36. Greenberg, DA; Pyron, RA; Johnson, LGW; Upham, NS; Jetz, W; Mooers, AO. (2021) Evolutionary legacies in contemporary tetrapod imperilment.Ecol. Lett. 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
34. Guzman, LM; Johnson, SA; Mooers, AO; M'Gonigle, LK. (2021) Using historical data to estimate bumble bee occurrence: Variable trends across species provide little support for community-level declines.Biol. Conserv. 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
33. Wicke, K; Mooers, A; Steel, M. (2021) Formal Links between Feature Diversity and Phylogenetic Diversity.Syst. Biol. 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
32. Cantalapiedra, JL; Aze, T; Cadotte, MW; Dalla Riva, GV; Huang, D; Mazel, F; Pennell, MW; Rios, M; Mooers, AO. (2019) Conserving evolutionary history does not result in greater diversity over geological time scales.Proc. R. Soc. B-Biol. Sci. 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
30. Chaudhary, A; Pourfaraj, V; Mooers, AO. (2018) Projecting global land use-driven evolutionary history loss.Divers. Distrib. 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
29. Greenberg, DA; Palen, WJ; Chan, KC; Jetz, W; Mooers, AO. (2018) Evolutionarily distinct amphibians are disproportionately lost from human-modified ecosystems.Ecology Letters 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
28. Lewthwaite, JMM; Angert, AL; Kembel, SW; Goring, SJ; Davies, TJ; Mooers, AO; Sperling, FAH; Vamosi, SM; Vamosi, JC; Kerr, JT. (2018) Canadian butterfly climate debt is significant and correlated with range size.Ecography 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
27. Mazel, F; Pennell, MW; Cadotte, MW; Diaz, S; Dalla Riva, GV; Grenyer, R; Leprieur, F; Mooers, AO; Mouillot, D; Tucker, CM; Pearse, WD. (2018) Prioritizing phylogenetic diversity captures functional diversity unreliably.Nat. Commun. 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
24. Stein, RW; Mull, CG; Kuhn, TS; Aschliman, NC; Davidson, LNK; Joy, JB; Smith, GJ; Dulvy, NK; Mooers, AO. (2018) Global priorities for conserving the evolutionary history of sharks, rays and chimaeras.Nat. Ecol. Evol. 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
23. Greenberg, DA; Palen, WJ; Mooers, AO. (2017) Amphibian species traits, evolutionary history and environment predict Batrachochytrium dendrobatidis infection patterns, but not extinction risk.Evol. Appl. 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
22. Mazel, F; Mooers, AO; Dalla Riva, GV; Pennell, MW. (2017) Conserving Phylogenetic Diversity Can Be a Poor Strategy for Conserving Functional Diversity.Syst. Biol. 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
20. 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. (2017) A guide to phylogenetic metrics for conservation, community ecology and macroecology.Biol. Rev. 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
19. Waldron, A; Miller, DC; Redding, D; Mooers, A; Kuhn, TS; Nibbelink, N; Roberts, JT; Tobias, JA; Gittleman, JL. (2017) Reductions in global biodiversity loss predicted from conservation spending.Nature 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
18. Hurteau, LA; Mooers, AO; Reynolds, JD; Hocking, MD. (2016) Salmon nutrients are associated with the phylogenetic dispersion of riparian flowering-plant assemblages.Ecology 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
17. Dembo, M; Matzke, NJ; Mooers, AO; Collard, M. (2015) Bayesian analysis of a morphological supermatrix sheds light on controversial fossil hominin relationships.Proceedings of the Royal Society B-Biological Sciences 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
16. Gudde, RM; Joy, JB; Mooers, AO. (2013) Imperilled phylogenetic endemism of Malagasy lemuriformes.Diversity and Distributions 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
14. Thomas, GH; Hartmann, K; Jetz, W; Joy, JB; Mimoto, A; Mooers, AO. (2013) PASTIS: an R package to facilitate phylogenetic assembly with soft taxonomic inferences.Methods in Ecology and Evolution 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
13. 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. (2012) Approaching a state shift in Earth's biosphere.Nature 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
12. Jetz, W; Thomas, GH; Joy, JB; Hartmann, K; Mooers, AO. (2012) The global diversity of birds in space and time.Nature 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
11.Mooers, A; Gascuel, O; Stadler, T; Li, HY; Steel, M. (2012) Branch Lengths on Birth-Death Trees and the Expected Loss of Phylogenetic Diversity.Systematic Biology 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
10. Kuhn, TS; Mooers, AO; Thomas, GH. (2011) A simple polytomy resolver for dated phylogenies.Methods in Ecology and Evolution 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
9. 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. (2010) EARLY BURSTS OF BODY SIZE AND SHAPE EVOLUTION ARE RARE IN COMPARATIVE DATA.Evolution 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
8. Kuhn, TS; McFarlane, KA; Groves, P; Mooers, AO; Shapiro, B. (2010) Modern and ancient DNA reveal recent partial replacement of caribou in the southwest Yukon.Molecular Ecology 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
7.Mooers, AO; Doak, DF; Findlay, CS; Green, DM; Grouios, C; Manne, LL; Rashvand, A; Rudd, MA; Whitton, J. (2010) Science, Policy, and Species at Risk in Canada.Bioscience 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
6. Redding, DW; DeWolff, CV; Mooers, AO. (2010) Evolutionary Distinctiveness, Threat Status, and Ecological Oddity in Primates.Conservation Biology 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
5. Magnuson-Ford, K; Ingram, T; Redding, DW; Mooers, AO. (2009) Rockfish (Sebastes) that are evolutionarily isolated are also large, morphologically distinctive and vulnerable to overfishing.Biological Conservation 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
3. Parker, JDK; Bradley, BA; Mooers, AO; Quarmby, LM. (2007) Phylogenetic Analysis of the Neks Reveals Early Diversification of Ciliary-Cell Cycle Kinases.PLoS One 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
2.Mooers, AO; Holmes, EC. (2000) The evolution of base composition and phylogenetic inference.Trends in Ecology & Evolution 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.
