Phylogenetic relationships in the gymnopoid and marasmioid fungi (Basidiomycetes, euagarics clade) (original) (raw)
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One hundred and seventeen clades of euagarics
Molecular Phylogenetics and Evolution, 2002
This study provides a first broad systematic treatment of the euagarics as they have recently emerged in phylogenetic systematics. The sample consists of 877 homobasidiomycete taxa and includes approximately one tenth (ca. 700 species) of the known number of species of gilled mushrooms that were traditionally classified in the order Agaricales. About 1000 nucleotide sequences at the 5′ end of the nuclear large ribosomal subunit gene (nLSU) were produced for each taxon. Phylogenetic analyses of nucleotide sequence data employed unequally weighted parsimony and bootstrap methods. Clades revealed by the analyses support the recognition of eight major groups of homobasidiomycetes that cut across traditional lines of classification, in agreement with other recent phylogenetic studies. Gilled fungi comprise the majority of species in the euagarics clade. However, the recognition of a monophyletic euagarics results in the exclusion from the clade of several groups of gilled fungi that have been traditionally classified in the Agaricales and necessitates the inclusion of several clavaroid, poroid, secotioid, gasteroid, and reduced forms that were traditionally classified in other basidiomycete orders. A total of 117 monophyletic groups (clades) of euagarics can be recognized on the basis on nLSU phylogeny. Though many clades correspond to traditional taxonomic groups, many do not. Newly discovered phylogenetic affinities include for instance relationships of the true puffballs (Lycoperdales) with Agaricaceae, of Panellus and the poroid fungi Dictyopanus and Favolaschia with Mycena, and of the reduced fungus Caripia with Gymnopus. Several clades are best supported by ecological, biochemical, or trophic habits rather than by morphological similarities.
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.
A higher-level phylogenetic classification of the Fungi
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.
Fungal Biodiversity Profiles 31-40
Cryptogamie, Mycologie, 2017
In this new series of Fungal Biodiversity Profiles, the authors describe ten Basidiomycetes, one recombination and nine taxa new to science, using both morphological and molecular data. Descriptions are provided for Craterellus parvogriseus sp. nov. (Cantharellales); for Lactifluus maenanensis sp.nov., Russula albidogrisea sp. nov., R. aureorubra sp. nov., R. aureoviridis sp nov., R. obscuricolor sp. nov. and R. pauriensis sp.nov. (Russulales), for Xerocomus reticulostipitatus sp. nov. (Boletales) and for Leucocybe houghtonii comb. nov. and Amanita rahendrae sp. nov. (Agaricales).
Fungal Systematics and Evolution: FUSE 2
Sydowia, 2016
The present study introduces two new genera, 14 new species, five new combinations and 12 interesting host and/or geographical records. A majority of the fungi are Ascomycetes, but the study also includes a Basidiomycete, Xerocomellus fulvus described from Pakistan. Under single name nomenclature Zeuctomorpha arecae is reduced to synonymy under Acroconidiellina arecae (Sympoventuriaceae, Venturiales, Dothideomycetes). Based on morphology and phylogenetic affinities, Wojnowicia dactylidis, W. lonicerae and W. spartii are moved to the genus Wojnowiciella (Phaeosphaeriaceae, Pleosporales, Dothideomycetes) and Zalerion arboricola is now accommodated in Lophium (Mytilinidiaceae, Mytilinidiales, Dothideomycetes). Novel genera include: Alfariacladiella gen. nov. (Stachybotryaceae, Hypocreales, Sordariomycetes) with A. spartii sp. nov. as type species, and Calvolachnella gen. nov. (Chaetosphaeriales, Sordariomycetes) to accommodate Calvolachnella guaviyuensis comb. nov., previously included...
Molecular Ecology, 1998
We have assembled a sequence database for 80 genera of Basidiomycota from the Hymenomycete lineage (sensu Swann & Taylor 1993) for a small region of the mitochondrial large subunit rRNA gene. Our taxonomic sample is highly biased toward known ectomycorrhizal (EM) taxa, but also includes some related saprobic species. This gene fragment can be amplified directly from mycorrhizae, sequenced, and used to determine the family or subfamily of many unknown mycorrhizal basidiomycetes. The method is robust to minor sequencing errors, minor misalignments, and method of phylogenetic analysis. Evolutionary inferences are limited by the small size and conservative nature of the gene fragment. Nevertheless two interesting patterns emerge: (i) the switch between ectomycorrhizae and saprobic lifestyles appears to have happened convergently several and perhaps many times; and (ii) at least five independent lineages of ectomycorrhizal fungi are characterized by very short branch lengths. We estimate that two of these groups radiated in the mid-Tertiary, and we speculate that these radiations may have been caused by the expanding geographical range of their host trees during this period. The aligned database, which will continue to be updated, can be obtained from the following site on the WorldWide Web: http://mendel.berkeley.edu/boletus.html.
Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi
Molecular Phylogenetics and Evolution, 2007
A phylogeny of the fungal phylum Basidiomycota is presented based on a survey of 160 taxa and five nuclear genes. Two genes, rpb2, and tef1, are presented in detail. The rpb2 gene is more variable than tef1 and recovers well-supported clades at shallow and deep taxonomic levels. The tef1 gene recovers some deep and ordinal-level relationships but with greater branch support from nucleotides compared to amino acids. Intron placement is dynamic in tef1, often lineage-specific, and diagnostic for many clades. Introns are fewer in rpb2 and tend to be highly conserved by position. When both protein-coding loci are combined with sequences of nuclear ribosomal RNA genes, 18 inclusive clades of Basidiomycota are strongly supported by Bayesian posterior probabilities and 16 by parsimony bootstrapping. These numbers are greater than produced by single genes and combined ribosomal RNA gene regions. Combination of nrDNA with amino acid sequences, or exons with third codon positions removed, produces strong measures of support, particularly for deep internodes of Basidiomycota, which have been difficult to resolve with confidence using nrDNA data alone. This study produces 1055-7903/$ -see front matter Ó (P. Brandon Matheny).
Molecular Phylogenetics and Evolution, 2007
Cortinarius is the most species rich genus of mushroom forming fungi with an estimated 2000 spp. worldwide. However, species delimitation within the genus is often controversial. This is particularly true in the section Calochroi (incl. section Fulvi), where the number of accepted taxa in Europe ranges between c.60 and c.170 according to diVerent taxonomic schools. Here, we evaluated species delimitation within this taxonomically diYcult group of species and estimated their phylogenetic relationships. Species were delimited by phylogenetic inference and by comparison of ITS sequence data in combination with morphological characters. A total of 421 ITS sequences were analyzed, including data from 53 type specimens. The phylogenetic relationships of the identiWed species were estimated by analyzing ITS data in combination with sequence data from the two largest subunits of RNA polymerase II (RPB1 and RPB2). Seventy-nine species were identiWed, which are believed to constitute the bulk of the diversity of this group in Europe. The delimitation of species based on ITS sequences is more consistent with a conservative morphological species concept for most groups. ITS sequence data from 30 of the 53 types were identical to other taxa, and most of these can be readily treated as synonyms. This emphasizes the importance of critical analysis of collections before describing new taxa. The phylogenetic separation of species was, in general, unambiguous and there is considerable potential for using ITS sequence data as a barcode for the group. A high level of homoplasy and phenotypic plasticity was observed for morphological and ecological characters. Whereas most species and several minor lineages can be recognized by morphological and ecological character states, these same states are poor indicators at higher levels.
Marasmioid and gymnopoid fungi of the Republic of Korea. 7. Gymnopus sect. Androsacei
Mycological Progress, 2014
Collections of Gymnopus sect. Levipedes from the Republic of Korea have been studied. Two new species, Gymnopus dryophiloides and G. brunneodiscus, are described based on their macro-and micromorphological and phylogenetic characteristics. Three other species, referred to as Gymnopus spp. 1, 2, and 3, are distinguished as separate taxa without formal descriptions. Taxonomic and phylogenetic positions of all taxa have been inferred and confirmed by analyses of ITS and LSU sequence data. Their detailed descriptions, illustrations and an identification key are provided.
2006
Alnicola ( D Naucoria, pro parte) is a mushroom genus of strictly temperate, obligately ectomycorrhizal species, traditionally included in the family Cortinariaceae. Most Alnicola spp. are primarily host speciWc on Alnus, although a few are mycobionts of Salix or other hosts. The diVerent species of Alnicola exhibit unique morphological (cystidia, pileipellis) and cytological (dikaryotic or monokaryotic hyphae) characters. This makes the genus Alnicola of particular interest for studying the evolution of host speciWcity and morphological characters in ectomycorrhizal basidiomycetes. We used a combination of classical morphological and phylogenetic methods (rDNA ITS and LSU sequences) to address the following questions: (i) Is Alnicola monophyletic? And (ii) Are characters like host speciWcity or microscopical structures synapomorphic for certain clades? The study included nearly all currently known European Alnicola sp. Our results demonstrated that, on one hand, the genus Alnicola is polyphyletic, with sistergroup relationships to Hebeloma, Anamika or the clades /Hymenogaster I and /Hymenogaster II. On the other hand, Alnicola splits into three well-supported clades corresponding to the sections Alnicola, Submelinoides, and Salicicolae. The strict host-speciWcity to Alnus is a derived character and has occurred at least twice. The following morphological characters are synapomorphic for deWned clades: the spindle-shaped hymenial cystidia for sect. Alnicola, the hymeniform pileipellis for sect. Submelinoides, and monocaryotic/clampless hyphae for sect. Salicicolae and its sistergroup /Hymenogaster II. As a taxonomical consequence, polyphyly of Alnicola implies that the sects. Submelinoides and Salicicolae need to be segregated from Alnicola.