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This classification is restricted to organisms that belong in the monophyletic kingdom Fungi, including sexual and asexual forms. It does not consider other organisms formerly included in the kingdom but which are now known not to belong there, even if still studied by mycologists, such as the oomycetes and slime moulds. The classification adopted here uses a Linnean hierarchy as modified by the International Code of Botanical Nomenclature [Code] (McNeill et al. 2006), and uses seven ranks, including: order (suffix: -ales), subclass (-mycetidae), class (-mycetes), subphylum (- mycotina), phylum (-mycota; except Microsporidia), subkingdom, and kingdom. The rankings of taxa reflect the preferences and past practices of various authors, as well as the need to keep the nested hierarchies of clades and Linnean categories parallel. Taxa placed at the same rank are not necessarily equivalent in age (except sister taxa), number of species, or degree of morphological divergence. The classification is limited to taxa down to the level of order. In many orders, especially those representing larger groups, such as Agaricales, there is still not enough resolution or taxon sampling to structure a comprehensive family-level classification. The challenge of creating family-level classifications is made even more difficult by the Code (McNeill et al. 2006), which requires that names of taxa at the rank of family or lower follow the principle of priority (which does not apply to higher ranks). Ideally, construction of consensus classifications within many of the orders recognized here will involve the coordinated efforts of groups of taxonomic specialists. It is hoped that the present classification will facilitate those endeavors. The taxa included here are all supported as monophyletic by at least one published phylogenetic analysis (not applicable to monotypic taxa), with the exception of the Lahmiales and Triblidiales (Pezizomycotina) and Asellariales (Kickxellomycotina), for which molecular data are not available. Support for the monophyly of each group is 10
summarized in Tables 1-3, which list selected phylogenetic studies, the type of data that were analyzed, the number of OTUs sampled, and bootstrap frequencies and Bayesian posterior probabilities. No attempt has been made to cite all of the relevant studies for each group. The analyses chosen for inclusion in the Tables are those that have the greatest numbers of loci or taxa, and that provide the strongest support for monophyly of the clades in question. To supplement the information in the tables, brief comments on synonyms, phylogenetic relationships, and composition are provided below for some taxa, along with bibliographic citations for all taxon names. However, it is beyond the scope of this article to discuss each taxon in detail. For additional literature on the phylogeny and taxonomy of individual taxa, readers should consult the studies listed in Tables 1-3 and below, and the references therein. The classification is also presented as a set of tree diagrams (Figs 1-3). Taxa of uncertain position are listed as incertae sedis, and have been placed at the least inclusive level in the hierarchy where they can be assigned with confidence. There are several nodes resolved in the tree figure that are not reflected in the classification (Figs 1-3). These unnamed clades, for which there is strong to moderate support in recent studies, include the Dacrymycetes plus Agaricomycetes (Basidiomycota) (Matheny et al. 2006, 2007a), Saccharomycotina plus Pezizomycotina (Ascomycota) (James et al. 2006; Spatafora et al. 2007), and the inoperculate euascomycetes (Ascomycota) (e.g. Lumbsch et al. 2002). The inoperculate euascomycetes has been recognized as a superclass, the Leotiomyceta (Eriksson & Winka 1997; Lumbsch et al. 2002), which is a rank that is not employed here, while the Dacrymycetes plus Agaricomycetes correspond to the subclass Hymenomycetidae of Swann & Taylor (1995). The absence of these groups from the present classification should not be interpreted as a judgment on their monophyly. Rather, it reflects a desire to keep the classification simple, and to minimize the number 11
Page 1 and 2: Elsevier Editorial System(tm) for M
Page 3 and 4: Cover Letter February 8, 2007 Dr. D
Page 5 and 6: A higher-level phylogenetic classif
Page 7 and 8: 18 Institute of Applied Ecology, Ch
Page 9 and 10: 47 Systematic Mycology and Lichenol
Page 11 and 12: classifications. Two important work
Page 13: promote communication and awareness
Page 17 and 18: Pucciniomycotina, and Ustilaginomyc
Page 19 and 20: Many of the citations and authoriti
Page 21 and 22: Class: Chytridiomycetes Caval.-Sm.,
Page 23 and 24: ibosomal aggregation, and rumposome
Page 25 and 26: Synonym: Allomycetes Caval.-Sm., Bi
Page 27 and 28: Order: Paraglomerales C. Walker & A
Page 29 and 30: Fungi pathogenici obligate animalib
Page 31 and 32: Synonym: Zoopagales Bessey, Morph.
Page 33 and 34: Unicellular or filamentous Fungi, l
Page 35 and 36: Class: Pneumocystidomycetes O. E. E
Page 37 and 38: Order: Dothideales Lindau, in Engle
Page 39 and 40: Lichenized, parasitic, and saprobic
Page 41 and 42: Order: Onygenales Cif. ex Benny & K
Page 43 and 44: vel infirme ramosae, septatae, medi
Page 45 and 46: Exemplar genera: Coccocarpia Pers.
Page 47 and 48: Lecanoromycetes incertae sedis (not
Page 49 and 50: Based on current character and taxo
Page 51 and 52: Order: Coronophorales Nannf., Nova
Page 53 and 54: Order: Coniochaetales Huhndorf, A.
Page 55 and 56: Exemplar genera: Huangshania O. E.
Page 57 and 58: Order: Cystobasidiales R. Bauer, Be
Page 59 and 60: Exemplar genera: Microbotryum Lév.
Page 61 and 62: Class: Ustilaginomycetes R. Bauer,
Page 63 and 64: Emend. Bauer, Oberwinkler & Vánky,
Page 65 and 66:
Order: Cystofilobasidiales Fell, Ro
Page 67 and 68:
Order: Agaricales Underw., Moulds,
Page 69 and 70:
phylogenetics of Cantharellales. An
Page 71 and 72:
cylindrical or suballantoid, with t
Page 73 and 74:
subicular hyphae with or without am
Page 75 and 76:
REFERENCES 1 Adl SM, Simpson AGB, F
Page 77 and 78:
Begerow D, Bauer R, Oberwinkler F,
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Clements FE, Shear CL. 1931. The Ge
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Galagan JE, Henn MR, Ma L-J, Cuomo
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Lecanoromycetes (Ascomycota). Molec
Page 85 and 86:
Keeling PJ, 2003. Congruent evidenc
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Lindau G, 1896. Hysteriineae. In: E
Page 89 and 90:
Margulis L, Corliss JO, Melkonian M
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Nannfeldt JA, 1932. Studien über d
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Sampaio JP, Gadanho M, Bauer R, Wei
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Sugiyama J, Hosaka K, Suh S-O, 2007
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Glomeromycota. Mycological Research
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Sordariomycetes systematics: An ove
Page 102 and 103:
MICROSPORIDIA Kickxellales Dimargar
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Agaricostilbales Agaricostilbomycet
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James et al. (2007) lsu, ssu, 5.8S
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Table 2. Support for major groups o
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MPbs < 50 SC Dothideomycetidae Scho
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4 Bpp = 1.00 MLbs = 100 WPbs > 70 9
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pb2, tef1 MLbs = 93 Bpp = 1.00 Miad
Page 116 and 117:
Reeb et al. (2004, fig. 1) lsu, ssu
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tef1 WPbs = 96 MLbs = 90 Bpp = 1.00
Page 120 and 121:
Bpp = 1.00 Miller & Huhndorf (2005,
Page 122 and 123:
Table 3. Support for major groups o
Page 124 and 125:
Sampaio (2004, fig. 1) lsu 7 Bpp =
Page 126 and 127:
O Ustilaginales Matheny et al. (200
Page 128 and 129:
pb2, tef1 MPbs = 50-69 Fell et al.
Page 130:
Larsson et al. (2007, fig. 3) lsu,
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