6. 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
5. 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
4. 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
3.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
2.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
1.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
