One hundred and seventeen clades of euagarics (original) (raw)
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D. S. Hibbett). a v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / m y c r e s m y c o l o g i c a l r e s e a r c h 1 1 1 ( 2 0 0 7 ) 5 0 9 -5 4 7 Eumycota Lichens Molecular phylogenetics Mycota Nomenclature Systematics a b s t r a c t A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae.
Specimens belonging to taxa traditionally assigned to the subsection Spadiceogriseae of the genus Psathyrella were analyzed both morphologically and molecularly. Samples included mainly European collections, selected GenBank accessions, and specimens of various North American taxa described by Smith (1972) and deposited at the Herbarium of the University of Michigan (MICH). Three additional taxa from Africa and Central America were also included. Bayesian and Maximum Likelihood analyses of two loci (ITS and Tef-1α) independently and together supported the monophyletic nature of the subsection Spadiceogriseae, and identified nine statistically supported clades within the subsection. North American and European species often fell within the same clade, suggesting a relatively recent origin of the subsection or human induced intercontinental movement. While this study determines for the first time that the presence of a white veil is diagnostic for the entire subsection, very few morphological traits were associated with individual clades, but clades were often distinctively different in terms of habitat association, suggesting that trophic interactions may have driven the evolution of this group of fungi.
Genetica, 2015
During the last two decades, the unprecedented development of molecular phylogenetic tools has propelled an opportunity to revisit the fungal kingdom under an evolutionary perspective. Mycology has been profoundly changed but a sustained effort to elucidate large sections of the astonishing fungal diversity is still needed. Here we fill this gap in the case of Lyophyllaceae, a species-rich and ecologically diversified family of mushrooms. Assembly and genealogical concordance multigene phylogenetic analysis of a large dataset that includes original, vouchered material from expert field mycologists reveal the phylogenetic topology of the family, from higher (generic) to lower (species) levels. A comparative analysis of the most widely used phylogenetic markers in Fungi indicates that the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and portions of the genes for RNA polymerase II second largest subunit (RPB2) is the most performing combination to resolve the broadest range of taxa within Lyophyllaceae. Eleven distinct evolutionary lineages are identified, that display partial overlap with traditional genera as well as with the phylogenetic framework previously proposed for the family. Eighty phylogenetic species are delineated, which shed light on a large number of morphological concepts, including rare and poorly documented ones. Probing these novel phylogenetic species to the barcoding method of species limit delineation, indicates that the latter method fully resolves Lyophyllaceae species, except in one clade. This case study provides the first comprehensive phylogenetic overview of Lyophyllaceae, a necessary step towards a taxonomical, ecological and nomenclatural revision of this family of mushrooms. It also proposes a set of methodological guidelines that may be of relevance for future taxonomic works in other groups of Fungi.
Fungal systematics and evolution: FUSE 1
Sydowia, 2015
Fungal Systematics and Evolution (FUSE) is introduced as a new series to expedite the publication of issues relating to the epitypification of formerly described species, report new sexual-asexual connections, the merging of sexual and asexual gen¬era following the end of dual nomenclature, and to describe species or note interesting observations regarding fungi. This first paper includes 18 new combinations, 13 new species, three new genera and one new family. All taxa are ascomycetes, except one novel species, which is a basidiomycete. Based on its acervular conidioma, Septoria capensis is allocated to the genus Ac¬ervuloseptoria (Mycosphaerellaceae, Capnodiales, Dothideomycetes). Cheirospora botryospora is shown to have a Phialophora synasexual morph, and to belong to the Helotiales (Leotiomycetes). The genus Circinotrichum (Xylariaceae, Xylariales) is shown to be paraphyletic, and in need of revision. Dictyochaeta triseptata (Chaetosphaeriaceae, Chaetosphaeriales, Sordariomycete...
Phylogenetic relationships in the gymnopoid and marasmioid fungi (Basidiomycetes, euagarics clade)
Mycologia, 2005
Three distinct lineages of gymnopoid and marasmioid fungi are recognized in parsimony and Bayesian analyses of nLSU rDNA sequences. One lineage contains the genera Lentinula, Rhodocollybia, Tetrapyrgos, a resurrected and redefined Mycetinis, and two unresolved clades designated /marasmiellus and /gymnopus. /marasmiellus includes the type species of Marasmiellus and is dominated by members of Gymnopus sect. Vestipedes. /gymnopus includes the type species of Gymnopus, Micromphale and Setulipes, and members of Gymnopus sect. Levipedes. A second lineage includes the genera Marasmius s.s. and Crinipellis and represents a redefined /marasmiaceae. A third lineage includes the genera Cylindrobasidium, Flammulina, Gloiocephala, Physalacria, Strobilurus, Xerula and Marasmius sect. Epiphylli and represents /physalacriaceae. One new combination in Rhodocollybia and four new combinations in Mycetinis are proposed. A discussion of the taxonomic implications resulting from the phylogenetic reconstruction is presented.
Studies in Mycology, 2020
Typhuloid fungi are a very poorly known group of tiny clavarioid homobasidiomycetes. The phylogenetic position and family classification of the genera targeted here, Ceratellopsis, Macrotyphula, Pterula sensu lato and Typhula, are controversial and based on unresolved phylogenies. Our six-gene phylogeny with an expanded taxon sampling shows that typhuloid fungi evolved at least twice in the Agaricales (Pleurotineae, Clavariineae) and once in the Hymenochaetales. Macrotyphula, Pterulicium and Typhula are nested within the Pleurotineae. The type of Typhula (1818) and Sclerotium (1790), T. phacorrhiza and S. complanatum (synonym T. phacorrhiza), are encompassed in the Macrotyphula clade that is distantly related to a monophyletic group formed by species usually assigned to Typhula. Thus, the correct name for Macrotyphula (1972) and Typhula is Sclerotium and all Typhula species but those in the T. phacorrhiza group need to be transferred to Pistillaria (1821). To avoid undesirable nomenclatural changes, we suggest to conserve Typhula with T. incarnata as type. Clavariaceae is supported as a separate, early diverging lineage within Agaricales, with Hygrophoraceae as a successive sister taxon to the rest of the Agaricales. Ceratellopsis s. auct. is polyphyletic because C. acuminata nests in Clavariaceae and C. sagittiformis in the Hymenochaetales. Ceratellopsis is found to be an earlier name for Pterulicium, because the type, C. queletii, represents Pterulicium gracile (synonym Pterula gracilis), deeply nested in the Pterulicium clade. To avoid re-combining a large number of names in Ceratellopsis we suggest to conserve it with C. acuminata as type. The new genus Bryopistillaria is created to include C. sagittiformis. The families Sarcomyxaceae and Phyllotopsidaceae, and the suborder Clavariineae, are described as new. Six new combinations are proposed and 15 names typified.
D. S. Hibbett). a v a i l a b l e a t w w w . s c i e n c e d i r e c t . c o m j o u r n a l h o m e p a g e : w w w . e l s e v i e r . c o m / l o c a t e / m y c r e s m y c o l o g i c a l r e s e a r c h 1 1 1 ( 2 0 0 7 ) 5 0 9 -5 4 7 Eumycota Lichens Molecular phylogenetics Mycota Nomenclature Systematics a b s t r a c t A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae.
Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences
Systematic …, 2000
Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 59 end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets. {Fungal evolution; higher phylogeny; homobasidiomycete; large-scale molecular phylogeny; tree support.}