selection on sperm bindin in the same populations). However, these populations shared the same alleles that were under selection for amino acid differences at multiple codons (unlike the pattern of selection for population divergence in sperm bindin). The significance of positively selected EBR1 domains and alleles could be tested in functional analyses of fertilization rates associated with EBR1 (and bindin) polymorphisms. DOI
384. Hocking, MD; Dulvy, NK; Reynolds, JD; Ring, RA; Reimchen, TE.Salmon subsidize an escape from a size spectrum.Proceedings of the Royal Society B-Biological Sciences, 2013, 280 Salmon subsidize an escape from a size spectrum
SPECIES ABUNDANCE DISTRIBUTIONS; BODY MASS RELATIONSHIPS; STRUCTURED FOOD WEBS; PACIFIC SALMON; POPULATION-DENSITY; ENERGY USE; COMMUNITIES; ECOSYSTEMS; PREDATION; NUTRIENTS
A general rule in ecology is that the abundance of species or individuals in communities sharing a common energy source decreases with increasing body size. However, external energy inputs in the form of resource subsidies can modify this size spectrum relationship. Here, we provide the first test of how a marine resource subsidy can affect size spectra of terrestrial communities, based on energy derived from Pacific salmon carcasses affecting a forest soil community beside streams in western Canada. Using both species-based and individual approaches, we found size structuring in this forest soil community, and transient community-wide doubling of standing biomass in response to energy pulses from Pacific salmon carcasses. One group of species were clear outliers in the middle of the size spectrum relationship: larval calliphorid and dryomyzid flies, which specialize on salmon carcasses, and which showed a tenfold increase in biomass in their size class when salmon were available. Thus, salmon subsidize their escape from the size spectrum. These results suggest that using a size-based perspective of resource subsidies can provide new insights into the structure and functioning of food webs. DOI
383. Joy, JB.Symbiosis catalyses niche expansion and diversification.Proceedings of the Royal Society B-Biological Sciences, 2013, 280 Symbiosis catalyses niche expansion and diversification
INSECT-FUNGUS ASSOCIATION; ASTEROMYIA-CARBONIFERA; DIPTERA CECIDOMYIIDAE; REGRESSION-MODELS; FEEDING INSECTS; PLANTS; GALLS; CURCULIONIDAE; COEVOLUTION; HYMENOPTERA
Interactions between species are important catalysts of the evolutionary processes that generate the remarkable diversity of life. Symbioses, conspicuous and inherently interesting forms of species interaction, are pervasive throughout the tree of life. However, nearly all studies of the impact of species interactions on diversification have concentrated on competition and predation leaving unclear the importance of symbiotic interaction. Here, I show that, as predicted by evolutionary theories of symbiosis and diversification, multiple origins of a key innovation, symbiosis between gall-inducing insects and fungi, catalysed both expansion in resource use (niche expansion) and diversification. Symbiotic lineages have undergone a more than sevenfold expansion in the range of host-plant taxa they use relative to lineages without such fungal symbionts, as defined by the genetic distance between host plants. Furthermore, symbiotic gall-inducing insects are more than 17 times as diverse as their non-symbiotic relatives. These results demonstrate that the evolution of symbiotic interaction leads to niche expansion, which in turn catalyses diversification. DOI
382. Juan-Jorda, MJ; Mosqueira, I; Freire, J; Dulvy, NK.The Conservation and Management of Tunas and Their Relatives: Setting Life History Research Priorities.PLOS One, 2013, 8 The Conservation and Management of Tunas and Their Relatives: Setting Life History Research Priorities
MACKEREL SCOMBER-JAPONICUS; SOUTHERN BLUEFIN TUNA; EXTINCTION RISK; MARINE FISHES; INTRASPECIFIC VARIATION; REPRODUCTIVE-BIOLOGY; THUNNUS-ORIENTALIS; AGE-DETERMINATION; GROWTH; WATERS
Scombrids (tunas, bonitos, Spanish mackerels and mackerels) support important fisheries in tropical, subtropical and temperate waters around the world, being one of the most economically- and socially-important marine species globally. Their sustainable exploitation, management and conservation depend on accurate life history information for the development of quantitative fisheries stock assessments, and in the fishery data-poor situations for the identification of vulnerable species. Here, we assemble life history traits (maximum size, growth, longevity, maturity, fecundity, spawning duration and spawning interval) for the 51 species of scombrids globally. We identify major biological gaps in knowledge and prioritize life history research needs in scombrids based on their biological gaps in knowledge, the importance of their fisheries and their current conservation status according to the International Union for Conservation of Nature Red List. We find that the growth and reproductive biology of tunas and mackerel species have been more extensively studied than for Spanish mackerels and bonitos, although there are notable exceptions in all groups. We also reveal that reproductive biology of species, particular fecundity, is the least studied biological aspect in scombrids. We identify two priority groups, including 32 species of scombrids, and several populations of principal market tunas, for which life history research should be prioritized following the species-specific life history gaps identified in this study in the coming decades. By highlighting the important gaps in biological knowledge and providing a priority setting for life history research in scombrid species this study provides guidance for management and conservation and serves as a guide for biologists and resource managers interested in the biology, ecology, and management of scombrid species. DOI
381. Keever, CC; Nieman, C; Ramsay, L; Ritland, CE; Bauer, LS; Lyons, DB; Cory, JS.Microsatellite population genetics of the emerald ash borer (Agrilus planipennis Fairmaire): comparisons between Asian and North American populations.Biological Invasions, 2013, 15: 1537-1559 Microsatellite population genetics of the emerald ash borer (Agrilus planipennis Fairmaire): comparisons between Asian and North American populations
COLEOPTERA BUPRESTIDAE; NATURAL ENEMIES; BIOLOGY; DIFFERENTIATION; DIVERSITY; EVOLUTION; VARIANCE; SOFTWARE; CHINA; PHYLOGEOGRAPHY
The emerald ash borer (EAB) (Agrilus planipennis Fairmaire) (Coleoptera; Buprestidae), is an invasive wood-boring beetle native to northeast Asia. This species was first detected in Michigan USA in 2002, and is a significant threat to native and ornamental ash tree species (Fraxinus spp.) throughout North America. We characterized seven polymorphic microsatellite markers for EAB and used these to investigate EAB population structure in the early invasive populations within North America and in comparison with Asia. We found 2-9 alleles per microsatellite locus, no evidence of linkage disequilibrium, and no association with known coding sequences, suggesting that these markers are suitable for population genetic analysis. Microsatellite population genetic structure was examined in 48 EAB populations sampled between 2003 and 2008 from five regions, three in the introduced range, Michigan (US) and Ontario and Quebec (Canada) and two Asian regions, China and South Korea, where EAB is native. We found significant genetic variation geographically but not temporally in EAB populations. Bayesian clustering analyses of individual microsatellite genotypes showed strong clustering among multiple North American populations and populations in both China and South Korea. Finally, allelic richness and expected heterozygosity were higher in the native range of EAB, but there was no difference in observed heterozygosity, suggesting a significant loss of alleles upon introduction but no significant change in the distribution of alleles within and among individuals. DOI
380. Kennedy, CM; Lonsdorf, E; Neel, MC; Williams, NM; Ricketts, TH; Winfree, R; Bommarco, R; Brittain, C; Burley, AL; Cariveau, D; Carvalheiro, LG; Chacoff, NP; Cunningham, SA; Danforth, BN; Dudenhoffer, JH; Elle, E; Gaines, HR; Garibaldi, LA; Gratton, C; Holzschuh, A; Isaacs, R; Javorek, SK; Jha, S; Klein, AM; Krewenka, K; Mandelik, Y; Mayfield, MM; Morandin, L; Neame, LA; Otieno, M; Park, M; Potts, SG; Rundlof, M; Saez, A; Steffan-Dewenter, I; Taki, H; Viana, BF; Westphal, C; Wilson, JK; Greenleaf, SS; Kremen, C.A global quantitative synthesis of local and landscape effects on wild bee pollinators in agroecosystems.Ecology Letters, 2013, 16: 584-599 A global quantitative synthesis of local and landscape effects on wild bee pollinators in agroecosystems
DIFFERENT SPATIAL SCALES; AGRICULTURAL LANDSCAPES; CROP POLLINATION; ECOSYSTEM SERVICES; SPECIES RICHNESS; NATIVE BEES; BIODIVERSITY; INTENSIFICATION; CONTEXT; METAANALYSIS
Bees provide essential pollination services that are potentially affected both by local farm management and the surrounding landscape. To better understand these different factors, we modelled the relative effects of landscape composition (nesting and floral resources within foraging distances), landscape configuration (patch shape, interpatch connectivity and habitat aggregation) and farm management (organic vs. conventional and local-scale field diversity), and their interactions, on wild bee abundance and richness for 39 crop systems globally. Bee abundance and richness were higher in diversified and organic fields and in landscapes comprising more high-quality habitats; bee richness on conventional fields with low diversity benefited most from high-quality surrounding land cover. Landscape configuration effects were weak. Bee responses varied slightly by biome. Our synthesis reveals that pollinator persistence will depend on both the maintenance of high-quality habitats around farms and on local management practices that may offset impacts of intensive monoculture agriculture. DOI
379. Konefal, S; Elliot, M; Crespi, B.The adaptive significance of adult neurogenesis: an integrative approach.Frontiers in Neuroanatomy, 2013, 7 The adaptive significance of adult neurogenesis: an integrative approach
LONG-TERM POTENTIATION; NEURAL STEM-CELLS; GENERATED GRANULE CELLS; ENHANCED SYNAPTIC PLASTICITY; BORN HIPPOCAMPAL-NEURONS; OLFACTORY-BULB NEURONS; DENTATE GYRUS; PATTERN SEPARATION; ENTORHINAL CORTEX; NEWBORN NEURONS
Adult neurogenesis in mammals is predominantly restricted to two brain regions, the dentate gyrus (DG) of the hippocampus and the olfactory bulb (OB), suggesting that these two brain regions uniquely share functions that mediate its adaptive significance. Benefits of adult neurogenesis across these two regions appear to converge on increased neuronal and structural plasticity that subserves coding of novel, complex, and fine-grained information, usually with contextual components that include spatial positioning. By contrast, costs of adult neurogenesis appear to center on potential for dysregulation resulting in higher risk of brain cancer or psychological dysfunctions, but such costs have yet to be quantified directly. The three main hypotheses for the proximate functions and adaptive significance of adult neurogenesis, pattern separation, memory consolidation, and olfactory spatial, are not mutually exclusive and can be reconciled into a simple general model amenable to targeted experimental and comparative tests. Comparative analysis of brain region sizes across two major social ecological groups of primates, gregarious (mainly diurnal haplorhines, visually-oriented, and in large social groups) and solitary (mainly noctural, territorial, and highly reliant on olfaction, as in most rodents) suggest that solitary species, but not gregarious species, show positive associations of population densities and home range sizes with sizes of both the hippocampus and OB, implicating their functions in social territorial systems mediated by olfactory cues. Integrated analyses of the adaptive significance of adult neurogenesis will benefit from experimental studies motivated and structural by ecologically and socially relevant selective contexts. DOI
378. Kraus, RHS; Van Hooft, P; Megens, HJ; Tsvey, A; Fokin, SY; Ydenberg, RC; Prins, HHT.Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms.Molecular Ecology, 2013, 22: 41-55 Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms
Anas platyrhynchos; ascertainment bias; coalescent analysis; conservation management; population genomics; single nucleotide polymorphisms
Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population. DOI
377. Magner, DB; Wollam, J; Shen, YD; Hoppe, C; Li, DL; Latza, C; Rottiers, V; Hutter, H; Antebi, A.The NHR-8 Nuclear Receptor Regulates Cholesterol and Bile Acid Homeostasis in C. elegans.Cell Metabolism, 2013, 18: 212-224 The NHR-8 Nuclear Receptor Regulates Cholesterol and Bile Acid Homeostasis in C. elegans
CAENORHABDITIS-ELEGANS; LIFE-SPAN; DAUER FORMATION; SERUM-CHOLESTEROL; SIGNALING PATHWAY; METABOLISM; DISEASE; MECHANISMS; LONGEVITY; OXYGENASE
Hormone-gated nuclear receptors (NRs) are conserved transcriptional regulators of metabolism, reproduction, and homeostasis. Here we show that C. elegans NHR-8 NR, a homolog of vertebrate liver X and vitamin D receptors, regulates nematode cholesterol balance, fatty acid desaturation, apolipoprotein production, and bile acid metabolism. Loss of nhr-8 results in a deficiency in bile acid-like steroids, called the dafachronic acids, which regulate the related DAF-12/NR, thus controlling entry into the long-lived dauer stage through cholesterol availability. Cholesterol supplementation rescues various nhr-8 phenotypes, including developmental arrest, unsaturated fatty acid deficiency, reduced fertility, and shortened life span. Notably, nhr-8 also interacts with daf-16/FOXO to regulate steady-state cholesterol levels and is synthetically lethal in combination with insulin signaling mutants that promote unregulated growth. Our studies provide important insights into nuclear receptor control of cholesterol balance and metabolism and their impact on development, reproduction, and aging in the context of larger endocrine networks. DOI
376. Mahyari, ZL; Cannell, A; de Mello, EVL; Ishikado, M; Eisaki, H; Liang, RX; Bonn, DA; Sonier, JE.Universal inhomogeneous magnetic-field response in the normal state of cuprate high-T-c superconductors.Physical Review B, 2013, 88 Universal inhomogeneous magnetic-field response in the normal state of cuprate high-T-c superconductors
We report the results of a muon spin rotation (mu SR) study of the bulk of Bi2+xSr2-xCaCu2O8+delta, as well as pure and Ca-doped YBa2Cu3Oy, which together with prior measurements reveal a universal inhomogeneous magnetic-field response of hole-doped cuprates extending to temperatures far above the critical temperature T-c. The primary features of our data are incompatible with the spatially inhomogeneous response being dominated by known charge-density-wave and spin-density-wave orders. Instead, the normal-state inhomogeneous line broadening is found to scale with the maximum value T-c(max) for each cuprate family, indicating it is controlled by the same energy scale as T-c. Since the degree of chemical disorder varies widely among the cuprates we have measured, the observed scaling constitutes evidence for an intrinsic electronic tendency toward inhomogeneity above T-c. DOI
375. Marlatt, VL; Veldhoen, N; Lo, BP; Bakker, D; Rehaume, V; Vallee, K; Haberl, M; Shang, DY; van Aggelen, GC; Skirrow, RC; Elphick, JR; Helbing, CC.Triclosan exposure alters postembryonic development in a Pacific tree frog (Pseudacris regilla) Amphibian Metamorphosis Assay (TREEMA).Aquatic Toxicology, 2013, 126: 85-94 Triclosan exposure alters postembryonic development in a Pacific tree frog (Pseudacris regilla) Amphibian Metamorphosis Assay (TREEMA)
Tree frog tadpole; Postembryonic development; Thyroid hormone receptor; Gelatinase B; Proliferating nuclear antigen; Metamorphosis assay
The Amphibian Metamorphosis Assay (AMA), developed for Xenopus laevis, is designed to identify chemicals that disrupt thyroid hormone (TH)-mediated biological processes. We adapted the AMA for use on an ecologically-relevant North American species, the Pacific tree frog (Pseudacris regilla), and applied molecular endpoints to evaluate the effects of the antibacterial agent, triclosan (TCS). Premetamorphic (Gosner stage 26-28) tadpoles were immersed for 21 days in solvent control, 1.5 mu g/L thyroxine (T-4), 0.3, 3 and 30 mu g/L (nominal) TCS, or combined T-4/TCS treatments. Exposure effects were scored by morphometric (developmental stage, wet weight, and body, snout-vent and hindlimb lengths) and molecular (mRNA abundance using quantitative real time polymerase chain reaction) criteria. T-4 treatment alone accelerated development concomitant with altered levels of TH receptors alpha and beta, proliferating cell nuclear antigen, and gelatinase B mRNAs in the brain and tail. We observed TCS-induced perturbations in all of the molecular and morphological endpoints indicating that TCS exposure disrupts coordination of postembryonic tadpole development. Clear alterations in molecular endpoints were evident at day 2 whereas the earliest morphological effects appeared at day 4 and were most evident at day 21. Although TCS alone (3 and 30 mu g/L) was protective against tadpole mortality, this protection was lost in the presence of T-4. The Pacific tree frog is the most sensitive species examined to date displaying disruption of TH-mediated development by a common antimicrobial agent. (C) 2012 Elsevier B.V. All rights reserved. DOI
374. Menounos, B; Clague, JJ; Osborn, G; Davis, PT; Ponce, F; Goehring, B; Maurer, M; Rabassa, J; Coronato, A; Marr, R.Latest Pleistocene and Holocene glacier fluctuations in southernmost Tierra del Fuego, Argentina.Quat. Sci. Rev., 2013, 77: 70-79 Latest Pleistocene and Holocene glacier fluctuations in southernmost Tierra del Fuego, Argentina
Glacier fluctuations; Holocene; Patagonia; Surface exposure dating; Tephrochronology
Some researchers propose that summer Insolation controls long-term changes in glacier extent during the Holocene. If this hypothesis is correct, the record of glacier fluctuations at high latitudes in the Southern Hemisphere should differ from that in the Northern Hemisphere. Although the chronology of Holocene glacier fluctuations in the Northern Hemisphere is well established, much uncertainty remains in the ages of Holocene glacier fluctuations in the Southern Hemisphere, especially South America. Here we report on latest Pleistocene and Holocene glacier fluctuations at the southern end of the Andes north and west of Ushuaia, Argentina. Surface exposure ages (Be-10) from glaciated bedrock beyond cirque moraines indicate that alpine areas were free of ice by ca 16.9 ka. One, and in some cases two, closely spaced moraines extend up to 2 km beyond Little Ice Age moraines within many of the cirques in the region. The mean age of five Be-10 ages from two pre-Little Ice Age moraines is 14.27-12.67 ka, whereas a minimum limiting radiocarbon age for a smaller, recessional moraine in one cirque is 12.38-12.01 ka. Our ages imply that, following glacier retreat beginning about 18.52-17.17 ka, cirque glaciers first advanced during the Antarctic Cold Reversal (14.5-12.9 ka) and may have later advanced or stabilized in the Younger Dryas Chronozone (12.9-11.7 ka). Based on the distribution of thick, geochemically distinct, and well-dated Hudson tephra, no Holocene moraines appear to be older than 7.96-7.34 ka. At some sites, there is evidence for one or more advances of glaciers sometime between 7.96-7.34 ka and 5.29-5.05 ka to limits only tens of meters beyond Little Ice Age maximum positions. Taken together, the data: 1) do not support the summer insolation hypothesis to explain Holocene glacier fluctuations in southernmost Patagonia; 2) confirm paleobotanical evidence for a warm, dry early Holocene; and 3) suggest that some glaciers in the region reached extents comparable to those of the Little Ice Age shortly before 5.29-5.05 ka. (C) 2013 Elsevier Ltd. All rights reserved. DOI
373. Moore, K.D., and J.W. Moore.Ecological restoration and enabling behavior: a new metaphoric lens?Conservation Letters, 2013, 6:1-5 Ecological restoration and enabling behavior: a new metaphoric lens?
Ecological restoration practices are changing rapidly, dramatically, and in complex ways, with higher and higher stakes both for the restoration industries themselves and for the future of biodiversity and ecosystem services. Even as ecosystem degradation has accelerated, restoration has grown into a transnational, multibillion dollar industry. These changes create an imperative for correspondingly rapid and dramatic changes in the metaphoric lenses through which we view restoration projects. In this Policy Perspectives paper, we explore a metaphor that views ecological restoration through the lens of codependency theories about enabling behaviors in the lives of addicts. The metaphor raises questions about the nature of the relation between restoration practices and an industrial growth economy “addicted” to cheap fuel and consumer goods. It suggests some policy changes that might prevent development of co-dependencies between restoration industries and ecologically destructive practices.PDF DOI
372. Muller, K; Levesque-Tremblay, G; Bartels, S; Weitbrecht, K; Wormit, A; Usadel, B; Haughn, G; Kermode, AR.Demethylesterification of Cell Wall Pectins in Arabidopsis Plays a Role in Seed Germination.Plant Physiology, 2013, 161: 305-316 Demethylesterification of Cell Wall Pectins in Arabidopsis Plays a Role in Seed Germination
ENDO-BETA-MANNANASE; ABSCISIC-ACID; XYLOGLUCAN ENDOTRANSGLYCOSYLASE; METHYLESTERASE INHIBITORS; ENDOSPERM CAP; DORMANCY; GROWTH; THALIANA; ESTERIFICATION; EXPRESSION
The methylesterification status of cell wall homogalacturonans, mediated through the action of pectin methylesterases (PMEs), influences the biophysical properties of plant cell walls such as elasticity and porosity, important parameters for cell elongation and water uptake. The completion of seed germination requires cell wall extensibility changes in both the radicle itself and in the micropylar tissues surrounding the radicle. In wild-type seeds of Arabidopsis (Arabidopsis thaliana), PME activities peaked around the time of testa rupture but declined just before the completion of germination (endosperm weakening and rupture). We overexpressed an Arabidopsis PME inhibitor to investigate PME involvement in seed germination. Seeds of the resultant lines showed a denser methylesterification status of their cell wall homogalacturonans, but there were no changes in the neutral sugar and uronic acid composition of the cell walls. As compared with wild-type seeds, the PME activities of the overexpressing lines were greatly reduced throughout germination, and the low steady-state levels neither increased nor decreased. The most striking phenotype was a significantly faster rate of germination, which was not connected to altered testa rupture morphology but to alterations of the micropylar endosperm cells, evident by environmental scanning electron microscopy. The transgenic seeds also exhibited an apparent reduced sensitivity to abscisic acid with respect to its inhibitory effects on germination. We speculate that PME activity contributes to the temporal regulation of radicle emergence in endospermic seeds by altering the mechanical properties of the cell walls and thereby the balance between the two opposing forces of radicle elongation and mechanical resistance of the endosperm. DOI
371. Munshaw, RG; Palen, WJ; Courcelles, DM; Finlay, JC.Predator-Driven Nutrient Recycling in California Stream Ecosystems.PLOS One, 2013, 8 Predator-Driven Nutrient Recycling in California Stream Ecosystems
CRITICAL THERMAL MAXIMA; FOOD-WEB STRUCTURE; FRESH-WATER; PHOSPHORUS-LIMITATION; SALAMANDER DENSITY; MOUNTAIN LAKES; WESTERN OREGON; RAINBOW-TROUT; UNITED-STATES; GIZZARD SHAD
Nutrient recycling by consumers in streams can influence ecosystem nutrient availability and the assemblage and growth of photoautotrophs. Stream fishes can play a large role in nutrient recycling, but contributions by other vertebrates to overall recycling rates remain poorly studied. In tributaries of the Pacific Northwest, coastal giant salamanders (Dicamptodon tenebrosus) occur at high densities alongside steelhead trout (Oncorhynchus mykiss) and are top aquatic predators. We surveyed the density and body size distributions of D. tenebrosus and O. mykiss in a California tributary stream, combined with a field study to determine mass-specific excretion rates of ammonium (N) and total dissolved phosphorus (P) for D. tenebrosus. We estimated O. mykiss excretion rates (N, P) by bioenergetics using field-collected data on the nutrient composition of O. mykiss diets from the same system. Despite lower abundance, D. tenebrosus biomass was 2.5 times higher than O. mykiss. Mass-specific excretion summed over 170 m of stream revealed that O. mykiss recycle 1.7 times more N, and 1.2 times more P than D. tenebrosus, and had a higher N:P ratio (8.7) than that of D. tenebrosus (6.0), or the two species combined (7.5). Through simulated trade-offs in biomass, we estimate that shifts from salamander biomass toward fish biomass have the potential to ease nutrient limitation in forested tributary streams. These results suggest that natural and anthropogenic heterogeneity in the relative abundance of these vertebrates and variation in the uptake rates across river networks can affect broad-scale patterns of nutrient limitation. DOI
370. Ocampo, CB; Caicedo, PA; Jaramillo, G; Bedoya, RU; Baron, O; Serrato, IM; Cooper, DM; Lowenberger, C.Differential Expression of Apoptosis Related Genes in Selected Strains of Aedes aegypti with Different Susceptibilities to Dengue Virus.PLOS One, 2013, 8(4): e61187. doi:10.1371/journal.pone.0061187 Differential Expression of Apoptosis Related Genes in Selected Strains of Aedes aegypti with Different Susceptibilities to Dengue Virus
YELLOW-FEVER MOSQUITO; EQUINE ENCEPHALOMYELITIS VIRUS; QUANTITATIVE TRAIT LOCI; VECTOR COMPETENCE; RNA INTERFERENCE; INNATE IMMUNITY; DROSOPHILA-MELANOGASTER; ORAL INFECTION; CULICIDAE; DIPTERA
Aedes aegypti is the principal vector of Dengue viruses worldwide. We identified field collected insects with differential susceptibility to Dengue-2 virus (DENv-2) and used isofemale selection to establish susceptible and refractory strains based on midgut infection barriers. Previous experiments had identified higher expression of apoptosis-related genes in the refractory strain. To identify potential molecular mechanisms associated with DENv susceptibility, we evaluated the differential expression of Caspase-16, Aedronc, Aedredd, Inhibitor of apoptosis (AeIAP1) and one member of the RNAi pathway, Argonaute-2 in the midguts and fat body tissues of the selected strains at specific times post blood feeding or infection with DENv-2. In the refractory strain there was significantly increased expression of caspases in midgut and fatbody tissues in the presence of DENv-2, compared to exposure to blood alone, and significantly higher caspase expression in the refractory strain compared with the susceptible strain at timepoints when DENv was establishing in these tissues. We used RNAi to knockdown gene expression; knockdown of AeIAP1 was lethal to the insects. In the refractory strain, knockdown of the pro-apoptotic gene Aedronc increased the susceptibility of refractory insects to DENv-2 from 53% to 78% suggesting a contributing role of this gene in the innate immune response of the refractory strain. DOI
369. Pardo, SA; Cooper, AB; Dulvy, NK.Avoiding fishy growth curves.Methods in Ecology and Evolution, 2013, 4: 353-360 Avoiding fishy growth curves
GULF-OF-MEXICO; LIFE-HISTORY; BIOLOGICAL PARAMETERS; MULTIMODEL INFERENCE; HAMMERHEAD SHARK; GEAR SELECTIVITY; ATLANTIC-OCEAN; AGE; MODEL; SIZE
Somatic growth is a fundamental property of living organisms, and is of particular importance for species with indeterminate growth that can change in size continuously throughout their life. For example, fishes can increase in size by 26 orders of magnitude during their lifetime, resulting in changes in production, consumption and function at the ecosystem scale. Within species, growth rates are traded off against other life-history parameters, hence an accurate description of growth is essential to understand the comparative demography, productivity, fisheries yield and extinction risk of populations and species. The growth trajectory of indeterminate growing sharks and rays (elasmobranchs) and bony fishes (teleosts) is usually modelled using a three-parameter logarithmic function, the von Bertalanffy growth function (VBGF), to describe the total length of the average individual at any given age. Recently, however, a two-parameter form has gained popularity. Rather than being estimated in the model fitting process, the third y-intercept parameter (L0) of the VBGF has been interpreted as being biologically equivalent to, and thus fixed as, the empirically estimated size at birth. We tested the equivalence assumption that L0 is the same or similar to size at birth by comparing empirical estimates of size at birth available from the literature with estimates of L0 from published data from elasmobranchs, and found that even though there is an overlap of values, there is a high degree of variability between them. We calculate the bias in the growth coefficient (k) of the VBGF by comparison between the two- and three-parameter estimation methods. We show that slight deviations in fixed L0 can cause considerable bias in growth estimates in the two-parameter VBGF while providing no benefit even when L0 matches the true value. We show that the effect of this biased growth estimate has profound consequences for fisheries stock status. We strongly recommend the use of the three-parameter VBGF and discourage use of the two-parameter VBGF because it results in substantially biased growth estimates even with slight variations in the value of fixed L0. DOI
368. Perry, CT; Murphy, GN; Kench, PS; Smithers, SG; Edinger, EN; Steneck, RS; Mumby, PJ.Caribbean-wide decline in carbonate production threatens coral reef growth.Nat. Commun., 2013, 4 Caribbean-wide decline in carbonate production threatens coral reef growth
Global-scale deteriorations in coral reef health have caused major shifts in species composition. One projected consequence is a lowering of reef carbonate production rates, potentially impairing reef growth, compromising ecosystem functionality and ultimately leading to net reef erosion. Here, using measures of gross and net carbonate production and erosion from 19 Caribbean reefs, we show that contemporary carbonate production rates are now substantially below historical (mid-to late-Holocene) values. On average, current production rates are reduced by at least 50%, and 37% of surveyed sites were net erosional. Calculated accretion rates (mm year(-1)) for shallow fore-reef habitats are also close to an order of magnitude lower than Holocene averages. A live coral cover threshold of similar to 10% appears critical to maintaining positive production states. Below this ecological threshold carbonate budgets typically become net negative and threaten reef accretion. Collectively, these data suggest that recent ecological declines are now suppressing Caribbean reef growth potential. DOI
367. Phillis, CC; O'Regan, SM; Green, SJ; Bruce, JEB; Anderson, SC; Linton, JN; Favaro, B.Multiple pathways to conservation success.Conservation Letters, 2013, 6: 98-106 Multiple pathways to conservation success
PERSISTENT ORGANIC POLLUTANTS; IVORY TRADE; DDT; DICHLORODIPHENYLTRICHLOROETHANE; HEXACHLOROCYCLOHEXANES; ELEPHANTS; TRENDS; RAIN
Conservation successes can and do happen, however, the process by which society achieves them remains unclear. Using a novel culturomics approach, we analyse word usage within digitized texts to assess the chronological order in which scientists, the public, and policymakers engage in the conservation process for three prominent conservation issues: acid rain in North America, global DDT contamination, and the overexploitation of African elephants for ivory. Variation in the order and magnitude of sector responses among the three issues emphasizes that there are multiple pathways to conservation success and that science is just one component. Our study highlights that while scientists can initiate the process, policy change does not occur in the absence of public interest. We suggest that the fate of conservation action is not solely determined by the scientific soundness of the conservation plan, but rather requires the engagement of scientists, public, and policy makers alike. DOI
366. Ramser, EM; Gan, KJ; Decker, H; Fan, EY; Suzuki, MM; Ferreira, ST; Silverman, MA.Amyloid-beta oligomers induce tau-independent disruption of BDNF axonal transport via calcineurin activation in cultured hippocampal neurons.Mol. Biol. Cell, 2013, 24: 2494-2505 Amyloid-beta oligomers induce tau-independent disruption of BDNF axonal transport via calcineurin activation in cultured hippocampal neurons
Disruption of fast axonal transport (FAT) is an early pathological event in Alzheimer's disease (AD). Soluble amyloid-beta oligomers (A beta Os), increasingly recognized as proximal neurotoxins in AD, impair organelle transport in cultured neurons and transgenic mouse models. A beta Os also stimulate hyperphosphorylation of the axonal microtubule-associated protein, tau. However, the role of tau in FAT disruption is controversial. Here we show that A beta Os reduce vesicular transport of brain-derived neurotrophic factor (BDNF) in hippocampal neurons from both wild-type and tau-knockout mice, indicating that tau is not required for transport disruption. FAT inhibition is not accompanied by microtubule destabilization or neuronal death. Significantly, inhibition of calcineurin (CaN), a calcium-dependent phosphatase implicated in AD pathogenesis, rescues BDNF transport. Moreover, inhibition of protein phosphatase 1 and glycogen synthase kinase 3 beta, downstream targets of CaN, prevents BDNF transport defects induced by A beta Os. We further show that A beta Os induce CaN activation through nonexcitotoxic calcium signaling. Results implicate CaN in FAT regulation and demonstrate that tau is not required for A beta O-induced BDNF transport disruption. DOI PubMed
364. Ryan, CP; Crespi, BJ.Androgen receptor polyglutamine repeat number: models of selection and disease susceptibility.Evolutionary Applications, 2013, 6: 180-196 Androgen receptor polyglutamine repeat number: models of selection and disease susceptibility
PROSTATE-CANCER RISK; BULBAR MUSCULAR-ATROPHY; GENE CAG REPEAT; SIMPLE SEQUENCE REPEATS; CORONARY-ARTERY-DISEASE; BONE-MINERAL DENSITY; ACID TANDEM REPEATS; HUMAN BREAST-CANCER; MALE-INFERTILITY; PERSONALITY-TRAITS
Variation in polyglutamine repeat number in the androgen receptor (AR CAGn) is negatively correlated with the transcription of androgen-responsive genes and is associated with susceptibility to an extensive list of human disease. Only a small portion of the heritability for many of these diseases is explained by conventional SNP-based genome-wide association studies, and the forces shaping AR CAGn among humans remains largely unexplored. Here, we propose evolutionary models for understanding selection at the AR CAG locus, namely balancing selection, sexual conflict, accumulation-selection, and antagonistic pleiotropy. We evaluate these models by examining AR CAGn-linked susceptibility to eight extensively studied diseases representing the diverse physiological roles of androgens, and consider the costs of these diseases by their frequency and fitness effects. Five diseases could contribute to the distribution of AR CAGn observed among contemporary human populations. With support for disease susceptibilities associated with long and short AR CAGn, balancing selection provides a useful model for studying selection at this locus. Gender-specific differences AR CAGn health effects also support this locus as a candidate for sexual conflict over repeat number. Accompanied by the accumulation of AR CAGn in humans, these models help explain the distribution of repeat number in contemporary human populations. DOI
363. Salehzadeh, O; Kavanagh, KL; Watkins, SP.Geometric limits of coherent III-V core/shell nanowires.Journal of Applied Physics, 2013, 114 Geometric limits of coherent III-V core/shell nanowires
We demonstrate the application of a simple equilibrium model based on elasticity theory to estimate the geometric limits of dislocation-free core/shell nanowires (NWs). According to these calculations, in a coherent core/shell structure, tangential strain is the dominant component in the shell region and it decreases quickly away from the heterointerface, while axial strain is the dominant component in the core and is independent of the radial position. These strain distributions energetically favour the initial relief of axial strain in agreement with the experimental appearance of only edge dislocations with line directions perpendicular to the NW growth axis at the core/shell interfaces. Such dislocations were observed for wurtzite InAs/InP and zincblende GaAs/GaP core/shell NWs with dimensions above the coherency limits predicted by the model. Good agreement of the model was also found for experimental results previously reported for GaAs/InAs and GaAs/GaSb core/shell NWs. (C) 2013 AIP Publishing LLC. DOI
362. Sandkam, BA; Joy, JB; Watson, CT; Gonzalez-Bendiksen, P; Gabor, CR; Breden, F.HYBRIDIZATION LEADS TO SENSORY REPERTOIRE EXPANSION IN A GYNOGENETIC FISH, THE AMAZON MOLLY (POECILIA FORMOSA): A TEST OF THE HYBRID-SENSORY EXPANSION HYPOTHESIS.Evolution, 2013, 67: 120-130 HYBRIDIZATION LEADS TO SENSORY REPERTOIRE EXPANSION IN A GYNOGENETIC FISH, THE AMAZON MOLLY (POECILIA FORMOSA): A TEST OF THE HYBRID-SENSORY EXPANSION HYPOTHESIS
Evolutionary genomics; gene duplication; opsin; Poeciliidae; sensory system; visual system
Expansions in sensory systems usually require processes such as gene duplication and divergence, and thus evolve slowly. We evaluate a novel mechanism leading to rapid sensory repertoire expansion: hybrid-sensory expansion (HSE). HSE occurs when two species with differently tuned sensory systems form a hybrid, bringing together alleles from each of the parental species. In one generation, a sensory repertoire is created that is the sum of the variance between parental species. The Amazon molly presents a unique opportunity to test the HSE hypothesis in a frozen hybrid. We compared opsin sequences of the Amazon molly, Poecilia formosa, to those of the parental species. Both parental species are homozygous at the RH21 locus and each of the four long wavelength sensitive loci, while P. formosa possess two different alleles at these loci; one matching each parental allele. Gene expression analysis showed P. formosa use the expanded opsin repertoire that was the result of HSE. Additionally, behavioral tests revealed P. formosa respond to colored stimuli in a manner similar or intermediate to the parental species P. mexicana and P. latipinna. Together these results strongly support the HSE hypothesis. Hybrid-sensory repertoire expansion is likely important in other hybrid species and in other sensory systems.Website DOI
361. Schwander, T; Arbuthnott, D; Gries, R; Gries, G; Nosil, P; Crespi, BJ.Hydrocarbon divergence and reproductive isolation in Timema stick insects.BMC Evolutionary Biology, 2013, 13 Hydrocarbon divergence and reproductive isolation in Timema stick insects
HOST-PLANT ADAPTATION; CRISTINAE WALKING-STICKS; MALE MATE CHOICE; CUTICULAR HYDROCARBONS; SEXUAL SELECTION; DROSOPHILA-MOJAVENSIS; MORPHOLOGICAL EVOLUTION; CACTOPHILIC DROSOPHILA; INCIPIENT SPECIATION; MATING PREFERENCES
Background: Individuals commonly prefer certain trait values over others when choosing their mates. If such preferences diverge between populations, they can generate behavioral reproductive isolation and thereby contribute to speciation. Reproductive isolation in insects often involves chemical communication, and cuticular hydrocarbons, in particular, serve as mate recognition signals in many species. We combined data on female cuticular hydrocarbons, interspecific mating propensity, and phylogenetics to evaluate the role of cuticular hydrocarbons in diversification of Timema walking-sticks. Results: Hydrocarbon profiles differed substantially among the nine analyzed species, as well as between partially reproductively-isolated T. cristinae populations adapted to different host plants. In no-choice trials, mating was more likely between species with similar than divergent hydrocarbon profiles, even after correcting for genetic divergences. The macroevolution of hydrocarbon profiles, along a Timema species phylogeny, fits best with a punctuated model of phenotypic change concentrated around speciation events, consistent with change driven by selection during the evolution of reproductive isolation. Conclusion: Altogether, our data indicate that cuticular hydrocarbon profiles vary among Timema species and populations, and that most evolutionary change in hydrocarbon profiles occurs in association with speciation events. Similarities in hydrocarbon profiles between species are correlated with interspecific mating propensities, suggesting a role for cuticular hydrocarbon profiles in mate choice and speciation in the genus Timema. DOI
360. Schwander, T; Crespi, BJ; Gries, R; Gries, G.Neutral and selection-driven decay of sexual traits in asexual stick insects.Proceedings of the Royal Society B-Biological Sciences, 2013, 280 Neutral and selection-driven decay of sexual traits in asexual stick insects
TIMEMA WALKING-STICKS; WOLBACHIA-INDUCED PARTHENOGENESIS; LEPTOPILINA-CLAVIPES HYMENOPTERA; EVOLUTION; REPRODUCTION; ANCIENT; VESTIGIALIZATION; PHYLOGENETICS; PARASITOIDS; APHELINIDAE
Environmental shifts and lifestyle changes may result in formerly adaptive traits becoming non-functional or maladaptive. The subsequent decay of such traits highlights the importance of natural selection for adaptations, yet its causes have rarely been investigated. To study the fate of formerly adaptive traits after lifestyle changes, we evaluated sexual traits in five independently derived asexual lineages, including traits that are specific to males and therefore not exposed to selection. At least four of the asexual lineages retained the capacity to produce males that display normal courtship behaviours and are able to fertilize eggs of females from related sexual species. The maintenance of male traits may stem from pleiotropy, or from these traits only regressing via drift, which may require millions of years to generate phenotypic effects. By contrast, we found parallel decay of sexual traits in females. Asexual females produced altered airborne and contact signals, had modified sperm storage organs, and lost the ability to fertilize their eggs, impeding reversals to sexual reproduction. Female sexual traits were decayed even in recently derived asexuals, suggesting that trait changes following the evolution of asexuality, when they occur, proceed rapidly and are driven by selective processes rather than drift. DOI
359. Shelley, LK; Osachoff, HL; van Aggelen, GC; Ross, PS; Kennedy, CJ.Alteration of immune function endpoints and differential expression of estrogen receptor isoforms in leukocytes from 17 beta-estradiol exposed rainbow trout (Oncorhynchus mykiss).General and Comparative Endocrinology, 2013, 180: 24-32 Alteration of immune function endpoints and differential expression of estrogen receptor isoforms in leukocytes from 17 beta-estradiol exposed rainbow trout (Oncorhynchus mykiss)
PERIPHERAL-BLOOD LEUKOCYTES; FLOW-CYTOMETRIC ANALYSIS; PERSONAL CARE PRODUCTS; GENE-EXPRESSION; IN-VITRO; CYPRINUS-CARPIO; ENVIRONMENTAL ESTROGENS; DISEASE RESISTANCE; TERM EXPOSURE; COMMON CARP
While the endocrine system is known to modulate immune function in vertebrates, the role of 17 beta-estradiol (E2) in cellular immune function of teleosts is poorly understood. The cellular and molecular responses of juvenile rainbow trout (Oncorhynchus mykiss) to E2 treatment were evaluated by exposing fish to 0.47 +/- 0.02 mu g/L E2 (mean +/- SEM) for either 2 or 7 d, with a subsequent 14 d recovery period. After 2 and 7 d of exposure to E2, hematocrit was significantly lower than in control fish. Lipopolysaccharide-induced lymphocyte proliferation was elevated on day 2 and concanavalin A-induced lymphocyte proliferation was reduced following 7 d of E2 exposure. Four estrogen receptor (ER) transcripts were identified in purified trout head kidney leukocytes (HKL) and peripheral blood leukocytes (PBL). While the mRNA abundance of ER beta 1 and ER beta 2 was unaffected by treatment, ER alpha 1 was up-regulated in HKL and PBL following 7 d of E2 exposure. ER alpha 2 was up-regulated in HKL after 7 d of E2 exposure, but down-regulated in PBL after 2 and 7 d of treatment. All parameters that were altered during the E2 exposure period returned to baseline levels following the recovery period. This study reports the presence of the full repertoire of ERs in purified HKL for the first time, and demonstrates that ER alpha transcript abundance in leukocytes can be regulated by waterborne E2 exposure. It also demonstrated that physiologically-relevant concentrations of E2 can modulate several immune functions in salmonids, which may have widespread implications for xenoestrogen-associated immunotoxicity in feral fish populations inhabiting contaminated aquatic environments. (C) 2012 Elsevier Inc. All rights reserved. DOI
358. Smith, RA; Schuetz, M; Roach, M; Mansfield, SD; Ellis, B; Samuels, L.Neighboring Parenchyma Cells Contribute to Arabidopsis Xylem Lignification, while Lignification of Interfascicular Fibers Is Cell Autonomous.Plant Cell, 2013, 25: 3988-3999 Neighboring Parenchyma Cells Contribute to Arabidopsis Xylem Lignification, while Lignification of Interfascicular Fibers Is Cell Autonomous
Lignin is a critical structural component of plants, providing vascular integrity and mechanical strength. Lignin precursors (monolignols) must be exported to the extracellular matrix where random oxidative coupling produces a complex lignin polymer. The objectives of this study were twofold: to determine the timing of lignification with respect to programmed cell death and to test if nonlignifying xylary parenchyma cells can contribute to the lignification of tracheary elements and fibers. This study demonstrates that lignin deposition is not exclusively a postmortem event, but also occurs prior to programmed cell death. Radiolabeled monolignols were not detected in the cytoplasm or vacuoles of tracheary elements or neighbors. To experimentally define which cells in lignifying tissues contribute to lignification in intact plants, a microRNA against CINNAMOYL CoA-REDUCTASE1 driven by the promoter from CELLULOSE SYNTHASE7 (ProCESA7:miRNA CCR1) was used to silence monolignol biosynthesis specifically in cells developing lignified secondary cell walls. When monolignol biosynthesis in ProCESA7:miRNA CCR1 lines was silenced in the lignifying cells themselves, but not in the neighboring cells, lignin was still deposited in the xylem secondary cell walls. Surprisingly, a dramatic reduction in cell wall lignification of extraxylary fiber cells demonstrates that extraxylary fibers undergo cell autonomous lignification. DOI
357. Soares, MC; Cardoso, SC; Nicolet, KJ; Côté, IM; Bshary, R.Indo-Pacific parrotfish exert partner choice in interactions with cleanerfish but Caribbean parrotfish do not.Animal Behaviour, 2013, 86: 611-615 Indo-Pacific parrotfish exert partner choice in interactions with cleanerfish but Caribbean parrotfish do not
CLIENT REEF FISH; LABROIDES-DIMIDIATUS; TACTILE STIMULATION; CLEANING GOBIES; SERVICE QUALITY; CONTROL MECHANISMS; MUTUALISM; COOPERATION; PUNISHMENT; EVOLUTION
Cooperation theory puts a strong emphasis on partner control mechanisms that have evolved to stabilize cooperation against the temptation of cheating. The marine cleaning mutualism between the Indo-Pacific bluestreack cleaner wrasse, Labroides dimidiatus, and its reef fish 'clients' has been a model system to study partner control mechanisms and counterstrategies. These cleaners cooperate by eating ectoparasites; however, they can cheat by taking client mucus, which they prefer. Such a conflict may be the exception. For example, Caribbean cleaning gobies, Elacatinus spp., prefer to eat ectoparasites instead of mucus. While partner control mechanisms and counterstrategies seem to be absent in cleaning gobies, no study has directly compared cleaner wrasses and cleaning gobies by using the same methods. We examined systematic differences in cleaning interaction patterns and strategic behaviour exhibited by 12 closely related parrotfish species in the two systems. Parrotfish seeking cleaner wrasses visited them more often and spent more time with their cleaner than parrotfish seeking cleaning gobies. Moreover, the clients of cleaner wrasses returned more often to the same cleaner following a positive interaction, whereas the clients of cleaning gobies were less influenced by the outcome of previous interactions. We hypothesize that the higher frequency and repeated nature of interactions observed in the cleaner wrasse system, combined with the need to resolve conflicts, might have been prerequisites for the development of complex behavioural strategies. (C) 2013 The Association for the Study of Animal Behaviour. Published by Elsevier Ltd. All rights reserved. DOI
356. Squires, S and Bisgrove, S.The Microtubule-Associated Protein END BINDING1b, Auxin, and Root Responses to Mechanical Cues.Journal of Plant Growth Regulation, 2013, 32: 681-691 The Microtubule-Associated Protein END BINDING1b, Auxin, and Root Responses to Mechanical Cues
The ability of roots to penetrate through the soil
and maneuver around rocks and other impenetrable objects
requires a system for modulating output from mechanosensory
response networks. The microtubule-associated protein END BINDING1b (EB1b) has a role in this process; it represses root responses to mechanical cues. In this study, a possible relationship between EB1b and auxin during root responses to mechanical cues was investigated. We found that eb1b-1-mutant roots are more sensitive than wild-type roots to chemicals that disrupt auxin transport, whereas the roots of mutants with defects in auxin transport are resistant to these treatments. Using seedlings that express the auxin-sensitive DR5rev::GFP construct, we also found that wild-type and eb1b-1 roots treated with the auxin transport inhibitor naphthylphthalamic acid exhibited dose-dependent reductions in basipetal auxin transport that were indistinguishable from each other. The responses of eb1b-1 roots to mechanical cues were also enhanced over wild type in the presence of p-chlorophenoxyisobutyric acid, a chemical thought to inhibit auxin signaling. Finally, roots of eb1b-1 and wild-type plants exhibited slight increases in loop formation in response to increasing levels of exogenously applied indole-3-acetic acid or 1-naphthalene acetic acid. Taken together, these results suggest that the repression of loop formation by EB1b and auxin transport/signaling occurs by different mechanisms.
355. Steimel, A; Suh, J; Hussainkhel, A; Deheshi, S; Grants, JM; Zapf, R; Moerman, DG; Taubert, S; Hutter, H.The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation.Developmental Biology, 2013, 377: 385-398 The C. elegans CDK8 Mediator module regulates axon guidance decisions in the ventral nerve cord and during dorsal axon navigation
RNA-POLYMERASE-II; CHROMOSOME DOSAGE COMPENSATION; LIM HOMEOBOX GENE; CAENORHABDITIS-ELEGANS; TRANSCRIPTIONAL ACTIVATION; NEURONAL DIFFERENTIATION; PHARYNX DEVELOPMENT; COMBINATORIAL CODE; COLORECTAL-CANCER; ROBO RECEPTORS
Receptors expressed on the growth cone of outgrowing axons detect cues required for proper navigation. The pathway choices available to an axon are in part defined by the set of guidance receptors present on the growth cone. Regulated expression of receptors and genes controlling the localization and activity of receptors ensures that axons respond only to guidance cues relevant for reaching their targets. In genetic screens for axon guidance mutants, we isolated an allele of let-19/mdt-13, a component of the Mediator, a large similar to 30 subunit protein complex essential for gene transcription by RNA polymerase II. LET-19/MDT-13 is part of the CDK8 module of the Mediator. By testing other Mediator components, we found that all subunits of the CDK8 module as well as some other Mediator components are required for specific axon navigation decisions in a subset of neurons. Expression profiling demonstrated that let-19/mdt-13 regulates the expression of a large number of genes in interneurons. A mutation in the sax-3 gene, encoding a receptor for the repulsive guidance cue SLT-1, suppresses the commissure navigation defects found in cdk-8 mutants. This suggests that the CDK8 module specifically represses the SAX-3/ROBO pathway to ensure proper commissure navigation. (C) 2013 Elsevier Inc. All rights reserved. DOI
354. Stein, RW; Williams, TD.Extreme Intraclutch Egg-Size Dimorphism in Eudyptes Penguins, an Evolutionary Response to Clutch-Size Maladaptation.American Naturalist, 2013, 182: 260-270 Extreme Intraclutch Egg-Size Dimorphism in Eudyptes Penguins, an Evolutionary Response to Clutch-Size Maladaptation
BREEDING BIOLOGY; ROCKHOPPER PENGUINS; MACARONI PENGUINS; PYGOSCELIS-PAPUA; SPHENISCUS-HUMBOLDTI; MAGELLANIC PENGUINS; CRESTED PENGUINS; SOUTH GEORGIA; BIRD ISLAND; SUCCESS
Eudyptes penguins (six species) are uniquely characterized by a two-egg clutch with extreme intraclutch egg-size dimorphism (ESD): the first-laid A-egg is 17.5%-56.9% smaller than the B-egg. Although A-eggs are viable, they almost never produce fledged chicks (genus average <1%). Using classical life-history theory and phylogenetic comparative methods, we demonstrate a marked slow-down in the life history of Eudyptes: age of first reproduction is 52% later and annual fecundity 48% lower compared with other two-egg clutch penguin species. All six Eudyptes species have retained a two-egg clutch, despite this pronounced life-history slow-down; this suggests evolutionary mismatch between clutch size and chicks fledged per clutch. Consistent with this, we show that Eudyptes fledge 43% fewer chicks per clutch than other two-egg clutch penguin species. Extreme intraclutch ESD in Eudyptes is associated primarily with a uniform (5%) increase in relative B-egg size, and B-egg size has evolved in accord with life history. We further show that intraclutch ESD is positively correlated with age of first reproduction in Eudyptes but not in other two-egg clutch penguin species. We argue that Eudyptes' persistent failure to evolve a one-egg clutch constitutes a unique genus-wide evolutionary maladaptation and that extreme intraclutch ESD evolved as a correlated response to selection favoring a slower life history imposed by their extreme pelagic overwintering and migration ecology. DOI
353. Stencel, A; Crespi, B.What is a genome?Molecular Ecology, 2013, 22: 3437-3443 What is a genome?
HORIZONTAL GENE-TRANSFER; TRANSPOSABLE ELEMENTS; EVOLUTION; CHROMOSOME; HISTORY; ENCODE; DNA; INTROGRESSION; DIVERSITY; SEQUENCES
The field of genomics is expanding rapidly, yet the meanings of the word genome' have yet to be conceptualized in explicit, coherent and useful frameworks. We develop and apply an evolutionary conceptualization of the genome, which represents a logical extension of the evolutionary definition of a gene developed by George C. Williams. An evolutionary genome thus represents a set of genetic material, in a lineage, that due to common interests tends to favour the same or similar phenotypes. This conceptualization provides novel perspectives on genome functions, boundaries and evolution, which should help to guide theoretical and empirical genomics research. DOI
352. Suraci, JP; Dill, LM.Short timescale rate maximization by gulls and implications for predation on size-structured prey.Behavioral Ecology, 2013, 24: 280-292 Short timescale rate maximization by gulls and implications for predation on size-structured prey
diet breadth; glaucous-winged gull; intertidal ecology; Pisaster ochraceus; prey encounter rate
The timescale over which a predator estimates changes in prey encounter rates will play an important role in maximization of energetic returns from foraging in habitats where prey availability is highly variable through time. However, studies that explicitly test the temporal scale over which foragers track changes in prey availability are surprisingly rare. The increasingly well-recognized impact of terrestrial predators (e.g., birds) on intertidal food webs is likely to depend on their ability to track prey fluctuations in these highly variable environments. Here, we compare the predictions of 2 optimal diet models: a "classic" model in which prey encounter rate estimates are based on long-term, site-level abundance averages, and a model in which encounter rate estimates change at regular intervals throughout the foraging period. We parameterized these models using data from a field study on glaucous-winged gulls (Larus glaucescens) foraging on various sizes of the sea star Pisaster ochraceus. Predictions from the classic model, which assumes constant diet breadth throughout the tide cycle, did not match field observations of diet breadth. The "tide-sensitive" model, which assumes that gulls track tide-related changes in prey abundance, provided a better fit to observational data, explaining the full range of Pisaster sizes consumed by gulls. We conclude that gulls track short-term changes in prey encounter rates within a single low tide period to maximize foraging returns. We also present data for high rates of Pisaster removal by gulls, challenging the view of this sea star as a top predator in its intertidal communities. DOI
351. Taylor, RG; Scanlon, B; Doll, P; Rodell, M; van Beek, R; Wada, Y; Longuevergne, L; Leblanc, M; Famiglietti, JS; Edmunds, M; Konikow, L; Green, TR; Chen, JY; Taniguchi, M; Bierkens, MFP; MacDonald, A; Fan, Y; Maxwell, RM; Yechieli, Y; Gurdak, JJ; Allen, DM; Shamsudduha, M; Hiscock, K; Yeh, PJF; Holman, I; Treidel, H.Ground water and climate change.Nat. Clim. Chang., 2013, 3: 322-329 Ground water and climate change
As the world's largest distributed store of fresh water, ground water plays a central part in sustaining ecosystems and enabling human adaptation to climate variability and change. The strategic importance of ground water for global water and food security will probably intensify under climate change as more frequent and intense climate extremes (droughts and floods) increase variability in precipitation, soil moisture and surface water. Here we critically review recent research assessing the impacts of climate on ground water through natural and human-induced processes as well as through groundwater-driven feedbacks on the climate system. Furthermore, we examine the possible opportunities and challenges of using and sustaining groundwater resources in climate adaptation strategies, and highlight the lack of groundwater observations, which, at present, limits our understanding of the dynamic relationship between ground water and climate. DOI
350. Thomas, GH; Hartmann, K; Jetz, W; Joy, JB; Mimoto, A; Mooers, AO.PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences.Methods in Ecology and Evolution, 2013, 4: 1011-1017 PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences
MOLECULAR PHYLOGENIES; DIVERSIFICATION; BIRDS; DIVERSITY; MAMMALS; SPACE; TRAIT
1. Phylogenetic trees that include all member lineages are necessary for many questions in macroevolution, biogeography and conservation. Currently, producing such trees when genetic data or phenotypic characters for some tips are missing generally involves assigning missing species to the root of their most exclusive clade, essentially grafting them onto existing and static topologies as polytomies. 2. We describe an R package, PASTIS', that enables a two-stage Bayesian method using MrBayes version 3.2 (or higher) to incorporate lineages lacking genetic data at the tree inference stage. The inputs include a consensus topology, a set of taxonomic statements (e.g. placing species in genera and aligning some genera with each other or placing subspecies within species) and user-defined priors on edge lengths and topologies. PASTIS produces input files for execution in MrBayes that will produce a posterior distribution of complete ultrametric trees that captures uncertainty under a homogeneous birth-death prior model of diversification and placement constraints. If the age distribution of a focal node is known (e.g. from fossils), the ultrametric tree distribution can be converted to a set of dated trees. We also provide functions to visualize the placement of missing taxa in the posterior distribution. 3. The PASTIS approach is not limited to the level of species and could equally be applied to higher or lower levels of organization (e.g. accounting for all recognized subspecies or populations within a species) given an appropriate choice of priors on branching times. DOI
349. Thompson, O; Edgley, M; Strasbourger, P; Flibotte, S; Ewing, B; Adair, R; Au, V; Chaudhry, I; Fernando, L; Hutter, H; Kieffer, A; Lau, J; Lee, N; Miller, A; Raymant, G; Shen, B; Shendure, J; Taylor, J; Turner, EH; Hillier, LW; Moerman, DG; Waterston, RH.The million mutation project: A new approach to genetics in Caenorhabditis elegans.Genome Research, 2013, 23: 1749-1762 The million mutation project: A new approach to genetics in Caenorhabditis elegans
SACCHAROMYCES-CEREVISIAE GENOME; C-ELEGANS; FUNCTIONAL GENOMICS; RNA INTERFERENCE; LINKED SITES; GENES; YEAST; IDENTIFICATION; DROSOPHILA; DELETION
We have created a library of 2007 mutagenized Caenorhabditis elegans strains, each sequenced to a target depth of 15-fold coverage, to provide the research community with mutant alleles for each of the worm's more than 20,000 genes. The library contains over 800,000 unique single nucleotide variants (SNVs) with an average of eight nonsynonymous changes per gene and more than 16,000 insertion/deletion (indel) and copy number changes, providing an unprecedented genetic resource for this multicellular organism. To supplement this collection, we also sequenced 40 wild isolates, identifying more than 630,000 unique SNVs and 220,000 indels. Comparison of the two sets demonstrates that the mutant collection has a much richer array of both nonsense and missense mutations than the wild isolate set. We also find a wide range of rDNA and telomere repeat copy number in both sets. Scanning the mutant collection for molecular phenotypes reveals a nonsense suppressor as well as strains with higher levels of indels that harbor mutations in DNA repair genes and strains with abundant males associated with him mutations. All the strains are available through the Caenorhabditis Genetics Center and all the sequence changes have been deposited in WormBase and are available through an interactive website. DOI
348. Thomson, JA; Cooper, AB; Burkholder, DA; Heithaus, MR; Dill, LM.Correcting for heterogeneous availability bias in surveys of long-diving marine turtles.Biological Conservation, 2013, 165: 154-161 Correcting for heterogeneous availability bias in surveys of long-diving marine turtles
AERIAL SURVEYS; SEA-TURTLE; WESTERN-AUSTRALIA; LOGGERHEAD TURTLE; SHARK BAY; BUOYANCY CONTROL; CARETTA-CARETTA; HARBOR PORPOISE; GREEN TURTLES; ABUNDANCE
Effective conservation requires reliable data on the abundance and distribution of animals in space and time. During ship-based or aerial surveys for diving marine vertebrates such as sea turtles and marine mammals, a proportion of animals in a surveyed area will be missed because they are diving and out of view. While it is likely that dive and surface times vary with environmental conditions, such variation is rarely incorporated into survey-based research and its consequences for analyses of survey data are not well known. We quantified the effects of neglecting to account for variation in the dive-surfacing patterns of green turtles (Chelonia mydas) and loggerhead turtles (Caretta caretta) when analyzing boat-based survey data from a foraging ground in Western Australia. We found that analyses of turtle sightings data can be confounded by variation in the probability of turtles being at the surface where they are available for detection. For example, during the cold season in deeper areas in Shark Bay, green and loggerhead turtle density was underestimated by 45% and 21%, respectively, if extended dive times relative to population medians were not accounted for. These results have important implications for applications of survey data for a variety of taxa including other sea turtles, marine mammals and large sharks that are surveyed by boat or plane. Diving and depth use studies have much to contribute to the assessment and management of these groups, which include many species of conservation concern. (C) 2013 Elsevier Ltd. All rights reserved. DOI
347. Trebilco, R., Baum, J.K., Salomon, A.K. and Dulvy, N. K.Ecosystem ecology: size-based constraints on the pyramids of life.Trends in Ecology & Evolution, 2013, 28: 423–431. Ecosystem ecology: size-based constraints on the pyramids of life
Biomass distribution and energy flow in ecosystems are traditionally described with trophic pyramids, and increasingly with size spectra, particularly in aquatic ecosystems. Here, we show that these methods are equivalent and interchangeable representations of the same information. Although pyramids are visually intuitive, explicitly linking them to size spectra connects pyramids to metabolic and size-based theory, and illuminates size-based constraints on pyramid shape. We show that bottom-heavy pyramids should predominate in the real world, whereas top-heavy pyramids indicate overestimation of predator abundance or energy subsidies. Making the link to ecological pyramids establishes size spectra as a central concept in ecosystem ecology, and provides a powerful framework both for understanding baseline expectations of community structure and for evaluating future scenarios under climate change and exploitation.Website DOI
346. Turner, DG; Ward, BC; Bond, JD; Jensen, BJL; Froese, DG; Telka, AM; Zazula, GD; Bigelow, NH.Middle to Late Pleistocene ice extents, tephrochronology and paleoenvironments of the White River area, southwest Yukon.Quat. Sci. Rev., 2013, 75: 59-77 Middle to Late Pleistocene ice extents, tephrochronology and paleoenvironments of the White River area, southwest Yukon
Dating; Pleistocene; Beringia; Last Interglacial; Paleoenvironments; Tephrochronology; Macrofossil; Pollen
Sedimentary deposits from two Middle to Late Pleistocene glaciations and intervening non-glacial intervals exposed along the White River in southwest Yukon, Canada, provide a record of environmental change for much of the past 200 000 years. The study sites are beyond the Marine Isotope stage (MIS) 2 glacial limit, near the maximum regional extent of Pleistocene glaciation. Non-glacial deposits include up to 25 m of loess, peat and gravel with paleosols, pollen, plant and insect macrofossils, large mammal fossils and tephra beds. Finite and non-finite radiocarbon dates, and twelve different tephra beds constrain the chronology of these deposits. Tills correlated to MIS 4 and 6 represent the penultimate and maximum Pleistocene glacial limits, respectively. The proximity of these glacial limits to each other, compared to limits in central Yukon, suggests precipitation conditions were more consistent in southwest Yukon than in central Yukon during the Pleistocene. Conditions in MIS 5e and 5a are recorded by two boreal forest beds, separated by a shrub birch tundra, that indicate environments as warm or warmer than present. A dry, treeless steppe-tundra, dominated by Artemisia frigida, upland grasses and forbs existed during the transition from late MIS 3 to early MIS 2. These glacial and non-glacial deposits constrain the glacial limits and paleoenvironments during the Middle to Late Pleistocene in southwest Yukon. (c) 2013 Elsevier Ltd. All rights reserved. DOI
345. Unsoeld, T; Park, JO; Hutter, H.Discoidin domain receptors guide axons along longitudinal tracts in C. elegans.Developmental Biology, 2013, 374: 142-152 Discoidin domain receptors guide axons along longitudinal tracts in C. elegans
TYROSINE KINASE FAMILY; BASEMENT-MEMBRANE COLLAGEN; CAENORHABDITIS-ELEGANS; IV COLLAGEN; MATRIX METALLOPROTEINASE-2; EXTRACELLULAR-MATRIX; PROTEIN-KINASES; GENE-EXPRESSION; CELL-MIGRATION; XIII COLLAGEN
Discoidin domain receptors are a family of receptor tyrosine kinases activated by collagens. Here we characterize the role of the two discoidin domain receptors, ddr-1 and ddr-2, of the nematode C. elegans during nervous system development. ddr-2 mutant animals exhibit axon guidance defects in major longitudinal tracts most prominently in the ventral nerve cord. ddr-1 mutants show no significant phenotype on their own but significantly enhance guidance defects of ddr-2 in double mutants. ddr-1 and ddr-2 GFP-reporter constructs are expressed in neurons with axons in all affected nerve tracts. DDR-1 and DDR-2 GFP fusion proteins localize to axons. DDR-2 is required cell-autonomously in the PVPR neuron for the guidance of the PVPR pioneer axon, which establishes the left ventral nerve cord tract and serves as substrate for later outgrowing follower axons. Our results provide the first insight on discoidin domain receptor function in invertebrates and establish a novel role for discoidin domain receptors in axon navigation and axon tract formation. (c) 2012 Elsevier Inc. All rights reserved.Website DOI
344. Vines, TH; Andrew, RL; Bock, DG; Franklin, MT; Gilbert, KJ; Kane, NC; Moore, JS; Moyers, BT; Renaut, S; Rennison, DJ; Veen, T; Yeaman, S.Mandated data archiving greatly improves access to research data.FASEB Journal, 2013, 27: 1304-1308 Mandated data archiving greatly improves access to research data
AUTHORS
The data underlying scientific papers should be accessible to researchers both now and in the future, but how best can we ensure that these data are available? Here we examine the effectiveness of four approaches to data archiving: no stated archiving policy, recommending (but not requiring) archiving, and two versions of mandating data deposition at acceptance. We control for differences between data types by trying to obtain data from papers that use a single, widespread population genetic analysis, STRUCTURE. At one extreme, we found that mandated data archiving policies that require the inclusion of a data availability statement in the manuscript improve the odds of finding the data online almost 1000-fold compared to having no policy. However, archiving rates at journals with less stringent policies were only very slightly higher than those with no policy at all. We also assessed the effectiveness of asking for data directly from authors and obtained over half of the requested datasets, albeit with similar to 8 d delay and some disagreement with authors. Given the long-term benefits of data accessibility to the academic community, we believe that journal-based mandatory data archiving policies and mandatory data availability statements should be more widely adopted.-Vines, T. H., Andrew, R. L., Bock, D. G., Franklin, M. T., Gilbert, K. J., Kane, N. C., Moore, J-S., Moyers, B. T., Renaut, S., Rennison, D. J., Veen, T., Yeaman, S. Mandated data archiving greatly improves access to research data. FASEB J. 27, 1304-1308 (2013). www.fasebj.org DOI
343. Watson, CT; Steinberg, KM; Huddleston, J; Warren, RL; Malig, M; Schein, J; Willsey, AJ; Joy, JB; Scott, JK; Graves, TA; Wilson, RK; Holt, RA; Eichler, EE; Breden, F.Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation.Am. J. Hum. Genet., 2013, 92: 530-546 Complete Haplotype Sequence of the Human Immunoglobulin Heavy-Chain Variable, Diversity, and Joining Genes and Characterization of Allelic and Copy-Number Variation
The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of similar to 1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large gemiline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (F-st = 0.3-0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested. DOI PubMed
342. Wilson, S; Anderson, EM; Wilson, ASG; Bertram, DF; Arcese, P.Citizen Science Reveals an Extensive Shift in the Winter Distribution of Migratory Western Grebes.PLOS One, 2013, 8 Citizen Science Reveals an Extensive Shift in the Winter Distribution of Migratory Western Grebes
CURRENT ECOSYSTEM; BIRD POPULATIONS; PACIFIC-OCEAN; ABUNDANCE; CLIMATE; FOOD; SEA; SEABIRDS; DECLINES; RECOVERY
Marine waterbirds have shown variable trends in abundance over the past four decades with some species displaying steep declines along the Pacific coast from British Columbia through California. One of the most dramatic changes has been that of western grebes (Aechmophorus occidentalis) in the Salish Sea. This region was a former core of the species wintering distribution but they have become increasingly rare prompting calls for conservation action. A more thorough understanding of this situation requires the analysis of trends at broader geographic scales as well as a consideration of mechanisms that might have led to a change in abundance. We used hierarchical modeling with a Bayesian framework applied to 36 years of Audubon Christmas Bird Count data to assess continent-wide and regional population trends in western and Clark's grebes (A. clarkii) from 1975 to 2010. Our results show that the North American wintering population of Aechmophorus grebes decreased by similar to 52% after 1975, but also that western grebes displayed strongly opposing regional patterns. Abundance decreased by about 95% over 36 years in the Salish Sea but increased by over 300% along coastal California. As a result, the mean centre of the species distribution shifted south by an estimated 895 km between 1980 and 2010. Mechanisms underlying this shift require further study but we hypothesize that it may be related to a change in the abundance and availability of their forage fish prey base. Since the mid-1980s, the Pacific sardine stock off the California coast increased from a few thousand metric tonnes to over two million. At the same time both the abundance and availability of Pacific herring declined in the Salish Sea. Studies are needed to examine this hypothesis further and additional consideration should be directed at other changes in the marine environment that may have contributed to a range shift. DOI
341. Winter, V; Elliott, JE; Letcher, RJ; Williams, TD.Validation of an egg-injection method for embryotoxicity studies in a small, model songbird, the zebra finch (Taeniopygia guttata).Chemosphere, 2013, 90: 125-131 Validation of an egg-injection method for embryotoxicity studies in a small, model songbird, the zebra finch (Taeniopygia guttata)
In ova exposure; Embryotoxicity; Developmental effects; Zebra finch; Flame retardant; PBDE-99
Female birds deposit or 'excrete' lipophilic contaminants to their eggs during egg formation. Concentrations of xenobiotics in bird eggs can therefore accurately indicate levels of contamination in the environment and sampling of bird eggs is commonly used as a bio-monitoring tool. It is widely assumed that maternally transferred contaminants cause adverse effects on embryos but there has been relatively little experimental work confirming direct developmental effects (cf. behaviorally-mediated effects). We validated the use of egg injection for studies of in ovo exposure to xenobiotics for a small songbird model species, the zebra finch (Taeniopygia guttata), where egg weight averages only 1 g. We investigated a) the effect of puncturing eggs with or without vehicle (DMSO) injection on egg fate (embryo development), chick hatching success and subsequent growth to 90 days (sexual maturity), and b) effects of two vehicle solutions (DMSO and safflower oil) on embryo and chick growth. PBDE-99 and -47 were measured in in ovo PBDE-treated eggs, chicks and adults to investigate relationships between putative injection amounts and the time course of metabolism (debromination) of PBDE-99 during early development. We successfully injected a small volume (5 mu L) of vehicle into eggs, at incubation day 0, with no effects on egg or embryo fate and with hatchability similar to that for non-manipulated eggs in our captive-breeding colony (43% vs. 48%). We did find some evidence for an inhibitory effect of DMSO vehicle on post-hatching chick growth, in male chicks only. This method can be used to treat eggs in a dose-dependent, and ecologically-relevant, manner with PBDE-99, based on chemical analysis of eggs, hatchling and adults. (C) 2012 Elsevier Ltd. All rights reserved. DOI
340. Winter, V; Williams, TD; Elliott, JE.A three-generational study of In ovo exposure to PBDE-99 in the zebra finch.Environmental Toxicology and Chemistry, 2013, 32: 562-568 A three-generational study of In ovo exposure to PBDE-99 in the zebra finch
POLYBROMINATED DIPHENYL ETHERS; BROMINATED FLAME RETARDANTS; KESTRELS FALCO-SPARVERIUS; CHICKEN GALLUS-GALLUS; HERRING GULL EGGS; AMERICAN KESTRELS; 2,2',4,4',5-PENTABROMODIPHENYL ETHER; TAENIOPYGIA-GUTTATA; REPRODUCTIVE EFFORT; NEONATAL EXPOSURE
Based on a literature review of avian data for polybrominated diphenyl ethers (PBDEs), ecologically relevant doses, low (10ng/egg), medium (100ng/egg), and high (1,000ng/egg) of the 2,2,4,4,5-pentabromodiphenyl ether (BDE-99) congener along with dimethylsulfoxide (DMSO) control were injected into the yolk sac of un-incubated eggs of zebra finch, Taeniopygia guttata. Offspring development and adult phenotype were followed over three generations. No effects of in ovo PBDE exposure on hatching success, chick growth, thyroid hormone levels, or hematological traits were measured at sexual maturity (90d posthatching). However, the authors did detect significant effects of BDE-99 treatment on adult phenotype of in ovoexposed birds by breeding observations, in which clutch size was significantly smaller in all PBDE-dosed birds (low, medium, and high) compared with controls. A trend was also seen for longer laying intervals in PBDE-dosed birds (1314d) compared with control birds (8d). In addition, a significant effect of PBDE was found on growth of the second-generation offspring of in ovotreated females; body mass was significantly lower in the high-PBDE dosed birds compared with controls from hatch through to fledging (day 30). The authors found no evidence of effects over the longer term and in successive generations, whether in adult, reproductive phenotype of the second-generation offspring of in ovotreated birds, or in the growth of their (third-generation) offspring. Their results suggest that egg levels as low as 10ng/g BDE-99 may affect reproduction in small passerines by reducing clutch size. Environ. Toxicol. Chem. 2013;32:562568. (c) 2012 SETAC DOI
339. Yeakel, J.D., J.W. Moore, M. de Aguiar, and P. Guimarães.Stability and synchronization in river networks.Ecology Letters, 2013, In Press Stability and synchronization in river networks.
Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations.PDF
338. Zanette, LY; Hobson, KA; Clinchy, M; Travers, M; Williams, TD.Food use is affected by the experience of nest predation: implications for indirect predator effects on clutch size.Oecologia, 2013, 172: 1031-1039 Food use is affected by the experience of nest predation: implications for indirect predator effects on clutch size
SNOWSHOE HARE CYCLE; EGG-PRODUCTION; PREY INTERACTIONS; SONG SPARROWS; RISK; STRESS; REPRODUCTION; COST; ELK; CONSEQUENCES
Indirect predator effects on prey demography include any effect not attributable to direct killing and can be mediated by perceived predation risk. Though perceived predation risk clearly affects foraging, few studies have yet demonstrated that it can chronically alter food intake to an extent that affects demography. Recent studies have used stable isotopes to gauge such chronic effects. We previously reported an indirect predator effect on the size of subsequent clutches laid by song sparrows (Melospiza melodia). Females that experienced frequent experimental nest predation laid smaller clutches and were in poorer physiological condition compared to females not subject to nest predation. Every female was provided with unlimited supplemental food that had a distinctive C-13 signature. Here, we report that frequent nest predation females had lower blood delta C-13 values, suggesting that the experience of nest predation caused them to eat less supplemental food. Females that ate less food gained less fat and were in poorer physiological condition, consistent with the effect on food use contributing to the indirect predator effect on clutch size. Tissue delta N-15 values corroborated that clutch size was not likely constrained by endogenous resources. Finally, we report that the process of egg production evidently affects egg delta C-13 values, and this may mask the source of nutrients to eggs. Our results indicate that perceived predation risk may impose food limitation on prey even where food is unlimited and such predator-induced food limitation ought to be added to direct killing when considering the total effect of predators on prey numbers. DOI
337. Zeng, Y; Zhao, TH; Kermode, AR.A Conifer ABI3-Interacting Protein Plays Important Roles during Key Transitions of the Plant Life Cycle.Plant Physiology, 2013, 161: 179-195 A Conifer ABI3-Interacting Protein Plays Important Roles during Key Transitions of the Plant Life Cycle
LATERAL ROOT DEVELOPMENT; OF-FUNCTION MUTATION; ABSCISIC-ACID; ARABIDOPSIS-THALIANA; GENE-EXPRESSION; STORAGE PROTEIN; FLOWERING TIME; ABI3 GENE; CELL ELONGATION; SEED DORMANCY
ABI3 (for ABSCISIC ACID INSENSITIVE3), a transcription factor of the abscisic acid signal transduction pathway, plays a major role during seed development, dormancy inception, and dormancy maintenance. This protein appears to also function in meristematic and vegetative plant tissues and under certain stress conditions. We have isolated the ABI3 gene ortholog (CnABI3) from yellow cedar (Callitropsis nootkatensis) and found that it was functionally similar to other ABI3 genes of angiosperms. Here, we report that using a yeast (Saccharomyces cerevisiae) two-hybrid approach, we have identified another protein of yellow cedar (CnAIP2; for CnABI3 INTERACTING PROTEIN2) that physically interacts with CnABI3. Functional analyses revealed that CnAIP2 plays important roles during key transitions in the plant life cycle: (1) CnAIP2 impaired seed development and reduced seed dormancy; (2) CnAIP2 promoted root development, particularly the initiation of lateral roots, and the CnAIP2 gene promoter was exquisitely auxin sensitive; and (3) CnAIP2 promoted the transition from vegetative growth to reproductive initiation (i.e. flowering). The nature of the effects of CnAIP2 on these processes and other evidence place CnAIP2 in the category of a "global" regulator, whose actions are antagonistic to those of ABI3. DOI
336. Zhao, S; Salehzadeh, O; Alagha, S; Kavanagh, KL; Watkins, SP; Mi, Z.Probing the electrical transport properties of intrinsic InN nanowires.Applied Physics Letters, 2013, 102 Probing the electrical transport properties of intrinsic InN nanowires
We have studied the electrical transport properties of intrinsic InN nanowires using an electrical nanoprobing technique in a scanning electron microscope environment. It is found that such intrinsic InN nanowires exhibit an ohmic conduction at low bias and a space charge limited conduction at high bias. It is further derived that such InN nanowires can exhibit a free carrier concentration as low as similar to 10(13) cm(-3) and possess a very large electron mobility in the range of 8000-12 000 cm(2)/V s, approaching the theoretically predicted maximum electron mobility at room temperature. In addition, charge traps are found to distribute exponentially just below the conduction band edge, with a characteristic energy similar to 65 meV. (C) 2013 American Institute of Physics. [http://dx.doi.org/10.1063/1.4792699] DOI
335. Antolin, MF; Jenkins, KP; Bergstrom, CT; Crespi, BJ; De, S; Hancock, A; Hanley, KA; Meagher, TR; Moreno-Estrada, A; Nesse, RM; Omenn, GS; Stearns, SC.EVOLUTION AND MEDICINE IN UNDERGRADUATE EDUCATION: A PRESCRIPTION FOR ALL BIOLOGY STUDENTS.Evolution, 2012, 66: 1991-2006 EVOLUTION AND MEDICINE IN UNDERGRADUATE EDUCATION: A PRESCRIPTION FOR ALL BIOLOGY STUDENTS
Biomedical research; evolution of disease; host-pathogen interactions; human genetics; medical practice; mismatch hypothesis; premedical curriculum; public health; science education
The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to explore. However, gaps persist between evolution and medicine, for historical reasons and because they are often perceived as having disparate goals. Evolutionary biologists have a role in building a bridge between the disciplines by presenting evolutionary biology in the context of human health and medical practice to undergraduates, including premedical and preprofessional students. We suggest that students will find medical examples of evolution engaging. By making the connections between evolution and medicine clear at the undergraduate level, the stage is set for future health providers and biomedical scientists to work productively in this synthetic area. Here, we frame key evolutionary concepts in terms of human health, so that biomedical examples may be more easily incorporated into evolution courses or more specialized courses on evolutionary medicine. Our goal is to aid in building the scientific foundation in evolutionary biology for all students, and to encourage evolutionary biologists to join in the integration of evolution and medicine. DOI
334. Barnosky, AD; Hadly, EA; Bascompte, J; Berlow, EL; Brown, JH; Fortelius, M; Getz, WM; Harte, J; Hastings, A; Marquet, PA; Martinez, ND; Mooers, A; Roopnarine, P; Vermeij, G; Williams, JW; Gillespie, R; Kitzes, J; Marshall, C; Matzke, N; Mindell, DP; Revilla, E; Smith, AB.Approaching a state shift in Earth's biosphere.Nature, 2012, 486: 52-58 Approaching a state shift in Earth's biosphere
Localized ecological systems are known to shift abruptly and irreversibly from one state to another when they are forced across critical thresholds. Here we review evidence that the global ecosystem as a whole can react in the same way and is approaching a planetary-scale critical transition as a result of human influence. The plausibility of a planetary-scale 'tipping point' highlights the need to improve biological forecasting by detecting early warning signs of critical transitions on global as well as local scales, and by detecting feedbacks that promote such transitions. It is also necessary to address root causes of how humans are forcing biological changes. DOI
333. Blanchard, JL; Jennings, S; Holmes, R; Harle, J; Merino, G; Allen, JI; Holt, J; Dulvy, NK; Barange, M.Potential consequences of climate change for primary production and fish production in large marine ecosystems.Philosophical Transactions of the Royal Society B-Biological Sciences, 2012, 367: 2979-2989 Potential consequences of climate change for primary production and fish production in large marine ecosystems
global environmental change; benthic-pelagic coupling; fisheries ecology; marine macroecology; marine communities; size spectrum
Existing methods to predict the effects of climate change on the biomass and production of marine communities are predicated on modelling the interactions and dynamics of individual species, a very challenging approach when interactions and distributions are changing and little is known about the ecological mechanisms driving the responses of many species. An informative parallel approach is to develop size-based methods. These capture the properties of food webs that describe energy flux and production at a particular size, independent of species' ecology. We couple a physical-biogeochemical model with a dynamic, size-based food web model to predict the future effects of climate change on fish biomass and production in 11 large regional shelf seas, with and without fishing effects. Changes in potential fish production are shown to most strongly mirror changes in phytoplankton production. We project declines of 30-60% in potential fish production across some important areas of tropical shelf and upwelling seas, most notably in the eastern Indo-Pacific, the northern Humboldt and the North Canary Current. Conversely, in some areas of the high latitude shelf seas, the production of pelagic predators was projected to increase by 28-89%. DOI
332. Bomfim, TR; Forny-Germano, L; Sathler, LB; Brito-Moreira, J; Houzel, JC; Decker, H; Silverman, MA; Kazi, H; Melo, HM; McClean, PL; Holscher, C; Arnold, SE; Talbot, K; Klein, WL; Munoz, DP; Ferreira, ST; De Felice, FG.An anti-diabetes agent protects the mouse brain from defective insulin signaling caused by Alzheimer's disease-associated A beta oligomers.Journal of Clinical Investigation, 2012, 122: 1339-1353 An anti-diabetes agent protects the mouse brain from defective insulin signaling caused by Alzheimer's disease-associated A beta oligomers
Defective brain insulin signaling has been suggested to contribute to the cognitive deficits in patients with Alzheimer's disease (AD). Although a connection between AD and diabetes has been suggested, a major unknown is the mechanism(s) by which insulin resistance in the brain arises in individuals with AD. Here, we show that serine phosphorylation of IRS-1 (IRS-1pSer) is common to both diseases. Brain tissue from humans with AD had elevated levels of IRS-1pSer and activated JNK, analogous to what occurs in peripheral tissue in patients with diabetes. We found that amyloid-beta peptide (A beta) oligomers, synaptotoxins that accumulate in the brains of AD patients, activated the JNK/TNF-alpha pathway, induced IRS-1 phosphorylation at multiple serine residues, and inhibited physiological IRS-1pTyr in mature cultured hippocarnpal neurons. Impaired IRS-1 signaling was also present in the hippocampi of Tg mice with a brain condition that models AD. Importantly, intracerebroventricular injection of A beta oligomers triggered hippocampal IRS-1pSer and JNK activation in cynomolgus monkeys. The oligomer-induced neuronal pathologies observed in vitro, including impaired axonal transport, were prevented by exposure to exendin-4 (exenatide), an anti-diabetes agent. In Tg mice, exendin-4 decreased levels of hippocampal IRS-1pSer and activated JNK and improved behavioral measures of cognition. By establishing molecular links between the dysregulated insulin signaling in AD and diabetes, our results open avenues for the investigation of new therapeutics in AD. DOI
331. Braun, DC; Reynolds, JD.Cost-effective variable selection in habitat surveys.Methods in Ecology and Evolution, 2012, 3: 388-396 Cost-effective variable selection in habitat surveys
conservation; cost-effectiveness; diminishing returns; efficiency; monitoring; multicollinearity; survey design
1. Researchers usually expect to understand the ecological systems better when they examine more variables. However, we cannot measure everything because time and money are limited, so we need to make difficult choices. Decisions are complicated by the fact that variables are often either uninformative or highly correlated, leading to diminishing returns on information with new variables. Correlated variables and diminishing returns on information per variable can be explicitly incorporated with costs of data collection to design cost-effective survey programmes. 2. We develop a step-by-step quantitative protocol to evaluate the cost-effectiveness of survey designs under different cost scenarios to help scientists and managers design cost-effective surveys. We illustrate this protocol using a case study that relates physical stream habitat variables to variation in sockeye salmon spawning populations. 3. We present our protocol by comparing linear regression models containing different combinations of variables representing different survey designs. The steps of the protocol are to (i) eliminate redundant variables, (ii) calculate costs scenarios, (iii) calculate survey performance metrics and (iv) identify and compare a subset of survey designs that maximize effectiveness at a given cost. Survey designs are compared by their ranked performance using R 2, AICc, average cost-effectiveness ratio and incremental cost-effectiveness ratio. 4. Our case study shows diminishing returns on the information provided by the addition of more variables as survey costs increase. The protocol supports the design of cost-effective monitoring programmes and leads to a general discussion relating changing environmental conditions to survey costs, including the need for clear and measurable objectives, which allow scientific information to be translated into management options. DOI
330. Chatterton, S; Punja, ZK.Colonization of geranium foliage by Clonostachys rosea f. catenulata, a biological control agent of botrytis grey mould.Botany-Botanique, 2012, 90: 1-10 Colonization of geranium foliage by Clonostachys rosea f. catenulata, a biological control agent of botrytis grey mould
biological control; geranium; leaf colonization; Gliocladium catenulatum
The ecological requirements for the colonization of geranium leaves by the biocontrol agent Clonostachys rosea f. catenulata strain J1446 were investigated. Although this biocontrol agent is a soil-inhabiting fungus, treatment of geranium foliage with the agent can reduce grey mould caused by Botrytis cinerea in the greenhouse. To characterize the extent of foliar colonization, a GUS-transformed isolate of C. rosea f. catenulata was applied to foliage of two geranium cultivars, Pelargonium x hortorum and Pelargonium x domesticum. Population levels of C. rosea f. catenulata were found to be highest on senescent leaves and stems, followed by fully expanded leaves, and lowest on newly emerged leaves of both cultivars. Optimum temperature for leaf and petiole colonization was 20-25 degrees C for both cultivars. The biocontrol agent required at least 12 h of continuous leaf wetness to achieve maximum population densities on the leaves and stems of both cultivars. On whole plants, colonization was significantly higher on wounded leaves, stems, and senescing leaves compared with that on nonwounded leaves, stems, and mature leaves, respectively. GUS staining indicated that the fungus preferentially colonized the wound sites of leaves and the cut portions of stems. Results indicate that this biocontrol agent can successfully colonize the foliage of geraniums, thus demonstrating the endophytic ability of C. rosea f. catenulata in both root and foliar tissues. DOI
329. Chin A, White J, Dulvy NK.Aquatic conservation: Environment in Queensland at risk.Nature, 2012, 490: 176. Aquatic conservation: Environment in Queensland at risk
In the state of Queensland, Australia, hard-won environmental protections are under threat.
In April this year, Queensland elected a new government that is pro-development and pro-mining. These activities have been burgeoning over the past few years, prompting the United Nations Educational, Scientific and Cultural Organization (UNESCO) to investigate whether the Great… DOI
328. Connors, B.M., Braun, D.C., Peterman, R.M., Cooper, A.B., Reynolds, J.D., Dill, L.M., Ruggerone, G.T. & Krkosek, M.Migration links ocean-scale competition and local ocean conditions with exposure to farmed salmon to shape wild salmon dynamics.Conservation Letters, 2012, 2012, 1-9 Migration links ocean-scale competition and local ocean conditions with exposure to farmed salmon to shape wild salmon dynamics.
Climate, competition, and disease are well-recognized drivers of population
dynamics. These stressors can be intertwined by animal migrations, leading to
uncertainty about the roles of natural and anthropogenic factors in conservation
and resource management. We quantitatively assessed the four leading
hypotheses for an enigmatic long-term decline in productivity of Canada’s
iconic Fraser River sockeye salmon: (1) delayed density-dependence, (2) local
oceanographic conditions, (3) pathogen transmission from farmed salmon, and
(4) ocean-basin scale competition with pink salmon. Our findings suggest that
the long-term decline is primarily explained by competition with pink salmon,
which can be amplified by exposure to farmed salmon early in sockeye marine
life, and by a compensatory interaction between coastal ocean temperature
and farmed-salmon exposure. These correlative relationships suggest oceanicscale
processes, which are beyond the reach of current regulatory agencies,
may exacerbate local ecological processes that challenge the coexistence of
fisheries and aquaculture-based economies in coastal seas.Website DOI
327. Crespi, B; Schwander, T.Asexual evolution: do intragenomic parasites maintain sex?Molecular Ecology, 2012, 21: 3893-3895 Asexual evolution: do intragenomic parasites maintain sex?
adaptation; animal mating; breeding systems; ecological genetics; evolution of sex
Resolving the paradox of sex, with its twofold cost to genic transmission, remains one of the major unresolved questions in evolutionary biology. Counting this genetic cost has now gone genomic. In this issue of Molecular Ecology, Kraaijeveld (2012) describe the first genome-scale comparative study of related sexual and asexual animal lineages, to test the hypothesis that asexuals bear heavier loads of deleterious transposable elements. A much higher density of such parasites might be expected, due to the inability of asexual lineages to purge transposons via mechanisms exclusive to sexual reproduction. They find that the answer is yesand nodepending upon the family of transposons considered. Like many such advances in testing theory, more questions are raised by this study than answered, but a door has been opened to molecular evolutionary analyses of how responses to selection from intragenomic parasites might mediate the costs of sex. DOI
325. Crossin GT, Poisbleau M, Demongin L, Chastel O, Williams TD, Eens M, Quillfeldt P.Migratory constraints on yolk precursors limit yolk androgen deposition and underlie a brood reduction strategy in rockhopper penguins.Biol Lett. 2012 Dec 23;8(6):1055-8. Epub 2012 Jul 18., 2012, 8: 1055-1058 Migratory constraints on yolk precursors limit yolk androgen deposition and underlie a brood reduction strategy in rockhopper penguins.
androstenedione; testosterone; physiological epiphenomenon hypothesis; vitellogenin; maternal effects; carryover effects
Hormonally mediated maternal effects link maternal phenotype and environmental conditions to offspring phenotype. The production of lipid-rich maternal yolk precursors may provide a mechanism by which lipophilic steroid hormones can be transported to developing yolks, thus predicting a positive correlation between yolk precursors in mothers and androgen levels in eggs. Using rockhopper penguins (Eudyptes chrysocome), which produce a two-egg clutch characterized by extreme egg-size dimorphism, reversed hatching asynchrony and brood-reduction, we examined correlations between circulating concentrations of the primary yolk-precursor vitellogenin (VTG) and levels of yolk androgens. Previous work in Eudyptes penguins has shown that egg-size dimorphism is the product of migratory constraints on yolk precursor production. We predicted that if yolk precursors are constrained, androgen transport to developing yolks would be similarly constrained. We reveal positive linear relationships between maternal VTG and androgens in small A-eggs but not larger B-eggs, which is consistent with a migratory constraint operating on the A-egg. Results suggest that intra-clutch variation in total yolk androgen levels depends on the production and uptake of yolk precursors. The brood reduction strategy common to Eudyptes might thus be best described as the result of a migratory constraint.
DOI
324. Crossin, GT; Dawson, A; Phillips, RA; Trathan, PN; Gorman, KB; Adlard, S; Williams, TD.Seasonal patterns of prolactin and corticosterone secretion in an Antarctic seabird that moults during reproduction.General and Comparative Endocrinology, 2012, 175: 74-81 Seasonal patterns of prolactin and corticosterone secretion in an Antarctic seabird that moults during reproduction
Prolactin; Corticosterone; Physiological conflict; Incubation; Chick rearing; Giant petrel; Macronectes; Life-history; Foraging behaviour; Parental care
In avian species that have evolved life-history strategies wherein molt and breeding overlap, there are potential conflicts between the regulatory roles of baseline prolactin and corticosterone in parental care (positive) and moult (negative). We describe seasonal patterns of hormonal secretion, moult, and parental behaviour in sibling species of giant petrels (Macronectes spp.) which begin moult during the incubation/early chick-rearing stage of reproduction. With the exception of male Southern giant petrels (Macronectes giganteus), prolactin secretion and moult in Northern (Macronectes halli) and female Southern giant petrels conformed to those observed in all other avian species, with the initiation of moult coincident with decreases from peak prolactin levels. However, male Southern giant petrels began moulting early in incubation when prolactin was increasing and had not yet peaked, which suggests a requirement of prolactin for incubation behaviour and a dissociation of prolactin from moult. Corticosterone showed little seasonal variation and no relationship with moult. When comparing prolactin, corticosterone, and moult in failed vs. active breeders, we found that failed breeding enabled a more rapid down-regulation of prolactin, thus facilitating a more rapid moult. We present specific examples of the behavioural ecology of giant petrels which we conclude help mediate any potential hormonal conflicts between parental care and moult. Crown Copyright (C) 2011 Published by Elsevier Inc. All rights reserved. DOI
323. Crossin, GT; Phillips, RA; Trathan, PN; Fox, DS; Dawson, A; Wynne-Edwards, KE; Williams, TD.Migratory carryover effects and endocrinological correlates of reproductive decisions and reproductive success in female albatrosses.General and Comparative Endocrinology, 2012, 176: 151-157 Migratory carryover effects and endocrinological correlates of reproductive decisions and reproductive success in female albatrosses
Trade-offs; Vitellogenin; Physiological conflict; Yolk precursors; Reproductive hormones; Seabirds
Physiological mechanisms mediating carryover effects, wherein events or activities occurring in one season, habitat, or life-history stage affect important processes in subsequent life-history stages, are largely unknown. The mechanism most commonly invoked to explain carryover effects from migration centres on the acquisition and utilization of resources (e.g. body mass, or individual 'condition'). However, other mechanisms are plausible, e.g. trade-offs reflecting conflict or incompatibility between physiological regulatory systems required for different activities or life-history stages (migration vs. reproduction). Here we show that in female black-browed albatrosses (Thalassarche melanophris) the decision to reproduce or to defer reproduction, made prior to their arrival at breeding colonies after long-distance migration, is associated with condition-related (body mass, hematocrit, hemoglobin concentrations) and hormonal (progesterone, testosterone, estrogen-dependent yolk precursors) traits. In contrast, reproductive success showed little association with condition but showed significant associations with the steroidogenic processes underlying follicle development. Specifically, success was determined by reproductive readiness via differences in steroid hormones and hormone-dependent traits. Successful albatrosses were characterized by high progesterone and high estradiol-dependent yolk precursor levels, whereas failed albatrosses had high testosterone and low yolk precursor levels. Results are discussed with reference to migratory carryover effects and how these can differentially affect the physiologies influencing reproductive decisions and reproductive success. (C) 2012 Elsevier Inc. All rights reserved. DOI
322. Crossin, GT; Trathan, PN; Phillips, RA; Gorman, KB; Dawson, A; Sakamoto, KQ; Williams, TD.Corticosterone Predicts Foraging Behavior and Parental Care in Macaroni Penguins.American Naturalist, 2012, 180: E31-E41 Corticosterone Predicts Foraging Behavior and Parental Care in Macaroni Penguins
allostasis; time-depth recorders; telemetry; parental care; reproductive investment; stress hormones
Corticosterone has received considerable attention as the principal hormonal mediator of allostasis or physiological stress in wild animals. More recently, it has also been implicated in the regulation of parental care in breeding birds, particularly with respect to individual variation in foraging behavior and provisioning effort. There is also evidence that prolactin can work either inversely or additively with corticosterone to achieve this. Here we test the hypothesis that endogenous corticosterone plays a key physiological role in the control of foraging behavior and parental care, using a combination of exogenous corticosterone treatment, time-depth telemetry, and physiological sampling of female macaroni penguins (Eudyptes chrysolophus) during the brood-guard period of chick rearing, while simultaneously monitoring patterns of prolactin secretion. Plasma corticosterone levels were significantly higher in females given exogenous implants relative to those receiving sham implants. Increased corticosterone levels were associated with significantly higher levels of foraging and diving activity and greater mass gain in implanted females. Elevated plasma corticosterone was also associated with an apparent fitness benefit in the form of increased chick mass. Plasma prolactin levels did not correlate with corticosterone levels at any time, nor was prolactin correlated with any measure of foraging behavior or parental care. Our results provide support for the corticosterone-adaptation hypothesis, which predicts that higher corticosterone levels support increased foraging activity and parental effort. DOI
321. Darling, ES; Alvarez-Filip, L; Oliver, TA; McClanahan, TR; Côté, IM.Evaluating life-history strategies of reef corals from species traits.Ecology Letters, 2012, 15: 1378-1386 Evaluating life-history strategies of reef corals from species traits
Community assembly; coral reefs; C-S-R triangle; ecological strategies; functional diversity; selection pressure
Classifying the biological traits of organisms can test conceptual frameworks of life-history strategies and allow for predictions of how different species may respond to environmental disturbances. We apply a trait-based classification approach to a complex and threatened group of species, scleractinian corals. Using hierarchical clustering and random forests analyses, we identify up to four life-history strategies that appear globally consistent across 143 species of reef corals: competitive, weedy, stress-tolerant and generalist taxa, which are primarily separated by colony morphology, growth rate and reproductive mode. Documented shifts towards stress-tolerant, generalist and weedy species in coral reef communities are consistent with the expected responses of these life-history strategies. Our quantitative trait-based approach to classifying life-history strategies is objective, applicable to any taxa and a powerful tool that can be used to evaluate theories of community ecology and predict the impact of environmental and anthropogenic stressors on species assemblages. DOI
320. Dashtgard, SE; Gingras, MK.Chapter 10: Marine invertebrate neoichnology.Trace Fossils as Indicators of Sedimentary Environments (Knaust, D; Bromley, RG (eds.)), 2012, Developments in Sedimentology 64: 273-295 Chapter 10: Marine invertebrate neoichnology
DOI
319. Dashtgard, SE; MacEachern, JA; Frey, SE; Gingras, MK.Tidal effects on the shoreface: Towards a conceptual framework.Sediment. Geol., 2012, 279: 42-61 Tidal effects on the shoreface: Towards a conceptual framework
Tides; Beach; Facies models; Sedimentology; Ichnology; Storm-dominated
Tidal processes can have a significant impact on the sedimentological and ichnological character of wave-dominated shoreface deposits. As the influence of tides increases, the resulting shoreface successions begin to depart markedly from those postulated by the conventional, wave-dominated shoreface model, which was built upon essentially non-tidal shoreline settings. In shoreface settings subject to stronger tidal flux, tides can be manifest either directly or indirectly. Direct tidal effects refer to those characteristics imparted by tidal energy (e.g., tidal currents) per se, and are best expressed in offshore and lower shoreface positions. Key evidence of direct tidal control includes uniform sediment calibres from the upper shoreface to the offshore, and little or no mud preserved in the lower shoreface. Additionally, sands in the lower shoreface and offshore tend to be intensely bioturbated. Where primary stratification is preserved, it largely comprises current-generated structures. Such shoreface deposits are referred to herein as "tide-influenced shorefaces", and are expected in settings with low storm-wave input coupled with strong tidal currents (e.g., straits). Indirect tidal influences are manifest by the lateral translation of wave zones across the shoreface profile owing to changes in water depth during the tidal cycle. This is best developed in macrotidal to megatidal settings. Indirect tidal influences are more pronounced in the upper and lower shoreface, and are recorded through the interbedding of sedimentary structures produced by shoaling waves, breakers and surf, swash-backwash, and surface runoff. The boundaries between shoreface subenvironments are correspondingly poorly defined. The foreshore in settings of elevated tidal range is also generally much thicker (typically 4 to 5 m). Bioturbation tends to be patchy in distribution across the shoreface, and dominated by vertical structures. Such systems are defined as "tidally modulated shorefaces". Using well-established sedimentological and ichnological criteria for recognizing wave-dominated (nontidal) shorefaces - wherein sediment deposition is nearly wholly controlled by fair-weather wave and storm-wave processes - a conceptual model is developed for discriminating fair-weather (non-tidal) shorefaces, storm-influenced (non-tidal) shorefaces, and tidally influenced shorefaces. Five shoreface archetypes are defined: storm-affected, storm-influenced, storm-dominated, tide-influenced, and tidally modulated. (C) 2010 Elsevier B.V. All rights reserved. DOI
318. Davis, BD; Dill, LM.Intraspecific kleptoparasitism and counter-tactics in the archerfish (Toxotes chatareus).Behaviour, 2012, 149: 1367-1394 Intraspecific kleptoparasitism and counter-tactics in the archerfish (Toxotes chatareus)
FISH LEARN; REEF FISH; PREY; BEHAVIOR; SIZE; EVOLUTION; CROWS; JACULATRIX; PARASITISM; REFRACTION
The mechanics of the archerfish's remarkable ability to spit down aerial prey is well studied. Relatively unknown, however, are the social consequences of this hunting method. To explore how physical factors and behavioural choices affect the use and success of intraspecific kleptoparasitism in socially foraging archerfish, 10 tagged, juvenile archerfish (Toxotes chatareus) were presented in groups of 3, 5, and 7 with single crickets of 3 sizes overhanging the water by either 15 or 30 cm. Video review revealed all spits, jumps, attempted thefts, and consumptions. Kleptoparasitism attempts were common, resulting in a 43.6% loss rate to the fish that successfully brought down the prey. Group size affected the probability of kleptoparasitism asymptotically: loss rate increased as group size increased from 3 to 5 members, but with no further increase at 7 members. As observed with other kleptoparasitic species, the rate and success of kleptoparasitism increased with both prey size and prey height (analogous to handling time). Several counter-kleptoparasitism behaviours were observed, including jumping to grab prey directly, aggression, spitting technique, and positioning. DOI
317. Favaro, B; Lichota, C; Côté, IM; Duff, SD.TrapCam: an inexpensive camera system for studying deep-water animals.Methods in Ecology and Evolution, 2012, 3: 39-46 TrapCam: an inexpensive camera system for studying deep-water animals
behaviour; bycatch; deep water; digital video; rockfish; spot prawn; underwater cameras
1. Behavioural research in deep water (>40 m depth) has traditionally been expensive and logistically challenging, particularly because the light and sound produced by underwater vehicles make them unsuitably disruptive. Yet, understanding the behaviour of deep-water animals, especially those targeted by exploitation, is important for conservation. For example, understanding interactions between animals and deep-water fishing gear could inform the design of devices that minimize bycatch. 2. We describe the ` TrapCam', a self- contained, high- definition video system that requires neither the support of a vessel once deployed nor special equipment to deploy or retrieve. This system can record 13-h videos at 1080p resolution and is deployable on any substrata at depths of up to 100 m. The system is inexpensive (<$ 3000 USD), versatile and suited to the study of animal behaviour at depths inaccessible to scuba divers. 3. We evaluate the performance and cost effectiveness of TrapCam and analyse videos retrieved frompilot deployments to observe spot prawn (Pandalus platyceros) traps at 100 mdepth. Preliminary analyses of animal- prawn trap interactions yield novel insights. We provide future directions for researchers to use this type of camera system to study deep water- dwelling species around the world. DOI
316. Greig, HS; Kratina, P; Thompson, PL; Palen, WJ; Richardson, JS; Shurin, JB.Warming, eutrophication, and predator loss amplify subsidies between aquatic and terrestrial ecosystems.Global Change Biology, 2012, 18: 504-514 Warming, eutrophication, and predator loss amplify subsidies between aquatic and terrestrial ecosystems
allochthonous resources; amphibians; climate warming; detritus decomposition; global change; insect emergence; spatial subsidies; top-down control
The exchange of organisms and energy among ecosystems has major impacts on food web structure and dynamics, yet little is known about how climate warming combines with other pervasive anthropogenic perturbations to affect such exchanges. We used an outdoor freshwater mesocosm experiment to investigate the interactive effects of warming, eutrophication, and changes in top predators on the flux of biomass between aquatic and terrestrial ecosystems. We demonstrated that predatory fish decoupled aquatic and terrestrial ecosystems by reducing the emergence of aquatic organisms and suppressing the decomposition of terrestrial plant detritus. In contrast, warming and nutrients enhanced cross-ecosystem exchanges by increasing emergence and decomposition, and these effects were strongest in the absence of predators. Furthermore, we found that warming advanced while predators delayed the phenology of insect emergence. Our results demonstrate that anthropogenic perturbations may extend well beyond ecosystem boundaries by influencing cross-ecosystem subsidies. We find that these changes are sufficient to substantially impact recipient communities and potentially alter the carbon balance between aquatic and terrestrial ecosystems and the atmosphere. DOI
315. Hanson, MA; Lian, OB; Clague, JJ.The sequence and timing of large late Pleistocene floods from glacial Lake Missoula.Quat. Sci. Rev., 2012, 31: 67-81 The sequence and timing of large late Pleistocene floods from glacial Lake Missoula
Glacial Lake Missoula; Outburst floods; Stratigraphy; Sedimentology; Varves; Optical dating
Glacial Lake Missoula formed when the Purcell Trench lobe of the Cordilleran ice sheet dammed Clark Fork River in Montana during the Fraser Glaciation (marine oxygen isotope stage 2). Over a period of several thousand years, the lake repeatedly filled and drained through its ice dam, and floodwaters coursed across the landscape in eastern Washington. In this paper, we describe the stratigraphy and sedimentology of a significant new section of fine-grained glacial Lake Missoula sediment and compare this section to a similar, previously described sequence of sediments at Ninemile Creek, 26 km to the northwest. The new exposure, which we informally term the rail line section, is located near Missoula, Montana, and exposes 29 units, each of which consists of many silt and clay couplets that we interpret to be varves. The deposits are similar to other fine-grained sediments attributed to glacial Lake Missoula. Similar varved sediments overlie gravelly flood deposits elsewhere in the glacial Lake Missoula basin. Each of the 29 units represents a period when the lake was deepening, and all units show evidence for substantial draining of glacial Lake Missoula that repeatedly exposed the lake floor. The evidence includes erosion and deformation of glaciolacustrine sediment that we interpret happened during draining of the lake, desiccation cracks that formed during exposure of the lake bottom, and fluvial sand deposited as the lake began to refill. The floods date to between approximately 21.4 and 13.4 cal ka ago based on regional chronological data. The total number of varves at the rail line and Ninemile sites are, respectively, 732 and 583. Depending on lake refilling times, each exposure probably records 1350-1500 years of time. We present three new optical ages from the rail line and Ninemile sites that further limit the age of the floods. These ages, in calendar years, are 15.1 +/- 0.6 ka at the base of the Ninemile exposure, and 14.8 +/- 0.7 and 12.6 +/- 0.6 ka midway through the rail line exposure. The sediment at the two sections was deposited during later stages of glacial Lake Missoula, after the largest outburst events. (C) 2011 Elsevier Ltd. All rights reserved. DOI
314. Harnik, PG; Lotze, HK; Anderson, SC; Finkel, ZV; Finnegan, S; Lindberg, DR; Liow, LH; Lockwood, R; McClain, CR; McGuire, JL; O'Dea, A; Pandolfi, JM; Simpson, C; Tittensor, DP.Extinctions in ancient and modern seas.Trends in Ecology & Evolution, 2012, 27: 608-617 Extinctions in ancient and modern seas
PERMIAN MASS EXTINCTION; EOCENE THERMAL MAXIMUM; CLIMATE-CHANGE; OCEAN ACIDIFICATION; MARINE BIODIVERSITY; FOSSIL RECORD; LEVEL CHANGE; RISK; ECOSYSTEMS; CORAL
In the coming century, life in the ocean will be confronted with a suite of environmental conditions that have no analog in human history. Thus, there is an urgent need to determine which marine species will adapt and which will go extinct. Here, we review the growing literature on marine extinctions and extinction risk in the fossil, historical, and modern records to compare the patterns, drivers, and biological correlates of marine extinctions at different times in the past. Characterized by markedly different environmental states, some past periods share common features with predicted future scenarios. We highlight how the different records can be integrated to better understand and predict the impact of current and projected future environmental changes on extinction risk in the ocean. DOI
313. Hart, MW.New sea urchin phylogeography reveals latitudinal shifts associated with speciation.Molecular Ecology, 2012, 21: 26-27 New sea urchin phylogeography reveals latitudinal shifts associated with speciation
allopatry; echinoderms; ecological speciation; hybridization; phylogeography
Where do new species arise? When do they form and how do they diverge from a common ancestor? A new comprehensive study of Arbacia sea urchins provides surprising answers to these questions. By combining mtDNA phylogeographic markers with a nuclear locus (encoding the sperm acrosomal protein bindin) known to be susceptible to high rates of adaptive codon evolution, Lessios (2012) show that new species and lineages arose relatively recently, most often in association with latitudinal shifts between the temperate zones and the tropics, and in one case, in association with a significant geological barrier to gene flow (the rise of the Isthmus of Panama). In addition to the where and when of Arbacia speciation, these new data resolve an important question about whoArbacia species are by revealing extensive allele sharing at both loci between a pair of broadly sympatric nominal species (that should perhaps be considered a single taxon). HowArbacia diverge from each other is less easily resolved: there is no evidence for reinforcement (via selection on bindin) as an important source of divergence between nominal species, and there are few other data to decide among the alternative hypotheses to explain Arbacia speciation. DOI
312. Hart, MW.NEXT-GENERATION STUDIES OF MATING SYSTEM EVOLUTION.Evolution, 2012, 66: 1675-1680 NEXT-GENERATION STUDIES OF MATING SYSTEM EVOLUTION
ARIS; asterosap; bindin; fertilization; guanylate cyclase; lysin
The specificity of mate selection can vary from wantonly indiscriminate to extraordinarily choosy, and depends in large part on molecules expressed on the surfaces of sperm and eggs. Understanding the evolution of this specificity of gamete recognition leads to important insights into the evolution of reproductive isolation and speciation. One productive area of research has focused on genes that encode gamete recognition proteins in broadcast-spawning marine invertebrates. These gene products are relatively accessible to biochemical and cellular analyses of expression and function, and they mediate almost all of the elements of mate selection and specificity between males and females of such species. However, genetic analyses of their evolution are currently limited to a few combinations of molecules and taxa, and may miss the broader view of adaptive responses to selection on mating specificity across many genes and many types of mating systems. A transcriptomic study shows how next-generation sequencing methods and analyses could relatively easily broaden such studies to more clades, deepen those studies to include more of the interacting molecular parts that mediate gamete recognition, and eventually lead to a more complete understanding of the molecular basis for mating system variation and its evolutionary response to selection. DOI
311. Hart, MW; Popovic, I; Emlet, RB.LOW RATES OF BINDIN CODON EVOLUTION IN LECITHOTROPHIC HELIOCIDARIS SEA URCHINS.Evolution, 2012, 66: 1709-1721 LOW RATES OF BINDIN CODON EVOLUTION IN LECITHOTROPHIC HELIOCIDARIS SEA URCHINS
Bindin; fertilization; polyspermy; sexual selection
Life-history variables including egg size affect the evolutionary response to sexual selection in broadcast-spawning sea urchins and other marine animals. Such responses include high or low rates of codon evolution at gamete recognition loci that encode sperm- and egg-surface peptides. Strong positive selection on such loci affects intraspecific mating success and interspecific reproductive divergence (and may play a role in speciation). Here, we analyze adaptive codon evolution in the sperm acrosomal protein bindin from a brooding sea urchin (Heliocidaris bajulus, with large eggs and nonfeeding or lecithotrophic larval development) and compare our results to previously published data for two closely related congeners. Purifying selection and low relative rates of bindin nonsynonymous substitution in H. bajulus were significantly different from selectively neutral bindin evolution in H. erythrogramma despite similar large egg size in those two species, but were similar to the background rate of nonsynonymous bindin substitution for other closely related sea urchins (including H. tuberculata, all with small egg size and feeding planktonic larval development). Bindin evolution is not driven by egg size variation among Heliocidaris species, but may be more consistent with an alternative mechanism based on the effects of high or low spatial density of conspecific mates. DOI
310. He, X; Haselhorst, T; von Itzstein, M; Kolarich, D; Packer, NH; Gloster TM;Vocadlo, DJ; Clarke, LA; Qian, Y; Kermode, AR.Production of α-L-iduronidase in maize for the potential treatment of a human lysosomal storage disease.Nature Communications, 2012, 3: Article number: 1062 Production of α-L-iduronidase in maize for the potential treatment of a human lysosomal storage disease
Lysosomal storage diseases are a class of over 70 rare genetic diseases that are amenable to enzyme replacement therapy. Towards developing a plant-based enzyme replacement therapeutic for the lysosomal storage disease mucopolysaccharidosis I, here we expressed α-L-iduronidase in the endosperm of maize seeds by a previously uncharacterized mRNA-targeting-based mechanism. Immunolocalization, cellular fractionation and in situ RT-PCR demonstrate that the α-L-iduronidase protein and mRNA are targeted to endoplasmic reticulum (ER)-derived protein bodies and to protein body-ER regions, respectively, using regulatory (5′- and 3′-UTR) and signal-peptide coding sequences from the γ-zein gene. The maize α-L-iduronidase exhibits high activity, contains high-mannose N-glycans and is amenable to in vitro phosphorylation. This mRNA-based strategy is of widespread importance as plant N-glycan maturation is controlled and the therapeutic protein is generated in a native form. For our target enzyme, the N-glycan structures are appropriate for downstream processing, a prerequisite for its potential as a therapeutic protein. DOI PubMed
309. Henry, L; Schwander, T; Crespi, BJ.Deleterious Mutation Accumulation in Asexual Timema Stick Insects.Molecular Biology and Evolution, 2012, 29: 401-408 Deleterious Mutation Accumulation in Asexual Timema Stick Insects
CYTOCHROME-OXIDASE-I; FRESH-WATER SNAIL; SEXUAL REPRODUCTION; ANCIENT ASEXUALITY; BDELLOID ROTIFERS; EVOLUTION; SELECTION; PATTERNS; PARTHENOGENESIS; RECOMBINATION
Sexual reproduction is extremely widespread in spite of its presumed costs relative to asexual reproduction, indicating that it must provide significant advantages. One postulated benefit of sex and recombination is that they facilitate the purging of mildly deleterious mutations, which would accumulate in asexual lineages and contribute to their short evolutionary life span. To test this prediction, we estimated the accumulation rate of coding (nonsynonymous) mutations, which are expected to be deleterious, in parts of one mitochondrial (COI) and two nuclear (Actin and Hsp70) genes in six independently derived asexual lineages and related sexual species of Timema stick insects. We found signatures of increased coding mutation accumulation in all six asexual Timema and for each of the three analyzed genes, with 3.6- to 13.4-fold higher rates in the asexuals as compared with the sexuals. In addition, because coding mutations in the asexuals often resulted in considerable hydrophobicity changes at the concerned amino acid positions, coding mutations in the asexuals are likely associated with more strongly deleterious effects than in the sexuals. Our results demonstrate that deleterious mutation accumulation can differentially affect sexual and asexual lineages and support the idea that deleterious mutation accumulation plays an important role in limiting the long-term persistence of all-female lineages. DOI
308. Huang, W; Pacradouni, V; Kennett, MP; Komiya, S; Sonier, JE.Precision search for magnetic order in the pseudogap regime of La2-xSrxCuO4 by muon spin relaxation.Physical Review B, 2012, 85 Precision search for magnetic order in the pseudogap regime of La2-xSrxCuO4 by muon spin relaxation
We report a high-precision search for orbital-like magnetic order in the pseudogap region of La2-xSrxCuO4 single crystals using zero-field muon spin relaxation (ZF-mu SR). In contrast to previous studies of this kind, the effects of the dipolar and quadrupolar interactions of the muon with nearby nuclei are calculated. ZF-mu SR spectra with a high number of counts were also recorded to determine whether a magnetically ordered phase exists in dilute regions of the sample. Despite these efforts, we find no evidence for static magnetic order of any kind in the pseudogap region above the hole-doping concentration p = 0.13. DOI
307. Jetz, W; Thomas, GH; Joy, JB; Hartmann, K; Mooers, AO.The global diversity of birds in space and time.Nature, 2012, 491: 444-448 The global diversity of birds in space and time
Current global patterns of biodiversity result from processes that operate over both space and time and thus require an integrated macroecological and macroevolutionary perspective(1-4). Molecular time trees have advanced our understanding of the tempo and mode of diversification(5-7) and have identified remarkable adaptive radiations across the tree of life(8-10). However, incomplete joint phylogenetic and geographic sampling has limited broad-scale inference. Thus, the relative prevalence of rapid radiations and the importance of their geographic settings in shaping global biodiversity patterns remain unclear. Here we present, analyse and map the first complete dated phylogeny of all 9,993 extant species of birds, a widely studied group showing many unique adaptations. We find that birds have undergone a strong increase in diversification rate from about 50 million years ago to the near present. This acceleration is due to a number of significant rate increases, both within songbirds and within other young and mostly temperate radiations including the waterfowl, gulls and woodpeckers. Importantly, species characterized with very high past diversification rates are interspersed throughout the avian tree and across geographic space. Geographically, the major differences in diversification rates are hemispheric rather than latitudinal, with bird assemblages in Asia, North America and southern South America containing a disproportionate number of species from recent rapid radiations. The contribution of rapidly radiating lineages to both temporal diversification dynamics and spatial distributions of species diversity illustrates the benefits of an inclusive geographical and taxonomical perspective. Overall, whereas constituent clades may exhibit slowdowns(10,11), the adaptive zone into which modern birds have diversified since the Cretaceous may still offer opportunities for diversification. DOI
306. Joy, JB; Crespi, BJ.Island phytophagy: explaining the remarkable diversity of plant-feeding insects.Proceedings of the Royal Society B-Biological Sciences, 2012, 279: 3250-3255 Island phytophagy: explaining the remarkable diversity of plant-feeding insects
macroevolution; plant-insect interactions; diversification; island biogeography; plant genetic distinctiveness; insularity
Plant-feeding insects have undergone unparalleled diversification among different plant taxa, yet explanations for variation in their diversity lack a quantitative, predictive framework. Island biogeographic theory has been applied to spatially discrete habitats but not to habitats, such as host plants, separated by genetic distance. We show that relationships between the diversity of gall-inducing flies and their host plants meet several fundamental predictions from island biogeographic theory. First, plant-taxon genetic distinctiveness, an integrator for long-term evolutionary history of plant lineages, is a significant predictor of variance in the diversity of gall-inducing flies among host-plant taxa. Second, range size and structural complexity also explain significant proportions of the variance in diversity of gall-inducing flies among different host-plant taxa. Third, as with other island systems, plant-lineage age does not predict species diversity. Island biogeographic theory, applied to habitats defined by genetic distance, provides a novel, comprehensive framework for analysing and explaining the diversity of plant-feeding insects and other host-specific taxa. DOI
305. Juan-Jordá, M.J., Mosqueira, I., Freire, J. & Dulvy, N.K.Life in 3-D: life history strategies in tunas, mackerels and bonitos.Reviews in Fish Biology and Fisheries, 2012, Life in 3-D: life history strategies in tunas, mackerels and bonitos
Sexual dimorphism
Life history trade-offs
Mortality
Data-poor species
Data-poor methods
Conservation
Mammals
Life history data set
The scombrids (tunas, bonitos, Spanish mackerels and mackerels) sustain some of the most important fisheries in the world and their sustainable management depends on better understanding of their life history strategies. Here, we first assemble life history information on maximum size, growth, longevity, maturity, fecundity and spawning duration and interval for all scombrid species. Second we characterize their life history patterns and trait co-variation and evaluate how many principal axes of trait variation underlie scombrid life history strategies. Most of their life history variation can be explained along three axes or dimensions: size, speed, and reproductive schedule. Body size governs the first axis ranking species along a small-large continuum. The second axis was mostly influenced by time-related traits, such as longevity, growth rates, spawning duration, time between spawning events, ranking species along a slow-fast continuum of life histories. Scombrid species with the slowest life histories such as Atlantic bluefin tuna Thunnus thynnus and Atlantic mackerel Scomber scombrus tend to inhabit more temperate waters while species with faster life histories such as yellowfin tuna Thunnus albacares and short mackerel Rastrelliger brachysoma are typically found in more tropical waters. The third axis comprises the negative relationship between number of eggs produced at length of maturity and rate in gain of fecundity with size describing the schedule of reproductive allocation which reflects a fundamental trade-off between reproduction and growth. Finally, in addition we show that the life history strategies of scombrids conform more closely to the Periodic and Opportunistic strategists within the triangular model of fish life histories. DOI
304. Kaiser, CV; Huang, W; Komiya, S; Hussey, NE; Adachi, T; Tanabe, Y; Koike, Y; Sonier, JE.Curie-like paramagnetism due to incomplete Zhang-Rice singlet formation in La2-xSrxCuO4.Physical Review B, 2012, 86 Curie-like paramagnetism due to incomplete Zhang-Rice singlet formation in La2-xSrxCuO4
In an effort to elucidate the origin of the Curie-like paramagnetism that is generic for heavily overdoped cuprates, we have performed high-transverse-field muon spin rotation (TF-mu SR) measurements of La2-xSrxCuO4 single crystals over the Sr content range 0.145 <= x <= 0.33. We show that the x dependence of the previously observed field-induced broadening of the internalmagnetic field distribution above the superconducting transition temperature T-c reflects the presence of two distinct contributions. One of these becomes less pronounced with increasing x and is attributed to diminishing antiferromagnetic correlations. The other grows with increasing x, but decreases above x similar to 0.30, and is associated with the Curie-like term in the bulk magnetic susceptibility.. In contrast to the Curie-like term, however, this second contribution to the TF-mu SR linewidth extends back into the underdoped regime. Our findings imply a coexistence of antiferromagnetically correlated and paramagnetic moments, with the latter becoming dominant beyond x similar to 0.185. This suggests that the doped holes do not neutralize all Cu spins via the formation of Zhang-Rice singlets. Moreover, the paramagnetic component of the TF-mu SR linewidth is explained by holes progressively entering the Cu 3d(x2-y2) orbital with doping. DOI
303. Keith, SA; Webb, TJ; Bohning-Gaese, K; Connolly, SR; Dulvy, NK; Eigenbrod, F; Jones, KE; Price, T; Redding, DW; Owens, IPF; Isaac, NJB.What is macroecology?Biology Letters, 2012, 8: 904-906 What is macroecology?
macroecology; spatial scale; process-based model; theory; ecosystem; disease
The symposium 'What is Macroecology?' was held in London on 20 June 2012. The event was the inaugural meeting of the Macroecology Special Interest Group of the British Ecological Society and was attended by nearly 100 scientists from 11 countries. The meeting reviewed the recent development of the macroecological agenda. The key themes that emerged were a shift towards more explicit modelling of ecological processes, a growing synthesis across systems and scales, and new opportunities to apply macroecological concepts in other research fields. DOI
302. Kuwae, T; Miyoshi, E; Hosokawa, S; Ichimi, K; Hosoya, J; Amano, T; Moriya, T; Kondoh, M; Ydenberg, RC; Elner, RW.Variable and complex food web structures revealed by exploring missing trophic links between birds and biofilm.Ecology Letters, 2012, 15: 347-356 Variable and complex food web structures revealed by exploring missing trophic links between birds and biofilm
Behavioural ecology; feeding ecology; foraging behaviour; functional morphology; omnivory; phylogeny; tongue spine; trophic relationship; wader
Food webs are comprised of a network of trophic interactions and are essential to elucidating ecosystem processes and functions. However, the presence of unknown, but critical networks hampers understanding of complex and dynamic food webs in nature. Here, we empirically demonstrate a missing link, both critical and variable, by revealing that direct predator-prey relationships between shorebirds and biofilm are widespread and mediated by multiple ecological and evolutionary determinants. Food source mixing models and energy budget estimates indicate that the strength of the missing linkage is dependent on predator traits (body mass and foraging action rate) and the environment that determines food density. Morphological analyses, showing that smaller bodied species possess more developed feeding apparatus to consume biofilm, suggest that the linkage is also phylogenetically dependent and affords a compelling re-interpretation of niche differentiation. We contend that exploring missing links is a necessity for revealing true network structure and dynamics. DOI
301. Law, HT; Bonazzi, M; Jackson, J; Cossart, P; Guttman, JA.Nexilin is a dynamic component of Listeria monocytogenes and enteropathogenic Escherichia coli actin-rich structures.Cellular Microbiology, 2012, 14: 1097-1108 Nexilin is a dynamic component of Listeria monocytogenes and enteropathogenic Escherichia coli actin-rich structures
The bacterial pathogens Listeria monocytogenes and enteropathogenic Escherichia coli (EPEC) generate motile actin-rich structures (comet tails and pedestals) as part of their infectious processes. Nexilin, an actin-associated protein and a component of focal adhesions, has been suggested to be involved in actin-based motility. To determine whether nexilin is commandeered during L. monocytogenes and EPEC infections, we infected cultured cells and found that nexilin is crucial for L. monocytogenes invasion as levels of internalized bacteria were significantly decreased in nexilin-targeted siRNA-treated cells. In addition, nexilin is a component of the machinery that drives the formation of L. monocytogenes comet tails and EPEC pedestals. Nexilin colocalizes with stationary bacteria and accumulates at the distal portion of comet tails and pedestals of motile bacteria. We also show that nexilin is crucial for efficient comet tail formation as cells pre-treated with nexilin siRNA generate malformed comet tails, whereas nexilin is dispensable during EPEC pedestal generation. These findings demonstrate that nexilin is required for efficient infection with invasive and adherent bacteria and is key to the actin-rich structures these microbes generate. DOI
300. Lee, YS; Otton, SV; Campbell, DA; Moore, MM; Kennedy, CJ; Gobas, FAPC.Measuring In Vitro Biotransformation Rates of Super Hydrophobic Chemicals in Rat Liver S9 Fractions Using Thin-Film Sorbent-Phase Dosing.Environmental Science & Technology, 2012, 46: 410-418 Measuring In Vitro Biotransformation Rates of Super Hydrophobic Chemicals in Rat Liver S9 Fractions Using Thin-Film Sorbent-Phase Dosing
Methods for rapid and cost-effective assessment of the biotransformation potential of very hydrophobic and potentially bioaccumulative chemicals in mammals are urgently needed for the ongoing global evaluation of the environmental behavior of commercial chemicals. We developed and tested a novel solvent-free, thin-film sorbent-phase in vitro dosing system to measure the in vitro biotransformation rates of very hydrophobic chemicals in male Sprague-Dawley rat liver S9 homogenates and compared the rates to those measured by conventional solvent-delivery dosing. The thin-film sorbent-phase dosing system using ethylene vinyl acetate coated vials was developed to eliminate the incomplete dissolution of very hydrophobic substances in largely aqueous liver homogenates, to determine biotransformation rates at low substrate concentrations, to measure the unbound fraction of substrate in solution, and to simplify chemical analysis by avoiding the difficult extraction of test chemicals from complex biological matrices. Biotransformation rates using sorbent-phase dosing were 2-fold greater than those measured using solvent-delivery dosing. Unbound concentrations of very hydrophobic test chemicals were found to decline with increasing S9 and protein concentrations, causing measured biotransformation rates to be independent of S9 or protein concentrations. The results emphasize the importance of specifying both protein content and unbound substrate fraction in the measurement and reporting of in vitro biotransformation rates of very hydrophobic substances, which can be achieved in a thin-film sorbent-phase dosing system. DOI PubMed
299. Leung, SSW; Busto, JV; Keyvanloo, A; Goni, FM; Thewalt, J.Insights into Sphingolipid Miscibility: Separate Observation of Sphingomyelin and Ceramide N-Acyl Chain Melting.Biophysical Journal, 2012, 103: 2465-2474 Insights into Sphingolipid Miscibility: Separate Observation of Sphingomyelin and Ceramide N-Acyl Chain Melting
NUCLEAR-MAGNETIC-RESONANCE; LIPID MONOLAYERS; PHASE-BEHAVIOR; BIOPHYSICAL PROPERTIES; ACID SPHINGOMYELINASE; MEMBRANE DOMAINS; ENRICHED DOMAINS; ORDERED DOMAINS; MODEL MEMBRANE; CHOLESTEROL
Ceramide produced from sphingomyelin in the plasma membrane is purported to affect signaling through changes in the membrane's physical properties. Thermal behavior of N-palmitoyl sphingomyelin (PSM) and N-palmitoyl ceramide (PCer) mixtures in excess water has been monitored by H-2 NMR spectroscopy and compared to differential scanning calorimetry (DSC) data. The alternate use of either perdeuterated or proton-based N-acyl chain PSM and PCer in our H-2 NMR studies has allowed the separate observation of gel-fluid transitions in each lipid in the presence of the other one, and this in turn has provided direct information on the lipids' miscibility over a wide temperature range. The results provide further evidence of the stabilization of the PSM gel state by PCer. Moreover, overlapping NMR and DSC data reveal that the DSC-signals parallel the melting of the major component (PSM) except at intermediate (20 and 30 mol %) fractions of PCer. In such cases, the DSC endotherm reports on the presumably highly cooperative melting of PCer. Up to at least 50 mol % PCer, PSM and PCer mix ideally in the liquid crystalline phase; in the gel phase, PCer becomes incorporated into PSM: PCer membranes with no evidence of pure solid PCer. DOI
298. Liu, C; Salehzadeh, O; Poole, PJ; Watkins, SP; Kavanagh, KL.Insights into semiconductor nanowire conductivity using electrodeposition.Semiconductor Science and Technology, 2012, 27 Insights into semiconductor nanowire conductivity using electrodeposition
Copper (Cu) and iron (Fe) electrical contacts to gallium arsenide (GaAs) and indium arsenide (InAs) nanowires (NWs) have been fabricated via electrodeposition. For undoped or low carbon-doped (10(17)/cm(-3)), p-type GaAs NWs, Cu or Fe nucleate and grow only on the gold catalyst at the NW tip, avoiding the sidewalls. Metal growth is limited by the Au contact resistance due to thick sidewall depletion layers. For InAs NWs and heavier-doped, core-shell (undoped core-C-doped shell) GaAs NWs, metal nucleation and growth occurs on the sidewalls as well as on the gold catalyst limited now by the ion electrolyte diffusivity. DOI
297. M'Gonigle, LK; Mazzucco, R; Otto, SP; Dieckmann, U.Sexual selection enables long-term coexistence despite ecological equivalence.Nature, 2012, 484: 506-509 Sexual selection enables long-term coexistence despite ecological equivalence
Empirical data indicate that sexual preferences are critical for maintaining species boundaries(1-4), yet theoretical work has suggested that, on their own, they can have only a minimal role in maintaining biodiversity(5-9). This is because long-term coexistence within overlapping ranges is thought to be unlikely in the absence of ecological differentiation(9). Here we challenge this widely held view by generalizing a standard model of sexual selection to include two ubiquitous features of populations with sexual selection: spatial variation in local carrying capacity, and mate-search costs in females. We show that, when these two features are combined, sexual preferences can single-handedly maintain coexistence, even when spatial variation in local carrying capacity is so slight that it might go unnoticed empirically. This theoretical study demonstrates that sexual selection alone can promote the long-term coexistence of ecologically equivalent species with overlapping ranges, and it thus provides a novel explanation for the maintenance of species diversity. DOI
296. Maurer, MK; Menounos, B; Luckman, BH; Osborn, G; Clague, JJ; Beedle, MJ; Smith, R; Atkinson, N.Late Holocene glacier expansion in the Cariboo and northern Rocky Mountains, British Columbia, Canada.Quat. Sci. Rev., 2012, 51: 71-80 Late Holocene glacier expansion in the Cariboo and northern Rocky Mountains, British Columbia, Canada
Holocene; Glacier advance; Environmental reconstruction
Castle Creek Glacier in the Cariboo Mountains of British Columbia remained close to its Little Ice Age limit for most of the past 1500 years, without significant recession until the 20th century. This conclusion is based on radiocarbon-dated detrital and in-situ plant material overrun by the glacier, and the sedimentary record from informally named On-off Lake, which received clastic sediments only when Castle Creek Glacier crossed a hydrologic divide 330 m upvalley of the Little Ice Age limit. Plant macrofossils recovered from the transition between basal inorganic silt and overlying organic silty clay in a sediment core from the lake indicate that the glacier first retreated behind the divide ca. 10.92-9.70 ka. Ages of 8.97-8.61 and 5.58-5.53 ka on detrital wood from the glacier's forefield may record earlier advances, but the first unequivocal evidence of glacier expansion is from an overridden stump with an age of 4.96-4.45 ka. Continuous accumulation of gyttja within On-off Lake, however, indicates that Castle Creek Glacier did not cross the hydrologic divide at any time during the first half of the Holocene. Glacigenic sediments began to accumulate in the lake between 2.73 and 2.49 ka, indicating that Castle Creek Glacier expanded beyond the hydrologic divide at that time. A coincident advance is also recorded in the northern Rocky Mountains of British Columbia at Kwadacha Glacier, which overran a vegetated surface at 2.69-2.36 ka. Clastic sedimentation in On-off Lake ceased soon after the Bridge River volcanic eruption (2.70-2.35 ka), indicating that Castle Creek glacier retreat to a position upvalley of the divide at that time. Sedimentation resumed before 1.87-1.72 ka when the glacier advanced again past the hydrologic divide. Following a second retreat, Castle Creek Glacier advanced across the divide a final time at ca. 1.54-1.42 ka. The snout of the glacier remained less than 330 m upvalley of the Little Ice Age moraine until the early twentieth century when annual moraines indicate rapid frontal recession to a position upvalley of the hydrologic divide. These data collectively indicate that glaciers in the Cariboo Mountains of British Columbia nearly achieved their all-time Holocene limits as early as 2.73-2.49 ka and climatic conditions in the early 20th century abruptly ended a 1500-year period favoring glacier expansion. (C) 2012 Elsevier Ltd. All rights reserved. DOI
295. McClenachan, L; Cooper, AB; Carpenter, KE; Dulvy, NK.Extinction risk and bottlenecks in the conservation of charismatic marine species.Conservation Letters, 2012, 5: 73-80 Extinction risk and bottlenecks in the conservation of charismatic marine species
CITES; climate change; elasmobranchs; fishing impacts; IUCN Red List; reef fish; taxonomic bias
The oceans face a biodiversity crisis, but the degree and scale of extinction risk remains poorly characterized. Charismatic species are most likely to garner greatest support for conservation and thus provide a best-case scenario of the status of marine biodiversity. We summarize extinction risk and diagnose impediments to successful conservation for 1,568 species in 16 families of marine animals in the movie Finding Nemo. Sixteen percent (1234%) of those that have been evaluated are threatened, ranging from 9% (728%) of bony fishes to 100% (83100%) of marine turtles. A lack of scientific knowledge impedes analysis of threat status for invertebrates, which have 1,000 times fewer conservation papers than do turtles. Legal protection is severely deficient for sharks and rays; only 8% of threatened species in our analysis are protected. Extinction risk among wide-ranging taxa is higher than most terrestrial groups, suggesting a different conservation focus is required in the sea. DOI
294. Merino, G; Barange, M; Blanchard, JL; Harle, J; Holmes, R; Allen, I; Allison, EH; Badjeck, MC; Dulvy, NK; Holt, J; Jennings, S; Mullon, C; Rodwell, LD.Can marine fisheries and aquaculture meet fish demand from a growing human population in a changing climate?Global Environmental Change-Human and Policy Dimensions, 2012, 22: 795-806 Can marine fisheries and aquaculture meet fish demand from a growing human population in a changing climate?
Global environmental change; Fish production; Fisheries; Aquaculture; Adaptation
Expansion in the world's human population and economic development will increase future demand for fish products. As global fisheries yield is constrained by ecosystems productivity and management effectiveness, per capita fish consumption can only be maintained or increased if aquaculture makes an increasing contribution to the volume and stability of global fish supplies. Here, we use predictions of changes in global and regional climate (according to IPCC emissions scenario A1B), marine ecosystem and fisheries production estimates from high resolution regional models, human population size estimates from United Nations prospects, fishmeal and oil price estimations, and projections of the technological development in aquaculture feed technology, to investigate the feasibility of sustaining current and increased per capita fish consumption rates in 2050. We conclude that meeting current and larger consumption rates is feasible, despite a growing population and the impacts of climate change on potential fisheries production, but only if fish resources are managed sustainably and the animal feeds industry reduces its reliance on wild fish. Ineffective fisheries management and rising fishmeal prices driven by greater demand could, however, compromise future aquaculture production and the availability of fish products. (C) 2012 Elsevier Ltd. All rights reserved. DOI
293. Mitchell-Foster, K; Ma, BO; Warsame-Ali, S; Logan, C; Rau, ME; Lowenberger, C.The influence of larval density, food stress, and parasitism on the bionomics of the dengue vector Aedes aegypti (Diptera: Culicidae): implications for integrated vector management.Journal of Vector Ecology, 2012, 37: 221-229 The influence of larval density, food stress, and parasitism on the bionomics of the dengue vector Aedes aegypti (Diptera: Culicidae): implications for integrated vector management
Aedes aegypti; Plagiorchis elegans; fitness consequences; biocontrol
New larval control strategies for integrated vector management of Aedes aegypti are in high demand, including the use of biological control agents. Exposure of Aedes aegypti to parasites, starvation, and overcrowded conditions during larval development reduces the probability of survival to eclosion, can directly affect fitness parameters such as adult size and fecundity, and can affect the size, provisioning, and viability of eggs produced by females. We compared these parameters after exposing larvae to 1) abundant food at low larval densities, 2) food deprivation and high larval density, and 2) infection with the endoparasite Plagiorchis elegans, an entomopathogenic digenean trematode. Female mosquitoes that eclosed from larval conditions of starvation and overcrowding were smaller and laid fewer and smaller eggs than controls. The proportion of females to complete an oviposition cycle was reduced in the P. elegans-infected treatment group. Parasite load was negatively correlated with wing length and egg size. Infection of Ae. aegypti with P. elegans has sublethal effects and may reduce population-level reproductive output, but one-time low-density P. elegans exposure does not have sufficient effect on Ae. aegypti fitness parameters to be considered a viable biocontrol option. DOI
292. Mooers, A; Gascuel, O; Stadler, T; Li, HY; Steel, M.Branch Lengths on Birth-Death Trees and the Expected Loss of Phylogenetic Diversity.Systematic Biology, 2012, 61: 195-203 Branch Lengths on Birth-Death Trees and the Expected Loss of Phylogenetic Diversity
EVOLUTIONARY HISTORY; DIVERSIFICATION RATES; NONRANDOM EXTINCTION; SPECIATION RATES; NEUTRAL MODELS; PATTERNS; SHAPE; TIME
Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where pendant branches leading to tips can be very short compared with branches deeper in the tree. Here, we analyze alternative and more realistic Yule and birth-death models. We show how censoring at the present both makes average branches one half what we might expect and makes pendant and interior branches roughly equal in length. Although dependent on whether we condition on the size of the tree, its age, or both, these results hold both for the Yule model and for birth-death models with moderate extinction. Importantly, the rough equivalency in interior and exterior branch lengths means that the loss of evolutionary history with loss of species can be roughly linear. Under these models, the Tree of Life may offer limited redundancy in the face of ongoing species loss. DOI PubMed
291. Muller, K; Linkies, A; Leubner-Metzger, G; Kermode, AR.Role of a respiratory burst oxidase of Lepidium sativum (cress) seedlings in root development and auxin signalling.Journal of Experimental Botany, 2012, 63: 6325-6334 Role of a respiratory burst oxidase of Lepidium sativum (cress) seedlings in root development and auxin signalling
AtrbohB; auxin; Lepidium sativum; Rboh; reactive oxygen species; RNAi; root development; superoxide
Reactive oxygen species are increasingly perceived as players in plant development and plant hormone signalling pathways. One of these species, superoxide, is produced in the apoplast by respiratory burst oxidase homologues (rbohs), a family of proteins that is conserved throughout the plant kingdom. Because of the availability of mutants, the focus of research into plant rbohs has been on Arabidopsis thaliana, mainly on AtrbohD and AtrbohF. This study investigates: (i) a different member of the Atrboh family, AtrbohB, and (ii) several rbohs from the close relative of A. thaliana, Lepidium sativum (ocress'). Five cress rbohs (Lesarbohs) were sequenced and it was found that their expression patterns were similar to their Arabidopsis orthologues throughout the life cycle. Cress plants in which LesarbohB expression was knocked down showed a strong seedling root phenotype that resembles phenotypes associated with defective auxin-related genes. These transgenic plants further displayed altered expression of auxin marker genes including those encoding the auxin responsive proteins 14 and 5 (IAA14 and IAA5), and LBD16 (LATERAL ORGAN BOUNDARIES DOMAIN16), an auxin-responsive protein implicated in lateral root initiation. It is speculated that ROS produced by rbohs play a role in root development via auxin signalling. DOI
290. Osborn, G; Menounos, B; Ryane, C; Riedel, J; Clague, JJ; Koch, J; Clark, D; Scott, K; Davis, PT.Latest Pleistocene and Holocene glacier fluctuations on Mount Baker, Washington.Quat. Sci. Rev., 2012, 49: 33-51 Latest Pleistocene and Holocene glacier fluctuations on Mount Baker, Washington
Pleistocene; Holocene; Glacial history; Mount Baker; Tephrochronology
Glaciers on stratovolcanoes of the Pacific Northwest of North America offer opportunities for dating late Pleistocene and Holocene glacier advances because tephra and fossil wood are common in lateral moraines and in glacier forefields. We capitalize on this opportunity by examining the Holocene glacial record at Mount Baker, an active stratovolcano in northwest Washington. Earlier workers concluded that glaciers on Mount Baker during the early Holocene were more extensive than during the Little Ice Age and hypothesized that the explanation lay in unusual climatic or hypsometric effects peculiar to large volcanoes. We show that the main argument for an early Holocene glacier advance on Mount Baker, namely the absence of ca 10,000-year-old tephra on part of the south flank of the mountain, is incorrect. Moreover, a lake-sediment core indicates that a small cirque moraine previously thought be of early Holocene age is also likely older than the tephra and consequently of late Pleistocene age. Lateral and end moraines and wood mats ca 2 km downvalley of the present snout of Deming Glacier indicate that an advance during the Younger Dryas interval was little more extensive than the climactic Little Ice Age advance. Tephra and wood between tills in the left lateral moraine of Easton Glacier suggest that ice on Mount Baker was restricted in the early Holocene and that Neoglaciation began ca 6 ka. A series of progressively more extensive Neoglacial advances, dated to about 2.2, 1.6, 0.9, and 0.4 ka, are recorded by stacked tills in the right lateral moraine of Deming Glacier. Intervening retreats were long enough to allow establishment of forests on the moraine. Wood mats in moraines of Coleman and Easton glaciers indicate that Little Ice Age expansion began before 0.7 ka and was followed by retreat and a readvance ca 0.5 ka. Tree-ring and lichen data indicate glaciers on the south side of the mountain reached their maximum extents in the mid-1800s. The similarity between glacier fluctuations at Mount Baker and those elsewhere in the Cascades and in British Columbia suggests a coherent history of Holocene climate change over a broad area of the western Cordillera. We found no evidence that glaciers on stratovolcanoes behave differently than glaciers elsewhere. (C) 2012 Elsevier Ltd. All rights reserved. DOI
289. Pacheco, MA; Reid, MJC; Schillaci, MA; Lowenberger, CA; Galdikas, BMF; Jones-Engel, L; Escalante, AA.The Origin of Malarial Parasites in Orangutans.PLOS One, 2012, 7(4): e34990. Epub Apr 20 The Origin of Malarial Parasites in Orangutans
Background: Recent findings of Plasmodium in African apes have changed our perspectives on the evolution of malarial parasites in hominids. However, phylogenetic analyses of primate malarias are still missing information from Southeast Asian apes. In this study, we report molecular data for a malaria parasite lineage found in orangutans. Methodology/Principal Findings: We screened twenty-four blood samples from Pongo pygmaeus (Kalimantan, Indonesia) for Plasmodium parasites by PCR. For all the malaria positive orangutan samples, parasite mitochondrial genomes (mtDNA) and two antigens: merozoite surface protein 1 42 kDa (MSP-1(42)) and circumsporozoite protein gene (CSP) were amplified, cloned, and sequenced. Fifteen orangutans tested positive and yielded 5 distinct mitochondrial haplotypes not previously found. The haplotypes detected exhibited low genetic divergence among them, indicating that they belong to one species. We report phylogenetic analyses using mitochondrial genomes, MSP-1(42) and CSP. We found that the orangutan malaria parasite lineage was part of a monophyletic group that includes all the known non-human primate malaria parasites found in Southeast Asia; specifically, it shares a recent common ancestor with P. inui (a macaque parasite) and P. hylobati (a gibbon parasite) suggesting that this lineage originated as a result of a host switch. The genetic diversity of MSP-1(42) in orangutans seems to be under negative selection. This result is similar to previous findings in non-human primate malarias closely related to P. vivax. As has been previously observed in the other Plasmodium species found in non-human primates, the CSP shows high polymorphism in the number of repeats. However, it has clearly distinctive motifs from those previously found in other malarial parasites. Conclusion: The evidence available from Asian apes indicates that these parasites originated independently from those found in Africa, likely as the result of host switches from other non-human primates. DOI
288. Porszt, EJ; Peterman, RM; Dulvy, NK; Cooper, AB; Irvine, JR.Reliability of Indicators of Decline in Abundance.Conservation Biology, 2012, 26: 894-904 Reliability of Indicators of Decline in Abundance
COSEWIC; IUCN; receiver operating characteristic (ROC); sockeye salmon; threat indicators; caracteristica de operacion del receptor; COR; COSEWIC; indicadores de amenaza; IUCN; Oncorhynchus nerka
Although there are many indicators of endangerment (i.e., whether populations or species meet criteria that justify conservation action), their reliability has rarely been tested. Such indicators may fail to identify that a population or species meets criteria for conservation action (false negative) or may incorrectly show that such criteria have been met (false positive). To quantify the rate of both types of error for 20 commonly used indicators of declining abundance (threat indicators), we used receiver operating characteristic curves derived from historical (19382007) data for 18 sockeye salmon (Oncorhynchus nerka) populations in the Fraser River, British Columbia, Canada. We retrospectively determined each population's yearly status (reflected by change in abundance over time) on the basis of each indicator. We then compared that population's status in a given year with the status in subsequent years (determined by the magnitude of decline in abundance across those years). For each sockeye population, we calculated how often each indicator of past status matched subsequent status. No single threat indicator provided error-free estimates of status, but indicators that reflected the extent (i.e., magnitude) of past decline in abundance (through comparison of current abundance with some historical baseline abundance) tended to better reflect status in subsequent years than the rate of decline over the previous 3 generations (a widely used indicator). We recommend that when possible, the reliability of various threat indicators be evaluated with empirical analyses before such indicators are used to determine the need for conservation action. These indicators should include estimates from the entire data set to take into account a historical baseline. DOI
286. Reynolds, J.D., Favaro, B. & Côté.Canada: A bleak day for the environment.Nature, 2012, 487, 171 Canada: A bleak day for the environment
It was a dark day for environmental science and policy in Canada on 29 June.
The country's Conservative Party has been steadily dismantling environmental protection since winning a majority government last year (see, for example, Nature http://doi.org/h2v; 2012). Further alarming changes to environmental laws were concealed in a 'budget bill' that was ratified by the Senate on 29 June.
For example, the Canadian Environmental Assessment Act has been replaced by a weaker law that reduces government oversight of the environmental impact of a proposed pipeline from the Alberta oil sands to tankers off British Columbia. Canada's Fisheries Act now allows for more pollution and no longer protects fish habitats, except for fisheries. The National Round Table on the Environment and the Economy, which provides independent scientific advice on sustainable development, will be dissolved in March 2013. A finance committee that had no scientific or public input has decided that this massive legislative overhaul could proceed as written.
Globally significant research facilities have already been axed, including the renowned Experimental Lakes Area and the Polar Environment Atmospheric Research Laboratory in the high Arctic. Scientific agencies such as Fisheries and Oceans Canada (DFO), Environment Canada and Parks Canada have had to sack most of the personnel responsible for habitat management and monitoring, including those in the DFO's marine-pollution programme.
The new legislative framework marginalizes science in environmental management, and could do irreparable harm to the environment and the economy it supports. Such tactics match Canada's intransigence on climate change: the same bill made it the first country to pull out of the Kyoto agreement.Website DOI
285. Salehzadeh, O; Zhang, X; Gates, BD; Kavanagh, KL; Watkins, SP.p-type doping of GaAs nanowires using carbon.J. Appl. Phys., 2012, 112 p-type doping of GaAs nanowires using carbon
We report on the electrical properties of Au-catalyzed C-doped GaAs nanowires (NWs) grown by metal organic vapor phase epitaxy. Transport measurements were carried out using a tungsten nanoprobe inside a scanning electron microscope by contacting to the Au catalyst particle of individual nanowires. The doping level could be varied from approximately (4 +/- 1) x 10(16) cm(-3) to (1.0 +/- 0.3) x 10(19) cm(-3) by varying the molar flow of the gas phase carbon precursor, as well as the group V to group III precursor ratio. It was found that the current transport mechanism switches from generation-recombination to tunnelling field emission by increasing the doping level to 1 x 10(19) cm(-3). Based on a diameter-dependent analysis of the apparent resistivity of the C-doped NWs, we propose that C incorporates into GaAs NWs through the triple boundary at the Au/NW interface. The p-type conductivity of the C-doped NWs was inferred by observing a rectification at negative bias (applied to the Au electrode) and confirmed by back-gating measurements performed on field effect transistor devices. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4759368] DOI
284. Suh, J; Hutter, H.A survey of putative secreted and transmembrane proteins encoded in the C-elegans genome.BMC Genomics, 2012, 13 A survey of putative secreted and transmembrane proteins encoded in the C-elegans genome
NEMATODE CAENORHABDITIS-ELEGANS; GENE FAMILY; SUBCELLULAR-LOCALIZATION; EXPRESSION ANALYSIS; AXON FASCICULATION; CELL-ADHESION; DATABASE; PREDICTION; RNAI; CLASSIFICATION
Background: Almost half of the Caenorhabditis elegans genome encodes proteins with either a signal peptide or a transmembrane domain. Therefore a substantial fraction of the proteins are localized to membranes, reside in the secretory pathway or are secreted. While these proteins are of interest to a variety of different researchers ranging from developmental biologists to immunologists, most of secreted proteins have not been functionally characterized so far. Results: We grouped proteins containing a signal peptide or a transmembrane domain using various criteria including evolutionary origin, common domain organization and functional categories. We found that putative secreted proteins are enriched for small proteins and nematode-specific proteins. Many secreted proteins are predominantly expressed in specific life stages or in one of the two sexes suggesting stage- or sex-specific functions. More than a third of the putative secreted proteins are upregulated upon exposure to pathogens, indicating that a substantial fraction may have a role in immune response. Slightly more than half of the transmembrane proteins can be grouped into broad functional categories based on sequence similarity to proteins with known function. By far the largest groups are channels and transporters, various classes of enzymes and putative receptors with signaling function. Conclusion: Our analysis provides an overview of all putative secreted and transmembrane proteins in C. elegans. This can serve as a basis for selecting groups of proteins for large-scale functional analysis using reverse genetic approaches. DOI
283. Sunday, JM; Bates, AE; Dulvy, NK.Thermal tolerance and the global redistribution of animals.Nature Climate Change, 2012, 2: 686-690 Thermal tolerance and the global redistribution of animals
The redistribution of life on Earth has emerged as one of the most significant biological responses to anthropogenic climate warming(1-3). Despite being one of the most long-standing puzzles in ecology(4), we still have little understanding of how temperature sets geographic range boundaries(5). Here we show that marine and terrestrial ectotherms differ in the degree to which they fill their potential latitudinal ranges, as predicted from their thermal tolerance limits. Marine ectotherms more fully occupy the extent of latitudes tolerable within their thermal tolerance limits, and are consequently predicted to expand at their poleward range boundaries and contract at their equatorward boundaries with climate warming. In contrast, terrestrial ectotherms are excluded from the warmest regions of their latitudinal range; thus, the equatorward, or 'trailing' range boundaries, may not shift consistently towards the poles with climate warming. Using global observations of climate-induced range shifts, we test this prediction and show that in the ocean, shifts at both range boundaries have been equally responsive, whereas on land, equatorward range boundaries have lagged in response to climate warming. These results indicate that marine species' ranges conform more closely to their limits of thermal tolerance, and thus range shifts will be more predictable and coherent. However, on land, warmer range boundaries are not at equilibrium with heat tolerance. Understanding the relative contribution of factors other than temperature in controlling equatorward range limits is critical for predicting distribution changes, with implications for population and community viability. DOI
282. Sutherland, WJ; Aveling, R; Bennun, L; Chapman, E; Clout, M; Côté, IM; Depledge, MH; Dicks, LV; Dobson, AP; Fellman, L; Fleishman, E; Gibbons, DW; Keim, B; Lickorish, F; Lindenmayer, DB; Monk, KA; Norris, K; Peck, LS; Prior, SV; Scharlemann, JPW; Spalding, M; Watkinson, AR.A horizon scan of global conservation issues for 2012.Trends in Ecology & Evolution, 2012, 27: 12-18 A horizon scan of global conservation issues for 2012
Our aim in conducting annual horizon scans is to identify issues that, although currently receiving little attention, may be of increasing importance to the conservation of biological diversity in the future. The 15 issues presented here were identified by a diverse team of 22 experts in horizon scanning, and conservation science and its application. Methods for identifying and refining issues were the same as in two previous annual scans and are widely transferable to other disciplines. The issues highlight potential changes in climate, technology and human behaviour. Examples include warming of the deep sea, increased cultivation of perennial grains, burning of Arctic tundra, and the development of nuclear batteries and hydrokinetic in-stream turbines. DOI
281. Thomson, JA; Cooper, AB; Burkholder, DA; Heithaus, MR; Dill, LM.Heterogeneous patterns of availability for detection during visual surveys: spatiotemporal variation in sea turtle dive-surfacing behaviour on a feeding ground.Methods in Ecology and Evolution, 2012, 3: 378-387 Heterogeneous patterns of availability for detection during visual surveys: spatiotemporal variation in sea turtle dive-surfacing behaviour on a feeding ground
abundance estimation; availability bias; detectability; diving; green turtle; loggerhead turtle; sightability; transect sampling
1. During aerial or boat-based surveys for large-bodied diving taxa (e.g. marine mammals and marine turtles), a proportion of animals present will be missed because they are submerged and out of view, leading to availability bias in abundance indices. Information on divesurfacing patterns can improve corrections for availability bias. However, as dive data are typically limited, availability correction factors are often based on poorly resolved dive and surface times, and diving heterogeneity is not considered. 2. We collected dive records for green turtles Chelonia mydas, Linnaeus 1758, and loggerhead turtles Caretta caretta, Linnaeus 1758, on a foraging ground in Shark Bay, Western Australia to quantify dive-surfacing patterns and assess potential correlations with easily measured environmental features: habitat depth and water temperature. Bayesian regression models were used to predict dive and surface interval durations across temperature-depth gradients and assess their uncertainty. We used these predictions to quantify variation in availability correction factors, which were multipliers designed, in this case, to adjust surface sightings data to incorporate diving animals. 3. Dive and surface interval durations for both species varied positively with depth and negatively with temperature, consistent with a priori expectations, although temperature effects were not always significant. Dive metrics were predictable, although uncertainty increased in deeper habitat with few observed dives. 4. Availability correction factors were highly heterogeneous, with larger corrections necessary in colder, deeper conditions (long-diving, infrequent surfacing behaviour) and smaller corrections required in warmer, shallower conditions (short-diving, frequent-surfacing behaviour). 5. Predictable variation in the diving behaviour of chelonid sea turtles across environmental gradients on a foraging ground reveals that site-specific knowledge of dive-surfacing patterns can be important to mitigate the effects of availability bias during population surveys. Accounting for such trends may improve the reliability of ecological inferences (e. g. spatiotemporal distribution trends) and the efficacy of applications (e. g. conservation planning) based on survey data. DOI
280. Twardochleb, L.A., M. Novak, and J.W. Moore.Using the functional response of a consumer to predict biotic resistance to invasive prey.Ecological Applications, 2012, 22: 1162-1171 Using the functional response of a consumer to predict biotic resistance to invasive prey.
biotic resistance; crayfish; New Zealand mud snail; Pacifastacus leniusculus; Potamopyrgus antipodarum; predation; propagule pressure; San Lorenzo River, California, USA; stream; type 3 functional response
Predators sometimes provide biotic resistance against invasions by nonnative prey. Understanding and predicting the strength of biotic resistance remains a key challenge in invasion biology. A predator's functional response to nonnative prey may predict whether a predator can provide biotic resistance against nonnative prey at different prey densities. Surprisingly, functional responses have not been used to make quantitative predictions about biotic resistance. We parameterized the functional response of signal crayfish (Pacifastacus leniusculus) to invasive New Zealand mud snails (Potamopyrgus antipodarum; NZMS) and used this functional response and a simple model of NZMS population growth to predict the probability of biotic resistance at different predator and prey densities. Signal crayfish were effective predators of NZMS, consuming more than 900 NZMS per predator in a 12-h period, and Bayesian model fitting indicated their consumption rate followed a type 3 functional response to NZMS density. Based on this functional response and associated parameter uncertainty, we predict that NZMS will be able to invade new systems at low crayfish densities (<0.2 crayfish/m(2)) regardless of NZMS density. At intermediate to high crayfish densities (>0.2 crayfish/m(2)), we predict that low densities of NZMS will be able to establish in new communities; however, once NZMS reach a threshold density of similar to 2000 NZMS/m(2), predation by crayfish will drive negative NZMS population growth. Further, at very high densities, NZMS overwhelm predation by crayfish and invade. Thus, interacting thresholds of propagule pressure and predator densities define the probability of biotic resistance. Quantifying the shape and uncertainty of predator functional responses to nonnative prey may help predict the outcomes of invasions.PDF
278. Vezina, F; Williams, TD; Piersma, T; Morrison, RIG.Phenotypic compromises in a long-distance migrant during the transition from migration to reproduction in the High Arctic.Functional Ecology, 2012, 26: 500-512 Phenotypic compromises in a long-distance migrant during the transition from migration to reproduction in the High Arctic
arrival biology; basal metabolic rate; breeding; energetics; life-history stages; phenotypic flexibility; physiological conflicts; polar environment; reproduction; thermoregulation
1. Seasonal carry-over effects may be important structuring components of avian life-history cycles. However, little is known on physiological transitions between stages and on phenotypic compromises that may be made at such time to improve fitness. 2. We studied postmigratory body remodelling in red knots (Calidris canutus islandica) arriving on the Arctic breeding grounds. Our objectives were to determine the effects of body reconstruction and preparation for breeding on maintenance energy costs and to determine whether weather conditions can force compromises between functions required for postmigration recovery of body composition, thermoregulation and breeding. 3. During two consecutive springs at the northernmost land on Earth (Alert, Ellesmere Island, Canada, 82 degrees 30' N), we monitored changes in knots post- arrival body stores. Using ultrasonography, we also tracked changes in gizzard size, an indicator of gut size, and pectoral muscle thickness, not only an endogenous protein source but also a thermogenic organ. We measured basal metabolic rate (BMR) throughout reconstruction and compared it with BMR of nonbreeding red knots wintering in the Dutch Wadden Sea. 4. Arriving knots faced temperatures up to 13 degrees C lower than during midwinter. Birds arrived with large body stores and pectoral muscles, which declined in size while they grew their gizzard and prepared for breeding. BMR at arrival was indistinguishable from winter BMR and increased linearly throughout reconstruction. BMR increased up to 69% faster in females than males, likely due to the development of their reproductive organs. 5. Birds had lower body stores but larger muscles in the colder year, and muscle loss was correlated with the warming of spring temperatures. Therefore, muscles would not only serve as a nutrient source, but their thermogenic function could also provide the flexibility to cope with high thermostatic costs in the spring. However, retaining muscles for shivering may limit protein recirculation and delay the onset of breeding. 6. Postmigratory recovery therefore involves significant energy costs and arriving birds likely have to make physiological compromises, depending on spring conditions, which may impact on fitness. Although this period is clearly critical in the life cycle of red knots, it is one of the least understood life- history stages in Arctic- breeding shorebirds. DOI
277. Waliwitiya, R; Belton, P; Nicholson, RA; Lowenberger, CA.Plant Terpenoids: Acute Toxicities and Effects on Flight Motor Activity and Wing Beat Frequency in the Blow Fly Phaenicia sericata.Journal of Economic Entomology, 2012, 105: 72-84 Plant Terpenoids: Acute Toxicities and Effects on Flight Motor Activity and Wing Beat Frequency in the Blow Fly Phaenicia sericata
flight muscles; eugenol; pulegone; alpha-terpineol; citronellal
We evaluated the acute toxicities and the physiological effects of plant monoterpenoids (eugenol, pulegone, citronellal and alpha-terpineol) and neuroactive insecticides (malathion, dieldrin and RH3421) on flight muscle impulses (FMI) and wing beat signals (WBS) of the blow fly (Phaenicia sericata). Topically-applied eugenol, pulegone, citronellal, and alpha-terpineol produced neurotoxic symptoms, but were less toxic than malathion, dieldrin, or RH3421. Topical application of eugenol, pulegone, and citronellal reduced spike amplitude in one of the two banks of blow fly dorsolongitudinal flight muscles within 6-8 min, but with citronellal, the amplitude of FMIs reverted to a normal pattern within 1 hr. In contrast to pulegone and citronellal, where impulse frequency remained relatively constant, eugenol caused a gradual increase, then a decline in the frequency of spikes in each muscle bank. Wing beating was blocked permanently within 6-7 min of administering pulegone or citronellal and within 16 mins with eugenol. alpha-Terpineol-treated blow flies could not beat their wings despite normal FMI patterns. The actions of these monoterpenoids on blow fly flight motor patterns are discussed and compared with those of dieldrin, malathion, RH3421, and a variety of other neuroactive substances we have previously investigated in this system. Eugenol, pulegone and citronellal readily penetrate blow fly cuticle and interfere with flight muscle and/or central nervous function. Although there were differences in the effects of these compounds, they mainly depressed flight-associated responses, and acted similarly to compounds that block sodium channels and facilitate GABA action. DOI
276. Waliwitiya, R; Nicholson, RA; Kennedy, CJ; Lowenberger, CA.The Synergistic Effects of Insecticidal Essential Oils and Piperonyl Butoxide on Biotransformational Enzyme Activities in Aedes aegypti (Diptera: Culicidae).Journal of Medical Entomology, 2012, 49: 614-623 The Synergistic Effects of Insecticidal Essential Oils and Piperonyl Butoxide on Biotransformational Enzyme Activities in Aedes aegypti (Diptera: Culicidae)
ethoxyresorufin O-deethylase; glutathione S-transferase; esterase; essential oil; Ae. Aegypti
The biochemical mechanisms underlying the increased toxicity of several plant essential oils (thymol, eugenol, pulegone, terpineol, and citronellal) against fourth instar of Aedes aegypti L. when exposed simultaneously with piperonyl butoxide (PBO) were examined. Whole body biotransformational enzyme activities including cytochrome P450-mediated oxidation (ethoxyresorufin O-dethylase [EROD]), glutathione S-transferase (GST), and beta-esterase activity were measured in control, essential oil-exposed only (single chemical), and essential oil + PBO (10 mg/liter) exposed larvae. At high concentrations, thymol, eugenol, pulegone, and citronellal alone reduced EROD activity by 5-25% 16 h postexposure. Terpineol at 10 mg/liter increased EROD activity by 5 +/- 1.8% over controls. The essential oils alone reduced GST activity by 3-20% but PBO exposure alone did not significantly affect the activity of any of the measured enzymes. All essential oils in combination with PBO reduced EROD activity by 58-76% and reduced GST activity by 3-85% at 16 h postexposure. This study indicates a synergistic interaction between essential oils and PBO in inhibiting the cytochrome P450 and GST detoxification enzymes in Ae. aegypti. DOI
275. Williams, TD; Fronstin, RB; Otomo, A; Wagner, E.Validation of the use of phenylhydrazine hydrochloride (PHZ) for experimental manipulation of haematocrit and plasma haemoglobin in birds.Ibis, 2012, 154: 21-29 Validation of the use of phenylhydrazine hydrochloride (PHZ) for experimental manipulation of haematocrit and plasma haemoglobin in birds
European Starlings; experimental manipulation; haemolytic anaemia; individual variation; Zebra Finches
The levels of haematocrit (Hct) and plasma haemoglobin (Hb) vary markedly through the annual cycle of birds, as well as among individuals at all life-stages (embryos, chicks, adults). It is thus surprising that the functional, fitness-related consequences of this variation are poorly understood. Putative adaptive variation in these haematological traits has been associated with varying demands for aerobic capacity and oxygen transport, for example during migration, winter acclimatization, with increasing altitude, or during parental care. It has also been proposed that changes in Hct might reflect costs of parental investment, for example during reproductive anaemia. However, almost all studies to date have been correlative. Here we describe a series of experiments that validate the use of phenylhydrazine hydrochloride (PHZ) for the transient, reversible experimental manipulation of Hct and Hb in birds. A single bolus injection (12.5 mu g PHZ/g body weight delivered via intra-muscular injection) caused a rapid decrease in Hct and plasma Hb within 24 h, from pretreatment values of 5054% to 4044% in non-breeding Zebra Finches Taenipoygia guttata and European Starlings Sturnus vulgaris, and to 35% in breeding female Zebra Finches, changes within the normal physiological range. Hct and Hb returned to pre-injection levels within 510 days of treatment. Changes in plasma Hb paralleled those for Hct. We suggest that PHZ treatment provides a widely applicable technique for use in experimental work to establish relationships between haematological status, aerobic capacity, workload (e.g. migration, parental care, thermoregulation), individual quality (of both adults and chicks) and trade-offs such as costs of reproduction. DOI
273. Alvarez-Filip L., Gill J.A., Dulvy N.K.Complex reef architecture supports more small-bodied fishes and longer food chains on Caribbean reefs.Ecosphere, 2011, 2, art118 Complex reef architecture supports more small-bodied fishes and longer food chains on Caribbean reefs
Coral community shifts towards reefs dominated by stress-resistant corals have contributed to rapid declines in the architectural complexity of reefs throughout the Caribbean. Complex reef architecture provides important niches and refuges for many reef fishes and thus widespread declines in reef complexity could have important consequences for the structure and function of fish assemblages. We explore the influence of reef architecture on fish assemblages by comparing the size and trophic structure of reef fishes along a 20 km-long 15-reef gradient of coral cover, coral species dominance and architectural complexity in Cozumel, Mexico. Our results show that reefs with high architectural complexity, in particular those dominated by robust Montastraea corals, supported fish assemblages with larger numbers of individuals in the smallest size classes (<20 cm) and longer food chains (higher mean trophic levels). The association between coral complexity and fish communities is highly size-structured and is greatest for smallest size classes. The greater abundance of both small fish and the key early life stages of larger fishes on more complex reefs suggests that architectural complexity may influence entire reef fish assemblages, even though larger fish are less dependent on reef complexity. Key reef-building corals such as Montastraea are thus likely to be disproportionately important for maintaining reef fish communities, and shifts in Caribbean coral communities may compromise fish recruitment and truncate food chains, reducing resilience and inhibiting reef recovery from degradation.PDF DOI
272. Alvarez-Filip, L; Côté, IM; Gill, JA; Watkinson, AR; Dulvy, NK.Region-wide temporal and spatial variation in Caribbean reef architecture: is coral cover the whole story?Global Change Biology, 2011, 17: 2470-2477 Region-wide temporal and spatial variation in Caribbean reef architecture: is coral cover the whole story?
climate change; ecosystem services; foundation species; habitat loss; reef degradation
The architectural complexity of coral reefs is largely generated by reef-building corals, yet the effects of current regional-scale declines in coral cover on reef complexity are poorly understood. In particular, both the extent to which declines in coral cover lead to declines in complexity and the length of time it takes for reefs to collapse following coral mortality are unknown. Here we assess the extent of temporal and spatial covariation between coral cover and reef architectural complexity using a Caribbean-wide dataset of temporally replicated estimates spanning four decades. Both coral cover and architectural complexity have declined rapidly over time, with little evidence of a time-lag. However, annual rates of change in coral cover and complexity do not covary, and levels of complexity vary greatly among reefs with similar coral cover. These findings suggest that the stressors influencing Caribbean reefs are sufficiently severe and widespread to produce similar regional-scale declines in coral cover and reef complexity, even though reef architectural complexity is not a direct function of coral cover at local scales. Given that architectural complexity is not a simple function of coral cover, it is important that conservation monitoring and restoration give due consideration to both architecture and coral cover. This will help ensure that the ecosystem services supported by architectural complexity, such as nutrient recycling, dissipation of wave energy, fish production and diversity, are maintained and enhanced. DOI
271. Alvarez-Filip, L; Dulvy, NK; Côté, IM; Watkinson, AR; Gill, JA.Coral identity underpins architectural complexity on Caribbean reefs.Ecological Applications, 2011, 21: 2223-2231 Coral identity underpins architectural complexity on Caribbean reefs
biodiversity; coral; Cozumel; Mexico; dominance; functional groups; habitat complexity; landscape ecology; reef
The architectural complexity of ecosystems can greatly influence their capacity to support biodiversity and deliver ecosystem services. Understanding the components underlying this complexity can aid the development of effective strategies for ecosystem conservation. Caribbean coral reefs support and protect millions of livelihoods, but recent anthropogenic change is shifting communities toward reefs dominated by stress-resistant coral species, which are often less architecturally complex. With the regionwide decline in reef fish abundance, it is becoming increasingly important to understand changes in coral reef community structure and function. We quantify the influence of coral composition, diversity, and morpho-functional traits on the architectural complexity of reefs across 91 sites at Cozumel, Mexico. Although reef architectural complexity increases with coral cover and species richness, it is highest on sites that are low in taxonomic evenness and dominated by morpho-functionally important, reef-building coral genera, particularly Montastraea. Sites with similar coral community composition also tend to occur on reefs with very similar architectural complexity, suggesting that reef structure tends to be determined by the same key species across sites. Our findings provide support for prioritizing and protecting particular reef types, especially those dominated by key reef-building corals, in order to enhance reef complexity. DOI
270. Archibald, SB; Johnson, KR; Mathewes, RW; Greenwood, DR.Intercontinental dispersal of giant thermophilic ants across the Arctic during early Eocene hyperthermals.Proceedings of the Royal Society B-Biological Sciences, 2011, 278: 3679-3686 Intercontinental dispersal of giant thermophilic ants across the Arctic during early Eocene hyperthermals
Formicidae; Formiciinae; Titanomyrma; Holarctic dispersal; hyperthermals
Early Eocene land bridges allowed numerous plant and animal species to cross between Europe and North America via the Arctic. While many species suited to prevailing cool Arctic climates would have been able to cross throughout much of this period, others would have found dispersal opportunities only during limited intervals when their requirements for higher temperatures were met. Here, we present Titanomyrma lubei gen. et sp. nov. from Wyoming, USA, a new giant (greater than 5 cm long) formiciine ant from the early Eocene (approx. 49.5 Ma) Green River Formation. We show that the extinct ant subfamily Formiciinae is only known from localities with an estimated mean annual temperature of about 20 degrees C or greater, consistent with the tropical ranges of almost all of the largest living ant species. This is, to our knowledge, the first known formiciine of gigantic size in the Western Hemisphere and the first reported cross-Arctic dispersal by a thermophilic insect group. This implies intercontinental migration during one or more brief high-temperature episodes (hyperthermals) sometime between the latest Palaeocene establishment of intercontinental land connections and the presence of giant formiciines in Europe and North America by the early middle Eocene. DOI
268. Calvert, AJ; Preston, LA; Farahbod, AM.Sedimentary underplating at the Cascadia mantle-wedge corner revealed by seismic imaging.Nat. Geosci., 2011, 4: 545-548 Sedimentary underplating at the Cascadia mantle-wedge corner revealed by seismic imaging
Earth's largest earthquakes occur in subduction zones, along the boundary between the subducting and overriding plates(1). Non-volcanic tremor generated by slow slip between the plates is thought to originate on, or near, this boundary(2,3). Earthquakes also occur in the down-going plate as fluids are released(4), and zones of anomalously low seismic velocities observed beneath several subduction zones are interpreted to be the subducting oceanic crust(5-10). Yet, the exact location of the plate boundary remains uncertain(5). Here we interpret a three-dimensional seismic tomography model from the northern Cascadia subduction zone in the northwest USA. We find that the low-velocity zone varies considerably along the Cascadia margin. In places, we observe the low-velocity zone to crop out at the surface and separate from the descending plate at depths of 35-40 km. We argue that the low-velocity zone here cannot represent oceanic crust as previously suggested, and instead the zone mostly represents sediments that have been subducted and underplated beneath the North American continent. We also find that tremor signals correlate with the position of the low-velocity zone, implying that slow slip and tremor may be facilitated by trapped fluids and high pore fluid pressures in subducted sedimentary rocks at, or close to the plate boundary. Our results also imply that the plate boundary beneath Cascadia is much deeper than previously thought. DOI
267. Casanova, M; Preissner, T; Cerase, A; Poot, R; Yamada, D; Li, XZ; Appanah, R; Bezstarosti, K; Demmers, J; Koseki, H; Brockdorff, N.Polycomblike 2 facilitates the recruitment of PRC2 Polycomb group complexes to the inactive X chromosome and to target loci in embryonic stem cells.Development, 2011, 138: 1471-1482 Polycomblike 2 facilitates the recruitment of PRC2 Polycomb group complexes to the inactive X chromosome and to target loci in embryonic stem cells
ES cell; Polycomb; X inactivation; Mouse
Polycomb group (PcG) proteins play an important role in the control of developmental gene expression in higher organisms. In mammalian systems, PcG proteins participate in the control of pluripotency, cell fate, cell cycle regulation, X chromosome inactivation and parental imprinting. In this study we have analysed the function of the mouse PcG protein polycomblike 2 (Pcl2), one of three homologues of the Drosophila Polycomblike (Pcl) protein. We show that Pcl2 is expressed at high levels during early embryogenesis and in embryonic stem (ES) cells. At the biochemical level, Pcl2 interacts with core components of the histone H3K27 methyltransferase complex Polycomb repressive complex 2 (PRC2), to form a distinct substoichiometric biochemical complex, Pcl2-PRC2. Functional analysis using RNAi knockdown demonstrates that Pcl2-PRC2 facilitates both PRC2 recruitment to the inactive X chromosome in differentiating XX ES cells and PRC2 recruitment to target genes in undifferentiated ES cells. The role of Pcl2 in PRC2 targeting in ES cells is critically dependent on a conserved PHD finger domain, suggesting that Pcl2 might function through the recognition of a specific chromatin configuration. DOI PubMed
266. Chassot, E; Bonhommeau, S; Reygondeau, G; Nieto, K; Polovina, JJ; Huret, M; Dulvy, NK; Demarcq, H.Satellite remote sensing for an ecosystem approach to fisheries management.ICES Journal of Marine Science, 2011, 68 Satellite remote sensing for an ecosystem approach to fisheries management
ecosystem approach; fisheries; mesoscale; satellite; tracking
Satellite remote sensing (SRS) of the marine environment has become instrumental in ecology for environmental monitoring and impact assessment, and it is a promising tool for conservation issues. In the context of an ecosystem approach to fisheries management (EAFM), global, daily, systematic, high-resolution images obtained from satellites provide a good data source for incorporating habitat considerations into marine fish population dynamics. An overview of the most common SRS datasets available to fishery scientists and state-of-the-art data-processing methods is presented, focusing on recently developed techniques for detecting mesoscale features such as eddies, fronts, filaments, and river plumes of major importance in productivity enhancement and associated fish aggregation. A comprehensive review of remotely sensed data applications in fisheries over the past three decades for investigating the relationships between oceanographic conditions and marine resources is provided, emphasizing how synoptic and information-rich SRS data have become instrumental in ecological analyses at community and ecosystem scales. Finally, SRS data, in conjunction with automated in situ data-acquisition systems, can provide the scientific community with a major source of information for ecosystem modelling, a key tool for implementing an EAFM. DOI
264. Crespi, B.The evolutionary biology of child health.Proceedings of the Royal Society B-Biological Sciences, 2011, 278: 1441-1449 The evolutionary biology of child health
evolutionary medicine; child health; cancer; growth
I apply evolutionary perspectives and conceptual tools to analyse central issues underlying child health, with emphases on the roles of human-specific adaptations and genomic conflicts in physical growth and development. Evidence from comparative primatology, anthropology, physiology and human disorders indicates that child health risks have evolved in the context of evolutionary changes, along the human lineage, affecting the timing, growth-differentiation phenotypes and adaptive significance of prenatal stages, infancy, childhood, juvenility and adolescence. The most striking evolutionary changes in humans are earlier weaning and prolonged subsequent pre-adult stages, which have structured and potentiated maladaptations related to growth and development. Data from human genetic and epigenetic studies, and mouse models, indicate that growth, development and behaviour during pre-adult stages are mediated to a notable degree by effects from genomic conflicts and imprinted genes. The incidence of cancer, the primary cause of non-infectious childhood mortality, mirrors child growth rates from birth to adolescence, with paediatric cancer development impacted by imprinted genes that control aspects of growth. Understanding the adaptive significance of child growth and development phenotypes, in the context of human-evolutionary changes and genomic conflicts, provides novel insights into the causes of disease in childhood. DOI
263. Elmhirst, JF; Haselhan, C; Punja, ZK.Evaluation of biological control agents for control of botrytis blight of geranium and powdery mildew of rose.Canadian Journal of Plant Pathology-Revue Canadienne de Phytopathologie, 2011, 33: 499-505 Evaluation of biological control agents for control of botrytis blight of geranium and powdery mildew of rose
biological control; botrytis; geranium; ornamental disease management; powdery mildew; rose
Four commercially formulated biological control products, containing Gliocladium catenulatum (Prestop (R) WP), Trichoderma harzianum (PlantShield (R)) and Bacillus subtilis [Serenade (R) MAX (TM) (wettable powder) and Rhapsody (R) ASO (TM) (liquid)] were evaluated for control of rose powdery mildew (Podosphaera pannosa) on outdoor, container-grown roses and botrytis blight (Botrytis cinerea) on greenhouse-grown zonal geraniums in 2006 and 2007. The products were applied every 7-14 days and disease incidence and severity were compared to the fungicides captan for botrytis blight control and myclobutanil for powdery mildew control. Gliocladium catenulatum provided the best control of botrytis blight of geranium in both years, and disease incidence was significantly lower compared with plants treated with captan. Both G. catenulatum and B. subtilis (Serenade MAX (TM) applied every 14 days or Rhapsody ASO (TM) every 7 days) provided significant control of rose powdery mildew, which was comparable to that provided by myclobutanil. These preventative disease-suppressive biological control products may have a useful role in commercial nursery crop production. DOI
262. Field, RD; Reynolds, JD.Sea to sky: impacts of residual salmon-derived nutrients on estuarine breeding bird communities.Proceedings of the Royal Society B-Biological Sciences, 2011, 278: 3081-3088 Sea to sky: impacts of residual salmon-derived nutrients on estuarine breeding bird communities
coastal watersheds; ecosystem-based management; biodiversity; wetlands; fisheries; Great Bear Rainforest
Pacific salmon (Oncorhynchus spp.) returning to streams around the North Pacific Rim provide a nutrient subsidy to these ecosystems. While many species of animals feed directly on salmon carcasses each autumn, salmon-derived nutrients can also be stored in coastal habitats throughout the year. The effects of this storage legacy on vertebrates in other seasons are not well understood, especially in estuaries, which can receive a large portion of post-spawning salmon nutrients. We examine the effects of residual salmon-derived nutrients, forest habitats and landscape features on summer breeding birds in estuary forests. We compared models containing environmental variables and combined chum (Oncorhynchus keta) and pink (Oncorhynchus gorbuscha) salmon biomass to test predictions concerning bird density and diversity. We discovered that total bird, insectivore, golden-crowned kinglet and Pacific wren densities and Shannon's diversity in the summer were strongly predicted by salmon biomass in the autumn. For most metrics, this relationship approaches an asymptote beyond 40 000 kg of salmon biomass. Foliage height diversity, watershed catchment area and estuary area were also important predictors of avian communities. Our study suggests that the legacy of salmon nutrients influences breeding bird density and diversity in estuaries that vary across a wide gradient of spawning salmon biomass. DOI
261. Frank, SA; Crespi, BJ.Pathology from evolutionary conflict, with a theory of X chromosome versus autosome conflict over sexually antagonistic traits.Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 10886-10893 Pathology from evolutionary conflict, with a theory of X chromosome versus autosome conflict over sexually antagonistic traits
BECKWITH-WIEDEMANN-SYNDROME; PRADER-WILLI-SYNDROME; SILVER-RUSSELL-SYNDROME; ANGELMAN-SYNDROME; TUMOR RISK; PARENTAL ANTAGONISM; GENE-EXPRESSION; BIRTH-WEIGHT; FETAL-GROWTH; SELECTION
Evolutionary conflicts cause opponents to push increasingly hard and in opposite directions on the regulation of traits. One can see only the intermediate outcome from the balance of the exaggerated and opposed forces. Intermediate expression hides the underlying conflict, potentially misleading one to conclude that trait regulation is designed to achieve efficient and robust expression, rather than arising by the precarious resolution of conflict. Perturbation often reveals the underlying nature of evolutionary conflict. Upon mutation or knockout of one side in the conflict, the other previously hidden and exaggerated push on the trait may cause extreme, pathological expression. In this regard, pathology reveals hidden evolutionary design. We first review several evolutionary conflicts between males and females, including conflicts over mating, fertilization, and the growth rate of offspring. Perturbations of these conflicts lead to infertility, misregulated growth, cancer, behavioral abnormalities, and psychiatric diseases. We then turn to antagonism between the sexes over traits present in both males and females. For many traits, the different sexes favor different phenotypic values, and constraints prevent completely distinct expression in the sexes. In this case of sexual antagonism, we present a theory of conflict between X-linked genes and autosomal genes. We suggest that dysregulation of the exaggerated conflicting forces between the X chromosome and the autosomes may be associated with various pathologies caused by extreme expression along the male-female axis. Rapid evolution of conflicting X-linked and autosomal genes may cause divergence between populations and speciation. DOI
260. Hart, M., P. Belton & R. Kuhn.The Risler Manuscript,European Mosquito Bulletin, 2011, 29: 103-113 The Risler Manuscript,
Aedes vexans, Johnston's organ, hearing
An unpublished manuscript “The Auditory Organ of Male Mosquitoes (Culicidae) (Studies on Aëdes vexans
Meigen 1830)” describes the structure of the pedicels and flagella of male and female Aedes vexans (=
Aedimorphus1vexans) from scanning and transmission electron micrographs. We reproduce diagrams from the
manuscript showing an in-depth section of the pedicel and first few flagellar segments, a hinge involved in
extending and collapsing the long fibrils on the male flagellum that has not been described before in the Culicinae
and the structure and arrangement of two different types of sensory units (scolopidia), one of which we speculate
might be involved in vibrating the flagellum and increasing the sensitivity of Johnston’s organ.Website
259. Hart, MW.THE SPECIES CONCEPT AS AN EMERGENT PROPERTY OF POPULATION BIOLOGY.Evolution, 2011, 65 THE SPECIES CONCEPT AS AN EMERGENT PROPERTY OF POPULATION BIOLOGY
Metapopulation lineage; speciation; species delimitation; unified species concept
Resurgent interest in the genetics of population divergence and speciation coincides with recent critical evaluation of species concepts and proposals for species delimitation. An important result of these parallel trends is a slight but important conceptual shift in focus away from species diagnoses based on prior species concepts or definitions, and toward analyses of the processes acting on lineages of metapopulations that eventually lead to differences recognizable as species taxa. An advantage of this approach is that it identifies quantitative metapopulation differences in continuous variables, rather than discrete entities that do or do not conform to a prior species concept, and species taxa are recognized as an emergent property of population-level processes. The tension between species concepts and diagnosis versus emergent recognition of species taxa is at least as old as Darwin, and is unlikely to be resolved soon in favor of either view, because the products of both approaches (discrete utilitarian taxon names for species, process-based understanding of the origins of differentiated metapopulations) continue to have important applications. DOI
258. Hocking, MD; Reynolds, JD.Impacts of Salmon on Riparian Plant Diversity.Science, 2011, 331 Impacts of Salmon on Riparian Plant Diversity
The study of natural gradients in nutrient subsidies between ecosystems allows for predictions of how changes in one system can affect biodiversity in another. We performed a large-scale empirical test of the role of Pacific salmon (Oncorhynchus spp.) in structuring riparian plant communities. A comparison of 50 watersheds in the remote Great Bear Rainforest of British Columbia's central coast in Canada shows that salmon influence nutrient loading to plants, shifting plant communities toward nutrient-rich species, which in turn decreases plant diversity. These effects are mediated by interactions between salmon density and the physical characteristics of watersheds. Predicting how salmon affect terrestrial ecosystems is central to conservation plans that aim to better integrate ecosystem values into resource management. DOI
257. Jayaraman, J; Norrie, J; Punja, ZK.Commercial extract from the brown seaweed Ascophyllum nodosum reduces fungal diseases in greenhouse cucumber.Journal of Applied Phycology, 2011, 23: 353-361 Commercial extract from the brown seaweed Ascophyllum nodosum reduces fungal diseases in greenhouse cucumber
Ascophyllum; Cucumber; Fungal diseases; Resistance; Mechanism
This study examined the effects of Stimplex (TM), a marine plant extract formulation from Ascophyllum nodosum, on some common cucumber fungal pathogens. Greenhouse cucumber plants were sprayed and/or root drenched using Stimplex (TM) at 0.5% or 1% concentration twice at 10-day intervals. Treatments also included application of fungicide (chlorothalonil, 2 g L(-1)) alternating with Stimplex (TM) application. Treated plants were inoculated with four cucumber fungal pathogens including Alternaria cucumerinum, Didymella applanata, Fusarium oxysporum, and Botrytis cinerea. Stimplex (TM) application resulted in a significant reduction in disease incidence of all the pathogens tested. The disease control effect was greater for Alternaria and Fusarium infection, followed by Didymella and Botrytis. Combined spray and root drenching with Stimplex (TM) was more effective than either spray or root drenching alone. The alternation of one fungicide application, alternated with Stimplex (TM) application, was highly effective and found to be the best treatment in reducing the disease ratings. Plants treated with Stimplex T showed enhanced activities of various defense-related enzymes including chitinase, beta-1,3-glucanase, peroxidase, polyphenol oxidase, phenylalanine ammonia lyase, and lipoxygenase. Altered transcript levels of various defense genes, including chitinase, lipoxygenase, glucanase, peroxidase, and phenylalanine ammonia lyase were observed in treated plants. Cucumber plants treated with Stimplex (TM) also accumulated higher level of phenolics compared to water controls. These results suggest that seaweed extracts enhance disease resistance in cucumber probably through induction of defense genes or enzymes. DOI
256. Jensen, EL; Dill, LM; Cahill, JE.Applying Behavioral-Ecological Theory to Plant Defense: Light-Dependent Movement in Mimosa pudica Suggests a Trade-Off between Predation Risk and Energetic Reward.American Naturalist, 2011, 177 Applying Behavioral-Ecological Theory to Plant Defense: Light-Dependent Movement in Mimosa pudica Suggests a Trade-Off between Predation Risk and Energetic Reward
plant behavioral ecology; predation-risk hypothesis; sensitive plant; light response
Many animal species tolerate different amounts of predation risk based on environmental conditions and the individual's own condition, often accepting greater risk when energetically stressed. We studied the sensitive plant Mimosa pudica to see whether it too accepts greater risk of predation when less light energy is available. This plant displays a defensive behavior of rapidly folding its leaves when stimulated by touch, thereby decreasing visibility to herbivores. Averting herbivory involves a trade-off because leaf closure results in a reduction in light foraging. We manipulated the light environment of individual M. pudica plants and recorded the time it took a plant to reopen its leaves following stimulation as a measure of tolerance of predation risk. As predicted by theory, avoidance behavior was sustained longer under high light conditions than under more light-limited conditions. These findings suggest this species balances the risk and reward of antiherbivore behavior in relation to current environmental conditions and that behavioral-ecological theory is a useful framework for understanding plant responses to predators. DOI
255. Juan-Jorda, MJ; Mosqueira, I; Cooper, AB; Freire, J; Dulvy, NK.Global population trajectories of tunas and their relatives.Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 20650-20655 Global population trajectories of tunas and their relatives
Tunas and their relatives dominate the world's largest ecosystems and sustain some of the most valuable fisheries. The impacts of fishing on these species have been debated intensively over the past decade, giving rise to divergent views on the scale and extent of the impacts of fisheries on pelagic ecosystems. We use all available age-structured stock assessments to evaluate the adult biomass trajectories and exploitation status of 26 populations of tunas and their relatives (17 tunas, 5 mackerels, and 4 Spanish mackerels) from 1954 to 2006. Overall, populations have declined, on average, by 60% over the past half century, but the decline in the total adult biomass is lower (52%), driven by a few abundant populations. The trajectories of individual populations depend on the interaction between life histories, ecology, and fishing pressure. The steepest declines are exhibited by two distinct groups: the largest, longest lived, highest value temperate tunas and the smaller, short-lived mackerels, both with most of their populations being overexploited. The remaining populations, mostly tropical tunas, have been fished down to approximately maximum sustainable yield levels, preventing further expansion of catches in these fisheries. Fishing mortality has increased steadily to the point where around 12.5% of the tunas and their relatives are caught each year globally. Overcapacity of these fisheries is jeopardizing their long-term sustainability. To guarantee higher catches, stabilize profits, and reduce collateral impacts on marine ecosystems requires the rebuilding of overexploited populations and stricter management measures to reduce overcapacity and regulate threatening trade. DOI
254. Krkosek, M; Connors, BM; Ford, H; Peacock, S; Mages, P; Ford, JS; Morton, A; Volpe, JP; Hilborn, R; Dill, LM; Lewis, MA.Fish farms, parasites, and predators: implications for salmon population dynamics.Ecological Applications, 2011, 21: 897-914 Fish farms, parasites, and predators: implications for salmon population dynamics
aquaculture; behavior; fish farms; Lepeophtheirus salmonis; Oncorhynchus spp.; parasites; population dynamics; predation; salmon; sea lice
For some salmon populations, the individual and population effects of sea lice (Lepeophtheirus salmonis) transmission from sea cage salmon farms is probably mediated by predation, which is a primary natural source of mortality of juvenile salmon. We examined how sea lice infestation affects predation risk and mortality of juvenile pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon, and developed a mathematical model to assess the implications for population dynamics and conservation. A risk-taking experiment indicated that infected juvenile pink salmon accept a higher predation risk in order to obtain foraging opportunities. In a schooling experiment with juvenile chum salmon, infected individuals had increased nearest-neighbor distances and occupied peripheral positions in the school. Prey selection experiments with cutthroat trout (O. clarkii) predators indicated that infection reduces the ability of juvenile pink salmon to evade a predatory strike. Group predation experiments with coho salmon (O. kisutch) feeding on juvenile pink or chum salmon indicated that predators selectively consume infected prey. The experimental results indicate that lice may increase the rate of prey capture but not the handling time of a predator. Based on this result, we developed a mathematical model of sea lice and salmon population dynamics in which parasitism affects the attack rate in a type II functional response. Analysis of the model indicates that: (1) the estimated mortality of wild juvenile salmon due to sea lice infestation is probably higher than previously thought; (2) predation can cause a simultaneous decline in sea louse abundance on wild fish and salmon productivity that could mislead managers and regulators; and (3) compensatory mortality occurs in the saturation region of the type II functional response where prey are abundant because predators increase mortality of parasites but not overall predation rates. These findings indicate that predation is an important component of salmon-louse dynamics and has implications for estimating mortality, reducing infection, and developing conservation policy. DOI
253. Krkosek, M; Connors, BM; Morton, A; Lewis, MA; Dill, LM; Hilborn, R.Effects of parasites from salmon farms on productivity of wild salmon.Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 14700-14704 Effects of parasites from salmon farms on productivity of wild salmon
The ecological risks of salmon aquaculture have motivated changes to management and policy designed to protect wild salmon populations and habitats in several countries. In Canada, much attention has focused on outbreaks of parasitic copepods, sea lice (Lepeophtheirus salmonis), on farmed and wild salmon in the Broughton Archipelago, British Columbia. Several recent studies have reached contradictory conclusions on whether the spread of lice from salmon farms affects the productivity of sympatric wild salmon populations. We analyzed recently available sea lice data on farms and spawner-recruit data for pink (Oncorhynchus gorbuscha) and coho (Oncorhynchus kisutch) salmon populations in the Broughton Archipelago and nearby regions where farms are not present. Our results show that sea lice abundance on farms is negatively associated with productivity of both pink and coho salmon in the Broughton Archipelago. These results reconcile the contradictory findings of previous studies and suggest that management and policy measures designed to protect wild salmon from sea lice should yield conservation and fishery benefits. DOI
252. Kuhn, TS; Mooers, AO; Thomas, GH.A simple polytomy resolver for dated phylogenies.Methods in Ecology and Evolution, 2011, 2: 427-436 A simple polytomy resolver for dated phylogenies
MOLECULAR PHYLOGENIES; SPECIATION; EXTINCTION; EVOLUTION; DIVERSIFICATION; RESOLUTION; SUPERTREE; MAMMALS; RATES
1. Unresolved nodes in phylogenetic trees (polytomies) have long been recognized for their influences on specific phylogenetic metrics such as topological imbalance measures, diversification rate analysis and measures of phylogenetic diversity. However, no rigorously tested, biologically appropriate method has been proposed for overcoming the effects of this phylogenetic uncertainty. 2. Here, we present a simple approach to polytomy resolution, using biologically relevant models of diversification. Using the powerful and highly customizable phylogenetic inference and analysis software beast and R, we present a semi-automated 'polytomy resolver' capable of providing a distribution of tree topologies and branch lengths under specified biological models. 3. Utilizing both simulated and empirical data sets, we explore the effects and characteristics of this approach on two widely used phylogenetic tree statistics, Pybus' gamma (gamma) and Colless' normalized tree imbalance (I-c). Using simulated pure birth trees, we find no evidence of bias in either estimate using our resolver. Applying our approach to a recently published Cetacean phylogeny, we observed the expected small positive bias in gamma and decrease in I-c. 4. We further test the effect of polytomy resolution on diversification rate analysis using the Cetacean phylogeny. We demonstrate that using a birth-death model to resolve the Cetacean tree with 20%, 40% and 60% of random nodes collapsed to polytomies gave qualitatively similar patterns regarding the tempo and mode of diversification as the same analyses on the original, fully resolved phylogeny. 5. Finally, we applied the birth-death polytomy resolution approach to a large (>5000 tips), but unresolved, supertree of extant mammals. We report a distribution of fully resolved model-based trees, which should be useful for many future analysis of the mammalian supertree. DOI
251. Leung, DC; Dong, KB; Maksakova, IA; Goyal, P; Appanah, R; Lee, S; Tachibana, M; Shinkai, Y; Lehnertz, B; Mager, DL; Rossi, F; Lorincz, MC.Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing.Proc. Natl. Acad. Sci. U. S. A., 2011, 108: 5718-5723 Lysine methyltransferase G9a is required for de novo DNA methylation and the establishment, but not the maintenance, of proviral silencing
epigenetics; covalent histone modification; long terminal repeat
Methylation on lysine 9 of histone H3 (H3K9me) and DNA methylation play important roles in the transcriptional silencing of specific genes and repetitive elements. Both marks are detected on class I and II endogenous retroviruses (ERVs) in murine embryonic stem cells (mESCs). Recently, we reported that the H3K9-specific lysine methyltransferase (KMTase) Eset/Setdb1/KMT1E is required for H3K9me3 and the maintenance of silencing of ERVs in mESCs. In contrast, G9a/Ehmt2/KMT1C is dispensable, despite the fact that this KMTase is required for H3K9 dimethylation (H3K9me2) and efficient DNA methylation of these retroelements. Transcription of the exogenous retrovirus (XRV) Moloney murine leukemia virus is rapidly extinguished after integration in mESCs, concomitant with de novo DNA methylation. However, the role that H3K9 KMTases play in this process has not been addressed. Here, we demonstrate that G9a, but not Suv39h1 or Suv39h2, is required for silencing of newly integrated Moloney murine leukemia virus-based vectors in mESCs. The silencing defect in G9a(-/-) cells is accompanied by a reduction of H3K9me2 at the proviral LTR, indicating that XRVs are direct targets of G9a. Furthermore, de novo DNA methylation of newly integrated proviruses is impaired in the G9a(-/-) line, phenocopying proviral DNA methylation and silencing defects observed in Dnmt3a-deficient mESCs. Once established, however, maintenance of silencing of XRVs, like ERVs, is dependent exclusively on the KMTase Eset. Taken together, these observations reveal that in mESCs, the H3K9 KMTase G9a is required for the establishment, but not for the maintenance, of silencing of newly integrated proviruses. DOI PubMed
250. Lin, AE; Benmerah, A; Guttman, JA.Eps15 and Epsin1 Are Crucial for Enteropathogenic Escherichia coli Pedestal Formation Despite the Absence of Adaptor Protein 2.Journal of Infectious Diseases, 2011, 204: 695-703 Eps15 and Epsin1 Are Crucial for Enteropathogenic Escherichia coli Pedestal Formation Despite the Absence of Adaptor Protein 2
Enteropathogenic Escherichia coli (EPEC) are primarily extracellular pathogens that generate actin-rich structures known as pedestals during their pathogenesis. Surprising evidence has demonstrated that despite maintaining an extracellular location, EPEC require the endocytic protein, clathrin, for pedestal formation. To evaluate the strategies EPEC use to usurp endocytic machinery, we investigated the roles of a number of clathrin-coated pits components, adaptor protein 2 (AP-2), Eps15 and epsin1, during EPEC infections. We demonstrated that in conjunction with clathrin, pedestal formation also required the recruitment of Eps15 and epsin1 but not AP-2. Because AP-2 orchestrates the recruitment of clathrin, Eps15, and epsin1, as well as other adaptors, during assembly of clathrin-coated pits at the plasma membrane, our findings reveal a novel internalization subversion strategy employed by EPEC. These results further emphasize the recent paradigm that endocytic proteins are important for EPEC-mediated disease. DOI
249. Love, OP; Williams, TD.Manipulating developmental stress reveals sex-specific effects of egg size on offspring phenotype.Journal of Evolutionary Biology, 2011, 24: 1497-1504 Manipulating developmental stress reveals sex-specific effects of egg size on offspring phenotype
STARLING STURNUS-VULGARIS; FLUCTUATING ASYMMETRY; FLIGHT PERFORMANCE; REARING CONDITIONS; REPRODUCTIVE INVESTMENT; HAEMATOPUS-OSTRALEGUS; COMPENSATORY GROWTH; IMMUNE-RESPONSE; TIT NESTLINGS; SURVIVAL
The general lack of experimental evidence for strong, positive effects of egg size on offspring phenotype has led to suggestions that avian egg size is a neutral trait. To better understand the functional significance of intra-specific variation in egg size as a determinant of offspring fitness within a life-history (sex-specific life-history strategies) and an environmental (poor rearing conditions) context, we experimentally increased developmental stress (via maternal feather-clipping) in the sexually size-dimorphic European starling (Sturnus vulgaris) and measured phenotypic traits in offspring across multiple biological scales. As predicted by life-history theory, sons and daughters had different responses when faced with developmental stress and variation in egg size. In response to developmental stress, small egg size in normally faster-growing sons was associated with catch-up growth prior to attaining larger adult size, resulting in a reduction in developmental stability. Daughters apparently avoided this developmental instability by reducing growth rate and eventual adult body mass and size. Interestingly, large egg size provided offspring with greater developmental flexibility under poor growth conditions. Large-egg sons and daughters avoided the reduction in developmental stability, and daughters also showed enhanced escape performance during flight trials. Furthermore, large egg size resulted in elevated immune responses for both sexes under developmental stress. These findings show that there can be significant, but complex, context-specific effects of egg size on offspring phenotype at least up to fledging, but these can only be demonstrated by appreciating variation in the quality of the offspring environment and life histories. Results are therefore consistent with egg size playing a significant role in shaping the phenotypic outcome of offspring in species that show even greater intra-specific variation in egg size than starlings. DOI
248. M'Gonigle, LK; Otto, SP.Ploidy and the evolution of parasitism.Proceedings of the Royal Society B-Biological Sciences, 2011, 278: 2814-2822 Ploidy and the evolution of parasitism
hosts; parasites; coevolution; ploidy; modifier
Levels of parasitism are continuously distributed in nature. Models of host-parasite coevolution, however, typically assume that species can be easily characterized as either parasitic or non-parasitic. Consequently, it is poorly understood which factors influence the evolution of parasitism itself. We investigate how ploidy level and the genetic mechanisms underlying infection influence evolution along the continuum of parasitism levels. In order for parasitism to evolve, selective benefits to the successful invasion of hosts must outweigh the losses when encountering resistant hosts. However, we find that exactly where this threshold occurs depends not only on the strength of selection, but also on the genetic model of interaction, the ploidy level in each species, and the nature of the costs to virulence and resistance. With computer simulations, we are able to incorporate more realistic dynamics at the loci underlying species interactions and to extend our analyses in a number of directions, including finite population sizes, multiple alleles and different generation times. DOI
247. Marko, PB; Hart, MW.The complex analytical landscape of gene flow inference.Trends in Ecology & Evolution, 2011, 26: 448-456 The complex analytical landscape of gene flow inference
Gene flow estimation is essential for characterizing local adaptation, speciation potential and connectivity among threatened populations. New model-based population genetic methods can resolve complex demographic histories, but many studies in fields such as landscape genetics continue to rely on simple rules of thumb focused on gene flow to explain patterns of spatial differentiation. Here, we show how methods that use gene genealogies can reveal cryptic demographic histories and provide better estimates of gene flow with other parameters that contribute to genetic variation across landscapes and seascapes. We advocate for the expanded use and development of methods that consider spatial differentiation as the product of multiple forces interacting over time, and caution against a routine reliance on post-hoc gene flow interpretations. DOI
246. Mull, CG; Yopak, KE; Dulvy, NK.Does more maternal investment mean a larger brain? Evolutionary relationships between reproductive mode and brain size in chondrichthyans.Marine and Freshwater Research, 2011, 62: 567-575 Does more maternal investment mean a larger brain? Evolutionary relationships between reproductive mode and brain size in chondrichthyans
allometry; encephalisation; pGLS; relative brain size; reproductive mode
Chondrichthyans have the most diverse array of reproductive strategies of any vertebrate group, ranging from egg-laying to live-bearing with placental matrotrophy. Matrotrophy is defined as additional maternal provisioning beyond the yolk to the developing neonate; in chondrichthyans, this occurs through a range of mechanisms including uterine milk, oophagy, uterine cannibalism and placentotrophy. Chondrichthyans also exhibit a wide range of relative brain sizes and highly diverse patterns of brain organisation. Brains are energetically expensive to produce and maintain, and represent a major energetic constraint during early life in vertebrates. In mammals, more direct maternal-fetal placental connections have been associated with larger brains (steeper brain-body allometric scaling relationships). We test for a relationship between reproductive mode and relative brain size across 85 species from six major orders of chondrichthyans by using several phylogenetic comparative analyses. Ordinary least-squares (OLS) and reduced major axis (RMA) regression of body mass versus brain mass suggest that increased maternal investment results in a larger relative brain size. Our findings were supported by phylogenetic generalised least-squares models (pGLS), which also highlighted that these results vary with evolutionary tempo, as described by different branch-length assumptions. Across all analyses, maximum body size had a significant influence on the relative brain size, with large-bodied species (body mass > 100 kg) having relatively smaller brains. The present study suggests that there may be a link between reproductive investment and relative brain size in chondrichthyans; however, a more definitive test requires a better-resolved phylogeny and a more nuanced categorisation of the level of maternal investment in chondrichthyans. DOI
245. Novak, M., J.W. Moore, and R.A. Leidy.Nestedness patterns and the dual nature of community reassembly in California streams: a multivariate permutation-based approach.Global Change Biology, 2011, 17: 3714-3723 Nestedness patterns and the dual nature of community reassembly in California streams: a multivariate permutation-based approach.
body size; conservation; disturbance; extinction risk; freshwater stream fishes; invasion risk; metacommunity structure; multivariate gradient analysis; trait-based biogeography
Many factors contribute to the nonrandom processes of extinctions and invasions that are changing the structure of ecological communities worldwide. These factors include the attributes of the species, their abiotic environment, and the interactions and feedbacks between them. The relative importance of these factors has been difficult to quantify. We used nested subset theory and a novel permutation-based extension of gradient analysis to disentangle the direct and indirect pathways by which these factors affect the metacommunity structure of freshwater fishes inhabiting the streams tributary to the San Francisco Bay. Our analyses provide quantitative measures of how species and stream attributes may influence extinction vulnerability and invasion risk, highlight the need for considering the multiple interacting drivers of community change concurrently, and indicate that the ongoing disassembly and assembly of Bay Area freshwater fish communities are not fully symmetric processes. Fish communities are being taken apart and put back together in only partially analogous trajectories of extinction and invasion for which no single explanatory hypothesis is sufficient. Our study thereby contributes to the forecasting of continued community change and its effects on the functioning of freshwater ecosystems.Website DOI
244. Perry, CT; Kench, PS; Smithers, SG; Riegl, B; Yamano, H; O'Leary, MJ.Implications of reef ecosystem change for the stability and maintenance of coral reef islands.Glob. Change Biol., 2011, 17: 3679-3696 Implications of reef ecosystem change for the stability and maintenance of coral reef islands
climate change; ecological change; island vulnerability; reef islands; reef sediments
Coral reef islands are among the most vulnerable environments on Earth to climate change because they are low lying and largely constructed from unconsolidated sediments that can be readily reworked by waves and currents. These sediments derive entirely from surrounding coral reef and reef flat environments and are thus highly sensitive to ecological transitions that may modify reef community composition and productivity. How such modifications - driven by anthropogenic disturbances and on-going and projected climatic and environmental change - will impact reef island sediment supply and geomorphic stability remains a critical but poorly resolved question. Here, we review the unique ecological-geomorphological linkages that underpin this question and, using different scenarios of environmental change for which reef sediment production responses can be projected, explore the likely resilience of different island types. In general, sand-dominated islands are likely to be less resilient than those dominated by rubble grade material. However, because different islands typically have different dominant sediment constituents (usually either coral, benthic foraminifera or Halimeda) and because these respond differently to individual ecological disturbances, island resilience is likely to be highly variable. Islands composed of coral sands are likely to undergo major morphological change under most near-future ecological change scenarios, while those dominated by Halimeda may be more resilient. Islands composed predominantly of benthic foraminifera (a common state through the Pacific region) are likely to exhibit varying degrees of resilience depending upon the precise combination of ecological disturbances faced. The study demonstrates the critical need for further research bridging the ecological-geomorphological divide to understand: (1) sediment production responses to different ecological and environmental change scenarios; and (2) dependant landform vulnerability. DOI
243. Punja, ZK.American Ginseng: Research Developments, Opportunities, and Challenges.Journal of Ginseng Research, 2011, 35: 368-374 American Ginseng: Research Developments, Opportunities, and Challenges
Panax quinquefolius; Genetic variation; Disease; Transgenic research
American ginseng (Panax quinquefolius L.) is grown in some regions of the USA and Canada and marketed for its health promoting attributes. While cultivation of this plant species has taken place in North America for over 100 years, there are many challenges that need to be addressed. In this article, the current production method used by growers is described and the challenges and opportunities for research on this valuable plant are discussed. These include studies on pharmacological activity, genetic diversity within the species, genetic improvement of currently grown plants, molecular characterization of gene expression, and management of diseases affecting plant productivity. The current research developments in these areas are reviewed and areas requiring further work are summarized. Additional research should shed light on the nature of the bioactive compounds and their clinical effects, and the molecular basis of active ingredient biosynthesis, and provide more uniform genetic material as well as improved plant growth, and potentially reduce losses due to pathogens. DOI
242. Raj, S; Brautigam, K; Hamanishi, ET; Wilkins, O; Thomas, BR; Schroeder, W; Mansfield, SD; Plant, AL; Campbell, MM.Clone history shapes Populus drought responses.Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 12521-12526 Clone history shapes Populus drought responses
epigenetics; forest trees; poplar
Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome-level drought responses of three economically important hybrid genotypes-DN34 (Populus deltoides x Populus nigra), Walker [P. deltoides var. occidentalis x (Populus laurifolia x P. nigra)], and Okanese [Walker x (P. laurifolia x P. nigra)]-derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, whereby the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenomic basis for the clone history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for the industrial application of Populus trees and the evolution and persistence of these important tree species and their associated hybrids. DOI
241. Reuter, KE; Lotterhos, KE; Crim, RN; Thompson, CA; Harley, CDG.Elevated pCO(2) increases sperm limitation and risk of polyspermy in the red sea urchin Strongylocentrotus franciscanus.Global Change Biology, 2011, 17: 163-171 Elevated pCO(2) increases sperm limitation and risk of polyspermy in the red sea urchin Strongylocentrotus franciscanus
anthropogenic climate change; carbon dioxide; echinoid; fertilization; marine invertebrates; ocean acidification
Anthropogenic carbon dioxide (CO2) emissions and the resultant acidification of surface ocean waters are predicted to have far-reaching consequences for biological processes in the marine environment. For example, because changes in pH and pCO(2) can alter sperm performance, ocean acidification may be accompanied by reductions in the success of fertilization in marine broadcast spawners. Several studies have attempted to determine the effects of elevated pCO(2) on marine invertebrate fertilization success, albeit with differing results. These conflicts may stem from the use of inappropriate sperm-egg contact times and, in several cases, the lack of measurements over a range of sperm concentrations extending from sperm-limited conditions to polyspermy scenarios. In our study, we used biologically realistic sperm-egg contact times and a full range of sperm concentrations to assess the effect of elevated pCO(2) on fertilization in the broadcast spawning sea urchin, Strongylocentrotus franciscanus. Fertilization experiments were carried out in seawater bubbled with CO2 to 400 (control), 800, and 1800 ppm. Using a fertilization kinetics model, we estimate that elevated pCO(2) levels both increased sperm limitation and reduced the efficiency of fast blocks to polyspermy. Thus, elevated pCO(2) decreased the range of sperm concentrations over which high fertilization success was likely. Given the inherent difficulties in achieving high fertilization success in broadcast spawners, raised pCO(2) levels are likely to exacerbate low fertilization success in low-density populations or in areas with high water turbulence. DOI
239. Salomon, AK; Gaichas, SK; Jensen, OP; Agostini, VN; Sloan, NA; Rice, J; McClanahan, TR; Ruckelshaus, MH; Levin, PS; Dulvy, NK; Babcock, EA.BRIDGING THE DIVIDE BETWEEN FISHERIES AND MARINE CONSERVATION SCIENCE.Bulletin of Marine Science, 2011, 87: 251-274 BRIDGING THE DIVIDE BETWEEN FISHERIES AND MARINE CONSERVATION SCIENCE
Researchers from traditionally disparate disciplines and practitioners with typically incongruent mandates have begun working together to better understand and solve marine conservation and sustainable yield problems. Conservation practitioners are recognizing the need to achieve conservation goals in seascapes that are a source of livelihood and food security, while fisheries management is realizing that achieving economically and ecologically sustainable fisheries requires an understanding of the role of biodiversity and ecosystem dynamics in fishery production. Yet, tensions still exist due to the unique histories, epistemologies, cultures, values, and quantitative techniques of fisheries and marine conservation science, and the often-divergent objectives of the institutions and organizations these academic disciplines inform. While there is general agreement on what needs to be achieved (less overfishing, recovery of depleted fish stocks, reduction in bycatch and habitat impacts, jobs, food production), specific objectives and how best to achieve them remain contentious and unresolved. By analyzing three contemporary yet controversial marine policies (ecosystem-based fishery management, marine protected areas, and catch shares) and specific case studies, we demonstrate how both fisheries and marine conservation science can be used to provide clear scientific advice to practitioners and provide empirical evidence of the benefits of bridging the disciplinary divide. Finally, we discuss future prospects for collaboration in an emerging issue at the nexus of conservation and fishery management: eco-certification. Drawing on lessons learned from these empirical examples, we outline general processes necessary for clearly defining multiple conservation and fisheries objectives in working seascapes. By bridging the divide, we illuminate the process of navigating trade-offs between multiple objectives in a finite world. DOI
238. Schwander, T; Henry, L; Crespi, BJ.Molecular Evidence for Ancient Asexuality in Timema Stick Insects.Current Biology, 2011, 21: 1129-1134 Molecular Evidence for Ancient Asexuality in Timema Stick Insects
SEXUAL REPRODUCTION; BDELLOID ROTIFERS; HYBRID ORIGINS; DNA-SEQUENCES; EVOLUTION; RECOMBINATION; POPULATION; LINEAGES; PARTHENOGENESIS; PATTERNS
Asexuality is rare in animals in spite of its apparent advantage relative to sexual reproduction, indicating that it must be associated with profound costs [1-9]. One expectation is that reproductive advantages gained by new asexual lineages will be quickly eroded over time [3, 5-7]. Ancient asexual taxa that have evolved and adapted without sex would be "scandalous" exceptions to this rule, but it is often difficult to exclude the possibility that putative asexuals deploy some form of "cryptic" sex, or have abandoned sex more recently than estimated from divergence times to sexual relatives [10]. Here we provide evidence, from high intraspecific divergence of mitochondrial sequence and nuclear allele divergence patterns, that several independently derived Timema stick-insect lineages have persisted without recombination for more than a million generations. Nuclear alleles in the asexual lineages displayed significantly higher intraindividual divergences than in related sexual species. In addition, within two asexuals, nuclear allele phylogenies suggested the presence of two clades, with sequences from the same individual appearing in both clades. These data strongly support ancient asexuality in Timema and validate the genus as an exceptional opportunity to attack the question of how asexual reproduction can be maintained over long periods of evolutionary time. DOI
237. Sherren, CN; Mu, CH; Webb, MI; McKenzie, I; McCollum, BM; Brodovitch, JC; Percival, PW; Storr, T; Seddon, KR; Clyburne, JAC; Walsby, CJ.Merging the chemistry of electron-rich olefins with imidazolium ionic liquids: radicals and hydrogen-atom adducts.Chem. Sci., 2011, 2: 2173-2177 Merging the chemistry of electron-rich olefins with imidazolium ionic liquids: radicals and hydrogen-atom adducts
To probe the reactivity of ionic liquids relevant to their use in electrochemical applications, the ionic liquid 1-ethyl-3-methylimidazolium tetrachloroaluminate(III) was reacted with metallic lithium to produce a persistent radical, which can be considered a hydrogen-atom adduct of an electron-rich olefin (ERO). Reaction of tetrakis(dimethylamino) ethene, a bona fide ERO, with muonium, produces a structurally similar radical. DOI
236. Simpfendorfer, CA; Heupel, MR; White, WT; Dulvy, NK.The importance of research and public opinion to conservation management of sharks and rays: a synthesis.Marine and Freshwater Research, 2011, 62: 518-527 The importance of research and public opinion to conservation management of sharks and rays: a synthesis
chondrichthyes; research priorities; sustainable use
Growing concern for the world's shark and ray populations is driving the need for greater research to inform conservation management. A change in public perception, from one that we need to protect humans from sharks to one where we must protect sharks from humans, has added to calls for better management. The present paper examines the growing need for research for conservation management of sharks and rays by synthesising information presented in this Special Issue from the 2010 Sharks International Conference and by identifying future research needs, including topics such as taxonomy, life history, population status, spatial ecology, environmental effects, ecosystem role and human impacts. However, this biological and ecological research agenda will not be sufficient to fully secure conservation management. There is also a need for research to inform social and economic sustainability. Effective conservation management will be achieved by setting clear priorities for research with the aid of stakeholders, implementing well designed research projects, building the capacity for research, and clearly communicating the results to stakeholders. If this can be achieved, it will assure a future for this iconic group, the ecosystems in which they occur and the human communities that rely on them. DOI
235. Sparks, TH; Butchart, SHM; Balmford, A; Bennun, L; Stanwell-Smith, D; Walpole, M; Bates, NR; Bomhard, B; Buchanan, GM; Chenery, AM; Collen, B; Csirke, J; Diaz, RJ; Dulvy, NK; Fitzgerald, C; Kapos, V; Mayaux, P; Tierney, M; Waycott, M; Wood, L; Green, RE.Linked indicator sets for addressing biodiversity loss.Oryx, 2011, 45: 411-419 Linked indicator sets for addressing biodiversity loss
2010 target; CBD; Convention on Biological Diversity; ecosystem services; humid tropical forest; marine fisheries; response
The target adopted by world leaders of significantly reducing the rate of biodiversity loss by 2010 was not met but this stimulated a new suite of biodiversity targets for 2020 adopted by the Parties to the Convention on Biological Diversity (CBD) in October 2010. Indicators will be essential for monitoring progress towards these targets and the CBD will be defining a suite of relevant indicators, building on those developed for the 2010 target. Here we argue that explicitly linked sets of indicators offer a more useful framework than do individual indicators because the former are easier to understand, communicate and interpret to guide policy. A Response-Pressure-State-Benefit framework for structuring and linking indicators facilitates an understanding of the relationships between policy actions, anthropogenic threats, the status of biodiversity and the benefits that people derive from it. Such an approach is appropriate at global, regional, national and local scales but for many systems it is easier to demonstrate causal linkages and use them to aid decision making at national and local scales. We outline examples of linked indicator sets for humid tropical forests and marine fisheries as illustrations of the concept and conclude that much work remains to be done in developing both the indicators and the causal links between them. DOI
234. Springer, SA; Crespi, BJ; Swanson, WJ.Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture.Molecular Ecology, 2011, 20: 2240-2257 Beyond the phenotypic gambit: molecular behavioural ecology and the evolution of genetic architecture
adaptation; behaviour; social evolution; evolutionary conflict; genetic architecture
Most studies of behaviour examine traits whose proximate causes include sensory input and neural decision-making, but conflict and collaboration in biological systems began long before brains or sensory systems evolved. Many behaviours result from non-neural mechanisms such as direct physical contact between recognition proteins or modifications of development that coincide with altered behaviour. These simple molecular mechanisms form the basis of important biological functions and can enact organismal interactions that are as subtle, strategic and interesting as any. The genetic changes that underlie divergent molecular behaviours are often targets of selection, indicating that their functional variation has important fitness consequences. These behaviours evolve by discrete units of quantifiable phenotypic effect (amino acid and regulatory mutations, often by successive mutations of the same gene), so the role of selection in shaping evolutionary change can be evaluated on the scale at which heritable phenotypic variation originates. We describe experimental strategies for finding genes that underlie biochemical and developmental alterations of behaviour, survey the existing literature highlighting cases where the simplicity of molecular behaviours has allowed insight to the evolutionary process and discuss the utility of a genetic knowledge of the sources and spectrum of phenotypic variation for a deeper understanding of how genetic and phenotypic architectures evolve. DOI
233. Sunday, JM; Bates, AE; Dulvy, NK.Global analysis of thermal tolerance and latitude in ectotherms.Proceedings of the Royal Society B-Biological Sciences, 2011, 278: 1823-1830 Global analysis of thermal tolerance and latitude in ectotherms
macroecology; macrophysiology; thermal tolerance breadth; latitude; thermal niche; climate variability hypothesis
A tenet of macroecology is that physiological processes of organisms are linked to large-scale geographical patterns in environmental conditions. Species at higher latitudes experience greater seasonal temperature variation and are consequently predicted to withstand greater temperature extremes. We tested for relationships between breadths of thermal tolerance in ectothermic animals and the latitude of specimen location using all available data, while accounting for habitat, hemisphere, methodological differences and taxonomic affinity. We found that thermal tolerance breadths generally increase with latitude, and do so at a greater rate in the Northern Hemisphere. In terrestrial ectotherms, upper thermal limits vary little while lower thermal limits decrease with latitude. By contrast, marine species display a coherent poleward decrease in both upper and lower thermal limits. Our findings provide comprehensive global support for hypotheses generated from studies at smaller taxonomic subsets and geographical scales. Our results further indicate differences between terrestrial and marine ectotherms in how thermal physiology varies with latitude that may relate to the degree of temperature variability experienced on land and in the ocean. DOI
232. Sutherland, WJ; Bardsley, S; Bennun, L; Clout, M; Côté, IM; Depledge, MH; Dicks, LV; Dobson, AP; Fellman, L; Fleishman, E; Gibbons, DW; Impey, AJ; Lawton, JH; Lickorish, F; Lindenmayer, DB; Lovejoy, TE; Mac Nally, R; Madgwick, J; Peck, LS; Pretty, J; Prior, SV; Redford, KH; Scharlemann, JPW; Spalding, M; Watkinson, AR.Horizon scan of global conservation issues for 2011.Trends in Ecology & Evolution, 2011, 26 Horizon scan of global conservation issues for 2011
This review describes outcomes of a 2010 horizon-scanning exercise building upon the first exercise conducted in 2009. The aim of both horizon scans was to identify emerging issues that could have substantial impacts on the conservation of biological diversity, and to do so sufficiently early to encourage policy-relevant, practical research on those issues. Our group included professional horizon scanners and researchers affiliated with universities and non- and inter-governmental organizations, including specialists on topics such as invasive species, wildlife diseases and coral reefs. We identified 15 nascent issues, including new greenhouse gases, genetic techniques to eradicate mosquitoes, milk consumption in Asia and societal pessimism. DOI
231. Ursic-Bedoya, R; Buchhop, J; Joy, JB; Durvasula, R; Lowenberger, C.Prolixicin: a novel antimicrobial peptide isolated from Rhodnius prolixus with differential activity against bacteria and Trypanosoma cruzi.Insect Molecular Biology, 2011, 20: 775-786 Prolixicin: a novel antimicrobial peptide isolated from Rhodnius prolixus with differential activity against bacteria and Trypanosoma cruzi
hemiptera; innate immunity; antimicrobial peptide; attacin; diptericin; Trypanosoma cruzi
We identified and characterized the activity of prolixicin, a novel antimicrobial peptide (AMP) isolated from the hemipteran insect, Rhodnius prolixus. Sequence analysis reveals one region of prolixicin that may be related to the diptericin/attacin family of AMPs. Prolixicin is an 11-kDa peptide containing a putative 21 amino acid signal peptide, two putative phosphorylation sites and no glycosylation sites. It is produced by both adult fat body and midgut tissues in response to bacterial infection of the haemolymph or the midgut. Unlike most insect antibacterial peptides, the prolixicin gene does not seem to be regulated by NF-kappa B binding sites, but its promoter region contains several GATA sites. Recombinant prolixicin has strong activity against the Gram-negative bacterium Escherichia coli and differential activity against several Gramnegative and Gram-positive bacteria. No significant toxicity was demonstrated against Trypanosoma cruzi, the human parasite transmitted by R. prolixus. DOI
230. Voegele, A; Linkies, A; Muller, K; Leubner-Metzger, G.Members of the gibberellin receptor gene family GID1 (GIBBERELLIN INSENSITIVE DWARF1) play distinct roles during Lepidium sativum and Arabidopsis thaliana seed germination.Journal of Experimental Botany, 2011, 62: 5131-5147 Members of the gibberellin receptor gene family GID1 (GIBBERELLIN INSENSITIVE DWARF1) play distinct roles during Lepidium sativum and Arabidopsis thaliana seed germination
Arabidopsis thaliana; endosperm weakening; expansin; GIBBERELLIN INSENSITIVE DWARF1; Lepidium sativum; seed germination; xyloglucan endo-transglycosylase; hydrolase
Germination of endospermic seeds is partly regulated by the micropylar endosperm, which acts as constraint to radicle protrusion. Gibberellin (GA) signalling pathways control coat-dormancy release, endosperm weakening, and organ expansion during seed germination. Three GIBBERELLIN INSENSITIVE DWARF1 (GID1) GA receptors are known in Arabidopsis thaliana: GID1a, GID1b, and GID1c. Molecular phylogenetic analysis of angiosperm GID1s reveals that they cluster into two eudicot (GID1ac, GID1b) groups and one monocot group. Eudicots have at least one gene from each of the two groups, indicating that the different GID1 receptors fulfil distinct roles during plant development. A comparative Brassicaceae approach was used, in which gid1 mutant and whole-seed transcript analyses in Arabidopsis were combined with seed-tissue-specific analyses of its close relative Lepidium sativum (garden cress), for which three GID1 orthologues were cloned. GA signalling via the GID1ac receptors is required for Arabidopsis seed germination, GID1b cannot compensate for the impaired germination of the gid1agid1c mutant. Transcript expression patterns differed temporarily, spatially, and hormonally, with GID1b being distinct from GID1ac in both species. Endosperm weakening is mediated, at least in part, through GA-induced genes encoding cell-wall-modifying proteins. A suppression subtraction hybridization (SSH) cDNA library enriched for sequences that are highly expressed during early germination in the micropylar endosperm contained expansins and xyloglucan endo-transglycosylases/hydrolases (XTHs). Their transcript expression patterns in both species strongly suggest that they are regulated by distinct GID1-mediated GA signalling pathways. The GID1ac and GID1b pathways seem to fulfil distinct regulatory roles during Brassicaceae seed germination and seem to control their downstream targets distinctly. DOI
229. Watson, CT; Gray, SM; Hoffmann, M; Lubieniecki, KP; Joy, JB; Sandkam, BA; Weigel, D; Loew, E; Dreyer, C; Davidson, WS; Breden, F.Gene Duplication and Divergence of Long Wavelength-Sensitive Opsin Genes in the Guppy, Poecilia reticulata.J. Mol. Evol., 2011, 72: 240-252 Gene Duplication and Divergence of Long Wavelength-Sensitive Opsin Genes in the Guppy, Poecilia reticulata
Opsin; Gene duplication; Sexual selection; Gene conversion
Female preference for male orange coloration in the genus Poecilia suggests a role for duplicated long wavelength-sensitive (LWS) opsin genes in facilitating behaviors related to mate choice in these species. Previous work has shown that LWS gene duplication in this genus has resulted in expansion of long wavelength visual capacity as determined by microspectrophotometry (MSP). However, the relationship between LWS genomic repertoires and expression of LWS retinal cone classes within a given species is unclear. Our previous study in the related species, Xiphophorus helleri, was the first characterization of the complete LWS opsin genomic repertoire in conjunction with MSP expression data in the family Poeciliidae, and revealed the presence of four LWS loci and two distinct LWS cone classes. In this study we characterized the genomic organization of LWS opsin genes by BAC clone sequencing, and described the full range of cone cell types in the retina of the colorful Cumana guppy, Poecilia reticulata. In contrast to X. helleri, MSP data from the Cumana guppy revealed three LWS cone classes. Comparisons of LWS genomic organization described here for Cumana to that of X. helleri indicate that gene divergence and not duplication was responsible for the evolution of a novel LWS haplotype in the Cumana guppy. This lineage-specific divergence is likely responsible for a third additional retinal cone class not present in X. helleri, and may have facilitated the strong sexual selection driven by female preference for orange color patterns associated with the genus Poecilia. DOI PubMed
228. Weitbrecht, K; Muller, K; Leubner-Metzger, G.First off the mark: early seed germination.Journal of Experimental Botany, 2011, 62: 3289-3309 First off the mark: early seed germination
Abscisic acid; cold stratification; energy metabolism; gibberellins; imbibition; novel techniques; testa rupture; transcriptome
Most plant seeds are dispersed in a dry, mature state. If these seeds are non-dormant and the environmental conditions are favourable, they will pass through the complex process of germination. In this review, recent progress made with state-of-the-art techniques including genome-wide gene expression analyses that provided deeper insight into the early phase of seed germination, which includes imbibition and the subsequent plateau phase of water uptake in which metabolism is reactivated, is summarized. The physiological state of a seed is determined, at least in part, by the stored mRNAs that are translated upon imbibition. Very early upon imbibition massive transcriptome changes occur, which are regulated by ambient temperature, light conditions, and plant hormones. The hormones abscisic acid and gibberellins play a major role in regulating early seed germination. The early germination phase of Arabidopsis thaliana culminates in testa rupture, which is followed by the late germination phase and endosperm rupture. An integrated view on the early phase of seed germination is provided and it is shown that it is characterized by dynamic biomechanical changes together with very early alterations in transcript, protein, and hormone levels that set the stage for the later events. Early seed germination thereby contributes to seed and seedling performance important for plant establishment in the natural and agricultural ecosystem. DOI
227. Wiegmann, BM; Trautwein, MD; Winkler, IS; Barr, NB; Kim, JW; Lambkin, C; Bertone, MA; Cassel, BK; Bayless, KM; Heimberg, AM; Wheeler, BM; Peterson, KJ; Pape, T; Sinclair, BJ; Skevington, JH; Blagoderov, V; Caravas, J; Kutty, SN; Schmidt-Ott, U; Kampmeier, GE; Thompson, FC; Grimaldi, DA; Beckenbach, AT; Courtney, GW; Friedrich, M; Meier, R; Yeates, DK.Episodic radiations in the fly tree of life.Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 5690-5695 Episodic radiations in the fly tree of life
molecular systematics; phylogenetics; Insecta; adaptive radiation
Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic estimate of fly relationships based on molecules and morphology from 149 of 157 families, including 30 kb from 14 nuclear loci and complete mitochondrial genomes combined with 371 morphological characters. Multiple analyses show support for traditional groups (Brachycera, Cyclorrhapha, and Schizophora) and corroborate contentious findings, such as the anomalous Deuterophlebiidae as the sister group to all remaining Diptera. Our findings reveal that the closest relatives of the Drosophilidae are highly modified parasites (including the wingless Braulidae) of bees and other insects. Furthermore, we use micro-RNAs to resolve a node with implications for the evolution of embryonic development in Diptera. We demonstrate that flies experienced three episodes of rapid radiation-lower Diptera (220 Ma), lower Brachycera (180 Ma), and Schizophora (65 Ma)-and a number of life history transitions to hematophagy, phytophagy, and parasitism in the history of fly evolution over 260 million y. DOI
226. Winn, AA; Elle, E; Kalisz, S; Cheptou, PO; Eckert, CG; Goodwillie, C; Johnston, MO; Moeller, DA; Ree, RH; Sargent, RD; Vallejo-Marin, M.ANALYSIS OF INBREEDING DEPRESSION IN MIXED-MATING PLANTS PROVIDES EVIDENCE FOR SELECTIVE INTERFERENCE AND STABLE MIXED MATING.Evolution, 2011, 65: 3339-3359 ANALYSIS OF INBREEDING DEPRESSION IN MIXED-MATING PLANTS PROVIDES EVIDENCE FOR SELECTIVE INTERFERENCE AND STABLE MIXED MATING
Age-specific expression of inbreeding depression; gynodioecy; mating-system evolution; outcrossing; purging; selfing
Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Lower average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary transition will have intermediate ID. We compared the magnitude of ID from published estimates for highly selfing (r > 0.8), mixed-mating (0.2 =r= 0.8), and highly outcrossing (r < 0.2) plant populations across 58 species. We found that mixed-mating and outcrossing taxa have equally high average lifetime ID (d= 0.58 and 0.54, respectively) and similar ID at each of four life-cycle stages. These results are not consistent with evolution toward selfing in most mixed-mating taxa. We suggest that prevention of purging by selective interference could explain stable mixed mating in many natural populations. We identify critical gaps in the empirical data on ID and outline key approaches to filling them. DOI
225. Zazula, GD; Turner, DG; Ward, BC; Bond, J.Last interglacial western camel (Camelops hesternus) from eastern Beringia.Quat. Sci. Rev., 2011, 30: 2355-2360 Last interglacial western camel (Camelops hesternus) from eastern Beringia
Western camel; C. hesternus; Beringia; Fauna; Yukon; Pleistocene; Stratigraphy; Last interglacial; Sangamonian; Rancholabrean
Western camel (C. hesternus) fossils are rare from Eastern Beringia, thus there is little available information on their chronology, paleoecology, and biogeography in this region. In August of 2010, a partial proximal phalanx of a western camel was recovered from a sedimentary exposure along the White River, in the formerly glaciated terrain of southwest Yukon, northwest Canada. The fossil specimen was recovered in situ from sediments that are correlated by stratigraphic, tephra and radiocarbon data to the Marine Isotope Stage (MIS) 5 interglacial period (Sangamonian). Associated paleoenvironmental data indicates that this western camel inhabited a shrub tundra ecosystem that did not include spruce trees or boreal forest during a relatively cold interval between MIS Se and 5a. This is the oldest reliably dated western camel fossil from Eastern Beringia and supports the model of range expansion for this species to the high latitudes of northwest North America during the last interglacial (sensu lato). Crown Copyright (C) 2011 Published by Elsevier Ltd. All rights reserved. DOI
224. Anderson, JH; Faulds, PL; Atlas, WI; Pess, GR; Quinn, TP.Selection on breeding date and body size in colonizing coho salmon, Oncorhynchus kisutch.Molecular Ecology, 2010, 19: 2562-2573 Selection on breeding date and body size in colonizing coho salmon, Oncorhynchus kisutch
behaviour; conservation; dams; natural selection; reintroduction; sexual selection
Selection during the colonization of new habitat is critical to the process of local adaptation, but has rarely been studied. We measured the form, direction, and strength of selection on body size and date of arrival to the breeding grounds over the first three cohorts (2003-2005) of a coho salmon (Oncorhynchus kisutch) population colonizing 33 km of habitat made accessible by modification of Landsburg Diversion Dam, on the Cedar River, Washington, USA. Salmon were sampled as they bypassed the dam, parentage was assigned based on genotypes from 10 microsatellite loci, and standardized selection gradients were calculated using the number of returning adult offspring as the fitness metric. Larger fish in both sexes produced more adult offspring, and the magnitude of the effect increased in subsequent years for males, suggesting that low densities attenuated traditional size-biased intrasexual competition. For both sexes, directional selection favoured early breeders in 2003, but stabilizing selection on breeding date was observed in 2004 and 2005. Adults that arrived, and presumably bred, early produced stream-rearing juvenile offspring that were larger at a common date than offspring from later parents, providing a possible mechanism linking breeding date to offspring viability. Comparison to studies employing similar methodology indicated selection during colonization was strong, particularly with respect to reproductive timing. Finally, female mean reproductive success exceeded that needed for replacement in all years so the population expanded in the first generation, demonstrating that salmon can proficiently exploit vacant habitat. DOI
223. Ash, PEA; Zhang, YJ; Roberts, CM; Saldi, T; Hutter, H; Buratti, E; Petrucelli, L; Link, CD.Neurotoxic effects of TDP-43 overexpression in C-elegans.Human Molecular Genetics, 2010, 19: 3206-3218 Neurotoxic effects of TDP-43 overexpression in C-elegans
RNA-binding protein TDP-43 has been associated with multiple neurodegenerative diseases, including amyotrophic lateral sclerosis and frontotemporal lobar dementia. We have engineered pan-neuronal expression of human TDP-43 protein in Caenorhabditis elegans, with the goal of generating a convenient in vivo model of TDP-43 function and neurotoxicity. Transgenic worms with the neuronal expression of human TDP-43 exhibit an 'uncoordinated' phenotype and have abnormal motorneuron synapses. Caenorhabditis elegans contains a single putative ortholog of TDP-43, designated TDP-1, which we show can support alternative splicing of CFTR in a cell-based assay. Neuronal overexpression of TDP-1 also results in an uncoordinated phenotype, while genetic deletion of the tdp-1 gene does not affect movement or alter motorneuron synapses. By using the uncoordinated phenotype as a read-out of TDP-43 overexpression neurotoxicty, we have investigated the contribution of specific TDP-43 domains and subcellular localization to toxicity. Full-length (wild-type) human TDP-43 expressed in C. elegans is localized to the nucleus. Deletion of either RNA recognition domain (RRM1 or RRM2) completely blocks neurotoxicity, as does deletion of the C-terminal region. These deleted TDP-43 variants still accumulate in the nucleus, although their subnuclear distribution is altered. Interestingly, fusion of TDP-1 C-terminal sequences to TDP-43 missing its C-terminal domain restores normal subnuclear localization and toxicity in C. elegans and CFTR splicing in cell-based assays. Overexpression of wild-type, full-length TDP-43 in mammalian cells (differentiated M17 cells) can also result in cell toxicity. Our results demonstrate that in vivo TDP-43 neurotoxicity can result from nuclear activity of overexpressed full-length protein. DOI
222. Baron, OL; Ursic-Bedoya, RJ; Lowenberger, CA; Ocampo, CB.Differential gene expression from midguts of refractory and susceptible lines of the mosquito, Aedes aegypti, infected with Dengue-2 virus.Journal of Insect Science, 2010, 10: 41 Differential gene expression from midguts of refractory and susceptible lines of the mosquito, Aedes aegypti, infected with Dengue-2 virus
suppressive subtractive hybridization
Suppressive subtractive hybridization was used to evaluate the differential expression of midgut genes of feral populations of Aedes aegypti (Diptera: Culicidae) from Colombia that are naturally refractory or susceptible to Dengue-2 virus infection. A total of 165 differentially expressed sequence tags (ESTs) were identified in the subtracted libraries. The analysis showed a higher number of differentially expressed genes in the susceptible Ae. aegypti individuals than the refractory mosquitoes. The functional annotation of ESTs revealed a broad response in the susceptible library that included immune molecules, metabolic molecules and transcription factors. In the refractory strain, there was the presence of a trypsin inhibitor gene, which could play a role in the infection. These results serve as a template for more detailed studies aiming to characterize the genetic components of refractoriness, which in turn can be used to devise new approaches to combat transmission of dengue fever.Website DOI
221. Chassot, E; Bonhommeau, S; Dulvy, NK; Melin, F; Watson, R; Gascuel, D; Le Pape, O.Global marine primary production constrains fisheries catches.Ecology Letters, 2010, 13: 495-505 Global marine primary production constrains fisheries catches
Bottom-up; Large Marine Ecosystem; quantile regression; sustainable fishing
P>Primary production must constrain the amount of fish and invertebrates available to expanding fisheries; however the degree of limitation has only been demonstrated at regional scales to date. Here we show that phytoplanktonic primary production, estimated from an ocean-colour satellite (SeaWiFS), is related to global fisheries catches at the scale of Large Marine Ecosystems, while accounting for temperature and ecological factors such as ecosystem size and type, species richness, animal body size, and the degree and nature of fisheries exploitation. Indeed we show that global fisheries catches since 1950 have been increasingly constrained by the amount of primary production. The primary production appropriated by current global fisheries is 17-112% higher than that appropriated by sustainable fisheries. Global primary production appears to be declining, in some part due to climate variability and change, with consequences for the near future fisheries catches. DOI
219. Crespi, B; Stead, P; Elliot, M.Comparative genomics of autism and schizophrenia.Proceedings of the National Academy of Sciences of the United States of America, 2010, 107: 1736-1741 Comparative genomics of autism and schizophrenia
genetics; evolution; psychiatry
We used data from studies of copy-number variants (CNVs), single-gene associations, growth-signaling pathways, and intermediate phenotypes associated with brain growth to evaluate four alternative hypotheses for the genomic and developmental relationships between autism and schizophrenia: (i) autism subsumed in schizophrenia, (ii) independence, (iii) diametric, and (iv) partial overlap. Data from CNVs provides statistical support for the hypothesis that autism and schizophrenia are associated with reciprocal variants, such that at four loci, deletions predispose to one disorder, whereas duplications predispose to the other. Data from single-gene studies are inconsistent with a hypothesis based on independence, in that autism and schizophrenia share associated genes more often than expected by chance. However, differentiation between the partial overlap and diametric hypotheses using these data is precluded by limited overlap in the specific genetic markers analyzed in both autism and schizophrenia. Evidence from the effects of risk variants on growth-signaling pathways shows that autism-spectrum conditions tend to be associated with up-regulation of pathways due to loss of function mutations in negative regulators, whereas schizophrenia is associated with reduced pathway activation. Finally, data from studies of head and brain size phenotypes indicate that autism is commonly associated with developmentally-enhanced brain growth, whereas schizophrenia is characterized, on average, by reduced brain growth. These convergent lines of evidence appear most compatible with the hypothesis that autism and schizophrenia represent diametric conditions with regard to their genomic underpinnings, neurodevelopmental bases, and phenotypic manifestations as reflecting under-development versus dysregulated over-development of the human social brain. DOI
218. Crespi, B; Summers, K; Dorus, S.Evolutionary genomics of human intellectual disability.Evolutionary Applications, 2010, 3: 52-63 Evolutionary genomics of human intellectual disability
LINKED MENTAL-RETARDATION; NIJMEGEN-BREAKAGE-SYNDROME; AARSKOG-SCOTT-SYNDROME; REGULATING BRAIN SIZE; RHO-FAMILY GTPASES; FRAGILE-X-SYNDROME; POSITIVE SELECTION; DNA-DAMAGE; ADAPTIVE EVOLUTION; COGNITIVE-ABILITY
Previous studies have postulated that X-linked and autosomal genes underlying human intellectual disability may have also mediated the evolution of human cognition. We have conducted the first comprehensive assessment of the extent and patterns of positive Darwinian selection on intellectual disability genes in humans. We report three main findings. First, as noted in some previous reports, intellectual disability genes with primary functions in the central nervous system exhibit a significant concentration to the X chromosome. Second, there was no evidence for a higher incidence of recent positive selection on X-linked than autosomal intellectual disability genes, nor was there a higher incidence of selection on such genes overall, compared to sets of control genes. However, the X-linked intellectual disability genes inferred to be subject to recent positive selection were concentrated in the Rho GTP-ase pathway, a key signaling pathway in neural development and function. Third, among all intellectual disability genes, there was evidence for a higher incidence of recent positive selection on genes involved in DNA repair, but not for genes involved in other functions. These results provide evidence that alterations to genes in the Rho GTP-ase and DNA-repair pathways may play especially-important roles in the evolution of human cognition and vulnerability to genetically-based intellectual disability. DOI
216. Crossin, GT; Trathan, PN; Phillips, RA; Dawson, A; Le Bouard, F; Williams, TD.A Carryover Effect of Migration Underlies Individual Variation in Reproductive Readiness and Extreme Egg Size Dimorphism in Macaroni Penguins.American Naturalist, 2010, 176: 357-366 A Carryover Effect of Migration Underlies Individual Variation in Reproductive Readiness and Extreme Egg Size Dimorphism in Macaroni Penguins
carryover effect; Eudyptes; physiological conflict; egg development; reproductive trade-off; vitellogenin
Where life-history stages overlap, there is the potential for physiological conflicts that might be important in mediating carryover effects. However, our knowledge of the specific physiological mechanisms underlying carryover effects remains rudimentary, and specific examples remain rare. Here we show that female macaroni penguins (Eudyptes chrysolophus) initiate vitellogenesis and yolk formation while at sea during return migrations to breeding colonies; yolk formation takes approximately 16 days, but females lay only 7-14 days after their return. Once on land, Eudyptes penguins show a unique reproductive pattern of extreme egg size dimorphism in which the smaller, first-laid A-egg is 55%-75% of the size of the larger B-egg. We show that the degree of egg size dimorphism is inversely correlated with time between arrival and laying; that is, females that begin reproductive development well in advance of their return produce more dimorphic eggs. Furthermore, late-arriving females that produce the most dimorphic eggs have lower plasma levels of the yolk precursor vitellogenin on arrival; that is, they show lower reproductive readiness. These data support the hypothesis that extreme egg size dimorphism in Eudyptes penguins is due to a physiological constraint imposed by a migratory carryover effect and argue against small A-eggs having a specific, adaptive function. DOI
215. Decker, H; Lo, KY; Unger, SM; Ferreira, ST; Silverman, MA.Amyloid-beta Peptide Oligomers Disrupt Axonal Transport through an NMDA Receptor-Dependent Mechanism That Is Mediated by Glycogen Synthase Kinase 3 beta in Primary Cultured Hippocampal Neurons.Journal of Neuroscience, 2010, 30: 9166-9171 Amyloid-beta Peptide Oligomers Disrupt Axonal Transport through an NMDA Receptor-Dependent Mechanism That Is Mediated by Glycogen Synthase Kinase 3 beta in Primary Cultured Hippocampal Neurons
Disruption of axonal transport is a hallmark of several neurodegenerative diseases, including Alzheimer's disease (AD). Even though defective transport is considered an early pathologic event, the mechanisms by which neurodegenerative insults impact transport are poorly understood. We show that soluble oligomers of the amyloid-beta peptide (A beta Os), increasingly recognized as the proximal neurotoxins in AD pathology, induce disruption of organelle transport in primary hippocampal neurons in culture. Live imaging of fluorescent protein-tagged organelles revealed a marked decrease in axonal trafficking of dense-core vesicles and mitochondria in the presence of 0.5 mu M A beta Os. NMDA receptor (NMDAR) antagonists, including D-AP5, MK-801, and memantine, prevented the disruption of trafficking, thereby identifying signals for A beta O action at the cell membrane. Significantly, both pharmacological inhibition of glycogen synthase kinase-3 beta (GSK-3 beta) and transfection of neurons with a kinase-dead form of GSK-3 beta prevented the transport defect. Finally, we demonstrate by biochemical and immunocytochemical means that A beta Os do not affect microtubule stability, indicating that disruption of transport involves a more subtle mechanism than microtubule destabilization, likely the dysregulation of intracellular signaling cascades. Results demonstrate that A beta Os negatively impact axonal transport by a mechanism that is initiated by NMDARs and mediated by GSK-3 beta and establish a new connection between toxic A beta oligomers and AD pathology.Website
214. Eckert, CG; Kalisz, S; Geber, MA; Sargent, R; Elle, E; Cheptou, PO; Goodwillie, C; Johnston, MO; Kelly, JK; Moeller, DA; Porcher, E; Ree, RH; Vallejo-Marin, M; Winn, AA.Plant mating systems in a changing world.Trends in Ecology & Evolution, 2010, 25: 35-43 Plant mating systems in a changing world
There is increasing evidence that human disturbance can negatively impact plant-pollinator interactions such as outcross pollination. We present a meta-analysis of 22 studies involving 27 plant species showing a significant reduction in the proportion of seeds outcrossed in response to anthropogenic habitat modifications. We discuss the evolutionary consequences of disturbance on plant mating systems, and in particular whether reproductive assurance through selfing effectively compensates for reduced outcrossing. The extent to which disturbance reduces pollinator versus mate availability could generate diverse selective forces on reproductive traits. Investigating how anthropogenic change influences plant mating will lead to new opportunities for better understanding of how mating systems evolve, as well as of the ecological and evolutionary consequences of human activities and how to mitigate them. DOI
213. Goodwillie, C; Sargent, RD; Eckert, CG; Elle, E; Geber, MA; Johnston, MO; Kalisz, S; Moeller, DA; Ree, RH; Vallejo-Marin, M; Winn, AA.Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation.New Phytologist, 2010, 185: 311-321 Correlated evolution of mating system and floral display traits in flowering plants and its implications for the distribution of mating system variation
LEPTOSIPHON-JEPSONII POLEMONIACEAE; NUMBER TRADE-OFF; SELF-FERTILIZATION; INBREEDING DEPRESSION; RESOURCE-ALLOCATION; FEMALE FUNCTIONS; POLLINATOR VISITATION; PHYLOGENETIC EVIDENCE; FITNESS CONSEQUENCES; INFLORESCENCE SIZE
P> Reduced allocation to structures for pollinator attraction is predicted in selfing species. We explored the association between outcrossing and floral display in a broad sample of angiosperms. We used the demonstrated relationship to test for bias against selfing species in the outcrossing rate distribution, the shape of which has relevance for the stability of mixed mating. Relationships between outcrossing rate, flower size, flower number and floral display, measured as the product of flower size and number, were examined using phylogenetically independent contrasts. The distribution of floral displays among species in the outcrossing rate database was compared with that of a random sample of the same flora. The outcrossing rate was positively associated with the product of flower size and number; individually, components of display were less strongly related to outcrossing. Compared with a random sample, species in the outcrossing rate database showed a deficit of small floral display sizes. We found broad support for reduced allocation to attraction in selfing species. We suggest that covariation between mating systems and total allocation to attraction can explain the deviation from expected trade-offs between flower size and number. Our results suggest a bias against estimating outcrossing rates in the lower half of the distribution, but not specifically against highly selfing species. DOI
212. Guttman, JA; Lin, AEJ; Li, YL; Bechberger, J; Naus, CC; Vogl, AW; Finlay, BB.Gap junction hemichannels contribute to the generation of diarrhoea during infectious enteric disease.Gut, 2010, 59: 218-226 Gap junction hemichannels contribute to the generation of diarrhoea during infectious enteric disease
Objective The attaching and effacing (A/E) pathogens enterohaemorrhagic Escherichia coli, enteropathogenic E coli and Citrobacter rodentium colonise intestinal tracts, attach to enterocytes, collapse infected cell microvilli and alter numerous host cell processes during infection. Enterocyte alterations result in numerous small molecules being released from host cells that likely contribute to diarrhoeal phenotypes observed during these infections. One possible route for small molecules to be released from intestinal cells may be through functional gap junction hemichannels. Here we examine the involvement of these hemichannels during the diarrhoeal disease caused by A/E pathogens in vivo. Design Mice were infected with the diarrhoea-causing murine A/E pathogen C rodentium for 7 days. Connexin43 (Cx43) protein levels and immunolocalisation in the colon were initially used to determine alterations during A/E bacterial infections in vivo. Connexin mimetic peptides and connexin permeable tracer molecules were used to gage the presence and function of unpaired connexin hemichannels. The role of Cx43 in diarrhoea generation was assessed by comparing infections of wild-type mice to Cx43 mutant mice and determining the water abundance in the colonic luminal material. Results We demonstrate that Cx43 protein levels are increased in colonocytes during in vivo A/E bacterial infections, resulting in functionally open connexon hemichannels in apical membranes of infected cells. Moreover, infected Cx43 +/- mice do not suffer from diarrhoeal disease. Conclusions This study provides the first evidence that functional connexon hemichannels can occur in the intestine and are a novel molecular mechanism of water release during infectious diarrhoea. DOI
211. Hamanishi, ET; Raj, S; Wilkins, O; Thomas, BR; Mansfield, SD; Plant, AL; Campbell, MM.Intraspecific variation in the Populus balsamifera drought transcriptome.Plant Cell and Environment, 2010, 33: 1742-1755 Intraspecific variation in the Populus balsamifera drought transcriptome
balsam poplar; drought; genotypic variation; microarray; transcriptome
Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of genome responsiveness to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome using six different Populus balsamifera L. genotypes and Affymetrix GeneChip technology. Within a given genotype there was a positive correlation between the magnitude of water-deficit induced changes in transcript abundance across the transcriptome, and the capacity of that genotype to maintain growth following water deficit. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses. DOI
210. Harmon, LJ; Losos, JB; Davies, TJ; Gillespie, RG; Gittleman, JL; Jennings, WB; Kozak, KH; McPeek, MA; Moreno-Roark, F; Near, TJ; Purvis, A; Ricklefs, RE; Schluter, D; Schulte, JA; Seehausen, O; Sidlauskas, BL; Torres-Carvajal, O; Weir, JT; Mooers, AO.EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA.Evolution, 2010, 64: 2385-2396 EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA
Adaptive radiation; Brownian motion; comparative methods; model fitting; phylogeny
George Gaylord Simpson famously postulated that much of life's diversity originated as adaptive radiations-more or less simultaneous divergences of numerous lines from a single ancestral adaptive type. However, identifying adaptive radiations has proven difficult due to a lack of broad-scale comparative datasets. Here, we use phylogenetic comparative data on body size and shape in a diversity of animal clades to test a key model of adaptive radiation, in which initially rapid morphological evolution is followed by relative stasis. We compared the fit of this model to both single selective peak and random walk models. We found little support for the early-burst model of adaptive radiation, whereas both other models, particularly that of selective peaks, were commonly supported. In addition, we found that the net rate of morphological evolution varied inversely with clade age. The youngest clades appear to evolve most rapidly because long-term change typically does not attain the amount of divergence predicted from rates measured over short time scales. Across our entire analysis, the dominant pattern was one of constraints shaping evolution continually through time rather than rapid evolution followed by stasis. We suggest that the classical model of adaptive radiation, where morphological evolution is initially rapid and slows through time, may be rare in comparative data. DOI
208. Heath, JP; Gilchrist, HG; Ydenberg, RC.Interactions between rate processes with different timescales explain counterintuitive foraging patterns of arctic wintering eiders.Proceedings of the Royal Society B-Biological Sciences, 2010, 277: 3179-3186 Interactions between rate processes with different timescales explain counterintuitive foraging patterns of arctic wintering eiders
foraging; diving; digestion; scale; time series; arctic ecology
To maximize fitness, animals must respond to a variety of processes that operate at different rates or timescales. Appropriate decisions could therefore involve complex interactions among these processes. For example, eiders wintering in the arctic sea ice must consider locomotion and physiology of diving for benthic invertebrates, digestive processing rate and a nonlinear decrease in profitability of diving as currents increase over the tidal cycle. Using a multi-scale dynamic modelling approach and continuous field observations of individuals, we demonstrate that the strategy that maximizes long-term energy gain involves resting during the most profitable foraging period (slack currents). These counterintuitive foraging patterns are an adaptive trade-off between multiple overlapping rate processes and cannot be explained by classical rate-maximizing optimization theory, which only considers a single timescale and predicts a constant rate of foraging. By reducing foraging and instead digesting during slack currents, eiders structure their activity in order to maximize long-term energetic gain over an entire tide cycle. This study reveals how counterintuitive patterns and a complex functional response can result from a simple trade-off among several overlapping rate processes, emphasizing the necessity of a multi-scale approach for understanding adaptive routines in the wild and evaluating mechanisms in ecological time series. DOI
207. Hoffmann, M; Hilton-Taylor, C; Angulo, A; Bohm, M; Brooks, TM; Butchart, SHM; Carpenter, KE; Chanson, J; Collen, B; Cox, NA; Darwall, WRT; Dulvy, NK; Harrison, LR; Katariya, V; Pollock, CM; Quader, S; Richman, NI; Rodrigues, ASL; Tognelli, MF; Vie, JC; Aguiar, JM; Allen, DJ; Allen, GR; Amori, G; Ananjeva, NB; Andreone, F; Andrew, P; Ortiz, ALA; Baillie, JEM; Baldi, R; Bell, BD; Biju, SD; Bird, JP; Black-Decima, P; Blanc, JJ; Bolanos, F; Bolivar, W; Burfield, IJ; Burton, JA; Capper, DR; Castro, F; Catullo, G; Cavanagh, RD; Channing, A; Chao, NL; Chenery, AM; Chiozza, F; Clausnitzer, V; Collar, NJ; Collett, LC; Collette, BB; Fernandez, CFC; Craig, MT; Crosby, MJ; Cumberlidge, N; Cuttelod, A; Derocher, AE; Diesmos, AC; Donaldson, JS; Duckworth, JW; Dutson, G; Dutta, SK; Emslie, RH; Farjon, A; Fowler, S; Freyhof, J; Garshelis, DL; Gerlach, J; Gower, DJ; Grant, TD; Hammerson, GA; Harris, RB; Heaney, LR; Hedges, SB; Hero, JM; Hughes, B; Hussain, SA; Icochea, J; Inger, RF; Ishii, N; Iskandar, DT; Jenkins, RKB; Kaneko, Y; Kottelat, M; Kovacs, KM; Kuzmin, SL; La Marca, E; Lamoreux, JF; Lau, MWN; Lavilla, EO; Leus, K; Lewison, RL; Lichtenstein, G; Livingstone, SR; Lukoschek, V; Mallon, DP; McGowan, PJK; McIvor, A; Moehlman, PD; Molur, S; Alonso, AM; Musick, JA; Nowell, K; Nussbaum, RA; Olech, W; Orlov, NL; Papenfuss, TJ; Parra-Olea, G; Perrin, WF; Polidoro, BA; Pourkazemi, M; Racey, PA; Ragle, JS; Ram, M; Rathbun, G; Reynolds, RP; Rhodin, AGJ; Richards, SJ; Rodriguez, LO; Ron, SR; Rondinini, C; Rylands, AB; de Mitcheson, YS; Sanciangco, JC; Sanders, KL; Santos-Barrera, G; Schipper, J; Self-Sullivan, C; Shi, YC; Shoemaker, A; Short, FT; Sillero-Zubiri, C; Silvano, DL; Smith, KG; Smith, AT; Snoeks, J; Stattersfield, AJ; Symes, AJ; Taber, AB; Talukdar, BK; Temple, HJ; Timmins, R; Tobias, JA; Tsytsulina, K; Tweddle, D; Ubeda, C; Valenti, SV; van Dijk, PP; Veiga, LM; Veloso, A; Wege, DC; Wilkinson, M; Williamson, EA; Xie, F; Young, BE; Akcakaya, HR; Bennun, L; Blackburn, TM; Boitani, L; Dublin, HT; da Fonseca, GAB; Gascon, C; Lacher, TE; Mace, GM; Mainka, SA; McNeely, JA; Mittermeier, RA; Reid, GM; Rodriguez, JP; Rosenberg, AA; Samways, MJ; Smart, J; Stein, BA; Stuart, SN.The Impact of Conservation on the Status of the World's Vertebrates.Science, 2010, 330: 1503-1509 The Impact of Conservation on the Status of the World's Vertebrates
Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species. DOI
206. Holt, BG; Côté, IM; Emerson, BC.Signatures of speciation? Distribution and diversity of Hypoplectrus (Teleostei: Serranidae) colour morphotypes.Global Ecology and Biogeography, 2010, 19: 432-441 Signatures of speciation? Distribution and diversity of Hypoplectrus (Teleostei: Serranidae) colour morphotypes
Caribbean; colour polymorphism; co-occurrence; coral reef; evolution; fish; hamlets; marine; sympatry
Aim To test historical and current influences on the distributions of sympatric colour morphotypes in the coral reef fish genus Hypoplectrus. Location The Caribbean and surrounding tropical waters. These areas cover the entire distribution of the genus. Methods A large and extensive database of Hypoplectrus sightings was used to establish the distribution of colour morphotypes and test a long-standing hypothesis regarding their origin. First, we considered the evidence for the previously proposed 'population centre' hypothesis, which suggests that current morphotype distributions reflect past conditions where these colour forms evolved in allopatry. Using morphotype sighting data, the existence of clusters in occurrence and density was tested. Second, we examined whether the observed patterns of morphotype co-occurrence deviate from random expectations using null model simulations, within subregions of the distribution of the genus, to infer ecological influences on distribution. Results There is considerable variation in morphotype distribution, with even widespread morphotypes showing geographical clustering. There is also little evidence to suggest past or current geographical isolation, with only one of the 11 morphotypes (Hypoplectrus chlorurus) showing a density distribution that is consistent with the population centre hypothesis. Null model analyses show that variation in local morphotype co-occurrence is typically significantly lower than expected under random dispersal conditions. Main conclusions Our results strongly suggest that morphotype co-occurrence is not random, but there is no evidence to suggest a past allopatric radiation in Hypoplectrus colour. Current distributions are likely to be driven by competitive interactions and/or habitat preferences. Our study highlights the value of the Hypoplectrus species complex as a system for the study of speciation in the marine environment, and implies that these closely related morphotypes have ecological relevance rather than being simple colour variants of a single polymorphic species. DOI
205. Kuhn, TS; McFarlane, KA; Groves, P; Mooers, AO; Shapiro, B.Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon.Molecular Ecology, 2010, 19: 1312-1323 Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon
ancient DNA; caribou; conservation genetics; microsatellite
The long-term persistence of forest-dwelling caribou (Rangifer tarandus caribou) will probably be determined by management and conservation decisions. Understanding the evolutionary relationships between modern caribou herds, and how these relationships have changed through time will provide key information for the design of appropriate management strategies. To explore these relationships, we amplified microsatellite and mitochondrial markers from modern caribou from across the Southern Yukon, Canada, as well as mitochondrial DNA from Holocene specimens recovered from alpine ice patches in the same region. Our analyses identify a genetically distinct group of caribou composed of herds from the Southern Lakes region that may warrant special management consideration. We also identify a partial genetic replacement event occurring 1000 years before present, coincident with the deposition of the White River tephra and the Medieval Warm Period. These results suggest that, in the face of increasing anthropogenic pressures and climate variability, maintaining the ability of caribou herds to expand in numbers and range may be more important than protecting the survival of any individual, isolated sedentary forest-dwelling herd. DOI
204. Kurvers, R.H.J.M., H.H.T. Prins, S.E. van Wieren, K. van Oers, B.A. Nolet and R.C. Ydenberg.The effect of personality on social foraging: shy barnacle geese scrounge more.Proceedings of the Royal Society B-Biological Sciences, 2010, 277: 601-608 The effect of personality on social foraging: shy barnacle geese scrounge more.
Animals foraging in groups can either search for food themselves (producing) or search for the food discoveries of other individuals (scrounging). Tactic use in producer-scrounger games is partly flexible but individuals tend to show consistency in tactic use under different conditions suggesting that personality might play a role in tactic use in producer-scrounger games. Here we studied the use of producing and scrounging tactics by bold and shy barnacle geese (Branta leucopsis), where boldness is a personality trait known to be repeatable over time in this species. We defined individuals as bold, shy or intermediate based on two novel object tests. We scored the frequency of finding food patches (the outcome of investing in producing) and joining patches (the outcome of investing in scrounging) by bold and shy individuals and their feeding time. Shy individuals had a higher frequency of joining than bold individuals, demonstrating for the first time that personality is associated with tactic use in a producer-scrounger game. Bold individuals tended to spend more time feeding than shy individuals. Our results highlight the importance of including individual behavioural variation in models of producer-scrounger games.
DOI
203. Kurvers, RHJM; van Oers, K; Nolet, BA; Jonker, RM; van Wieren, SE; Prins, HHT; Ydenberg, RC.Personality predicts the use of social information.Ecology Letters, 2010, 13: 829-837 Personality predicts the use of social information
Barnacle goose; boldness; Branta leucopsis; personality; social information
P>The use of social information is known to affect various important aspects of an individual's ecology, such as foraging, dispersal and space use and is generally assumed to be entirely flexible and context dependent. However, the potential link between personality differences and social information use has received little attention. In this study, we studied whether use of social information was related to personality, using barnacle geese, Branta leucopsis, where boldness is a personality trait known to be consistent over time. We found that the use of social information decreased with increasing boldness score of the individuals. Individuals had lower feeding times when they did not follow the social information and this effect was unrelated to boldness score. When manipulating social information, thereby making it incorrect, individuals irrespective of their boldness score, learned that it was incorrect and ignored it. Our results show that social information use depends on the personality type of an individual, which calls for incorporation of these personality-related differences in studies of spatial distribution of animals in which social information use plays a role. DOI
202. M'Gonigle, LK; FitzJohn, RG.ASSORTATIVE MATING AND SPATIAL STRUCTURE IN HYBRID ZONES.Evolution, 2010, 64: 444-455 ASSORTATIVE MATING AND SPATIAL STRUCTURE IN HYBRID ZONES
Assortative mating; dispersal; hybrid zones; long distance; mosaic
The spatial genetic composition of hybrid zones exhibits a range of possible patterns, with many characterized by patchy distributions. While several hypothetical explanations exist for the maintenance of these "mosaic" hybrid zones, they remain virtually unexplored theoretically. Using computer simulations we investigate the roles of dispersal and assortative mating in the formation and persistence of hybrid zone structure. To quantify mosaic structure we develop a likelihood method, which we apply to simulation and empirical data. We find that long distance dispersal can lead to a patchy distribution that assortative mating can then reinforce, ultimately producing a mosaic capable of persisting over evolutionarily significant periods of time. By reducing the mating success of rare males, assortative mating creates a positive within-patch frequency-dependent selective pressure. Selection against heterozygotes can similarly create a rare-type disadvantage and we show that it can also preserve structure. We find that mosaic structure is maintained across a range of assumptions regarding the form and strength of assortative mating. Interestingly, we find that higher levels of mosaic structure are sometimes observed for intermediate assortment strengths. The high incidence of assortment documented in hybrid zones suggests that it may play a key role in stabilizing their form and structure. DOI
201. MacNeil, MA; Graham, NAJ; Cinner, JE; Dulvy, NK; Loring, PA; Jennings, S; Polunin, NVC; Fisk, AT; McClanahan, TR.Transitional states in marine fisheries: adapting to predicted global change.Philosophical Transactions of the Royal Society B-Biological Sciences, 2010, 365: 3753-3763 Transitional states in marine fisheries: adapting to predicted global change
climate change; fish communities; social-ecological systems; biodiversity
Global climate change has the potential to substantially alter the production and community structure of marine fisheries and modify the ongoing impacts of fishing. Fish community composition is already changing in some tropical, temperate and polar ecosystems, where local combinations of warming trends and higher environmental variation anticipate the changes likely to occur more widely over coming decades. Using case studies from the Western Indian Ocean, the North Sea and the Bering Sea, we contextualize the direct and indirect effects of climate change on production and biodiversity and, in turn, on the social and economic aspects of marine fisheries. Climate warming is expected to lead to (i) yield and species losses in tropical reef fisheries, driven primarily by habitat loss; (ii) community turnover in temperate fisheries, owing to the arrival and increasing dominance of warm-water species as well as the reduced dominance and departure of cold-water species; and (iii) increased diversity and yield in Arctic fisheries, arising from invasions of southern species and increased primary production resulting from ice-free summer conditions. How societies deal with such changes will depend largely on their capacity to adapt-to plan and implement effective responses to change-a process heavily influenced by social, economic, political and cultural conditions. DOI
200. Marko, PB; Hoffman, JM; Emme, SA; McGovern, TM; Keever, CC; Cox, LN.The 'Expansion-Contraction' model of Pleistocene biogeography: rocky shores suffer a sea change?Molecular Ecology, 2010, 19: 146-169 The 'Expansion-Contraction' model of Pleistocene biogeography: rocky shores suffer a sea change?
BARNACLE BALANUS-GLANDULA; EFFECTIVE POPULATION-SIZE; CRYPTIC GLACIAL REFUGIA; CLIMATE-CHANGE; GENETIC-STRUCTURE; THERMAL-STRESS; LIFE-HISTORY; GEOGRAPHICAL VARIATION; MYTILUS-CALIFORNIANUS; INTERACTION STRENGTH
Approximately 20 000 years ago the last glacial maximum (LGM) radically altered the distributions of many Northern Hemisphere terrestrial organisms. Fewer studies describing the biogeographic responses of marine species to the LGM have been conducted, but existing genetic data from coastal marine species indicate that fewer taxa show clear signatures of post-LGM recolonization. We have assembled a mitochondrial DNA (mtDNA) data set for 14 co-distributed northeastern Pacific rocky-shore species from four phyla by combining new sequences from ten species with previously published sequences from eight species. Nuclear sequences from four species were retrieved from GenBank, plus we gathered new elongation factor 1-alpha sequences from the barnacle Balanus glandula. Results from demographic analyses of mtDNA for five (36%) species (Evasterias troschelii, Pisaster ochraceus, Littorina sitkana, L. scutulata, Xiphister mucosus) were consistent with large population expansions occurring near the LGM, a pattern expected if these species recently recolonized the region. However, seven (50%) species (Mytilus trossulus, M. californianus, B. glandula, S. cariosus, Patiria miniata, Katharina tunicata, X. atropurpureus) exhibited histories consistent with long-term stability in effective population size, a pattern indicative of regional persistence during the LGM. Two species of Nucella with significant mtDNA genetic structure showed spatially variable demographic histories. Multilocus analyses for five species were largely consistent with mtDNA: the majority of multilocus interpopulation divergence times significantly exceeded the LGM. Our results indicate that the LGM did not extirpate the majority of species in the northeastern Pacific; instead, regional persistence during the LGM appears a common biogeographic history for rocky-shore organisms in this region. DOI
199. McGovern, TM; Keever, CC; Saski, CA; Hart, MW; Marko, PB.Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species.Molecular Ecology, 2010, 19: 5043-5060 Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co-distributed species
ancestral polymorphism; biogeography; coalescence; divergence time; gene flow; glaciation; larval development; pseudo-congruence; vicariance
Coalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent-based inferences about demographic processes to reconstruct the population histories of two co-distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation. DOI
198. Mills, SC; Côté, IM.Crime and punishment in a roaming cleanerfish.Proceedings of the Royal Society B-Biological Sciences, 2010, 277: 3617-3622 Crime and punishment in a roaming cleanerfish
conflict; cooperation; biological markets; cheating; partner switching; territory size
Cheating is common in cooperative interactions, but its occurrence can be controlled by various means ranging from rewarding cooperators to active punishment of cheaters. Punishment occurs in the mutualism involving the cleanerfish Labroides dimidiatus and its reef fish clients. When L. dimidiatus cheats, by taking scales and mucus rather than ectoparasites, wronged clients either chase or withhold further visits to the dishonest cleaner, which leads to more cooperative future interactions. Punishment of cheating L. dimidiatus may be effective largely because these cleaners are strictly site-attached, increasing the potential for repeated interactions between individual cleaners and clients. Here, we contrast the patterns of cheating and punishment in L. dimidiatus with its close relative, the less site-attached Labroides bicolor. Overall, L. bicolor had larger home ranges, cheated more often and, contrary to our prediction, were punished by cheated clients as frequently as, and not less often than, L. dimidiatus. However, adult L. bicolor, which had the largest home ranges, did not cheat more than younger conspecifics, suggesting that roaming, and hence the frequency of repeated interactions, has little influence on cheating and retaliation in cleaner-client relationships. We suggest that roaming cleaners offer the only option available to many site-attached reef fish seeking a cleaning service. This asymmetry in scope for partner choice encourages dishonesty by the partner with more options (i.e. L. bicolor), but to be cleaned by a cleaner that sometimes cheats may be a better option than not to be cleaned at all. DOI
197. Mooers, AO; Doak, DF; Findlay, CS; Green, DM; Grouios, C; Manne, LL; Rashvand, A; Rudd, MA; Whitton, J.Science, Policy, and Species at Risk in Canada.Bioscience, 2010, 60 Science, Policy, and Species at Risk in Canada
endangered species; critical habitat; listing; recovery; transparency
The meaningful incorporation of independent scientific advice into effective public policy is a hurdle for any conservation legislation. Canada's Species at Risk Act (SARA; 2002) was designed to separate the science-based determination of a species' risk status from the decision to award it legal protection. However, thereafter, the input of independent science into policy has not been clearly identifiable. Audits of SARA have identified clear deficiencies in the protection and recovery of listed species; for example, of the 176 species legally protected in 2003, only one has a legal implementation plan for its recovery We argue that clearly distinguishing science from policy at all relevant stages would improve the scientific integrity, transparency, accountability, and public acceptance of the legal listing and recovery implementation processes in SARA. Such delineation would also clarify exactly what trade-offs are being made between at-risk species recovery and competing policy objectives. DOI
196. Moore, J.W., and D.E. Schindler.Spawning salmon and the phenology of emergence in stream insects.Proceedings of the Royal Society B-Biological Sciences, 2010, 277: 1695-1703 Spawning salmon and the phenology of emergence in stream insects
ecosystem engineer; disturbance regime; bioturbation; marine-derived nutrients
Phenological dynamics are controlled by environmental factors, disturbance regimes and species interactions that alter growth or mortality risk. Ecosystem engineers can be a key source of disturbance, yet their effects on the phenologies of co-occurring organisms are virtually unexplored. We investigated how the abundance of a dominant ecosystem engineer, spawning sockeye salmon (Oncorhynchus nerka), alters the emergence phenology of stream insects. In streams with high densities of salmon, peak insect emergence occurred in early July, immediately prior to salmon spawning. By contrast, peak insect emergence in streams with low densities of salmon was weeks later and more protracted. The emergence of specific taxa was also significantly related to salmon density. A common rearing experiment revealed that differences in emergence timing are maintained in the absence of spawning salmon. We hypothesize that these patterns are probably driven by predictable and severe disturbance from nest-digging salmon driving local adaptation and being a trait filter of insect emergence. Thus, salmon regulate the timing and duration of aquatic insect emergence, a cross-ecosystem flux from streams to riparian systems. DOI
195. Palen, WJ; Schindler, DE.Water clarity, maternal behavior, and physiology combine to eliminate UV radiation risk to amphibians in a montane landscape.Proceedings of the National Academy of Sciences of the United States of America, 2010, 107: 9701-9706 Water clarity, maternal behavior, and physiology combine to eliminate UV radiation risk to amphibians in a montane landscape
amphibian declines; ultraviolet radiation; risk analysis; dissolved organic matter; oviposition behavior
Increasing UV-B radiation (UV-B; 290-320 nm) due to stratospheric ozone depletion has been a leading explanation for the decline in amphibians for nearly 2 decades. Yet, the likelihood that UV-B can influence amphibians at the large spatial scales relevant to population declines has not yet been evaluated. A key limitation has been in relating results from individual sites to the effect of UV-B for populations distributed across heterogeneous landscapes. We measured critical embryonic exposures to UV-B for two species of montane amphibians with contrasting physiological sensitivities, long-toed salamander (Ambystoma macrodactylum) and Cascades frog (Rana cascadae), at field sites spanning a gradient of UV-B attenuation in water. We then used these experimental results to estimate the proportion of embryos exposed to harmful UV-B across a large number of breeding sites. By combining surveys of the incubation timing, incident UV-B, optical transparency of water, and oviposition depth and light exposure of embryos at each site, we present a comprehensive assessment of the risk posed by UV-B for montane amphibians of the Pacific Northwest. We found that only 1.1% of A. macrodactylum and no R. cascadae embryos across a landscape of breeding sites are exposed to UV-B exceeding lethal levels. These results emphasize that accurately estimating the risk posed by environmental stressors requires placing experimental results in a broader ecological context that accounts for the heterogeneity experienced by populations distributed across natural landscapes. DOI
194. Pavey, SA; Nielsen, JL; Hamon, TR.RECENT ECOLOGICAL DIVERGENCE DESPITE MIGRATION IN SOCKEYE SALMON (ONCORHYNCHUS NERKA).Evolution, 2010, 64: 1773-1783 RECENT ECOLOGICAL DIVERGENCE DESPITE MIGRATION IN SOCKEYE SALMON (ONCORHYNCHUS NERKA)
Colonization; divergence with migration; ecological speciation; isolation with migration (IM); rapid evolution; sympatric speciation
Ecological divergence may result when populations experience different selection regimes, but there is considerable discussion about the role of migration at the beginning stages of divergence before reproductive isolating mechanisms have evolved. However, detection of past migration is difficult in current populations and tools to differentiate genetic similarities due to migration versus recent common ancestry are only recently available. Using past volcanic eruption times as a framework, we combine morphological analyses of traits important to reproduction with a coalescent-based genetic analysis of two proximate sockeye salmon (Oncorhynchus nerka) populations. We find that this is the most recent (similar to 500 years, 100 generations) natural ecological divergence recorded in a fish species, and report that this divergence is occurring despite migration. Although studies of fish divergence following the retreat of glaciers (10,000-15,000 years ago) have contributed extensively to our understanding of speciation, the Aniakchak system of sockeye salmon provides a rare example of the initial stages of ecological divergence following natural colonization. Our results show that even in the face of continued migration, populations may diverge in the absence of a physical barrier. DOI
193. Peery, MZ; Hall, LA; Sellas, A; Beissinger, SR; Moritz, C; Berube, M; Raphael, MG; Nelson, SK; Golightly, RT; McFarlane-Tranquilla, L; Newman, S; Palsboll, PJ.Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation.Proceedings of the Royal Society B-Biological Sciences, 2010, 277: 697-706 Genetic analyses of historic and modern marbled murrelets suggest decoupling of migration and gene flow after habitat fragmentation
dispersal; genetic variation; habitat fragmentation; marbled murrelet; old-growth forest; rescue effects
The dispersal of individuals among fragmented populations is generally thought to prevent genetic and demographic isolation, and ultimately reduce extinction risk. In this study, we show that a century of reduction in coastal old-growth forests, as well as a number of other environmental factors, has probably resulted in the genetic divergence of marbled murrelets (Brachyramphus marmoratus) in central California, despite the fact that 7 per cent of modern-sampled murrelets in this population were classified as migrants using genetic assignment tests. Genetic differentiation appears to persist because individuals dispersing from northern populations contributed relatively few young to the central California population, as indicated by the fact that migrants were much less likely to be members of parent-offspring pairs than residents (10.5% versus 45.4%). Moreover, a recent 1.4 per cent annual increase in the proportion of migrants in central California, without appreciable reproduction, may have masked an underlying decline in the resident population without resulting in demographic rescue. Our results emphasize the need to understand the behaviour of migrants and the extent to which they contribute offspring in order to determine whether dispersal results in gene flow and prevents declines in resident populations. DOI
192. Redding, DW; DeWolff, CV; Mooers, AO.Evolutionary Distinctiveness, Threat Status, and Ecological Oddity in Primates.Conservation Biology, 2010, 24: 1052-1058 Evolutionary Distinctiveness, Threat Status, and Ecological Oddity in Primates
conservation priorities; phylogenetic isolation; triage
The EDGE (evolutionarily distinct and globally endangered) conservation program (www.edgeofexistence.org) uses a composite measure of threat and phylogenetic isolation to rank species for conservation attention. Using primates as a test case, we examined how species that rank highly with this metric represent the collective from which they are drawn. We considered the ecological and morphological traits, including body mass, diet, terrestriality, and home range size, of all 233 species of primates. Overall, EDGE score and the level of deviance from the mean of 20 different ecological, reproductive, and morphological variables were correlated (mean correlation r = 0.14, combined p = 1.7 x 10(-14)). Although primates with a high EDGE score had characteristics that made them seem odd, they did not seem to express more ancestral characteristics than expected. Sets of primate species with high EDGE scores will, therefore, collectively capture a broader than expected range of the biology of the clade. If similar patterns hold in other groups, the EDGE metric may be useful for prioritizing biodiversity for conservation. DOI
191. Rintoul, GL; Reynolds, IJ.Mitochondrial trafficking and morphology in neuronal injury.Biochimica et Biophysica Acta-Molecular Basis of Disease, 2010, 1802: 143-150 Mitochondrial trafficking and morphology in neuronal injury
Mitochondria; Neurodegeneration; Fission; Fusion
Alterations in mitochondrial function may have a central role in the pathogenesis of many neurodegenerative diseases. The study of mitochondrial dysfunction has typically focused on ATP generation, calcium homeostasis and the production of reactive oxygen species. However, there is a growing appreciation of the dynamic nature of mitochondria within cells. Mitochondria are highly motile organelles, and also constantly undergo fission and fusion. This raises the possibility that impairment of mitochondrial dynamics could contribute to the pathogenesis of neuronal injury. In this review we describe the mechanisms that govern mitochondrial movement, fission and fusion. The key proteins that are involved in mitochondrial fission and fusion have also been linked to some inherited neurological diseases, including autosomal dominant optic atrophy and Charcot-Marie-Tooth disease 2A. We will discuss the evidence that altered movement, fission and fusion are associated with impaired neuronal viability. There is a growing collection of literature that links impaired mitochondrial dynamics to a number of disease models. Additionally, the concept that the failure to deliver a functional mitochondrion to the appropriate site within a neuron could contribute to neuronal dysfunction provides an attractive framework for understanding the mechanisms underlying neurologic disease. However, it remains difficult to clearly establish that altered mitochondrial dynamics clearly represent a cause of neuronal dysfunction. (C) 2009 Elsevier B.V. All rights reserved. DOI
190. Schlotterer, A; Hamann, A; Kukudov, G; Ibrahim, Y; Heckmann, B; Bozorgmehr, F; Pfeiffer, M; Hutter, H; Stern, D; Du, XL; Brownlee, M; Bierhaus, A; Nawroth, P; Morcos, M.Apurinic/apyrimidinic endonuclease 1, p53, and thioredoxin are linked in control of aging in C-elegans.Aging Cell, 2010, 9: 420-432 Apurinic/apyrimidinic endonuclease 1, p53, and thioredoxin are linked in control of aging in C-elegans
Aging; C; elegans; DNA repair; mitochondrial DNA; reactive oxygen species; p53
P>Deletions in mitochondrial DNA (mtDNA) accumulate during aging. Expression of the Caenorhabditis elegans apurinic/apyrimidinic endonuclease 1 (APE1) ortholog exo-3, involved in DNA repair, is reduced by 45% (P < 0.05) during aging of C. elegans. Suppression of exo-3 by treatment with RNAi resulted in a threefold increase in mtDNA deletions (P < 0.05), twofold enhanced generation of reactive oxygen species (ROS) (P < 0.01), distortion of the structural integrity of the nervous system, reduction of head motility by 43% (P < 0.01) and whole animal motility by 38% (P < 0.05). Suppression of exo-3 significantly reduced life span: mean life span decreased from 18.5 +/- 0.4 to 15.4 +/- 0.1 days (P < 0.001) and maximum life span from 25.9 +/- 0.4 to 23.2 +/- 0.1 days (P = 0.001). Additional treatment of exo-3-suppressed animals with a mitochondrial uncoupler decreased ROS levels, reduced neuronal damage, and increased motility and life span. Additional suppression of the C. elegans p53 ortholog cep-1 in exo-3 RNAi-treated animals similarly decreased ROS levels, preserved neuronal integrity, and increased motility and life span. In wild-type animals, suppression of cep-1, involved in downregulation of exo-3, increased expression of exo-3 without a significant effect on ROS levels, preserved neuronal integrity, and increased motility and life span. Suppression of the C. elegans thioredoxin orthologs trx-1 and trx-2, involved in the redox chaperone activity of exo-3, overrides the protective effect of cep-1 RNAi treatment on neuronal integrity, neuronal function, mean and maximum life span. These results show that APE1/EXO-3, p53/CEP-1, and thioredoxin affect each other and that these interactions determine aging as well as neuronal structure and function. DOI
189. Schwander, T; Vuilleumier, S; Dubman, J; Crespi, BJ.Positive feedback in the transition from sexual reproduction to parthenogenesis.Proceedings of the Royal Society B-Biological Sciences, 2010, 277: 1435-1442 Positive feedback in the transition from sexual reproduction to parthenogenesis
Understanding how new phenotypes evolve is challenging because intermediate stages in transitions from ancestral to derived phenotypes often remain elusive. Here we describe and evaluate a new mechanism facilitating the transition from sexual reproduction to parthenogenesis. In many sexually reproducing species, a small proportion of unfertilized eggs can hatch spontaneously ('tychoparthenogenesis') and develop into females. Using an analytical model, we show that if females are mate-limited, tychoparthenogenesis can result in the loss of males through a positive feedback mechanism whereby tychoparthenogenesis generates female-biased sex ratios and increasing mate limitation. As a result, the strength of selection for tychoparthenogenesis increases in concert with the proportion of tychoparthenogenetic offspring in the sexual population. We then tested the hypothesis that mate limitation selects for tychoparthenogenesis and generates female-biased sex ratios, using data from natural populations of sexually reproducing Timema stick insects. Across 41 populations, both the tychoparthenogenesis rates and the proportions of females increased exponentially as the density of individuals decreased, consistent with the idea that low densities of individuals result in mate limitation and selection for reproductive insurance through tychoparthenogenesis. Our model and data from Timema populations provide evidence for a simple mechanism through which parthenogenesis can evolve rapidly in a sexual population. DOI
188. Shames, SR; Deng, WY; Guttman, JA; de Hoog, CL; Li, YL; Hardwidge, PR; Sham, HP; Vallance, BA; Foster, LJ; Finlay, BB.The pathogenic E-coli type III effector EspZ interacts with host CD98 and facilitates host cell prosurvival signalling.Cellular Microbiology, 2010, 12: 1322-1339 The pathogenic E-coli type III effector EspZ interacts with host CD98 and facilitates host cell prosurvival signalling
Cell Biology; Microbiology
Enterohaemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC respectively) are diarrhoeal pathogens that cause the formation of attaching and effacing (A/E) lesions on infected host cells. These pathogens encode a type III secretion system (T3SS) used to inject effector proteins directly into host cells, an essential requirement for virulence. In this study, we identified a function for the type III secreted effector EspZ. Infection with EPEC Delta espZ caused increased cytotoxicity in HeLa and MDCK cells compared with wild-type EPEC, and expressing espZ in cells abrogated this effect. Using yeast two-hybrid, proteomics, immunofluorescence and co-immunoprecipitation, it was demonstrated that EspZ interacts with the host protein CD98, which contributes to protection against EPEC-mediated cytotoxicity. EspZ enhanced phosphorylation of focal adhesion kinase (FAK) and AKT during infection with EPEC, but CD98 only appeared to facilitate FAK phosphorylation. This study provides evidence that EspZ and CD98 promote host cell survival mechanisms involving FAK during A/E pathogen infection. DOI
187. Steimel, A; Wong, LN; Najarro, EH; Ackley, BD; Garriga, G; Hutter, H.The Flamingo ortholog FMI-1 controls pioneer-dependent navigation of follower axons in C. elegans.Development, 2010, 137: 3663-3673 The Flamingo ortholog FMI-1 controls pioneer-dependent navigation of follower axons in C. elegans
Axon guidance; flamingo; C. elegans; Pioneer; Follower; Nervous system; Cadherin; Adhesion; GPCR
Development of a functional neuronal network during embryogenesis begins with pioneer axons creating a scaffold along which later-outgrowing axons extend. The molecular mechanism used by these follower axons to navigate along pre-existing axons remains poorly understood. We isolated loss-of-function alleles of fmi-1, which caused strong axon navigation defects of pioneer and follower axons in the ventral nerve cord (VNC) of C. elegans. Notably follower axons, which exclusively depend on pioneer axons for correct navigation, frequently separated from the pioneer. fmi-1 is the sole C. elegans ortholog of Drosophila flamingo and vertebrate Celsr genes, and this phenotype defines a new role for this important molecule in follower axon navigation. FMI-1 has a unique and strikingly conserved structure with cadherin and C-terminal G-protein coupled receptor domains and could mediate cell-cell adhesion and signaling functions. We found that follower axon navigation depended on the extracellular but not on the intracellular domain, suggesting that FMI-1 mediates primarily adhesion between pioneer and follower axons. By contrast, pioneer axon navigation required the intracellular domain, suggesting that FMI-1 acts as receptor transducing a signal in this case. Our findings indicate that FMI-1 is a cell-type dependent axon guidance factor with different domain requirements for its different functions in pioneers and followers. DOI
186. Stroeven, AP; Fabel, D; Codilean, AT; Kleman, J; Clague, JJ; Miguens-Rodriguez, M; Xu, S.Investigating the glacial history of the northern sector of the Cordilleran Ice Sheet with cosmogenic Be-10 concentrations in quartz.Quat. Sci. Rev., 2010, 29: 3630-3643 Investigating the glacial history of the northern sector of the Cordilleran Ice Sheet with cosmogenic Be-10 concentrations in quartz
Exposure durations of glacial landforms in widely separated areas of central Yukon Territory affected by the northern sector of the Cordilleran Ice Sheet (OS) and alpine glaciers have been determined using cosmogenic Be-10 in quartz. The aim of our research is to test previous reconstructions of glacial history and to begin to address the paucity of chronological control for the lateral and vertical extent of the northern CIS. Chronological evidence for CIS expansion predating the Last Glacial Maximum comes from minimum surface exposure durations of c 100 ka for two bedrock samples within the Reid glacial limit, indicating a possible marine Oxygen Isotope Stage (OIS) 6 age for this event, and from minimum exposure durations of about 40 ka for boulders on moraines constructed by alpine glaciers on a nunatak within the McConnell glacial limit (OIS 2), indicating a possible OIS 4 age. High elevation minimum surface exposure durations within the McConnell limit indicate that some areas formerly mapped as nunataks were covered by cold-based ice prior to 30 ka. Montane glaciation in the Mackenzie Mountains, outside the McConnell glacial limit, was contemporaneous with nearby CIS advance at 17 ka, with CIS retreat by 15 ka. Deglaciation of the Tintina Trench, a major ice discharge route, was completed by 12 ka. At this time ice in an adjacent discharge route to the south was still entering higher-elevation valleys in the Pelly Mountains. A Lateglacial readvance may have peaked at ca 10 ka in the Ogilvie Mountains. Considerable variation in ages from individual landforms, and possible complex histories, require additional cosmogenic nuclide measurements to confirm interpretations. (C) 2010 Elsevier Ltd. All rights reserved. DOI
185. Summers, K; Crespi, BJ.Xmrks the spot: life history tradeoffs, sexual selection and the evolutionary ecology of oncogenesis.Molecular Ecology, 2010, 19: 3022-3024 Xmrks the spot: life history tradeoffs, sexual selection and the evolutionary ecology of oncogenesis
In a classic paper, George Williams (1957) argued that alleles promoting reproductive success early in life may be favoured by selection, even if they reduce the lifespan of individuals that bear the allele. A variety of evidence supports the theory that such 'antagonistic pleiotropy' is a major factor contributing to the evolution of senescence (Ljubuncic & Reznick 2009), but examples of specific alleles known to fulfil Williams' criteria remain rare, in both humans and other animals (e.g. Alexander et al. 2007; Kulminski et al. 2010). An intriguing example in this issue of Molecular Ecology (Fernandez & Bowser 2010) demonstrates that both natural and sexual selection may favour melanoma-promoting oncogene alleles in the fish genus Xiphophorus. DOI
184. Sutherland, WJ; Clout, M; Côté, IM; Daszak, P; Depledge, MH; Fellman, L; Fleishman, E; Garthwaite, R; Gibbons, DW; De Lurio, J; Impey, AJ; Lickorish, F; Lindenmayer, D; Madgwick, J; Margerison, C; Maynard, T; Peck, LS; Pretty, J; Prior, S; Redford, KH; Scharlemann, JPW; Spalding, M; Watkinson, AR.A horizon scan of global conservation issues for 2010.Trends in Ecology & Evolution, 2010, 25: 1-7 A horizon scan of global conservation issues for 2010
Horizon scanning identifies emerging issues in a given field sufficiently early to conduct research to inform policy and practice. Our group of horizon scanners, including academics and researchers, convened to identify fifteen nascent issues that could affect the conservation of biological diversity. These include the impacts of and potential human responses to climate change, novel biological and digital technologies, novel pollutants and invasive species. We expect to repeat this process and collation annually. DOI
183. Travers, M; Clinchy, M; Zanette, L; Boonstra, R; Williams, TD.Indirect predator effects on clutch size and the cost of egg production.Ecology Letters, 2010, 13: 980-988 Indirect predator effects on clutch size and the cost of egg production
Clutch size; cost of reproduction; egg production; nest predation; non-consumptive effects; oxidative stress; predator-prey ecology
Predator-induced changes in physiology and behaviour may negatively affect a prey's birth rate. Evidence of such indirect predator effects on prey demography remains scarce in birds and mammals despite invertebrate and aquatic studies that suggest ignoring such effects risks profoundly underestimating the total impact of predators. We report the first experimental demonstration of indirect predator effects on the annual 'birth' rate resulting from negative effects on the size of subsequent clutches laid by birds. We manipulated the probability of nest predation and measured the size of subsequent clutches and multiple indices of the mother's physiological condition, while controlling for food availability, date and stage of breeding. Females subject to frequent experimental nest predation laid smaller subsequent clutches and were in poorer physiological condition, particularly regarding non-resource-based indices (e.g. oxidative stress and glucocorticoid mobilization) consistent with both a response to the threat of predation and an increased cost of egg production. DOI
182. Trefry, SA; Hik, DS.Variation in pika (Ochotona collaris, O-princeps) vocalizations within and between populations.Ecography, 2010, 33: 784-795 Variation in pika (Ochotona collaris, O-princeps) vocalizations within and between populations
Understanding geographic call variation can resolve evolutionary and behavioural questions, yet the factors influencing divergent acoustic signals remain poorly understood in mammals. We explored call variation between collared pikas in Yukon and Alaska and American pikas in Alberta, and between individuals within a population of collared pikas. Classification trees were used to determine the extent of call divergence between populations and the elements of calls driving these differences. Pika populations had significant differences in call structure, and individual pikas were classified to their correct populations with up to 94% accuracy. To investigate possible mechanisms responsible for interspecific variability, we tested the acoustic adaptation hypothesis by using a playback experiment to explore whether American and collared pika calls transmit with less degradation across their own species' habitat than the habitat of their congener. We found no support for the acoustic adaptation hypothesis. Geographic call variation in these two species of pikas likely reflects genetic divergence, and may be a result of separate evolutionary histories. We calculated the potential for individual coding for both time and frequency measurements of calls. High frequency harmonics showed greater between- than within-individual variation, and may act as sources of information regarding individual identity. DOI
181. Wade, MJ; Wilson, DS; Goodnight, C; Taylor, D; Bar-Yam, Y; de Aguiar, MAM; Stacey, B; Werfel, J; Hoelzer, GA; Brodie, ED; Fields, P; Breden, F; Linksvayer, TA; Fletcher, JA; Richerson, PJ; Bever, JD; Van Dyken, JD; Zee, P.Multilevel and kin selection in a connected world.Nature, 2010, 463: E8-E9 Multilevel and kin selection in a connected world
DOI
180. Waliwitiya, R; Belton, P; Nicholson, RA; Lowenberger, CA.Effects of the essential oil constituent thymol and other neuroactive chemicals on flight motor activity and wing beat frequency in the blowfly Phaenicia sericata.Pest Management Science, 2010, 66: 277-289 Effects of the essential oil constituent thymol and other neuroactive chemicals on flight motor activity and wing beat frequency in the blowfly Phaenicia sericata
flight motor activity; wing beat; thymol; GABA
BACKGROUND: The effects were evaluated of the plant terpenoid thymol and eight other neuroactive compounds on flight muscle impulses (FMIs) and wing beat frequency (WBF) of tethered blowflies (Phaenicia sericata Meig.). RESULTS: The electrical activity of the dorsolongitudinal flight muscles was closely linked to the WBF of control insects. Topically applied thymol inhibited WBF within 15-30 min and reduced FMI frequency. Octopamine and chlordimeform caused a similar, early-onset bursting pattern that decreased in amplitude with time. Desmethylchlordimeform blocked wing beating within 60 min and generated a profile of continuous but lower-frequency FMIs. Fipronil suppressed wing beating and induced a pattern of continuous, variable-frequency spiking that diminished gradually over 6 h. Cypermethrin- and rotenone-treated flies had initial strong FMIs that declined with time. In flies injected with GABA, the FMIs were generally unidirectional and frequency was reduced, as was seen with thymol. CONCLUSIONS: Thymol readily penetrates the cuticle and interferes with flight muscle and central nervous function in the blowfly. The similarity of the action of thymol and GABA suggests that this terpenoid acts centrally in blowflies by mimicking or facilitating GABA action. (C) 2009 Society of Chemical Industry DOI
179. Wally, O; Punja, ZK.Enhanced disease resistance in transgenic carrot (Daucus carota L.) plants over-expressing a rice cationic peroxidase.Planta, 2010, 232: 1229-1239 Enhanced disease resistance in transgenic carrot (Daucus carota L.) plants over-expressing a rice cationic peroxidase
Peroxidase; Lignin; Hydrogen peroxide; Pathogen resistance; Oxidative burst
Plant class III peroxidases are involved in numerous responses related to pathogen resistance including controlling hydrogen peroxide (H2O2) levels and lignin formation. Peroxidases catalyze the oxidation of organic compounds using H2O2 as an oxidant. We examined the mechanisms of disease resistance in a transgenic carrot line (P23) which constitutively over-expresses the rice cationic peroxidase OsPrx114 (previously known as PO-C1) and which exhibits enhanced resistance to necrotrophic foliar pathogens. OsPrx114 over-expression led to a slight enhancement of constitutive transcript levels of pathogenesis-related (PR) genes. These transcript levels were dramatically increased in line P23 compared to controls [GUS construct under the control of 35S promoter (35S::GUS)] when tissues were treated with cell wall fragments of the fungal pathogen Sclerotinia sclerotiorum (SS-walls), and to a lesser extent with 2,6-dichloroisonicotinic acid. There was no basal increase in basal H2O2 levels in tissues of the line P23. However, during an oxidative burst response elicited by SS-walls, H2O2 accumulation was reduced in line P23 despite, typical media alkalinization associated with oxidative burst responses was observed, suggesting that OsPrx114 was involved in rapid H2O2 consumption during the oxidative burst response. Tap roots of line P23 had increased lignin formation in the outer periderm tissues, which was further increased during challenge inoculation with Alternaria radicina. Plant susceptibility to a biotrophic pathogen, Erysiphe heraclei, was not affected. Disease resistance to necrotrophic pathogens in carrot as a result of OsPrx114 over-expression is manifested through increased PR transcript accumulation, rapid removal of H2O2 during oxidative burst response and enhanced lignin formation. DOI
178. Watson, CT; Lubieniecki, KP; Loew, E; Davidson, WS; Breden, F.Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri.BMC Evol. Biol., 2010, 10 Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri
Background: Long wave-sensitive (LWS) opsin genes have undergone multiple lineage-specific duplication events throughout the evolution of teleost fishes. LWS repertoire expansions in live-bearing fishes (family Poeciliidae) have equipped multiple species in this family with up to four LWS genes. Given that color vision, especially attraction to orange male coloration, is important to mate choice within poeciliids, LWS opsins have been proposed as candidate genes driving sexual selection in this family. To date the genomic organization of these genes has not been described in the family Poeciliidae, and little is known about the mechanisms regulating the expression of LWS opsins in any teleost. Results: Two BAC clones containing the complete genomic repertoire of LWS opsin genes in the green swordtail fish, Xiphophorus helleri, were identified and sequenced. Three of the four LWS loci identified here were linked in a tandem array downstream of two tightly linked short wave-sensitive 2 (SWS2) opsin genes. The fourth LWS opsin gene, containing only a single intron, was not linked to the other three and is the product of a retrotransposition event. Genomic and phylogenetic results demonstrate that the LWS genes described here share a common evolutionary origin with those previously characterized in other poeciliids. Using qualitative RT-PCR and MSP we showed that each of the LWS and SWS2 opsins, as well as three other cone opsin genes and a single rod opsin gene, were expressed in the eyes of adult female and male X. helleri, contributing to six separate classes of adult retinal cone and rod cells with average lambda(max) values of 365 nm, 405 nm, 459 nm, 499 nm, 534 nm and 568 nm. Comparative genomic analysis identified two candidate teleost opsin regulatory regions containing putative CRX binding sites and hormone response elements in upstream sequences of LWS gene regions of seven teleost species, including X. helleri. Conclusions: We report the first complete genomic description of LWS and SWS2 genes in poeciliids. These data will serve as a reference for future work seeking to understand the relationship between LWS opsin genomic organization, gene expression, gene family evolution, sexual selection and speciation in this fish family. DOI PubMed
177. Weiser, J. P.Belton, Z. Ziska & J. Holusa.Ultrastructure of the Microsporidian, Duboscqia legeri, the type species of the Genus Duboscqia Perez 1908.Acta Protozool., 2010, 49: 125-131 Ultrastructure of the Microsporidian, Duboscqia legeri, the type species of the Genus Duboscqia Perez 1908
Summary. The type species of the genus Duboscqia Perez, 1908 (Opisthokonta, Microspora), D. legeri is a pathogen of termites. It was
found again in Zootermopsis angusticollis in British Columbia and the material is used for emendation of data on ultrastructures of this old
genus. The sporogony of this microsporidian ends with 16 oval spores closed in sporophorous vesicles. The isofilar polar filament coiled in
13 coils, the arched anchoring disc and the polaroplast with tightly packed lamellae are typical for the ultrastructures of uninucleate spores.
The sporophorous vesicle is persistent. The microsporidian infects cyst-like lobes of the fat body hanging free in the body cavity. Relations
to other related genera are discussed.
176. Willie, J; Travers, M; Williams, TD.Female Zebra Finches (Taeniopygia guttata) Are Chronically but Not Cumulatively "Anemic" during Repeated Egg Laying in Response to Experimental Nest Predation.Physiological and Biochemical Zoology, 2010, 83: 119-126 Female Zebra Finches (Taeniopygia guttata) Are Chronically but Not Cumulatively "Anemic" during Repeated Egg Laying in Response to Experimental Nest Predation
STARLING STURNUS-VULGARIS; HEMATOCRIT VALUES; BODY CONDITION; CLUTCH SIZE; DYNAMICS; SPARROWS; COSTS; MANIPULATIONS; REPEATABILITY; REPRODUCTION
Recently it has been recognized that reproduction itself, or the regulatory processes controlling reproduction, might contribute to physiological costs of reproduction. Reproductive anemia, a decrease in hematocrit and hemoglobin concentration, might provide one such mechanism underlying the costs of egg production in birds. In this study, we investigated the effect of repeated cycles of egg production in response to experimental nest predation (egg removal) on hematological traits in female zebra finches (Taeniopygia guttata). We predicted that if the negative effect of egg production on hematocrit and hemoglobin concentration was cumulative, with anemia being proportional to reproductive effort, then females laying more clutches, or laying successive clutches without recovery during incubation, would show greater reproductive anemia. In contrast, if females maintain hematocrit and hemoglobin concentration at some minimum functional level independent of reproductive effort, then there should be no difference in hematological traits among females laying two or more successive clutches. Our results supported the second of these hypotheses: egg-laying females had reduced hematocrit (-7.5%) and hemoglobin concentrations (-10%), but the extent of reproductive anemia did not differ among females laying either two or three successive clutches, with or without recovery during incubation, or in females laying 7-21 eggs. Females maintained low hematocrit and hemoglobin for 20-35 d, and we suggest that prolonged periods of anemia might be common and functionally important in free-living birds, for example, where females produce multiple successive clutches in response to high levels of nest predation or where they initiate a second clutch while still rearing first brood chicks. DOI
175. Willing, EM; Bentzen, P; van Oosterhout, C; Hoffmann, M; Cable, J; Breden, F; Weigel, D; Dreyer, C.Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.Molecular Ecology, 2010, 19: 968-984 Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies
F-ST outlier methods; Neighbor-net; Poecilia reticulata; population genetics; principal component analysis; single nucleotide polymorphism
Adaptation of guppies (Poecilia reticulata) to contrasting upland and lowland habitats has been extensively studied with respect to behaviour, morphology and life history traits. Yet population history has not been studied at the whole-genome level. Although single nucleotide polymorphisms (SNPs) are the most abundant form of variation in many genomes and consequently very informative for a genome-wide picture of standing natural variation in populations, genome-wide SNP data are rarely available for wild vertebrates. Here we use genetically mapped SNP markers to comprehensively survey genetic variation within and among naturally occurring guppy populations from a wide geographic range in Trinidad and Venezuela. Results from three different clustering methods, Neighbor-net, principal component analysis (PCA) and Bayesian analysis show that the population substructure agrees with geographic separation and largely with previously hypothesized patterns of historical colonization. Within major drainages (Caroni, Oropouche and Northern), populations are genetically similar, but those in different geographic regions are highly divergent from one another, with some indications of ancient shared polymorphisms. Clear genomic signatures of a previous introduction experiment were seen, and we detected additional potential admixture events. Headwater populations were significantly less heterozygous than downstream populations. Pairwise F-ST values revealed marked differences in allele frequencies among populations from different regions, and also among populations within the same region. F-ST outlier methods indicated some regions of the genome as being under directional selection. Overall, this study demonstrates the power of a genome-wide SNP data set to inform for studies on natural variation, adaptation and evolution of wild populations. DOI
174. Almedom, RB; Liewald, JF; Hernando, G; Schultheis, C; Rayes, D; Pan, J; Schedletzky, T; Hutter, H; Bouzat, C; Gottschalk, A.An ER-resident membrane protein complex regulates nicotinic acetylcholine receptor subunit composition at the synapse.EMBO Journal, 2009, 28: 2636-2649 An ER-resident membrane protein complex regulates nicotinic acetylcholine receptor subunit composition at the synapse
ELEGANS NEUROMUSCULAR-JUNCTION; NEMATODE CAENORHABDITIS-ELEGANS; ALPHA-SUBUNIT; TGF-BETA; GENE ENCODES; C. ELEGANS; MUSCLE; IDENTIFICATION; VISUALIZATION; TRAFFICKING
Nicotinic acetylcholine receptors (nAChRs) are homo- or heteropentameric ligand-gated ion channels mediating excitatory neurotransmission and muscle activation. Regulation of nAChR subunit assembly and transfer of correctly assembled pentamers to the cell surface is only partially understood. Here, we characterize an ER transmembrane (TM) protein complex that influences nAChR cell-surface expression and functional properties in Caenorhabditis elegans muscle. Loss of either type I TM protein, NRA-2 or NRA-4 (nicotinic receptor associated), affects two different types of muscle nAChRs and causes in vivo resistance to cholinergic agonists. Sensitivity to subtype-specific agonists of these nAChRs is altered differently, as demonstrated by whole-cell voltage-clamp of dissected adult muscle, when applying exogenous agonists or after photo-evoked, channelrhodopsin-2 (ChR2) mediated acetylcholine (ACh) release, as well as in single-channel recordings in cultured embryonic muscle. These data suggest that nAChRs desensitize faster in nra-2 mutants. Cell-surface expression of different subunits of the 'levamisole-sensitive' nAChR (L-AChR) is differentially affected in the absence of NRA-2 or NRA-4, suggesting that they control nAChR subunit composition or allow only certain receptor assemblies to leave the ER. The EMBO Journal (2009) 28, 2636-2649. doi: 10.1038/emboj.2009.204; Published online 16 July 2009 Subject Categories: membranes & transport; neuroscience DOI
173. Brandt, R; Gergou, A; Wacker, I; Fath, T; Hutter, H.A Caenorhabditis elegans model of tau hyperphosphorylation: Induction of developmental defects by transgenic overexpression of Alzheimer's disease-like modified tau.Neurobiology of Aging, 2009, 30: 22-33 A Caenorhabditis elegans model of tau hyperphosphorylation: Induction of developmental defects by transgenic overexpression of Alzheimer's disease-like modified tau
Tauopathy; Neurodegenerative disease; Animal model; Cytoskeleton; Phosphorylation; Aggregation
The microtubule-associated tau proteins become functionally and structurally altered in Alzheimer's disease (AD). To analyze tau modification and its role in a non-vertebrate animal model, we produced transgenic Caenorhabditis elegans strains with a panneuronal expression of human tau and a pseudohyperphosphorylated (PHP) tau construct that mimics AD-relevant tau modification. We show that human tau in C. elegans becomes highly phosphorylated and exhibits conformational changes similar to PHP tau and human PHF tau. Both, wt tau and PHP tau induced a progressive age-dependent development of a phenotype of uncoordinated locomotion (unc) in the absence of neuronal degeneration. However, only PHP tau induced a defective pattern of motor neuron development as indicated by the presence of gaps in the dorsal cord. commissures on the wrong side and local broadening of axons. The data indicate that C. elgans is capable of highly phosphorylating human tau to an AD-like state whereas only stable disease-like tau modification induce developmental defects suggesting a specific interference of pathologic tau with intracellular mechanisms of axonal out-growth and pathfinding. (C) 2007 Elsevier Inc. All rights reserved. DOI
172. Clague, JJ; Menounos, B; Osborn, G; Luckman, BH; Koch, J.Nomenclature and resolution in Holocene glacial chronologies.Quat. Sci. Rev., 2009, 28: 2231-2238 Nomenclature and resolution in Holocene glacial chronologies
Most Quaternary research in Canada during the first half of the twentieth century focused on Pleistocene glaciation. Given the dramatic shifts in climate during the Pleistocene, it is not surprising that the Holocene was viewed as a time of benign climate. Holocene climate variability was first recognized around the middle of the century when paleoecologists found evidence that the early part of the epoch was warmer and drier than the later part. In 1970s and 1980s, another generation of geologists, geographers, and botanists began to recognize more complexity in Holocene climate and vegetation in western Canada. Several millennial-scale glacier "advances" postdating the early Holocene warm interval were defined, including the Garibaldi Phase (6.9-5.6 ka), the Tiedemann-Peyto Advance (3.5-1.9 ka), and the Little Ice Age (AD 1200-1900). Subsequently, application of dendrochronological techniques and stratigraphic studies in glacier forefields showed that the Little Ice Age was itself more complex than previously thought. During that 700-year period, glaciers repeatedly advanced and retreated in response to climatic variability on time scales ranging from centuries to decades. Recent work shows that the glacier record of the Garibaldi Phase and the Tiedemann and Peyto advances are similar in complexity to the Little Ice Age, with multiple advances of glaciers separated by intervals of more restricted ice cover. Researchers have also identified other times in the Holocene when glaciers expanded from restricted positions - 8.20, 4.90-3.80, and 1.70-1.40 ka. Continued research undoubtedly will reveal additional complexities, but with what is currently known the appropriateness of terms such as "Tiedemann Advance Peyto Advance," and "Little Ice Age" can be questioned. Only short periods of time separate these episodes as currently defined, and it seems likely that intervals of restricted glacier cover within each of these millennial-length intervals are just as long as the intervals separating them. (C) 2008 Elsevier Ltd. All rights reserved. DOI
171. Cooper, DM; Chamberlain, CM; Lowenberger, C.Aedes FADD: A novel death domain-containing protein required for antibacterial immunity in the yellow fever mosquito, Aedes aegypti.Insect Biochemistry and Molecular Biology, 2009, 39: 47-54 Aedes FADD: A novel death domain-containing protein required for antibacterial immunity in the yellow fever mosquito, Aedes aegypti
KAPPA-B KINASE; DROSOPHILA-MELANOGASTER; SIGNALING PATHWAYS; ANOPHELES-GAMBIAE; INSECT IMMUNITY; FACTOR RELISH; EXPRESSION; CASPASE; INFECTION; APOPTOSIS
Microbial infections in insects activate a series of immune responses that culminate in the production of antimicrobial peptides (AMPS). In Drosophila, two signaling pathways, govern the challenge-dependent expression of AMPS; the Toll and IMD pathways. While AMPS have been the subject of much research in mosquitoes, the regulation of the pathways required for AMP expression remains largely unknown. We report here the identification of Aedes FADD (AeFADD), a death domain protein in Aedes aegypti. AeFadd is expressed in all immune-competent tissues and all developmental stages examined. At the transcriptional level, AeFadd transcripts increased when challenged with Escherichia coli but not Micrococcus luteus. In both cases, we observed the induction of two AMP genes; cecropin and defensin. Loss of AeFadd function by dsRNA interference impaired the inducible expression of both AMPS, and rendered adult mosquitoes susceptible to both types of bacteria. Identifying molecules that regulate mosquito immunity may help elucidate the factors that contribute to the vectorial capacity and provide insights into general mechanisms that regulate innate immunity. (C) 2008 Elsevier Ltd. All rights reserved. DOI
170. Cooper, DM; Granville, DJ; Lowenberger, C.The insect caspases.Apoptosis, 2009, 14: 247-256 The insect caspases
PROGRAMMED CELL-DEATH; YELLOW-FEVER MOSQUITO; DROSOPHILA CASPASE; AEDES-AEGYPTI; COMPENSATORY PROLIFERATION; BACULOVIRUS INHIBITOR; DOMAIN SUPERFAMILY; MOLECULAR-CLONING; IAP PROTEINS; IN-VIVO
Developmental and tissue homeostasis is a delicate balance between cell proliferation and cell death. The activation of caspases, a conserved family of cysteine proteases, is a main event in the initiation and execution of programmed cell death. While caspases have been characterized from many organisms, comparatively little is known about insect caspases. In Drosophila melanogaster, seven caspases have been characterized; three initiators and four effectors. In mosquitoes, several putative caspases have been identified in the genomes of Aedes aegypti and Anopheles gambiae. A small number of caspases have been identified in the Lepidoptera, the flour beetle, Tribolium castaneum, and the pea aphid, Acyrthosiphon pisum. The availability of new insect genome sequences will provide a unique opportunity to examine the caspase family across an evolutionarily diverse phylum and will provide valuable insights into their function and regulation. DOI
169. Crespi, B.Gender, biology, and mathematics performance.Proceedings of the National Academy of Sciences of the United States of America, 2009, 106: E102-E102 Gender, biology, and mathematics performance
DOI
168. Dashtgard, SE; Gingras, MK; MacEachern, JA.Tidally modulated shorefaces.J. Sediment. Res., 2009, 79: 793-807 Tidally modulated shorefaces
Tidally modulated shorefaces (TMS) are wave-dominated, but differ from conventional shorefaces in that sediments deposited in water depths equivalent to the upper, middle, and lower shoreface (depending upon the tidal range) are regularly subjected to variable wave processes, including swash-backwash, breaking-wave and surf processes, and shoaling waves; during the tidal cycle. In upper macrotidal and megatidal settings, it is also possible that these shoreface deposits are subaerially exposed during low tide. TMS exhibit the morphology, seaward decrease in sediment caliber, and dominance of wave-generated sedimentary structures consistent with beach-shoreface settings. However, the sedimentological and ichnological structures of deposits exposed in the laterally extensive intertidal zone are more akin to those of the upper and lower shoreface, and not the beach. Four major differences permit the ready differentiation of tidally modulated shoreface successions from conventional shorefaces. (1) Sedimentary structures generated by swash-backwash (plane beds), surf and breaking waves (current ripples and trough cross-beds), shoaling waves (oscillation ripples), and storm waves (hummocky and swaly cross-stratification) are interbedded with one another across the shoreface. (2) Ebb-oriented tidal currents and surface runoff during the failing tide and at low tide deposit offshore-directed current ripples and combined-flow ripples in sandy sediments, or trough cross beds in gravel-dominated sediments. (3) Ichnologically, TMS exhibit a reduction in both the diversity of ichnogenera and density of burrowing across the entire shoreface profile. However, the incipient-trace associations are most similar to the Skolithos Ichnofacies in the upper shoreface-equiva lent zone, and to the Cruziana Ichnofacies in the lower shoreface-equiva lent zone. (4) The sedimentological and ichnological criteria commonly employed to identify the middle shoreface are spread out across the upper and lower shoreface, making this subenvironment difficult to differentiate. DOI
166. Ericsson, JD; Janmaat, AF; Lowenberger, C; Myers, JH.Is decreased generalized immunity a cost of Bt resistance in cabbage loopers Trichoplusia ni?Journal of Invertebrate Pathology, 2009, 100: 61-67 Is decreased generalized immunity a cost of Bt resistance in cabbage loopers Trichoplusia ni?
INSECTICIDE BACILLUS-THURINGIENSIS; PROPHENOLOXIDASE-ACTIVATING SYSTEM; MOTH EPHESTIA-KUEHNIELLA; CRY1AB TOXIN; PEPTIDOGLYCAN RECOGNITION; ANTIMICROBIAL PEPTIDES; DIAMONDBACK MOTH; DELTA-ENDOTOXIN; AEDES-AEGYPTI; BACTERIA
We studied the immune response to Bacillus thuringiensis kurstaki (Btk) in Susceptible (Bt-RS) and resistant (Bt-R) Trichoplusia ni after exposure to low doses of Btk and injection with Escherichia coli. We measured the levels of resistance, the expression profiles of hemolymph proteins, the phenoloxidase (PO) activity, and the differential number of circulating hemocytes in resistant and susceptible individuals. Individuals from the Bt-RS line became more resistant following a previous exposure to sub lethal concentrations of Btk, but the resistance to Btk of the Bt-R line did not change significantly, Similarly the Bt-R strain showed no significant changes in any of the potential immune responses, hemolymph protein levels or PO activity. The number of circulating hemocytes was significantly lower in the Bt-R strain than in the Bt-RS strain. Exposure to Btk decreased the hemocyte Counts and reduced PO activity of Bt-RS larvae. Hemolymph protein concentrations also declined significantly in the susceptible larvae continually exposed to Btk. Seven peptides with antibacterial activity were identified in the hemolymph of Bt-RS larvae after exposure to Btk and five Were found in the Bt-R larvae. When exposed to a low level Bt challenge the susceptible strain increases in tolerance and there are concomitant reductions in hemolymph protein concentrations, PO activity and the number of circulating hemocytes. (C) 2008 Elsevier Inc. All rights reserved. DOI
165. Hall, LA; Palsboll, PJ; Beissinger, SR; Harvey, JT; Berube, M; Raphael, MG; Nelson, SK; Golightly, RT; Mcfarlane-Tranquilla, L; Newman, SH; Peery, MZ.Characterizing dispersal patterns in a threatened seabird with limited genetic structure.Molecular Ecology, 2009, 18: 5074-5085 Characterizing dispersal patterns in a threatened seabird with limited genetic structure
MURRELET BRACHYRAMPHUS-MARMORATUS; SEX-BIASED DISPERSAL; SOURCE-SINK DYNAMICS; MARBLED MURRELET; CATHARACTA-MACCORMICKI; MULTILOCUS GENOTYPES; POPULATION-STRUCTURE; ASSIGNMENT METHODS; SIMULATION; CONSERVATION
Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age classes. We demonstrate that assignment methods can be rigorously used to characterize dispersal patterns in a marbled murrelet (Brachyramphus marmoratus) population from central California that numbers approximately 600 individuals and is only moderately differentiated (F-ST similar to 0.03) from larger populations to the north. We used coalescent simulations to select a significance level that resulted in a low and approximately equal expected number of type I and II errors and then used this significance level to identify a population of origin for 589 individuals genotyped at 13 microsatellite loci. The proportion of migrants in central California was greatest during winter when 83% of individuals were classified as migrants compared to lower proportions during the breeding (6%) and post-breeding (8%) seasons. Dispersal was also biased toward young and female individuals, as is typical in birds. Migrants were rarely members of parent-offspring pairs, suggesting that they contributed few young to the central California population. A greater number of migrants than expected under equilibrium conditions, a lack of individuals with mixed ancestry, and a small number of potential source populations (two), likely allowed us to use assignment methods to rigorously characterize dispersal patterns for a population that was larger and less differentiated than typically thought required for the identification of migrants. DOI
164. Hart, MW; Grosberg, RK.Caterpillars did not evolve from onychophorans by hybridogenesis.Proceedings of the National Academy of Sciences of the United States of America, 2009, 106: 19906-19909 Caterpillars did not evolve from onychophorans by hybridogenesis
MARINE-INVERTEBRATES; LIFE-CYCLES; GENOME; LARVAE; EVOLUTION; ADAPTATION; ORIGINS
The evolution and loss of distinctive larval forms in animal life cycles have produced complex patterns of similarity and difference among life-history stages and major animal lineages. One example of this similarity is the morphological forms of Onychophora (velvet worms) and the caterpillar-like larvae of some insects. Williamson [(2009) Proc Natl Acad Sci USA 106: 15786-15790] has made the astonishing and unfounded claim that the ancestors of the velvet worms directly gave rise to insect caterpillars via hybridization and that evidence of this ancient "larval transfer'' could be found in comparisons among the genomes of extant onychophorans, insects with larvae, and insects without larvae. Williamson has made a series of predictions arising from his hypothesis and urged genomicists to test them. Here, we use data already in the literature to show these predictions to be false. Hybridogenesis between distantly related animals does not explain patterns of morphological and life-history evolution in general, and the genes and genomes of animals provide strong evidence against hybridization or larval transfer between a velvet worm and an insect in particular. DOI
163. James, T; Gowan, EJ; Hutchinson, I; Clague, JJ; Barrie, JV; Conway, KW.Sea-level change and paleogeographic reconstructions, southern Vancouver Island, British Columbia, Canada.Quat. Sci. Rev., 2009, 28: 1200-1216 Sea-level change and paleogeographic reconstructions, southern Vancouver Island, British Columbia, Canada
Forty-eight new and previously published radiocarbon ages constrain deglacial and postglacial sea levels on southern Vancouver Island, British Columbia. Sea level fell rapidly from its high stand of about +75 m elevation just before 14000 cal BP (12000 radiocarbon yrs BP) to below the present shoreline by 13 200 cal BP (11400 radiocarbon years BP). The sea fell below its present level 1000 years later in the central Strait of Georgia and 2000 years later in the northern Strait of Georgia, reflecting regional differences in ice sheet retreat and downwasting. Direct observations only constrain the low stand to be below -11 m and above -40 m. Analysis of the crustal isostatic depression with equations utilizing exponential decay functions appropriate to the Cascadia subduction zone, however, places the low stand at -30 +/- 5 m at about 11200 cal BP (9800 BP). The inferred low stand for southern Vancouver Island, when compared to the sea-level curve previously derived for the central Strait of Georgia to the northwest, generates differential isostatic depression that is consistent with the expected crustal response between the two regions. Morphologic and sub-bottom features previously interpreted to indicate a low stand of -50 to -65 m are re-evaluated and found to be consistent with a low stand of -30 +/- 5 m. Submarine banks in eastern Juan de Fuca Strait were emergent at the time of the low stand, but marine passages persisted between southern Vancouver island and the mainland. The crustal uplift presently occurring in response to the Late Pleistocene collapse of the southwestern sector of the Cordilleran Ice Sheet amounts to about 0.1 mm/yr. The small glacial isorstatic adjustment rate is a consequence of low-viscosity mantle in this tectonically active region. Crown Copyright (C) 2008 Published by Elsevier Ltd. All rights reserved. DOI
162. JANSSEN, M.H., ARCESE, P., KYSER, T.K., BERTRAM, D.F., MCFARLANE TRANQUILLA, L., WILLIAMS, T.D. & NORRIS, R.D.Pre-breeding diet, condition, and timing of breeding in a threatened seabird, the Marbled Murrelet Brachyramphus marmoratus.Marine Ornithology 37: 33-40., 2009, Pre-breeding diet, condition, and timing of breeding in a threatened seabird, the Marbled Murrelet Brachyramphus marmoratus.
Murrelets; Marbled Murrelets;
Marbled Murrelets Brachyramphus marmoratus are small, threatened seabirds that nest in old growth coniferous forests along the west coast of North America and spend most of their lives in nearshore waters. Recent evidence suggests that long term declines in pre-breeding trophic feeding level may be associated with reduced reproductive success. To test the hypothesis that pre-breeding trophic feeding level positively influences breeding success, we investigated relationships between timing of breeding, female body condition, and pre-breeding trophic feeding level. We predicted that females feeding on higher trophic level prey prior to breeding would be in better condition, and initiate egg production earlier, than females feeding on lower trophic level prey. Egg producing females were identified based on elevated yolk precursor (vitellogenin) levels, and diet composition was inferred using stable-carbon (δ13C) and -nitrogen (δ15N) analysis of murrelet and prey tissues during the pre-breeding seasons of 1999, 2000, 2006, and 2007 in Desolation Sound, British Columbia. Contrary to our predictions, females feeding on a higher proportion of low trophic level prey in 2007 were in better condition and more likely to produce an egg early in the breeding season. However, differences in pre-breeding diet between egg-producing females and non-egg producers were not consistent among years. Although our results suggest that low trophic level prey in pre-breeding diet promoted egg production and breeding success in 2007, this was likely not the case in others years studied. To reconcile results presented here and previous work on diet composition and breeding success in the Marbled Murrelet, we propose an alternative hypothesis of diet quality incorporating optimal foraging theory, whereby the net energy gain from feeding on a prey type is a function of its relative availability. PDF
161. Keever, CC; Sunday, J; Puritz, JB; Addison, JA; Toonen, RJ; Grosberg, RK; Hart, MW.DISCORDANT DISTRIBUTION OF POPULATIONS AND GENETIC VARIATION IN A SEA STAR WITH HIGH DISPERSAL POTENTIAL.Evolution, 2009, 63: 3214-3227 DISCORDANT DISTRIBUTION OF POPULATIONS AND GENETIC VARIATION IN A SEA STAR WITH HIGH DISPERSAL POTENTIAL
LIFE-HISTORY; MAXIMUM-LIKELIHOOD; LARVAL DISPERSAL; MARINE FISH; CONTRASTING PATTERNS; INTEGRATED SOFTWARE; SEQUENCE ALIGNMENT; STATISTICAL TESTS; BRITISH-COLUMBIA; SPECIES COMPLEX
Patiria miniata, a broadcast-spawning sea star species with high dispersal potential, has a geographic range in the intertidal zone of the northeast Pacific Ocean from Alaska to California that is characterized by a large range gap in Washington and Oregon. We analyzed spatial genetic variation across the P. miniata range using multilocus sequence data (mtDNA, nuclear introns) and multilocus genotype data (microsatellites). We found a strong phylogeographic break at Queen Charlotte Sound in British Columbia that was not in the location predicted by the geographical distribution of the populations. However, this population genetic discontinuity does correspond to previously described phylogeographic breaks in other species. Northern populations from Alaska and Haida Gwaii were strongly differentiated from all southern populations from Vancouver Island and California. Populations from Vancouver Island and California were undifferentiated with evidence of high gene flow or very recent separation across the range disjunction between them. The surprising and discordant spatial distribution of populations and alleles suggests that historical vicariance (possibly caused by glaciations) and contemporary dispersal barriers (possibly caused by oceanographic conditions) both shape population genetic structure in this species. DOI
160. Korup, O; Clague, JJ.Natural hazards, extreme events, and mountain topography.Quat. Sci. Rev., 2009, 28: 977-990 Natural hazards, extreme events, and mountain topography
The hazard of any natural process can be expressed as a function of its magnitude and the annual probability of its occurrence in a particular region. Here we expand on the hypothesis that natural hazards have size-frequency relationships that in parts resemble inverse power laws. We illustrate that these trends apply to extremely large events, such as mega-land slides, huge volcanic debris avalanches, and outburst flows from failures of natural dams. We review quantitative evidence that supports the important contribution of extreme events to landscape development in mountains throughout the world, and propose that their common underreporting in the Quaternary record may lead to substantial underestimates of mean process rates. We find that magnitude-frequency relationships provide a link between Quaternary science and natural hazard research, with a degree of synergism and societal importance that neither discipline alone can deliver. Quaternary geomorphology, stratigraphy, and geochronology allow the reconstruction of times, magnitudes, and frequencies of extreme events, whereas natural hazard research raises public awareness of the importance of reconstructing events that have not happened historically, but have the potential to cause extreme destruction and loss of life in the future. (C) 2009 Elsevier Ltd. All rights reserved. DOI
159. Magnuson-Ford, K; Ingram, T; Redding, DW; Mooers, AO.Rockfish (Sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing.Biological Conservation, 2009, 142: 1787-1796 Rockfish (Sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing
MARINE FISHES; PHYLOGENETIC DIVERSITY; EXTINCTION RISK; BODY-SIZE; FUNCTIONAL DIVERSITY; DIVERSIFICATION; SCORPAENIFORMES; REDESCRIPTION; RESURRECTION; SPECIATION
In an age of triage,me must prioritize species for conservation effort. Species more isolated on the tree of life are candidates for increased attention. The rockfish genus Sebastes is speciose (>100 spp.), morphologically and ecologically diverse and many species are heavily fished. We used a complete Sebastes phylogeny to calculate a measure of evolutionary isolation for each species and compared this to their morphology and imperilment. We found that evolutionarily isolated species in the northeast Pacific are both larger-bodied and, independent of body size, morphologically more distinctive. We examined extinction risk within rockfish using a compound measure of each species' intrinsic vulnerability to overfishing and categorizing species as commercially fished or not. Evolutionarily isolated species in the northeast Pacific are more likely to be fished, and, due to their larger sizes and to life history traits such as long lifespan and slow maturation rate, they are also intrinsically more vulnerable to overfishing. Finally, the set of northeast Pacific species that are both fished and most intrinsically vulnerable to fishing are among the most evolutionarily distinctive. These findings suggest that, at least for this clade, extra attention should be paid to evolutionary distinctiveness when prioritizing species for conservation. (C) 2009 Elsevier Ltd. All rights reserved. DOI
158. Menendez, A; Arena, ET; Guttman, JA; Thorson, L; Vallance, BA; Vogl, W; Finlay, BB.Salmonella Infection of Gallbladder Epithelial Cells Drives Local Inflammation and Injury in a Model of Acute Typhoid Fever.Journal of Infectious Diseases, 2009, 200: 1703-1713 Salmonella Infection of Gallbladder Epithelial Cells Drives Local Inflammation and Injury in a Model of Acute Typhoid Fever
ACUTE ACALCULOUS CHOLECYSTITIS; IN-VIVO; PEYERS-PATCHES; BILIARY-TRACT; TYPHIMURIUM; BILE; MACROPHAGES; RESISTANCE; IDENTIFICATION; PERFORATION
The gallbladder is often colonized by Salmonella during typhoid fever, yet little is known about bacterial pathogenesis in this organ. With use of a mouse model of acute typhoid fever, we demonstrate that Salmonella infect gallbladder epithelial cells in vivo. Bacteria in the gallbladder showed a unique behavior as they replicated within gallbladder epithelial cells and remained confined to those cells without translocating to the mucosa. Infected gallbladders showed histopathological damage characterized by destruction of the epithelium and massive infiltration of neutrophils, accompanied by a local increase of proinflammatory cytokines. Damage was determined by the ability of Salmonella to invade gallbladder epithelial cells and was independent of high numbers of replication-competent, although invasion-deficient, bacteria in the lumen. Our results establish gallbladder epithelial cells as a novel niche for in vivo replication of Salmonella and reveal the involvement of these cells in the pathogenesis of Salmonella in the gallbladder during the course of acute typhoid fever. DOI
157. Menounos, B; Osborn, G; Clague, JJ; Luckman, BH.Latest Pleistocene and Holocene glacier fluctuations in western Canada.Quat. Sci. Rev., 2009, 28: 2049-2074 Latest Pleistocene and Holocene glacier fluctuations in western Canada
We summarize evidence of the latest Pleistocene and Holocene glacier fluctuations in the Canadian Cordillera. Our review focuses primarily on studies completed after 1988, when the first comprehensive review of such evidence was published. The Cordilleran ice sheet reached its maximum extent about 16 ka and then rapidly decayed. Some lobes of the ice sheet, valley glaciers, and cirque glaciers advanced one or more times between 15 and 11 ka. By 11 ka, or soon thereafter, glacier cover in the Cordillera was no more extensive than at the end of the 20th century. Glaciers were least extensive between 11 and 7 ka. A general expansion of glaciers began as early as 8.4 ka when glaciers overrode forests in the southern Coast Mountains; it culminated with the climactic advances of the Little Ice Age. Holocene glacier expansion was not continuous, but rather was punctuated by advances and retreats on a variety of timescales. Radiocarbon ages of wood collected from glacier forefields reveal six major periods of glacier advance: 8.59-8.18, 7.36-6.45, 4.40-3.97, 3.54-2.77, 1.71-1.30 ka, and the past millennium. Tree-ring and lichenometric dating shows that glaciers began their Little Ice Age advances as early as the 11th century and reached their maximum Holocene positions during the early 18th or mid-19th century. Our data confirm a previously suggested pattern of episodic but successively greater Holocene glacier expansion from the early Holocene to the climactic advances of the Little Ice Age, presumably driven by decreasing summer insolation throughout the Holocene. Proxy climate records indicate that glaciers advanced during the Little Ice Age in response to cold conditions that coincided with times of sunspot minima. Priority research required to further advance our understanding of late Pleistocene and Holocene glaciation in western Canada includes constraining the age of late Pleistocene moraines in northern British Columbia and Yukon Territory, expanding the use of cosmogenic surface exposure dating techniques, using multi-proxy paleoclimate approaches, and directing more of the research effort to the northern Canadian Cordillera. (C) 2008 Elsevier Ltd. All rights reserved. DOI
156. Mitchell, MGE; Cahill, JF; Hik, DS.Plant interactions are unimportant in a subarctic-alpine plant community.Ecology, 2009, 90: 2360-2367 Plant interactions are unimportant in a subarctic-alpine plant community
Artemisia norvegica; Carex consimilis; community structure; competition; facilitation; importance; intensity; plant interactions; regression trees; subarctic-alpine; Yukon, Canada
We investigated whether plant interaction intensity in a subarctic-alpine meadow is important for determining community structure and species abundance. Using two common species as phytometers, we measured interaction intensity using a neighbor removal approach. Eight biotic and abiotic variables known to influence species abundance and community structure were measured, with regression trees used to examine how plant interactions and the biotic and abiotic variables were related to species evenness, richness, and phytometer spatial cover. A range of interactions was present, with both strong competition and facilitation present over small-scale abiotic and biotic gradients. Despite the variation in interaction intensity, it was generally unrelated to either community structure or phytometer cover. In other words, plant interactions were intense in many cases but were not important to community structure. This may be due to the prevalence of clonal species in this system and the influence of previous year's interactions on plant survival and patterns of community structure. These results also suggest how conflicting theories of the role of competition in unproductive environments may be resolved. Our findings suggest that plant interactions may be intense in reducing individual growth, while simultaneously not important in the context of community structure. Plant interactions need to be viewed and tested relative to other factors and stresses to accurately evaluate their importance in plant communities, with continued differentiation between the intensity of plant interactions and their relative importance in communities. DOI
155. Paddack, MJ; Reynolds, JD; Aguilar, C; Appeldoorn, RS; Beets, J; Burkett, EW; Chittaro, PM; Clarke, K; Esteves, R; Fonseca, AC; Forrester, GE; Friedlander, AM; Garcia-Sais, J; Gonzalez-Sanson, G; Jordan, LKB; McClellan, DB; Miller, MW; Molloy, PP; Mumby, PJ; Nagelkerken, I; Nemeth, M; Navas-Camacho, R; Pitt, J; Polunin, NVC; Reyes-Nivia, MC; Robertson, DR; Rodriguez-Ramirez, A; Salas, E; Smith, SR; Spieler, RE; Steele, MA; Williams, ID; Wormald, CL; Watkinson, AR; Côté, IM.Recent Region-wide Declines in Caribbean Reef Fish Abundance.Current Biology, 2009, 19: 590-595 Recent Region-wide Declines in Caribbean Reef Fish Abundance
GREAT-BARRIER-REEF; MASS MORTALITY; CORAL-REEFS; DIADEMA-ANTILLARUM; TROPHIC CASCADES; MARINE RESERVES; PROTECTED AREAS; COMMUNITIES; POPULATIONS; ECOSYSTEMS
Profound ecological changes are occurring on coral reefs throughout the tropics [1-3], with marked coral cover losses and concomitant algal increases, particularly in the Caribbean region [4]. Historical declines in the abundance of large Caribbean reef fishes likely reflect centuries of overexploitation [5-7]. However, effects of drastic recent degradation of reef habitats on reef fish assemblages have yet to be established. By using meta.-analysis, we analyzed time series of reef fish density obtained from 48 studies that include 318 reefs across the Caribbean and span the time period 1955-2007. Our analyses show that overall reef fish density has been declining significantly for more than a decade, at rates that are consistent across all subregions of the Caribbean basin (2.7% to 6.0% loss per year) and in three of six trophic groups. Changes in fish density over the past half-century are modest relative to concurrent changes in benthic cover on Caribbean reefs. However, the recent significant decline in overall fish abunclance and its consistency across several trophic groups. and among both fished and nonfished species indicate that Caribbean fishes have begun to respond negatively to habitat degradation. DOI
154. Plunkett, RM; Murray, SI; Lowenberger, CA.Generation and characterization of the antibacterial activity of a novel hybrid antimicrobial peptide comprising functional domains from different insect cecropins.Canadian Journal of Microbiology, 2009, 55: 520-528 Generation and characterization of the antibacterial activity of a novel hybrid antimicrobial peptide comprising functional domains from different insect cecropins
ESCHERICHIA-COLI; GENE-REGULATION; AEDES-AEGYPTI; EXPRESSION; DROSOPHILA; CLONING; MOSQUITO; IMMUNITY; PURIFICATION; HEMOLYMPH
The search for new antimicrobial compounds involves finding novel sources of chemotherapeutic compounds or manipulating and combining structures from existing molecules. Small antimicrobial peptides (AMPs) are components of innate immune defenses characterized in greatest detail in insect-derived AMPs. We have generated hybrid AMPs (hAMPs) by combining functional motifs from different insect AMPs as a proof of principle that we can generate molecules with lower minimum inhibitory concentrations, and with different activity and target specificity than either parent molecule. A two-helix, cecropin-like hAMP was created by linking the N-terminal a helix of cecropin A from Aedes aegypti to the C-terminal a helix of cecropin A1 from Drosophila melanogaster. This molecule exhibits antibacterial activity at sub-micromolar concentrations with a target specificity that differs from either parent molecule. Antibacterial activity of the hybrid molecule was found to be greater against Gram-negative than Gram-positive bacteria. No hemolysis was observed in sheep red blood cells exposed to concentrations up to 50 mu mol/L, suggesting the peptide is not detrimental to eukaryotic cells. DOI
153. Schlotterer, A; Kukudov, G; Bozorgmehr, F; Hutter, H; Du, XL; Oikonomou, D; Ibrahim, Y; Pfisterer, F; Rabbani, N; Thornalley, P; Sayed, A; Fleming, T; Humpert, P; Schwenger, V; Zeier, M; Hamann, A; Stern, D; Brownlee, M; Bierhaus, A; Nawroth, P; Morcos, M.C-elegans as Model for the Study of High Glucose-Mediated Life Span Reduction.Diabetes, 2009, 58: 2450-2456 C-elegans as Model for the Study of High Glucose-Mediated Life Span Reduction
CAENORHABDITIS-ELEGANS; GLYOXALASE SYSTEM; DAF-16; METHYLGLYOXAL; GENES
OBJECTIVE-Establishing Caenorhabditis elegans as a model for glucose toxicity-mediated life span reduction. RESEARCH DESIGN AND METHODS-C. elegans were maintained to achieve glucose concentrations resembling the hyperglycemic conditions in diabetic patients. The effects of high glucose on life span, glyoxalase-1 activity, advanced glycation end products (AGEs), and reactive oxygen species (ROS) formation and on mitochondrial function were studied. RESULTS-High glucose conditions reduced mean life span from 18.5 +/- 0.4 to 16.5 +/- 0.6 days and maximum life span from 25.9 +/- 0.4 to 23.2 +/- 0.4 days, independent of glucose effects on cuticle or bacterial metabolization of glucose. The formation of methylglyoxal-modified mitochondrial proteins and ROS was significantly increased by high glucose conditions and reduced by mitochondrial uncoupling and complex IIIQo inhibition. Overexpression of the methylglyoxal-detoxifying enzyme glyoxalase-1 attenuated the life-shortening effect of glucose by reducing AGE accumulation (by 65%) and ROS formation (by 50%) and restored mean (16.5 +/- 0.6 to 20.6 +/- 0.4 days) and maximum life span (23.2 +/- 0.4 to 27.7 +/- 2.3 days). In contrast, inhibition of glyoxalase-1 by RNAi further reduced mean (16.5 +/- 0.6 to 13.9 +/- 0.7 days) and maximum life span (23.2 +/- 0.4 to 20.3 +/- 1.1 days). The life span reduction by glyoxalase-1 inhibition was independent from the insulin signaling pathway because high glucose conditions also affected daf-2 knockdown animals in a similar manner. CONCLUSIONS-C. elegans is a suitable model organism to study glucose toxicity, in which high glucose conditions limit the life span by increasing ROS formation and AGE modification of mitochondrial proteins in a daf-2 independent manner. Most importantly, glucose toxicity can be prevented by improving glyoxalase-l-dependent methylglyoxal detoxification or preventing mitochondrial dysfunction. Diabetes 58:2450-2456, 2009 DOI
152. Schwander, T; Crespi, BJ.MULTIPLE DIRECT TRANSITIONS FROM SEXUAL REPRODUCTION TO APOMICTIC PARTHENOGENESIS IN TIMEMA STICK INSECTS.Evolution, 2009, 63: 84-103 MULTIPLE DIRECT TRANSITIONS FROM SEXUAL REPRODUCTION TO APOMICTIC PARTHENOGENESIS IN TIMEMA STICK INSECTS
CRISTINAE WALKING-STICKS; DROSOPHILA-MERCATORUM; PHYLOGENETIC-RELATIONSHIPS; GEOGRAPHIC PARTHENOGENESIS; LEAF BEETLES; GENE FLOW; EVOLUTION; SELECTION; HYBRIDIZATION; ADAPTATION
Transitions from sexual reproduction to parthenogenesis may occur along multiple evolutionary pathways and involve various cytological mechanisms to produce diploid eggs. Here, we investigate routes to parthenogenesis in Timema stick insects, a genus comprising five obligate parthenogens. By combining information from microsatellites and karyotypes with a previously published mitochondrial phylogeny, we show that all five parthenogens likely evolved spontaneously from sexually reproducing species, and that the sexual ancestor of one of the five parthenogens was probably of hybrid origin. The complete maintenance of heterozygosity between generations in the five parthenogens strongly suggests that eggs are produced by apomixis. Virgin females of the sexual species were also able to produce parthenogenetic offspring, but these females produced eggs by automixis. High heterozygosity levels stemming from conserved ancestral alleles in the parthenogens suggest, however, that automixis has not generated the current parthenogenetic Timema lineages but that apomixis appeared abruptly in several sexual species. A direct transition from sexual reproduction to (at least functional) apomixis results in a relatively high level of allelic diversity and high efficiency for parthenogenesis. Because both of these traits should positively affect the demographic success of asexual lineages, spontaneous apomixis may have contributed to the origin and maintenance of asexuality in Timema. DOI
151. Schwander, T; Crespi, BJ.Twigs on the tree of life? Neutral and selective models for integrating macroevolutionary patterns with microevolutionary processes in the analysis of asexuality.Molecular Ecology, 2009, 18: 28-42 Twigs on the tree of life? Neutral and selective models for integrating macroevolutionary patterns with microevolutionary processes in the analysis of asexuality
NEW-ZEALAND SNAIL; MITOCHONDRIAL-DNA SEQUENCES; EVOLUTIONARY DEAD-END; GEOGRAPHICAL PARTHENOGENESIS; PHYLOGENETIC-RELATIONSHIPS; DELETERIOUS MUTATIONS; BDELLOID ROTIFERS; POTAMOPYRGUS-ANTIPODARUM; MOLECULAR PHYLOGENETICS; ENDOSYMBIOTIC BACTERIA
Neutral models characterize evolutionary or ecological patterns expected in the absence of specific causal processes, such as natural selection or ecological interactions. In this study, we describe and evaluate three neutral models that can, in principle, help to explain the apparent 'twigginess' of asexual lineages on phylogenetic trees without involving the negative consequences predicted for the absence of recombination and genetic exchange between individuals. Previously, such phylogenetic twiggyness of asexual lineages has been uncritically interpreted as evidence that asexuality is associated with elevated extinction rates and thus represents an evolutionary dead end. Our first model uses simple phylogenetic simulations to illustrate that, with sexual reproduction as the ancestral state, low transition rates to stable asexuality, or low rates of ascertained 'speciation' in asexuals, can generate twiggy distributions of asexuality, in the absence of high extinction rates for asexual lineages. The second model, developed by Janko et al. (2008), shows that a dynamic equilibrium between origins and neutral losses of asexuals can, under some conditions, generate a relatively low mean age of asexual lineages. The third model posits that the risk of extinction for asexual lineages may be higher than that of sexuals simply because asexuals inhabit higher latitudes or altitudes, and not due to effects of their reproductive systems. Such neutral models are useful in that they allow quantitative evaluation of whether empirical data, such as phylogenetic and phylogeographic patterns of sex and asexuality, indeed support the idea that asexually reproducing lineages persist over shorter evolutionary periods than sexual lineages, due to such processes as mutation accumulation, slower rates of adaptive evolution, or relatively lower levels of genetic variability. DOI
150. Silverman, MA; Leroux, MR.Intraflagellar transport and the generation of dynamic, structurally and functionally diverse cilia.Trends Cell Biol., 2009, 19: 306-316 Intraflagellar transport and the generation of dynamic, structurally and functionally diverse cilia
Cilia are organelles that project from most eukaryotic organisms and cell types. Their pervasiveness stems from having remarkably versatile propulsive and sensory functions, which in humans are recognized to have essential roles in physiology and development. Under-appreciated, however, are their diverse ultrastructures and typically bipartite organization consisting of doublet and singlet microtubules. Moreover, the overall shapes of the membrane-ensheathed cilia are varied, as exemplified by differences between hair-like olfactory cilia and rod- or cone-shaped photoreceptor connecting cilia-outer segments. Although cell-specific transcriptional programs are evidently crucial in establishing ciliary morphological specialization, few players directly involved in generating such diversity are known. Recent findings suggest that at least two molecular motors (kinesin-II and OSM-3/KIF17) can differentially mobilize the intraflagellar transport machinery required for ciliogenesis and, presumably, different cargo to help generate dynamic, structurally and functionally distinct cilia. DOI PubMed
149. Ursic-Bedoya, R; Buchhop, J; Lowenberger, C.Cloning and characterization of Dorsal homologues in the hemipteran Rhodnius prolixus.Insect Molecular Biology, 2009, 18: 681-689 Cloning and characterization of Dorsal homologues in the hemipteran Rhodnius prolixus
NF-KAPPA-B; MOSQUITO AEDES-AEGYPTI; IMMUNE-RESPONSE; TRANSCRIPTION FACTOR; ANOPHELES-GAMBIAE; CHAGAS-DISEASE; FACTOR RELISH; DROSOPHILA; GENE; DEFENSE
Rhodnius prolixus is an ancient haematophagous hemipteran insect capable of mounting a powerful immune response. This response is transcriptionally regulated in part by transcription factors of the Rel/Nuclear Factor kappa B (Rel/NF-kappa B) family. We have cloned and characterized three members of this transcription factor family in this insect. Dorsal 1A is primarily expressed in early developmental stages. In contrast, dorsal 1B and 1C, both differentially spliced products of dorsal 1A, are expressed primarily in the adult fat body in response to septic injury, suggesting their exclusive role in immunity. Additionally, we identified putative kappa B binding sites in the 5' upstream regions of target genes known to be involved in the innate immune response of insects. DOI
148. Valdez, Y; Grassl, GA; Guttman, JA; Coburn, B; Gros, P; Vallance, BA; Finlay, BB.Nramp1 drives an accelerated inflammatory response during Salmonella-induced colitis in mice.Cellular Microbiology, 2009, 11: 351-362 Nramp1 drives an accelerated inflammatory response during Salmonella-induced colitis in mice
ENTERICA SEROTYPE TYPHIMURIUM; SLC11A1 FORMERLY NRAMP1; NATURAL-RESISTANCE; SEROVAR TYPHIMURIUM; INTRACELLULAR PARASITES; DENDRITIC CELLS; BCG/ITY/LSH LOCUS; CANDIDA-ALBICANS; GENETIC-CONTROL; C57BL/6J MICE
A recently developed model for enterocolitis in mice involves pre-treatment with the antibiotic streptomycin prior to infection with Salmonella enterica serovar Typhimurium (S. Typhimurium). The contribution of Nramp1/Slc11a1 protein, a critical host defence mechanism against S. Typhimurium, to the development of inflammation in this model has not been studied. Here, we analysed the impact of Nramp1 expression on the early development of colitis using isogenic Nramp1(+/+) and Nramp1(-/-) mice. We hypothesized that Nramp1 acts by rapidly inducing an inflammatory response in the gut mucosa creating an antibacterial environment and limiting spread of S. Typhimurium to systemic sites. We observed that Nramp1(+/+) mice showed lower numbers of S. Typhimurium in the caecum compared with Nramp1(-/-) mice at all times analysed. Acute inflammation was much more pronounced in Nramp1(+/+) mice 1 day after infection. The effect of Nramp1 on development of colitis was characterized by higher secretion of the pro-inflammatory cytokines IFN-gamma, TNF-alpha and MIP-1 alpha and a massive infiltration of neutrophils and macrophages, compared with Nramp1(-/-) animals. These data show that an early and rapid inflammatory response results in protection against pathological effects of S. Typhimurium infection in Nramp1(+/+) mice. DOI
147. Vergnon, R; Dulvy, NK; Freckleton, RP.Niches versus neutrality: uncovering the drivers of diversity in a species-rich community.Ecology Letters, 2009, 12: 1079-1090 Niches versus neutrality: uncovering the drivers of diversity in a species-rich community
ABUNDANCE DISTRIBUTIONS; RELATIVE ABUNDANCE; BIODIVERSITY; PHYTOPLANKTON; COEXISTENCE; DYNAMICS; PLANKTON; ECOLOGY; MODEL; SIZE
Ecological models suggest that high diversity can be generated by purely niche-based, purely neutral or by a mixture of niche-based and neutral ecological processes. Here, we compare the degree to which four contrasting hypotheses for coexistence, ranging from niche-based to neutral, explain species richness along a body mass niche axis. We derive predictions from these hypotheses and confront them with species body-mass patterns in a highly sampled marine phytoplankton community. We find that these patterns are consistent only with a mechanism that combines niche and neutral processes, such as the emergent neutrality mechanism. In this work, we provide the first empirical evidence that a niche-neutral model can explain niche space occupancy pattern in a natural species-rich community. We suggest this class of model may be a useful hypothesis for the generation and maintenance of species diversity in other size-structured communities. DOI
146. Waliwitiya, R., Kennedy, C., and Lowenberger, C.Larvicidal and antiovipositional activity of monoterpenoids and rosemary oil to the yellow fever mosquito Aedes aegypti (Diptera: Culicidae).Pest Management Science, 2009, 65: 241-248. Larvicidal and antiovipositional activity of monoterpenoids and rosemary oil to the yellow fever mosquito Aedes aegypti (Diptera: Culicidae)
Aedes aegypti, acute toxicity, essential oils, larvicides, monoterpenoids, oviposition, piperonyl butoxide
Aedes aegypti L. is the major vector of dengue fever and dengue hemorrhagic fever. In an effort to find effective tools for control programs to reduce mosquito populations, the authors assessed the acute toxicities of 14 monoterpenoids, trans-anithole and the essential oil of rosemary against different larval stages of Ae. aegypti. The potential for piperonyl butoxide (PBO) to act as a synergist for these compounds to increase larvicidal activity was also examined, and the oviposition response of gravid Ae. aegypti females to substrates containing these compounds was evaluated in behavioral bioassays.
RESULTS: Pulegone, thymol, eugenol, trans-anithole, rosemary oil and citronellal showed high larvicidal activity against all larval stages of Ae. aegypti (LC50 values 10.3-40.8 mg L-1). The addition of PBO significantly increased the larvicidal activity of all test compounds (3-250-fold). Eugenol, citronellal, thymol, pulegone, rosemary oil and cymene showed oviposition deterrent and/or repellent activities, while the presence of borneol, camphor and -pinene increased the number of eggs laid in test containers.
CONCLUSIONS: This study quantified the lethal and sublethal effects of several phytochemical compounds against all larval stages of Aedes aegypti, providing information that ultimately may have potential in mosquito control programs through acute toxicity and/or the ability to alter reproductive behaviorsWebsite DOI
145. Wally, O; Jayaraj, J; Punja, ZK.Broad-spectrum disease resistance to necrotrophic and biotrophic pathogens in transgenic carrots (Daucus carota L.) expressing an Arabidopsis NPR1 gene.Planta, 2009, 231: 131-141 Broad-spectrum disease resistance to necrotrophic and biotrophic pathogens in transgenic carrots (Daucus carota L.) expressing an Arabidopsis NPR1 gene
SYSTEMIC ACQUIRED-RESISTANCE; FOLIAR FUNGAL PATHOGENS; DISPLAY ENHANCED RESISTANCE; SALICYLIC-ACID; DEFENSE RESPONSES; SCLEROTINIA-SCLEROTIORUM; SIGNALING PATHWAY; BOTRYTIS-CINEREA; NPR1-LIKE GENES; RICE
The development of transgenic plants highly resistant to a range of pathogens using traditional signal gene expression strategies has been largely ineffective. Modification of systemic acquired resistance (SAR) through the overexpression of a controlling gene such as NPR1 (non-expressor of PR genes) offers an attractive alternative for augmenting the plants innate defense system. The Arabidopsis (At) NPR1 gene was successfully introduced into 'Nantes Coreless' carrot under control of a CaMV 35S promoter and two independent transgenic lines (NPR1-I and NPR1-XI) were identified by Southern and Northern blot hybridization. Both lines were phenotypically normal compared with non-transformed carrots. Northern analysis did not indicate constitutive or spontaneous induction in carrot cultures of SAR-related genes (DcPR-1, 2, 4, 5 or DcPAL). The duration and intensity of expression of DcPR-1, 2 and 5 genes were greatly increased compared with controls when the lines were treated with purified cell wall fragments of Sclerotinia sclerotiorum as well as with 2,6-dichloroisonicotinic acid. The two lines were challenged with the necrotrophic pathogens Botrytis cinerea, Alternaria radicina and S. sclerotiorum on the foliage and A. radicina on the taproots. Both lines exhibited 35-50% reduction in disease symptoms on the foliage and roots when compared with non-transgenic controls. Leaves challenged with the biotrophic pathogen Erysiphe heraclei or the bacterial pathogen Xanthomonas hortorum exhibited 90 and 80% reduction in disease development on the transgenic lines, respectively. The overexpression of the SAR controlling master switch in carrot tissues offers the ability to control a wide range of different pathogens, for which there is currently little genetic resistance available. DOI
144. Wang, Y; Zhang, ZQ; Garbow, JR; Rowland, DJ; Lubet, RA; Sit, D; Law, F; You, M.Chemoprevention of Lung Squamous Cell Carcinoma in Mice by a Mixture of Chinese Herbs.Cancer Prevention Research, 2009, 2: 634-640 Chemoprevention of Lung Squamous Cell Carcinoma in Mice by a Mixture of Chinese Herbs
RANDOMIZED-TRIAL; BETA-CAROTENE; VITAMIN-A; CANCER; MODELS; EFFICACY; MATRINE
Antitumor B (ATB) is a Chinese herbal mixture of six plants. Previous studies have shown significant chemopreventive efficacy of ATB against human esophageal and lung cancers. We have recently developed a new mouse model for lung squamous cell carcinomas (SCC). In this study, lung SCC mouse model was characterized using small-animal imaging techniques (magnetic resonance imaging and computed tomography). ATB decreased lung SCC significantly (3.1-fold; P<0.05) and increased lung hyperplastic lesions by 2.4-fold (P<0.05). This observation suggests that ATB can block hyperplasia from progression to SCC. ATB tissue distribution was determined using matrine as a marker chemical. We found that ATB is rapidly absorbed and then distributes to various tissues including the lung. These results indicate that ATB is a potent chemopreventive agent against the development of mouse lung SCCs. DOI
143. Zhang, DP; Xiong, HL; Mennigen, JA; Popesku, JT; Marlatt, VL; Martyniuk, CJ; Crump, K; Cossins, AR; Xia, X; Trudeau, VL.Defining Global Neuroendocrine Gene Expression Patterns Associated with Reproductive Seasonality in Fish.PLOS One, 2009, 4 Defining Global Neuroendocrine Gene Expression Patterns Associated with Reproductive Seasonality in Fish
Background: Many vertebrates, including the goldfish, exhibit seasonal reproductive rhythms, which are a result of interactions between external environmental stimuli and internal endocrine systems in the hypothalamo-pituitary-gonadal axis. While it is long believed that differential expression of neuroendocrine genes contributes to establishing seasonal reproductive rhythms, no systems-level investigation has yet been conducted. Methodology/Principal Findings: In the present study, by analyzing multiple female goldfish brain microarray datasets, we have characterized global gene expression patterns for a seasonal cycle. A core set of genes (873 genes) in the hypothalamus were identified to be differentially expressed between May, August and December, which correspond to physiologically distinct stages that are sexually mature (prespawning), sexual regression, and early gonadal redevelopment, respectively. Expression changes of these genes are also shared by another brain region, the telencephalon, as revealed by multivariate analysis. More importantly, by examining one dataset obtained from fish in October who were kept under long-day-length photoperiod (16 h) typical of the springtime breeding season (May), we observed that the expression of identified genes appears regulated by photoperiod, a major factor controlling vertebrate reproductive cyclicity. Gene ontology analysis revealed that hormone genes and genes functionally involved in G-protein coupled receptor signaling pathway and transmission of nerve impulses are significantly enriched in an expression pattern, whose transition is located between prespawning and sexually regressed stages. The existence of seasonal expression patterns was verified for several genes including isotocin, ependymin II, GABA(A) gamma2 receptor, calmodulin, and aromatase b by independent samplings of goldfish brains from six seasonal time points and real-time PCR assays. Conclusions/Significance: Using both theoretical and experimental strategies, we report for the first time global gene expression patterns throughout a breeding season which may account for dynamic neuroendocrine regulation of seasonal reproductive development. DOI
141. Bisgrove, SR; Lee, YRJ; Liu, B; Peters, NT; Kropf, DL.The microtubule plus-end binding protein EB1 functions in root responses to touch and gravity signals in Arabidopsis.Plant Cell, 2008, 20: 396-410 The microtubule plus-end binding protein EB1 functions in root responses to touch and gravity signals in Arabidopsis
Microtubules function in concert with associated proteins that modify microtubule behavior and/or transmit signals that effect changes in growth. To better understand how microtubules and their associated proteins influence growth, we analyzed one family of microtubule-associated proteins, the END BINDING1 (EB1) proteins, in Arabidopsis thaliana (EB1a, EB1b, and EB1c). We find that antibodies directed against EB1 proteins colocalize with microtubules in roots, an observation that confirms previous reports using EB1-GFP fusions. We also find that T-DNA insertion mutants with reduced expression from EB1 genes have roots that deviate toward the left on vertical or inclined plates. Mutant roots also exhibit extended horizontal growth before they bend downward after tracking around an obstacle or after a 908 clockwise reorientation of the root. These observations suggest that leftward deviations in root growth may be the result of delayed responses to touch and/or gravity signals. Root lengths and widths are normal, indicating that the delay in bend formation is not due to changes in the overall rate of growth. In addition, the genotype with the most severe defects responds to low doses of microtubule inhibitors in a manner indistinguishable from the wild type, indicating that microtubule integrity is not a major contributor to the leftward deviations in mutant root growth. DOI
140. Crespi, B.Genomic imprinting in the development and evolution of psychotic spectrum conditions.Biological Reviews, 2008, 83: 441-493 Genomic imprinting in the development and evolution of psychotic spectrum conditions
schizophrenia; psychosis; autism; genomic imprinting; evolution; genomic conflict PRADER-WILLI-SYNDROME; BIPOLAR AFFECTIVE-DISORDER; PARENT-OF-ORIGIN; MATERNAL UNIPARENTAL DISOMY; FAMILY-BASED ASSOCIATION; SMITH-MAGENIS-SYNDROME; ATTENTION-DEFICIT/HYPERACTIVITY DISORDER; LINKED MENTAL-RETARDATION; GENOMEWIDE LINKAGE SCAN; FACTOR BDNF GENE
I review and evaluate genetic and genomic evidence salient to the hypothesis that the development and evolution of psychotic spectrum conditions have been mediated in part by alterations of imprinted genes expressed in the brain. Evidence from the genetics and genomics of schizophrenia, bipolar disorder, major depression, Prader-Willi syndrome, Klinefelter syndrome, and other neurogenetic conditions support the hypothesis that the etiologies of psychotic spectrum conditions commonly involve genetic and epigenetic imbalances in the effects of imprinted genes, with a bias towards increased relative effects from imprinted genes with maternal expression or other genes favouring maternal interests. By contrast, autistic spectrum conditions, including Kanner autism, Asperger syndrome, Rett syndrome, Turner syndrome, Angelman syndrome, and Beckwith-Wiedemann syndrome, commonly engender increased relative effects from paternally expressed imprinted genes, or reduced effects from genes favouring maternal interests. Imprinted-gene effects on the etiologies of autistic and psychotic spectrum conditions parallel the diametric effects of imprinted genes in placental and foetal development, in that psychotic spectrum conditions tend to be associated with undergrowth and relatively-slow brain development, whereas some autistic spectrum conditions involve brain and body overgrowth, especially in foetal development and early childhood. An important role for imprinted genes in the etiologies of psychotic and autistic spectrum conditions is consistent with neurodevelopmental models of these disorders, and with predictions from the conflict theory of genomic imprinting. DOI
139. Darling, ES; Côté, IM.Quantifying the evidence for ecological synergies.Ecology Letters, 2008, 11: 1278-1286 Quantifying the evidence for ecological synergies
meta-analysis, mortality, multiple stressors, non-additive effects, synergy.
There is increasing concern that multiple drivers of ecological change will interact synergistically to accelerate biodiversity loss. However, the prevalence and magnitude of these interactions remain one of the largest uncertainties in projections of future ecological change. We address this uncertainty by performing a meta-analysis of 112 published factorial experiments that evaluated the impacts of multiple stressors on animal mortality in freshwater, marine and terrestrial communities. We found that, on average, mortalities from the combined action of two stressors were not synergistic and this result was consistent across studies investigating different stressors, study organisms and life-history stages. Furthermore, only one-third of relevant experiments displayed truly synergistic effects, which does not support the prevailing ecological paradigm that synergies are rampant. However, in more than three-quarters of relevant experiments, the outcome of multiple stressor interactions was non-additive (i.e. synergies or antagonisms), suggesting that ecological surprises may be more common than simple additive effects.PDF DOI
138. Dashtgard, SE; Gingras, MK; Pemberton, SG.Grain-size controls on the occurrence of bioturbation.Paleogeogr. Paleoclimatol. Paleoecol., 2008, 257: 224-243 Grain-size controls on the occurrence of bioturbation
ichnology; neoichnology; bioturbation; Bay of Fundy; grain size; intertidal; gravel; conglomerate
Grain size and grain-size related stresses impart a significant influence on the ichnological character of marginal-marine deposits. This is evident on the New Brunswick coastline of the Bay of Fundy, Canada, where three coarse-grained marginal-marine deposits are studied to assess grain-size controls on the occurrence and type of bioturbation. Firm mud and sand substrates exhibit the greatest diversity and density of bioturbation (i.e., bioturbation intensity). The types of organisms colonizing sands and firm-mud substrates are variable; however, the resultant trace assemblages are similar. Thixotropic muds exhibit significantly reduced trace diversity and density relative to firm mud, reflecting the additional stress placed on the organisms by the relatively soupy consistency of the sediment. A significant change in the trace assemblage occurs when sediment caliber passes the gradational sand-fine gravel boundary. Four main conclusions can be drawn from this study. First, for mixed sand and gravel, fine gravel, and coarse-gravel deposits, the degree of bioturbation (diversity * density) decreases more rapidly onshore (across the intertidal zone) than is noted in sand or mud deposits. Second, there is a decrease in the degree of bioturbation with increasing grain size for substrates composed of sand-sized and larger clasts. Third, burrows in gravels tend to be lined and/or robust, likely to maintain a stable environment within the burrow. Fourth, in coarse-gravel substrates or substrates with a significant component of coarse gravel, burrows are developed between the clasts and tend to be more permanent structures (than those developed in sand or mud), which are generally continuously occupied. The degree of burrowing noted in these modem gravel deposits contrasts with the relative paucity of biogenic structures reported in conglomerates preserved in the rock record. Based on the intensity of burrowing observed in the gravels, we hypothesize that ancient marginal-marine conglomerates are likely bioturbated, but that these burrows are likely distorted during burial and compaction. (C) 2007 Elsevier B.V. All rights reserved. DOI
137. Dolgosheina, EV; Morin, RD; Aksay, G; Sahinalp, SC; Magrini, V; Mardis, ER; Mattsson, J; Unrau, PJ.Conifers have a unique small RNA silencing signature.RNA-Publ. RNA Soc., 2008, 14: 1508-1515 Conifers have a unique small RNA silencing signature
RNA silencing; Dicer (DCL); small RNA processing; plant evolution; gymnosperms
Plants produce small RNAs to negatively regulate genes, viral nucleic acids, and repetitive elements at either the transcriptional or post-transcriptional level in a process that is referred to as RNA silencing. While RNA silencing has been extensively studied across the different phyla of the animal kingdom (e. g., mouse, fly, worm), similar studies in the plant kingdom have focused primarily on angiosperms, thus limiting evolutionary studies of RNA silencing in plants. Here we report on an unexpected phylogenetic difference in the size distribution of small RNAs among the vascular plants. By extracting total RNA from freshly growing shoot tissue, we conducted a survey of small RNAs in 24 vascular plant species. We find that conifers, which radiated from the other seed-bearing plants; 260 million years ago, fail to produce significant amounts of 24-nucleotide (nt) RNAs that are known to guide DNA methylation and heterochromatin formation in angiosperms. Instead, they synthesize a diverse population of small RNAs that are exactly 21-nt long. This finding was confirmed by high-throughput sequencing of the small RNA sequences from a conifer, Pinus contorta. A conifer EST search revealed the presence of a novel Dicer-like (DCL) family, which may be responsible for the observed change in small RNA expression. No evidence for DCL3, an enzyme that matures 24-nt RNAs in angiosperms, was found. We hypothesize that the diverse class of 21-nt RNAs found in conifers may help to maintain organization of their unusually large genomes. DOI PubMed
136. Dong, KB; Maksakova, IA; Mohn, F; Leung, D; Appanah, R; Lee, S; Yang, HW; Lam, LL; Mager, DL; Schubeler, D; Tachibana, M; Shinkai, Y; Lorincz, MC.DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity.Embo J., 2008, 27: 2691-2701 DNA methylation in ES cells requires the lysine methyltransferase G9a but not its catalytic activity
chromatin; DNA methylation; ERV; H3K9 methylation; HP1 alpha
Histone H3K9 methylation is required for DNA methylation and silencing of repetitive elements in plants and filamentous fungi. In mammalian cells however, deletion of the H3K9 histone methyltransferases (HMTases) Suv39h1 and Suv39h2 does not affect DNA methylation of the endogenous retrovirus murine leukaemia virus, indicating that H3K9 methylation is dispensable for DNA methylation of retrotransposons, or that a different HMTase is involved. We demonstrate that embryonic stem (ES) cells lacking the H3K9 HMTase G9a show a significant reduction in DNA methylation of retrotransposons, major satellite repeats and densely methylated CpG-rich promoters. Surprisingly, demethylated retrotransposons remain transcriptionally silent in G9a(-/-) cells, and show only a modest decrease in H3K9me2 and no decrease in H3K9me3 or HP1 alpha binding, indicating that H3K9 methylation per se is not the relevant trigger for DNA methylation. Indeed, introduction of catalytically inactive G9a transgenes partially 'rescues' the DNA methylation defect observed in G9a(-/-) cells. Taken together, these observations reveal that H3K9me3 and HP1 alpha recruitment to retrotransposons occurs independent of DNA methylation in ES cells and that G9a promotes DNA methylation independent of its HMTase activity. DOI PubMed
135. Flowers, GE; Bjornsson, H; Geirsdottir, A; Miller, GH; Black, JL; Clarke, GKC.Holocene climate conditions and glacier variation in central Iceland from physical modelling and empirical evidence.Quat. Sci. Rev., 2008, 27: 797-813 Holocene climate conditions and glacier variation in central Iceland from physical modelling and empirical evidence
Lacustrine sediment cores from proglacial lake Hvitarvatn, central Iceland, reveal a detailed chronology of Holocene sedimentation, from which environmental conditions and the attendant fluctuations of Langjokull ice cap have been interpreted. We apply a numerical ice-sheet model to determine the climatic conditions under which the empirical reconstruction is glaciologically plausible. Modelling constraints are derived from core records of diatom concentration, benthic diatom fraction, and ice-rafted debris occurrence, as well as lake bottom morphology and the present-day ice-cap geometry. Holocene simulations driven by the NGRIP delta O-18 record that are consistent with the empirical constraints show the most extensive advance of Langjokull ice cap to be its most recent, beginning somewhere between 5 and 3 ka BP. Ice advance in response to the 8.2 ka BP cold event is followed by several thousand years of nearly ice-free conditions in the mid-Holocene. All simulations suggest that the maximum Holocene stand of the ice cap occurred during the Little Ice Age (LIA); those consistent with the constraints show little to no ice advance into Hvitarvatn before similar to 1 ka BP and indicate the lake area occupied by ice was much greater during the LIA than at any previous time. The most plausible simulation results were obtained for a maximum Holocene warming of 3-4 degrees C relative to the 1961-1990 reference, twice the Arctic average, and for Holocene Thermal Maximum (HTM) precipitation amounts comparable to or slightly greater than the modern. Reconciling the simulated subglacial discharge record to the empirically derived sediment volumes and emplacement times requires mean Holocene sediment concentrations of 0.8-1.6 kg m(-3). These estimates increase to 1.4-2.0 kg m(-3) when sedimentation rates are highest. (C) 2008 Published by Elsevier Ltd. DOI
132. Ikeda, DD; Duan, Y; Matsuki, M; Kunitomo, H; Hutter, H; Hedgecock, EM; Iino, Y.CASY-1, an ortholog of calsyntenins/alcadeins, is essential for learning in Caenorhabditis elegans.Proceedings of the National Academy of Sciences of the United States of America, 2008, 105: 5260-5265 CASY-1, an ortholog of calsyntenins/alcadeins, is essential for learning in Caenorhabditis elegans
ectodomain shedding; learning and memory
Calsyntenins/alcadeins are type I transmembrane proteins with two extracellular cadherin domains highly expressed in mammalian brain. They form a tripartite complex with X11/X11L and APP (amyloid precursor protein) and are proteolytically processed in a similar fashion to APP. Although a genetic association of calsyntenin-2 with human memory performance has recently been reported, physiological roles and molecular functions of the protein in the nervous system are poorly understood. Here, we show that CASY-1, the Caenorhabditis elegans ortholog of calsyntenins/alcadeins, is essential for multiple types of learning. Through a genetic screen, we found that casy-1 mutants show defects in salt chemotaxis learning. casy-1 mutants also show defects in temperature learning, olfactory adaptation, and integration of two sensory signals. casy-1 is widely expressed in the nervous system. Expression of casy-1 in a single sensory neuron and at the post-developmental stage is sufficient for its function in salt chemotaxis learning. The fluorescent protein-tagged ectodomain of CASY-1 is released from neurons. Moreover, functional domain analyses revealed that both cytoplasmic and transmembrane domains of this protein are dispensable, whereas the ectodomain, which contains the LG/LNS-like domain, is critically required for learning. These results suggest that learning is modulated by the released ectodomain of CASY-1. DOI
131. Jayaraj, J; Devlin, R; Punja, Z.Metabolic engineering of novel ketocarotenoid production in carrot plants.Transgenic Research, 2008, 17: 489-501 Metabolic engineering of novel ketocarotenoid production in carrot plants
beta-carotene ketolase; carotenoid pathway engineering; ketocarotenoids; astaxanthin; root pigmentation; biopharming
Carotenoids constitute a vast group of pigments that are ubiquitous throughout nature. Carrot (Daucus carota L.) roots provide an important source of dietary beta-carotene (provitamin A), alpha-carotene and lutein. Ketocarotenoids, such as canthaxanthin and astaxanthin, are produced by some algae and cyanobacteria but are rare in plants. Ketocarotenoids are strong antioxidants that are chemically synthesized and used as dietary supplements and pigments in the aquaculture and neutraceutical industries. We engineered the ketocarotenoid biosynthetic pathway in carrot tissues by introducing a beta-carotene ketolase gene isolated from the alga Haematococcus pluvialis. Gene constructs were made with three promoters (double CaMV 35S, Arabidopsis-ubiquitin, and RolD from Agrobacterium rhizogenes). The pea Rubisco small sub-unit transit peptide was used to target the enzyme to plastids in leaf and root tissues. The phosphinothricin acetyl transferase (bar) gene was used as a selectable marker. Following Agrobacterium-mediated transformation, 150 plants were regenerated and grown in a glasshouse. All three promoters provided strong root expression, while the double CaMV 35S and Ubiquitin promoters also had strong leaf expression. The recombinant ketolase protein was successfully targeted to the chloroplasts and chromoplasts. Endogenous expression of carrot beta-carotene hydroxylases was up-regulated in transgenic leaves and roots, and up to 70% of total carotenoids was converted to novel ketocarotenoids, with accumulation up to 2,400 mu g/g root dry weight. Astaxanthin, adonirubin, and canthaxanthin were most prevalent, followed by echinenone, adonixanthin and beta-cryptoxanthin. Our results show that carrots are suitable for biopharming ketocarotenoid production for applications to the functional food, neutraceutical and aquaculture industries. DOI
130. Katz, MJ; Sakai, K; Leznoff, DB.The use of aurophilic and other metal-metal interactions as crystal engineering design elements to increase structural dimensionality.Chem. Soc. Rev., 2008, 37: 1884-1895 The use of aurophilic and other metal-metal interactions as crystal engineering design elements to increase structural dimensionality
Research in the field of supramolecular chemistry has rapidly grown in recent years due to the generation of fascinating structural topologies and their associated physical properties. In order to rationally synthesize such high-dimensionality systems, several different classes of non-covalent intermolecular interactions in the crystal engineering toolbox can be utilized. Among these, attractive metallophilic interactions, such as those observed for d(10) gold(I), have been increasingly harnessed as a design element to synthesize functional high-dimensional systems. This tutorial review will explore the methods by which gold(I) and other d(10) and d(8) metal centres have been employed to increase structural dimensionality via the formation of metal-metal interactions. Physical and optical properties associated with metallophilicity-based supramolecular structures will also be highlighted. DOI PubMed
128. Lardeux, F; Tejerina, R; Aliaga, C; Ursic-Bedoya, R; Lowenberger, C; Chavez, T.Optimization of a semi-nested multiplex PCR to identify Plasmodium parasites in wild-caught Anopheles in Bolivia, and its application to field epidemiological studies.Transactions of the Royal Society of Tropical Medicine and Hygiene, 2008, 102: 485-492 Optimization of a semi-nested multiplex PCR to identify Plasmodium parasites in wild-caught Anopheles in Bolivia, and its application to field epidemiological studies
PCR; Anopheles; Plasmodium; prevalence; entomology; Bolivia
Without an adequate DNA extraction protocol, the identification of Plasmodium species in whole mosquitoes by PCR is difficult because of the presence of reaction inhibitors from the insects. In this study, eight DNA extraction protocols were tested, from which a chelex-based protocol was selected. Then a semi-nested multiplex PCR technique that detects and distinguishes among the four human Plasmodium species in single mosquitoes and in pools of up to 100 mosquitoes was optimized. The technique was used to detect P. vivax in wild-caught Anopheles pseudopunctipennis from a village in the Andean valleys of Bolivia in May 2003. The prevalence of infection was 0.9%. This is the first direct evidence of P vivax transmission by this vector in this country. The extraction and PCR technique presented here can be useful to: (1) estimate Plasmodium prevalence in Anopheles populations in low prevalence areas where large numbers of individual mosquitoes would need to be processed to obtain a reliable estimate; (2) incriminate Anopheles species as malaria vectors; (3) identify all the circulating Plasmodium species in vectors from an area; (4) detect mixed infections in mosquitoes; and (5) detect mosquitoes with low-level parasite infections. (C) 2008 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved. DOI
127. Lavigueur, C; Foster, EJ; Williams, VE.Self-assembly of discotic mesogens in solution and in liquid crystalline phases: Effects of substituent position and hydrogen bonding.J. Am. Chem. Soc., 2008, 130: 11791-11800 Self-assembly of discotic mesogens in solution and in liquid crystalline phases: Effects of substituent position and hydrogen bonding
The effects of functional group position on the phase behavior of discotic mesogens was examined for a series of dibenzophenazine derivatives bearing a carboxylic acid, methyl carboxylate, or nitro group. In all cases, changing the position of the group from the "top" to the "side" of the aromatic core led to dramatic differences in the phase behavior, both in terms of the stability of the liquid crystalline phases as well as the types of mesophases; formed. For the non-hydrogen bonding ester and nitro derivatives, moving the substituent to the side of the core led to a lowering of the clearing temperatures or loss of liquid crystallinity. Carboxylic acid derivatives exhibit broad mesophases irrespective of the position of the acid group, but mesogens bearing this group on the side of the core exclusively form COl(h) phases, whereas those with an acid group on the top of the core exhibit more varied mesomorphism, with the formation of Col(h), Col(r), and nematic phases. Contrary to expectations, the presence of a carboxylic acid group on the side of the core does not appear to lead to the formation of dimeric structures in the liquid crystalline phase, although the columnar structures appear to be stabilized by intermolecular hydrogen bonding along the columns. These derivatives also form pi-stacked dimers in solution; the structure of these dimers are consistent with the proposed structure of the columnar phases. DOI PubMed
126. Leighton, BJ; Roitberg, BD; Belton, P; Lowenberger, CA.Host antibodies in mosquito bloodmeals: A potential tool to detect and monitor infectious diseases in wildlife.Journal of Medical Entomology, 2008, 45: 470-475 Host antibodies in mosquito bloodmeals: A potential tool to detect and monitor infectious diseases in wildlife
mosquito; enzyme-linked immunosorbent assay; bloodmeal; antibody; wildlife disease
When a female mosquito bites, it carries away a blood sample containing specific antibodies that can provide a history of the immune responses of its vertebrate host. This research examines the limits and reliability of a technique to detect antibodies in blood-fed mosquitoes in the laboratory. Mosquitoes were fed on blood containing a specific antibody, and then they were assayed using an enzyme-linked immunosorbent assay to determine the limits of detection of antibody over time, at different temperatures and initial antibody concentrations. The antibody, at an initial concentration of 1 mu g/ml, could be detected in mosquitoes for 24-48 h after feeding. Blind tests simulating the assay of feral mosquitoes were used to test the reliability of the method and detected positive mosquitoes with few false negatives and no false positives. Specific antibodies also could be detected in mosquitoes that had been air-dried or preserved in ethanol. This research indicates that, in theory, the collection and immunological assay of blood-fed mosquitoes could be developed to detect and monitor infectious disease in wildlife.
125. Martinez-Fleites, C; Macauley, MS; He, Y; Shen, DL; Vocadlo, DJ; Davies, GJ.Structure of an O-GlcNAc transferase homolog provides insight into intracellular glycosylation.Nat. Struct. Mol. Biol., 2008, 15: 764-765 Structure of an O-GlcNAc transferase homolog provides insight into intracellular glycosylation
N-Acetylglucosamine (O-GlcNAc) modification of proteins provides a mechanism for the control of diverse cellular processes through a dynamic interplay with phosphorylation. UDP-GlcNAc:polypeptidyl transferase (OGT) catalyzes O-GlcNAc addition. The structure of an intact OGT homolog and kinetic analysis of human OGT variants reveal a contiguous superhelical groove that directs substrates to the active site. DOI PubMed
124. Menounos, B; Clague, JJ.Reconstructing hydro-climatic events and glacier fluctuations over the past millennium from annually laminated sediments of Cheakamus Lake, southern Coast Mountains, British Columbia, Canada.Quat. Sci. Rev., 2008, 27: 701-713 Reconstructing hydro-climatic events and glacier fluctuations over the past millennium from annually laminated sediments of Cheakamus Lake, southern Coast Mountains, British Columbia, Canada
We recovered sediment cores from Cheakamus Lake in the southern Coast Mountains, southwest British Columbia, to reconstruct late Holocene environmental conditions in the watershed. The cored sediments are inorganic, rhythmically laminated clayey silt. Radiocarbon ages and correlation of lamina thickness with the magnitude of the annual flood recorded at a nearby gauging station indicate that the laminae are varves. We discriminate seven types of varves on the basis of couplet thickness and internal structure, and compare them to annual hydrographs over the period of record. The seven varve types record summer snowmelt floods, autumn floods, mid-season floods, years with two major floods, years with three major floods, years with more than three major floods, and periods of sustained glacier runoff. Varves attributed to autumn storms and glacier runoff are dominant, exhibit serial dependence, and are most common during six periods: AD 1300-1320, 1380-1410, 1470-1500, 1710-1730, 1880-1906, and 1916-1945. In contrast, varves attributed to summer snowmelt floods are randomly distributed through time. Thickest varves occur during the decades AD 1090-1110, 1120-1170, 1210-1250, 1310-1330, 1390-1450, 1720-1780, 1860-1900, and 1920-1945. The relation between Little lee Age glacier activity and lake sedimentation is complex, but the thickest varves coincide with times of rapid glacier retreat and periods when air temperatures were warmer than average. The results confirm the importance of sediment transfers during the summer and autumn runoff season in the British Columbia Coast Mountains. (C) 2008 Elsevier Ltd. All rights reserved. DOI
123. Moore, J.W., and B.X. Semmens.Incorporating uncertainty and prior information into stable isotope mixing models.Ecology Letters, 2008, 11: 470-480 Incorporating uncertainty and prior information into stable isotope mixing models
bayesian; carbon; diet; food web; isotopic fractionation; MixSIR; nitrogen; rainbow trout; salmon; sampling importance resampling
Stable isotopes are a powerful tool for ecologists, often used to assess contributions of different sources to a mixture (e.g. prey to a consumer). Mixing models use stable isotope data to estimate the contribution of sources to a mixture. Uncertainty associated with mixing models is often substantial, but has not yet been fully incorporated in models. We developed a Bayesian-mixing model that estimates probability distributions of source contributions to a mixture while explicitly accounting for uncertainty associated with multiple sources, fractionation and isotope signatures. This model also allows for optional incorporation of informative prior information in analyses. We demonstrate our model using a predator-prey case study. Accounting for uncertainty in mixing model inputs can change the variability, magnitude and rank order of estimates of prey (source) contributions to the predator (mixture). Isotope mixing models need to fully account for uncertainty in order to accurately estimate source contributions. DOI
122. Morcos, M; Du, XL; Pfisterer, F; Hutter, H; Sayed, AAR; Thornalley, P; Ahmed, N; Baynes, J; Thorpe, S; Kukudov, G; Schlotterer, A; Bozorgmehr, F; El Baki, RA; Stern, D; Moehrlen, F; Ibrahim, Y; Oikonomou, D; Hamann, A; Becker, C; Zeier, M; Schwenger, V; Miftari, N; Humpert, P; Hammes, HP; Buechler, M; Bierhaus, A; Brownlee, M; Nawroth, PP.Glyoxalase-1 prevents mitochondrial protein modification and enhances lifespan in Caenorhabditis elegans.Aging Cell, 2008, 7: 260-269 Glyoxalase-1 prevents mitochondrial protein modification and enhances lifespan in Caenorhabditis elegans
aging; lifespan; C; elegans; Advanced Glycation Endproducts; mitochondria; metabolic rate; reactive oxygen species; glyoxalase-1
Studies of mutations affecting lifespan in Caenorhabditis elegans show that mitochondrial generation of reactive oxygen species (ROS) plays a major causative role in organismal aging. Here, we describe a novel mechanism for regulating mitochondrial ROS production and lifespan in C. elegans: progressive mitochondrial protein modification by the glycolysis-derived dicarbonyl metabolite methylglyoxal (MG). We demonstrate that the activity of glyoxalase-1, an enzyme detoxifying MG, is markedly reduced with age despite unchanged levels of glyoxalase-1 mRNA. The decrease in enzymatic activity promotes accumulation of MG-derived adducts and oxidative stress markers, which cause further inhibition of glyoxalase-1 expression. Over-expression of the C. elegans glyoxalase-1 orthologue CeGly decreases MG modifications of mitochondrial proteins and mitochondrial ROS production, and prolongs C. elegans lifespan. In contrast, knock-down of CeGly increases MG modifications of mitochondrial proteins and mitochondrial ROS production, and decreases C. elegans lifespan. DOI
121. Napier, DG; Shizgal, BD.Sound dispersion in single-component systems.Physica A, 2008, 387: 4099-4118 Sound dispersion in single-component systems
Boltzmann equation; sound dispersion; Maxwell molecules
The present paper considers the theoretical description of the propagation of sound waves in a one component monatomic gas. The interatomic potential is assumed to vary as the inverse fourth power of the interatomic separation, that is for so-called Maxwell molecules. The eigenvalues and eigenfunctions of the linearized Boltzmann collision operator are known for this model. We emphasize the behaviour of this system in the rarefied, large Knudsen number regime for which the convergence of solutions of the Boltzmann equation can be very slow. We carry out a detailed comparison of the previous formalisms by Wang Chang and Uhlenbeck [C.S. Wang Chang, G.E. Uhlenbeck, The kinetic theory of gases, in: G.E. Uhlenbeck, De Boer, (Eds.), Studies in Statistical Mechanics, vol. 5, Elsevier, New York, 1970, pp. 43-75], Alexeev [B.V. Alexeev, Philos. Trans. R. Soc. A 349 (1994) 357] and Sirovich and Thurber [L. Sirovich, J. K. Thurber, J. Math. Phys. 10 (1969) 239]. The latter exploit a general method of solution of the Boltzmann equation developed by Gross and Jackson. We demonstrate that the Generalized Boltzmann Equation proposed by Alexeev is not appropriate and we show the reasoning for the success of the Sirovich Thurber approach over the Wang Chang and Uhlenbeck calculations. Comparisons are made with experimental data. (c) 2008 Elsevier B.V. All rights reserved. DOI
120. Nelson, AR; Sawai, Y; Jennings, AE; Bradley, LA; Gerson, L; Sherrod, BL; Sabean, J; Horton, BP.Great-earthquake paleogeodesy and tsunamis of the past 2000 years at Alsea Bay, central Oregon coast, USA.Quat. Sci. Rev., 2008, 27: 747-768 Great-earthquake paleogeodesy and tsunamis of the past 2000 years at Alsea Bay, central Oregon coast, USA
The width of plate-boundary fault rupture at the Cascadia subduction zone, a dimension related to earthquake magnitude, remains uncertain because of the lack of quantitative information about land-level movements during past great-earthquake deformation cycles. Beneath a marsh at Alsea Bay, on the central Oregon coast, four sheets of tsunami-deposited sand blanket contacts between tidal mud and peat. Radiocarbon ages for the sheets match ages for similar evidence of regional coseismic subsidence and tsunamis during four of Cascadia's great earthquakes. Barring rapid, unrecorded postseismic uplift, reconstruction of changes in land level from core samples using diatom and foraminiferal transfer functions includes modest coseismic subsidence (0.4 +/- 0.2m) during the four earthquakes. Interpretation is complicated, however, by the 30-38% of potentially unreliable transfer function values from samples with poor analogs in modern diatom and foraminiferal assemblages. Reconstructions of coseismic subsidence using good-analog samples range from 0.46 +/- 0.12 to 0.09 +/- 0.20m showing greater variability than implied by sample-specific errors. From apparent high rates of land uplift following subsidence and tsunamis, we infer that postseismic rebound caused by slip on deep parts of the plate boundary and (or) viscoelastic stress relaxation in the upper plate may be almost as large as coseismic subsidence. Modest coseismic subsidence 100km landward of the deformation front implies that plate-boundary ruptures in central Oregon were largely offshore. Ruptures may have been long and narrow during earthquakes near magnitude 9, as suggested for the AD 1700 earthquake, or of smaller and more variable dimensions and magnitudes. (C) 2008 Elsevier Ltd. All rights reserved. DOI
119. Parent, CE; Caccone, A; Petren, K.Colonization and diversification of Galapagos terrestrial fauna: a phylogenetic and biogeographical synthesis.Philosophical Transactions of the Royal Society B-Biological Sciences, 2008, 363: 3347-3361 Colonization and diversification of Galapagos terrestrial fauna: a phylogenetic and biogeographical synthesis
adaptive radiation; diversification; evolution; phylogeny; phylogeography; speciation
Remote oceanic islands have long been recognized as natural models for the study of evolutionary processes involved in diversification. Their remoteness provides opportunities for isolation and divergence of populations, which make islands remarkable settings for the study of diversification. Groups of islands may share a relatively similar geological history and comparable climate, but their inhabitants experience subtly different environments and have distinct evolutionary histories, offering the potential for comparative studies. A range of organisms have colonized the Galapagos Islands, and various lineages have radiated throughout the archipelago to form unique assemblages. This review pays particular attention to molecular phylogenetic studies of Galapagos terrestrial fauna. We find that most of the Galapagos terrestrial fauna have diversified in parallel to the geological formation of the islands. Lineages have occasionally diversified within islands, and the clearest cases occur in taxa with very low vagility and on large islands with diverse habitats. Ecology and habitat specialization appear to be critical in speciation both within and between islands. Although the number of phylogenetic studies is continuously increasing, studies of natural history, ecology, evolution and behaviour are essential to completely reveal how diversification proceeded on these islands. DOI
117. Schwander, T; Humbert, JY; Brent, CS; Cahan, SH; Chapuis, L; Renai, E; Keller, L.Maternal effect on female caste determination in a social insect.Current Biology, 2008, 18: 265-269 Maternal effect on female caste determination in a social insect
Caste differentiation and division of labor are the hallmarks of social insect colonies [1, 2]. The current dogma for female caste differentiation is that female eggs are totipotent, with morphological and physiological differences between queens and workers stemming from a developmental switch during the larval stage controlled by nutritional and other environmental factors (e.g., [3-8]). In this study, we tested whether maternal effects influence caste differentiation in Pogonomyrmex harvester ants. By conducting crossfostering experiments we identified two key factors in the process of caste determination. New queens were produced only from eggs laid by queens exposed to cold. Moreover, there was a strong age effect, with development into queens occurring only in eggs laid by queens that were at least two years old. Biochemical analyses further revealed that the level of ecdysteroids was significantly lower in eggs developing into queens than workers. By contrast, we found no significant effect of colony size or worker exposure to cold, suggesting that the trigger for caste differentiation may be independent of the quantity and quality of resources provided to larvae. Altogether these data demonstrate that the developmental fate of female brood is strongly influenced by maternal effects in ants of the genus Pogonomyrmex. DOI
115. Ursic-Bedoya, RJ; Nazzari, H; Cooper, D; Triana, O; Wolff, M; Lowenberger, C.Identification and characterization of two novel lysozymes from Rhodnius prolixus, a vector of Chagas disease.Journal of Insect Physiology, 2008, 54: 593-603 Identification and characterization of two novel lysozymes from Rhodnius prolixus, a vector of Chagas disease
Rhodnius prolixus; lysozyme; antimicrobial peptides; Chagas disease; innate immunity; Trypanosoma cruzi
Lysozymes have been described in invertebrates as digestive or immune molecules. We report here the characterization of two novel c-type lysozymes, RpLys-A (EU250274) and RpLys-B (EU250275), isolated from the fat body and digestive tract of immune stimulated Rhodnius prolixus, a major vector of Chagas disease. Transcriptional profiles indicate that the temporal and spatial expression patterns of these two peptides are very different. RpLys-A is expressed predominantly in the midgut after ingestion of Trypanosoma cruzi in a bloodmeal, or after injection of bacteria into the hemocoel. RpLys-B is expressed primarily in the fat body after bacterial injection. Phylogenetic alignments indicate that RpLys-A aligns best with molecules from other hemipterans whose major expression is found in the intestinal tract whereas RpLys-B aligns best with mosquito and tick molecules whose expression is found principally in hemocytes and fat body and whose role has been described as immune-related. These data suggest a differential compartmentalized role of two closely related molecules; one for immunity in the hemocoel and the other for digestion in the midgut. (c) 2007 Elsevier Ltd. All rights reserved. DOI
114. Valdez, Y; Diehl, GE; Vallance, BA; Grassl, GA; Guttman, JA; Brown, NF; Rosenberger, CM; Littman, DR; Gros, P; Finlay, BB.Nramp1 expression by dendritic cells modulates inflammatory responses during Salmonella Typhimurium infection.Cellular Microbiology, 2008, 10: 1646-1661 Nramp1 expression by dendritic cells modulates inflammatory responses during Salmonella Typhimurium infection
Host resistance against Salmonella enterica serovar Typhimurium (S. Typhimurium) is mediated by natural resistance-associated macrophage protein 1 (Nramp1/Slc11a1). Nramp1 is critical to host defence, as mice lacking Nramp1 fail to control bacterial replication and succumb to low doses of S. Typhimurium. Despite this crucial role, the mechanisms underlying Nramp1's protective effects are unclear. Dendritic cells (DCs) that sample the intestinal lumen are among the first cells encountered by S. Typhimurium following oral infection and act as a conduit for S. Typhimurium to cross the intestinal epithelial barrier. We report that DCs, including intestinal, splenic and bone marrow-derived DCs (BMDCs), express Nramp1 protein. In the small intestine, Nramp1 expression is greater in a subset of DCs (CD11c(+)CD103(-)) characterized by the elevated expression of pro-inflammatory cytokines in response to bacterial products. While Nramp1 expression did not affect S. Typhimurium replication in BMDCs, infected Nramp1+/+ BMDCs and intestinal CD11c(+)CD103(-) DCs secreted more inflammatory cytokines (IL-6, IL-12 and TNF-alpha) than Nramp1-/-, suggesting that Nramp1 expression may promote a more rapid inflammatory response following infection. Collectively, these findings reveal a new role for DCs and Nramp1 in modulating the host inflammatory response to S. Typhimurium. DOI
113. Wang, XL; Zhang, W; Cheever, T; Schwarz, V; Opperman, K; Hutter, H; Koepp, D; Chen, L.The C-elegans L1CAM homologue LAD-2 functions as a coreceptor in MAB-20/Sema2-mediated axon guidance.Journal of Cell Biology, 2008, 180: 233-246 The C-elegans L1CAM homologue LAD-2 functions as a coreceptor in MAB-20/Sema2-mediated axon guidance
The L1 cell adhesion molecule (L1CAM) participates in neuronal development. Mutations in the human L1 gene can cause the neurological disorder CRASH (corpus callosum hypoplasia, retardation, adducted thumbs, spastic paraplegia, and hydrocephalus). This study presents genetic data that shows that L1-like adhesion gene 2 (LAD-2), a Caenorhabditis elegans L1CAM, functions in axon pathfinding. In the SDQL neuron, LAD-2 mediates dorsal axon guidance via the secreted MAB-20/Sema2 and PLX-2 plexin receptor, the functions of which have largely been characterized in epidermal morphogenesis. We use targeted misexpression experiments to provide in vivo evidence that MAB-20/Sema2 acts as a repellent to SDQL. Coimmunoprecipitation assays reveal that MAB-20 weakly interacts with PLX-2; this interaction is increased in the presence of LAD-2, which can interact independently with MAB-20 and PLX-2. These results suggest that LAD-2 functions as a MAB-20 coreceptor to secure MAB-20 coupling to PLX-2. In vertebrates, L1 binds neuropilin1, the obligate receptor to the secreted Sema3A. However, invertebrates lack neuropilins. LAD-2 may thus function in the semaphorin complex by combining the roles of neuropilins and L1CAMs. DOI
112. Ward, BC; Bond, JD; Froese, D; Jensen, B.Old Crow tephra (140+/-10 ka) constrains penultimate Reid glaciation in central Yukon Territory.Quat. Sci. Rev., 2008, 27: 1909-1915 Old Crow tephra (140+/-10 ka) constrains penultimate Reid glaciation in central Yukon Territory
Old Crow tephra (140 +/- 10 ka) is closely associated with deposits from the penultimate Reid glaciation along the Pelly River in central Yukon Territory. The elevation of the tephra above present base level and association with deglacial sediments Suggests a close minimum age estimate, confirming a MIS 6 age for the Reid glaciation. This is in contrast to a MIS 4 age for the penultimate Gladstone glaciation in Southwest Yukon. This study demonstrates that the assumed synchrony of the penultimate advance of the Cordilleran Ice Sheet has little support, and regional controls on the mass balance of source regions of the ice sheet are more important than previously considered. (C) 2008 Elsevier Ltd. All rights reserved. DOI
111. Williams, TD.Individual variation in endocrine systems: moving beyond the 'tyranny of the Golden Mean'.Philosophical Transactions of the Royal Society B-Biological Sciences, 2008, 363: 1687-1698 Individual variation in endocrine systems: moving beyond the 'tyranny of the Golden Mean'
endocrine systems; inter-individual variation; reaction norms; heritability; plasticity
Twenty years ago, Albert Bennett published a paper in the influential book New directions in ecological physiology arguing that individual variation was an 'underutilized resource'. In this paper, I review our state of knowledge of the magnitude, mechanisms and functional significance of phenotypic variation, plasticity and flexibility in endocrine systems, and argue for a renewed focus on inter-individual variability. This will provide challenges to conventional wisdom in endocrinology itself, e. g. re-evaluation of relatively simple, but unresolved questions such as structure-function relationships among hormones, binding globulins and receptors, and the functional significance of absolute versus relative hormone titres. However, there are also abundant opportunities for endocrinologists to contribute solid mechanistic understanding to key questions in evolutionary biology, e. g. how endocrine regulation is involved in evolution of complex suites of traits, or how hormone pleiotropy regulates trade-offs among life-history traits. This will require endocrinologists to embrace the raw material of adaptation (heritable, individual variation and phenotypic plasticity) and to take advantage of conceptual approaches widely used in evolutionary biology (selection studies, reaction norms, concepts of evolutionary design) as well as a more explicit focus on the endocrine basis of life-history traits that are of primary interest to evolutionary biologists (cf. behavioural endocrinology). DOI
110. Wilson, SK; Fisher, R; Pratchett, MS; Graham, NAJ; Dulvy, NK; Turner, RA; Cakacaka, A; Polunin, NVC; Rushton, SP.Exploitation and habitat degradation as agents of change within coral reef fish communities.Global Change Biology, 2008, 14: 2796-2809 Exploitation and habitat degradation as agents of change within coral reef fish communities
climate change; density dependence; disturbance; food webs; trophic cascades GREAT-BARRIER-REEF; SOUTH-EASTERN AUSTRALIA; TROPHIC CASCADES; CLIMATE-CHANGE; MARINE RESERVES; TOP-DOWN; BOTTOM-UP; FOOD WEBS; ECOSYSTEMS; FISHERIES
Over-exploitation and habitat degradation are the two major drivers of global environmental change and are responsible for local extinctions and declining ecosystem services. Here we compare the top-down effect of exploitation by fishing with the bottom-up influence of habitat loss on fish communities in the most diverse of ecological systems, coral reefs. Using a combination of multivariate techniques and path analyses, we illustrate that the relative importance of coral cover and fishing in controlling fish abundance on remote Fijian reefs varies between species and functional groups. A decline in branching Acropora coral is strongly associated with a decline in abundance of coral-feeding species, and a decrease in coral-associated habitat complexity, which has indirectly contributed to reduced abundance of small-bodied damselfish. In contrast, reduced fishing pressure, brought about by declining human populations and a shift to alternate livelihoods, is associated with increased abundance of some piscivores and fisheries target species. However, availability of prey is controlled by coral-associated habitat complexity and appears to be a more important driver of total piscivore abundance compared with fishing pressure. Effects of both fishing and coral loss are stronger on individual species than functional groups, as variation in the relative importance of fishing or coral loss among species within the same functional group attenuated the impact of either of these potential drivers at the functional level. Overall, fishing continues to have an influence on Fijian fish communities; however, habitat loss is currently the overriding agent of change. The importance of coral loss mediated by climate change is expected to have an increasing contribution to fish community dynamics, particularly in remote locations or where the influence of fishing is waning. DOI
109. Wingfield, JC; Visser, ME; Williams, TD.Introduction. Integration of ecology and endocrinology in avian reproduction: a new synthesis.Philosophical Transactions of the Royal Society B-Biological Sciences, 2008, 363: 1581-1588 Introduction. Integration of ecology and endocrinology in avian reproduction: a new synthesis
ecology; endocrinology; evolution; global warming; climate change; maternal effects
Birds are some of the most familiar organisms of global ecosystems. Changes in the visibility and abundance of birds are therefore excellent indicators of population and physiological responses to habitat changes and are a major focus for public concern about detrimental environmental changes. In order to understand how birds respond to these challenges, it is essential to determine how the environment affects reproduction under natural conditions. The continuum from environmental variables (cues) to reproductive life-history traits depends upon a cascade of neural and physiological processes that determine the extent and rate at which birds will be able to adapt to changes in their environment. For a full understanding of this ability to adapt, ecologists and endocrinologists need to collaborate and build a common framework. The objective of this theme issue is to bring together a series of papers addressing how evolutionary ecologists and endocrinologists can collaborate directly using avian reproduction as a model system. First, we address the need to integrate ecology and endocrinology and what benefits to biological knowledge will be gained. The papers collected in this issue represent a new synthesis of ecology and endocrinology as discussed in three E-BIRD workshops. The three main foci are trade-offs and constraints, maternal effects and individual variation. Authors within each group present ecological and endocrinological aspects of their topics and many go on to outline testable hypotheses. Finally, we discuss where the major problems remain and how this issue points out where these need collaborative efforts of ecologists and endocrinologists. Specific challenges are raised to future researchers to break through intellectual barriers and explore new frontiers. This framework of topics will ultimately apply to all taxa because the principles involved are universal and hopefully will have direct application to programmes integrating organisms and genes throughout biological sciences. DOI
108. Bhavsar A, Guttman, JA., Finlay, BB.Manipulation of host-cell pathways by bacterial pathogens.Nature, 2007, 449:827-834. Manipulation of host-cell pathways by bacterial pathogens.
Bacterial pathogens operate by attacking crucial intracellular pathways in their hosts. These pathogens
usually target more than one intracellular pathway and often interact at several points in each of these
pathways to commandeer them fully. Although different bacterial pathogens tend to exploit similar pathway
components in the host, the way in which they ‘hijack’ host cells usually differs. Knowledge of how pathogens
target distinct cytoskeletal components and immune-cell signalling pathways is rapidly advancing, together
with the understanding of bacterial virulence at a molecular level. Studying how these bacterial pathogens
subvert host-cell pathways is central to understanding infectious disease. PDF DOI
107. Chesnaux, R; Allen, DM; Graham, G.Assessment of the impact of nutrient management practices on nitrate contamination in the abbotsford-sumas aquifer.Environ. Sci. Technol., 2007, 41: 7229-7234 Assessment of the impact of nutrient management practices on nitrate contamination in the abbotsford-sumas aquifer
The impact of recent changes to nutrient management practices in raspberry fields on the loading and subsequent transport of nitrate through the vadose zone of the Abbotsford-Sumas aquifer is investigated numerically. Previous studies have shown that nitrate concentrations in the aquifer have remained relatively stable despite a shift in nutrient management practices. Using an estimate of net annual available nitrogen in fields that are fertilized using synthetic fertilizer, nitrate concentrations as a function of time and depth through the vadose zone are simulated from spring to late fall. Results indicate rapid leaching of nitrate owing to the permeable nature of the aquifer and suggest that nitrate loading to the water table may occur earlier than previously thought, possibly due to spring rains. For an average fertilizer application rate of 90 kg of N/ha, the simulated nitrate concentration on Oct 1 within the top I m of soil is 33 mg of N/kg, while the residual soil nitrate measured in late September was 37 mg of N/kg. Taking into account the effects of dilution within the saturated zone,the simulated peak nitrate concentration is similar to average observed peak concentrations in a shallow monitoring well. A solution is offered for estimating nitrate concentration at the water table as a function of the rate of synthetic fertilizer applied to raspberry fields. DOI PubMed
106. Cooper, DM; Pio, F; Thi, EP; Theilmann, D; Lowenberger, C.Characterization of Aedes Dredd: A novel initiator caspase from the yellow fever mosquito, Aedes aegypti.Insect Biochem. Mol. Biol., 2007, 37: 559-569 Characterization of Aedes Dredd: A novel initiator caspase from the yellow fever mosquito, Aedes aegypti
Caspases play an essential role during programmed cell death in all metazoans. These enzymes are cysteine proteases and comprise a multi-gene family with more than a dozen mammalian family members. Although caspases have been characterized in many animals, including Drosophila melanogaster, little is known about the laspases that exist in mosquitoes. Here we describe the identification and characterization of Aedes Dredd (AeDredd), a novel caspase in the yellow fever mosquito, Aedes aegypti. AeDredd contains two N-terminal death effector domains and the well conserved caspase catalytic domain. Multiple sequence alignments and functional substrate assays of recombinant protein Suggest that AcDredd is an orthologue of Drosophila Dredd and human caspase-8, both central effectors of the death receptor-inediated apoptotic pathway. AeDredd exhibits substrate specificity most similar to human caspase-8. AeDredd transcripts were found in all developmental stages with highest expression in early pupae. Within adults, AeDredd was found in all the tissues examined, with the highest transcript levels detected in fat body tissues. This is the first functional characterization of a death domain-containing caspase in in insect vector of human disease, and will initiate Studies on the role of apoptosis in the innate immune response of vectors towards intracellular parasites Such as Viruses. (c) 2007 Elsevier Ltd. All rights reserved. DOI PubMed
105. Cooper, DM; Thi, EP; Chamberlain, CM; Pio, F; Lowenberger, C.Aedes Dronc: a novel ecdysone-inducible caspase in the yellow fever mosquito, Aedes aegypti.Insect Mol. Biol., 2007, 16: 563-572 Aedes Dronc: a novel ecdysone-inducible caspase in the yellow fever mosquito, Aedes aegypti
apoptosis; caspase; Aedes aegypti; ecdysone; development
Caspases are cysteinyl-aspartate-specific proteases known for their role in apoptosis. Here, we describe the characterization of Aedes Dronc, a novel caspase in the yellow fever mosquito, Aedes aegypti. Aedes Dronc is predicted to contain an N-terminal caspase recruitment domain and is a homologue of Drosophila Dronc and human caspase-9. An increase in transcripts and caspase activity coincides with developmental changes in the mosquito, suggesting that Aedes Dronc plays a role in developmental apoptosis. Exposure of third instar larvae to ecdysone resulted in a significant increase in both transcript levels and caspase activity. We present here a functional characterization of the first caspase recruitment domain-containing caspase in mosquitoes, and will initiate studies on the role of apoptosis in the innate immune response of vectors. DOI PubMed
104. Cornelissen, JHC; van Bodegom, PM; Aerts, R; Callaghan, TV; van Logtestijn, RSP; Alatalo, J; Chapin, FS; Gerdol, R; Gudmundsson, J; Gwynn-Jones, D; Hartley, AE; Hik, DS; Hofgaard, A; Jonsdottir, IS; Karlsson, S; Klein, JA; Laundre, J; Magnusson, B; Michelsen, A; Molau, U; Onipchenko, VG; Quested, HM; Sandvik, SM; Schmidt, IK; Shaver, GR; Solheim, B; Soudzilovskaia, NA; Stenstrom, A; Tolvanen, A; Totland, O; Wada, N; Welker, JM; Zhao, XQ.Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes.Ecology Letters, 2007, 10: 619-627 Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes
alpine; carbon; circum-arctic; global change; growth form; litter turnover; mass loss; vegetation change
Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide. Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition. DOI
103. Crespi, BJ.Sly FOXP2: genomic conflict in the evolution of language.Trends in Ecology & Evolution, 2007, 22: 174-175 Sly FOXP2: genomic conflict in the evolution of language
MIRROR SYSTEM; SCHIZOPHRENIA; AUTISM; SPEECH; GENE
102. Danby, RK; Hik, DS.Variability, contingency and rapid change in recent subarctic alpine tree line dynamics.J. Ecol., 2007, 95: 352-363 Variability, contingency and rapid change in recent subarctic alpine tree line dynamics
climate change; dendroecology; ecotones; forest-tundra; non-linearity; Picea glauca; Salix glauca; stand dynamics; timberline; Yukon: alpine
Boundaries between forest and tundra ecosystems, tree lines, are expected to advance in altitude and latitude in response to climate warming. However, varied responses to 20th century warming suggest that in addition to temperature, tree line dynamics are mediated by species-specific traits and environmental conditions at landscape and local scales. We examined recent tree line dynamics at six topographically different, but climatically similar, sites in south-west Yukon, Canada. Dendroecological techniques were used to reconstruct changes in density of the dominant tree species, white spruce (Picea glauca), and to construct static age distributions of willow (Salix spp.), one of two dominant shrub genera. Data were analysed to identify periods and rates of establishment and mortality and to relate these to past climate. Tree line elevation and stand density increased significantly during the early to mid 20th century. However, this change was not uniform across sites. Spruce advanced rapidly on south-facing slopes and tree line rose 65-85 m in elevation. Tree line did not advance on north-facing slopes, but stand density increased 40-65%. Differences observed between aspects were due primarily to the differential presence of permafrost. Additional variability among sites was related to slope and vegetation type. Results were less conclusive for willow, but evidence for an advance was found at two sites. Increases in stand density were strongly correlated with summer temperatures. The period of rapid change coincided with a 30-year period of above average temperatures, beginning in 1920. The highest correlations were obtained using a forward average of 30-50 years, supporting the hypothesis that tree line dynamics are controlled more by conditions influencing recruitment than by establishment alone. The changes observed at several sites are suggestive of a threshold response and challenge the notion that tree lines respond gradually to climate warming. Overall, the results provide further evidence to support the idea that the pattern and timing of change is contingent on local, landscape, and regional-scale factors, as well as species' biology. DOI
101. Danby, RK; Hik, DS.Responses of white spruce (Picea glauca) to experimental warming at a subarctic alpine treeline.Glob. Change Biol., 2007, 13: 437-451 Responses of white spruce (Picea glauca) to experimental warming at a subarctic alpine treeline
climate change; experimental warming; open-top chamber; Picea glauca; seedling growth; timberline; treeline dynamics; Yukon: alpine
From 2001 to 2004 we experimentally warmed 40 large, naturally established, white spruce [Picea glauca (Moench) Voss] seedlings at alpine treeline in southwest Yukon, Canada, using passive open-top chambers (OTCs) distributed equally between opposing north and south-facing slopes. Our goal was to test the hypothesis that an increase in temperature consistent with global climate warming would elicit a positive growth response. OTCs increased growing season air temperatures by 1.8 degrees C and annual growing degree-days by one-third. In response, warmed seedlings grew significantly taller and had higher photosynthetic rates compared with control seedlings. On the south aspect, soil temperatures averaged 1.0 degrees C warmer and the snow-free period was nearly 1 month longer. These seedlings grew longer branches and wider annual rings than seedlings on the north aspect, but had reduced Photosystem-II efficiency and experienced higher winter needle mortality. The presence of OTCs tended to reduce winter dieback over the course of the experiment. These results indicate that climate warming will enhance vertical growth rates of young conifers, with implications for future changes to the structure and elevation of treeline contingent upon exposure-related differences. Our results suggest that the growth of seedlings on north-facing slopes is limited by low soil temperature in the presence of permafrost, while growth on south-facing slopes appears limited by winter desiccation and cold-induced photoinhibition. DOI
100. Fielenbach, N; Guardavaccaro, D; Neubert, K; Chan, T; Li, DL; Feng, Q; Hutter, H; Pagano, M; Antebi, A.DRE-1: An evolutionarily conserved F box protein that regulates C-elegans developmental age.Developmental Cell, 2007, 12: 443-455 DRE-1: An evolutionarily conserved F box protein that regulates C-elegans developmental age
During metazoan development, cells acquire both positional and temporal identities. The Caenorhabditis elegans heterochronic loci are global regulators of larval temporal fates. Most encode conserved transcriptional and translational factors, which affect stage-appropriate programs in various tissues. Here, we describe dre-1, a heterochronic gene, whose mutant phenotypes include precocious terminal differentiation of epidermal stem cells and altered temporal patterning of gonadal outgrowth. Genetic interactions with other heterochronic loci place dre-1 in the larval-to-adult switch. dre-1 encodes a highly conserved F box protein, suggesting a role in an SCF ubiquitin ligase complex. Accordingly, RNAi knockdown of the C. elegans SKP1-like homolog SKR-1, the cullin CUL-1, and ring finger RBX homologs yielded similar heterochronic phenotypes. DRE-1 and SKR-1 form a complex, as do the human orthologs, hFBX011 and SKP1, revealing a phyletically ancient interaction. The identification of core components involved in SCF-mediated modification and/or proteolysis suggests an important level of regulation in the heterochronic hierarchy. DOI
99. Flowers, GE; Bjornsson, H; Geirsdottir, A; Miller, GH; Clarke, GKC.Glacier fluctuation and inferred climatology of Langjokull ice cap through the Little Ice Age.Quat. Sci. Rev., 2007, 26: 2337-2353 Glacier fluctuation and inferred climatology of Langjokull ice cap through the Little Ice Age
Emerging paleoclimate records from proglacial lake Hvitarvatn, central Iceland, suggest that Langjokull ice cap attained its maximum Holocene extent within the last 400 years. With the aim of constructing glaciological models and appropriate model inputs for Holocene simulations of Langjokull, we begin by simulating the evolution of Langjokull through the Little Ice Age to present, a period for which we have some constraint on ice-cap geometry. Using modern measured mass balance distributions (1997-2003) and meteorological data from nearby Hveravellir, we derive a reference precipitation field for the period 1961-1990 over the ice cap. Our simulations suggest Langjokull attained its maximum Little Ice Age volume around 1840 with a second local maximum around 1890. The two outlet glaciers terminating in Hvitarvatn, Norourjokull and Suourjokull, advance slowly into the lake, occupying their maximum lake area in the late 19th century, and retreat comparatively rapidly in the mid- to late 20th century. Simulations of Norourjokull are much more faithful to the geomorphic evidence than are simulations of Suourjokull, potentially suggesting a difference in dynamics between these two glaciers. While only 35% of the Hvitarvatn catchment area is ice-covered, meltwater from Langjokull comprises similar to 70% of the water input to the lake. Two-thirds of this input from the ice cap is transported as groundwater. Simulated glacier-derived discharge to the lake through the Little Ice Age suggests that a sediment concentration of 1.5 kg m(-3) would have resulted in the transport of 1.5 x 10(11) kg of material to the lake over the last 300 years, comparable to the estimated mass of sediment in the most recently deposited sedimentary unit in the lake. (C) 2007 Elsevier Ltd. All rights reserved. DOI
98. Gray, SM; McKinnon, JS.Linking color polymorphism maintenance and speciation.Trends in Ecology & Evolution, 2007, 22: 71-79 Linking color polymorphism maintenance and speciation
Here, we review the recently burgeoning literature on color polymorphisms, seeking to integrate studies of the maintenance of genetic variation and the evolution of reproductive isolation. Our survey reveals that several mechanisms, some operating between populations and others within them, can contribute to both color polymorphism persistence and speciation. As expected, divergent selection clearly can couple with gene flow to maintain color polymorphism and mediate speciation. More surprisingly, recent evidence suggests that diverse forms of with in-population sexual selection can generate negative frequency dependence and initiate reproductive isolation. These findings deserve additional study, particularly concerning the roles of heterogeneous visual environments and correlational selection. Finally, comparative studies and more comprehensive approaches are required to elucidate when color polymorphism evolves, persists, or leads to speciation. DOI
97. Koh, S; Hik, DS.Herbivory mediates grass-endophyte relationships.Ecology, 2007, 88: 2752-2757 Herbivory mediates grass-endophyte relationships
endophytic fungi; Festuca altaica; herbivory; mutualism; Neotyphodium; optimal defense theory; subarctic; symbiosis
Endophytic fungi are plant symbionts living asymptomatically within plant tissues. Neotyphodium spp., which are asexual vertically transmitted systemic fungal endophytes of cool-season grasses, are predicted to be plant mutualists. These endophytes increase host plant resistance to environmental stresses and/or increase the production of alkaloid-based herbivore deterrents. The ubiquity of this defense mutualism is unclear, and a variety of alternative mechanisms may explain the observed variation in infection rates, levels of deterrence, and the maintenance of asexual endophytes in grass populations. We found that grass-endophyte interactions are variable and ordered along an herbivory gradient in an undisturbed subarctic alpine ecosystem. Native grass populations in grazed sites had significantly greater frequency of Neotyphodium infection compared to ungrazed sites. Tillers from grazed sites had significantly higher hyphal densities compared to ungrazed sites. The ability of grass-Neotyphodium constituents to deter vertebrate herbivory in natural systems is thought to be rare. In grazed meadows, we showed that endophyte infection resulted in the deterrence of grazing by native vertebrate herbivores. However, the same herbivores did not distinguish between infected and uninfected grass harvested from ungrazed areas. These results demonstrate that the relationship between vertically transmitted endophytes and grasses in the alpine tundra vary greatly within populations. This may be based in part on defense mutualism and is consistent, under varying levels of herbivory, with the predictions of optimal defense theory. DOI
96. Kyle, CJ; Karels, TJ; Davis, CS; Mebs, S; Clark, B; Strobeck, C; Hik, DS.Social structure and facultative mating systems of hoary marmots (Marmota caligata).Mol. Ecol., 2007, 16: 1245-1255 Social structure and facultative mating systems of hoary marmots (Marmota caligata)
hoary marmot; Marmota caligata; mating system; microsatellites; parentage; social structure
Mate-choice theory predicts different optimal mating systems depending on resource availability and habitat stability. Regions with limited resources are thought to promote monogamy. We tested predictions of monogamy in a social rodent, the hoary marmot (Marmota caligata), at the northern climatic extreme of its distribution. Mating systems, social structure and genetic relationships were investigated within and among neighbouring colonies of marmots within a 4 km(2) valley near Kluane National Park, Yukon, Canada, using 21 microsatellite loci. While both monogamous and polygynous populations of hoary marmots have been observed in the southern reaches of this species' range; northern populations of this species are thought to be predominantly monogamous. Contrary to previous studies, we did not find northern hoary marmot social groups to be predominantly monogamous; rather, the mating system seemed to be facultative, varying between monogamy and polygyny within, as well as among, social groups. These findings reveal that the mating systems within colonies of this species are more flexible than previously thought, potentially reflecting local variation in resource availability. DOI
94. Morrison, SF; Hik, DS.Demographic analysis of a declining pika Ochotona collaris population: linking survival to broad-scale climate patterns via spring snowmelt patterns.J. Anim. Ecol., 2007, 76: 899-907 Demographic analysis of a declining pika Ochotona collaris population: linking survival to broad-scale climate patterns via spring snowmelt patterns
collared pika; fertility; life-table response experiment; Pacific Decadal Oscillation; snowmelt
1. Demographic analysis is essential in order to determine which factors, such as survival, fertility and other life-history characteristics, have the greatest influence on a population's rate of growth (lambda). 2. We used life-table response experiments (LTREs) to assess the relative importance of survival and fertility rates for an alpine lagomorph, the collared pika Ochotona collaris, using 12 years (1995-2006) of census data. The LTRE analysis was repeated for each of three subpopulations within the main study site that were defined by aspect (east, west and south). 3. Across the entire study site, the survival and fertility of adults contributed 35.6 and 43.5%, respectively, to the variance observed in the projected population growth rate, V(lambda), whereas juvenile survival contributed 20.9%. Adult survival and fertility contributed approximately equal amounts for each subpopulation when considered separately, although their rank order varied spatially. 4. Adult survival across the entire site was positively correlated to the Pacific Decadal Oscillation (PDO) with a time lag of 1 year, and was uncorrelated to adult density. The PDO was negatively correlated to the timing of spring snowmelt at our site, implicating the importance of earlier spring conditions and plant phenology on the subsequent winter survival of adults and therefore, population growth. 5. When subpopulations were analysed separately, survivals and fertilities were variously correlated to lagged PDO and adult densities, but the patterns varied spatially. Therefore, the mechanisms underlying V(lambda) can vary substantially over relatively short distances. DOI
93. Newton, K; Côté, IM; Pilling, GM; Jennings, S; Dulvy, NK.Current and future sustainability of island coral reef fisheries.Current Biology, 2007, 17: 655-658 Current and future sustainability of island coral reef fisheries
Overexploitation is one of the principal threats to coral reef diversity, structure, function, and resilience [1, 2]. Although it is generally held that coral reef fisheries are unsustainable [3-5], little is known of the overall scale of exploitation or which reefs are overfished [6]. Here, on the basis of ecological footprints and a review of exploitation status [7, 8], we report widespread unsustainability of island coral reef fisheries. Over half (55%) of the 49 island countries considered are exploiting their coral reef fisheries in an unsustainable way. We estimate that total landings of coral reef fisheries are currently 64% higher than can be sustained. Consequently, the area of coral reef appropriated by fisheries exceeds the available effective area by similar to 75,000 km(2), or 3.7 times the area of Australia's Great Barrier Reef, and an extra 196,000 km(2) of coral reef may be required by 2050 to support the anticipated growth in human populations. The large overall imbalance between current and sustainable catches implies that management methods to reduce social and economic dependence on reef fisheries are essential to prevent the collapse of coral reef ecosystems while sustaining the well-being of burgeoning coastal populations. DOI
92. Osborn, G; Menounos, B; Koch, J; Clague, JJ; Vallis, V.Multi-proxy record of Holocene glacial history of the Spearhead and Fitzsimmons ranges, southern Coast Mountains, British Columbia.Quat. Sci. Rev., 2007, 26: 479-493 Multi-proxy record of Holocene glacial history of the Spearhead and Fitzsimmons ranges, southern Coast Mountains, British Columbia
Evidence from glacier forefields and lakes is used to reconstruct Holocene glacier fluctuations in the Spearhead and Fitzsimmons ranges in southwest British Columbia. Radiocarbon ages on detrital wood and trees killed by advancing ice and changes in sediment delivery to downstream proglacial lakes indicate that glaciers expanded from minimum extents in the early Holocene to their maximum extents about two to three centuries ago during the Little Ice Age. The data indicate that glaciers advanced 8630-8020, 6950-6750, 3580-2990, and probably 4530-4090 cal yr BP, and repeatedly during the past millennium. Little Ice Age moraines dated using dendrochronology and lichenometry date to early in the 18th century and in the 1830s and 1890s. Limitations inherent in lacustrine and terrestrial-based methods of documenting Holocene glacier fluctuations are minimized by using the two records together. (c) 2006 Published by Elsevier Ltd. DOI
91. Parker, JDK; Bradley, BA; Mooers, AO; Quarmby, LM.Phylogenetic Analysis of the Neks Reveals Early Diversification of Ciliary-Cell Cycle Kinases.PLoS One, 2007, 2 Phylogenetic Analysis of the Neks Reveals Early Diversification of Ciliary-Cell Cycle Kinases
Background. NIMA-related kinases (Neks) have been studied in diverse eukaryotes, including the fungus Aspergillus and the ciliate Tetrahymena. In the former, a single Nek plays an essential role in cell cycle regulation; in the latter, which has more than 30 Neks in its genome, multiple Neks regulate ciliary length. Mammalian genomes encode an intermediate number of Neks, several of which are reported to play roles in cell cycle regulation and/or localize to centrosomes. Previously, we reported that organisms with cilia typically have more Neks than organisms without cilia, but were unable to establish the evolutionary history of the gene family. Methodology/Principle Findings. We have performed a large-scale analysis of the Nek family using Bayesian techniques, including tests of alternate topologies. We find that the Nek family had already expanded in the last common ancestor of eukaryotes, a ciliated cell which likely expressed at least five Neks. We suggest that Neks played an important role in the common ancestor in regulating cilia, centrioles, and centrosomes with respect to mitotic entry, and that this role continues today in organisms with cilia. Organisms that lack cilia generally show a reduction in the number of Nek clades represented, sometimes associated with lineage specific expansion of a single clade, as has occurred in the plants. Conclusion/Significance. This is the first rigorous phylogenetic analysis of a kinase family across a broad array of phyla. Our findings provide a coherent framework for the study of Neks and their roles in coordinating cilia and cell cycle progression.Website DOI PubMed
90. Ursic-Bedoya, RJ; Lowenberger, CA.Rhodnius prolixus: Identification of immune-related genes up-regulated in response to pathogens and parasites using suppressive subtractive hybridization.Developmental and Comparative Immunology, 2007, 31: 109-120 Rhodnius prolixus: Identification of immune-related genes up-regulated in response to pathogens and parasites using suppressive subtractive hybridization
Rhodnius prolixus; parasitic infection; innate immunity; suppressive subtractive hybridization; expressed sequence tags
We report the identification of immune-related molecules from the fat body, and intestine of Rhodnius prolixus, an important vector of Chagas disease. Insects were challenged by introducing pathogens or Trypanosoma cruzi, the parasite that causes Chagas disease, into the hemocoel. RNA from intestines, or fat body were isolated 24 h after stimulation. We used suppressive subtractive hybridization to identify immune-related genes, generated three subtracted libraries, sequenced the clones and assembled the sequences. The functional annotation revealed expressed sequence tags (ESTs) generated in response to various stimuli in all tissues, and included pathogen recognition molecules, regulatory molecules, and effector molecules. (c) 2006 Elsevier Ltd. All rights reserved.
89. Verma, N; MacDonald, L; Punja, ZK.Environmental and host requirements for field infection of blueberry fruits by Colletotrichum acutatum in British Columbia.Plant Pathology, 2007, 56: 107-113 Environmental and host requirements for field infection of blueberry fruits by Colletotrichum acutatum in British Columbia
anthracnose; disease prediction; epidemiology; ripe-rot; Vaccinium corymbosum; weather conditions
Higher recovery of Colletotrichum acutatum, the causal agent of anthracnose (ripe-rot), from blueberry tissues during the growing seasons of 2002 and 2003 was found at bloom and ripe berry than at other stages of plant development. The effects of leaf-wetness duration and ambient temperature on fruit infection frequency were determined during the growing seasons of 2001-03. Potted 2-year-old blueberry plants were exposed for 1-week periods to prevailing environmental conditions and natural inoculum in a commercial field, and grown to harvest, when fruit infection was assessed. Three peaks of infection were observed: early during bloom, mid-season during the mature green berry stage, and later in the season when berries had ripened. Weather data collected simultaneously indicated that a minimum of 10 h of leaf wetness at 11 degrees C was sufficient for fruit infection. These conditions preceded each peak of infection. To determine whether peaks of infection in the field were also caused by changes in host susceptibility or available inoculum, groups of potted blueberry plants were artificially inoculated at weekly intervals during the growing season of 2004, exposed to prevailing environmental conditions, and fruit infection assessed at harvest. Flowers and developing fruits were found to be susceptible throughout the season, indicating that specific peaks of infection were associated with environmental conditions and availability of inoculum. DOI
88. Whiteley, J; Bendell-Young, L.Ecological implications of intertidal mariculture: observed differences in bivalve community structure between farm and reference sites.Journal of Applied Ecology, 2007, 44: 495-505 Ecological implications of intertidal mariculture: observed differences in bivalve community structure between farm and reference sites
bivalves; clam aquaculture; community structure; predator exclusion; Venerupis philippinarum
1. Despite recent growth in shellfish aquaculture in British Columbia, Canada, the impacts of common practices on non-target species are poorly understood. Two practices employed on clam farms to increase production of the exotic clam Venerupis philippinarum include the addition of juvenile 'seed' clams to the sediment and covering seeded clam beds with protective netting, ostensibly to exclude large mobile epibenthic predators. 2. We expected the effects of predator exclusion to be most evident among other bivalves, which made up more than 80% of the infaunal macrobenthos at all sites surveyed. A field study across three regions collected infaunal bivalve density and biomass data. We compared species richness, composition and abundances of communities between clam farms and reference sites, paired on the basis of physical characteristics such as sediment type, slope and aspect. 3. Venerupis philippinarum was the only species found in higher abundance on farm sites in low intertidal areas (227 +/- 241.6 clams m(-2), P = 0.02; 872.9 +/- 792.9 g m(-2), P = 0.037). Farmed sites showed no difference in mid-intertidal areas, nor in density of the other 25 bivalve species, although an increase would be expected if netting excluded important predators. Although statistically non-significant, there were indications that biomass of species other than V. philippinarum may have been lower on farm sites. 4. Bivalve species composition was not significantly different between farm and reference sites. Nevertheless, farm sites were more similar to each other as a group than reference sites, leading to a loss of regional distinctness that was evident among reference sites. 5. Synthesis and applications. Our findings support the hypothesis that predation and competition play minor roles in structuring communities in soft-bottomed environments. Given the potential for cumulative effects of seeding and netting at large scales, a precautionary approach is recommended in future development of intertidal clam aquaculture.PDF DOI
86. Boulanger, N; Bulet, P; Lowenberger, C.Antimicrobial peptides in the interactions between insects and flagellate parasites.Trends Parasitol, 2006, 22: 262-268 Antimicrobial peptides in the interactions between insects and flagellate parasites
Innate immunity has a key role in the control of microbial infections in both vertebrates and invertebrates. In insects, including vectors that transmit parasites that cause major human and animal diseases, antimicrobial peptides (AMPs) are important components of innate immunity. AMPs are induced upon parasitic infections and can participate in regulating parasite development in the digestive tract and in the hemolymph. This review presents our current knowledge of a field that is in its infancy: the role of innate immunity in different models of insects infected with flagellate parasites, and in particular the potential role of AMPs in regulating these parasitic infections.
84. Christians, JK; Hoeflich, A; Keightley, PD.PAPPA2, an enzyme that cleaves an insulin-like growth-factor-binding protein, is a candidate gene for a quantitative trait locus affecting body size in mice.Genetics, 2006, 173: 1547-1553 PAPPA2, an enzyme that cleaves an insulin-like growth-factor-binding protein, is a candidate gene for a quantitative trait locus affecting body size in mice
Identifying genes responsible for quantitative variation remains a major challenge. We previously identified a quantitative trait locus (QTL) affecting body size that segregated between two inbred strains of mice. By fine mapping, we have refined the location of this QTL to a genomic region containing only four protein-coding genes. One of these genes, PAPPA2, is a strong candidate because it codes for an enzyme that cleaves insulin-like growth-factor-binding protein 5 (IGFBP-5), an important stimulator of bone formation. Among littermates that segregate only for the four-gene region, we show that the QTL has a significant effect on the circulating levels of IGFBP-5 and IGFBP-3 (the latter subject to limited degradation by PAPPA2), but not on levels of IGFBP-2 and IGFBP-4, which are not cleaved by PAPPA2. There are 14 nonsynonymous SNPs among QTL alleles, which may affect the activity of the translated protein. The refinement of the target region to four genes and the finding that the QTL affects IGFBP-5 levels suggest that PAPPA2 may be involved with normal postnatal growth. Our mapping results also illustrate the potentially fractal nature of QTL: as we mapped our QTL with increasing resolution, what appeared to be a single QTL resolved into three closely linked QTL (previous work), and then one of these was further dissected into two in this study.PDF
83. Cory, JS; Hoover, K.Plant-mediated effects in insect-pathogen interactions.Trends in Ecology & Evolution, 2006, 21: 278-286 Plant-mediated effects in insect-pathogen interactions
Interactions between insect herbivores and their pathogens can be modulated by host plants. Inter- and intraspecific differences in plant chemistry and structure can after the susceptibility of insects to infection and the production and environmental persistence of pathogens. Whether plants can manipulate insect pathogens to act as 'bodyguards' and increase their own fitness remains to be shown. Reduced insect performance owing to poor plant quality can enhance the susceptibility of an insect to disease while these same phytochemicals can also reduce the effectiveness of entomopathogens in killing the host. As we discuss here, plants have an important role in the evolution of insect-pathogen relationships and a tritrophic perspective should thus be incorporated into the study of insects and their pathogens. DOI
80. Foster, EJ; Jones, RB; Lavigueur, C; Williams, VE.Structural factors controlling the self-assembly of columnar liquid crystals.J. Am. Chem. Soc., 2006, 128: 8569-8574 Structural factors controlling the self-assembly of columnar liquid crystals
A series of disc-shaped molecules were prepared by the condensation of 1,2-diamines with 2,3,6,7-tetrakis(hexyloxy) phenanthrene-9,10-dione to investigate the relationship between changes in molecular structure and the self-assembly of columnar liquid crystalline phases. A comparison of compounds with different core sizes indicated that molecules with larger aromatic cores had a greater propensity to form columnar phases, as did compounds substituted with electron-withdrawing groups. In contrast, molecules with electron-donating substituents were nonmesogenic. The clearing temperature of columnar phases increased linearly with the electron-withdrawing ability of the substituents, as quantified by Hammett sigma-values. The observed trends can be rationalized in terms of the strength of pi-pi interactions between aromatic cores in the liquid crystalline phases and suggest that both electrostatic interactions and dispersion forces play important roles in the self-assembly of these materials. DOI PubMed
79. Molloy, PP; Gage, MJG.Evolution: Vertebrate reproductive strategies get mixed up.Curr Biol, 2006, 16: R876-R879 Evolution: Vertebrate reproductive strategies get mixed up
The mangrove killifish is the only vertebrate known to have a mixed-mating strategy, where hermaphrodites reproduce by either self-fertilisation or cross-breeding. New molecular evidence from this species reveals that occasional cross-breeding between common hermaphroditic individuals and rare pure males results in an injection of genetic variation into otherwise highly homozygous 'clonal' lineages.
78. Nosil, P.Frequency-dependent selection: When being different makes you not stand out.Curr Biol, 2006, 16: R806-R808 Frequency-dependent selection: When being different makes you not stand out
A recent study reports frequency-dependent survival within highly variable guppy populations. Fitness advantages to rare genotypes may help maintain variation within populations, but the mechanisms underlying these advantages require further study.
77. Park, Y; Chen, XB; Punja, ZK.Molecular and biological characterization of a mitovirus in Chalara elegans (Thielaviopsis basicola).Phytopathology, 2006, 96: 468-479 Molecular and biological characterization of a mitovirus in Chalara elegans (Thielaviopsis basicola)
black root rot; fungal virus; mycovirus
A 2.8-kb double-stranded RNA (dsRNA) element in strain BK18 of Chalara elegans originally isolated from cotton soil in California was characterized by obtaining a full-length cDNA sequence (2,896 nucleotides in length) from a series of overlapping clones. Sequence analysis revealed the presence of one large open reading frame (ORF I) using the initochondrial genetic code, with 20 to 34% amino acid identity to the ORF I of other previously reported fungal mitochondrial RNA viruses. The ORF I encoded a putative protein of 705 amino acids and contained the conserved motif characteristic of RNA-dependent RNA polymerases. Purification of mitochondria from strain BK 18 confirmed the co-localization of this dsRNA. and northern blot hybridization with a strand-specific probe revealed the (+) single-stranded nature. This Chalara elegans mitovirus (CeMV) is designated as a new member of the genus Mitovirus of the family Narnaviridae. Using dsRNA-specific primers. the ORF I region (positions 427 to 2544) was obtained from an additional 2.8-kb dsRNA element in strain HA2 originating from carrot roots in the Netherlands. Both ORFs had 98% homology at the nucleotide and amino acid levels. CeMV was also found to be present in five additional strains of C. elegans from different geographic locations worldwide, and a 97 to 100% nucleotide sequence identity was observed within a 300-bp region of ORF I in these strains. To determine the biological effects of CeMV on C. elegans, attempts to cure strain BK 18 of the dsRNA were made. Sequential transfers of mycelium at 35 to 37 degrees C yielded a colony which lacked the 2.8-kb dsRNA when visualized on agarose gels and also in northern blot hybridization analysis. However. reverse transcription-polymerase chain reaction with specific primer sets revealed a band., indicating that dsRNA replication had been significantly repressed (latent). The wild type and latently infected strains were compared for colony morphology, growth rate, melanin production, various enzymatic assays (polyphenoloxidase, laccase. tyrosinase, and esterase), and virulence on carrot roots. Colony morphology on V8 agar was comparable between the two strains. while growth rate, melanin production, and virulence were enhanced in the latently infected strain. There were no detectable differences in enzymatic activity. Transmission electron microscopy of hyphae of the wild type and latently infected strains revealed differences in the number and size of the mitochondria, which were enhanced in the latently infected strain. Our results show that CeMV is a new member of the genus Mitovirus with some disruptive effects on its fungal host and is present in C. elegans strains from different locations worldwide.
76. Rahman, M; Punja, ZK.Influence of iron on cylindrocarpon root rot development on ginseng.Phytopathology, 2006, 96: 1179-1187 Influence of iron on cylindrocarpon root rot development on ginseng
Cylindrocarpon root rot, caused by Cylindrocarpon destructans, is an important disease on ginseng (Panax quinquefolius) in Canada. We studied the effects of iron (Fe) on disease severity and pathogen growth. When Hoagland's solution was amended with Fe at 56 and 112 mu g/ml compared with 0 mu g/ml, disease initiation and final severity on hydroponically maintained ginseng roots was significantly (P < 0.0001) enhanced. Under field conditions. wounding of roots with a fine needle followed by application of 0.05% FeNaEDTA to the rhizosphere of treated plants significantly enhanced Cylindrocarpon root rot in 2003 and 2004 compared with unwounded roots with Fe or wounded roots without Fe. Foliar applications of Fe (as FeNaEDTA) to ginseng plants three times during the 2002 and 2003 growing seasons significantly increased Fe levels in root tissues. These roots developed larger lesions following inoculation with C. destructons in vitro. When radioactive Fe (Fe-59) was applied to the foliage of ginseng plants, it was detected in the secondary phloem and in cortical and epidermal tissues within I week. Artificially wounded areas on the roots accumulated more Fe-59 than healthy areas. Diseased tissue also had threefold higher levels of phenolic compounds and Fe compared with adjoining healthy tissues. High-performance liquid chromatography analysis revealed enhanced levels of protocatechuic acid, chlorogenic acid, caffeic acid, ferulic acid, cinnamic acid, phloridizin, and quercetin. Phenolic compounds produced in diseased and wounded tissues sequestered Fe in vitro. The effects of Fe on mycelial growth, conidial germ tube length, and secondary branching of germ tubes of C destructans were examined in vitro. When grown on Chrome-azurol S medium, Fe also was sequestered by C. destructans through siderophore production, which was visualized as a clearing pigmented zone at the margin of colonies. Mycelial dry weight was significantly increased in glucose/yeast broth containing Fe at 56 or 112 mu g/ml. Conidial germ tube length and secondary branching of hyphae also were enhanced after 8 and 16 h by Fe. Colony growth of C. destructans was not enhanced by Fe, but significantly greater spore production was observed with Fe at 56 and 112 mu g/ml compared with no Fe in the medium. Although these levels of Fe had no effect on fungal pectinase enzyme activity, polyphenoloxidase (PPO) activity was significantly (P < 0.0001) enhanced. We conclude that Fe enhances Cylindrocarpon root rot through enhanced pathogen growth, sporulation, and PPO enzyme activity. Fe sequestered by phenolic cornpounds produced in wounded tissues can enhance Fe levels at the site of infection. The pathogen also has the ability to sequester Fe at these sites.
75. Reid, MJC; Ursic, R; Cooper, D; Nazzari, H; Griffiths, M; Galdikas, BM; Garriga, RM; Skinner, M; Lowenberger, C.Transmission of human and macaque Plasmodium spp. to ex-captive Orangutans in Kalimantan, Indonesia.Emerg Infect Dis, 2006, 12: 1902-1908 Transmission of human and macaque Plasmodium spp. to ex-captive Orangutans in Kalimantan, Indonesia
Data are lacking on the specific diseases to which great apes are susceptible and the transmission dynamics and overall impact of these diseases. We examined the prevalence of Plasmodium spp. infections in semicaptive orangutans housed at the Orangutan Care Center and Quarantine, Central Kalimantan, Indonesia, by using a combination of microscopic and DNA molecular techniques to identify the Plasmodium spp. in each animal. Previous studies indicated 2 orangutan-specific Plasmodium spp., but our data show 4 Plasmodium spp. These findings provide evidence for P vivax transmission between humans and orangutans and for P cynomolgi transmission between macaques and orangutans. These data have potential implications for the conservation of orangutans and also for the bidirectional transmission of parasites between orangutans and humans visiting or living in the region.
74. Verma, N; MacDonald, L; Punja, ZK.Inoculum prevalence, host infection and biological control of Colletotrichum acutatum: causal agent of blueberry anthracnose in British Columbia.Plant Pathol, 2006, 55: 442-450 Inoculum prevalence, host infection and biological control of Colletotrichum acutatum: causal agent of blueberry anthracnose in British Columbia
biological control; diagnostics; epidemiology; Gliocladium catenulatum; Trichoderma harzianum; Vaccinium corymbosum
To identify the causal organism of anthracnose (ripe-rot), which reduces yield and postharvest quality of blueberries grown in British Columbia, Canada, 80 isolates were recovered from diseased fruits collected from commercial blueberry fields during 2002-04 and identified as Colletotrichum acutatum using colony morphology, growth rate and species-specific PCR primers. In vitro incubation of replicated sets of inoculated detached berries at various temperatures produced infection at temperatures of 7-30 degrees C, with an optimum at 20 degrees C. Colletotrichum acutatum could not survive on the soil surface as mummified berries but the pathogen was detected mostly within flower buds and less so in blueberry twigs and fruit trusses. Infection of developing flower buds in May-June of the preceding growing season gave the highest inoculum recovery in the following year. Two commercial fungal biocontrol agents, Prestop (Gliocladium catenulatum) and PlantShield (Trichoderma harzianum), each reduced anthracnose development in 2003 and 2004 by up to 45% when sprayed three times onto plants between flowering and fruit ripening.
69. Crespi, B; Summers, K.Evolutionary biology of cancer.Trends in Ecology & Evolution, 2005, 20: 545-552 Evolutionary biology of cancer
Cancer is driven by the somatic evolution of cell lineages that have escaped controls on replication and by the population-level evolution of genes that influence cancer risk. We describe here how recent evolutionary ecological studies have elucidated the roles of predation by the immune system and competition among normal and cancerous cells in the somatic evolution of cancer. Recent analyses of the evolution of cancer at the population level show how rapid changes in human environments have augmented cancer risk, how strong selection has frequently led to increased cancer risk as a byproduct, and how anticancer selection has led to tumor-suppression systems, tissue designs that slow somatic evolution, constraints on morphological evolution and even senescence itself. We discuss how applications of the tools of ecology and evolutionary biology are poised to revolutionize our understanding and treatment of this disease.
68. Foster, EJ; Lavigueur, C; Ke, YC; Williams, VE.Self-assembly of hydrogen-bonded molecules: discotic and elliptical mesogens.J. Mater. Chem., 2005, 15: 4062-4068 Self-assembly of hydrogen-bonded molecules: discotic and elliptical mesogens
The effect of hydrogen bonding on the phase behaviour of discotic mesogens was investigated with a series of dibenzophenazine carboxylic acids and their methyl ester analogues. The esters exhibit only columnar hexagonal phases, while the acids form columnar hexagonal, columnar rectangular and nematic mesophases. The acids have much higher transition temperatures and supercool to room temperature while maintaining the liquid crystalline ordering. These differences could be explained by the ability of the acids to form hydrogen-bonded dimers, which may also be regarded as supramolecular elliptically-shaped mesogens. DOI
66. Morrissey, CA; Bendell-Young, LI; Elliott, JE.Identifying sources and biomagnification of persistent organic contaminants in biota from mountain streams of southwestern British Columbia, Canada.Environmental Science & Technology, 2005, 39: 8090-8098 Identifying sources and biomagnification of persistent organic contaminants in biota from mountain streams of southwestern British Columbia, Canada
We assessed whether biota occupying mountain streams accumulate and biomagnify remotely derived organic pollutants originating from atmospheric inputs to snowpack and glacial runoff and from marine sources introduced by migrating anadromous salmon. Several persistent organic pollutants including polychlorinated biphenyls (PCBs), p,p'-dichloro-diphenyl-dichloroethylene, hexachlorobenzene, and trans-nonachlor were commonly detected in benthic invertebrates, salmon fry (Oncorhynchus spp.), and eggs of an aquatic passerine, the American dipper (Cinclus mexicanus) from the Chilliwack River watershed, British Columbia, Canada. Total PCBs and several organochlorines (M) biomagnified from benthic invertebrate composites to salmon fry to dipper eggs. Invertebrate samples generally did not differ significantly in contaminant burdens between the river main stem where salmon are more abundant and higher-elevation tributaries where the salmon density is lower. Concentrations of total OCs and total PCBs in dipper eggs were positively related to drainage basin area and collection year but not to elevation. No differences in PCB congener patterns existed between dipper egg samples from the Chilliwack watershed and other watersheds in southwestern British Columbia. However, principal component analysis revealed significant spatial differences in egg PCB congener patterns between the main Chilliwack River and the higher-elevation tributaries. This difference was primarily due to a greater occurrence of lower chlorinated PCB congeners (66 and 105) in dipper eggs collected from the tributaries and higher loadings of the more stable and persistent congeners (153, 138, 130, and 128) in eggs from the river main stem. The results suggest that atmospheric sources are the main contributor of contaminants detected in biota from the region and that biomagnification is a common pathway for accumulation in lotic predators such as the American dipper.
65. Oliver, F. , Christians, J.K. , Liu, X, Rhind, S., Verma, V., Davison, C., Brown, S.D.M, Denny, P., and Keightley, P.D.Regulatory variation at glypican-3 underlies a major growth QTL in mice.PLOS Biology, 2005, 3: e135. Regulatory variation at glypican-3 underlies a major growth QTL in mice.
The genetic basis of variation in complex traits remains poorly understood, and few genes underlying variation have been identified. Previous work identified a quantitative trait locus (QTL) responsible for much of the response to selection on growth in mice, effecting a change in body mass of approximately 20%. By fine-mapping, we have resolved the location of this QTL to a 660-kb region containing only two genes of known function, Gpc3 and Gpc4, and two other putative genes of unknown function. There are no non-synonymous polymorphisms in any of these genes, indicating that the QTL affects gene regulation. Mice carrying the high-growth QTL allele have approximately 15% lower Gpc3 mRNA expression in kidney and liver, whereas expression differences at Gpc4 are non-significant. Expression profiles of the two other genes within the region are inconsistent with a factor responsible for a general effect on growth. Polymorphisms in the 3' untranslated region of Gpc3 are strong candidates for the causal sequence variation. Gpc3 loss-of-function mutations in humans and mice cause overgrowth and developmental abnormalities. However, no deleterious side-effects were detected in our mice, indicating that genes involved in Mendelian diseases also contribute to complex trait variation. Furthermore, these findings show that small changes in gene expression can have substantial phenotypic effects.PDF
64. Park, YJ; James, D; Punja, ZK.Co-infection by two distinct totivirus-like double-stranded RNA elements in Chalara eleganse (Thielaviopsis basicola).Virus Research, 2005, 109: 71-85 Co-infection by two distinct totivirus-like double-stranded RNA elements in Chalara eleganse (Thielaviopsis basicola)
Chalara elegans; dsRNA sequence; Totiviridae; fungal viruses
A full-length cDNA clone was developed from a 5.3 kb double-stranded (ds) RNA element present in strain CKP of the plant pathogenic fungus Chalara elegans. The complete nucleotide sequence was 5310bp in length and sequence analysis revealed that it contained three large putative open reading frames (ORFs). ORFI was initiated at nucleotide position 329 and encoded a putative coat protein, which shared some homology (35-45% amino acid identity) to other dsRNAs in the family Totiviridae. Both ORF2 and ORF3 were initiated at nucleotide positions 2619 and 4071, respectively, and encoded a putative RNA-dependent RNA polymerase (RdRp). Sequence comparison using deduced amino acid sequences of both ORF2 and ORF3 revealed that all RdRp conserved motifs shared highest homology (41% identity) to that of SsRNA1 of Totiviridae. This dsRNA in C. elegans was designated Chalara elegans RNA Virus 1 (CeRV1). During the development of the full-length cDNA clone of CeRV1, several partial cDNA clones from an additional dsRNA fragment in strain CKP were obtained, which when aligned with each other, produced one linear fragment which was 2336 bp long. Northern blot and sequence analysis of this second clone showed it differed in sequence composition from CeRV1. This dsRNA in C. elegans was designated Chalara elegans RNA Virus 2 (CeRV2). Sequence analysis of CeRV2 showed it contained all conserved motifs and shared some homology (45% amino acid identity) to RdRp regions of Totiviridae. The nucleotide and amino acid sequences of the conserved motifs of the RdRp regions between CeRV1 and CeRV2 showed an identity of 56% and 50%, respectively. These findings suggest that co-infection of two distinct totivirus-like dsRNAs (CeRV1 and CeRV2) in C. elegans, a first report in this fungus. Transmission electron microscopy of strain CKP of C. elegans revealed the presence of putative virus-like particles in the cytoplasm, which were similar both in shape and size to viruses in the Totiviridae. (C) 2004 Elsevier B.V. All rights reserved.
63. Patterson, RT; Dalby, AP; Roe, HM; Guilbault, JP; Hutchinson, I; Clague, JJ.Relative utility of foraminifera, diatoms and macrophytes as high resolution indicators of paleo-sea level in coastal British Columbia, Canada.Quat. Sci. Rev., 2005, 24: 2002-2014 Relative utility of foraminifera, diatoms and macrophytes as high resolution indicators of paleo-sea level in coastal British Columbia, Canada
A multiproxy analysis was carried out on diatom, foraminiferal and macrophyte assemblages across the saltmarsh at Zeballos, Vancouver Island, British Columbia. To determine which group, or combination of groups provided the most accurate elevational zonations, 36 stepwise multiple linear regressions (SMLR) were carried out using a variety of data transformations on an elevational training set. Adjusted R-2 values yielded statistically significant results in all analyses as follows: foraminifera (0.658-0.870); diatoms (0.888-0.974); macrophytes (0.671-0.844); foraminifera/diatoms (0.941-0.981); foraminifera/diatoms/macrophytes (0.958-0.993). The most realistic SMLR results were obtained when data transformations comprised of (In) normalized fractional abundance data was carried out on species present in statistically significant numbers (NrfaEQ). Of the individual proxies assessed, diatoms yielded the most significant adjusted R2 results, with the low marsh diatom Achnanthes hauckiana being one of the most important predictor variables (pv's). Amongst the foraminifera, the low marsh species Miliammina fusca and high marsh Balticammina pseudomacrescens were determined to be the most significant pv's. For macrophytes, the low marsh species Carex lyngbyei, the high marsh species Juncus balticus, Shannon-Wiener Diversity Index (SDI) and absence of plant cover on the tidal flat were the most important pv's. As SMLR analysis of all individual groups and combinations of groups yielded statistically significant results, the choice of proxies, or combinations of proxies that are suitable for paleo-sea level research is at the discretion of the researcher. (c) 2005 Elsevier Ltd. All rights reserved. DOI
62. Perry, AL; Low, PJ; Ellis, JR; Reynolds, JD.Climate change and distribution shifts in marine fishes.Science, 2005, 308: 1912-1915 Climate change and distribution shifts in marine fishes
We show that the distributions of both exploited and nonexploited North Sea fishes have responded markedly to recent increases in sea temperature, with nearly two-thirds of species shifting in mean latitude or depth or both over 25 years. For species with northerly or southerly range margins in the North Sea, half have shown boundary shifts with warming, and all but one shifted northward. Species with shifting distributions have faster life cycles and smaller body sizes than nonshifting species. Further temperature rises are likely to have profound impacts on commercial fisheries through continued shifts in distribution and alterations in community interactions.
61. Rahman, M; Punja, ZK.Factors influencing development of root rot on ginseng caused by Cylindrocarpon destructans.Phytopathology, 2005, 95: 1381-1390 Factors influencing development of root rot on ginseng caused by Cylindrocarpon destructans
disappearing root rot; epidemiology; Panax quinquefolius; pathogenicity
The fungus Cylindrocarpon destructans (Zins) Scholten is the cause of root rot (disappearing root rot) in many ginseng production areas in Canada. A total of 80 isolates of C. destructans were recovered from diseased roots in a survey of ginseng gardens in British Columbia from 2002-2004. Among these isolates, 49% were classified as highly virulent (causing lesions on unwounded mature roots) and 51% were weakly virulent (causing lesions only on previously wounded roots). Pectinase and polyphenoloxidase enzymes were produced in vitro by C. destructans isolates when they were grown on pectin and phenol as a substrate, respectively. However, highly virulent isolates produced significantly (P < 0.001) higher enzyme levels compared with weakly virulent isolates. Histopathological studies of ginseng roots inoculated with a highly virulent isolate revealed direct hyphal penetration through the epidermis, followed by intracellular hyphal growth in the cortex. Subsequent cell disintegration and accumulation of phenolic compounds was observed. Radial growth of highly and weakly virulent isolates on potato dextrose agar was highest at 18 and 21 degrees C, respectively and there was no growth at 35 degrees C. Mycelial mass production as significantly (P <= 0.01) lower at pH 7.0 compared with pH 5.0. To study the effects of pH (5.0 and 7.0) and wounding on disease development, ginseng roots were grown hydroponically in Hoagland's solution. Lesions were significantly larger (P < 0.001) at pH 5.0 compared with pH 7.0 and wounding enhanced disease by a highly virulent isolate at both pHs. In artificially infested soil, 2-year-old ginseng roots were most susceptible to Cylindrocarpon root rot among all root ages tested (I to 4 years) when evaluated using a combined scale of disease incidence and severity. Root rot severity was significantly (P < 0.002) enhanced by increasing the inoculum density from 3.45 x 10(2) CFU/g of soil to 1.86 x 10(3) CFU/g of soil. Disease severity was higher at 20 degrees C compared with 15 and 25 degrees C and at -0.02 MPa soil moisture compared with -0.005 and -0.001 MPa. A significant interaction between soil moisture and temperature was observed for root rot severity.
59. Calvert, AJ.Seismic reflection imaging of two megathrust shear zones in the northern Cascadia subduction zone.Nature, 2004, 428: 163-167 Seismic reflection imaging of two megathrust shear zones in the northern Cascadia subduction zone
At convergent continental margins, the relative motion between the subducting oceanic plate and the overriding continent is usually accommodated by movement along a single, thin interface known as a megathrust(1). Great thrust earthquakes occur on the shallow part of this interface where the two plates are locked together(2). Earthquakes of lower magnitude occur within the underlying oceanic plate, and have been linked to geochemical dehydration reactions caused by the plate's descent(3-7). Here I present deep seismic reflection data from the northern Cascadia subduction zone that show that the inter-plate boundary is up to 16 km thick and comprises two megathrust shear zones that bound a >5-km-thick, similar to110-km-wide region of imbricated crustal rocks. Earthquakes within the subducting plate occur predominantly in two geographic bands where the dip of the plate is inferred to increase as it is forced around the edges of the imbricated inter-plate boundary zone. This implies that seismicity in the subducting slab is controlled primarily by deformation in the upper part of the plate. Slip on the shallower megathrust shear zone, which may occur by aseismic slow slip, will transport crustal rocks into the upper mantle above the subducting oceanic plate and may, in part, provide an explanation for the unusually low seismic wave speeds that are observed there(8,9). DOI PubMed
57. Clague, JJ; Wohlfarth, B; Ayotte, J; Eriksson, M; Hutchinson, I; Mathewes, RW; Walker, IR; Walker, L.Late Holocene environmental change at treeline in the Northern Coast Mountains, British Columbia, Canada.Quat. Sci. Rev., 2004, 23: 2413-2431 Late Holocene environmental change at treeline in the Northern Coast Mountains, British Columbia, Canada
An integrated stratigraphic, paleoecological, and geochronological study of lake and fen sediments just beyond the terminus of Berendon Glacier provides insights into late Holocene climate, vegetation, and glacier change in the northern Coast Mountains of British Columbia. Cores collected from two small lakes in the foreland of Berendon Glacier and pits dug in a nearby fen record Little lee Age and older glacier advances. The first Little Ice Age advance in this area began more than 500 years ago and peaked in the early 17th century. An earlier Neoglacial advance began about 2800-3000 cal yr ago and may have lasted for hundreds of years. There is also evidence for an intervening advance of even smaller magnitude around 1200-1300 cal yr ago. The advances are broadly synchronous with those in other parts of western North America, indicating that they were caused by regional, possibly global, changes in climate. Plant communities within the study area did not change dramatically during the late Holocene. The ranges of some plants, however, likely retracted or extended near treeline in response to changes in mean temperatures of perhaps 1-2degreesC, as A well as changes in summer snow cover. The greatest changes in vegetation occurred within and just beyond the forefields of Berendon, Frank Mackie, and other nearby glaciers. The largest climate shifts of the last 3000 years took place during the late Little Ice Age and the last century. Climate warmed about 1-2degreesC during the 20th century, accompanied by a rise in treeline, an increase in coniferous tree cover in the subalpine zone, and an increase in the temperature and biological productivity of ponds. These trends are likely to continue if climate, as expected, continues to warm. (C) 2004 Elsevier Ltd. All rights reserved. DOI
56. Crespi, BJ.Vicious circles: positive feedback in major evolutionary and ecological transitions.Trends in Ecology & Evolution, 2004, 19: 627-633 Vicious circles: positive feedback in major evolutionary and ecological transitions
Evolutionary biologists and ecologists often focus on equilibrium states that are subject to forms of negative feedback, such as optima for phenotypic traits or regulation of population sizes. However, recent theoretical and empirical studies show how positive feedback can be instrumental in driving many of the most important and spectacular processes in evolutionary ecology, including the evolution of sex and genetic systems, mating systems, life histories, complex cooperation in insects and humans, ecological specialization, species diversity, species ranges, speciation and extinction. Taken together, this work suggests that positive feedback is more common than is generally appreciated, and that its self-reinforcing dynamics generate the conditions for changes that might otherwise be difficult or impossible for selection or other mechanisms to achieve. Testing for positive feedback requires analysing each causal link in feedback loops, tracking genetic, character and population-dynamic changes across generations, and elucidating the conditions that can result in self-reinforcing change.
55. de Napoles, M; Mermoud, JE; Wakao, R; Tang, YA; Endoh, M; Appanah, R; Nesterova, TB; Silva, J; Otte, AP; Vidal, M; Koseki, H; Brockdorff, N.Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation.Dev. Cell, 2004, 7: 663-676 Polycomb group proteins Ring1A/B link ubiquitylation of histone H2A to heritable gene silencing and X inactivation
In many higher organisms, 5%-15% of histone H2A is ubiquitylated at lysine 119 (uH2A). The function of this modification and the factors involved in its establishment, however, are unknown. Here we demonstrate that uH2A occurs on the inactive X chromosome in female mammals and that this correlates with recruitment of Polycomb group (PcG) proteins belonging to Polycomb repressor complex 1 (PRC1). Based on our observations, we tested the role of the PRC1 protein Ring1B and its closely related homolog Ring1A in H2A ubiquitylation. Analysis of Ring1B null embryonic stem (ES) cells revealed extensive depletion of global uH2A levels. On the inactive X chromosome, uH2A was maintained in Ring1A or Ring1B null cells, but not in double knockout cells, demonstrating an overlapping function for these proteins in development. These observations link H2A ubiquitylation, X inactivation, and PRC1 PcG function, suggesting an unanticipated and novel mechanism for chromatin-mediated heritable gene silencing. DOI PubMed
54. Franken, RJ; Hik, DS.Influence of habitat quality, patch size and connectivity on colonization and extinction dynamics of collared pikas Ochotona collaris.J. Anim. Ecol., 2004, 73: 889-896 Influence of habitat quality, patch size and connectivity on colonization and extinction dynamics of collared pikas Ochotona collaris
area; isolation; metapopulation; occupancy; persistence
1. The effects of habitat quality, patch size and connectivity between patches on patterns of local extinction and colonization of collared pikas were studied over 7 years in alpine meadows in the south-west Yukon. 2. Although adult population size independently had a significant influence on patch extinction, its influence was minimal when other variables were included in generalized linear models. Instead, an index of habitat quality and the connectivity of a patch were found to be the best predictors of pika extinction. 3. Similarly, patch connectivity only partly explained the recolonization of talus patches by pikas. Other patch characteristics, including aspect, amount of vegetation within the patch and an index of habitat quality based on survival probability of pikas also had a significant influence on recolonization. 4. These results suggest that the influence of patch quality on local extinction and recolonization need to be more fully incorporated into metapopulation models. DOI
53. Mak, W; Nesterova, TB; de Napoles, M; Appanah, R; Yamanaka, S; Otte, AP; Brockdorff, N.Reactivation of the paternal X chromosome in early mouse embryos.Science, 2004, 303: 666-669 Reactivation of the paternal X chromosome in early mouse embryos
It is generally accepted that paternally imprinted X inactivation occurs exclusively in extraembryonic lineages of mouse embryos, whereas cells of the embryo proper, derived from the inner cell mass (ICM), undergo only random X inactivation. Here we show that imprinted X inactivation, in fact, occurs in all cells of early embryos and that the paternal X is then selectively reactivated in cells allocated to the ICM. This contrasts with more differentiated cell types where X inactivation is highly stable and generally irreversible. Our observations illustrate that an important component of genome plasticity in early development is the capacity to reverse heritable gene silencing decisions. DOI PubMed
52. Menounos, B; Koch, J; Osborn, G; Clague, JJ; Mazzucchi, D.Early Holocene glacier advance, southern Coast Mountains, British Columbia, Canada.Quat. Sci. Rev., 2004, 23: 1543-1550 Early Holocene glacier advance, southern Coast Mountains, British Columbia, Canada
Terrestrial and lake sediment records from several sites in the southern Coast Mountains, British Columbia, provide evidence for an advance of alpine glaciers during the early Holocene. Silty intervals within organic sediments recovered from two proglacial lakes are bracketed by AMS C-14-dated terrestrial macrofossils and Mazama tephra to 8780-6730 and 7940-6730 C-14 yr BP [10,150-7510 and 8990-7510 cal yr BP]. Radiocarbon ages ranging from 7720 to 7380 14C yr BP [8630-8020 cal yr BP] were obtained from detrital wood in recently deglaciated forefields of Sphinx and Sentinel glaciers. These data, together with previously published data from proglacial lakes in the Canadian Rockies, imply that glaciers in western Canada advanced during the early Holocene. The advance coincides with the well-documented 8200-yr cold event identified in climate proxy data sets in the North Atlantic region and elsewhere. (C) 2003 Elsevier Ltd. All rights reserved. DOI
51. Morrissey, CA; Bendell-Young, LI; Elliott, JE.Linking contaminant profiles to the diet and breeding location of American dippers using stable isotopes.Journal of Applied Ecology, 2004, 41: 502-512 Linking contaminant profiles to the diet and breeding location of American dippers using stable isotopes
biomonitor; mercury; (15)Nitrogen; organochlorines; PCB; rivers; salmon fry; selenium
1. Individual variation in contaminant levels is a common occurrence in many toxicology studies, but the exact cause is often unclear. We investigated the influence of diet and breeding location on individual bird contaminant profiles using a colour-marked population of American dippers Cinclus mexicanus. The population comprised two distinct groups within a single river system: resident dippers breeding on the main river and altitudinal migrants breeding on tributaries. 2. Residue analysis revealed that total organochlorines (OC), polychlorinated biphenyls (PCB) and mercury (Hg) were all significantly higher in eggs from river residents compared with tributary migrants. This trend was also apparent for the three most prevalent organochlorine compounds: p,p'-dichlorodiphenyl-dichloroethylene (DDE), hexachlorobenzene and trans-nonachlor. 3. We hypothesized that the observed differences in contaminant concentrations were partially related to the proportion of salmon fry Oncorhynchus spp. in the diet relative to aquatic invertebrates. Stable isotope analyses using delta(13)C and delta(15)N were conducted on blood and feathers of dippers in addition to aquatic invertebrates and salmon fry prey. Linear mixing models using the N-15 isotope in the dippers' diet and blood revealed considerable variability in the proportion of fish consumed (0-71%). Resident dippers on the main river ate significantly higher proportions of fish (42%) than tributary migrants (22%) (P = 0.01). 4. The difference in diet between migratory groups explained some of the observed variation in egg contaminant profiles, as total OC (P = 0.002) in dipper eggs was positively correlated with blood delta(15)N values, indicating fish may be the primary source of contamination. 5. Synthesis and applications. We conclude that dipper eggs represent local conditions at the breeding site, making them useful tools for biomonitoring aquatic contaminants in watersheds. However, given the distinct difference in contaminant profiles between resident and migrant dippers and the link with diet, the results emphasize the importance of understanding individual species' ecology for assessing toxicological effects at the population level.
50. Widmeyer, JR; Crozier, ED; Moore, MM; Jurgensen, A; Bendell-Young, LI.Role of Leptothrix discophora in mediating metal uptake in the filter-feeding bivalve Mytilus trossulus (edulis).Environmental Science & Technology, 2004, 38: 769-774 Role of Leptothrix discophora in mediating metal uptake in the filter-feeding bivalve Mytilus trossulus (edulis)
The potential for filter-feeding bivalves to accumulate metals from a wide range of food sources is an important consideration when examining trophic transfer of metals up the food chain. The objective of this study was to determine the role of Leptothrix discophora in mediating metal uptake in the filter-feeding bivalve Mytilus trossulus. The bacterium L. discophora SP-6 was cultured in the absence or presence of Mn, allowing for a naturally formed Mn oxide sheath to develop. Secondary metals (Cd and Pb) were then added to the cultures, allowing for potential Cd and Pb adsorption to the Mn oxide sheath. Resulting bacterial aggregates of known diameter were then fed to the bivalve M. trossulus using a flow-through system. Initial concentrations of both Pb and Cd on the bacterium did not differ significantly in the presence or absence of the Mn oxide; conversely both Pb (F = 7.39, p < 0.0001) and Cd (F = 33.65, P < 0.0001) were found at lower concentrations in the mussel tissue when the Mn oxide was present. To determine whether these differences in metal uptake could be attributed to sorting by the mussel based on food quality, nutritional analysis was performed. Bacterial food matrixes containing Mn oxides were found to have significantly lower levels of carbon (F = 256, p < 0.0001). Particle clearance rates for the various food matrixes were positively correlated with organic content (R-2 = 0.852, p > 0.008). The results of our study suggest that metal uptake in M. trossulus was significantly decreased for Cd with a similar trend for Pb when the SP-6 sheath contained Mn oxides. The mechanism mediating this differential uptake is best explained by food quality, in that a higher quality food source enhanced metal uptake due to an increased clearance rate of organic-rich particles by M. trossulus.
49. Worobey, M., M.L. Santiago, B.F. Keele, J.N. Ndjango, J. B. Joy, B. Labama, B.D. Dhed’a, A. Rambaut, P.M. Sharp, G.M. Shaw, B.H. Hahn.Origin of AIDS: Contaminated polio vaccine theory refuted.Nature, 2004, 428(6985):820 Origin of AIDS: Contaminated polio vaccine theory refuted
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48. Blais-Stevens, A; Clague, JJ; Mathewes, RW; Hebda, RJ; Bornhold, BD.Record of large, Late Pleistocene outburst floods preserved in Saanich Inlet sediments, Vancouver Island, Canada.Quat. Sci. Rev., 2003, 22: 2327-2334 Record of large, Late Pleistocene outburst floods preserved in Saanich Inlet sediments, Vancouver Island, Canada
Two anomalous, gray, silty clay beds are present in ODP cores collected from Saanich Inlet, Vancouver Island, British Columbia, Canada. The beds, which date to about 10,500 C-14 yr BP (11,000 calendar years BP), contain Tertiary pollen derived from sedimentary rocks found only in the Fraser Lowland, on the mainland of British Columbia and Washington just east of the Strait of Georgia. Abundant illite-muscovite in the sediments supports a Fraser Lowland provenance. The clay beds are probably distal deposits of huge floods that swept through the Fraser Lowland at the end of the Pleistocene. Muddy overflow plumes from these floods crossed the Strait of Georgia and entered Saanich Inlet, where the sediment settled from suspension and blanketed diatom-rich mud on the fiord floor. The likely source of the floods is Late Pleistocene, ice-dammed lakes in the Fraser and Thompson valleys, which are known to have drained at about the time the floods occurred. (C) 2003 Elsevier Ltd. All rights reserved. DOI
47. Cory, JS; Myers, JH.The ecology and evolution of insect baculoviruses.Annual Review of Ecology Evolution and Systematics, 2003, 34: 239-272 The ecology and evolution of insect baculoviruses
virulence; resistance; pathogen; variation; transmission
Baculoviruses occur widely among Lepidoptera, and in some species of forest and agricultural insects, they cause epizootics in outbreak populations. Here we review recent developments in baculovirus ecology and evolution, in particular focusing on emerging areas of interest and studies relating to field populations. The expanding application of molecular techniques has started to reveal the structure of baculovirus populations and has highlighted how variable these pathogens are both genotypically and phenotypically at all levels from within individual hosts to among host populations. In addition, the detailed molecular knowledge available for baculoviruses has allowed the interpretation of gene functions across physiological and population levels in a way rarely possible in parasite-host systems and showed the diverse mechanisms that these viruses use to exploit their hosts. Analysis of the dynamic interactions between insects and baculoviruses, and their compatibility for laboratory and field experiments, has formed a basis for studies that have made a significant contribution to unraveling disease interactions in insect populations. In particular, manipulative studies on baculoviruses have been instrumental in developing an understanding of disease transmission dynamics. The results so far indicate that baculoviruses have the potential to be an excellent model for investigations of changes in virulence and resistance in fluctuating and stable host populations. DOI
46. Herniou, EA; Olszewski, JA; Cory, JS; O'Reilly, DR.The genome sequence and evolution of baculoviruses.Annual Review of Entomology, 2003, 48: 211-234 The genome sequence and evolution of baculoviruses
Baculoviridae; phylogeny; gene order; gene composition; gene function
Comparative analysis of the complete genome sequences of 13 baculoviruses revealed a core set of 30 genes, 20 of which have known functions. Phylogenetic analyses of these 30 genes yielded a tree with 4 major groups: the genus Granulovirus (GVs), the group I and II lepidopteran nucleopolyhedroviruses (NPVs), and the dipteran NPV, CuniNPV. These major divisions within the family Baculoviridae were also supported by phylogenies based on gene content and gene order. Gene content mapping has revealed the patterns of gene acquisitions and losses that have taken place during baculovirus evolution, and it has highlighted the fluid nature of baculovirus genomes. The identification of shared protein phylogenetic profiles provided evidence for two putative DNA repair systems and for viral proteins specific for infection of lymantrid hosts. Examination of gene order conservation revealed a core gene cluster of four genes, helicase, lef-5, ac96, and 38K(ac98), whose relative positions are conserved in all baculovirus genomes. DOI
44. Silva, J; Mak, W; Zvetkova, I; Appanah, R; Nesterova, TB; Webster, Z; Peters, AHFM; Jenuwein, T; Otte, AP; Brockdorff, N.Establishment of histone H3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 Polycomb group complexes.Dev. Cell, 2003, 4: 481-495 Establishment of histone H3 methylation on the inactive X chromosome requires transient recruitment of Eed-Enx1 Polycomb group complexes
Previous studies have implicated the Eed-Enx1 Polycomb group complex in the maintenance of imprinted X inactivation in the trophectoderm lineage in mouse. Here we show that recruitment of Eed-Enx1 to the inactive X chromosome (Xi) also occurs in random X inactivation in the embryo proper. Localization of Eed-Enx1 complexes to Xi occurs very early, at the onset of Xist expression, but then disappears as differentiation and development progress. This transient localization correlates with the presence of high levels of the complex in totipotent cells and during early differentiation stages. Functional analysis demonstrates that Eed-Enx1 is required to establish methylation of histone H3 at lysine 9 and/or lysine 27 on Xi and that this, in turn, is required to stabilize the Xi chromatin structure. DOI PubMed
43. Ward, BC; Wilson, MC; Nagorsen, DW; Nelson, DE; Driver, JC; Wigen, RJ.Port Eliza cave: North American West Coast interstadial environment and implications for human migrations.Quat. Sci. Rev., 2003, 22: 1383-1388 Port Eliza cave: North American West Coast interstadial environment and implications for human migrations
The timing of Late Pleistocene glacial advance, retreat, relative sea level and environmental viability between 25 and 12.5 ka (C-14 yrs BP) remain a key issue in the feasibility of a coastal migration route for the first North Americans. This is discussed on the basis of stratigraphic, radiometric and faunal data for Port Eliza cave, a raised sea cave, on the west coast of Vancouver Island, British Columbia. Ice cover is indicated by the occurrence of 2m of laminated clay, representing deposition in a subglacial take. From immediately below this clay a diverse vertebrate fauna of marmot, vote, marten, cervid and various species of birds and fish was recovered, yielding ages of 18-16 ka. These dates and others from the region show that ice cover on the outer coast was brief, from ca 15.5-14ka.. The fish species indicate that relative sea level was close to the cave and that salmon runs were likely present. The terrestrial vertebrate fauna is consistent with a cool, open parkland environment with maximum summer temperatures cooler than present; these conditions lasted until at least 16 ka. With a diverse fauna and favorable climate, humans could have survived here on a mixed marine-terrestrial diet, confirming the viability of the coastal migration hypothesis for this portion of the route. (C) 2003 Elsevier Science Ltd. All rights reserved. DOI
41. Clague, JJ; James, TS.History and isostatic effects of the last ice sheet in southern British Columbia.Quat. Sci. Rev., 2002, 21: 71-87 History and isostatic effects of the last ice sheet in southern British Columbia
The Late Wisconsinan Cordilleran ice sheet covered British Columbia, southern Yukon Territory, and parts of Alaska, Washington, Idaho, and Montana. Its major source areas were the high mountain ranges of the Canadian Cordillera, and flow was strongly controlled by topography. The last ice sheet began to develop about 30,000-25,000 (14)C yr ago, but it did not achieve its maximum extent until 15,000-14,000 (14)C yr BP. Ice sheet growth was interrupted locally by stillstands and retreat. Ice sheet decay was rapid and was characterized by complex frontal retreat at the periphery, accompanied locally by brief readvances, and by downwasting and stagnation. By 10,000 (14)C yr BP, < 5000 yr after the Last Glacial Maximum, ice cover in British Columbia was similar to that of today. The Cordilleran ice sheet depressed the crust over which it formed. Rapid isostatic rebound during deglaciation caused the sea to fall relative to the land along the southern British Columbia coast. A postglacial rebound model explains crustal tilting and rapid uplift in this region during retreat of the ice sheet in the late Pleistocene. Small values of modelled viscosity for the upper few hundred kilometers of the mantle deliver small present-day crustal tilt rates, consistent with mid- and late-Holocene sea-level observations. Rapid sea-level fall (land uplift) on eastern Vancouver Island during deglaciation requires, in addition to a low mantle viscosity, rapid unloading of the crust due to accelerated wastage of coastal portions of the southern Cordilleran ice sheet about 12,000 (14)C yr ago. (C) 2001 Elsevier Science Ltd. All rights reserved. DOI
40. Friele, PA; Clague, JJ.Younger Dryas readvance in Squamish river valley, southern Coast mountains, British Columbia.Quat. Sci. Rev., 2002, 21: 1925-1933 Younger Dryas readvance in Squamish river valley, southern Coast mountains, British Columbia
Stratigraphy and landforms in the Brohm Creek basin and lowermost Mamquam River valley provide evidence for a readvance of a valley glacier in the southern Coast Mountains of British Columbia during the Younger Dryas interval. At Brohm Creek, till containing wood 10,500 and 10,700 C-14 yr old (ca 12,500-12,900 cal yr old), overlies an ice-contact terrace that is correlative with similar terraces at the mouth of Mamquam River, 11 km to the south and 900 m lower in elevation. A line linking the two sites has a slope of 5degrees, which is similar to slopes of termini of present-day valley glaciers in the southern Coast Mountains. We used these observations to reconstruct the Younger Dryas glacier in Squamish valley at the head of Howe Sound. The glacier deflected landslide debris, derived from steep slopes at the head of Cheekye River basin on the west flank of Mt. Garibaldi, southward to an ice-marginal lake at the mouth of Mamquam River. Foreset-bedded sediments in the core of a large, fan at the mouth of Cheekye River indicate the glacier terminus had retreated up Squamish valley beyond Cheekye and Mamquam rivers by 10,200 C-14 yr BP (11,900 cal yr old). Radiocarbon ages on the oldest postglacial sediments in a kettle on the landslide debris show that stagnant ice in the study area had melted before 10,000 C-14 yr BP (11,500 cal yr BP). The readvance of the Squamish valley glacier during the Younger Dryas Chronozone was probably driven by a regional climate reversal. (C) 2002 Elsevier Science Ltd. All rights reserved. DOI
39. Froese, D; Westgate, J; Preece, S; Storer, J.Age and significance of the Late Pleistocene Dawson tephra in eastern Beringla.Quat. Sci. Rev., 2002, 21: 2137-2142 Age and significance of the Late Pleistocene Dawson tephra in eastern Beringla
Dawson tephra, recently recognized in the Klondike area of Yukon Territory, records one of the largest Quaternary volcanic eruptions in Beringia. Its composition is similar to that of Old Crow tephra, indicating a source in the Aleutian arc-Alaska Peninsula region of southwestern Alaska. Its primary thickness in central Yukon is nearly twice that of Old Crow tephra, which has an estimated eruption volume of > 50 km(3). The distribution of Dawson tephra is still poorly known, but based on its source area and occurrence in central Yukon, it should be widespread across southern Alaska, Yukon and the Gulf of Alaska. New radiocarbon ages indicate the eruption occurred at about 24,000 C-14 yr BP (ca 27,000 cal yr BP). The Dawson tephra is a valuable marker bed for correlating late Pleistocene records across large areas of eastern Beringia and adjacent marine records. (C) 2002 Elsevier Science Ltd. All rights reserved. DOI
38. Mcintire, EJB; Hik, DS.Grazing history versus current grazing: leaf demography and compensatory growth of three alpine plants in response to a native herbivore (Ochotona collaris).J. Ecol., 2002, 90: 348-359 Grazing history versus current grazing: leaf demography and compensatory growth of three alpine plants in response to a native herbivore (Ochotona collaris)
alpine meadows; collared pika; Erigeron humilis; grazing history; herbivory gradient; Kobresia myosuroides; Ochotona collaris; Oxytropis nigrescens
1 We measured leaf births, leaf deaths and leaf length of three alpine perennial species, Kobresia myosuroides, Erigeron humilis and Oxytropis nigrescens, from sites with different grazing histories (strong or weak) in response to two levels of current season grazing (present or absent) by collared pikas (Ochotona collaris), a small lagomorph, in the south-west Yukon. 2 All three species appeared to tolerate the removal of 58-61% of summer leaf production under natural conditions. Grazing history, which was defined by the location of plants located either < 2 m or > 6 m from boulderfields with a history of occupation by pikas, was the most significant factor determining shifts in leaf births and leaf deaths following herbivory. 3 The only detectable influence of current season herbivory for any measured species was a reduction of leaf length of Kobresia. 4 A comparison of historically grazed with historically ungrazed plants indicated several changes in leaf demography and morphology. Kobresia leaves were generally shorter and had higher rates of production of new leaves. Oxytropis had higher rates of new leaf production. Erigeron had fewer leaf births throughout the summer, but showed a large and highly significant delay in the timing of leaf senescence. 5 These responses can be largely understood as strategies to avoid the predictable intensive late season foraging that is characteristic of pikas. Morphological mechanisms allow these species to tolerate and, more importantly for the herbivore, persist under heavy and chronic grazing. DOI
37. Nosil, P; Crespi, BJ; Sandoval, CP.Host-plant adaptation drives the parallel evolution of reproductive isolation.Nature, 2002, 417: 440-443 Host-plant adaptation drives the parallel evolution of reproductive isolation
Parallel evolution of similar traits in independent populations that inhabit ecologically similar environments strongly implicates natural selection as the cause of evolution(1). Parallel speciation is a special form of parallel evolution where traits that determine reproductive isolation evolve repeatedly, in closely related populations, as by-products of adaptation to ecological conditions(1,2). The outcome of such parallel evolution is that ecologically divergent pairs of populations exhibit greater levels of reproductive isolation than ecologically similar pairs of populations of a similar or younger age(2-4). The parallel evolution of reproductive isolation provides strong evidence for natural selection in the process of speciation(1), but only one conclusive example from nature is known(2). Populations of the walking-stick insect Timema cristinae that use different host-plant species have diverged in body size and shape, host preference, behaviour and the relative frequency of two highly cryptic colour-pattern morphs(5,6). Here we report that divergent selection for host adaptation, and not genetic drift, has promoted the parallel evolution of sexual isolation in this species. Our findings represent a clear demonstration that host-plant adaptation can play a crucial and repeatable role in the early stages of speciation.
35. Crespi, BJ.The evolution of social behavior in microorganisms.Trends in Ecology & Evolution, 2001, 16: 178-183 The evolution of social behavior in microorganisms
Recent studies of microorganisms have revealed diverse complex social behaviors, including cooperation in foraging, building, reproducing, dispersing and communicating. These microorganisms should provide novel,tractable systems for the analysis of social evolution. The application of evolutionary and ecological theory to understanding their behavior will aid in developing better means to control the many pathogenic bacteria that use social interactions to affect humans.
34. Leavitt, BR; Guttman, JA; Hodgson, JG; Kimel, GH; Singaraja, R; Vogl, AW; Hayden, MR.Wild-type huntingtin reduces the cellular toxicity of mutant huntingtin in vivo.American Journal of Human Genetics, 2001, 68: 313-324 Wild-type huntingtin reduces the cellular toxicity of mutant huntingtin in vivo
We have developed yeast artificial chromosome (YAC) transgenic mice expressing normal (YAC18) and mutant (YAC46 or YAC72) human huntingtin (htt), in a developmental- and tissue-specific manner, that is identical to endogenous htt. YAC72 mice develop selective degeneration of medium spiny projection neurons in the lateral striatum, similar to what is observed in Huntington disease. Mutant human htt expressed by YAC transgenes can compensate for the absence of endogenous htt and can rescue the embryonic lethality that characterizes mice homozygous for targeted disruption of the endogenous Hdh gene (-/-). YAC72 mice lacking endogenous htt (YAC72 -/-) manifest a novel phenotype characterized by infertility, testicular atrophy, aspermia, and massive apoptotic cell death in the testes. The testicular cell death in YAC72 -/- mice can be markedly reduced by increasing endogenous htt levels. YAC72 mice with equivalent levels of both wild-type and mutant htt (YAC72 +/+) breed normally and have no evidence of increased testicular cell death. Similar findings are seen in YAC46 -/- mice compared with YAC46 +/+ mice, in which wild-type htt can completely counteract the proapoptotic effects of mutant htt. YAC18 -/- mice display no evidence of increased cellular apoptosis, even in the complete absence of endogenous htt, demonstrating that the massive cellular apoptosis observed in YAC46 -/- mice and YAC72 -/- mice is polyglutamine-mediated toxicity from the mutant transgene. These data provide the first direct in vivo evidence of a role for wild-type htt in decreasing the cellular toxicity of mutant htt. DOI
33. Berbee, ML, Carmean, D., and K. Winka.Ribosomal DNA and Resolution of Branching Order among the Ascomycota: How Many Nucleotides Are Enough?Molecular Phylogenetics and Evolution, 2000, 17: 337-344 Ribosomal DNA and Resolution of Branching Order among the Ascomycota: How Many Nucleotides Are Enough?
Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the “pattern of resolved nodes” method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade. DOI
31. Clague, JJ; Bobrowsky, PT; Hutchinson, I.A review of geological records of large tsunamis at Vancouver Island, British Columbia, and implications for hazard.Quat. Sci. Rev., 2000, 19: 849-863 A review of geological records of large tsunamis at Vancouver Island, British Columbia, and implications for hazard
Large tsunamis strike the British Columbia coast an average of once every several hundred years. Some of the tsunamis, including one from Alaska in 1964, are the result of distant great earthquakes. Most, however, are triggered by earthquakes at the Cascadia subduction zone, which extends along the Pacific coast from Vancouver Island to northern California. Evidence of these tsunamis has been found in tidal marshes and low-elevation coastal lakes on western Vancouver Island. The tsunamis deposited sheets of sand and gravel now preserved in sequences of peat and mud. These sheets commonly contain marine fossils, and they thin and fine landward, consistent with deposition by landward surges of water. They occur in low-energy settings where other possible depositional processes, such as stream flooding and storm surges, can be ruled out. The most recent large tsunami generated by an earthquake at the Cascadia subduction zone has been dated in Washington and Japan to AD 1700. The spatial distribution of the deposits of the 1700 tsunami, together with theoretical numerical modelling, indicate wave run-ups of up to 5 m asl along the outer coast of Vancouver Island and up to 15-20 m asl at the heads of some inlets. The waves attenuated as they moved eastward along Juan de Fuca Strait and into Puget Sound and the Strait of Georgia. No deposits of the 1700 event or, for that matter, any other tsunami, have yet been found in the Strait of Georgia, suggesting that waves were probably no more than 1 m high in this area. If a tsunami like the 1700 event were to occur today, communities along the outer Pacific coast from southern British Columbia to northern California would be severely damaged. There would be little time to evacuate these communities because the tsunami would strike the outer coast within minutes of the first ground shaking. Fortunately, such tsunamis are infrequent - perhaps as few as seven have occurred in the last 3500 yr. Other tsunamis that are much smaller and more localized, although probably more frequent, are caused by local crustal earthquakes and landslides along the British Columbia coast. Two such tsunamis have occurred in British Columbia in recent years, one in 1946 in the Strait of Georgia and another in 1975 at the head of a fiord on the northern mainland coast. (C) 2000 Elsevier Science Ltd. All rights reserved. DOI
30. Clague, JJ; Evans, SG.A review of catastrophic drainage of moraine-dammed lakes in British Columbia.Quat. Sci. Rev., 2000, 19: 1763-1783 A review of catastrophic drainage of moraine-dammed lakes in British Columbia
Moraine-dammed lakes are common in the high mountains of British Columbia. Most of these lakes formed when valley and cirque glaciers retreated from advanced positions achieved during the Little Ice Age. Many moraine dams in British Columbia are susceptible to failure because they are steep-sided, have relatively low width-to-height ratios, comprise loose, poorly sorted sediment, and may contain ice cores or interstitial ice. In addition, the lakes commonly are bordered by steep slopes that are prone to snow and ice avalanches and rockfalls. Moraine dams generally fail by overtopping and incision. The triggering event may be a heavy rainstorm, or an avalanche or rockfall that generates waves that overtop the dam. The dam can also be overtopped by an influx of water caused by sudden drainage of an upstream ice-dammed lake (jokulhlaup). Melting of moraine ice cores and piping are other possible failure mechanisms. Failures of moraine dams in British Columbia produce destructive floods orders of magnitude larger than normal streamflows. Most outburst floods are characterized by an exponential increase in discharge, followed by an abrupt drop to background levels when the water supply is exhausted. Peak discharges are controlled by dam characteristics, the volume of water in the reservoir, failure mechanisms, and downstream topography and sediment availability. For the same potential energy at the dam site, hoods from moraine-dammed lakes have higher peak discharges than floods from glacier-dammed lakes. The floodwaters may mobilize large amounts of sediment as they travel down steep valleys, producing highly mobile debris hows. Such flows have larger discharges and greater destructive impact than the floods from which they form. Moraine dam failures in British Columbia and elsewhere are most frequent following extended periods of cool climate when large lateral and end moraines are built. A period of protracted warming is required to trap lakes behind moraines and create conditions that lead to dam failure. This sequence of events occurred only a few times during the Holocene Epoch, most notably during the last several centuries. Glaciers built large moraines during the Little Ice Age, mainly during the 1700s and 1800s, and lakes formed behind these moraines when climate warmed in the 1900s. Twentieth-century climate warming is also responsible for recent moraine dam failures in mountains throughout the world. Warming from the late 1800s until about 1940 and again from 1965 to today destabilized moraine dams with interstitial or core ice. The warming also forced glaciers to retreat, prompting ice avalanches, landslides, and jokulhlaups that have destroyed some moraine dams. (C) 2000 Elsevier Science Ltd. All rights reserved. DOI
28. James, TS; Clague, JJ; Wang, KL; Hutchinson, I.Postglacial rebound at the northern Cascadia subduction zone.Quat. Sci. Rev., 2000, 19: 1527-1541 Postglacial rebound at the northern Cascadia subduction zone
Postglacial rebound is the response of the Earth to the decay of ice-sheets. A postglacial rebound model explains crustal tilting and rapid uplift at the northern Cascadia subduction zone that occurred during retreat of the Cordilleran ice-sheet. Observations explained by the model include the shoreline tilts of two proglacial lakes that formed at 13.5-14 ka (C-14 yr ago) and rapid sea level fall (land uplift) at 12-12.5 ka. Modelled mantle viscosity values range from 5 x 10(18) to 5 x 10(19) Pa s, and are consistent with previous viscosity inferences from observations of crustal deformation following subduction zone earthquakes (10(18)- 0(19) Pa s). No lower limit to subduction zone mantle viscosity is apparent from our model, but viscosity values equal to or larger than 10"0 Pa a are definitely ruled out. Our modelled subduction zone viscosity values are smaller than most upper-mantle viscosity estimates derived from postglacial rebound studies of tectonically less-active regions (10(20)-10(21) pa s). The rapid observed uplift at 12 ka requires, in addition to a low mantle viscosity, rapid unloading from a sudden collapse of remaining coastal portions of the southern Cordilleran ice-sheet. The sudden collapse provides 0.18 m of global eustatic sea level rise, approximately 0.7% of the sea level rise associated with melt-water pulse IA. Predictions of a global postglacial rebound model (ICE-3G) with a 10(21) Pa s upper-mantle viscosity were previously applied to geodetic data from this region to isolate signals associated with the earthquake cycle. Owing to the low-viscosity values, and resulting rapid recovery of glacial deformation, our model predicts present-day postglacial rebound uplift rates at least 10 times smaller than ICE-3G (less than about 0.1mm/yr). As the ICE-3G adjustments were substantial, this indicates the need for re-evaluation of the geodetic data. (C) 2000 Elsevier Science Ltd. All rights reserved. DOI
27. Mooers, AO; Holmes, EC.The evolution of base composition and phylogenetic inference.Trends in Ecology & Evolution, 2000, 15: 365-369 The evolution of base composition and phylogenetic inference
Base composition varies at all levels of the phylogenetic hierarchy and throughout the genome, and can be caused by active selection or passive mutation pressure. This variation can make reconstructing trees difficult. However, recent tree-based analyses have shed light on the forces responsible for the evolution of base composition, forces that might be very general. More explicit tree-based work is encouraged.
26. Bendell-Young, LI.Application of a kinetic model of bioaccumulation across a pH and salinity gradient for the prediction of cadmium uptake by the sediment dwelling chironomidae.Environmental Science & Technology, 1999, 33: 1501-1508 Application of a kinetic model of bioaccumulation across a pH and salinity gradient for the prediction of cadmium uptake by the sediment dwelling chironomidae
A kinetic model for the prediction of metal concentrations in aquatic organisms was applied for the prediction of cadmium concentrations in the sediment dwelling dipertan larvae, Chironomidae. Cadmium concentrations were determined in Chironomidae sampled along two distinct environmental gradients: (1) an acidity gradient(from pH 5.0-6.5) and (2) a salinity gradient (from 0 to 9.6 ppt). Comparison of predicted and observed values indicated that the kinetic model was successful in predicting concentrations in chironomids sampled along the acidity gradient but not the salinity gradient. Separation of routes of cadmium uptake into food and solute sources indicated that ingested sediment accounted for 60-100% of total invertebrate cadmium concentrations, however, the relative importance of water increased as a function of decreasing acidity and salinity. These results support the refinement of a kinetic model for predicting cadmium concentrations in sediment-living invertebrates, such as Chironomidae. By allowing for uptake from food and water the model highlighted the potential for routes of cadmium uptake to be pH and salinity dependent. For monitoring purposes, hath vectors and the potential for the relative importance for each vector to change needs to be considered when assessing the degree of metal exposure to sediment ingesting invertebrates which inhabit systems with either a natural or anthropogencially induced gradient in key water chemistry variables such as salinity or pH.
23. Carmean D, Kimsey L.Phylogenetic revision of the parasitoid wasp family Trigonalidae (Hymenoptera).Syst Entomol, 1998, 23: 35-76 Phylogenetic revision of the parasitoid wasp family Trigonalidae (Hymenoptera)
SYSTEMATIC Trigonalidae
A phylogenetic analysis of generic relationships and revised generic concepts for the Trigonalidae is presented. The Trigonalidae is divided into two subfamilies, the Orthogonalinae and the Trigonalinae. Orthogonalinae consists of a single primitive genus, Orthogonalys, sharing many generalized apocritan characters, but lacking advanced trigonalid characters including antennal tyloids and female metasomal armature. No synapomorphies have been detected for the Orthogonalinae. Trigonalinae are characterized by the presence of tyloids. The Trigonalinae were originally defined by the absence of female armature, and were therefore polyphyletic because armature has been lost several times. Within the revised concept of Trigonalinae, the tribe Trigonalini is characterized by the presence of elongate parameres and an intertorulus distance subequal to the distance between the torulus and the eye. A second tribe, Nomadinini, is based on the secondary loss of tyloids, and comprises the previous subfamilies Seminotinae, Nomadininae, Bareogonalinae and Lycogastrinae. The two tribes Trigonalini and Nomadinini share the presence of female armature, although in some Trigonalini it has been secondarily lost. The genera Labidogonalos Schulz, Lycogastroides Strand, Lycogonalos Bischoff, Nanogonalos Schulz, Poecilogonalos Schulz and Taiwanogonalos Tsuneki are synonymised under Taeniogonalos Schulz. The species Lycogaster zimmeri Bischoff, Tapinogonalos maschuna Schulz, and Trigonalys pictifrons Smith (placed in Lycogaster by Schulz, 1906a) are transferred to Taeniogonalos. The genera Discenea Enderlein and Stygnogonalos Schulz are synonymised under Trigonalys Westwood. The species Labidogonalos flavescens Bischoff, L. sanctaecatharinae Schulz, Trigonalys lachrymosa Westwood (placed in Lycogaster by Bischoff, 1938), T. maculifrons Cameron (placed in Labidogonalos by Bischoff, 1938) and T. rufiventris Magretti (placed in Lycogaster by Schulz, 1907a) are transferred to Trigonalys.Trigonalys costalis Cresson is synonymised with Taeniogonalos gundlachii (Cresson). Xanthogonalos fasciatus Bertoni and X.severini Schulz are synonymised with Trigonalys sanctaecatharinae (Schulz). Mimelogonalos partiglabra Riek and M. punctulata Riek are synonymised with M. bouvieri Schulz. Lectotypes are designated for Trigonalys melanoleuca Westwood and Taeniogonalos fasciatipennis (Cameron). The author of Trigonalys maculifrons is Sharp (1895), not Cameron (1897), and the author of Taeniogonalos enderleini is De Santis (1980), not Schulz 1906. Viereck (1914) designated Trigonalys pulchella Cresson as type of the genus Tapinogonalos Schulz, preceding Bischoff's (1938) designation, making Tapinogonalos a synonym of Orthogonalys. A new genus, Afrigonalys, is proposed for the three species that were described in ‘Tapinogonalos’sensu Bischoff, nec Viereck.PDF DOI
21. Kropf, DL; Bisgrove, SR; Hable, WE.Cytoskeletal control of polar growth in plant cells.Current Opinion in Cell Biology, 1998, 10: 117-122 Cytoskeletal control of polar growth in plant cells
There are two quite different modes of polar cell expansion in plant cells, namely, diffuse growth and tip growth. The direction of diffuse growth is determined by the orientation of cellulose microfibrils in the cell wall, which in turn are aligned by microtubules in the cell cortex. The orientation of the cortical microtubule array changes in response to developmental and environmental signals, and recent evidence indicates that microtubule disassembly/reassembly and microtubule translocation participate in reorientation of the array. Tip growth, in contrast, is governed mainly by F-actin, which has several putative forms and functions in elongating cells. Longitudinal cables are involved in vesicle transport to the expanding apical dome and, in some tip growers, a subapical ring of F-actin may participate in wall-membrane adhesions. The structure and function of F-actin within the apical dome may be variable, ranging from a dense meshwork to sparse single filaments. The presence of multiple F-actin structures in elongating tips suggests extensive regulation of this cytoskeletal array. DOI
20. MacFarlane, KS; Rettig, SJ; Liu, ZQ; James, BR.The co-crystallization of Ru((R)-binap)(eta(3)-Me-allyl)(2) and binap dioxide, and synthesis of Ru(Ph2P(CH2)(4)PPh2)(eta(3)-Me-allyl)(2).Journal of Organometallic Chemistry, 1998, 557: 213-219 The co-crystallization of Ru((R)-binap)(eta(3)-Me-allyl)(2) and binap dioxide, and synthesis of Ru(Ph2P(CH2)(4)PPh2)(eta(3)-Me-allyl)(2)
ruthenium(II) complexes; binap; allyl; X-ray crystal structure
The molecular structure of the 2-methylallyl species Ru((R)-binap)(eta(3)-Me-allyl)(2) (3) was established by X-ray crystallography of a crystal of 3a, the asymmetric unit of which is composed of half of a molecule of 3 and half of a (R)-(+)-2,2'-bis(-diphenylphosphinoyl)-1,1'-binaphthyl(binap dioxide) molecule, co-crystallized with two disordered deuterobenzenes; crystals of 3a are tetragonal, space group I422, with Z = 8, a = 21.344(1) Angstrom and c = 36.453(2) A. The structure was solved by direct methods and refined by full-matrix least-squares procedures to R = 0.034 and R-w = 0.032 for 3431 reflections with I greater than or equal to 3 sigma(I). The 1,4-bis(diphenylphosphino)butane (dppb) analogue (2) of 3 was also prepared and characterized by H-1 and P-31{H-1}-NMR spectroscopy and elemental analysis, and the reactivities of 2 and 3 toward halogen acids are discussed. (C) 1998 Elsevier Science S.A. All rights reserved. DOI
19. MacFarlane, KS; Thorburn, IS; Cyr, PW; Chau, DEKY; Rettig, SJ; James, BR.Triply-bridged diruthenium(II) 1,4-bis(diphenylphosphino)butane (dppb) and (R)-2,2 '-bis(diphenylphosphino)-1,1 '-binaphthyl (binap) complexes, including structural characterisation of [(dppb)ClRu(mu-D2O)-(mu-Cl)(2)RuCl(dppb)], [(eta(2)-H-2)(dppb)Ru(mu-Cl)(3)RuCl(dppb)] and the [(dppb)ClRu(mu-Cl)(3)RuCl(dppb)](-) anion.Inorganica Chimica Acta, 1998, 270: 130-144 Triply-bridged diruthenium(II) 1,4-bis(diphenylphosphino)butane (dppb) and (R)-2,2 '-bis(diphenylphosphino)-1,1 '-binaphthyl (binap) complexes, including structural characterisation of [(dppb)ClRu(mu-D2O)-(mu-Cl)(2)RuCl(dppb)], [(eta(2)-H-2)(dppb)Ru(mu-Cl)(3)RuCl(dppb)] and the [(dppb)ClRu(mu-Cl)(3)RuCl(dppb)](-) anion
crystal structures; ruthenium complexes; triply-bridged complexes; diphosphine complexes
Several triply-bridged diruthenium(II)(1,4-bis(diphenylphosphino)butane) complexes were synthesised and characterised by elemental analysis, UV-Vis, NMR and IR spectroscopies, The solid-state structures of [(dppb)ClRu(mu-D2O)(mu-Cl)(2)RuCl(dppb)] (1), [(eta(2)-H-2) (dppb)Ru(mu-Cl)(3)RuCl(dppb)] (2) and [TMP][(dppb)ClRu(mu-Cl)(3)RuCl(dppb)] (3) were established by X-ray crystallographic analyses (TMP=1,1,3-trimethyl-2,3-dihydroperimidinium; dppb = Ph2P(CH2)(4)PPh2). Crystals of 1.1.5C(6)D(6), 2.1.5C(7)D(8) and 3.2Me(2)CO.2H(2)O are all monoclinic, space groups P2(1)/c, P2(1)/n and C2/c, respectively, with Z=4: a=16.8681(6), b=13.3542(4), c=26.4966(7) Angstrom, beta=91.877(1)degrees for 1.1.5C(6)D(6); a = 19.8123(1), b=14.5246(2), c = 22.1803(1) Angstrom, beta=106.58(1)degrees for 2.1.5C(7)D(8); a=21.596(2), b=16.019(2), c=22.317(2) Angstrom, beta=106.15(1)degrees for 3.2Me(2)CO . 2H(2)O. The structures of 1 and 2 were salved by direct methods while 3 was solved by heavy atom methods and all were refined by full-matrix least-squares procedures to R-1 = 0.0433, 0.0612 and R = 0.039 (wR(2) = 0.0709 (1), 0.1178 (2)) for 7751, 6757 and 5237 reflections with I greater than or equal to 2 sigma(I) for 1 and 2 and I greater than or equal to 3 sigma(I) for 3, respectively, Complex I was also studied in the solid-state by P-31 CP/MAS NMR spectroscopy. The bromo- and iodo-analogues of 1 were prepared, and these three species were screened as catalysts for hydrogenation of aldimines. The complexes [H2NR2][{RuCl(P-P)}(2)(mu-Cl)(3)] were synthesised by the addition of NR3 or [H2NR2]Cl to RuCl2(P-P)(PPh3), where P-P = dppb or (R)-2,2'-bis(diphenylphosphino)-1,1'-binaphthyl (binap) and R =Et, n-Bu or n-Oct. The syntheses of [(DMA)(2)H][(PPh3)(2)ClRu(mu-Cl)(3)RuCl(PPh3)(2)], [(py)(dppb)Ru(mu-Cl)(3)RuCl(dppb)] and [(C2H4)(dppb)Ru(mu-Cl)(3)RuCl(dppb)] were also accomplished (DMA = N,N-dimethylacetamide; py = pyridine). (C) 1998 Elsevier Science S.A. DOI
18. Warner, TS; Sinclair, DAR; Fitzpatrick, KA; Singh, H; Devlin, RH; Honda, BM.The light gene of Drosophila melanogaster encodes a homologue of VPS41, a yeast gene involved in cellular-protein trafficking.Genome, 1998, 41: 236-243 The light gene of Drosophila melanogaster encodes a homologue of VPS41, a yeast gene involved in cellular-protein trafficking
vesicle transport; eye-colour gene; heterochromatin
Mutations in a number of genes affect eye colour in Drosophila melanogaster; some of these "eye-colour" genes have been shown to be involved in various aspects of cellular transport processes. In addition, combinations of viable mutant alleles of some of these genes, such as carnation (car) combined with either light (It) or deep-orange (dor) mutants, show lethal interactions. Recently, dor was shown to be homologous to the yeast gene PEP3 (VPS18), which is known to be involved in intracellular trafficking. We have undertaken to extend our earlier work on the It gene, in order to examine in more detail its expression pattern and to characterize its gene product via sequencing of a cloned cDNA. The gene appears to be expressed at relatively high levels in all stages and tissues examined, and shows strong homology to VPS41, a gene involved in cellular-protein trafficking in yeast and higher eukaryotes. Further genetic experiments also point to a role for It in transport processes: we describe lethal interactions between viable alleles of It and dor, as well as phenotypic interactions (reductions in eye pigment) between alleles of It and another eye-colour gene, garnet (g), whose gene product has close homology to a subunit of the human adaptor complex, AP-3. DOI PubMed
17. Davis, TJ; Keller, CP.Modelling uncertainty in natural resource analysis using fuzzy sets and Monte Carlo simulation: Slope stability prediction.Int. J. Geogr. Inf. Sci., 1997, 11: 409-434 Modelling uncertainty in natural resource analysis using fuzzy sets and Monte Carlo simulation: Slope stability prediction
The techniques of fuzzy logic and Monte Carlo simulation are combined to address two incompatible types of uncertainty present in most natural resource data: thematic classification uncertainty and variance in unclassified continuously distributed data. The resultant model of uncertainty is applied to an infinite slope stability model using data from Louise Island, British Columbia. Results are summarized so as to answer forestry decision support queries. The proposed model of uncertainty in resource data analysis is found to have utility in combining different types of uncertainty, and efficiently utilizing available metadata. Integration of uncertainty data models with visualization tools is considered a necessary prerequisite to effective implementation in decision support systems. DOI
16. Davis, TJ; Keller, CP.Modelling and visualizing multiple spatial uncertainties.Comput. Geosci., 1997, 23: 397-408 Modelling and visualizing multiple spatial uncertainties
GIS; visualization; uncertainty; fuzzy; slope stability modelling
This paper presents the results of research into the modelling and visualization of multiple types of uncertainty - each exhibiting distinct spatial characteristics. Slope stability modelling is utilized as a vehicle to bring together uncertainties in categorical spatial data and continuous spatial data. A variety of static visualization methods are discussed, as well as the implications of using an interactive animated display to explore multiple realizations of a continuous surface. The results indicate that careful definitions of allowable uncertainty, and the implications thereof, are required to calibrate an interactive animation that will be utilized by non-specialists. It is argued that this holds particularly true in the situation of risk management decisions. (C) 1997 Elsevier Science Ltd. DOI
15. Reynolds, JD.Animal breeding systems.Trends in Ecology & Evolution, 1996, 11: A68-A72 Animal breeding systems
The study of breeding systems explores relationships between mating behaviour and parental care. Recent findings have shown that in many birds, fishes, anurans, and insects, females play a more active role than previously thought, by engaging in mate choice, mating with more than one male, and selecting genetic partners separately from social partners, Theoretical advances have improved our understanding of the effect of parental care on sex differences in mating behaviour, though less attention has been devoted to feedback in the opposite direction, The original emphasis on the role of ecology in determining breeding systems has been overshadowed by studies of individual interactions, but modern comparative techniques may provide a new fusion between ecology, life histories, and reproductive behaviour.
14. Carmean, D; Crespi, BJ.Do long branches attract flies?Nature, 1995, 373: 666 Do long branches attract flies?
Strepsiptera and Diptera group together in phylogenetic analysis as an artefact resulting from the high substitution rates in their 18S rDNA sequences. The grouping is an excellent example of long-branch attraction resulting from the violation of the molecular clock for this gene. Website DOI
12. NAPIER, DG; SHIZGAL, BD.NONEQUILIBRIUM EFFECTS IN MODEL REACTIVE SYSTEMS - THE ROLE OF SPECIES TEMPERATURES.Phys. Rev. E, 1995, 52: 3797-3811 NONEQUILIBRIUM EFFECTS IN MODEL REACTIVE SYSTEMS - THE ROLE OF SPECIES TEMPERATURES
The nonequilibrium effects for a model reactive system, A + B --> products, that arise from the perturbation of the distribution function from the Maxwellian are studied. The main objective is the calculation of the fractional decrease of the nonequilibrium rate coefficient from the equilibrium value. This effect is examined with the Chapman-Enskog method of solution of the Boltzmann equation which treats the reactive processes as a weak perturbation. The approach is referred to as weak nonequilibrium. The reactive process causes the temperatures of the two species to differ from the system temperature and this effect can play an important role in the determination of the departure of the rate coefficient from the equilibrium value. A second method is an extension of the Chapman-Enskog approach and involves the expansion of the distribution functions about Maxwellians at different temperatures and is referred to as strong nonequilibrium (SNE). A third approach is a modification of SNE and is referred to as modified strong nonequilibrium. The three methods are described and departures of the rate coefficients from their equilibrium values are computed for each case and compared, along with an explicitly time-dependent solution of the Boltzmann equation. DOI PubMed
11. CORY, JS; HIRST, ML; WILLIAMS, T; HAILS, RS; GOULSON, D; GREEN, BM; CARTY, TM; POSSEE, RD; CAYLEY, PJ; BISHOP, DHL.FIELD TRIAL OF A GENETICALLY IMPROVED BACULOVIRUS INSECTICIDE.Nature, 1994, 370: 138-140 FIELD TRIAL OF A GENETICALLY IMPROVED BACULOVIRUS INSECTICIDE
IMPROVEMENT of biological pesticides through genetic modification has enormous potential and the insect baculoviruses are particularly amenable to this approach(1,2). A key aim of genetic engineering is to increase their speed of kill, primarily by the incorporation of genes which encode arthropod or bacterially derived insect-selective toxins(3-11), insect hormones(12,13) or enzymes(14,15). We report here the first, to our knowledge, field trial of a genetically improved nuclear polyhedrosis virus of the alfalfa looper, Autographa californica (AcNPV) that expresses an insect-selective toxin gene (AaHIT) derived from the venom of the scorpion Androctonus australis(16-18). Previous laboratory assays with the cabbage looper, Trichoplusia ni, demonstrated a 25% reduction in time to death compared to the wild-type virus, but unaltered pathogenicity(6) and host range(19). In the field, the modified baculovirus killed faster, resulting in reduced crop damage and it appeared to reduce the secondary cycle of infection compared to the wild-type virus.
10. MATHEWES, RW; CLAGUE, JJ.DETECTION OF LARGE PREHISTORIC EARTHQUAKES IN THE PACIFIC-NORTHWEST BY MICROFOSSIL ANALYSIS.Science, 1994, 264: 688-691 DETECTION OF LARGE PREHISTORIC EARTHQUAKES IN THE PACIFIC-NORTHWEST BY MICROFOSSIL ANALYSIS
Geologic and palynological evidence for rapid sea level change similar to 3400 and similar to 2000 carbon-14 years ago (3600 and 1900 calendar years ago) has been found at sites up to 110 kilometers apart in southwestern British Columbia. Submergence on southern Vancouver Island and slight emergence on the mainland during the older event are consistent with a great (magnitude M greater than or equal to 8) earthquake on the Cascadia subduction zone. The younger event is characterized by submergence throughout the region and may also record a plate-boundary earthquake or a very large crustal or intraplate earthquake. Microfossil analysis can detect small amounts of coseismic uplift and subsidence that leave little or no lithostratigraphic signature. DOI PubMed
6. Carmean, D., Kimsey, L. and M. Berbee.18S rDNA sequences and the holometabolous insects.Molecular Phylogenetics and Evolution, 1992, 1: 270-278 18S rDNA sequences and the holometabolous insects
The Holometabola (insects with complete metamorphosis: beetles, wasps, flies, fleas, butterflies, lacewings, and others) is a monophyletic group that includes the majority of the world's animal species. Holometabolous orders are well defined by morphological characters, but relationships among orders are unclear. In a search for a region of DNA that will clarify the interordinal relationships we sequenced approximately 1080 nucleotides of the 5? end of the 185 ribosomal RNA gene from representatives of 14 families of insects in the orders Hymenoptera (sawflies and wasps), Neuroptera (lacewing and antlion), Siphonaptera (flea), and Mecoptera (scorpionfly). We aligned the sequences with the published sequences of insects from the orders Coleoptera (beetle) and Diptera (mosquito and Drosophila), and the outgroups aphid, shrimp, and spider. Unlike the other insects examined in this study, the neuropterans have A-T rich insertions or expansion regions: one in the antlion was 260 by long. The dipteran 185 rDNA evolved rapidly, with over 3 times as many substitutions among the aligned sequences, and 2-3 times more unalignable nucleotides than other Holometabola, in violation of an insect-wide molecular clock. When we excluded the long-branched taxa (Diptera, shrimp, and spider) from the analysis, the most parsimonious (minimum-length) trees placed the beetle basal to other holometabolous orders, and supported a morphologically monophyletic clade including the fleas + scorpionflies (96% bootstrap support). However, most interordinal relationships were not significantly supported when tested by maximum likelihood or bootstrapping and were sensitive to the taxa included in the analysis. The most parsimonious and maximum-likelihood trees both separated the Coleoptera and Neuroptera, but this separation was not statistically significant. The position of the Hymenoptera relative to other orders was not clarified. Including the less derived members in the analysis made the Hymenoptera appear paraphyletic. The two representatives of Neuroptera grouped together as did the two Diptera, both pairs with very significant bootstrap support. DOI
5. HIK, DS; JEFFERIES, RL; SINCLAIR, ARE.FORAGING BY GEESE, ISOSTATIC UPLIFT AND ASYMMETRY IN THE DEVELOPMENT OF SALT-MARSH PLANT-COMMUNITIES.J. Ecol., 1992, 80: 395-406 FORAGING BY GEESE, ISOSTATIC UPLIFT AND ASYMMETRY IN THE DEVELOPMENT OF SALT-MARSH PLANT-COMMUNITIES
ARCTIC SALT-MARSHES; EDAPHIC PROCESSES; GRAZING LAWNS; LESSER SNOW GOOSE; MULTIPLE-STATE COMMUNITIES
1. The response of different salt-marsh plant communities to grazing by lesser snow geese and isostatic uplift was examined at La Perouse Bay, Manitoba on the Hudson Bay coast. Results are based on direct experimental manipulation of swards and previously published floristic and biomass data. 2. At the seaward end of the salt-marsh the vegetation is composed of Puccinellia phryganodes and Carex subspathacea. This assemblage of species is also present in the upper marsh, but only as a consequence of intense grazing by geese. Grazed swards of these species persist over a period of at least 10 years. 3. When swards are protected from grazing in the upper marsh, rapid changes in floristic composition of vegetation occur. There is a substantial increase in above-ground biomass and the vegetation is dominated by Calamagrostis deschampsiodes, Festuca rubra and dicotyledonous plants. When these swards are grazed the species composition does not revert to the Puccinellia-Carex assemblage. 4. In the presence of grazing this change from the Puccinellia-Carex assemblage to the Calamagrostis-Festuca assemblage occurs gradually as a consequence of changes in edaphic conditions associated with isostatic uplift. The geese delay the rate of vegetational development associated with the effects of isostatic uplift but they cannot arrest it. 5. Both types of plant assemblage may become extinct locally as a result of grubbing by the geese for roots and rhizomes of graminoid species. Habitat conditions are sufficiently altered following grubbing that the process of succession recommences from bare sediment. 6. The results of changes in floristic composition, above-ground biomass and replacement rates of vegetation are examined in relation to predictions of multiple-state models which emphasize the directional asymmetry in the development of plant communities. DOI
3. Belton. P.Sounds of Insects in Flight.Insect Flight: Dispersal and Migration, Springer Verlag, 1986, pp 60-70 Sounds of Insects in Flight
insect sounds
