| Introduction
We are developing a molecular phylogenetic classification for the major groups (families and genera) of mushroom fungi (Basidiomycota: Agaricales). Taxonomy of mushrooms has traditionally relied on morphological characters that are known to be subject to parallel evolution and phenotypic plasticity and, as a result, many modern families are artificial. In our view, development of a natural system of classification for the agaricoid fungi is still hampered by continued emphasis of certain aspects of the Friesian system together with preoccupation on nomenclatural stability and a lack of phylogenetic perspective. Even the most comprehensive taxonomy proposed to date (Singer, 1986, The Agaricales in Modern Taxonomy) holds a simplistic view that a phenetic classification (based on similarity or correlation of characters) is an appropriate approximation of natural classification (based on common possession of derived characters). Although phylogenetic approaches may sometimes conflict with traditional Linnaean classification, continued emphasis on characters (as synapomorphies) for delimiting taxa should assist transition to a phylogenetic system over time. We address the higher-level relationships among the major groups of
agarics and their non-agaricoid relatives (secotioids, puffballs and reduced
forms) by sequencing the genes coding for nuclear large (> 1,000 targeted
taxa) and small (> 150 targeted taxa) subunit ribosomal RNA (nLSU and nSSU
rDNA); mitochondrial ribosomal DNA genes, and nuclear and mitochondrial
protein-encoding genes, are also targeted for exemplar taxa representative
of the broadest nuclear rDNA diversity. The resulting molecular sequence
data bases should be helpful in the identification of environmental isolates
and new or unknown agarics. This study will also provide a basis
for comparative studies on different aspects of molecular and character
evolution, and for estimation of phylogenetic diversity in mushrooms.
It also addresses several general questions in systematic biology involving
problems of analysis of large data sets and data combinability in multi-gene
phylogenies.
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