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

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 relatio...

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Published inMicrobiology spectrum Vol. 5; no. 5
Main Authors Spatafora, Joseph W., Aime, M. Catherine, Grigoriev, Igor V., Martin, Francis, Stajich, Jason E., Blackwell, Meredith
Format Journal Article
LanguageEnglish
Published United States ASM Press 01.10.2017
American Society for Microbiology
Subjects
Animals
Classification
Eukaryotes: Fungi and Parasitology
Evolution, Molecular
Fungi
Fungi - classification
Fungi - genetics
Fungi - isolation & purification
Genome, Fungal
Phylogeny
Plants - microbiology
Online AccessGet full text
ISSN2165-0497
2165-0497
DOI10.1128/microbiolspec.FUNK-0053-2016

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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.
AbstractList 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.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.
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.
Author Blackwell, Meredith
Grigoriev, Igor V.
Stajich, Jason E.
Spatafora, Joseph W.
Martin, Francis
Aime, M. Catherine
Author_xml – sequence: 1
  givenname: Joseph W.
  surname: Spatafora
  fullname: Spatafora, Joseph W.
  organization: Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
– sequence: 2
  givenname: M. Catherine
  surname: Aime
  fullname: Aime, M. Catherine
  organization: Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907
– sequence: 3
  givenname: Igor V.
  surname: Grigoriev
  fullname: Grigoriev, Igor V.
  organization: U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598
– sequence: 4
  givenname: Francis
  surname: Martin
  fullname: Martin, Francis
  organization: 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
– sequence: 5
  givenname: Jason E.
  surname: Stajich
  fullname: Stajich, Jason E.
  organization: Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California–Riverside, Riverside, CA 92521
– sequence: 6
  givenname: Meredith
  surname: Blackwell
  fullname: Blackwell, Meredith
  organization: Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803 and Department of Biological Sciences, University of South Carolina, Columbia, SC 29208
BackLink https://www.ncbi.nlm.nih.gov/pubmed/28917057$$D View this record in MEDLINE/PubMed
https://www.osti.gov/biblio/1619079$$D View this record in Osti.gov
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Copyright 2017 American Society for Microbiology. All rights reserved.
2017 American Society for Microbiology. All rights reserved. 2017 American Society for Microbiology
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– notice: 2017 American Society for Microbiology. All rights reserved. 2017 American Society for Microbiology
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DocumentTitleAlternate Spatafora et al., The Fungal Tree of Life
Spatafora et al
EISSN 2165-0497
Editor Heitman, Joseph
James, Timothy Y.
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Snippet The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from...
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SubjectTerms Animals
Classification
Eukaryotes: Fungi and Parasitology
Evolution, Molecular
Fungi
Fungi - classification
Fungi - genetics
Fungi - isolation & purification
Genome, Fungal
Phylogeny
Plants - microbiology
Title The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies
URI https://www.ncbi.nlm.nih.gov/pubmed/28917057
https://journals.asm.org/doi/10.1128/microbiolspec.funk-0053-2016
https://www.proquest.com/docview/1940051639
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https://pubmed.ncbi.nlm.nih.gov/PMC11687545
Volume 5
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