Discussion of Phylogenetic Relationships
Understanding of the phylogenetic relationships of the Agaricomycetes has improved dramatically since the mid-1990s. As in all Fungi, the first wave of phylogenetic studies in Agaricomycetes was based on rRNA genes, following the description of conserved primer sequences for PCR amplification (White et al. 1990). This early work was summarized by Hibbett and Thorn (2001), who recognized eight major clades, labelled with informal names, such as “euagarics clade”, “russuloid clade”, “polyporoid clade”, etc.
One of the most commonly-sampled regions in Agaricomycete phylogenetics has been the nuclear-encoded large subunit (nuc-lsu) rRNA gene. At present, the most inclusive published trees are based on the nuc-lsu rRNA, including studies by Moncalvo et al. (2002), with 877 taxa, and Binder et al. (2005), with 656 taxa. An on-line project in automated phylogenetics of Agaricomycetes has generated trees with almost 3000 sequences, and this dataset is being automatically updated with new records from Genbank (Hibbett et al. 2005; http://mor.clarku.edu/).
While the nuc-lsu rRNA studies have been instrumental in fleshing out the sampling of Agaricomycetes, it has long been clear that these genes do not provide robust resolution of many of the deeper nodes. In an attempt to improve resolution of the major groups, Binder and Hibbett (2002) combined data from small and large subunits of nuclear and mitochondrial rDNA (3.8 kilobases per species) in 93 species that span much of the diversity of Agaricomycetes. This analysis provided strong support for seven of the eight major groups that Hibbett and Thorn (2001) proposed, and also suggested some novel relationships, such as a sister-group relationship between Agaricales and Boletales. Nevertheless, the deeper relationships among the major clades were poorly resolved, and the “polyporoid clade” remained weakly supported and controversial (Larsson et al. 2004).
Recently, analyses combining rRNA genes with protein-coding genes have begun to appear, and these have provided great improvements in resolution and support (Matheny et al. 2006, 2007). For example, the “polyporoid clade” has been strongly supported as monophyletic (Matheny et al. 2007).
The current classification of the Agaricomycetes is based on a combination of rRNA and combined protein/rRNA studies, which are too numerous to review here. For a compilation of the phylogenetic studies that inform the current classification, see Hibbett et al. (2007). The informal names of Hibbett and Thorn (2001) have now been replaced by formal taxonomic names, most of which were preexisting in the taxonomic literature. Thus, the current concept of Agaricales is equivalent to the “euagarics clade”, the Polyporales is equivalent to the “polyporoid clade”, the Phallomycetidae is equivalent to the “gomphoid-phalloid clade”, and so on.
There have been several independent clades discovered in recent years that were not included in Hibbett and Thorn’s (2001) overview. These include clades composed mostly of resupinate forms (Corticiales, Trechisporales, and Atheliales), as well as the “heterobasidiomycetous” Sebacinales, which includes coralloid, resupinate, and encrusting forms (Hibbett and Binder 2001; Larsson 2002; Lim 2001; Langer 2002; Weiss et al. 2004). With further study of the cryptic resupinate forms, it is entirely possible that additional major groups of Agaricomycetes will be discovered.
In the tree at the top of this page, the deepest “backbone” nodes in the Agaricomycetes are drawn as a large polytomy, reflecting lingering uncertainty about their resolution (this is a somewhat conservative view, because the multi-locus studies suggest some resolution; see Matheny et al. ). Resolving the earliest divergences in the Agaricomycetes is of interest, because this could provide insight into the form and ecology of the common ancestor of Agaricomycetes. Molecular data do not yet provide robust resolution of this problem, but ultrastructure of parenthesomes may provide some clues. Most Agaricomycetes have perforate parenthesomes, but the Cantharellales, Phallomycetidae, Hymenochaetales, and Trechisporales include species with imperforate parenthesomes. The Auriculariales and Dacrymycetes (see the Agaricomycotina page) also have imperforate parenthesomes, which may therefore be the plesiomorphic condition in the Agaricomycetes. Consistent with this view, the Cantharellales and Phallomycetidae clade have frequently been resolved as basal clades in the Agaricomycetes, albeit with weak bootstrap support (Hibbett and Binder 2002; Binder and Hibbett 2002; Matheny et al. 2007). Several authors have suggested that there is homoplasy in the evolution of parenthesomes in Agaricomycetes (Larsson 2002; Hibbett and Thorn 2001).
In sum, there are nineteen major clades of Agaricomycetes that are formally named in the current classification. The tree shown here also includes a few nodes that are resolved but are not named. Support for these groupings is moderate to strong in some analyses, and in the future these clades may also be recognized as formal taxa (if they are not refuted!).
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