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The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies

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  • Authors: Joseph W. Spatafora1, M. Catherine Aime2, Igor V. Grigoriev3, Francis Martin4, Jason E. Stajich5, Meredith Blackwell6
  • Editors: Joseph Heitman7, Timothy Y. James8
    Affiliations: 1: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331; 2: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907; 3: U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598; 4: Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Interactions Arbres/Microorganismes, Laboratoire d’Excellence Recherches Avancés sur la Biologie de l’Arbre et les Ecosystèmes Forestiers (ARBRE), Centre INRA-Lorraine, 54280 Champenoux, France; 5: Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California–Riverside, Riverside, CA 92521; 6: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208; 7: Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710; 8: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048
  • Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016
  • Received 06 June 2017 Accepted 11 June 2017 Published 15 September 2017
  • Joseph W. Spatafora, [email protected]
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  • Abstract:

    The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

  • Citation: Spatafora J, Aime M, Grigoriev I, Martin F, Stajich J, Blackwell M. 2017. The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. Microbiol Spectrum 5(5):FUNK-0053-2016. doi:10.1128/microbiolspec.FUNK-0053-2016.


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The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

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Fungal tree of life. Cladogram of the kingdom Fungi based on published multi-gene and genome-scale phylogenies ( 11 14 , 17 , 18 , 32 , 33 , 83 , 98 , 109 , 112 , 167 , 168 ). Polytomies represent regions of the tree currently unresolved by molecular and genomic data.

Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016
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Examples of zoosporic fungal diversity. (Cryptomycota) parasitizing hyphae of (Blastocladiomycota). Chytridiomycota: (Chytridiomycetes) monocentric, operculate zoosporangium with rhizoids; sp. (Chytridiomycetes) monocentric, operculate zoosporangium with rhizoids; (Monoblepharidomycetes) mature zygote or oospore, empty and mature antheridia and antherozoids or male gametes emerging from antheridium (by Marilyn M. N. Mollicone); sp. (Neocallimastigomycetes) monocentric thallus with rhizoids (by Gary Easton); () zoospores (photo by D’Ann Rochon); sp. (Neocallimastigomycetes) multiflagellate zoospores (photo by Gary Easton).

Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016
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Examples of zygomycete fungal diversity. Zoopagomycota: adult fly infected by a species of Entomophthorales; conidium; conidia; thallus with trichospores (photo by R.W. Lichtwardt); sporangium; sporangium; sporangium; sporangium. Mucoromycota: spore (photo from American Society for the Advancement of Science); sporocarp (photo by D. Redeker); arbuscule (photo by K. Wex); sporangium; sporangium; sporangium; sporangium; sporangium; zygosporangium; zygosporangium; sporocarp, zygospore (inset).

Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016
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Examples of Ascomycota diversity. Apothecia (yellow) of , Orbiliomycetes (J. H. Petersen/MycoKey). Apothecia of , Pezizomycetes (J. H. Petertsen/MycoKey). Thallus of with apothecia, Lecanoromycetes (B. McCune, Oregon State University). Thallus of , Lichinomycetes (B. McCune, Oregon State University). Bitunicate asci of , Dothideomycetes (S. Huhndorf, Field Museum). Thallus of with apothecia, Arthoniomycetes (B. McCune, Oregon State University). Thallus of , Laboulbeniomycetes (A. Weir, SUNY-ESF). Perithecia of , Sordariomycetes (N. B. Raju, Stanford University). Earth-tongue apothecia of , Leotiomycetes (Z. Wang, Iowa State University). Cleistothecia of , Eurotiomycetes (D. Geiser, Penn State University). Operculate ascus of (J. H. Petersen/MycoKey). Ascostroma of , Dothideomycetes (T. Volk, University of Wisconsin at La Crosse). Unitunicate asci (N. B. Raju, Stanford University). Prototunicate ascus of (D. Geiser, Penn State University).

Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016
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Examples of Basidiomycota diversity. Pucciniomycotina: uredinia of ; fruiting body of ; aecia of ; yeast state of . Ustilaginomycotina: smut galls of ; gall of ; culture of sp. Agaricomycotina: culture of ; stinkhorn fruiting body of (photo by Nu Nguyen). coral fruiting body of ; crust fruiting body of ; club fruiting body of ; polypore, conk fruiting body of ; gilled mushroom fruiting body of ; pored mushroom fruiting body of ; puffball fruiting body of .

Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016
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Classification of the kingdom Fungi

Source: microbiolspec September 2017 vol. 5 no. 5 doi:10.1128/microbiolspec.FUNK-0053-2016

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