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Since Carolus Linnaeus developed the system of biological classification we still use today, biologists have struggled to develop a good working definition of fungi. Fungi were not even placed into their own kingdom until the twentieth century. Today, most taxonomists prefer definitions based heavily or entirely on phylogeny, the evolutionary history and relationships of organisms. Yet little attention has been paid to working out a definition of this diverse kingdom based on fungi phylogeny.
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Defining Organisms Using Phylogeny
When defining a group of organisms using phylogeny, two major approaches are the apomorphy-based definition and the phylospace-based (or simply "phylogenetic") definition.
A definition based on apomorphies would define the group based on its unique characteristics, ones not shared with any other groups. While such a definition is based on phylogeny, it does not provide any information about the group's position on the Tree of Life.
A definition based on a group's position in "phylospace" (that is, its position among the branches of the Tree of Life) is more useful to science because it includes information about evolutionary relationships.
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Groups of Fungi
Fungi are closely related to animals, at least more closely than either is related to plants. There are other groups whose potential inclusion within Fungi has been debated.
The placement of the two groups of "higher" fungi is secure; these are the Ascomycota (truffles, lichens, morels, and most yeasts including those used in brewing and bakery) and the Basidiomycota (mushrooms, puffballs, smuts, rusts, and certain yeasts). Trichomycetes are fungi that are obligate symbiotes of insects, usually commensal (that is, harmless but not helpful to the host) but sometimes parasitic.
The highly simplified, single-celled, parasitic Microsporidia are now generally placed within Fungi as well. The most basal (primitive) group now generally placed within Fungi is the Chytridiomycota; these are the organisms thought to be responsible for the decline of some frogs and other amphibians worldwide.
Most slime molds (Mycetozoa and several other groups) share a more recent common ancestor with plants than with fungi and animals, so they should not be included within Fungi on the basis of phylogeny. One group of slime molds, the Phytomyxea, predates the last common ancestor of plants and animals-fungi, so they should not be included within Fungi either.
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A Phylogenetic Definition of Fungi
A phylogenetic definition of fungi should indicate their place on the Tree of Life, the phylogeny tree for all living organisms. If Microsporidia and Chytridiomycota are included within Fungi, then the closest sister group is Metazoa (animals). So a phylogenetic definition would be "all organisms closer to mushrooms than to animals." The phylogeny website Palaeos drolly puts this "toadstools > toads" (that is, all organisms closer to toadstools than to toads).
Apomorphy-based definitions of fungi, ones which list characteristics shared (or secondarily lost) by all fungi but not found in any other group, are difficult and clumsy due to the great diversity of Fungi. Phylogeny is a good, simple way to define this widely variable group.