Part One presents the current classification that includes all accepted genera and higher taxa above the generic level in the phylum Ascomycota. It is based on the changes listed in Myconet notes 4751–5113. In the current outline, three subphyla (Pezizomycotina, Saccharomycotina, Taphrinomycotina) are accepted. Taphrinomycotina includes four classes (Neolectomycetes, Pneumocystidomycetes, Schizosaccharomyces, Taphrinomycetes). Saccharomycotina consists of one class and Pezizomycotina includes eleven classes (Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Laboulbeniomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, Orbiliomycetes, Pezizomycetes, Sordariomycetes). Part Two presents 363 notes on the taxonomy and nomenclature of ascomycetes (Ascomycota) at the generic and higher levels. Numerous changes in higher levels resulted from multi-authored phylogenetic papers resulting from the AFTOL and Deep Hyphae projects, especially a publication on a revised fungal classifica...

https://bioone.org/journals/fieldiana-life-and-earth-sciences/volume-2010/issue-1/1557.1/Myconet-Volume-14-Part-One-Outline-of-Ascomycota2009-Part-Two/10.3158/1557.1.pdf

Myconet Volume 14. Part One. Outline of Ascomycota—2009. Part Two. Notes on Ascomycete Systematics. Nos. 4751–5113

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota.

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New primers for promising single-copy genes in fungal phylogenetics and systematics.

This study was supported by an National Health and Medical Research Council of Australia (NHM CNPq [350338/2000-0] and FAPERJ [E-26/103.157/2011] grants to RM Zancope-Oliveira; CNPq [308011/2010-4] and FAPESP [2007/08575-1] Fundacao de Amparo Pesquisa do Estado de So Paulo (FAPESP) grants to AL Colombo; PEst-OE/BIA/UI4050/2014 from Fundacao para a Ciencia e Tecnologia (FCT) to C Pais; the Belgian Science Policy Office (Belspo) to BCCM/IHEM; the MEXBOL program of CONACyT-Mexico, [ref. number: 1228961 to ML Taylor and [122481] to C Toriello; the Institut Pasteur and Institut de Veil le Sanitaire to F Dromer and D Garcia-Hermoso; and the grants from the Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq) and the Fundacao de Amparo a Pesquisa do Estado de Goias (FAPEG) to CM de Almeida Soares and JA Parente Rocha. I Arthur would like to thank G Cherian, A Higgins and the staff of the Molecular Diagnostics Laboratory, Division of Microbiology and Infectious Diseases, Path West, QEII Medial Centre. Dromer would like to thank for the technical help of the sequencing facility and specifically that of I, Diancourt, A-S Delannoy-Vieillard, J-M Thiberge (Genotyping of Pathogens and Public Health, Institut Pasteur). RM Zancope-Oliveira would like to thank the Genomic/DNA Sequencing Platform at Fundacao Oswaldo Cruz-PDTIS/FIOCRUZ [RPT01A], Brazil for the sequencing. B Robbertse and CL Schoch acknowledge support from the Intramural Research Program of the NIH, National Library of Medicine. T Sorrell's work is funded by the NHM she is a Sydney Medical School Foundation Fellow.

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International Society of Human and Animal Mycology (ISHAM)-ITS reference DNA barcoding database--the quality controlled standard tool for routine identification of human and animal pathogenic fungi.

Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were monophyletic, some were not, and others, previously believed to be unrelated, fell within single monophyletic groups, indicating the need for a revision of the generic delimitations. This study aims to give an overview of current knowledge of the major clades of all parmelioid lichens. For this, we assembled a dataset of 762 specimens, including 31 of 33 currently accepted parmelioid genera (and 63 of 84 accepted genera of Parmeliaceae). We performed maximum likelihood and Bayesian analyses of combined datasets including two, three and four loci. Based on these phylogenies and the correlation of morphological and chemical characters that characterize monophyletic groups, we accept 27 genera within nine main clades. We re-circumscribe several genera and reduce Parmelaria to synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo is described as a new genus (type: E. masonii). Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex A. Crespo & al. is elevated to generic rank and 15 new combinations are proposed (in the genera Flavoparmelia, Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A short discussion of the accepted genera is provided and remaining challenges and areas requiring additional taxon sampling are identified.

Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence

Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene.

Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species

Molecular phylogenies based on the ITS-LSU nrDNA and part of the s-tubulin region were used to investigate the position of Neuropogon in Usnea s. lat. Bayesian inference and maximum parsimony strongly supported the monophyly of Neuropogon. Subgenus Usnea and Neuropogon form a strongly supported group with subg. Eumitria and subg. Dolichousnea as consecutive monophyletic sister groups. The following generic classification is proposed: Usnea (subgenus Usnea only), Neuropogon, Eumitria, and Dolichousnea. Dolichousnea is elevated to generic rank. Usnea as presently conceived is clearly non-monophyletic but with the present recircumscription it may be monophyletic, or not; this requires further analysis. The genera are well characterised morphologically, and pending further investigations this classification is in agreement with current practice and minimises the need for nomenclatural changes. The following new combinations are made: Dolichousnea (Y. Ohmura) Articus, Dolichousnea longissima (Ach.) Articus, D. trichodeoides (Vain.) Articus, D. diffracta (Vain.) Articus, and Eumitria pectinata (Taylor) Articus.

/pdf/neuropogon-and-the-phylogeny-of-usnea-s-l-parmeliaceae-1ds0ztc9aa.pdf

Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes)

The monophyletic groups of cetrarioid lichens

This thesis deals with the phylogeny of the lichen genus Usnea (Parmeliaceae, Ascomycetes) The relationships and the morphological variation among Usnea species has been studied, as well as the relationship of Usnea to allied genera Two species, U florida and U subfloridana, which earlier were regarded to form two separate species have been synonymized In an analysis based on sequence data these two taxa formed a monophyletic group of intermixed specimens Usnea florida and U subfloridana have earlier been regarded to form a species pair, but the species pairs concept cannot be applied in this case The morphological characters traditionally used for species recognition of a number of European Usnea species have been analyzed regarding their reliability The evolution and distribution of the morphological characters was studied in relation to a phylogeny based on sequence data Most characters proved to be homoplastic in relation to the phylogeny Few characters were consistent in a clade, and the same character could be inconsistent in another clade Therefore a combination of several characters is recommended for species recognition The relationship of Neuropogon to Usnea was investigated based on sequence data Neuropogon showed to be closely related to Usnea subg Usnea The subgenera Eumitria and Dolichousnea formed the sister group to the clade comprising subg Usnea and Neuropogon Usnea is paraphyletic in this investigation Eumitria is treated as a genus and the subgenus Dolichousnea is elevated to generic rank The position of Usnea, Neuropogon, Eumitria, and Dolichousnea in the family Parmeliaceae was investigated based on a phylogeny obtained by sequence data Protousnea probably forms the sister group to the clade of Usnea, Neuropogon, Eumitria, and Dolichousnea Several monophyletic groups in the family Parmeliaceae were identified

Kristina Articus

Papers

Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene.

Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species

Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes)

The monophyletic groups of cetrarioid lichens

Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)