Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project ‘‘Assembling the Fungal Tree of Life’’ (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

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Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits

http://lutzonilab.org/publications/lutzoni_file180.pdf

Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming acarosporaceae and evolution of polyspory

Ninety years after Zahlbruckner, we present the most recent update to the classification of lichen fungi in the Ascomycota and Basidiomycota to genus level, with species numbers and references to changes compared to the 2010 Outline of Ascomycota and other recent classifications. Updated statistics on global species richness of lichen fungi and species richness at family, order and class level are given. The number of accepted species is 19,387 in 995 genera, 115 families, 39 orders and eight classes. Lichenized Basidiomycota amount to 172 species (0.9% of the total), 15 genera (1.5%), five families (4.3%), five orders (12.8%) and one class (12.5%). The most speciose genera are Xanthoparmelia, Lecanora, Arthonia, Cladonia, Pertusaria, Ocellularia, Graphis, Caloplaca, Usnea and Buellia. The average number of species per genus is 19.5 and 256 genera are monospecific. Using newly defined categories, two genera (Xanthoparmelia, Lecanora) are ultradiverse (more than 500 species), 17 hyperdiverse (201–500 species) and 12 megadiverse (101–200). The largest family is Parmeliaceae, with 2,765 species and 77 genera, followed by Graphidaceae (2,161; 79), Verrucariaceae (943; 43), Ramalinaceae (916; 43) and Lecanoraceae (791; 25). The largest order is Lecanorales, with 6,231 species and 234 genera, followed by Ostropales (3,261; 138), Arthoniales (1,541, 103), Peltigerales (1,301; 67) and Caliciales (1,276; 55). The largest class is Lecanoromycetes, with 15,131 species and 701 genera, followed by Arthoniomycetes (1,541; 103), Eurotiomycetes (1,203; 63), Dothideomycetes (812; 39) and Lichinomycetes (390; 50). A total of 751 out of 995 genera (75%) have molecular data. Fifty-nine genera remain in unresolved positions at the family, order or class level. The phylogenetic position of the 39 orders containing lichenized fungi suggests 20–30 independent lichenization events during the evolution of higher Fungi, 14–23 in the Ascomycota and 6–7 in the Basidiomycota. The following names are validated: Candelariomycetidae Miądl. et al. ex Timdal & M.Westb. subcl. nov., Cystocoleaceae Locq. ex Lucking, B.P.Hodk. & S.D.Leav. fam. nov, Letrouitineae Gaya & Lutzoni subordo nov., Rhizocarpales Miądl. & Lutzoni ordo nov. and Teloschistineae Gaya & Lutzoni subordo nov. Lectotypes are designated for Clathroporinopsis M.Choisy and Protoschistes M.Choisy, making both synonyms of Gyalecta Ach., and Stromatothelium Trevis., making it a synonym of Pyrenula Ach. Members of Cyphobasidiales, which are here interpreted as hyperlichenized fungi, as well as fossil lichen fungi, are added in additional classifications in two appendices.

https://bioone.org/journals/The-Bryologist/volume-119/issue-4/0007-2745-119.4.361/The-2016-classification-of-lichenized-fungi-in-the-Ascomycota-and/10.1639/0007-2745-119.4.361.pdf

The 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota – Approaching one thousand genera

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

The Lecanoromycetes includes most of the lichen-forming fungal species (>13 500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogeneti...

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New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, beta-tubulin and GAPDH sequences

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial beta-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and beta-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and beta-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.

Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and beta-tubulin sequences, morphology, anatomy and secondary chemistry.

Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.

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Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers

Various aspects of the lichen genus Xanthoparmelia have been investigated using ITS rDNA sequences. The delimitation of the genus and phylogeographic trends within the genus are reviewed. Three south African genera, Almbornia, Namakwa and Xanthomaculina, are synonymized with Xanthoparmelia. The transfer of Xanthoparmelia peruviensis to Psiloparmelia is strongly supported by a bootstrap analysis. Two new names are proposed, Xanthoparmelia aliphaticella and X ovealambornii, and four new combinations are made, Psiloparmelia peruviensis, Xanthoparmelia azaniensis, X. frondosa and X. hottentotta.

A contribution to the phylogeny and taxonomy of Xanthoparmelia (Ascomycota, Parmeliaceae)

Some European species of the genera Parmelia and Punctelia are analysed using molecular, morphological and chemical characters and notes on their distribution are presented. ITS sequences were compared from a total of 31 representative specimens. Parmelia ernstiae and P. serrana form a sister group to P. pinnatifida and P. saxatilis, whereas P. discordans and P. omphalodes are closely related and form a sister group to all former four species. Bootstrap support values from the PAUP and PHYLIP analyses are used to confirm relationships between Parmelia and Punctelia species. Parmelia ernstiae, P. serrana, Punctelia jeckeri and P. subrudecta are reported from additional countries and provinces. Parmelia ernstiae is reported from Bosnia-Herzegovina and Czech Republic for the first time, and P. serrana is new to Germany, Russia and Ukraine. Data on chemistry are collected both from the literature and from our own investigations. The chemical compounds present in Parmelia ernstiae, P. saxatilis and P. serrana were analysed and compared using HPLC. These morphologically similar species are chemically different. (Less)

Tassilo Feuerer

Papers

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, beta-tubulin and GAPDH sequences

Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and beta-tubulin sequences, morphology, anatomy and secondary chemistry.

Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers

A contribution to the phylogeny and taxonomy of Xanthoparmelia (Ascomycota, Parmeliaceae)

Notes on the systematics, chemistry and distribution of European Parmelia and Punctelia species (lichenized ascomycetes)