Chapter 3 : What Defines the “Kingdom” Fungi?

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It is a certainty that the tree of life can be broken up into large units of biodiversity that span such great evolutionary distances that one could call them kingdoms. However, if these units are to have any meaning, they must represent radiations of diverse groups underpinned by unique shared derived adaptations that drove the evolutionary success of each group. Without such evolutionary characters, these classifications are merely abstract concepts or arbitrarily demarcated lineages. Even the five kingdoms (commonly called plants, animals, fungi, protists, and prokaryotes) that gained popular acceptance from Whittaker ( ) were abstractly defined and nonmonophyletic. These kingdoms were defined based on cellular organization (prokaryote or eukaryote), multicellularity (protist or “higher” eukaryote), and trophic level (producer [plants], consumer [animals], or decomposer [fungi]). Somewhat more phylogenetically sound definitions ( ) have replaced these classifications, but the names, defining characters, and number of kingdoms are still not settled (e.g., ).

Citation: Richards T, Leonard G, Wideman J. 2017. What Defines the “Kingdom” Fungi?, p 57-77. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0044-2017
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Figure 1

Diversity and distribution of gene families known to function in chitin cell wall synthesis or remodeling. The diversity of domain architectures (as identified using PFAM [ ]) for chitin cell wall synthesis or remodeling gene families. Note the gene fusion between a myosin head domain motor protein and a chitin synthase which was previously suggested to be fungus-specific ( ). The taxonomic distribution of putative homologues across a subset of eukaryotic taxa identified using a custom-built set of domain-specific hidden Markov models kindly provided by Jason Stajich and Divya Sain ( ). The fungal component of the phylogenetic tree is based on Spatafora et al. ( ).

Citation: Richards T, Leonard G, Wideman J. 2017. What Defines the “Kingdom” Fungi?, p 57-77. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0044-2017
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Figure 2

Diversity and distribution of gene families known to function in hyphal growth. A cartoon illustrating how proteins interact relating to subprocesses which govern vesicle trafficking associated with hyphal growth. Functions are briefly discussed in the main body of this manuscript and are marked i to viii. The taxonomic distribution of putative orthologues identified using reciprocal BLAST searches and phylogenetic methods across a subset of eukaryotic taxa (data not shown). The fungal component of the phylogenetic tree is based on Spatafora et al. ( ).

Citation: Richards T, Leonard G, Wideman J. 2017. What Defines the “Kingdom” Fungi?, p 57-77. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0044-2017
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Figure 3

Cartoon illustration summarizing how features previously discussed as defining the protist-fungal transition have been shown to have a mosaic distribution within the Fungi and/or outside the Fungi among other eukaryotes. White connecting nodes illustrate linked characters/traits.

Citation: Richards T, Leonard G, Wideman J. 2017. What Defines the “Kingdom” Fungi?, p 57-77. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0044-2017
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Figure 4

Schematic phylogenetic tree illustrating additional groups branching proximate to the origin of the fungal clade and the phylogenetic uncertainty among the deep branches of the Fungi and associated groups. Basal clone group 1 is composed of environmental sequences, which in some analyses is placed close to fungi ( ).

Citation: Richards T, Leonard G, Wideman J. 2017. What Defines the “Kingdom” Fungi?, p 57-77. In Heitman J, Howlett B, Crous P, Stukenbrock E, James T, Gow N (ed), The Fungal Kingdom. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.FUNK-0044-2017
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