A higher-level phylogenetic classification of the Fungi

Mycological Research - Tập 111 - Trang 509-547 - 2007
David S. Hibbett1, Manfred Binder1, Joseph F. Bischoff2, Meredith Blackwell3, Paul F. Cannon4, Ove E. Eriksson5, Sabine Huhndorf6, Timothy James7, Paul M. Kirk4, Robert Lücking6, H. Thorsten Lumbsch6, François Lutzoni7, P. Brandon Matheny1, David J. McLaughlin8, Martha J. Powell9, Scott Redhead10, Conrad L. Schoch11, Joseph W. Spatafora11, Joost A. Stalpers12, Rytas Vilgalys7
1Biology Department, Clark University, Worcester, MA 01610, USA
2National Library of Medicine, National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20892-6510, USA
3Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
4CABI UK, Bakeham Lane, Egham, Surrey TW20 9TY, UK
5Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
6Department of Botany, The Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL 60605-2496, USA
7Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
8Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN 55108-1095, USA
9Department of Biological Sciences, Box 870344/319 Biology, University of Alabama, Tuscaloosa, AL 35487-0344, USA
10ECORC, Agriculture and Agri-Food Canada, CEF, Neatby Building, Ottawa, ON K1A 0C6, Canada
11Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, USA
12Centraalbureau voor Schimmelcultures, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands

Tài liệu tham khảo

Adl, 2005, The new higher level classification of eukaryotes with emphasis on the taxonomy of protists, Journal of Eukaryotic Microbiology, 52, 399, 10.1111/j.1550-7408.2005.00053.x Aime, 2007, . An overview of the higher-level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences, Mycologia, 98, 896, 10.3852/mycologia.98.6.896 Alexopoulos, 1996 von Arx, 1967 Balbiani, 1882, Sur les microsporides ou psorospermies des Articulés, Comptes rendus de l'Académie des Sciences, Paris, 95, 1168 Baldauf, 2000, A kingdom-level phylogeny of eukaryotes based on combined protein data, Science, 290, 972, 10.1126/science.290.5493.972 Barr, 1980, An outline for the reclassification of the Chytridiales, and for a new order, the Spizellomycetales, Canadian Journal of Botany, 58, 2380, 10.1139/b80-276 Barr, 1983, The ascomycete connection, Mycologia, 75, 1, 10.2307/3792917 Barr, 1987, New taxa and combinations in the Loculoascomycetes, Mycotaxon, 29, 501 Barr, 1987 Barron, 1975, Nematophagus fungi: Helicocephalum, Transactions of the British Mycological Society, 65, 309, 10.1016/S0007-1536(75)80015-5 Bauer, 2001, Ustilaginomycetes, 57 Bauer, 2006, The simple-septate basidiomycetes: a synopsis, Mycological Progress, 5, 41, 10.1007/s11557-006-0502-0 Bauer, 1997, Ultrastructural markers and systematics in smut fungi and allied taxa, Canadian Journal of Botany, 75, 1273, 10.1139/b97-842 Begerow, 2000, Phylogenetic placements of ustilaginomycetous anamorphs as deduced from nuclear LSU rDNA sequences, Mycological Research, 104, 53, 10.1017/S0953756299001161 Begerow, 1997, Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa, Canadian Journal of Botany, 75, 2045, 10.1139/b97-916 Begerow, 2007, A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data, Mycologia, 98, 906, 10.3852/mycologia.98.6.906 Benjamin, 1979, Zygomycetes and their spores, 573 Benny, 1980, A synopsis of the orders and families of Plectomycetes with keys to genera, Mycotaxon, 12, 1 Benny, 2001, The classification and phylogeny of Trichomycetes and Zygomycetes, 39 Berres, 1995, Phylogenetic relationships in auriculariaceous basidiomycetes based on 25S ribosomal DNA sequences, Mycologia, 87, 821, 10.2307/3760858 Binder, 2005, The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes), Systematics and Biodiversity, 3, 1, 10.1017/S1477200005001623 Binder, 2007, Molecular systematics and biological diversification of Boletales, Mycologia, 98, 971, 10.3852/mycologia.98.6.971 Blackwell, 2007, Research coordination networks: a phylogeny for kingdom Fungi, Mycologia, 98, 829, 10.3852/mycologia.98.6.829 Boidin, 1998, Taxonomie moléculaire des Aphyllophorales, Mycotaxon, 66, 445 Bold, 1957 Bullerwell, 2003, Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences, Nucleic Acids Research, 31, 1614, 10.1093/nar/gkg264 Campbell, 2003, Systematics of Halosarpheia based on morphological and molecular data, Mycologia, 95, 530, 10.2307/3761897 Campbell, 2005, A re-evaluation of Lulworthiales: relationships based on 18S and 28S rDNA, Mycological Research, 109, 556, 10.1017/S0953756205002716 Castlebury, 2002, A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences, Mycologia, 94, 1017, 10.2307/3761867 Castlebury, 2004, Multigene phylogeny reveals new lineage for Stachybotrys chartarum, the indoor air fungus, Mycological Research, 108, 864, 10.1017/S0953756204000607 Cavalier-Smith, 1981, Eukaryote kingdoms: seven or nine?, BioSystems, 14, 461, 10.1016/0303-2647(81)90050-2 Cavalier-Smith, 1998, A revised six-kingdom system of Life, Biological Reviews, 73, 203, 10.1017/S0006323198005167 Cejp, 1957 Clements, 1931 Cohn, 1879, Ueber ein Thallophytensystem, Jahresbericht der Schlesischen Gesellschaft für vaterländische Cultur, Breslau, 57, 279 2004 Currah, 1985, Taxonomy of the Onygenales: Arthrodermataceae, Gymnoacaceae, Myxotrichaceae and Onygenaceae, Mycotaxon, 24, 1 David, 2002, A preliminary catalogue of the names of fungi above the rank of order, Constancea, 83, 1 Del Prado, 2006, Molecular data place Trypetheliaceae in Dothideomycetes, Mycological Research, 110, 511, 10.1016/j.mycres.2005.08.013 Donk, 1964, A conspectus of the families of Aphyllophorales, Persoonia, 3, 199 Ekman, 2002, Most species of Lepraria and Leproloma form a monophyletic group closely related to Stereocaulon, Mycological Research, 106, 1262, 10.1017/S0953756202006718 Engler, 1898 Eriksson, 1982, Outline of the ascomycetes, Mycotaxon, 15, 203 Eriksson, 1986, Lahmia Körber (=Parkerella A. Funk) a misinterpreted genus with isolated position, Mycotaxon, 27, 347 Eriksson, 1992, Huangshania verrucosa gen. et sp. nov. (Triblidiaceae, Triblidiales ordo nov.), a discomycete on Pinus from China, Systema Ascomycetum, 11, 1 Eriksson, 1994, Pneumocystis carinii, a parasite in lungs of mammals, referred to a new family and order (Pneumocystidaceae, Pneumocystidales, Ascomycota), Systema Ascomycetum, 13, 165 Eriksson, 2003, Notes on ascomycete systematics. Nos 3580-3623, Myconet, 9, 91 Eriksson, 1993, Molecular evidence for the evolutionary hiatus between Saccharomyces cerevisiae and Schizosaccharomyces pombe, Systema Ascomycetum, 11, 119 Eriksson, 1997, Supraordinal taxa of Ascomycota, Myconet, 1, 1 Fell, 2001, Basidiomycetous yeasts, 3 Fell, 1999, a new order of basidiomycetous yeasts. International Journal of Systematic Bacteriology, Cystofilobasidiales, 49, 907 Fell, 2004, Reassignment of the basidiomycetous yeasts Trichosporon pullulans to Guehomyces pullulans gen. nov., comb. nov. and Hyalodendron lignicola to Trichosporon lignicola comb. nov, International Journal of Systematic and Evolutionary Microbiology, 54, 995, 10.1099/ijs.0.03017-0 Fischer, 1892, Phycomycetes. Rabenhorst's Kryptogamen-Flora von Deutschland, Österreich und der Schweiz, 1, 1 Fischer, 1898, Phallineae, 276 Fries, 1821 Fries, 1832 Galagan, 2005, Genomics of the fungal kingdom: insights into eukaryotic biology, Genome Research, 15, 1620, 10.1101/gr.3767105 Gamundí, 1971, Las Cyttariales sudamericanas, Darwiniana, 16, 461 Gäumann, 1926 Gäumann, 1928 Geiser, 2007, Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae, Mycologia, 98, 1054 Germot, 1997, Evidence for loss of mitochondria in microsporidia from a mitochondrial HSP70 in Nosema locustae, Molecular and Biochemical Parasitology, 87, 159, 10.1016/S0166-6851(97)00064-9 Gibson, 1986, Ultrastructural observations on Endogonaceae (Zygomycetes). II. Glaziellales ord. nov. and Glaziellaceae fam. nov.: new taxa based upon light and electron microscopic observations of Glaziella aurantiaca, Mycologia, 78, 941, 10.2307/3807435 Gilbert, 1931 Gill, 2006, Assessing the microsporidia–fungi relationship: combined phylogenetic analysis of eight genes, Gene, 375, 103, 10.1016/j.gene.2006.02.023 Grube, 2004, The phylogeny of Porinaceae (Ostropomycetidae) suggests a neotenic origin of perithecia in Lecanoromycetes, Mycological Research, 108, 1111, 10.1017/S0953756204000826 Gwynne-Vaughan, 1922 Hausner, 2004, The nuclear small subunit ribosomal genes of Sphaeronaemella helvellae, Sphaeronaemella fimicola, Gabarnaudia betae, and Cornuvesica falcata: phylogenetic implications, Canadian Journal of Botany, 82, 752, 10.1139/b04-046 Hawksworth, 1995 Henk, 2003, Laboulbeniopsis, an ectoparasite of termites newly recognized as a member of the Laboulbeniomycetes, Mycologia, 95, 561, 10.2307/3761931 Hennings, 1897, Exobasidiineae, 103 Hennings, 1898, Dacryomycetineae, 96 Henssen, 1973 Hibbett, 2007, A phylogenetic overview of the Agaricomycotina, Mycologia, 98, 917, 10.3852/mycologia.98.6.917 Hibbett, 1998, Integrating phylogenetic analysis and classification in fungi, Mycologia, 90, 347, 10.2307/3761391 Hibbett, 2001, Homobasidiomycetes, 121 Hirt, 1997, A mitochondrial Hsp70 orthologue in Vairimorpha necatrix: molecular evidence that Microsporidia once contained mitochondria, Current Biology, 7, 995, 10.1016/S0960-9822(06)00420-9 Hofstetter, 2007, Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota), Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2006.10.016 de Hoog, 2005, Evolution, taxonomy and ecology of the genus Thelebolus in Antarctica, Studies in Mycology, 51, 33 Hosaka, 2007, Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders, Mycologia, 98, 949, 10.3852/mycologia.98.6.949 Huhndorf, 2004, Molecular systematics of the Coronophorales and new species of Bertia, Lasiobertia and Nitschkia, Mycological Research, 108, 1384, 10.1017/S0953756204001273 Huhndorf, 2004, Molecular systematics of the Sordariales: the order and the family Lasiosphaeriaceae redefined, Mycologia, 96, 368, 10.2307/3762068 Inderbitzin, 2001, Aliquandostipitaceae, a new family for two new tropical ascomycetes with unusually wide hyphae and dimorphic ascomata, American Journal of Botany, 88, 52, 10.2307/2657126 Inderbitzin, 2004, The phylogenetic position of Spathulospora based on DNA sequences from dried herbarium material, Mycological Research, 108, 737, 10.1017/S0953756204000206 International Commission on Zoological Nomenclature, 1999 Jahn, 1949 James, 2006, Reconstructing the early evolution of the fungi using a six gene phylogeny, Nature, 443, 818, 10.1038/nature05110 James, 2007, A molecular phylogeny of the flagellated fungi (Chytridiomycota) and a proposal for a new phylum (Blastocladiomycota), Mycologia, 98, 860, 10.3852/mycologia.98.6.860 James, 2000, Molecular phylogenetics of the Chytridiomycota supports the utility of ultrastructural data in chytrid systematics, Canadian Journal of Botany, 78, 336, 10.1139/b00-009 Jülich, 1981, Higher taxa of basidiomycetes, Bibliotheca Mycologica, 85, 1 Kauff, 2002, Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): among and within order relationships based on nuclear ribosomal RNA small and large subunits, Molecular Phylogenetics and Evolution, 25, 138, 10.1016/S1055-7903(02)00214-2 Keeling, 2003, Congruent evidence for alpha-tubulin and beta-tubulin gene phylogenies for a zygomycete origin of Microsporidia, Fungal Genetics and Biology, 38, 298, 10.1016/S1087-1845(02)00537-6 Keeling, 2000, Evidence from beta-tubulin phylogeny that Microsporidia evolved from within the fungi, Molecular Biology and Evolution, 17, 23, 10.1093/oxfordjournals.molbev.a026235 1979 Kendrick, 1985 2001 Kohlmeyer, 2000, Lulworthiales, a new order of marine Ascomycota, Mycologia, 92, 453, 10.2307/3761504 Kruys, 2006, Phylogenetic relationships of coprophilous Pleosporales (Dothideomycetes, Ascomycota), and the classification of some bitunicate taxa of unknown position, Mycological Research, 110, 527, 10.1016/j.mycres.2006.03.002 Kuramae, 2006, Phylogenomics reveal a robust fungal tree of life, FEMS Yeast Research, 6, 1213, 10.1111/j.1567-1364.2006.00119.x Kudrjazew, 1960 Kurtzman, 2001, Ascomycetous yeasts and yeastlike taxa, 179 Landvik, 1994, Relationship of the genus Glaziella (Ascomycota) inferred from 18S rDNA sequences, Systema Ascomycetum, 13, 13 Landvik, 2001, Neolecta — a fungal dinosaur? Evidence from β-tubulin amino acid sequences, Mycologia, 93, 1151, 10.2307/3761675 Landvik, 1993, Relationships of the genus Neolecta (Neolectales ordo nov., Ascomycotina) inferred from 18S rDNA sequences, Systema Ascomycetum, 11, 107 Larsson, 2003, Phylogenetic relationships of russuloid basidiomycetes with emphasis on aphyllophoralean taxa, Mycologia, 95, 1037, 10.2307/3761912 Larsson, 2000, Folia Parasitologica, 47, 241, 10.14411/fp.2000.043 Larsson, 2004, High phylogenetic diversity among corticioid homobasidiomycetes, Mycological Research, 108, 983, 10.1017/S0953756204000851 Larsson, 2007, Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade, Mycologia, 98, 926, 10.3852/mycologia.98.6.926 Letcher, 2006, Ultrastructural and molecular phylogenetic delineation of a new order, the Rhizophydiales (Chytridiomycota), Mycological Research, 110, 898, 10.1016/j.mycres.2006.06.011 Li, 1993, The phylogenetic relationships of the anaerobic chytridiomycetous gut fungi (Neocallimasticaceae) and the Chytridiomycota. II. Cladistic analysis of structural data and description of Neocallimasticales ord. nov, Canadian Journal of Botany, 71, 393, 10.1139/b93-044 Lichtwardt, 1978, Validation of the Harpellales and Asellariales, Mycotaxon, 7, 441 Lindau, 1896, Hysteriineae, 265 Lindau, 1897, Dothideales, 373 Lindau, 1897, Hypocreales, 343 Lindau, 1897, Laboulbeniineae, 491 Lindemuth, 2001, Phylogenetic analysis of nuclear and mitochondrial rDNA sequences supports the view that loculoascomycetes (Ascomycota) are not monophyletic, Mycological Research, 105, 1176, 10.1016/S0953-7562(08)61988-7 Liu, 2004, Body plan evolution of ascomycetes, as inferred from an RNA polymerase II phylogeny, Proceedings of the National Academy of Sciences, USA, 101, 4507, 10.1073/pnas.0400938101 Liu, 2006, Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of kingdom Fungi inferred from RNA polymerase II subunit genes, BMC Evolutionary Biology, 6, 74, 10.1186/1471-2148-6-74 Locquin, 1984 Lücking, 2004, Phylogenetic relationships of Gomphillaceae and Asterothyriaceae: evidence from a combined Bayesian analysis of nuclear and mitochondrial sequences, Mycologia, 96, 283, 10.2307/3762064 Lumbsch, 2004, Supraordinal phylogenetic relationships of Lecanoromycetes based on Bayesian analysis of combined nuclear and mitochondrial sequences, Molecular Phylogenetics and Evolution, 31, 822, 10.1016/j.ympev.2003.11.001 Lumbsch, 2005, Performance of four ribosomal DNA regions to infer higher-level phylogenetic relationships of inoperculate euascomycetes (Leotiomyceta), Molecular Phylogenetics and Evolution, 34, 512, 10.1016/j.ympev.2004.11.007 Lumbsch, 2007, The phylogenetic placement of Ostropales within Lecanoromycetes (Ascomycota) revisited, Mycological Research, 111, 10.1016/j.mycres.2007.01.006 Lumbsch, 2002, Higher level phylogenetic relationships of euascomycetes (Pezizomycotina) inferred from a combined analysis of nuclear and mitochondrial sequence data, Mycological Progress, 1, 57, 10.1007/s11557-006-0005-z Lutzoni, 2004, Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits, American Journal of Botany, 91, 1446, 10.3732/ajb.91.10.1446 Manier, 1973, Quelques aspects ultrastructuraux du trichomycète asellariale, Asellaria ligae Tuzet et Manier, 1950 ex Manier, 1958, Comptes Rendu hebdomadaires des séances de l'Académie des Sciences de Paris, séries D, 276, 3429 Margulis, 1990 Matheny, 2007, Major clades of Agaricales: a multi-locus phylogenetic overview, Mycologia, 98, 984 Matheny, 2007, Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota, Canadian Journal of Botany, 84, 1794, 10.1139/b06-128 Matheny, 2006, Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi), Molecular Phylogenetics and Evolution 2001 2001 2006 Miądlikowska, 2007, New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes, Mycologia, 98, 1089 Miądlikowska, 2004, Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits, American Journal of Botany, 91, 449, 10.3732/ajb.91.3.449 Miller, 2004, A natural classification of Lasiosphaeria based on nuclear LSU rDNA sequences, Mycological Research, 108, 26, 10.1017/S0953756203008864 Miller, 2005, Multi-gene phylogenies indicate ascomal wall morphology is a better predictor of phylogenetic relationships than ascospore morphology in the Sordariales (Ascomycota, Fungi), Molecular Phylogenetics and Evolution, 35, 60, 10.1016/j.ympev.2005.01.007 Miller, 2007, Perspectives in the new Russulales, Mycologia, 98, 960, 10.3852/mycologia.98.6.960 Moncalvo, 2007, The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods, Mycologia, 98, 937, 10.3852/mycologia.98.6.937 Moncalvo, 2002, One hundred seventeen clades of euagarics, Molecular Phylogenetics and Evolution, 23, 357, 10.1016/S1055-7903(02)00027-1 Moore, 1980, Taxonomic proposals for the classification of marine yeasts and other yeast-like fungi including the smuts, Botanica Marina, 23, 361 Moore, 1990, Order Platygloeales ord. nov., Mycotaxon, 39, 245 Moreau, 1954 Morton, 1990, Revised classification of arbuscular mycorrhizal fungi (Zygomycetes): a new order, Glomales, two new suborders, Glomineae and Gigasporineae, and two new families, Acaulosporaceae and Gigasporaceae, with an emendation of Glomaceae, Mycotaxon, 37, 471 Moss, 1975, Septal structure in the Trichomycetes with special reference to Astreptonema gammari (Eccrinales), Transactions of the British Mycological Society, 65, 115, 10.1016/S0007-1536(75)80187-2 Nagahama, 2006, Phylogenetic relationship within the Erythrobasidium clade: molecular phylogenies, secondary structure, and intron positions inferred from partial sequences of ribosomal RNA and elongation factor-1α genes, Journal of General and Applied Microbiology, 52, 37, 10.2323/jgam.52.37 Nagahama, 1995, Phylogenetic divergence of the entomophthoralean fungi: evidence from nuclear 18S ribosomal RNA gene sequences, Mycologia, 87, 203, 10.2307/3760906 Nannfeldt, 1932, Studien über die Morphologie und Systematik der nicht-lichenisierten inoperculaten Discomyceten, Nova Acta Regiae Societatis Scientarum Upsaliensis, ser. 4, 8, 1 Nishida, 1994, Archiascomycetes: detection of a major new lineage within the Ascomycota, Mycoscience, 35, 361, 10.1007/BF02268506 Oberwinkler, 1976, Eine agaricoide Gattung der Thelephorales, Sydowia, 78, 359 Oberwinkler, 1977, Das neue System der Basidiomyceten, 59 Oberwinkler, 1982, A taxonomic survey of the gasteroid, auricularioid Heterobasidiomycetes, Canadian Journal of Botany, 60, 1726, 10.1139/b82-221 Oberwinkler, 1989, The systematics of gasteroid, auricularioid Heterobasidiomycetes, Sydowia, 41, 224 Oberwinkler, 1990, Cryptomycocolax: a new mycoparasitic heterobasidiomycete, Mycologia, 82, 671, 10.2307/3760154 O'Donnell, 1998, Phylogenetic relationships among the Harpellales and Kickxellales, Mycologia, 90, 286, 10.2307/3761222 Pang, 2002, Jahnulales (Dothideomycetes, Ascomycota): a new order of lignicolous freshwater ascomycetes, Mycological Research, 106, 1031, 10.1017/S095375620200638X Parmasto, 1986, On the origin of the hymenomycetes (what are corticioid fungi?), Windahlia, 16, 3 Peyretaillade, 1998, Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin, Molecular Biology and Evolution, 15, 683, 10.1093/oxfordjournals.molbev.a025971 Réblová, 2006, Molecular systematics of Ceratostomella sensu lato and morphologically similar fungi, Mycologia, 98, 68, 10.3852/mycologia.98.1.68 Réblová, 2004, New genera in the Calosphaeriales: Togniniella and its anamorph Phaeocrella, and Calosphaeriophora as anamorph of Calosphaeria, Studies in Mycology, 50, 533 Réblová, 2004, Cryptadelphia (Trichosphaeriales), a new genus for holomorphs with Brachysporium anamorphs and clarification of the taxonomic status of Wallrothiella, Mycologia, 96, 343, 10.2307/3762067 Reeb, 2004, Multilocus phylogenetic circumscription of the lichen-forming fungi family Acarosporaceae and its position within the Ascomycota, Molecular Phylogenetics and Evolution, 32, 1036, 10.1016/j.ympev.2004.04.012 Robbertse, 2006, A phylogenomic analysis of the Ascomycota, Fungal Genetics and Biology, 43, 715, 10.1016/j.fgb.2006.05.001 Rossman, 2004, The coelomycetous genera Chaetomella and Pilidium represent a newly discovered lineage of inoperculate discomycetes, Mycological Progress, 3, 275, 10.1007/s11557-006-0098-4 Ryvarden, 2002, A note on the genus Hydnodon Banker, Synopsis Fungorum, 15, 31 Saenz, 1999, Phylogenetic relationships of Meliola and Meliolina inferred from nuclear small subunit rRNA sequences, Mycological Research, 103, 1049, 10.1017/S0953756298008211 Saikawa, 1997, Electron microscopy of two trichomycetous fungi attached to the hindgut lining of pillbugs, Canadian Journal of Botany, 75, 1479, 10.1139/b97-862 Sampaio, 2003, Taxonomic studies in the Microbotryomycetidae: Leucosporidium golubevii sp. nov., Leucosporidiella gen. nov. and the new orders Leucosporidiales and Sporidiobolales, Mycological Progress, 2, 53, 10.1007/s11557-006-0044-5 Sampaio, 2004, Diversity, phylogeny and classification of basidiomycetous yeasts, 49 Schaffner, 1909, The classification of plants, IV, Ohio Naturalist, 9, 446 Schmitt, 2005, Ascoma morphology is homoplaseous and phylogenetically misleading in some pyrenocarpous lichens, Mycologia, 97, 362, 10.3852/mycologia.97.2.362 Schoch, 2007, A multigene phylogeny of the Dothideomycetes using four nuclear loci, Mycologia, 98, 1042 Schröter, 1889, Pilze, 382 Schröter, 1892, Phycomycetes, 63 Schröter, 1893, Monoblepharidineae, 106 Schröter, 1894, Pezizineae, 173 Schüßler, 2001, A new fungal phylum, the Glomeromycota: phylogeny and evolution, Mycological Research, 105, 1413, 10.1017/S0953756201005196 Seif, 2005, Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms, Nucleic Acids Research, 33, 734, 10.1093/nar/gki199 Serbinow, 1907, Organisazija I rasitie nekotorich gribow Chytridineae Schröt, Scripa Botanica Horti Universitatis Imperialis Petropolitana, 24, 1 Shenoy, 2006, Ribosomal and RPB2 DNA sequence analyses suggest that Sporidesmium and morphologically similar genera are polyphyletic, Mycological Research, 110, 916, 10.1016/j.mycres.2006.06.004 Sparrow, 1943 Sparrow, 1958, Interrelationships and phylogeny of the aquatic Phycomycetes, Mycologia, 50, 797, 10.2307/3755905 Spatafora, 2007, A five-gene phylogenetic analysis of the Pezizomycotina, Mycologia, 98, 1020 Sprague, 1998, Note on the name-author-date combination for the taxon Microsporidies Balbiani, 1882, when ranked as a phylum, Journal of Invertebrate Pathology, 71, 91, 10.1006/jipa.1997.4702 Starbäck, 1899, Ascomyceten der Ersten Regnellschen Expedition, Bihang till Kungliga Svenska Vetenskaps-Akademiens Handlingar, ser. 3, 25, 1 Steenkamp, 2006, The protistan origins of animals and fungi, Molecular Biology and Evolution, 23, 93, 10.1093/molbev/msj011 Sugiyama, 2007, Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas, Mycologia, 98, 998 Suh, 2007, Phylogenetics of Saccharomycetales, the ascomycete yeasts, Mycologia, 98, 1008 Swann, 2001, Urediniomycetes, 37 Swann, 1995, Phylogenetic perspectives on basidiomycete systematics: evidence from the 18S rRNA gene, Canadian Journal of Botany, 73, S862, 10.1139/b95-332 Takamatsu, 2004, Phylogeny and evolution of the powdery mildew fungi (Erysiphales, Ascomycota) inferred from nuclear ribosomal DNA sequences, Mycoscience, 45, 147, 10.1007/S10267-003-0159-3 Tanabe, 2000, Molecular phylogeny of parasitic Zygomycota (Dimargaritales, Zoopagales) based on nuclear small subunit ribosomal DNA sequences, Molecular Phylogenetics and Evolution, 16, 253, 10.1006/mpev.2000.0775 Tanabe, 2004, Molecular phylogeny of Zygomycota based on EF-1 and RPB1 sequences: limitations and utility of alternative markers to rDNA, Molecular Phylogenetics and Evolution, 30, 438, 10.1016/S1055-7903(03)00185-4 Tanabe, 2005, Evolutionary relationships among basal fungi (Chytridiomycota and Zygomycota): Insights from molecular phylogenetics, Journal of General and Applied Microbiology, 51, 267, 10.2323/jgam.51.267 Tang, 2007, Phylogenetic utility of protein (RPB2, B-tubulin) and ribosomal (LSU, SSU) gene sequences in the systematics of Sordariomycetes (Ascomycota, Fungi), Antonie van Leeuwenhoek, 10.1007/s10482-006-9120-8 Taylor, 2004, The fungi, 171 Tehler, 1988, A cladistic outline of the Eumycota, Cladistics, 4, 227, 10.1111/j.1096-0031.1988.tb00474.x Tehler, 2003, The full-length phylogenetic tree from 1551 ribosomal sequences of chitinous fungi, Fungi, Mycological Research, 107, 901, 10.1017/S0953756203008128 Thorn, 2000, Phylogenetic analyses and the distribution of nematophagy support a monophyletic Pleurotaceae within the polyphyletic pleurotoid-lentinoid fungi, Mycologia, 92, 241, 10.2307/3761557 Tibell, 2005, Chaenothecopsis in a molecular phylogeny based on nuclear rDNA ITS and LSU sequences, Taxon, 54, 427, 10.2307/25065370 Tibell, 2000, Mycocaliciales, a new order for nonlichenized calicioid fungi, Mycologia, 92, 577, 10.2307/3761518 Underwood, 1899 Vijaykrishna, 2004, Pleurostomophora, an anamorph of Pleurostoma (Calosphaeriales), a new anamorph genus morphologically similar to Phialophora, Studies in Mycology, 50, 387 Vossbrinck, 2005, Molecular phylogeny of the Microsporidia: ecological, ultrastructural and taxonomic considerations, Folia Parasitologica, 52, 131, 10.14411/fp.2005.017 Wagner, 2002, Proceedings towards a natural classification of the worldwide taxa Phellinus s.l. and Inonotus s.l., and phylogenetic relationships of allied genera, Mycologia, 94, 998, 10.2307/3761866 Walker, 2004, Nomenclatural clarifications and new taxa in the Glomeromycota, Mycological Research, 108, 981, 10.1017/S0953756204231173 Wang, 2006, Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): a nuclear rDNA phylogeny, Molecular Phylogenetics and Evolution, 41, 295, 10.1016/j.ympev.2006.05.031 Wang, 2007, Phylogenetic classification of the Leotiomycetes based on rDNA data, Mycologia, 98, 1066 Wedin, 2005, Phylogenetic relationships of Lecanoromycetes (Ascomycota) as revealed by analyses of mtSSU and nLSU rDNA sequence data, Mycological Research, 109, 159, 10.1017/S0953756204002102 Weir, 2001, Molecular data support the Laboulbeniales as a separate class of Ascomycota, Laboulbeniomycetes, Mycological Research, 105, 1182, 10.1016/S0953-7562(08)61989-9 Weiß, 2004, Spotlights on heterobasidiomycetes, 7 Weiß, 2001, Phylogenetic relationships in Auriculariales and related groups—hypotheses derived from nuclear ribosomal DNA sequences, Mycological Research, 105, 403, 10.1017/S095375620100363X Weiß, 2004, Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential, Mycological Research, 108, 1003, 10.1017/S0953756204000772 Wells, 2001, Heterobasidiomycetes, 85 White, 1990, Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, 315 White, 2007, Phylogeny of the Zygomycota based on nuclear ribosomal sequence data, Mycologia, 98, 872, 10.3852/mycologia.98.6.872 Whittaker, 1959, On the broad classification of organisms, Quarterly Review of Biology, 34, 210, 10.1086/402733 Wiklund, 2003, The phylogenetic relationships of the cyanobacterial lichens in the Lecanorales suborder Peltigerineae, Cladistics, 19, 419, 10.1111/j.1096-0031.2003.tb00312.x Wingfield, 1999, Phylogenetic relationships of ophiostomatoid fungi associated with Protea infrusctescences in South Africa, Mycological Research, 103, 1616, 10.1017/S0953756299008990 Winka K, 2000. Phylogenetic relationships within the Ascomycota based on 18S rDNA sequences. PhD thesis, Umeå University, Umeå. Winter, 1880, Schizomyceten, Saccharomyceten und Basidiomyceten Woronichin, 1925, Über die Capnodiales, Annales Mycologici, 23, 174 Zalar, 2005, Taxonomy and phylogeny of the xerophilic genus Wallemia (Wallemiomycetes and Wallemiales, cl. et ord. nov.), Antonie van Leeuwenhoek, 87, 311, 10.1007/s10482-004-6783-x Zhang, 2007, Sordariomycetes systematics: an overview of the systematics of the Sordariomycetes based on a four-gene phylogeny, Mycologia, 98, 1077