A higher-level phylogenetic classification of the Fungi - National ...

mycological research 111 (2007) 509–547available at www.sciencedirect.comjournal homepage: www.elsevier.com/locate/mycresA higher-level phylogenetic classification of the FungiDavid S. HIBBETT a, *, Manfred BINDER a , Joseph F. BISCHOFF b , Meredith BLACKWELL c , PaulF. CANNON d , Ove E. ERIKSSON e , Sabine HUHNDORF f , Timothy JAMES g , Paul M. KIRK d ,Robert LÜCKING f , H. THORSTEN LUMBSCH f , François LUTZONI g , P. Brandon MATHENY a ,David J. MCLAUGHLIN h , Martha J. POWELL i , Scott REDHEAD j , Conrad L. SCHOCH k ,Joseph W. SPATAFORA k , Joost A. STALPERS l , Rytas VILGALYS g , M. Catherine AIME m ,André APTROOT n , Robert BAUER o , Dominik BEGEROW p , Gerald L. BENNY q , Lisa A.CASTLEBURY m , Pedro W. CROUS l , Yu-Cheng DAI r , Walter GAMS l , David M. GEISER s ,Gareth W. GRIFFITH t ,Cécile GUEIDAN g , David L. HAWKSWORTH u , Geir HESTMARK v ,Kentaro HOSAKA w , Richard A. HUMBER x , Kevin D. HYDE y , Joseph E. IRONSIDE t , UrmasKÕLJALG z , Cletus P. KURTZMAN aa , Karl-Henrik LARSSON ab , Robert LICHTWARDT ac , JoyceLONGCORE ad , Jolanta MIĄDLIKOWSKA g , Andrew MILLER ae , Jean-Marc MONCALVO af ,Sharon MOZLEY-STANDRIDGE ag , Franz OBERWINKLER o , Erast PARMASTO ah , ValérieREEB g , Jack D. ROGERS ai , Claude ROUX aj , Leif RYVARDEN ak , José Paulo SAMPAIO al , ArthurSCHÜßLER am , Junta SUGIYAMA an , R. Greg THORN ao , Leif TIBELL ap , Wendy A.UNTEREINER aq , Christopher WALKER ar , Zheng WANG a , Alex WEIR as , Michael WEISS o ,Merlin M. WHITE at , Katarina WINKA e , Yi-Jian YAO au , Ning ZHANG ava Biology Department, Clark University, Worcester, MA 01610, USAb National Library of Medicine, National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20892-6510, USAc Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USAd CABI UK, Bakeham Lane, Egham, Surrey TW20 9TY, UKe Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Swedenf Department of Botany, The Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USAg Department of Biology, Duke University, Box 90338, Durham, NC 27708, USAh Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN 55108-1095, USAi Department of Biological Sciences, Box 870344/319 Biology, University of Alabama, Tuscaloosa, AL 35487-0344, USAj ECORC, Agriculture and Agri-Food Canada, CEF, Neatby Building, Ottawa, ON K1A 0C6, Canadak Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USAl Centraalbureau voor Schimmelcultures, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlandsm USDA ARS Systematic Botany and Mycology Laboratory, Bldg 011A Rm 319 BARC-WEST, 10300 Baltimore Ave,Beltsville, MD 20705 USAn ABL Herbarium, Gerrit van der Veenstraat 107, NL-3762 XK Soest, The Netherlandso Botanical Institute, University of Tübingen, Auf der Morgenstelle 1, D-72076 Tübingen, Germanyp Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, D-35043 Marburg, Germanyq Department of Plant Pathology, 1453 Fifield Hall, Hull Road, P.O. Box 110680, University of Florida, Gainesville FL 32611-0680, USAr Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, Chinas Department of Plant Pathology, Pennsylvania State University, University Park, PA 16802, USAt Institute of Biological Sciences, University of Wales, Aberystwyth SY23 3DA, UKu Departamento de Biología Vegetale II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza Ramón y Cajal, CiudadUniversitaria, E-28040 Madrid, Spain* Corresponding author.E-mail address: dhibbett@clarku.edu (D. S. Hibbett).0953-7562/$ – see front matter ª 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.doi:10.1016/j.mycres.2007.03.004

510 D. S. Hibbett et al.v Department of Biology, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norwayw Department of Botany, The Field Museum, 1400 S Lake Shore Dr., Chicago, IL 60605, USA,x USDA-ARS Plant Protection Research Unit, US Plant, Soil and Nutrition Laboratory, Tower Road, Ithaca, NY 14853-2901, USAy Centre for Research in Fungal Diversity, Department of Ecology & Biodiversity, University of Hong Kong, Pokfulam Road,Hong Kong SAR, Chinaz Institute of Botany and Ecology, Tartu University, 40 Lai Street, Tartu 51005, Estoniaaa Microbial Properties Research, NCAUR, ARS, USDA, 1815 N.University Street, Peoria, IL 61604-3999, USAab Göteborg University, Department of Plant and Environmental Sciences, P. O. Box 461, SE-405 30 Göteborg, Swedenac Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045-7534, USAad Department of Biological Sciences, University of Maine, 5722 Deering Hall, Orono, ME 04469-5722, USAae Center for Biodiversity, Illinois Natural History Survey, 1816 South Oak Street, Champaign, IL 61820-6970, USAaf Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, 100 Queen’s Park, Toronto, ON M5S 2C6, Canadaag Division of Natural Sciences, Mathematics, and Engineering, Middle Georgia College, 1100 Second Street, SE, Cochran,GA 31014-1599, USAah Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 181 Riia Street Tartu, 51014, Estoniaai Department of Plant Pathology, Washington State University, P.O. Box 646430, Pullman, WA 99164-6430, USAaj Chemin des Vignes vielles, 84120, Mirabeau, Franceak Botanical Institute, University of Oslo, P.O. Box 1066, Blindern, N-0316 Oslo, Norwayal CREM, SABT, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugalam Genetics Institute, Department Biology I, Ludwig-Maximilians-University, Maria-Ward-Strasse 1a, D-80638 Munich, Germanyan TechnoSuruga Co. Ltd, Tokyo Office, Ogawamachi Kita Building 4F, 1-8-3, Kanda Ogawamachi, Chiyoda-ku, Tokyo 101-0052, Japanao Department of Biology, University of Western Ontario, 213 Biological and Geological Sciences Building, 1151 Richmond Street North,London, ON, N6A 5B7, Canadaap Department of Systematic Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36, Uppsala, Swedenaq Botany Department, Brandon University, 270-18th Street, Brandon, MB R7A 6A9, Canadaar Royal Botanic Garden Edinburgh, 20A Inverlieth Row, Edinburgh Eh3 5LR, UKas Faculty of Environmental and Forest Biology, SUNY College, 242 Illick Hall, 1 Forestry Drive, Syracuse, NY 13210, USAat Department of Biology, Boise State University, 1910 University Drive, S/N Building, Room 210, Boise, ID 83725-1515, USAau Systematic Mycology and Lichenology Laboratory, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, Chinaav Department of Plant Pathology, Cornell University, Geneva, NY 14456, USAarticle infoArticle history:Received 31 January 2007Received in revised form22 February 2007Accepted 2 March 2007Published online 13 March 2007Corresponding Editor:David L. HawksworthKeywords:AFTOLEumycotaLichensMolecular phylogeneticsMycotaNomenclatureSystematicsabstractA comprehensive phylogenetic classification of the kingdom Fungi is proposed, withreference to recent molecular phylogenetic analyses, and with input from diverse membersof the fungal taxonomic community. The classification includes 195 taxa, down tothe level of order, of which 16 are described or validated here: Dikarya subkingdom nov.;Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetesclass. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.;Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales,Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classifiedas subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae.The most dramatic shifts in the classification relative to previous works concern the groupsthat have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycotais retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycotarepresenting segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycotaare distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina,Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia areincluded in the Fungi, but no further subdivision of the group is proposed. Several generaof ‘basal’ Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus,Caulochytrium, Olpidium, and Rozella.ª 2007 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.IntroductionThe molecular revolution in fungal taxonomy commenced inthe early 1990s, with analyses of PCR-amplified ribosomalRNA genes (White et al. 1990). Today, fungal molecular systematicsis a mature discipline in which multi-locus datasets,extensive taxon sampling, and rigorous analytical approachesare standard. To gain an overview of the current state of the

A higher-level phylogenetic classification of the Fungi 513Chytridiomycetes and Monoblepharidomycetes. The Blastocladiales,a traditional member of the Chytridiomycota, is heretreated as a phylum, the Blastocladiomycota, as in Jameset al. (2007). The Neocallimastigales, whose distinctivenessfrom other chytrids has long been recognized, is also elevatedto phylum, based on both morphology and molecular phylogeny.The genera Caulochytrium, Olpidium, and Rozella, whichhave traditionally been placed in the Chytridiomycota, andBasidiobolus, which has been classified in the Zygomycota(Entomophthorales), are not included in any higher taxa inthis classification, pending more definitive resolutions oftheir placements.The phylum Zygomycota is not accepted in this classification,pending resolution of relationships among the cladesthat have traditionally been placed in the Zygomycota (seediscussion under Mucoromycotina). The traditional Zygomycotaare here distributed among the phylum Glomeromycotaand four subphyla incertae sedis, including Mucoromycotina,Kickxellomycotina, Zoopagomycotina and Entomophthoromycotina.A clade containing the Glomeromycota and the Dikaryawas resolved previously based on ribosomal RNA genesand was classified as the Symbiomycota (Tehler et al. 2003).That taxon is not included here, because there was notstrong support for the clade in the analyses of James et al.(2006) or Liu et al. (2006). If the Symbiomycota is added tothis classification, it will need to be assigned a rank betweenkingdom and subkingdom, or perhaps be classified as an unrankedtaxon.Microsporidia, unicellular parasites of animals and protistswith highly reduced mitochondria (Germot et al. 1997; Hirtet al. 1997; Peyretaillade et al. 1998), are included here as a phylumof the Fungi, based on analyses by Keeling et al. (2000), Gill& Fast (2006), James et al. (2006), and Liu et al. (2006). The latterstudy concluded that Microsporidia are the sister group of therest of the Fungi and should not be classified as true Fungi,but that topology does not conflict with the delimitation ofthe monophyletic Fungi as proposed here. The analysis ofJames et al. (2006) suggested that Rozella, which was not sampledby Liu et al. (2006), is the sister group of the Microsporidia.No subdivision of the Microsporidia is proposed, owing to a lackof well-sampled multilocus analyses of this group (but seeVossbrinck & Debrunner-Vossbrinck 2005, for an analysis usingSSU rRNA genes).Phylogenetic classification of FungiMany of the citations and authorities in the list belowwere obtained from the Index Fungorum databases (www.indexfungorum.org). A brief list of exemplar genera, includingthe type for automatically typified names, is given for eachorder (for small orders, all included genera are listed). A numberof the genera listed are used in a modern, restrictedsense, and readers are urged to consult the primary literaturecited below and in the tables for information about currentgeneric concepts. Comprehensive lists of genera and familiesincluded in each order will be forthcoming in the Dictionary ofthe Fungi (10th edn; listing on-line at www.indexfungorum.org)and in the next revision of Myconet (for Ascomycota).Further information on the names of fungi (not only kingdomFungi) above the rank of order and their places of publicationmay be found in the preliminary catalogue compiled by David(2002).In accordance with the practice in recent editions of theCode, all scientific names regardless of rank are placed initalic type here except in the first line of the treatment ofeach accepted taxon where they are given in bold Romantype to make them stand out. When these names areused by other mycologists in their own publications, wewish to encourage the practice of the use of italics as recommendedin the Preface to the current Code (McNeillet al. 2006).Kingdom: Fungi R. T. Moore, Bot. Mar. 23: 371 (1980).Synonym: Fungi T. L. Jahn & F. F. Jahn, How to Know the Protozoa:7 (1949), nomen invalidum. (Table 1, Fig 1)The concept of the Fungi as one of six kingdoms of life wasintroduced by Jahn & Jahn (1949), and a five kingdom systemwas advanced by Whittaker (1959), but neither of these worksincluded a Latin diagnosis and the name was therefore invalidunder the Code until the required Latin was provided by Moore(1980). Although Moore did not make a specific reference toJahn & Jahn’s book, he was well aware that the name was inwidespread use in the rank of kingdom. Under the currentCode, Jahn & Jahn are not to be included in the author citation.However, a proposal to change this provision in the Code willbe made at the next International Botanical Congress (D. L.Hawksworth, unpubl.). If it is approved, the correct citationwould be Fungi T. L. Jahn & F. F. Jahn ex R. T. Moore (thisrule change would also affect the citations of Ascomycota andBasidiomycota).Phylum: Chytridiomycota M. J. Powell, phylum nov.MycoBank no.: MB 501278Synonyms: Archemycota Caval.-Sm., Biol. Rev. 73: 246 (1998), proparte.Thallus monocentricus vel polycentricus vel filamentosus;propagatio asexualis zoosporis, flagello retrorsum inserto, kinetosomateet centriolo supervacaneo praeditis, 9 munimentis flagelli,et complexu ‘‘microbody-corpore lipideo’’ descriptis; propagatiosexualis meiosi post copulationem perfecta; apparatus Golgi e cisternissuperimpositis constans; tegumentum nuclei mitosi procedentecircum polos fenestratum.Typus: Chytridium A. Braun 1851.Thallus monocentric, polycentric, or filamentous; asexualreproduction by zoospores with a single posteriorly-directedflagellum, both a kinetosome and non-functional centriole,nine flagellar props, and a microbody-lipid globule complex;sexual reproduction with zygotic meiosis where known; Golgiapparatus with stacked cisternae; nuclear envelope fenestratedat poles during mitosis.Used as a phylum name without Latin diagnosis or descriptionamong others by von Arx (1967) and Margulis et al. (1990).Equivalent to euchytrids of James et al. 2006, the ‘core chytridclade’ of James et al. (2007), or the ‘core chytrid clade’ plus theMonoblepharidales of James et al. (2000). Earlier usages are notindicated in the author citation of the name, because thecircumscription adopted here differs significantly from thatof those authors.

514 D. S. Hibbett et al.Table 1 – Support for major groups of Fungi in selected phylogenetic studies: basal fungi and DikaryaRank Taxon Reference Data a OTUs b Support cKingdom FUNGI Keeling (2003) a-tub, b-tub 38 MLBS ¼ 98NJBS ¼ 94Baldauf et al. (2000) act, a-tub, b-tub, tef1 12 MLBS ¼ 85MPBS ¼ 95Phylum CHYTRIDIOMYCOTA James et al. (2007) LSU, SSU, 5.8S 84 BPP 0.95Seif et al. (2005) mt-genome 5 BPP ¼ 1MLBS ¼ 100Class Chytridiomycetes James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 8 BPP 0.95MLBS 70James et al. (2007) LSU, SSU, 5.8S 75 BPP 0.95MLBS 70Keeling (2003) a-tub, b-tub 5 MLBS¼ 90NJBS ¼ 95Order Chytridiales James et al. (unpublished) LSU, SSU, 5.8S, rpb1, rpb2, tef1, atp6 9 MLBS¼ 98Order Rhizophydiales James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP 0.95MLBS 70Letcher et al. (2006) LSU, 5.8S 96 MPBS ¼ 100BPP ¼ 1Order Spizellomycetales James et al. (2007) LSU, SSU, 5.8S 9 MPBS ¼ 100Class/OrderPhylum/Class/OrderPhylum/Class/OrderMonoblepharidomycetes,MonoblepharidalesNEOCALLIMASTIGOMYCOTA,Neocallimastigomycetes,NeocallimastigalesBLASTOCLADIOMYCOTA,Blastocladiomycetes,BlastocladialesJames et al. (2007) LSU, SSU, 5.8S 9 BPP 0.95MLBS 70MPBS 70Bullerwell et al. (2003) cox 1,2,3; cob, atp6,9; nad 1,2,3,4, 4L,6 4 MLBS ¼ 100James et al. (2007) LSU, SSU, 5.8S 6 BPP 0.95MLBS 70MPBS 70James et al. (2007) LSU, SSU, 5.8S 10 BPP 0.95Liu et al. (2006) rpb1, rpb2 3 BPP ¼ 1MPBS ¼ 100Phylum MICROSPORIDIA James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP 0.95MLBS 70Keeling (2003) a-tub, b-tub 6 MLBS¼ 100NJBS ¼ 97Phylum/ClassGLOMEROMYCOTA,GlomeromycetesJames et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 5 BPP 0.95MLBS 70Schüßler et al. (2001) SSU 72 NJBS 90Order Archaeosporales Schüßler et al. (2001) SSU 5 NJBS 95Order Diversisporales Schüßler et al. (2001) SSU 32 NJBS 95Order Glomerales Schüßler et al. (2001) SSU 32 NJBS 95Order Paraglomerales Schüßler et al. (2001) SSU 3 NJBS 95Subphyla incertae sedis(not placed in any phylum)Subphylum Mucoromycotina James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 11 BPP ¼ 1Tanabe et al. (2004) rpb1 4 NJBS ¼ 82Order Mucorales James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 3 BPP 0.95MLBS 70Tanabe et al. (2004) rpb1 3 NJBS ¼ 100Keeling (2003) a-tub, b-tub 4 MLBS¼ 96NJBS ¼ 98White et al. (2007) LSU, SSU, 5.8S 28 BPP ¼ 1MPBS 70Order Endogonales White et al. (2007) LSU, SSU, 5.8S 2 BPP ¼ 1MPBS 70Order Mortierellales White et al. (2007) LSU, SSU, 5.8S 6 BPP ¼ 1MPBS 70Subphylum/OrderEntomophthoromycotina,EntomophthoralesJames et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP 0.95MLBS 70Subphylum/Order Zoopagomycotina, Zoopagales James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP 0.95MLBS 70Tanabe et al. (2004) rpb1 3 NJBS ¼ 86Subphylum Kickxellomycotina Tanabe et al. (2004) rpb1 6 NJBS ¼ 84Order Kickxellales O’Donnell et al. (1998) SSU 7 MPBS ¼ 100Order Dimargaritales Tanabe et al. (2000) SSU 3 NJBS ¼ 100

A higher-level phylogenetic classification of the Fungi 515Table 1 (continued)Rank Taxon Reference Data a OTUs b Support cOrder Harpellales Tanabe et al. (2004) rpb1 3 NJBS ¼ 98O’Donnell et al. (1998) SSU 4 MPBS ¼ 100Order Asellariales d d d dSubkingdom DIKARYA James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 161 BPP ¼ 1MLBS ¼ 71Steenkamp et al. (2006) act, a-tub, b-tub, tef1 10 BPP ¼ 1MLBS ¼ 84MPBS ¼ 82NJBS ¼ 96Seif et al. (2005) mt-genome 10 BPP ¼ 1MLBS ¼ 100Liu et al. (2006) rpb1, rpb2 27 BPP ¼ 1MPBS ¼ 100Taxa with only one subsidiary taxon included (i.e. redundant taxa) are listed on a single line, with rank abbreviations divided by a slash (e.g. theclass Agaricostilbomycetes, which contains a single order, Agaricostilbales, is indicated as Class/Order).a LSU, SSU, and 5.8S refer to nuclear rRNA genes, whereas mt-LSU and mt-SSU refer to mitochondrial rRNA genes, other genes follow standardabbreviations. Some datasets contain missing sequences.b Indicates the number of OTUs in the specified clade, not the total number of OTUs in the dataset.c BS, bootstrap %, jk, jackknife %,WP ¼ weighted parsimony, RML ¼ RaxML, PML ¼ PhyML, ME ¼ minimum evolution, BPP, Bayesian posteriorprobability, NA, not applicable because the group is monotypic, or only a single species was sampled in the reference study.Class: Chytridiomycetes Caval.-Sm., Biol. Rev. 73: 246 (1998).Synonym: Archimycetes A. Fisch. (Fischer 1892) pro parte(included Olpidiopsis, Hypochytrium).Type: Chytridium A. Braun 1851.Reproducing asexually by zoospores bearing a single posteriorly-directedflagellum; zoospores containing a kinetosomeand a non-flagellated centriole; thallus monocentric or rhizomycelialpolycentric; sexual reproduction not oogamous.Cavalier-Smith (1998) provided a brief, four-word, Latindescription that was not diagnostic for phyla of uniflagellatefungi, and has been revised above. The name Chytridiomyceteswas also used by Serbinow (1907), Cejp (1957), Sparrow (1958),and Alexopoulos et al. (1996). For further discussion of thenomenclatural history of the name, see David (2002).Order: Chytridiales Cohn, Jber. schles. Ges. vaterl. Kultur 57: 279(1879).Emend. Schröter (as ’Chytridineae’) in Engler & Prantl, Nat.Pflanzenfam. 1: 64 (1892). Emend. Barr, Can. J. Bot. 58: 2384(1980). Emend. Letcher & Powell, Mycol. Res. 110: 907 (2006).Type: Chytridium A. Braun 1851.Thallus monocentric or polycentric rhizomycelial; zoosporestypically with flagellar base containing an electron-opaque plug,microtubules extending from one side of the kinetosome ina parallel array, ribosomes aggregated near the nucleus, kinetosomeparallel to non-flagellated centriole and connected to it byfibrous material, nucleus not associated with kinetosome, fenestratedcisterna (rumposome) adjacent to lipid globule.Exemplar genera: Chytridium A. Braun 1851, ChytriomycesKarling 1945, Nowakowskiella J. Schröt. 1893.An emmended description is presented above to conformto the circumscription adopted here. Monophyly of this group,as currently delimited, is not certain; Polychytrium Ajello 1942and its allies and Chytriomyces angularis Longcore 1992 andits allies may eventually be segregated from Chytridiales s. str.Fig 1 – Phylogeny and classification of Fungi. Basal Fungi andDikarya. Branch lengths are not proportional to geneticdistances. See Table 1 for support values for clades.Order: Rhizophydiales Letcher, in Letcher et al., Mycol. Res. 110:908 (2006).Exemplar genera: Rhizophydium Schenk 1858, KappamycesLetcher & M.J. Powell 2005, Terramyces Letcher 2006,

516 D. S. Hibbett et al.Boothiomyces Letcher 2006; Batrachochytrium Longcore, Pessier &D.K. Nichols 1999 is on a long branch in this clade with no nearrelatives.Order: Spizellomycetales D. J. S. Barr, Can. J. Bot. 58: 2384 (1980).Exemplar genera: Spizellomyces D. J. S. Barr 1980, PowellomycesLongcore, D. J. S. Barr & Désauln. 1995, Kochiomyces D. J. S. Barr1980.This classification does not include Caulochytrium, Olpidium,Rozella, or the Rhizophlyctis rosea clade, which are consideredincertae sedis.Class: Monoblepharidomycetes J. H. Schaffn., Ohio Nat. 9: 449(1909), as ‘Monoblepharideae’.Type: Monoblepharis Cornu 1871.Thallus filamentous, either extensive or a simple unbranchedthallus, often with a basal holdfast; asexual reproductionby zoospores or autospores; zoospores containinga kinetosome parallel to a non-flagellated centriole, a striateddisk partially extending around the kinetosome, microtubulesradiating anteriorly from the striated disk, a ribosomal aggregation,and rumposome (fenestrated cisterna) adjacent toa microbody; sexual reproduction oogamous by means of posteriorlyuniflagellate antherozoids borne in antheridia andnonflagellate female gametes borne in oogonia.Schaffner (1909) used the name ‘Monoblepharideae’ as a classbut with the ending of a suborder; this must be changed withoutchange of authorship or date of publication (Code, Art. 16.3).Order: Monoblepharidales J. Schröt., in Engler & Prantl, Nat.Pflanzenfam. 1: 106 (1893), as ’Monoblepharidineae’.Emend. Sparrow, Aquatic Phycomycetes: 458 (1943).Emended description as for Monoblepharidomycetes.Exemplar genera: Monoblepharis Cornu 1871, HarpochytriumLagerh. 1890, Oedogoniomyces Tak. Kobay. & M. Ôkubo 1954.Phylum: Neocallimastigomycota M. J. Powell, phylum nov.MycoBank no.: MB 501279Thallus monocentricus vel polycentricus; fungi anaerobici, intratractum digestivum animalium herbivororum vel fortasse in substratisanaerobicis terrestribus vel limnicis; mitochondriis carentessed hydrogenosomatibus praediti; zoosporae retrorsumuni- vel multiflagellatae, kinetosoma praesens sed centriolumsupervacaneum absens; complexus kinetosomati affixus e radiomarginali et annulo circumflagellari compositus; microtubuli eradio entendentes circum nucleum radiantes et flabellum posteriusformantes; munimenta flagelli absentia; tegumentum nucleimitosi procedente integrum remanens.Typus: Neocallimastix Vavra & Joyon ex I. B. Heath 1983.Thallus monocentric or polycentric; anaerobic, found in digestivesystem of larger herbivorous mammals and possibly inother terrestrial and aquatic anaerobic environments; lacksmitochondria but contains hydrogenosomes of mitochondrialorigin; zoospores posteriorly unflagellate or polyflagellate, kinetosomepresent but non-functional centriole absent, kinetosome-associatedcomplex composed of a skirt, strut, spurand circumflagellar ring, microtubules extend from spur andradiate around nucleus, forming a posterior fan, flagellarprops absent; nuclear envelope remains intact throughoutmitosis.Class: Neocallimastigomycetes M. J. Powell, class. nov.MycoBank no.: MB 501280Diagnosis latina ut in Neocallimastigomycota (vide supra).Typus: Neocallimastix Vavra & Joyon ex I.B. Heath 1983.Order: Neocallimastigales J. L. Li, I. B. Heath & L. Packer, Can. J.Bot. 71: 403 (1993).Exemplar genera: Neocallimastix Vavra & Joyon ex I.B. Heath1983, Caecomyces J.J. Gold 1988, Orpinomyces D.J.S. Barr, H.Kudo, Jakober & K.J. Cheng 1989.Phylum: Blastocladiomycota T. Y. James, Mycologia 98: 867(2007) [‘2006’].Synonym: Allomycota Caval.-Sm., BioSystems 14: 465 (1981).This phylum was proposed to reflect phylogenetic informationfrom a number of molecular studies (James et al.2007; Liu et al. 2006).Class: Blastocladiomycetes T. Y. James, Mycologia 98: 868(2007) [‘2006’].Synonym: Allomycetes Caval.-Sm., Biol. Rev. 73: 246 (1998),based on Allomyces E. J. Butler 1911.Cavalier-Smith provided a brief, five-word Latin descriptionfor Allomycetes that is not diagnostic from other uniflagellatefungi. The name Allomycetes was not taken up, because itis appropriate to have a class name based on the same genusas an included ordinal name, and because Cavalier-Smith’s‘diagnosis’ was vague.Order: Blastocladiales 1910, H. E. Petersen, Bot. Tidsskr. 29: 357(1909) (‘Blastocladiineae’).Exemplar genera: Allomyces E. J. Butler 1911, BlastocladiaReinsch 1877, Coelomomyces Keilin. 1921.Phylum: Microsporidia Balbiani, C. R. Acad. Sci. Paris 95: 1168(1882).The nomenclatural status of Microsporidia is ambiguous. Ithas been treated as a phylum under the zoological Code (InternationalCommission on Zoological Nomenclature 1999),but there is disagreement about the correct author citation(Larsson 2000; Sprague & Becnel 1998), and it is uncertainif the name would be valid under the botanical Code. Thisuncertainty arises as Microsporidium Balbiani 1884 appearsto be a later synonym of Nosema Naegeli 1857. The presentwork follows the recommendation of Sprague & Becnel(1998) in attributing Microsporidia to Balbiani (1882), but thismust be regarded as provisional. Before the status of theMicrosporidia can be resolved, it will be necessary to decidewhether the nomenclature of the group as a whole shouldbe governed by the zoological or the botanical Code althoughthe latter now allows names of fungi described under thezoological Code to be accepted. The final decision will requireinput from the community of scientists who studyMicrosporidia.

A higher-level phylogenetic classification of the Fungi 517No subdivision of the group is proposed here, owing to thelack of well-sampled multi-gene phylogenies within thegroup. However, Vossbrinck & Debrunner-Vossbrinck (2005)proposed a class-level classification of microsporidia, basedon small-subunit rRNA gene sequences.Phylum: Glomeromycota C. Walker & A. Schuessler, inSchüßler et al., Mycol. Res. 105: 1416 (2001).Class: Glomeromycetes Caval.-Sm., Biol. Rev. 73: 246 (1998), as‘Glomomycetes’.Synonym: Geomycetes Caval.-Sm., Biol. Rev. 73: 247 (1998).Order: Archaeosporales C. Walker & A. Schuessler, in Schüßleret al., Mycol. Res. 105: 1418 (2001).Synonym: Geosiphonales Caval.-Sm., Biol. Rev. 73: 247 (1998).Exemplar genera: Archaeospora J.B. Morton & D. Redecker2001, Geosiphon F. Wettst. 1915.Order: Diversisporales C. Walker & A. Schuessler, Mycol. Res.108: 981 (2004).Exemplar genera: Acaulospora Gerd. & Trappe 1974, DiversisporaC. Walker & A. Schüßler 2004, Gigaspora Gerd. & Trappe1974, Pacispora Oehl & Sieverd. 2004.Order: Glomerales J. B. Morton & Benny, Mycotaxon 37: 473(1990), as‘Glomales’.Exemplar genus: Glomus Tul. & C. Tul. 1845.Order: Paraglomerales C. Walker & A. Schuessler, in Schüßleret al., Mycol. Res. 105: 1418 (2001).Exemplar genus: Paraglomus J. B. Morton & D. Redecker 2001.Subphyla incertae sedis (not assigned to any phylum):Subphylum: Mucoromycotina Benny, subphylum nov.MycoBank no.: MB 501281Fungi saprotrophici vel raro mycoparasiti facultativi, gallasfacientes, haustoriis carentes, raro ectomycorrhizam facientes.Mycelium ramosum, juvene coenocyticum, maturum aliquandoseptis microporosis divisum. Reproductio asexualis sporangiisvel sporangiolis vel merosporangiis, raro chlamydosporis velarthrosporis vel blastosporis effecta. Reproductio sexualis zygosporisplus minusve globosis e suspensoribus oppositis vel appositisformatis effecta.Typus: Mucor Fresen. 1850.Fungi saprobes, or rarely gall-forming, nonhaustorial, facultativemycoparasites, or forming ectomycorrhiza. Myceliumbranched, coenocytic when young, sometimes producingsepta that contain micropores at maturity. Asexual reproductionby sporangia, sporangiola, or merosporangia, or rarely bychlamydospores, arthrospores, or blastospores. Sexual reproductionby more or less globose zygospores formed on opposedor apposed suspensors.This group includes the Mucorales, which is the core group ofthe traditional Zygomycota. Monophyly of the traditional Zygomycota(including Mucorales, Glomerales, Entomophthorales andHarpellales) was suggested by a recent study by Liu et al. (2006)using rpb1 and rpb2, but that finding conflicts with results ofanalyses that included additional loci and taxa, which suggestedthat the traditional Zygomycota is polyphyletic (Jameset al. 2006).The name Zygomycota was first published without a Latin diagnosisby Moreau (1954) and is therefore invalid. At present,this classification does not include Zygomycota. When relationshipsamong basal fungal lineages are more clearly resolved, itmay be appropriate to resurrect and validate Zygomycota, toinclude Mucoromycotina and perhaps other clades.Order: Mucorales Fr., Syst. Mycol. 3 (2): 296 (1832).Exemplar genera: Mucor Fresen. 1850 ( pro parte), ParasitellaBainier 1903, Phycomyces Kunze 1823, Pilobolus Tode 1784, RhizopusEhrenb. 1821.Order: Endogonales Moreau ex R. K. Benj., in Kendrick (ed.),Whole Fungus 2: 599 (1979).Emend.: Morton & Benny, Mycotaxon 37: 473 (1990).Synonym: Endogonales Moreau, Encycl. Mycol. 23: 1231 (1954),nomen invalidum.Exemplar genera: Endogone Link 1809, Peridiospora C. G. Wu &S. J. Lin 1997, Sclerogone Warcup 1990, Youngiomyces Y. J. Yao1995.Order: Mortierellales Caval.-Sm., Biol. Rev. 73: 246 (1998).Exemplar genera: Mortierella Coem. 1863, Dissophora Thaxt.1914, Modicella Kanouse 1936.Subphylum: Entomophthoromycotina Humber, subphylumnov.MycoBank no.: MB 501282Fungi pathogenici obligate animalibus (praecipue invertebratis)vel plantis cryptogamicis vel saprotrophici, interdum inanimalibus vertebratis parasitici. Status somaticus myceliumcoenocyticum vel septatum, pariete circumdatum vel protoplasticum,in hospite culturisve saepe corpora hyphalia multinucleataformans; forma protoplastica hyphoidea vel amoeboideaforma variabilis; cystidia et rhizoidea in aliquot speciebusathropodicolis formata. Characteres nuclei, sicut magnitudo,nucleoli magnitudo et locus, praesentia aut absentia heterochromatiniintermitotici, familiis distinguendis iuvant. Conidiophorasimplicia ramosave. Sporae primariae conidia vera,uninucleatae vel plurinucleatae vel multinucleatae, variis modisvi propulsae vel passive liberatae, conidia secundaria persaepeformata. Sporae perdurantes crassituncatae, bistratosae velutzygosporae post conjugationem velut azygosporae singulaeformatae.Typus: Entomophthora Fresen. 1856.Obligate pathogens of animals (primarily arthropods), cryptogamicplants, or saprobes; occasionally facultative parasitesof vertebrates. Somatic state consisting of a well-defined mycelium,coenocytic or septate, walled or protoplastic, which mayfragment to form multinucleate hyphal bodies; protoplasts eitherhyphoid or amoeboid and changeable in shape; cystidia orrhizoids formed by some taxa. Such nuclear characters as overallsize, location and comparative size of nucleoli, presence orabsence of granular heterochromatin in chemically unfixedinterphasic nuclei, and mitotic patterns are important at thefamily level. Conidiophores branched or unbranched. Primaryspores true conidia, uni-, pluri-, or multinucleate, forcibly

518 D. S. Hibbett et al.discharged by diverse possible means or passively dispersed;secondary conidia often produced. Resting spores with thickbi-layered walls form as zygospores after conjugations of undifferentiatedgametangia from different or the same hyphalbodies or hypha or as azygospores arising without prior gametangialconjugations.Order: Entomophthorales G. Winter, Rabenh. Krypt.-Fl. 1: 74(1880).Exemplar genera: Entomophthora Fresen. 1856, BallocephalaDrechsler 1951, Conidiobolus Bref. 1884, Entomophaga Batko1964, Neozygites Witlaczil 1885.Subphylum: Zoopagomycotina Benny, subphylum nov.MycoBank no.: MB 501283Fungi endo- vel ectoparasitici microanimalium vel fungorum.Corpus vegetativum ex thallo simplici ramoso vel nonramosovel mycelio nonseptato plus minusve extense ramoso constans.Ectoparasitae haustoria intra hospitem formantes. Reproductioasexualis arthrosporis, chlamydosporis vel sporangiolis uni- velmultisporis perfecta; sporangiosporae sporangiolorum multispororumin catenenis (merosporangiis) simplicibus vel ramosisdispositae. Reproductio sexualis zygosporis paene globosis perficitur;hyphae sexuales hyphis vegetativis similes vel plus minusveampliatae.Typus: Zoopage Drechsler 1935.Endo- or ectoparasites of microanimals and fungi. Vegetativebody consisting of a simple, branched or unbranchedthallus or more of less extensively branched mycelium.Ectoparasites forming haustoria inside the host. Asexualreproduction by arthrospores, chlamydospores or uni- ormultispored sporangiola; sporangiospores of multispored sporangiolaformed in simple or branched chains (merosporangia).Sexual reproduction by nearly globose zygospores; sexual hyphaesimilar to the vegetative hyphae or more or less enlarged.The description of this group is based mostly on the validatingdescription for the Zoopagales by Benjamin (1979), exceptthat arthrospores have been added, based on Barron’s (1975) reportof arthrospores in Helicocephalum Thaxt. 1891.Order: Zoopagales Bessey ex R.K. Benj., in Kendrick (ed.),Whole Fungus 2: 590 (1979).Synonym: Zoopagales Bessey, Morph. Tax. Fungi : 177 (1950), nomeninvalidum.Exemplar genera: Cochlonema Drechsler 1935, RhopalomycesCorda 1839, Piptocephalis de Bary 1865, Sigmoideomyces Thaxt.1891, Syncephalis Tiegh. & G. Le Monn. 1873, Zoopage Drechsler1935.Subphylum: Kickxellomycotina Benny, subphylum nov.MycoBank no.: MB 501284Fungi saprotrophici vel mycoparasitici vel obligate symbiotici.Thallus in nonnullis generibus e tenaculo fungos alios parasitanset haustoriis penetrans; mycelium septatum, ramosum vel simplex;septa in medio excavata et obturata. Reproductio asexualismerosporangiis uni- vel bisporis vel trichosporis vel arthrosporiseffecta. Reproductio sexualis zygosporis globosis, biconicis velallantoideis circinatis effecta.Typus: Kickxella Coem. 1862.Fungi saprobes, mycoparasites, or obligate symbionts.Thallus arising from a holdfast on other fungi as a haustorialparasite, or branched, septate, subaerial hyphae. Myceliumbranched or unbranched, regularly septate. Septa with median,disciform cavities containing plugs. Asexual productionby 1- or 2-spored merosporangia, trichospores, or arthrospores.Sexual reproduction by zygospores that are globose,biconical, or allantoid and coiled.Order: Kickxellales Kreisel ex R. K. Benj., in Kendrick (ed.),Whole Fungus 2: 610 (1979).Synonym: Kickxellales Kreisel, Grundz. nat. Syst. Pilze: 65 (1969),nomen invalidum.Exemplar genera: Kickxella Coem. 1862, Coemansia Tiegh. &G. Le Monn. 1873, Linderina Raper & Fennell 1952, SpirodactylonR. K. Benj. 1959.Order: Dimargaritales R. K. Benj., in Kendrick (ed.), Whole Fungus2: 607 (1979).Exemplar genera: Dimargaris Tiegh. 1875, Dispira Tiegh. 1875,Tieghemiomyces R. K. Benj. 1959.Order: Harpellales Lichtw. & Manier, Mycotaxon 7: 441 (1978).The taxa in this order have been referred to as ‘Trichomycetes’.However, Trichomycetes is no longer a useful phylogenetictaxon because it describes a polyphyletic group. Theuse of the term should be restricted to ecological rather thanphylogenetic groupings, and not capitalized or italicized, i.e.as ‘trichomycetes’.Exemplar genera: Harpella L. Léger & Duboscq 1929, FurculomycesLichtw. & M. C. Williams 1992, Legeriomyces Pouzar 1972,Smittium R. Poiss. 1937.Order: Asellariales Manier ex Manier & Lichtw., Mycotaxon 7:442 (1978).Exemplar genera: Asellaria R. Poiss. 1932, Orchesellaria Manierex Manier & Lichtw. 1968.Asellariales are retained in the Fungi here due to their ultrastructuralcharacteristics (Benny & White 2001; Manier 1973;Moss 1975; Saikawa et al. 1997). Unpublished rpb1 and rpb2data also support their placement in the Kickxellomycotina(T. Y. James & M. M. White, unpubl.).Subkingdom: Dikarya Hibbett, T. Y. James & Vilgalys, subregnumnov.MycoBank no.: MB 501285Synonyms: Neomycota Caval.-Sm., Rev. Biol. 73: 209 (1998).Carpomycetaceae Bessey, Univ. Studies, Univ. Nebr. 7: 294(1907).Fungi unicellulares vel filamentosi, flagellis carentes, saepe stadiumdikaryoticum includentes. Ascomycota et Basidiomycotacomplectens.Unicellular or filamentous Fungi, lacking flagella, oftenwith a dikaryotic state. The least-inclusive clade that containsAscomycota and Basidiomycota.

A higher-level phylogenetic classification of the Fungi 519The name alludes to the putative synapomorphy of dikaryotichyphae (Tehler 1988) and was applied by James et al. (2006) withoutformal description. Kendrick (1985) and Tehler et al. (2003)referred to this group as the Dikaryomycota, but the termination‘–mycota’ denotes the rank of phylum under the Code. Cavalier-Smith (1998) referred to this group as Neomycota. Dikarya is usedhere, because it is more descriptive and is consistent with recentuse (James et al. 2006; Tehler et al. 2003; Kendrick 1985).Phylum: Ascomycota Caval.-Sm., Biol. Rev. 73: 247 (1998), as‘Ascomycota Berk. 1857. stat. nov.’Synonyms: Ascomycetes Berk., Intr. Crypt. Bot.: 270 (1857), rankuncertain; Whittaker (1959: 220).Ascomycota Bold, Morph. Pl.: 7, 180 (1958), nomen invalidum;Hawksworth et al. (1995: 30), Eriksson & Winka (1997: 4),etc, nomina nuda.Basic type: Peziza Fr. 1822.(Table 2, Fig 2) Cavalier-Smith was not the first to proposethe phylum name Ascomycota. It appears to have been used firstby Bold (1957: 7, 180), but without a Latin diagnosis. The namewas in widespread use before its validation by Cavalier-Smith,and its usage was popularized by its employment in the eighthedition of the Dictionary, which is listed in Cavalier-Smith’s(1998) bibliography. The Latin diagnosis provided by Cavalier-Smith consisted of only two words: ‘sporae intracellulares’. Itis questionable whether this description is diagnostic for theAscomycota, but as a validating diagnosis it is acceptable underthe Code. No detailed reference to the basionym was given, butis provided here. We also propose a basic type, Peziza, as we cannot be sure that the phylum will not be split in the future whenmore molecular data and material of ascomycetes and basidiomyceteshave been sequenced. Hawksworth et al. (1995) andEriksson & Winka (1997: 4) used the phylum names Ascomycotaand Basidiomycota; the latter authors listed 31 nucleotide signaturesin the nSSU rDNA genes in Basidiomycota. Since thenmany more sequences have become available, also frommany other genes that support monophyly of Ascomycota andBasidiomycota.The subdivision of Ascomycota used in the present paper isbased on the system of Eriksson & Winka (1997), which differsin many respects from that of Cavalier-Smith (1998).Subphylum: Taphrinomycotina O. E. Erikss. & Winka, Myconet1: 11 (1997).Class: Taphrinomycetes O. E. Erikss. & Winka, Myconet 1: 11(1997).Order: Taphrinales Gäum. & C. W. Dodge, Comp. morph. fun.:159 (1928).Exemplar genera: Taphrina Fr. 1815, Protomyces Unger1832.Class: Neolectomycetes O. E. Erikss. & Winka, Myconet 1: 8(1997).Order: Neolectales Landvik, O. E. Erikss, Gargas & P. Gustafss.,Syst. Ascom. 11: 114 (1993).Exemplar genus: Neolecta Speg. 1881.Class: Pneumocystidomycetes O. E. Erikss. & Winka, Myconet1: 9 (1997).Order: Pneumocystidales O. E. Erikss., Syst. Ascom. 13: 170(1994).Exemplar genus: Pneumocystis P. Delanoë & Delanoë 1912.Class: Schizosaccharomycetes O. E. Erikss. & Winka, Myconet1: 10 (1997).Order: Schizosaccharomycetales O. E. Erikss., Svedskog &Landvik, Syst. Ascom. 11: 146 (1993).Exemplar genus: Schizosaccharomyces Linder 1893.Subphylum: Saccharomycotina O. E. Erikss. & Winka, Myconet1: 10 (1997).Class: Saccharomycetes O. E. Erikss. & Winka, Myconet 1: 10(1997).Order: Saccharomycetales Kudryavtsev, System Hefen: 270(1960).Growth usually by individual yeast cells, often accompaniedby pseudohyphae and/or true hyphae. Cell walls predominatelyof b-glucan. Ascomata not formed; one to manyascospores formed in asci that often are converted from individualcells or borne on simple ascophores. Mitotic and meioticnuclear divisions within an intact nuclear membrane. Envelopingmembrane system in ascospore delimitation associatedindependently with postmeiotic nuclei. Asexual reproductionby holoblastic budding, conidia or fission (arthrospores).Exemplar genera: Saccharomyces Meyen ex E. C. Hansen 1838,Candida Berkhout 1923, Dipodascopsis L. R. Batra & Millner 1978,Metschnikowia T. Kamieński 1899.Subphylum: Pezizomycotina O. E. Erikss. & Winka, Myconet 1:9(1997).Class: Arthoniomycetes O. E. Erikss. & Winka, Myconet 1: 4(1997).Order: Arthoniales Henssen & Jahns ex D. Hawksw. & O. E.Erikss, Syst. Ascom. 5: 177 (1986).Synonym: Arthoniales Henssen & Jahns, Lichenes: 123 (1973)[‘1974’], nomen invalidum.Hawkworth & Eriksson (loc. cit.) listed only Henssen, butcited the book by Henssen & Jahns (loc. cit.) as place for theoriginal but invalid description so both should be cited althoughHenssen contributed the taxonomic system to thebook.Exemplar genera: Arthonia Ach. 1806, Chrysothrix Mont. 1852,Dirina Fr. 1825, Roccella DC. 1805.Class: Dothideomycetes O. E. Erikss. & Winka, Myconet 1: 5(1997).

520 D. S. Hibbett et al.Table 2 – Support for major groups of Fungi in selected phylogenetic studies: AscomycotaRank Taxon Reference Data OTUs SupportPhylum ASCOMYCOTA James et al. (2006, fig. 1) SSU, LSU, 5.8S,rpb1, rpb2, tef1Spatafora et al. (2007, fig. 2)LSU, SSU, rpb1,rpb2, tef1111 MLBS ¼ 94BPP ¼ 1177 WPBS ¼< 50MLBS ¼ 100BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 276 NJBS ¼ 67BPP ¼ 1Subphylum Taphrinomycotina James et al. (2006, fig. 2) SSU, LSU, 5.8S,rpb1, rpb2, tef1Spatafora et al. (2007, fig. 2)LSU, SSU, rpb1,rpb2, tef1Class/OrderClass/OrderClass/OrderClass/OrderTaphrinomycetes,TaphrinalesNeolectomycetes,NeolectalesPneumocystidomycetes,PneumocystidalesSchizosaccharomycetes,Schizosaccharomycetales4 MLBS ¼ 98BPP ¼ 18 WPBS ¼< 50MLBS ¼ 98BPP ¼ 1Liu et al. (2006, fig. 3) rpb1, rpb2 3 BPP ¼ 1Sugiyama et al. (2007, fig. 2) LSU, SSU rpb2, b-tub 11 BPP ¼ 1Kurtzman & Sugiyama (2001, fig. 7) SSU 8 NJBS ¼ 54Sugiyama et al. (2007, fig. 2) LSU, SSU rpb2, b-tub 6 BPP ¼ 1Kurtzman & Sugiyama (2001, fig. 7) SSU 4 NJBS ¼ 100Nishida & Sugiyama (1994, fig. 1) SSU 5 NJBS ¼ 100Lutzoni et al. (2004, fig. 2) LSU, SSU 1 NASugiyama et al. (2007, fig. 2) LSU, SSU, b-tub, rpb2 2 BPP ¼ 1Landvik et al. (2001, fig. 1) b-tub 2 MPBS ¼ 100Sugiyama et al. (2007, fig. 2) LSU, SSU, b-tub, rpb2 1 NALutzoni et al. (2004, fig. 2) LSU, SSU 1 NASugiyama et al. (2007, fig. 2) SSU, LSU, rpb2, b-tub 1 NALutzoni et al. (2004, fig. 2) LSU, SSU 2 BPP ¼ 1.0NJBS ¼ 100Taphrinomycotina incertaesedis (not placed in anysubphylum)Genus Saitoella Sugiyama et al. (2007, fig. 2) SSU, LSU, rpb2, b-tub 1 NANishida & Sugiyama (1994, fig. 1) SSU 1 NASubphylum/Class/Order Saccharomycotina,Saccharomycetes,SaccharomycetalesSpatafora et al. (2007, fig. 2)LSU, SSU, rpb1,rpb2, tef112 WPBS ¼ 55MLBS ¼ 100BPP ¼ 1Suh et al. (2007, fig. 2) LSU, SSU 87 MPBS ¼ 99BPP ¼ 1Subphylum Pezizomycotina James et al. (2006, fig. 1) SSU, LSU, 5.8S,rpb1, rpb2, tef1Class/OrderArthoniomycetes,Arthoniales46 BPP ¼ 1MLBS ¼ 94Robbertse et al. (2006, figs. 4,5,6) Genomes 11 MPBS ¼ 94-100NJBS ¼ 100MLBS ¼ 100Spatafora et al. (2007, fig. 2)Spatafora et al. (2007, fig. 2)Lumbsch et al. (2005, fig. 1)LSU, SSU, rpb1,rpb2, tef1LSU, SSU, rpb1,rpb2, tef1LSU, SSU,mt-SSU, mt-LSU157 WPBS ¼ 100MLBS ¼ 97BPP ¼ 14 WPBS ¼ 100MLBS ¼ 100BPP ¼ 16 MPBS ¼ 100BPP ¼ 1.0Class Dothideomycetes Schoch et al. (2007, fig.1) LSU, SSU, rpb2, tef1 96 BPP ¼ 1MPBS < 50MLBS ¼ 70Spatafora et al. (2007, fig. 2)LSU, SSU, rpb1,rpb2, tef117 WPBS < 50MLBS ¼ 84BPP ¼ 1Kruys et al. (2006, fig. 1) LSU, SSU, mt-SSU 51 BPP > 0.95MPBS < 50Subclass Dothideomycetidae Schoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 26 BPP ¼ 1MPBS > 50MLBS > 0.7

A higher-level phylogenetic classification of the Fungi 521Table 2 (continued)Rank Taxon Reference Data OTUs SupportKruys et al. (2006, fig. 1) LSU, SSU, mt-SSU 11 BPP > 0.95MPBS < 50Order Capnodiales Schoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 11 BPP ¼ 1MPBS > 70MLBS > 70Order Dothideales Schoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 9 BPP ¼ 1MPBS > 70MLBS > 70Kruys et al. (2006, fig. 1) LSU, SSU, mt-SSU 4 BPP > 0.95MPBS ¼ 100Lindemuth et al. (2001) LSU, SSU 6 MLBS ¼ 91NJBS ¼ 100Order Myriangiales Schoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 5 BPP ¼ 1MPBS > 70MLBS > 70Subclass/OrderPleosporomycetidae,PleosporalesSchoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 48 BPP ¼ 1MPBS > 70MLBS > 70Kruys et al. (2006, fig. 1) LSU, SSU, mt-SSU 35 BPP ¼ 1MPBS ¼ 100Dothideomycetesincertae sedis (not placedin any subclass)Order Botryosphaeriales Schoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 8 BPP ¼ 1MPBS > 70MLBS > 70Order Hysteriales Schoch et al. (2007, fig. 1) LSU, SSU, rpb2, tef1 3 BPP ¼ 1MPBS > 70MLBS > 70Order Patellariales Pang et al. (2002, fig. 26) SSU 1 NAInderbitzin et al. (2001, fig. 18) SSU 1 NAOrder Jahnulales Pang et al. (2002, fig. 26) SSU 6 MPBS ¼ 100Class Eurotiomycetes Spatafora et al. (2007, fig. 2) LSU, SSU, rpb1,rpb2, tef1Geiser et al. (2007, fig. 1)SSU, LSU, rpb1,rpb2, tef11 WPBS ¼ 89MLBS ¼ 84BPP ¼ 149 BPP ¼ 1MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100Ekman & Tønsberg (2002, fig. 1) SSU 13 BPP ¼ 0.99Del Prado et al. (2006, fig. 1) LSU, mt-SSU 15 BPP ¼ 1Lumbsch et al. (2005, fig. 1)LSU, SSU, mt-SSU,mt-LSU11 BPP > 0.95MPBS > 70Lutzoni et al. (2004, fig. 5) LSU, SSU, mt-SSU, rpb2 8 BPP ¼ 1BBS ¼ 61Reeb et al. (2004, fig. 1) SSU, LSU, rpb2 7 BPP ¼ 1BBS ¼ 89Subclass Chaetothyriomycetidae Reeb et al. (2004, fig. 1) SSU, LSU, rpb2 5 BPP ¼ 1BBS ¼ 100MLBS ¼ 100Lutzoni et al. (2004, fig. 5)LSU, SSU,mt-SSUSSU, rpb25 BPP ¼ 1BBS ¼ 100NJBS ¼ 99MPBS ¼ 98Del Prado et al. (2006, fig. 1) LSU, mt-SSU 11 BPP ¼ 1Spatafora et al. (2007, fig. 1)SSU, LSU, rpb1,rpb2, tef6 BPP ¼ 1MLBS ¼ 100WPBS > 70Geiser et al. (2007, fig. 1)SSU, LSU,rpb1, rpb2, tef21 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Order Chaetothyriales Lutzoni et al. (2004, fig. 2) LSU, SSU 5 BPP ¼ 1NJBS ¼ 94(continued on next page)

522 D. S. Hibbett et al.Table 2 (continued)Rank Taxon Reference Data OTUs SupportLiu & Hall (2004, fig. 3) rpb2 5 BPP ¼ 1MPBS ¼ 96Spatafora et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 4 BPP ¼ 1MLBS ¼ 100WPBS > 70Geiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 9 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Order Pyrenulales Lutzoni et al. (2004, fig. 8) LSU, SSU, mt-SSU, rpb2 2 BPP ¼ 1NJBS ¼ 100WPBS ¼ 100Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 2 BPP ¼ 1BBS ¼ 100MLBS ¼ 100Schmitt et al. (2004, fig. 1) LSU, mt-SSU 2 BPP ¼ 1Geiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 5 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Order Verrucariales Wedin et al. (2006, fig. 1) LSU, mt-SSU 3 BPP ¼ 1MPjk ¼ 100Geiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 7 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Lutzoni et al. (2004, fig. 2) LSU, SSU 3 BPP ¼ 1NJBS ¼ 98Gueidan et al. (2007, fig. 2) LSU, SSU, rpb1 83 BPP ¼ 1MLBS ¼ 100MPBS ¼ 100Subclass Eurotiomycetidae Geiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 24 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 98MLBS ¼ 100Lutzoni et al. (2004, fig. 2) LSU, SSU 11 NJBS ¼ 96BPP ¼ 1Order Coryneliales Winka (2000, fig. 1) SSU 2 MPBS ¼ 100NJBS ¼ 100Inderbitzin et al. (2004, fig. 14) SSU 1 NAGeiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 3 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Order Eurotiales Geiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 9 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Order Onygenales Geiser et al. (2007, fig. 1) SSU, LSU, rpb1, rpb2, tef 12 BPP ¼ 1MPBS ¼ 65WPBBS ¼ 68MLBS ¼ 88Subclass/OrderMycocaliciomycetidae,MycocalicialesTibell & Vinuesa (2005, fig. 1) LSU 20 BPP ¼ 1Geiser et al. (2007, fig. 1)SSU, LSU, rpb1,rpb2, tef4 BPP ¼ 1MPBS ¼ 100WPBBS ¼ 100MLBS ¼ 100Ekman & Tønsberg (2002, fig. 1) SSU 4 BPP ¼ 1Class Laboulbeniomycetes Weir & Blackwell (2001, fig. 2) SSU 4 MPBS ¼ 100Henk et al. (2003, fig. 1) SSU 6 MPBS ¼ 100Order Laboulbeniales Weir & Blackwell (2001, fig. 1) SSU 3 MPBS ¼ 100Henk et al. (2003, fig. 2) SSU 3 MPBS ¼ 57Order Pyxidiophorales Weir & Blackwell (2001, fig. 2) SSU 1 NAHenk et al. (2003, fig. 2) SSU 2 MPBS ¼ 99

A higher-level phylogenetic classification of the Fungi 523Table 2 (continued)Rank Taxon Reference Data OTUs SupportClass Lecanoromycetes Lutzoni et al. (2004, fig. 5) LSU, SSU, rpb2,mt-SSUSpatafora et al. (2007, fig. 2)LSU, SSU, rpb1,rpb2, tef1Subclass/OrderAcarosporomycetidae,AcarosporalesMiądlikowska et al. (2007, fig. 1)Hofstetter et al. (2007, fig. 1)Miądlikowska et al. (2007, fig. 1)LSU, SSU, rpb1,rpb2, mt-SSULSU, SSU, rpb1,rpb2, mt-SSULSU, SSU, rpb1,rpb2, mt-SSU34 BPP ¼ 1BBS ¼ 5638 WPBS < 50MLBS ¼ 93BPP ¼ 1264 RMLBS > 70BSBPP > 0.9582 RMLBS > 70BPP > 0.9515 RMLBS > 70 %PMLBS > 70 %BPP > 0.95Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 14 MLBS ¼ 100BPP ¼ 100Lutzoni et al. (2004, fig. 4) LSU, SSU, rpb2 14 BPP ¼ 1NJBS ¼ 100MPBS ¼ 100Subclass Lecanoromycetidae Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSUHofstetter et al. (2007, fig. 1)LSU, SSU, rpb1,rpb2, mt-SSU71 RMLBS > 70 %PMLBS > 70 %BPP > 0.9554 RMLBS > 70BPP > 0.95Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 14 MLBS ¼ 73BPP ¼ 100Order Lecanorales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSUHofstetter et al. (2007, fig. 1)LSU, SSU, rpb1,rpb2, mt-SSU86 RMLBS > 70BSBPP > 0.9530 RMLBS > 70BPP > 0.95Lumbsch et al. (2004, fig. 1) LSU, mt-SSU 14 BPP ¼ 1Lücking et al. (2004, fig. 3) LSU, mt-SSU 8 BPP ¼ 1Order Peltigerales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSU46 RMLBS > 70BSBPP > 0.95Miądlikowska & Lutzoni (2004, fig. 1) LSU, SSU 59 MPBS < 70BPP ¼ 0.92Wilklund & Wedin (2003, fig. 1) LSU, SSU 31 Bjk ¼ 99Order Teloschistales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSUSubclass Ostropomycetidae Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSU13 RMLBS > 70BPP > 0.9558 RMLBS > 70BSBPP > 0.95Grube et al. (2004, fig. 1) mt-SSU 30 BPP > 0.95Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 16 MLBS ¼ 100BPP ¼ 100Order Agyriales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSU8 RMLBS > 70BSBPP > 0.95Lücking et al. (2004, fig. 3) LSU, mt-SSU 11 BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 4 BPP ¼ 1NJBS ¼ 100Wedin et al. (2005, fig. 1) LSU, mt-SSU 8 MPjk ¼ 83BPP ¼ 0.99Order Baeomycetales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSU4 RMLBS > 70PMLBS > 70BPP > 0.95Wedin et al. (2005, fig. 1) LSU, mt-SSU 3 MPjk ¼ 99BPP ¼ 1.0Order Ostropales s.l. Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSU21 RMLBS > 70BSBPP > 0.95Schmitt et al. (2005, fig. 1) LSU, mt-SSU 12 BPP ¼ 1Wedin et al. (2005, fig. 1) LSU, mt-SSU 13 Bjk ¼ 94BPP ¼ 0.97(continued on next page)

524 D. S. Hibbett et al.Table 2 (continued)Rank Taxon Reference Data OTUs SupportLutzoni et al. (2004, fig. 4) LSU, SSU, rpb2 10 BPP ¼ 1NJBS ¼ 74MPBS ¼ 84Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 9 MLBS ¼ 99BPP ¼ 1BBS ¼ 1Order Pertusariales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1,rpb2, mt-SSU21 RMLBS > 70BSBpp > 0.95Lücking et al. (2004, fig. 3) LSU, mt-SSU 7 BPP ¼ 1Schmitt et al. (2005, fig. 1) LSU, mt-SSU 14 BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 11 BPP ¼ 1Lecanoromycetes incertaesedis (not placedin any subclass)Order Candelariales Wedin et al. (2005, fig. 1) LSU, mt-SSU 3 Jk ¼ 100BPP ¼ 0.96Hofstetter et al. (2007, fig. 1) LSU, SSU, mt-SSU, rpb1, rpb2 2 RMLBS > 70BPP > 0.95Miądlikowska et al. (2007, fig. 1) LSU, SSU, mt-SSU, rpb1, rpb2 3 RMLBS > 70PMLBS > 70BPP > 0.95Order Umbilicariales Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1, rpb2, mt-SSU 16 BSBSBPP > 0.95Miądlikowska et al. (2007, fig. 1) LSU, SSU, rpb1, rpb2, mt-SSU 9 RMLBS > 70PMLBS > 70BPP > 0.95Hofstetter et al. (2007, fig. 1) LSU, SSU, rpb1, rpb2, mt-SSU 8 RMLBS > 70BPP > 0.95Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 4 MLBS ¼ 70BPP ¼ 1BBS ¼ 88ClassLeotiomycetes(w/o Geoglossaceae)Spatafora et al. (2007, fig. 2) LSU, SSU, rpb1, rpb2, tef1 22 WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Wang et al. (2006, fig. 1) LSU, SSU, 5.8S 50 BPP ¼ 1Wang et al. (2007, fig. 2) LSU, SSU, 5.8S 78 MPBS ¼ 61BPP ¼ 1Order Cyttariales Wang et al. (2007, fig. 1) SSU, LSU, 5.8S 1 NAOrder Erysiphales Rossman et al. (2004, fig. 2) LSU 12 MPBS > 55Wang et al. (2007, fig. 1) SSU, LSU, 5.8S 16 MPBS ¼ 63BPP ¼ 0.97Takamatsu (2004, fig. 2) SSU 10 NJBS ¼ 99OrderHelotialesWang et al. (2007, fig. 1) SSU, LSU, 5.8S 40 BPP < 0.90(w/o Geoglossaceae)Order Rhytismatales Rossman et al. (2004, fig. 2) LSU 4 MPBS > 55Wang et al. (2007, fig. 1) SSU, LSU, 5.8S 5 MPBS ¼ 100BPP ¼ 1Order Thelebolales de Hoog et al. (2005, fig. 3) SSU 11 MPBS ¼ 56Class/OrderLichinomycetes,LichinalesSpatafora et al. (2007, fig. 2) LSU, SSU, rpb1, rpb2, tef1 1 NAClass/OrderClass/OrderOrbiliomycetes,OrbilialesPezizomycetes,PezizalesMiądlikowska et al. (2007, fig. 1)LSU, SSU, rpb1,rpb2, mt-SSU2 RMLBS > 70PMLBS > 70BPP > 0.95Reeb et al. (2004, fig. 1) LSU, SSU, rpb2 3 MLBS ¼ 100BBS ¼ 100BPP ¼ 1Spatafora et al. (2007, fig. 2) LSU, SSU, rpb1, rpb2, tef1 2 WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Spatafora et al. (2007, fig. 2) LSU, SSU, rpb1, rpb2, tef1 14 WPBS ¼ 54MLBS ¼ 99BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 21 BPP ¼ 0.96NJBS ¼ 70Class Sordariomycetes Spatafora et al. (2007, fig. 2) LSU, SSU, rpb1, rpb2, tef1 47 WPBS ¼ 100MLBS ¼ 100BPP ¼ 1

A higher-level phylogenetic classification of the Fungi 525Table 2 (continued)Rank Taxon Reference Data OTUs SupportZhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 106 MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 66 BPP ¼ 1NJBS ¼ 97Subclass Hypocreomycetidae Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 42 MPBS ¼ 92WPBS ¼ 96MLBS ¼ 90BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 26 NJBS < 50BPP ¼ 1Huhndorf et al. (2004b, figs. 38, 39) LSU 21 MPBS ¼ 67BPP >¼ 0.95Order Coronophorales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 2 MPBS < 50WPBS < 50MLBS ¼ 96BPP ¼ 1Huhndorf et al. (2004b, figs. 38, 39) LSU 16 WPBS ¼ 99BPP 95Miller & Huhndorf (2005, fig. 7) LSU, b-tub, rpb2 2 WPBS ¼ 100BPP 95Order Hypocreales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 21 MPBS ¼ 91WPBS ¼ 90MLBS ¼ 72BPP ¼ 1Castlebury et al. (2004, fig. 1) LSU, SSU 31 MPBS ¼ 70BPP ¼ 1Order Melanosporales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 2 MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100BPP ¼ 1OrderMicroascales(incl. Halosphaeriales)Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 15 MPBS ¼ 74WPBS ¼ 86MLBS ¼ 85BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 10 NJBS ¼ 80BPP ¼ 1Campbell et al. (2003, fig. 3) LSU, SSU 40 MPBS ¼ 100BPP ¼ 1Kohlmeyer et al. (2000, fig. 1) LSU, SSU 16 MPBS ¼ 97Subclass Sordariomycetidae Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 54 MPBS ¼ 82WPBS ¼ 85MLBS ¼ 77BPP ¼ 1Lutzoni et al. (2004, fig. 2) LSU, SSU 36 NJBS < 50BPP ¼ 0.97Order Boliniales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 4 MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Huhndorf et al. (2004a, fig. 1) LSU 3 WPBS ¼ 99BPP < 95Miller & Huhndorf (2005, fig. 7) LSU, b-tub, rpb2 2 WPBS ¼ 100BPP 95Order Chaetosphaeriales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 3 MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Miller & Huhndorf (2005, fig. 7) LSU, b-tub, rpb2 2 WPBS ¼ 100BPP 95Shenoy et al. (2006, fig. 3) LSU, rpb2 4 MPBS ¼ 100(continued on next page)

526 D. S. Hibbett et al.Table 2 (continued)Rank Taxon Reference Data OTUs SupportOrder Coniochaetales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 3 MPBS ¼ 93WPBS ¼ 100MLBS ¼ 87BPP ¼ 1Miller & Huhndorf (2005, fig. 7) LSU, b-tub, rpb2 2 WPBS ¼ 100BPP 95Miller & Huhndorf (2004, fig. 10) LSU 3 WPBS ¼ 98BPP 95Order Diaporthales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 19 MPBS ¼ 95WPBS ¼ 94MLBS ¼ 77BPP ¼ 1Castlebury et al. (2002, fig. 1) LSU 82 MPBS ¼ 100NJBS ¼ 100Lutzoni et al. (2004, fig. 2) LSU, SSU 10 NJBS ¼ 100BPP ¼ 1Miller & Huhndorf (2005, fig. 7) LSU, b-tub, rpb2 2 WPBS ¼ 100BPP 95Miller & Huhndorf (2004, fig. 10) LSU 3 WPBS ¼ 100BPP ¼ 95Order Ophiostomatales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 3 MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Hausner & Reid (2004, fig. 1) SSU 3 NJBS ¼ 99Wingfield et al. (1999, fig. 3) LSU 4 MPBS ¼ 99Order Sordariales Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 17 MPBS ¼ 80WPBS ¼ 77MLBS ¼ 84BPP ¼ 1Huhndorf et al. (2004a, fig. 1) LSU 22 WPBS ¼< 50BPP < 95Miller & Huhndorf (2005, fig. 7) LSU, b-tub, rpb2 41 WPBS ¼ 65BPP 95Subclass/OrderXylariomycetidae,XylarialesZhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 8 MPBS ¼ 98WPBS ¼ 99MLBS ¼ 78BPP ¼ 1Shenoy et al. (2006, fig. 1) LSU 16 MPBS ¼ 92Sordariomycetes incertaesedis (not placed inany subclass)Order Calosphaeriales Vijaykrishna et al. (2004, fig. 1) SSU 3 MPBS ¼ 100Réblová et al. (2004, fig. 1) LSU 6 MPBS ¼ 53Réblová (2006, fig. 1) SSU 2 MPBS ¼ 68OrderLulworthiales(incl. Spathulosporales)Zhang et al. (2007, fig. 2) LSU, SSU, rpb2, tef1 2 MPBS ¼ 100WPBS ¼ 100MLBS ¼ 100BPP ¼ 1Campbell et al. (2005, fig. 1) LSU, SSU 56 BPP ¼ 1Inderbitzin et al. (2004, fig. 15) LSU 15 MPBS ¼ 100NJBS ¼ 91BPP ¼ 86Kohlmeyer et al. (2000, fig. 1) LSU, SSU 7 MPBS ¼ 100Order Meliolales Saenz & Taylor (1999, fig. 1) LSU 2 MPBS ¼ 100Order Vijaykrishna et al. (2004, fig. 1) SSU 2 MPBS < 50Order Phyllachorales Inderbitzin et al. (2004, fig. 14) SSU 1 NAOrder Trichosphaeriales Réblová & Seifert (2004, fig. 1) LSU 8 MPBS < 50Pezizomycotina incertaesedis (not placedin any class)Order Lahmiales Eriksson (1986) d d dOrder Medeolariales Inderbitzin et al. (2004, fig. 14) SSU 1 NAOrder Triblidiales Eriksson (1992) d d dSee Table 1 for explanation.

A higher-level phylogenetic classification of the Fungi 527Order: Pleosporales Luttr. ex M. E. Barr, Prodr. Class Loculoasc.:67 (1987b).Synonym: Pleosporales Luttr., Mycologia 47: 520 (1955), nomeninvalidum.Exemplar genera: Pleospora Rabenh. ex Ces. & De Not.1863, Phaeosphaeria I. Miyake 1909, Lophiostoma Ces. & DeNot. 1863, Sporormiella Ellis & Everh.1892, Montagnula Berl.1896.Dothideomycetes incertae sedis (not placed in any subclass)Order: Botryosphaeriales C. L. Schoch, Crous & Shoemaker,Mycologia 98: 1051 (2007) [‘2006’].Exemplar genera: Botryosphaeria Ces. & De Not. 1863, GuignardiaViala & Ravaz 1892.Order: Hysteriales Lindau in Engler & Prantl (eds), Nat. Pflanzenfam.1: 265 (1896), as‘Hysteriinae’.Exemplar genera: Hysterium Pers. 1797, Hysteropatella Rehm.1890.Order: Patellariales D. Hawksw. & O. E. Erikss., Syst. Ascom. 5:181 (1986).Exemplar genus: Patellaria Fr. 1822.Order: Jahnulales Ka-Lai Pang, Abdel-Wahab, El-Shar., E. B. G.Jones & Sivichai, in Pang et al., Mycol. Res. 106: 1033 (2002).Exemplar genera: Aliquandostipite Inderb. 2001, JahnulaKirschst. 1936, Patescospora Abdel-Wahab & El-Shar. 2002.Class: Eurotiomycetes O. E. Erikss. & Winka, Myconet 1: 6 (1997).Fig 2 – Phylogeny and classification of Fungi. Ascomycota.See Table 2 for support values for clades. Dashed linesindicate taxa that are of uncertain placement.Subclass: Dothideomycetidae P. M. Kirk, P. F. Cannon, J. C. David& Stalpers ex Schoch et al., Mycologia 98: 1047 (2007)[‘2007’].Order: Capnodiales Woron., Annls Mycol. 23: 177 (1925).Exemplar genera: Capnodium Mont. 1848, Scorias Fr. 1825,Mycosphaerella Johanson 1884.Order: Dothideales Lindau, in Engler & Prantl (eds), Nat. Pflanzenfam.1(1): 373 (1897).Exemplar genera: Dothidea Fr. 1818, Dothiora Fr. 1849, SydowiaBres. 1895, Stylodothis Arx & E. Müll. 1975.Order: Myriangiales Starbäck, K. svenska Vetensk-Akad. Handl.,Bih., Afd. III 25: 37(1899).Exemplar genera: Myriangium Mont. & Berk. 1845, ElsinoëRacib. 1900.Subclass: Pleosporomycetidae C. L. Schoch, Spatafora, Crous& Shoemaker, Mycologia 98: 1049 (2007) [‘2006’].The circumscription of this class and the classificationwithin the Eurotiomycetes presented here are derived fromthe phylogenetic re-delimitation of this class by Ekman &Tønsberg (2002), Lutzoni et al. (2004) and Geiser et al. (2007),reflecting the inference of shared ancestry between Eurotiomycetes,comprising Coryneliales, Onygenales and Eurotiales andChaetothyriomycetes. Three subclasses, Chaetothyriomycetidae,Eurotiomycetidae, and Mycocaliciomycetidae, are defined to representthe major lineages within Eurotiomycetes.Subclass: Chaetothyriomycetidae Doweld, Prosyllabus: LXXVIII(2001).Lichenized, parasitic, and saprobic ascomycetes with mostlybitunicate/fissitunicate to evanescent asci, produced in perithecialascomata arranged superficially or immersed in a thallus.Thalli often produced on the surfaces of rocks, lichens, decayingplant material and other substrata. Ascospores variable, fromcolourless to pigmented, simple to muriform. Hamathecium,when present, consisting of pseudoparaphyses. Pigments,when present, generally related to melanin. Asexual stageswith phialidic and annellidic anamorphs observed in non-lichenizedtaxa.Order: Chaetothyriales M. E. Barr, Mycotaxon 29: 502 (1987).Exemplar genera: Capronia Sacc. 1883, Ceramothyrium Bat. &H. Maia 1956, Chaetothyrium Speg. 1888.

528 D. S. Hibbett et al.Order: Pyrenulales Fink ex D. Hawksw. & O. E. Erikss., Syst.Ascom. 5: 182 (1986).Synonym: Pyrenulales Fink, Ohio St. Univ. Bull. 19(28): 107 (1951),nomen invalidum.Exemplar genera: Pyrenula Ach. 1814, Pyrgillus Nyl. 1858.Order: Verrucariales Mattick ex D. Hawksw. & O. E. Erikss.,Syst. Ascom. 5: 183 (1986).Synonym: Verrucariales Mattick, in Engler, Syll. Pflanzenfam. (12edn): 208 (1954), nomen invalidum.Exemplar genera: Agonimia Zahlbr. 1909, DermatocarponEschw. 1824, Polyblastia A. Massal. 1852, Verrucaria Schrad. 1794.Subclass: Eurotiomycetidae Geiser & Lutzoni, subclass. nov.MycoBank no.: MB 501287Fungi saprotrophici vel parasitici vel mycorrhizales; asci globosi intoto ascomate sparsi, raro hymenium formantes; asci plerumqueevanescentes, nonnumquam bitunicati. Ascosporae plerumqueunicellulares, lenticulares, nonnumquam globosae vel ellipsoideae.Ascomata, si formata, plerumque cleistothecialia vel gymnothecialia,saepe textura stromatica circumdata. Structurae hamathecialesabsentes. Gametangia plerumque indistincta e glomere hyphaliconstantia. Fungi saepe laete colorati. Anamorphae variabiles, seuphialidicae seu arthroconidiales.Typus: Eurotium Link 1809.Saprotrophic, parasitic and mycorrhizal. Ascomata, whenpresent, usually cleistothecial/gymnothecial, globose, oftenproduced in surrounding stromatic tissue and brightly coloured;hamathecial elements lacking; gametangia usually undifferentiatedand consisting of hyphal coils. Asci usually evanescent,sometimes bitunicate, scattered throughout the ascoma, rarelyfrom a hymenium. Ascospores usually single-celled, lenticular,sometimes spherical or elliptical. Anamorphs variable, includingphialidic and arthroconidial forms.This name was employed by Lutzoni et al. (2004) and Geiseret al. (2007), in the same sense as the present classification, butwithout a formal diagnosis.Order: Coryneliales Seaver & Chardón, Scient. Surv. P. Rico: 40(1926).Exemplar genera: Corynelia Ach. 1823, Caliciopsis Peck 1880.Order: Eurotiales G. W. Martin ex Benny & Kimbr., Mycotaxon12: 23(1980).Synonym: Eurotiales G. W. Martin, Std. nat. Hist. Iowa Univ.18(Suppl.): 16 (1941), nomen invalidum.Exemplar genera: Eurotium Link 1809, Emericella Berk. 1857,Talaromyces C. R. Benj. 1955, Elaphomyces Nees 1820, TrichocomaJungh. 1838, Byssochlamys Westling 1909.Order: Onygenales Cif. ex Benny & Kimbr., Mycotaxon 12: 8 (1980).Synonym: Onygenales Cif., Atti Ist. Bot. Univ. Pavia, ser. 5, 14: 238(1957), nomen invalidum.Emend. Currah Mycotaxon 24: 13(1985).Exemplar genera: Onygena Pers. 1799, Gymnoascus Baran.1872, Arthroderma Curr. 1860.Subclass: Mycocaliciomycetidae Tibell. subclass nov.MycoBank no.: MB 501288Parasitae vel commensales in lichenibus vel saprotrophici.Ascomata disciformia, stipitata vel sessilia. Excipulum cupulatum,saltem partim scleroticum hyphis stipitis simile. Dispersiosporarum activa, raro passiva et tum mazedio parce evoluto.Asci unitunicati, cylindrici, vulgo apice distincte incrassato,8-spori. Ascosporae pallidae ad atrofuscae, ellipsoidales, nonseptataevel transversaliter 1–7-septatae. Paries sporae atrofuscus,laevis vel ornamento intra plasmalemma formato. Derivataacidi vulpinici in speciebus paucis praesentia. Anamorphae coelomycetumet hyphomycetum variae praesentes.Typus: Mycocalicium Vain. 1890.Parasites or commensals on lichens or saprobes. Ascomatadisciform, stalked or sessile. Excipulum cupulate, and like thestalk hyphae at least in part sclerotized. Spore dispersal active,more rarely passive and ascomata then with a moderately developedmazaedium. Asci unitunicate, cylindrical, mostly witha distinctly thickened apex, 8-spored. Ascospores pale to blackishbrown, ellipsoidal or spherical to cuboid, non-septate ortransversely 1–7-septate. Spore wall pigmented, smooth orwith an ornamentation formed within the plasmalemma. Vulpinicacid derivatives occur in a few species. A variety of coelomycetousand hyphomycetous anamorphs occur.Order: Mycocaliciales Tibell & Wedin, Mycologia 92: 579 (2000).Exemplar genera: Mycocalicium Vain. 1890, ChaenothecopsisVain. 1927, Stenocybe (Nyl.) Körb. 1855, Sphinctrina Fr. 1825.Class: Laboulbeniomycetes Engl., Syll. Pflanzenfam. (2nd edn):46 (1898).Order: Laboulbeniales Lindau, in Engler & Prantl (eds), Nat.Pflanzenfam. 1(1): 491 (1897), as‘Laboulbeniineae’.Exemplar genera: Laboulbenia Mont. & C.P. Robin 1835, RickiaCavara 1899, Ceratomyces Thaxt. 1892.Order: Pyxidiophorales P. F. Cannon, in Kirk et al., Ainsworth &Bisby’s Dict. Fungi (9th edn): xi (2001).Exemplar genus: Pyxidiophora Bref. & Tavel 1891.Class: Lecanoromycetes O. E. Erikss. & Winka, Myconet 1: 7(1997).Subclass: Acarosporomycetidae Reeb, Lutzoni & Cl. Roux, Mol.Phylogen. Evol. 32: 1053 (2004).Order: Acarosporales Reeb, Lutzoni & Cl. Roux, ord. nov.MycoBank no.: MB 501289Ascomycetes lichenisati algas virides thallo continentes. Ascomataimmersa vel sessilia, disciformia vel perithecioidea. Excipulumhyalinum, annulatum. Hymenium non-amyloideum. Paraphysesmediocriter vel infirme ramosae, septatae, mediocriter vel infirmeanastomosantes. Asci unitunicati, non-amyloidei vel satis infirmeamyloidei, polyspori. Ascosporae hyalinae, non-septatae, nonhalonatae.Typus: Acarospora A. Massal. 1852.Lichen-forming ascomycetes with chlorococcoid photobiont.Ascomata immersed or sessile, disciform or perithecioid.True exciple hyaline, annulate. Hymenium non-

A higher-level phylogenetic classification of the Fungi 529amyloid. Paraphyses moderately to poorly branched, septate,moderately to poorly anastomosing. Asci functionally unitunicate,lecanoralean, non-amyloid or with slightly amyloid tholi,polyspored, generally with more than 100 ascospores per ascus.Ascospores hyaline, small, non-septate, non-halonate.The members of this order were formerly classified withinthe Lecanorales, but Reeb et al. (2004) and Lutzoni et al. (2004)demonstrated that the Acarosporaceae diverged earlier thanthe Lecanoromycetidae and Ostropomycetidae. This early divergencewithin the Lecanoromycetes was confirmed by Wedinet al. (2005) and Miądlikowska et al. (2007).Exemplar genera: Acarospora A. Massal. 1852, PleopsidiumKörb. 1855, Sarcogyne Flot. 1851.Subclass: Lecanoromycetidae P. M. Kirk, P. F. Cannon, J. C. David& Stalpers ex Miądl., Lutzoni & Lumbsch, subclass. nov.MycoBank no.: MB 501290Synonym: Lecanoromycetidae P. M. Kirk, P. F. Cannon, J. C. David& Stalpers, Ainsworth & Bisby’s Dict. Fungi (9th edn): xi(2001), nomen invalidum.Ascomycetes lichenisati algas virides vel cyanobacteria thallocontinentes. Ascomata immersa, sessilia vel elevata, generaliterdisciformia. Excipulum hyalinum vel pigmentatum, annulatumvel cupulatum. Hymenium amyloideum vel non-amyloideum. Paraphysessimplices vel ramosae, septatae, anastomosantes velnon-anastomosantes. Asci bitunicati, unitunicati vel prototunicati,non-amyloidei vel amyloidei, generaliter octospori, sed etiam1- ad multispori. Ascosporae hyalinae vel brunneae, non-septatae,vel septate usque ad muriformes, halonatae vel non-halonatae.Typus: Lecanora Ach. 1809.Lichen-forming ascomycetes with green algal or cyanobacterialphotobiont. Ascomata immersed, sessile or stalked, usuallydisciform. True exciple hyaline or pigmented, annulate orcupulate. Hymenium amyloid or non-amyloid. Paraphysessimple or moderately to richly branched, septate, anastomosingor not. Asci bitunicate, functionally unitunicate, or prototunicate,lecanoralean, non-amyloid or amyloid, mostly8-spored, but varying from 1- to poly-spored. Ascosporeshyaline or brown, non-septate, trans-septate or muriform,halonate or non-halonate.This subclass includes the bulk of lichenized discomycetesand corresponds to the phylogenetic circumscription of thissubclass by Reeb et al. (2004), Lutzoni et al. (2004) and Miądlikowskaet al. (2007). It is in agreement with the Lecanorales ofLumbsch et al. (2004) and Wiklund & Wedin (2004). The ordersPeltigerales and Teloschistales are here accepted at the ordinallevel, following Miądlikowska & Lutzoni (2003) and Miądlikowskaet al. (2007).Order: Lecanorales Nannf., Nova Acta R. Soc. Scient. Upsal, ser. 48(2): 68 (1932).Exemplar genera: Cladonia Hill. ex P. Browne 1756, LecanoraAch. 1809, Parmelia Ach. 1803, Ramalina Ach. 1809, Usnea Dill.ex Adans. 1763Order: Peltigerales Walt. Watson, New Phytologist 28: 9 (1929).Exemplar genera: Coccocarpia Pers. 1827, Collema F. H. Wigg.1780, Nephroma Ach. 1810, Pannaria Del. ex Bory 1828, PeltigeraWilld. 1787.Order: Teloschistales D. Hawksw. & O. E. Erikss., Syst. Ascom.5: 183 (1986).Exemplar genera: Caloplaca Th. Fr. 1861, Teloschistes Norman1853, Xanthoria (Fr.) Th. Fr. 1860.Subclass: Ostropomycetidae Reeb, Lutzoni & Cl. Roux, Mol.Phylogen. Evol. 32: 1055 (2004).Order: Agyriales Clem. & Shear, Gen. Fungi: 141 (1931).Exemplar genera: Agyrium Fr. 1822, Placopsis (Nyl.) Linds. 1867,Trapelia M. Choisy 1929, Trapeliopsis Hertel & Gotth. Schneid.1980.Order: Baeomycetales Lumbsch, Huhndorf & Lutzoni, ord.nov.MycoBank no.: MB 501291Ascomycetes lichenisati algas virides thallo continentes.Ascomata elevata vel raro sessilia, disciformia. Excipulum hyalinumvel pigmentatum, annulatum vel cupulatum. Hymeniumnon-amyloideum. Paraphyses ramosae, septatae. Asci unitunicati,non-amyloidei vel satis infirme amyloidei, octospori.Ascosporae hyalinae, non-septatae vel septatae, halonatae velnon-halonatae.Typus: Baeomyces Pers. 1794.Lichen-forming ascomycetes with chlorococcoid photobiont.Ascomata sessile or rarely stalked, disciform. True exciplehyaline or pigmented, annulate or cupulate. Hymeniumnon-amyloid. Paraphyses moderately to richly branched, septate.Asci unitunicate, non-amyloid or with slightly amyloidtholi, 8-spored. Ascospores hyaline, non-septate or transseptate,halonate or non-halonate.Baeomycetales was shown to differ from Agyriales by Kauff &Lutzoni (2002) and this was confirmed by Miądlikowska et al.(2007) and Lumbsch et al. (2007).Exemplar genera: Ainoa Lumbsch & I. Schmitt 2001, BaeomycesPers. 1794, Phyllobaeis Gierl & Kalb 1993.Order: Ostropales Nannf., Nova Acta R. Soc. Scient. Upsal., ser. 48(2): 68 (1932).This order includes also taxa formerly classified in separateorders, such as Gomphillales, Graphidales, Gyalectales andTrichotheliales.Exemplar genera: Ostropa Fr. 1825, Stictis Pers. 1799, GyalectaAch. 1808, Gomphillus Nyl. 1855, Graphis Adans. 1763.,Odontotrema Nyl. 1858, Porina Müll. Arg. 1883, ThelotremaAch. 1803.Order: Pertusariales M. Choisy ex D. Hawksw. & O. E. Erikss.,Syst. Ascom. 5: 181 (1986).Synonym: Pertusariales M. Choisy, Bull. mens. Soc. linn. Lyon 18:12 (1949), nomen invalidum.This order may not be monophyletic as currently circumscribed,with Ochrolechiaceae and some groups of the heterogeneousPertusaria clustering in a separate clade, but withoutsupport. Nonetheless, a cluster of taxa in a ‘core’ group of Pertusarialeshas been strongly supported as monophyletic inphylogenetic analyses by Miądlikowska et al. (2007), Lücking

530 D. S. Hibbett et al.et al. (2004), Schmitt et al. (2005), Lutzoni et al. (2004), and Grubeet al. (2004).Exemplar genera: Coccotrema Müll. Arg. 1888, Icmadophila Trevis.1853, Ochrolechia A. Massal. 1852, Pertusaria DC. 1805.Lecanoromycetes incertae sedis (not placed in any subclass):Order: Candelariales Miadl., Lutzoni & Lumbsch, ord. nov.MycoBank no.: MB 501292Ascomycetes lichenisati algas virides thallo continentes. Ascomatasessilia, disciformia. Excipulum hyalinum, annulatum. Hymeniumamyloideum. Paraphyses ramosae, septatae. Asciunitunicati, amyloidei, ad typum Candelariae dictum pertinentes,octo- vel saepe multispori. Ascosporae hyalinae, non-septataevel raro 1-septatae.Typus: Candelaria A. Massal. 1853.Lichen-forming ascomycetes with chlorococcoid photobiont,predominantly nitrophilous. Thallus of various morphology,yellow to orange (pulvinic acid derivatives).Ascomata apothecial, sessile, with or without a distinct margin,yellow to orange. The ascomatal wall formed from denselyseptate twisted hyphae. paraphyses mostly simple. Excipulumhyaline, hymenium amyloid. Asci unitunicate of Candelariatypewith the amyloid lower part of the apical dome and broadapical cushion, often multispored. Ascospores hyaline, aseptate,rarely 1-septate.Candelariales was shown to differ from Lecanorales by Wedinet al. (2005) and this was confirmed by Hofstetter et al. (2007)and Miądlikowska et al. (2007).Exemplar genera: Candelaria A. Massal. 1853, CandelariellaMüll. Arg. 1894.Order: Umbilicariales Lumbsch, Hestmark & Lutzoni, ord. nov.MycoBank no.: MB 501293Ascomycetes lichenisati algas virides thallo continentes. Ascomatasessilia, raro immersa usque ad pauce elevata, plerumqueatra, irregularia, disciformia. Excipulum pigmentatum, annulatum.Hymenium amyloideum. Paraphyses simplices vel paulumramosae, septatae. Asci unitunicati, tholo inconspicue amyloideo,1–8-spori. Ascosporae hyalinae vel brunneae, non-septatae usquead muriformes.Typus: Umbilicaria Hoffm. 1789.Lichen-forming ascomycetes with chlorococcoid photobiont.Ascomata sessile, or rarely immersed or stalked, mostlyblack, irregular, disciform. True exciple pigmented, annulate.Hymenium amyloid. Paraphyses simple or slightly branched,septate, apically thickened. Asci unitunicate, with slightly amyloidtholi, 1–8-spored. Ascospores hyaline or brown, non-septateto muriform.Exemplar genera: Lasallia Mérat 1821, Umbilicaria Hoffm.1789.Class: Leotiomycetes O. E. Erikss. & Winka, Myconet 1: 7 (1997).Excluding Geoglossaceae (Wang et al. 2006).Order: Cyttariales Luttr. ex Gamundí, Darwiniana 16: 502(1971).Synonym: Cyttariales Luttr., Univ. Miss. Stud. 24(2): 109 (1951),nomen invalidum.Exemplar genus: Cyttaria Berk. 1842.Order: Erysiphales H. Gwynne-Vaughan, Fungi, Ascom., Ustilag.,Ured.: 78(1922).Exemplar genera: Erysiphe R. Hedw. ex DC. 1805, BlumeriaGolovin ex Speer 1975, Uncinula Lév. 1851.Order: Helotiales Nannf., Nova Acta R. Soc. Scient. Upsal., ser. 48(2): 68 (1932).Based on current character and taxon sampling (Wang et al.2006, 2007; Spatafora et al. 2007), the monophyly of Helotiales s.lat. is not well supported. There exists a minimum of fivehelotialean lineages that are intermixed with other leotiomycetantaxa (e.g. Cyttariales, Erysiphales) resulting in a paraphyleticHelotiales s. lat. The interrelationships of these taxa arepoorly resolved, however, thus preventing the synthesis ofan accurate phylogenetic classification at this time. Leotiomycetesrepresents one of the more undersampled higher taxaamong the Ascomycota, and it is likely that future samplingwill result in a phylogenetic classification of a more restrictedHelotiales and the recognition of additional orders based oncurrent helotialean families (e.g. Leotiaceae or Helotiaceae,Sclerotiniaceae).Exemplar genera: Mitrula Fr. 1821, Hymenoscyphus Gray 1821,Ascocoryne J.W. Groves & D.E. Wilson 1967.Order: Rhytismatales M. E. Barr ex Minter, in Hawksworth &Eriksson, Syst. Ascom. 5: 182 (1986).Synonym: Rhytismatales M. E. Barr, Mem. N. Y. Bot.Gdn 28: 6(1976), nomen invalidum.Exemplar genera: Rhytisma Fr. 1818, Lophodermium Chevall.1826, Cudonia Fr. 1849.Order: Thelebolales P. F. Cannon, in Kirk et al., Ainsworth & Bisby’sDict. Fungi (9th edn): xi (2001).Exemplar genera: Thelebolus Tode 1790, Coprotus Korf ex Korf& Kimbr. 1967, Ascozonus (Renny) E.C. Hansen 1876.Class: Lichinomycetes Reeb, Lutzoni & Cl. Roux., Mol. Phylogen.Evol. 32: 1055 (2004).Order: Lichinales Henssen & Büdel, in Hawksworth & Eriksson,Syst. Ascom. 5: 138 (1986).Exemplar genera: Heppia Nägeli ex A. Massal. 1854, Lichina C.Agardh 1817, Peltula Nyl. 1853.Class: Orbiliomycetes O. E. Erikss. & Baral, in Eriksson et al.,Myconet 9: 96 (2003).Order: Orbiliales Baral, O. E. Erikss., G. Marson & E. Weber, inEriksson et al., Myconet 9: 96(2003).Exemplar genera: Orbilia Fr. 1849, Hyalorbilia Baral & G. Marson2000.Class: Pezizomycetes O. E. Erikss. & Winka, Myconet 1: 8 (1997).

A higher-level phylogenetic classification of the Fungi 531Order: Pezizales J. Schröt., in Engler & Prantl (eds), Nat. Pflanzenfam.1: 173 (1894), as‘Pezizineae’.Exemplar genera: Peziza Fr. 1822, Glaziella Berk. 1880, MorchellaDill. ex Pers. 1794, Pyronema Carus 1835, Tuber F.H. Wigg. 1780.Glaziella has been described several times, inter alia asa zygomycete. Gibson et al. (1986) demonstrated it was an ascomyceteand proposed a new family and order close to Pezizales,but small subunit rRNA gene sequences show that itshould be included in Pezizales (Landvik & Eriksson 1994).Class: Sordariomycetes O. E. Erikss. & Winka, Myconet 1: 10(1997).Subclass: Hypocreomycetidae O. E. Erikss. & Winka, Myconet 1:6 (1997).Order: Coronophorales Nannf., Nova Acta R. Soc. Scient. Upsal,ser. 48: 54 (1932).Exemplar genera: Nitschkia G.H. Otth ex P. Karst. 1873, ScortechiniaSacc. 1885, Bertia De Not. 1844, Chaetosphaerella E. Müll. &C. Booth 1972.Order: Hypocreales Lindau, in Engler & Prantl (eds), Nat. Pflanzenfam.1: 343 (1897).Exemplar genera: Hypocrea Fr. 1825, Nectria (Fr.) Fr. 1849, Cordyceps(Fr.) Link 1833, Claviceps Tul. 1853, Niesslia Auersw. 1869.Order: Melanosporales N. Zhang & M. Blackw., ord. nov.MycoBank no.: MB 501294Ascomata perithecialia vel nonnumquam ostiolo carentia;peridium ascomatis e basi glomeris ascogonialis oriundum,translucidum; centrum pseudoparenchymaticum, paraphysibusabsentibus; asci unitunicati, evanescentes; ascosporae fuscae,poro germinationis utrinque praeditae; anamorphae hyphomycetales.Fungi saepe mycoparasitici.Typus: Melanospora Corda 1837.Ascoma perithecial or secondarily cleistothecial, peridiumderived from base of an ascogonial coil, translucent; centrumpseudoparenchymatous, paraphyses absent in development;asci unitunicate, evanescent; ascospores dark, with germ poresat both ends; anamorphs hyphomycetous; often mycoparasitic.Exemplar genus: Melanospora Corda 1837.Order: Microascales Luttr. ex Benny & Kimbr., Mycotaxon 12:40(1980).Synonym: Microascales Luttr., Univ. Miss. Stud. 24(2): 108 (1951),nomen invalidum.The group as recognized here includes members of theHalosphaeriales. InZhang et al. (2007) and Tang et al. (2007),the Halosphaeriales were maintained separate from theMicroascales.Exemplar genera: Microascus Zukal 1885, Petriella Curzi 1930,Halosphaeria Linder 1944, Lignincola Höhnk 1955, Nimbospora J.Koch 1982.Subclass: Sordariomycetidae O. E. Erikss. & Winka, Myconet 1:10 (1997).Order: Boliniales P. F. Cannon, in Kirk et al., Ainsworth & Bisby’sDict. Fungi (9th edn): x (2001).Exemplar genera: Camarops P. Karst. 1873, ApiocamaropsSamuels & J. D. Rogers 1987.Order: Calosphaeriales M. E. Barr, Mycologia 75: 11(1983).This order has not been placed in a subclass but the work ofRéblová et al. (2004) shows that it may be related to the Diaporthales.Members of this group were not included in Zhang et al.(2007) or Tang et al. (2007).Exemplar genera: Calosphaeria Tul. & C. Tul. 1863, TogniniellaRéblová, L. Mostert, W. Gams & Crous 2004, Pleurostoma Tul. &C. Tul. 1863.Order: Chaetosphaeriales Huhndorf, A. N. Mill. & F. A. Fernández,Mycologia 96: 378 (2004).Exemplar genera: Chaetosphaeria Tul. & C. Tul. 1863, MelanochaetaE. Müll., Harr & Sulmont 1969, Zignoëlla Sacc. 1878, StriatosphaeriaSamuels & E. Müll. 1979.Order: Coniochaetales Huhndorf, A. N. Mill. & F. A. Fernández,Mycologia 96: 378 (2004a).Exemplar genera: Coniochaeta (Sacc.) Cooke 1887, ConiochaetidiumMalloch & Cain 1971.Order: Diaporthales Nannf., Nova Acta R. Soc. Scient. upsal., ser.4 8: 53 (1932).Exemplar genera: Diaporthe Nitschke 1870, Gnomonia Ces. &De Not. 1863, Cryphonectria (Sacc.) Sacc. & D. Sacc. 1905, ValsaFr. 1849.Order: Ophiostomatales Benny & Kimbr., Mycotaxon 12: 48(1980).Exemplar genera: Ophiostoma Syd. & P. Syd. 1919, FragosphaeriaShear 1923.Order: Sordariales Chadef. ex D. Hawksw. & O. E. Erikss., Syst.Ascom. 5: 182 (1986).Synonym: Sordariales Chadef., in Chadefaud & Emberger, TraitéBot. 1: 594 (1960), nomen invalidum.Exemplar genera: Sordaria Ces. & De Not. 1863, Podospora Ces.1856, Neurospora Shear & B.O. Dodge 1927, Lasiosphaeria Ces. &De Not. 1863, Chaetomium Kunze 1817.Subclass: Xylariomycetidae O. E. Erikss. & Winka, Myconet 1:12(1997).Order: Xylariales Nannf., Nova Acta R. Soc. Scient. Upsal., ser. 4,8: 66 (1932).Exemplar genera: Xylaria Hill ex Schrank 1789, HypoxylonBull. 1791, Anthostomella Sacc. 1875, Diatrype Fr. 1849, GraphostromaPiroz. 1974.Sordariomycetes incertae sedis (not placed in any subclass)

532 D. S. Hibbett et al.Order: Lulworthiales Kohlm., Spatafora & Volkm-Kohlm.,Mycologia 92: 456 (2000).This order includes members formerly placed in theSpathulosporales.Exemplar genera: Lulworthia G. K. Sutherl. 1916, Lindra I.M.Wilson 1956.Order: Meliolales Gäum. ex D. Hawksw. & O. E. Erikss., Syst.Ascom. 5: 180 (1986).Synonym: Meliolales Gäum., Pilze (2nd edn): 158 (1964), nomeninvalidum.Exemplar genus: Meliola Fr. 1825.Order: Phyllachorales M. E. Barr, Mycologia 75: 10 (1983).Exemplar genus: Phyllachora Nitschke ex Fuckel 1870.Order: Trichosphaeriales M. E. Barr, Mycologia 75: 11 (1983).Exemplar genus: Trichosphaeria Fuckel 1870.Pezizomycotina incertae sedis (not placed in any class)Order: Lahmiales O. E. Erikss., Mycotaxon 27: 357 (1986).Exemplar genus: Lahmia Körb. 1861.Order: Medeolariales Korf, in Eriksson Mycotaxon 15: 232(1982).Exemplar genus: Medeolaria Thaxt. 1922.Order: Triblidiales O. E. Erikss., Syst. Ascom. 11: 9 (1992).Exemplar genera: Huangshania O. E. Erikss. 1992, PseudographisNyl. 1855, Triblidium Rebent. 1804.Phylum: Basidiomycota R. T. Moore, Bot. Mar. 23: 371 (1980).Synonyms: Basidiomycota Bold, Morph. Pl.: 7, 198 (1958), nomeninvalidum;Basidiomycetes Whittaker (1959: 220), nomen invalidum. (Table 3,Fig 3) As in the case of Fungi, Moore (1980) validated a namethat had already been used by Bold (1957), but he did notcite Bold’s work.Subphylum: Pucciniomycotina R. Bauer, Begerow, J. P. Samp.,M. Weiß & Oberw., Mycol. Progr. 5: 45 (2006).Equivalent to Urediniomycetes (Kirk et al. 2001; Swann &Taylor 1995; Swann et al. 2001). The classification of Pucciniomycotinaemployed here parallels that of Bauer et al. (2006)and Aime et al. (2007).Class: Pucciniomycetes R. Bauer, Begerow, J. P. Samp., M. Weiß& Oberw., Mycol. Progr. 5: 48 (2006).Equivalent to Urediniomycetidae (Swann et al. 2001).Order: Septobasidiales Couch ex Donk, Persoonia 3: 243(1964).Synonym: Septobasidiales Couch, Gen. Septobasidium: 65 (1938),nomen invalidum.Exemplar genera: Septobasidium Pat. 1892, AuriculoscyphaD. A. Reid & Manim. 1985.Order: Pachnocybales R. Bauer, Begerow, J. P. Samp., M. Weiß& Oberw., Mycol. Progr. 5: 48 (2006).Exemplar genus: Pachnocybe Berk. 1836.Order: Helicobasidiales R. Bauer, Begerow, J. P. Samp., M. Weiß& Oberw., Mycol. Progr. 5: 48 (2006).Exemplar genera: Helicobasidium Pat. 1885, Tuberculina Todeex Sacc. 1880.Order: Platygloeales R. T. Moore, Mycotaxon 39: 247 (1990).Equivalent to Platygloeales s. str. (Swann et al. 2001).Exemplar genera: Platygloea J. Schröt. 1887 s. str., EocronartiumG.F. Atk. 1902.Order: Pucciniales Clem. & Shear, Gen. Fungi (2nd edn): 147(1931).Equivalent to Uredinales.Exemplar genera: Puccinia Pers. 1801, Uromyces (Link) Unger1832.Class: Cystobasidiomycetes R. Bauer, Begerow, J. P. Samp., M.Weiß & Oberw., Mycol. Progr. 5: 46 (2006).Equivalent to the Erythrobasidium–Naohidea–Sakaguchiaclade (Swann et al. 2001) and Cystobasidiaceae lineage (Weißet al. 2004a). Genera of Cystobasidiomycetes that are not placedin any order include Sakaguchia Y. Yamada, K. Maeda & Mikata1994, and Cyrenella Goch. 1981 (Aime et al. 2007; Bauer et al.2006).Order: Cystobasidiales R. Bauer, Begerow, J. P. Samp., M. Weiß& Oberw., Mycol. Progr. 5: 46 (2006).Exemplar genera: Cystobasidium (Lagerh.) Neuhoff 1924,Occultifur Oberw. 1990, Rhodotorula F.C. Harrison 1927 pro parte.Order: Erythrobasidiales R. Bauer, Begerow, J. P. Samp.,M. Weiß & Oberw., Mycol. Progr. 5: 46 (2006).Exemplar genera: Erythrobasidium Hamam. Sugiyama &Komag. 1988, Rhodotorula F. C. Harrison 1927 pro parte, SporobolomycesKluyver & C. B. Niel 1924 pro parte, Bannoa Hamam. 2002.Order: Naohideales R. Bauer, Begerow, J. P. Samp., M. Weiß &Oberw., Mycol. Progr. 5: 46 (2006).Exemplar genus: Naohidea Oberw. 1990.Class: Agaricostilbomycetes R. Bauer, Begerow, J. P. Samp.,M. Weiß & Oberw., Mycol. Progr. 5: 45 (2006).Equivalent to Agaricostilbomycetidae (Swann et al. 2001;Weiß et al. 2004a).Order: Agaricostilbales Oberw. & R. Bauer, Sydowia 41: 240(1989).Exemplar genera: Agaricostilbum J. E. Wright 1970 (emend.Wright, Bandoni & Oberw. 1981), Chionosphaera D. E. Cox1976, Kondoa Y. Yamada, Nakagawa & I. Banno 1989 (emend.Fonseca, Sampaio, Inácio & Fell 2000).Order: Spiculogloeales R. Bauer, Begerow, J. P. Samp., M. Weiß& Oberw., Mycol. Progr. 5: 45 (2006).Equivalent to Mycogloea group (Weiß et al. 2004a).Exemplar genera: Mycogloea L. S. Olive 1950, Spiculogloea P.Roberts 1996, Sporobolomyces Kluyver & C. B. Niel 1924 pro parte.

A higher-level phylogenetic classification of the Fungi 533Table 3 – Support for major groups of Fungi in selected phylogenetic studies: BasidiomycotaRank Taxon Reference Data OTUs SupportPhylum BASIDIOMYCOTA James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 50 BPP ¼ 1MLBS ¼ 80Subphylum Pucciniomycotina Matheny et al. (2007a, fig. 4) SSU, LSU, 5.8S, rpb1, rpb2, tef1 17 BPP ¼ 1MPBS ¼ 100Aime et al. (2007, fig. 2) LSU, SSU 109 BPP ¼ 1MPBS ¼ 100Class Pucciniomycetes Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 7 BPP > 0.95MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 24 BPP ¼ 0.97MPBS 70Aime et al. (2007, fig. 2) LSU, SSU 19 BPP ¼ 1MPBS ¼ 100Aime et al. (2007, fig. 3) LSU, SSU 41 MPBS ¼ 86Order Septobasidiales Arun Kumar et al. (2007, fig. 7) LSU, SSU 4 BPP ¼ 1MPBS ¼ 100Order Pachnocybales Bauer et al. (2006, fig. 1) LSU 1 NABerres et al. (1995, fig. 4) LSU 1 NAOrder Helicobasidiales Aime et al. (2007, fig. 2) LSU, SSU 2 BPP ¼ 1MPBS ¼ 96NJBS ¼ 98Aime et al. (2007, fig. 3) LSU, SSU 10 MPBS ¼ 87Order Platygloeales Aime et al. (2007, fig. 2) LSU, SSU 4 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Aime et al. (2007, fig. 3) LSU, SSU 8 MPBS ¼ 99Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP > 0.95MPBS > 70Order Pucciniales Aime et al. (2007, fig. 2) LSU, SSU 12 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Aime (2006) LSU 46 MPBS ¼ 99Wingfield et al. (2004) SSU 72 MPBS < 50Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 5 BPP > 0.95MPBS > 70Class Cystobasidiomycetes Aime et al. (2007, fig. 2) LSU, SSU 27 BPP ¼ 1MPBS ¼ 100NJBS ¼ 96Sampaio (2004, fig. 1) LSU 11 BPP ¼ 0.92Sampaio (2004, fig. 2) LSU 26 BPP ¼ 0.98Order Cystobasidiales Nagahama et al. (2006, fig. 2) LSU, SSU, 5.8S, tef1 9 MLBS ¼ 100Aime et al. (2007, fig. 2) LSU, SSU 12 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Sampaio (2004, fig. 2) LSU 8 BPP ¼ 1Order Erythrobasidiales Nagahama et al. (2006, fig. 2) LSU, SSU, 5.8S, tef1 21 MLBS ¼ 72Aime et al. (2007, fig. 2) LSU, SSU 14 BPP ¼ 1MPBS ¼ 83NJBS ¼ 91Sampaio (2004, fig. 2) LSU 18 BPP ¼ 1Order Naohideales Aime et al. (2007, fig. 3) LSU, SSU 2 MPBS ¼ 98Weiß et al. (2004) LSU 3 BPP ¼ 0.94NJBS < 50Class Agaricostilbomycetes Aime et al. (2007, fig. 2) LSU, SSU 25 BPP ¼ 1MPBS < 70NJBS < 70Bauer et al. (2006, fig. 2) LSU, SSU 4 NJBS ¼ 89Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 8 BPP ¼ 1MPBS > 70Order Agaricostilbales Aime et al. (2007, fig. 2) LSU, SSU 22 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Aime et al. (2007, fig. 2) LSU, SSU 34 MPBS ¼ 98Sampaio (2004, fig. 1) LSU 7 BPP ¼ 1Sampaio (2004, fig. 2) LSU 23 BPP ¼ 1(continued on next page)

534 D. S. Hibbett et al.Table 3 (continued)Rank Taxon Reference Data OTUs SupportFell et al. (2001) LSU 24 MPBS ¼ 64Order Spiculogloeales Aime et al. (2007, fig. 2) LSU, SSU 3 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Aime et al. (2007, fig. 3) LSU, SSU 7 MPBS ¼ 74Bauer et al. (2006, fig. 2) LSU, SSU 2 NJBS ¼ 90Class Microbotryomycetes Aime et al. (2007, fig. 2) LSU, SSU 31 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Aime et al. (2007, fig. 3) LSU, SSU 60 MPBS ¼ 74Matheny et al. (2007a, fig. 4)LSU, SSU, 5.8S,rpb1, rpb2, tef16 BPP > 0.95MPBS > 70Sampaio (2004, fig. 2) LSU 49* BPP ¼ 0.87Fell et al. (2001) LSU 78 MPBS ¼ 75Order Heterogastridiales Bauer et al. (2006, fig. 2) LSU, SSU 1 NAOrder Microbotryales Aime et al. (2007, fig. 2) LSU, SSU 4 BPP ¼ 1MPBS ¼ 99NJBS ¼ 94Aime et al. (2007, fig. 3) LSU, SSU 12 MPBS ¼ 82Order Leucosporidiales Aime et al. (2007, fig. 2) LSU, SSU 3 BPP ¼ 0.98MPBS ¼ 85NJBS ¼ 100Aime et al. (2007, fig. 3) LSU, SSU 9 MPBS ¼ 67Order Sporidiobolales Aime et al. (2007, fig. 2) LSU, SSU 13 BPP ¼ 1MPBS ¼ 74NJBS ¼ 68Aime et al. (2007, fig. 3) LSU, SSU 17 MPBS ¼ 69Sampaio (2004, fig. 2) LSU 20 BPP ¼ 0.98Class/OrderClass/OrderAtractiellomycetes,AtractiellalesClassiculomycetes,ClassiculalesAime et al. (2007, fig. 2) LSU, SSU 4 BPP ¼ 1MPBS ¼ 80NJBS ¼ 96Aime et al. (2007, fig. 3) LSU, SSU 8 MPBS ¼ 68Bauer et al. (2006, fig. 2) LSU, SSU 7 NJBS ¼ 68Aime et al. (2007, fig. 2) LSU, SSU 2 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100Weiß et al. (2004, figs. 1–2) LSU 2 BPP ¼ 1NJBS ¼ 99Class/Order Mixiomycetes, Mixiales Aime et al. (2007, fig. 2) LSU, SSU 1 NABauer et al. (2006, fig. 2) LSU, SSU 1 NAClass/Order Cryptomycocolacomycetes, Aime et al. (2007, fig. 3) LSU, SSU 1 NACryptomycocolacalesBauer et al. (2006, fig. 1) LSU 2 NJBS ¼ 100Subphylum Ustilaginomycotina Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S,rpb1, rpb2, tef124 BPP ¼ 1MPBS ¼ 100Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 59 BPP ¼ 1MPBS > 70Class Ustilaginomycetes Bauer et al. (2006, fig. 2) LSU, SSU 21 NJBS ¼ 100Matheny et al. (2007a, fig. 4)LSU, SSU, 5.8S,rpb1, rpb2, tef112 BPP > 0.95MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 25 BPP ¼ 1MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 53 BPP ¼ 1MPBS ¼ 83NJBS ¼ 77Bauer et al. (2001, figs. 33–34) LSU 36 MPBS ¼ 79NJBS ¼ 93Fell et al. (2001, fig. 24) LSU 27 NJBS ¼ 86Order Urocystales Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 5 BPP ¼ 1MPBS ¼ 66NJBS ¼ 96Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 1 NABauer et al. (2001, figs. 33–34) LSU 9 MPBS ¼ 95 3NJBS ¼ 96 3

A higher-level phylogenetic classification of the Fungi 535Table 3 (continued)Rank Taxon Reference Data OTUs SupportOrder Ustilaginales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 10 BPP > 0.95MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 23 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 46 BPP ¼ 1MPBS < 60NJBS < 60Class Exobasidiomycetes Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 12 BPP > 0.95MPBS < 50Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 35 BPP < 0.60MPBS < 60NJBS < 60Bauer et al. (2001, figs. 33–34) LSU 36 MPBS ¼ 85NJBS ¼ 56Order Doassansiales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 1 NAMatheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 4 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 4 BPP ¼ 1MPBS ¼ 84NJBS ¼ 77Bauer et al. (2001, figs. 33–34) LSU 5 MPBS ¼ 96NJBS ¼ 97Order Entylomatales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 4 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 3 BPP ¼ 1MPBS < 60NJBS < 60Bauer et al. (2001, figs. 33–34) LSU 9 MPBS ¼ 72NJBS ¼ 91Order Exobasidiales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP > 0.95MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU 6 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 8 BPP ¼ 1MPBS < 60NJBS ¼ 61Order Georgefischeriales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 5 BPP < 0.60MPBS < 60NJBS < 60Bauer et al. (2001, figs. 33–34) LSU 9 MPBS ¼ 86NJBS ¼ 65Order Microstromatales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 1 NAMatheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 3 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 5 BPP ¼ 1MPBS ¼ 63NJBS ¼ 67Order Tilletiales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 2 BPP > 0.95MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 7 BPP > 0.95MPBS > 70Begerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 5 BPP ¼ 1MPBS ¼ 76NJBS ¼ 64Ustilaginomycotinaincertae sedis (notplaced in any class)Order Malasseziales Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 1 NABegerow et al. (2007, fig. 1) LSU, ITS, atp6, btub 2 BPP ¼ 1MPBS ¼ 100NJBS ¼ 100(continued on next page)

536 D. S. Hibbett et al.Table 3 (continued)Rank Taxon Reference Data OTUs SupportBauer et al. (2001, figs. 33–34) LSU 4 MPBS ¼ 100NJBS ¼ 100Subphylum Agaricomycotina Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 125 BPP ¼ 1MPBS ¼ 95Class Tremellomycetes Matheny et al. (2007a, fig. 4) SSU, LSU, 5.8S, rpb1, rpb2, tef1 5 BPP > 0.95MPBS ¼ 50-69Fell et al. (2001, figs. 19, 22) LSU 139 MPBS ¼ 100Order Cystofilobasidiales Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 5 BPP ¼ 1MPBS 70Fell & Scorzetti (2004, fig. 1) LSU 16 BPP ¼ 1MPBS ¼ 83Order Filobasidiales Fell et al. (2001, figs. 19, 22) LSU 34 MPBS ¼ 96Order Tremellales Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 5 BPP 0.95MPBS 70Fell et al. (2001, figs. 19, 22) LSU 89 MPBS ¼ 56Class/OrderDacrymycetes,DacrymycetalesMatheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 4 BPP ¼ 1MPBS ¼ 100Weiß & Oberwinkler (2001, fig. 6) LSU 9 NJBS ¼ 99Class Agaricomycetes Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 119 BPP ¼ 1MPBS ¼ 95James et al. (2006) LSU, SSU, 5.8S, rpb1, rpb2, tef1 37 BPP ¼ 1MLBS ¼ 92Subclass Agaricomycetidae Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 63 BPP ¼ 1MPBS ¼ 96Binder & Hibbett (2007, fig. 2) LSU, SSU, 5.8S, mt-LSU, atp6 47 BPP > 0.98MLBS ¼ 88Binder et al. (2005, fig. 1) LSU, SSU, mt-LSU, mt-SSU 46 MPBS ¼ 62Order Agaricales Matheny et al. (2006, fig. 2) LSU, SSU, 5.8S 230 BPP ¼ 0.84Matheny et al. (2006, fig. 3) LSU, SSU, 5.8S, rpb1, rpb2 238 BPP ¼ 1MPBS ¼ 43Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 41 BPP ¼ 1MPBS ¼ 76Moncalvo et al. (2002, fig. 2) LSU 786 MPBS < 50Order Atheliales Larsson et al. (2004, fig. 1) LSU 8 MPBS ¼ 97Binder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 3 MPBS ¼ 75Order Boletales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 11 BPP ¼ 1MPBS ¼ 100Binder & Hibbett (2007, fig. 2) LSU, SSU, 5.8S, mt-LSU, atp6 42 BPP > 0.98MLBS ¼ 99Binder & Hibbett (2007, fig. 3) LSU 301 BPP > 0.98Subclass Phallomycetidae Hosaka et al. (2007, fig. 2) LSU, mt-SSU, atp6, rpb2, tef1 222 BPP ¼ 1MPBS ¼ 98Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 3 BPP ¼ 1MPBS ¼ 100Order Geastrales Hosaka et al. (2007, fig. 2) LSU, mt-SSU, atp6, rpb2, tef1 21 BPP ¼ 1MPBS ¼ 59Order Gomphales Hosaka et al. (2007, fig. 2) LSU, mt-SSU, atp6, rpb2, tef1 61 BPP ¼ 1MPBS ¼ 63Order Hysterangiales Hosaka et al. (2007, fig. 2) LSU, mt-SSU, atp6, rpb2, tef1 99 BPP ¼ 1MPBS ¼ 98Order Phallales Hosaka et al. (2007, fig. 2) LSU, mt-SSU, atp6, rpb2, tef1 41 BPP ¼ 1MPBS ¼ 84Agaricomycetes incertaesedis (not placed inany subclass):Order Auriculariales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 3 BPP ¼ 1MPBS ¼ 100Weiß & Oberwinkler (2001, fig. 6) LSU 43 NJBS < 60Order Cantharellales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 11 BPP ¼ 1MPBS ¼ 69Moncalvo et al. (2007, fig. 1) LSU, SSU, mtSSU, rpb2 29 BPP < 0.50MPBS < 50Binder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 31 MPBS < 50Order Corticiales Larsson et al. (2004, fig. 1) LSU 7 MPBS ¼ 96

A higher-level phylogenetic classification of the Fungi 537Table 3 (continued)Rank Taxon Reference Data OTUs SupportBinder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 8 MPBS ¼ 81Order Gloeophyllales Thorn et al. (2000, fig. 5) LSU 5 MPBS ¼ 71Binder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 6 MPBS ¼ 54Hymenochaetales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 7 BPP ¼ 1MPBS ¼ 63Larsson et al. (2007, fig. 3) LSU, 5.8S 174 BPP ¼ 1Wagner & Fischer (2002, fig. 2) LSU 104 NJBS ¼ 100Order Polyporales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 16 BPP ¼ 1MPBS ¼ 85Binder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 122 MPBS < 50Order Russulales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 8 BPP ¼ 1MPBS ¼ 99Larsson & Larsson (2003, fig. 1) LSU, 5.8S 127 MPBS ¼ 96Miller et al. (2007, fig. 2) LSU, ITS 143 MPBS ¼ 100Order Sebacinales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 2 BPP ¼ 1MPBS ¼ 100Weiß & Oberwinkler (2001, fig. 6) LSU 9 NJBS ¼ 99Order Thelephorales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 2 BPP ¼ 1MPBS ¼ 100Binder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 13 MPBS ¼ 97Larsson et al. (2004, fig. 1) LSU, 5.8S 11 MPBS ¼ 86Order Trechisporales Matheny et al. (2007b, fig. 6) LSU, SSU, 5.8S, rpb2, tef1 2 BPP ¼ 1MPBS ¼ 100Binder et al. (2005, fig. 4) LSU, SSU, mt-LSU, mt-SSU 20 MPBS ¼ 69Larsson et al. (2004, fig. 1) LSU, 5.8S 12 MPBS ¼ 99Basidiomycota incertaesedis (not placed inany subphylum):Class/OrderClass/OrderWallemiomycetes,WallemialesEntorrhizomycetes,EntorrhizalesSee Table 1 for explanation.Matheny et al. (2007a, fig. 4) LSU, SSU, 5.8S, rpb1, rpb2, tef1 3 BPP > 0.95MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 3 BPP ¼ 1MPBS > 70Matheny et al. (2007a, fig. 5) LSU, SSU, 5.8S 3 BPP ¼ 1MPBS > 70Bauer et al. (2001, figs. 33–34) LSU 2 MPBS ¼ 100NJBS ¼ 100Class: Microbotryomycetes R. Bauer, Begerow, J. P. Samp., M.Weiß & Oberw., Mycol. Progr. 5: 47 (2006).Equivalent to Microbotryomycetidae (Swann et al. 2001; Weißet al. 2004a). The backbone of the Microbotryomycetes remainspoorly resolved, and several genera of Microbotryomycetes arenot placed in any order, including Colacogloea Oberw. &R. Bauer 1991, Atractocolax R. Kirschner, R. Bauer & Oberw.1999, Krieglsteinera Pouzar 1987, Camptobasidium Marvanová& Suberkr. 1990, Kriegeria Bres. 1891 and certain species ofthe polyphyletic genera Sporobolomyces Kluyver & C. B. Niel1924 pro parte, Rhodotorula F. C. Harrison 1927 pro parte, and LeucosporidiumFell, Statzell, I. L. Hunter & Phaff 1970, and others(Aime et al. 2007; Bauer et al. 2006; Sampaio et al. 2003; Weißet al. 2004a).Order: Heterogastridiales Oberw., R. Bauer & Bandoni R. J.,Mycologia 82: 57(1990).Exemplar genus: Heterogastridium Oberw. & R. Bauer 1990.Bauer et al. (2006) placed Colacogloea, Atractocolax and Krieglsteinerain the Heterogastridiales. However, analyses of Baueret al. (2006) and Aime et al. (2007) suggest that Heterogastridiumand Colacogloea do not form a clade, while Atractocolax andKrieglsteinera have yet to be sampled in molecular phylogeneticstudies.Order: Microbotryales R. Bauer & Oberw., in Bauer et al., Can. J.Bot. 75: 1309 (1997).Exemplar genera: Microbotryum Lév. 1847, UstilentylomaSavile 1964.Order: Leucosporidiales J. P. Samp., M. Weiß & R. Bauer, inSampaio et al., Mycol. Progr. 2: 61 (2003).Exemplar genera: Leucosporidiella J. P. Samp. 2003, LeucosporidiumFell, Statzell, I. L. Hunter & Phaff 1970, MastigobasidiumGolubev 1999.Order: Sporidiobolales J. P. Samp., M. Weiß & R. Bauer, in Sampaioet al., Mycol. Progr. 2: 66 (2003).Exemplar genera: Sporidiobolus Nyland 1949, SporobolomycesKluyver & C. B. Niel 1924, Rhodosporidium I. Banno 1967, RhodotorulaF. C. Harrison 1927 pro parte.

538 D. S. Hibbett et al.Order: Cryptomycocolacales Oberw. & R. Bauer, Mycologia 82:672 (1990).Exemplar genera: Cryptomycocolax Oberw. & R. Bauer 1990,Colacosiphon R. Kirschner, R. Bauer & Oberw. 2001.Subphylum: Ustilaginomycotina R. Bauer, Begerow, J. P.Samp., M. Weiß & Oberw., Mycol. Progr. 5: 45 (2006).Equivalent to Ustilaginomycetes (Bauer et al. 1997, 2001;Swann & Taylor 1995).The classification of Ustilaginomycotina employed herelargely parallels that of Begerow et al. (2007), with the primarydifferences being that here the Entorrhizomycetes are classifiedas incertae sedis among Basidiomycota (rather than being a classwithin Ustilaginomycotina).Class: Ustilaginomycetes R. Bauer, Oberw. & Vánky, Can. J. Bot.75: 1311 (1997).Emend. Begerow, Stoll & Bauer, Mycologia 98: 908 (2007)[‘2006’].Equivalent to Ustilaginomycetidae Jülich as emmended byBauer & Oberwinkler (Bauer et al. 1997, 2001; Weiß et al. 2004a).Order: Urocystales R. Bauer & Oberw., in Bauer et al., Can. J. Bot.75: 1311 (1997).Exemplar genera: Urocystis Rabenh. ex Fuckel 1870, UstacystisZundel 1945, Doassansiopsis (Setch.) Dietel 1897.Fig 3 – Phylogeny and classification of Fungi. Basidiomycota.See Table 3 for support values for clades. Dashed lines indicatetaxa that are of uncertain placement.Class: Atractiellomycetes R. Bauer, Begerow, J. P. Samp.,M. Weiß & Oberw., Mycol. Progr. 5: 45 (2006).Order: Atractiellales Oberw. & Bandoni, Can. J. Bot. 60: 1740(1982).Emend. Oberw. & Bauer, Sydowia 41: 239 (1989).Exemplar genera: Atractiella Sacc. 1886, Saccoblastia A. Møller1895, Helicogloea Pat. 1892, Phleogena Link 1833.Class: Classiculomycetes R. Bauer, Begerow, J. P. Samp.,M. Weiß & Oberw., Mycol. Progr. 5: 46 (2006).Order: Classiculales R. Bauer, Begerow, Oberw. & Marvanová,Mycologia 95: 763 (2003).Exemplar genera: Classicula R. Bauer, Begerow, Oberw. &Marvanová 2003, Jaculispora H. J. Huds. & Ingold 1960.Class: Mixiomycetes R. Bauer, Begerow, J. P. Samp., M. Weiß &Oberw., Mycol. Progr. 5: 47 (2006).Order: Mixiales R. Bauer, Begerow, J. P. Samp., M. Weiß &Oberw., Mycol. Progr. 5: 47 (2006).Exemplar genus: Mixia C. L. Kramer 1959 [‘1958’].Class: Cryptomycocolacomycetes R. Bauer, Begerow, J. P.Samp., M. Weiß & Oberw., Mycol. Progr. 5: 46 (2006).Melanotaenium de Bary 1874 has also been placed in this order(Bauer et al. 2001; Weiß et al. 2004a), but analyses ofBegerow et al. (2007) and Matheny et al. (2007b) have supportedits transfer to Ustilaginales.Order: Ustilaginales G. Winter, Rabenh. Krypt.-Fl. 2nd ed.1(1.1): 73 (1880), as ‘Ustilagineae’.Emend. Bauer & Oberwinkler, in Bauer et al., Can. J. Bot. 75:1311 (1997).Exemplar genera: Ustilago (Pers.) Roussel 1806, CintractiaCornu 1883.Thecaphora Fingerh. 1836 has also been placed in this order(Bauer et al. 2001), but analyses of Begerow et al. (2007) andMatheny et al. (2007b) have suggested that it is not nested inUstilaginales. Thecaphora may be the sister group of Urocystales(Matheny et al. 2007b).Class: Exobasidiomycetes Begerow, Stoll & R. Bauer, Mycologia98: 908 (2007) [‘2006’].Equivalent to Exobasidiomycetidae Jülich 1981 emend. Bauer& Oberwinkler, except for exclusion of Malasseziales (Baueret al. 1997, 2001; Weiß et al. 2004a).Monophyly of the Exobasidiomycetidae, as delimited here, issupported with high Bayesian posterior probability in analysesof rpb1, rpb2, and tef1, and nuclear lsu, ssu, and 5.8S ribosomalgenes (Matheny et al. 2007b), but it is weaklysupported in analyses using atp6, b-tubulin, and nuc-lsu ribosomalRNA genes (Begerow et al. 2007). See comments regardingMalasseziales.Order: Doassansiales R. Bauer & Oberw., in Bauer et al., Can. J.Bot. 75: 1312 (1997).

A higher-level phylogenetic classification of the Fungi 539Exemplar genera: Doassansia Cornu 1883, Rhamphospora D. D.Cunn. 1888, Nannfeldtiomyces Vánky 1981.Order: Entylomatales R. Bauer & Oberw., in Bauer et al., Can. J.Bot. 75: 1311 (1997).Exemplar genera: Entyloma de Bary 1874, Tilletiopsis Derx1948.Begerow et al. (2007) erected the monotypic order CeraceosoralesBegerow, Stoll & R. Bauer for Ceraceosorus bombacis (B.K. Bakshi) B. K. Bakshi 1976, which was weakly supported asthe sister group of Tilletiopsis albescens Gokhale 1972. The Ceraceosorus-T.albescens clade was placed as the sister group ofEntylomatales, again with weak support. Ceraceosorales is notincluded in the present classification, pending more robustresolution of the relationships among Ceraceosorus, Tilletiopsis,and Entyloma.Order: Exobasidiales Henn., in Engler & Prantl (eds), Nat. Pflanzenfam.1(1**): 103 (1897), as‘Exobasidiineae’.Emend. Bauer, Oberwinkler & Vánky, Can. J. Bot. 75: 1312(1997).Exemplar genera: Exobasidium Woronin 1867, ClinoconidiumPat. 1898, Dicellomyces L. S. Olive 1945.Order: Georgefischeriales R. Bauer, Begerow & Oberw., inBauer et al., Can. J. Bot. 75: 1311 (1997).Exemplar genera: Georgefischeria Thirum. & Naras. emend.Gandhe 1980, Phragmotaenium R. Bauer, Begerow, A. Nagler &Oberw. 2001, Tilletiaria Bandoni & B. N. Johri 1972, TilletiopsisDerx 1948 pro parte.Order: Microstromatales R. Bauer & Oberw., in Bauer et al., Can.J. Bot. 75: 1311 (1997).Exemplar genera: Microstroma Niessl 1861, SympodiomycopsisSugiy., Tokuoka & Komag. 1991, Volvocisporium Begerow,R. Bauer & Oberw. 2001.Order: Tilletiales Kreisel ex R. Bauer & Oberw., in Bauer et al.,Can. J. Bot. 75: 1311 (1997).Exemplar genera: Tilletia Tul. & C. Tul. 1847, ConidiosporomycesVánky 1992, Erratomyces M. Piepenbr. & R. Bauer 1997.Ustilaginomycotina incertae sedis (not placed in any class):Order: Malasseziales R. T. Moore, Bot. Mar. 23: 371 (1980).Emend. Begerow, Bauer & Boekhout, Mycol. Res. 104: 59(2000).Exemplar genus: Malassezia Baill. 1889.Analyses of the protein-coding genes rpb1, rpb2, and tef1,alone or in combination with nuclear LSU, SSU, and 5.8S ribosomalgenes, suggest that Malasseziales are included in theUstilaginomycetes, but analyses of nuclear ribosomal genesalone or in combination with atp6 and b-tubulin suggest thatMalasseziales is in the Exobasidiomycetes (Bauer et al. 2001;Begerow et al. 2007; Matheny et al. 2007b; Weiß et al. 2004a).Subphylum: Agaricomycotina Dowell Prosyllabus LXXVII(2001).Homonym: Agaricomycotina R. Bauer, Begerow, J. P. Samp.,M. Weiß & Oberw., Mycol. Progr. 5: 45 (2006). Equivalent toHymenomycetes (Swann & Taylor 1995) orBasidiomycetes (Kirket al. 2001; Hibbett 2007).Class: Tremellomycetes Dowell, Prosyllabus: LXXVII (2001).Dimorphic fungi. Fruiting bodies gelatinous or absent,parenthesomes sacculate or absent, basidia septate or nonseptate.The least inclusive clade containing Tremellales, Filobasidialesand Cystofilobasidiales.Equivalent to Tremellomycetidae sensu Swann & Taylor(1995) and Weiß et al. (2004a). The name Tremellomycetidaewas earlier published by Locquin (1984), but without a Latin diagnosis,and it is therefore invalid under the Code.Order: Cystofilobasidiales Fell, Roeijmans & Boekhout, Int. J.Syst. Bacteriol. 49: 911 (1999).Exemplar genera: Cystofilobasidium Oberw. & Bandoni 1983,Mrakia Y. Yamada & Komag. 1987, Itersonilia Derx 1948.Order: Filobasidiales Jülich, Biblthca Mycol. 85: 324 (1981).Exemplar genera: Filobasidiella Kwon-Chung 1976, CryptococcusVuill. 1901 ( pro parte).Order: Tremellales Fr., Syst. Mycol. 1: 2(1821), as‘Tremellinae’.As delimited here, the group includes TrichosporonalesBoekhout & Fell 2001 (Fell et al. 2001) and Christianseniales F.Rath 1991 (Wells & Bandoni 2001). Filobasidiales, which Weißet al. (2004a) included in Tremellales s. lat., has been resolvedas the sister group of Tremellales (Fell et al. 2001; Mathenyet al. 2007b; Swann & Taylor 1995).Exemplar genera: Tremella Pers. 1794, Trichosporon Behrend1890, Christiansenia Hauerslev 1969.Class: Dacrymycetes Dowell, Prosyllabus: LXXVII (2001)Fruiting bodies gelatinous, basidia furcate (rarely unisporous),parenthesomes imperforate.Containing the single order Dacrymycetales (Wells & Bandoni2001).Order: Dacrymycetales Henn., in Engler & Prantl (eds), Nat.Pflanzenfam. 1(1**): 96 (1898), as‘Dacryomycetineae’.Exemplar genera: Dacrymyces Nees 1861, Calocera (Fr.) Fr.1828, Guepiniopsis Pat. 1883.Class: Agaricomycetes Dowell, Prosyllabus: LXXVII (2001)Fruiting bodies hymenomycetous or gasteroid, basidiatwo- to eight-spored, parenthesomes perforate or imperforate.The least-inclusive clade containing Auriculariales, Sebacinales,Cantharellales, Phallomycetidae and Agaricomycetidae.This group is approximately equivalent to Homobasidiomycetessensu Hibbett & Thorn (2001) plus Auriculariales andSebacinales.Subclass: Agaricomycetidae Parmasto, Windahlia 16: 16 (1986).Synonym: Basidiosporeae Bessey, Univ. Studies, Univ. Nebr.7: 306 (1907).The least-inclusive clade containing Agaricales, Boletalesand Atheliales.The delimitation of Agaricomycetidae adopted here differsfrom that of Parmasto (1986), who described Agaricomycetidae

540 D. S. Hibbett et al.as a subclass of Cantharellomycetes Parm. 1986. For example,many of the resupinate forms in the Agaricomycetidae wereplaced by Parmasto in the Corticiomycetes Parm. 1986. Thename Agaricomycetidae was also published by Locquin (1984),but without a Latin diagnosis and it is therefore invalid underthe Code.Order: Agaricales Underw., Moulds, Mildews Mushrooms: 97(1899).Equivalent to euagarics clade (Hibbett & Thorn 2001).Exemplar genera: Agaricus L. 1753, Coprinus Pers. 1797, Pleurotus(Fr.) P. Kumm. 1871.Order: Atheliales Jülich, Biblthca Mycol. 85: 343 (1981).Equivalent to athelioid clade (Binder et al. 2005; Larssonet al. 2004).Exemplar genera: Athelia Pers. 1822, Piloderma Jülich 1969,Tylospora Donk 1960.Order: Boletales E.-J. Gilbert, Livres Mycol. 3: 83(1931).Equivalent to bolete clade (Binder & Hibbett 2006; Hibbett &Thorn 2001).Exemplar genera: Boletus Fr. 1821, Scleroderma Pers. 1801, ConiophoraDC. 1815, Rhizopogon Fr. & Nordholm 1817.Subclass: Phallomycetidae K. Hosaka, Castellano & Spatafora,Mycologia 98: 955 (2007) [‘2006’].Equivalent to Phallales sensu Kirk et al. (2001), and the gomphoid-phalloidclade (Hibbett & Thorn 2001; Hosaka et al.2007).Order: Geastrales K. Hosaka & Castellano, Mycologia 98: 957(2007) [‘2006’].Exemplar genera: Geastrum Pers. 1794, Radiigera Zeller 1944,Sphaerobolus Tode 1790.Order: Gomphales Jülich, Biblthca Mycol. 85: 348 (1981).Exemplar genera: Gomphus (Fr.) Weinm. 1826, Gautieria Vittad.1831, Ramaria Holmsk. 1790.Order: Hysterangiales K. Hosaka & Castellano, Mycologia 98:956 (2007) [‘2006’].Exemplar genera: Hysterangium Vittad. 1831, PhallogasterMorgan 1893, Gallacea Lloyd 1905, Austrogautieria E. L. Stewart& Trappe 1985.Order: Phallales E. Fisch., in Engler & Prantl (eds), Nat. Pflanzenfam.1(1**): 276 (1898).Equivalent to Phallomycetidae Locq. (Locquin 1984), whichwas invalidly published, owing to the absence of a Latindiagnosis.Exemplar genera: Phallus Junius ex L. 1753, Clathrus P. Micheliex L. 1753, Claustula K. M. Curtis 1926.Agaricomycetes incertae sedis (not placed in any subclass):Order: Auriculariales J. Schröt., in Cohn (ed.), Krypt.-Fl. Schlesien1: 382 (1889).Exemplar genera: Auricularia Bull. ex Juss. 1789, Exidia Fr.1822, Bourdotia (Bres.) Trotter 1913.Order: Cantharellales Gäum., Vergl. Morph. Pilze: 495 (1926).Equivalent to the cantharelloid clade (Hibbett & Thorn2001; Moncalvo et al. 2007). The Cantharellales as delimitedhere includes Tulasnella, which is distinguished by unusualbasidia with inflated sterigmata, and has been classified ina separate order, Tulasnellales Rea 1922 (e.g. Weiß et al.2004a). Extreme evolutionary rate heterogeneity in the nuclearribosomal RNA genes of Tulasnella, Cantharellus and Craterellusis a source of error in phylogenetics of Cantharellales. Analysesof Matheny et al. (2006) suggest that Tulasnella is nested withinthe Cantharellales, but it could also be the sister group to Cantharellaless.str. (Moncalvo et al. 2007). If so, then it may be appropriateto segregate Tulasnellales from Cantharellales s.str.Exemplar genera: Cantharellus Fr. 1821, Botryobasidium Donk1931, Craterellus Pers. 1825, Tulasnella J. Schröt. 1888.Order: Corticiales K. H. Larss., ord. nov.MycoBank no.: MB 501299Basidiomata resupinata, effuso-reflexa vel discoidea; hymenophoralaevia; systema hypharum monomiticum; dendrohyphidiararo absentia; basidia saepe e probasidiis oriuntur. Cystidia presentiavel absentia. Sporae hyalinae, tenuitunicatae, albae velaggregatae roseae.Typus: Corticium Pers. 1794.Basidiomycetes with effused or discoid (Cytidia) basidiomata,a smooth hymenophore, and a monomitic hyphalsystem with clamped, rarely simple-septate, hyphae. Dendrohyphidiacommon. Species with or without cystidia. A probasidialresting stage is present in many species. Spores smooth,in masses white to pink. Saprotrophic, parasitic, orlichenicolous.Equivalent to Vuilleminiales Boidin et al. 1998 and the corticioidclade (Binder et al. 2005; Larsson et al. 2004). Boidin et al.(1998) explicitly included Corticium in their new order, asa member of the family Vuilleminiaceae Maire 1902. Jülich(1981) also placed Corticium in Vuilleminiaceae but referredthem to Aleurodiscales Jülich 1981. Corticium is the type of CorticiaceaeHerter 1910, a family name conserved against Vuilleminiaceae.The introduction of Corticiales as a new name forthis order is, therefore, the preferred option.Exemplar genera: Corticium Pers. 1794, Vuilleminia Maire 1902,Punctularia Pat. 1895.Order: Gloeophyllales Thorn, ord. nov.MycoBank no.: MB 501300Basidiomata annua vel perennia, resupinata, effuso-reflexa,dimidiata vel pileata; hymenophora laevia, merulioidea, odontioideavel poroidea. Systema hypharum monomiticum, dimiticumvel trimiticum. Hyphae generativae fibulatae vel efibulatae. Leptocystidiaex trama in hymenium projecta, hyalina vel brunnea, tenuitunicatavel crassitunicata. Basidiosporae laeves, hyalinae,tenuitunicatae, ellipsoideae vel cylindricae vel allantoideae, inamyloideae.Lignum decompositum brunneum vel album.Typus: Gloeophyllum P. Karst. 1882.Fruiting bodies perennial or annual and long-lived, withhymenium maturing and thickening over time. Stature resupinate,effused-reflexed or dimidiate, with smooth, wrinkled,

A higher-level phylogenetic classification of the Fungi 541dentate, lamellate or regularly poroid hymenophore, orpileate-stipitate with lamellae. (Aborted, coralloid or flabelliformfruiting bodies may be formed under conditions of darknessor high carbon dioxide concentration). Leptocystidia orhyphoid hairs originating in the context and extending intoor protruding from the hymenial layer (or lamellar margin inNeolentinus) are common; these often with thick brown wallsand brownish incrustation. Context brown (but pallid in Neolentinus)and generally darkening in potassium hydroxide(the brownish incrustation in Boreostereum turning green inpotassium hydroxide). Monomitic (if so, with sclerified generativehyphae), dimitic, or trimitic; generative hyphae with orwithout clamp connections. Basidiospores hyaline, ellipsoidto cylindrical or suballantoid, with thin, smooth walls, andneither amyloid, dextrinoid nor cyanophilous. Where this isknown, basidiospores are binucleate and sexuality is heterothallicand bipolar (but tetrapolar in V. berkeleyi).Causing brown rots (Gloeophyllum, Neolentinus, Veluticeps)orstringy white rot (Boreostereum, Donkioporia) of wood of gymnosperms,monocots and dicots. Occurrence on ‘wood in service’(e.g. railway ties, paving blocks, wooden chests) seems to becommon (in Donkioporia, Gloeophyllum, Heliocybe and Neolentinus);often on charred wood (Boreostereum and Veluticeps).Equivalent to Gloeophyllum clade (Binder et al. 2005).Exemplar genera: Gloeophyllum P. Karst. 1882, NeolentinusRedhead & Ginns 1985, Veluticeps (Cooke) Pat. 1894.Order: Hymenochaetales Oberw., in Frey et al. (eds), Beitr. Biol.niederen Pflanz.: 89(1977).Equivalent to the hymenochaetoid clade (Hibbett & Thorn2001; Larsson et al. 2007).Exemplar genera: Hymenochaete Lév. 1846, Phellinus Quél.1886, Trichaptum Murrill 1904.Order: Polyporales Gäum., Vergl. Morph. Pilze: 503 (1926).Equivalent to polyporoid clade (Hibbett & Thorn 2001).Exemplar genera: Polyporus Fr. 1815, Fomitopsis P. Karst. 1881,Phanerochaete P. Karst. 1889.Order: Russulales Kreisel ex P. M. Kirk, P. F. Cannon & J. C. David,in Kirk et al., Ainsworth & Bisby’s Dict. Fungi (9th edn): xi(2001).Equivalent to the russuloid clade (Hibbett & Thorn 2001;Larsson & Larsson 2003; Miller et al. 2007).Exemplar genera: Russula Pers. 1796, Aleurodiscus Rabenh. exJ. Schröt. 1888, Bondarzewia Singer 1940, Hericium Pers. 1794,Peniophora Cooke 1879, Stereum Pers. 1794.Order: Sebacinales M. Weiß, Selosse, Rexer, A. Urb. & Oberw.,Mycol. Res. 108: 1007 (2004b).Exemplar genera: Sebacina Tul. 1871, Tremellodendron G. F.Atk. 1902, Piriformospora Sav. Verma, Aj. Varma, Rexer, G.Kost & P. Franken 1998.Order: Thelephorales Corner ex Oberw., Sydowia 78: 361 (1976).Equivalent to the thelephoroid clade (Hibbett & Thorn 2001).Exemplar genera: Thelephora Ehrh. ex Willd. 1787, BankeraCoker & Beers ex Pouzar 1955, Polyozellus Murrill 1910.Order: Trechisporales K. H. Larss., ord. nov.MycoBank no.: MB 501301Basidiomata resupinata, stipitata vel clavarioidea. Hymenophoralaevia, grandinioidea, hydnoidea vel poroidea. Systemahypharum monomiticum vel dimiticum. Hyphae fibulatae, septahypharum interdum inflata (ampullata). Cystidia praesentia velabsentia. Basidia 4-6 sterigmata formantia. Sporae laeves velornatae. Species lignicolae vel terricolae.Typus: Trechispora P. Karst. 1890.Basidiomycetes with effused, stipitate or clavarioid basidiomata.Hymenophore smooth, grandinioid, hydnoid orporoid. Hyphal system monomitic, hyphae clamped, subicularhyphae with or without ampullate septa. Cystidia presentin some species, mostly lacking. Basidia with four tosix sterigmata. Spores smooth or ornamented. On wood orsoil.Equivalent to Hydnodontales Jülich 1981 and trechisporoidclade (Binder et al. 2005; Larsson et al. 2004). Hydnodon Banker1913 was recently placed in synonomy under Trechispora(Ryvarden 2002) and this synonomy is supported by moleculardata (K.H. Larsson, unpubl.). The introduction of a new namefor the group, a name that connects to the clade name alreadyestablished and that is based on the most species-rich genusis, therefore, justified.Exemplar genera: Trechispora P. Karst. 1890, Sistotremastrum J.Erikss. 1958, Porpomyces Jülich 1982.Basidiomycota incertae sedis (not placed in any subphylum):Class: Wallemiomycetes Zalar, de Hoog & Schroers, Antonievan Leeuwenhoek 87: 322 (2005).Analyses of rpb1, rpb2, tef1, and nuc-lsu, nuc-ssu, and 5.8Sribosomal RNA genes suggest that the Wallemiomycetes is thesister group of the rest of the Basidiomycota (possibly alongwith Entorrhizomycetes, see below), but subsets of this datasetproduce alternative placements (Matheny et al. 2007b; Zalaret al. 2005).Order: Wallemiales Zalar, de Hoog & Schroers, Antonie vanLeeuwenhoek 87: 322 (2005).Exemplar genus: Wallemia Johan-Olsen 1887.Class: Entorrhizomycetes Begerow, Stoll & R. Bauer, Mycologia98: 908 (2007) [‘2006’].Equivalent to Entorrhizomycetidae R. Bauer & Oberw. (Baueret al. 1997). So far, only ribosomal RNA genes have beensequenced in Entorrhizomycetes. Analyses with broad samplingacross all groups of Basidiomycota and including Ascomycotaand Glomeromycota as outgroups suggest that Entorrhizomycetesis not nested within any subphylum, and may be the sistergroup of the rest of the Basidiomycota (Matheny et al. 2007a;also see Begerow et al. 1997).Order: Entorrhizales R. Bauer & Oberw., in Bauer et al., ,Can. J.Bot. 75: 1311 (1997).Exemplar genus: Entorrhiza C. A. Weber 1884.

542 D. S. Hibbett et al.AcknowledgmentsPreparation of this classification was facilitated by the Assemblingthe Fungal Tree of Life (AFTOL) project and the DeepHypha Research Coordination Network, which were supportedby the US National Science Foundation grants DEB-0228657,DEB-0228668, DEB-0228671, DEB-0228725 and NSF-0090301.Note added in proofAfter this article went to press, the authors became awareof the following publication, which includes alternative citationsfor many of the names included here: Doweld A, 2001.Prosyllabus tracheophytorum: Tentamen systematis plantarumvascularium (Tracheophyta). Geos, Moscow.references*Adl SM, Simpson AGB, Farmer MA, Andersen RA, Anderson OR,Barta JR, Bowser SS, Brugerolle G, Fensome RA, Fredericq S,James TY, Karpov S, Kugrens P, Krug J, Lane CE, Lewis LA,Lodge J, Lynn DH, Mann DG, McCourt RM, Mendoza L,Moestrup Ø, Mozley-Standridge SE, Nerad TA, Shearer CA,Smirnov AV, Spiegel FW, Taylor MFJR, 2005. 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