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Introduction to Systematic Biology-----Overview of Laboratory Methods------Overview of Fungal Systematics

III. Overview of Fungal Systematics, emphasizing Homobasidiomycetes


The higher-level phylogeny and Kingdom-level classification of eukaryotes has undergone dramatic changes:

  • In the Linnaean system, Fungi were included in the Plant Kingdom
  • The Linnaean 2 Kingdom system gave way to a 5-Kingdom system, in which fungi were in their own Kingdom
  • Small subunit rRNA analyses by Carl Woese demosntrated that there are three major domains of Life, of which two are prokaryotic
  • Molecular analyses within the eukaryotes indicate that the old Kingdom Protista is composed of many unique lineages
  • So, now we have a 3-domain/20+-Kingdom system
  • Fungi are not closely related to plants
  • The closest relative of the Fungi are the Animals, and Mycetozoa
  • Choanoflagellates are unicellular or colonial flagellated organisms that appear to be basal to the animals—compare to chytrids.

Some fungus-like organisms are no longer considered to be members of the true Fungi (Eumycota):

  • Oomycetes--include Phytophthora infestans, the causal agent of the Irish potato famine--now kown to be in the Stramenopila, with kelps and other "algae"
  • Slime molds--terrestrial heterotrophs that feed on bacteria--now in their own Kingdom, the Mycetozoa--unicellular or multicellular?

Some eukaryotes that were previously classified among the “Protista”, an artificial Kingdom, are now thought to be within the Fungi

  • Microsporidia--intracellular parasites of aquatic arthropods. Microsporidia lack mitochondria and were once thought to be very primitve eukaryotes—i.e., eukaryotes that evolved before the acquisition of mitochondria—now it appears that they lost their mitochondria secondarily.
  • Pneumocystis carinii--pathogen that infects lung tissue in mammals--a serious pathogen of AIDS patients

Recall that within the Fungi, four major groups ("Phyla") have been traditionally recognized, based largely on the structure of cells involved in production of spores by meiosis:

  • Chytridiomycota--"chytrids"
  • Zygomycota--"zygomycetes"--"pin fungi"
  • Ascomycota--"ascomycetes"--"cup fungi"
  • Basidiomycota--"basidiomycetes"--"gill fungi" or "club fungi"

Chytrids and zygomycetes are probably not monophyletic—they are part of the cluster of "basal fungal lineages"—this implies that there may have been more than one loss of flagella in the evolution of the Fungi.

Basidiomycota and Ascomycota are monophyletic and are sister groups

Homobasidiomycetes--"mushroom forming fungi"

  • Ca. 17,000 described species
  • The 18th centry “Friesian system” divided macrofungi according to gross morphology—in particular the form of the hymenophore (spore-producing structures). Thus, the Agaricales included all gilled fungi; Aphyllophroales included all non-gilled fungi (divided into poroid forms, toothed forms, etc); and the Gasteromycetes included all macrofungi with internal spore production.
  • Anatomical features (e.g., spore forms) suggested that Friesian system is artificial, and led to major rearragements, but the paucity of anatomical characters led to extensive taxonomic disagreements.
  • Molecular characters have provided a higher-level phylogenetic framework for homobasidiomcyetes, and have resolved many controversies. Many anatomy-based hypotheses have been upheld, many others have been refined or refuted.
  • Major “Friesian” forms have been shown to have evolved repeatedly—e.g., agarics (with cap and gills) and resupinate forms (crust-like flattened forms)<
  • We now think that there are approximately eight major clades and several minor clades of homobasidiomycetes, each containing strikingly dissimilar forms.


Examples of major clades of homobasidiomycetes recognized with molecular characters:

  • Euagarics clade
  • Ca. 8000 species
  • Mostly gilled mushrooms, also puffballs, coral fungi, even a few marine mushrooms

Exemplar families:

Amanitaceae—large family of ectomycorrhizal fungi, including some of the most deadly poisonous taxa. Includes Amanita, Limacella.Tricholomataceae—polyphyletic assemblage of white spored mushrooms with gills. Includes Megacollybia, Tricholoma, Mycena, Gymnopus and many others.Agaricaceae—includes edible button mushroom, Agaricus, and others.

  • Bolete clade
  • Ca 840 species
  • Mostly stalked poroid forms (boletes) but also some puffballs, resupiante forms, etc.
  • Mostly ectomycorrhizal, a few wood decayers

Exemplar genera: Xanthocomium, Tylopilus

  • Russuloid clade
  • Ca. 1000 species
  • Morphologically very diverse—many gilled forms, but also coral fungi, polypores, resupinate forms, etc

Exemplar families:
Russulaceae—large family of ectomycorrhizal mushrooms. Includes Russula.
Hericiaceae—morphologically variable family of wood decay fungi

  • Polyporoid clade
  • Ca 1350 species
  • Mostly wood-decaying polypores, also resupinate forms. Ecologically important in carbon cycle
  • No ectomycorrhizal taxa in this group

Exemplar genera:Oligoporus, Polyporus, Lentinus, Phanerochaete

  • Thelephoroid clade
  • Ca. 240 species
  • Morpholgically variable, many resupinate forms, also poroid, toothed, and coralloid forms
  • All ectomycorrhizal

Exemplar genera:Sarcodon, Thelephora

  • Gomphoid-phalloid clade
  • Ca 350 species
  • Morphology is very diverse in this relatively small group: coral fungi, earthstars, gilled mushrooms (including ‘chanterelles’), false truffles, cannon ball fungus, stinkhorns, etc

Exemplars:Cantharellus (chanterelles), Phallus, Ramaria, Sphaerobolus


Taylor, J. W., J. Spatafora, K. O’Donnell, F. Lutzoni, T. James, D. S. Hibbett, D. Geiser, T. D. Bruns, and M. Blackwell. The Kingdom Fungi. In:Assembling the Tree of Life [tentative title] (J. Cracraft and M. J. Donoghue, eds.) American Museum of Natural History. In press. This book, when it is finally published, should provide a good overview of the current knowledge of the phylogeny of life, not just fungi.

Hibbett, D. S., and R. G. Thorn. 2001. Basidiomycota: Homobasidiomycetes. Pp. 121-168 in: The Mycota, vol. VII part B, Systematics and Evolution (D. J. McLaughlin, E. G. McLaughlin, and P. A. Lemke, eds.). Springer Verlag. This is a rather technical review of homobasidiomycete systematics. Unfortunately, there are no non-technical reviews of this subject that I am aware of.

Hibbett, D. S., E. M. Pine, E. Langer, G. Langer, and M. J. Donoghue. 1997. Evolution of gilled mushrooms and puffballs inferred from ribosomal DNA sequences. Proceedings of the National Academy of Sciences, U.S.A. 94: 12002-12006.

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All content © 2005 AFTOL (Assembling the Fungal Tree of Life Project). Website managed by Jason Slot. AFTOL logo designed by Michal Skakuj. Contact Dr. David Hibbett with any questions. This page was last modified on 08/31/05. Development of this site is being supported by a grant from the National Science Foundation for research in fungal evolutionary biology (NSF award number DEB-0228657).