Skip to main content
SpringerLink
Log in

Recent Developments in the Molecular Taxonomy of Fungi

  • Chapter
  • First Online:
Physiology and Genetics

Part of the book series: The Mycota ((MYCOTA,volume 15))

Abstract

Chapter 1: This chapter gives an up-to-date account of the taxonomy of fungi, referring to the recent AFTOL (‘assembling the fungal tree of life') scheme. For each group, changes proposed since the publication of Mycota VIIA and VIIB in 2001 are discussed. Considerations include groups which no longer belong to the Fungi in a taxonomic sense, but continue to be studied by mycologists. Although AFTOL has potential to become the first global taxonomic scheme for fungi, there are several factors which could destabilise it. Likely or possible problem cases are indicated. This as indeed any previous ‘natural’ (i.e. phylogeny-based) classification scheme of fungi has grouped together biologically dissimilar species whilst separating others which show striking similarities in their life styles or morphologies. The impact of such rearrangements for the teaching of mycology is discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 229.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Adl S, et al (2005) The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. J Eukaryot Microbiol 52:399–451

    Article  PubMed  Google Scholar 

  • Adl S, et al (2007) Diversity, nomenclature, and taxonomy of protists. Syst Biol 56:684–689

    Article  PubMed  Google Scholar 

  • Aime MC, Matheny PB, Henk DA, Frieders EM, Nilsson RH, Piepenbring M, McLaughlin DJ, Szabo LJ, Begerow D, Sampaio JP, Bauer R, Weiss M, Oberwinkler F, Hibbett D (2006) An overview of the higher-level classification of Pucciniomycotina based on combined analyses of nuclear large and small subunit rDNA sequences. Mycologia 98:869–905

    Article  Google Scholar 

  • Alexopoulos CJ, Mims CW, Blackwell M (1996) Introductory mycology, fourth edn. Wiley, New York

    Google Scholar 

  • Archibald JM, Keeling PJ (2004) Actin and ubiquitin protein sequences support a cercozoan/foraminiferan ancestry for the plasmodiophorid plant pathogens. J Eukaryot Microbiol 51:113–118

    Article  CAS  PubMed  Google Scholar 

  • Baldauf SL, Roger AJ, Wenk-Siefert I, Doolittle WF (2000) A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972–977

    Article  CAS  PubMed  Google Scholar 

  • Bauer R, Oberwinkler F, Vánky K (1997) Ultrastructural markers and systematics in smut fungi and allied taxa. Can J Bot 75:1273–1314

    Article  Google Scholar 

  • Bauer R, Begerow D, Sampaio JP, Weiss M, Oberwinkler F (2006) The simple-septate basidiomycetes: a synopsis. Mycol Progr 5:41–66

    Article  Google Scholar 

  • Begerow D, Bauer R, Oberwinkler F (1997) Phylogenetic studies on the nuclear large subunit ribosomal DNA of smut fungi and related taxa. Can J Bot 75:2045–2056

    Article  CAS  Google Scholar 

  • Begerow M, Bauer R, Oberwinkler F (2002) The Exobasidiales: an evolutionary hypothesis. Mycol Prog 1:187–199

    Article  Google Scholar 

  • Begerow D, Stoll M, Bauer R (2006) A phylogenetic hypothesis of Ustilaginomycotina based on multiple gene analyses and morphological data. Mycologia 98:906–916

    Article  PubMed  Google Scholar 

  • Berbee ML, Taylor JW (2001) Fungal molecular evolution: gene trees and geologic time. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The Mycota VIIB: systematics and evolution. Springer, Heidelberg, pp 229–245

    Google Scholar 

  • Binder M, Hibbett DS (2006) Molecular systematics and biological diversification of Boletales. Mycologia 98:971–981

    Article  PubMed  Google Scholar 

  • Binder M, Hibbett DS, Larsson K-H, Larsson E, Langer E, Langer G (2005) The phylogenetic distribution of resupinate forms across the major clades of mushroom-forming fungi (Homobasidiomycetes). Syst Biodiv 3:113–157

    Article  Google Scholar 

  • Blackwell M, Hibbett DS, Taylor JW, Spatafora JW (2006) Research coordination networks: a phylogeny for kingdom Fungi (Deep Hypha). Mycologia 98:829–837

    Article  PubMed  Google Scholar 

  • Cafaro M (2005) Eccrinales (Trichomycetes) are not fungi, but a clade of protists at the early divergence of animals and fungi. Mol Phylogen Evol 35:21–34

    Article  CAS  Google Scholar 

  • Dick MW (2001) Straminipilous fungi. Kluwer, Dordrecht

    Google Scholar 

  • Eriksson OE, Winka K (1997) Supraordinal taxa of the Ascomycota. Myconet 1:1–16

    Google Scholar 

  • Fast NM, Xue L, Bingham S, Keeling PJ (2002) Re-examining alveolate evolution using multiple protein molecular phylogenies. J Eukaryot Microbiol 49:30–37

    Article  CAS  PubMed  Google Scholar 

  • Fell JW, Boekhout T, Fonseca A, Sampaio JP (2001) Basidiomycetous yeasts. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The Mycota VIIB: systematics and evolution. Springer, Heidelberg, pp 3–35

    Google Scholar 

  • Geiser DM, LoBuglio KF (2001) The monophyletic Plectomycetes: Ascosphaerales, Onygenales, Eurotiales. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The Mycota VIIA: systematics and evolution. Springer, Heidelberg, pp 201–219

    Google Scholar 

  • Geiser DM, Gueidan C, Miadlikowska J, Lutzoni F, Kauff F, Hofstetter V, Fraker E, Schoch CL, Tibell L, Untereiner WA, Aptroot A (2006) Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae. Mycologia 98:1953–1064

    Article  Google Scholar 

  • Hakariya M, Hirose D, Tokumasu S (2007) A molecular phylogeny of Haptoglossa species, terrestrial peronosporomycetes (oomycetes) endoparasitic on nematodes. Mycoscience 48:169–175

    Article  CAS  Google Scholar 

  • Hansen K, Pfister DH (2006) Systematics of the Pezizomycetes – the operculate discomycetes. Mycologia 98:1029–1040

    Article  CAS  PubMed  Google Scholar 

  • Hibbett DS (2006) A phylogenetic overview of the Agaricomycotina. Mycologia 98:917–925

    Article  PubMed  Google Scholar 

  • Hibbett DS, Thorn RG (2001) Basidiomycota: Homobasidiomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The Mycota VIIB: systematics and evolution. Springer, Heidelberg, pp 121–168

    Google Scholar 

  • Hibbett DS, Pine EM, Langer E, Langer G, Donoghue MJ (1997) Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proc Natl Acad Sci USA 94:12002–12006

    Article  CAS  PubMed  Google Scholar 

  • Hibbett DS, et al (2007) A higher-level phylogenetic classification of the Fungi. Mycol Res 111:509–547

    Article  PubMed  Google Scholar 

  • Hosaka K, Bates ST, Beever RE, Castellano MA, Colgan W, Domínguez LS, Nouhra ER, Geml J, Giachini AJ, Kenney SR, Simpson NB, Spatafora JW, Trappe J (2006) Molecular phylogenetics of the gomphoid–phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders. Mycologia 98:949–959

    Article  CAS  PubMed  Google Scholar 

  • Hudspeth DSS, Stenger D, Hudspeth MES (2003) A cox2 phylogenetic hypothesis for the downy mildews and white rusts. Fungal Divers 13:47–57

    Google Scholar 

  • Inagaki Y, Susko E, Fast NM, Roger AJ (2004) Covarion shifts cause a long-branch attraction artifact that unites Microsporidia and Archaebacteria in EF-1α phylogenies. Mol Biol Evol 21:1340–1349

    Article  CAS  PubMed  Google Scholar 

  • James TY, et al (2006a) Reconstructing the early evolution of fungi using a six-gene phylogeny. Nature 443:818–822

    Article  CAS  Google Scholar 

  • James TY, Letcher PM, Longcore JE, Mozley-Standridge SE, Powell MJ, Griffith GW, Vilgalys R (2006b) A molecular phylogeny of the flagellated fungi (Chytridiomycota) and description of a new phylum (Blastocladiomycota). Mycologia 98:860–871

    Article  Google Scholar 

  • Keeling PJ, Fast NM (2002) Microsporidia: biology and evolution of highly reduced intracellular parasites. Annu Rev Microbiol 56:93–116

    Article  CAS  PubMed  Google Scholar 

  • Keeling PJ, Luker MA, Palmer JD (2000) Evidence from beta-tubulin phylogeny that Microsporidia evolved from within the Fungi. Mol Biol Evol 17:23–31

    CAS  PubMed  Google Scholar 

  • Keeling PJ, Burger G, Durnford DG, Lang BF, Lee RW, Pearlman RE, Roger AJ, Gray MW (2005) The tree of eukaryotes. Trends Ecol Evol 20:670–676

    Article  PubMed  Google Scholar 

  • Kessin RH (2001) Dictyostelium. Evolution, cell biology, and the evolution of multicellularity. Cambridge University Press, Cambridge

    Book  Google Scholar 

  • Kirk PM, Cannon PF, David JC, Stalpers JA (eds) (2001) Ainsworth and Bisby's dictionary of the fungi, 9th edn. CABI, Wallingford

    Google Scholar 

  • Kurtzman CP, Sugiyama J (2001) Ascomycetous yeasts and yeastlike taxa. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The mycota VIIA: systematics and evolution. Springer, Heidelberg, pp 179–200

    Google Scholar 

  • Larsson K-H, Parmasto E, Fischer M, Langer E, Nakasone KK, Redhead SA (2006) Hymenochaetales: a molecular phylogeny for the hymenochaetoid clade. Mycologia 98:926–936

    Article  PubMed  Google Scholar 

  • Liu YJ, Hodson MC, Hall BD (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 Evol Biol 6:74

    Article  CAS  PubMed  Google Scholar 

  • Lutz M, Bauer R, Begerow D, Oberwinkler F (2004) Tuberculina – Thanatophytum/Rhizoctonia crocorum – Helicobasidium: a unique mycoparasitic–phytoparasitic life strategy. Mycol Res 108:227–238

    Article  PubMed  Google Scholar 

  • Matheny PB, et al (2006) Major clades of Agaricales: a multilocus phylogenetic overview. Mycologia 98:982–995

    Article  PubMed  Google Scholar 

  • Matheny PB, et al (2007) Contributions of rpb1 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Mol Phylogen Evol 43:430–451

    Article  CAS  Google Scholar 

  • McLaughlin DJ, McLaughlin EG, Lemke PA (eds) (2001) The mycota VIIA, VIIB: systematics and evolution. Springer, Heidelberg

    Google Scholar 

  • Miadlikowska J, et al (2006) New insights into classification and evolution od the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-encoding genes. Mycologia 98:1088–1103

    Article  CAS  PubMed  Google Scholar 

  • Miller SL, Larsson E, Larsson K-H, Verbeken A, Nuytinck J (2006) Perspectives in the new Russulales. Mycologia 98:960–970

    Article  PubMed  Google Scholar 

  • Moncalvo J-M, Vilgalys R, Redhead SA, Johnson JE, James TY, Aime MC, Hofstetter V, Verduin SJW, Larsson E, Baroni TJ, Thorn RG, Jacobsson S, Clémençon H, Miller OK (2002) One hundred and seventeen clades of euagarics. Mol Phylogen Evol 23:357–400

    Article  CAS  Google Scholar 

  • Moncalvo J-M, Nilsson RH, Koster B, Dunham SM, Bernauer T, Matheny PB, Porter TM, Margaritescu S, Weiss M, Garnica S, Danell E, Langer G, Langer E, Larsson E, Larsson K-H, Vilgalys R (2006) The cantharelloid clade: dealing with incongruent gene trees and phylogenetic reconstruction methods. Mycologia 98:937–948

    Article  PubMed  Google Scholar 

  • Morton JB, Benny GL (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 37:471–491

    Google Scholar 

  • Nishida H, Sugiyama J (1994) Archiascomycetes: detection of a major new lineage within the Ascomycota. Mycoscience 35:361–366

    Article  Google Scholar 

  • Redecker D, Raab P (2006) Phylogeny of the Glomeromycota (arbuscular mycorrhizal fungi): recent developments and new gene markers. Mycologia 98:885–895

    Article  PubMed  Google Scholar 

  • Riethmüller A, Voglmayr H, Göker M, Weiss M, Oberwinkler F (2002) Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences. Mycologia 94:834–849

    Article  PubMed  Google Scholar 

  • Samuels GJ, Blackwell M (2001) Pyrenomycetes – fungi with perithecia. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The mycota VIIA: systematics and evolution. Springer, Heidelberg, pp 221–255

    Google Scholar 

  • Schoch CL, Shoemaker RA, Seifert KA, Hambleton S, Spatafora JW, Crous PW (2006) A multigene phylogeny of the Dothideomycetes using four nuclear loci. Mycologia 98:1041–1052

    Article  CAS  PubMed  Google Scholar 

  • Schüssler A, Schwarzott D, Walker C (2001) A new fungal phylum, the Glomeromycota: phylogeny and evolution. Mycol Res 105:1413–1421

    Article  Google Scholar 

  • Simpson AGB, Roger AJ (2004) The real ‘kingdoms’ of eukaryotes. Curr Biol 14:R693–R696

    Article  CAS  PubMed  Google Scholar 

  • Spatafora JW, et al (2006) A five-gene phylogeny of Pezizomycotina. Mycologia 98:1018–1028

    Article  CAS  PubMed  Google Scholar 

  • Sugiyama J, Hosaka K, Suh S-U (2006) Early diverging Ascomycota: phylogenetic divergence and related evolutionary origins. Mycologia 98:996–1005

    Article  PubMed  Google Scholar 

  • Suh S-O, Blackwell M, Kurtzman CP, Lachance M-A (2006) Phylogenetics of Saccharomycetales, the ascomycete yeasts. Mycologia 98:1006–1017

    Article  CAS  PubMed  Google Scholar 

  • Swann EC, Taylor JW (1993) Higher taxa of basidiomycetes: an 18S rRNA perspective. Mycologia 85:923–936

    Article  CAS  Google Scholar 

  • Swann EC, Frieders EM, McLaughlin DJ (2001) Urediniomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The mycota VIIB: systematics and evolution. Springer, Heidelberg, pp 37–56

    Google Scholar 

  • Tanabe Y, Watanabe MM, Sugiyama J (2002) Are Microsporidia really related to Fungi? A reappraisal based on additional gene sequences from basal fungi. Mycol Res 106:1380–1391

    Article  CAS  Google Scholar 

  • Tanabe Y, Saikawa M, Watanabe MM, Sugiyama J (2004) Molecular phylogeny of Zygomycota based on EF-1α and RPB1 sequences: limitations and utility of alternative markers to rDNA. Mol Phylogen Evol 30:438–449

    Article  CAS  Google Scholar 

  • Thines M, Göker M, Telle S, Ryley M, Mathur K, Narayana YD, Spring O, Thakur RP (2008) Phylogenetic relationships of graminicolous downy mildews based on cox2 sequence data. Mycol Res 112:345–351

    Article  CAS  PubMed  Google Scholar 

  • Tsuneda A, Currah RS (2004) Ascomatal morphogenesis in Myxotrichum arcticum supports the derivation of Myxotrichaceae from a discomycetous ancestor. Mycologia 96:627–635

    Article  CAS  PubMed  Google Scholar 

  • Ustinova I, Krienitz L, Huss VAR (2000) Hyaloraphidium curvatum is not a green alga, but a lower fungus; Amoebidium parasiticum is not a fungus, but a member of the DRIPs. Protist 151:253–262

    Article  CAS  PubMed  Google Scholar 

  • Villa NO, Kageyama K, Asano T, Suga H (2006) Phylogenetic relationships of Pythium and Phytophthora species based on ITS rDNA, cytochrome oxidase II and β-tubulin gene sequences. Mycologia 98:410–422

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Johnston PR, Takamatsu S, Spatafora JW, Hibbett DS (2006) Toward a phylogenetic classification of the Leotiomycetes based on rDNA data. Mycologia 98:1065–1075

    Article  CAS  PubMed  Google Scholar 

  • Webster J, Weber RWS (2007) Introduction to fungi, 3rd edn. Cambridge University Press, Cambridge

    Google Scholar 

  • Weiss M, Selosse M-A, Rexer K-H, Urban A, Oberwinkler F (2004) Sebacinales: a hitherto overlooked cosm of heterobasidiomycetes with a broad mycorrhizal potential. Mycol Res 108:1003–1010

    Article  PubMed  Google Scholar 

  • Wells K, Bandoni RJ (2001) Heterobasidiomycetes. In: McLaughlin DJ, McLaughlin EG, Lemke PA (eds) The mycota VIIB: systematics and evolution. Springer, Heidelberg, pp 86–120

    Google Scholar 

  • White MW, James TY, O'Donnell K, Cafaro MJ, Tanabe Y, Sugiyama J (2006) Phylogeny of the Zygomycota based on nuclear ribosomal sequence data. Mycologia 98:872–884

    Article  PubMed  Google Scholar 

  • Zhang N, Castlebury LA, Miller AN, Huhndorf SM, Schoch CL, Seifert KA, Rossman AY, Rogers JD, Kohlmeyer J, Volkmann-Kohlmeyer B, Sung G-H (2006) An overview of the systematics of the Sordariomycetes based on a four-gene phylogeny. Mycologia 98:1076–1087

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Obstbau Versuchs- und Beratungszentrum/Fruit Research and Advisory Centre (OVB) Jork, Moorende 53, 21635, Jork, Germany

    Roland W.S. Weber

Authors
  1. Roland W.S. Weber
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Roland W.S. Weber .

Editor information

Editors and Affiliations

  1. Inst. Biotechnologie und, TU Kaiserslautern, Erwin-Schrödinger-Str. 56, Kaiserslautern, 67663, Germany

    Timm Anke

  2. MIP Pharma GmbH, Mühlstr. 50, St.Ingbert, 66386, Germany

    Daniela Weber

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Weber, R.W. (2009). Recent Developments in the Molecular Taxonomy of Fungi. In: Anke, T., Weber, D. (eds) Physiology and Genetics. The Mycota, vol 15. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-00286-1_1

Download citation

Publish with us

Policies and ethics

Search

Navigation