Data from: Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the
order Agaricales were addressed using nuclear large subunit ribosomal DNA
sequences. Approximately 900 bases of the 5' end of the
nucleus-encoded large subunit RNA gene (nLSU-rDNA) were sequenced for 154
selected taxa representing most families within the Agaricales. Several
phylogenetic methods were used, including weighted and equally weighted
parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The
starting tree for branch swapping in the ML analyses was the tree with the
highest ML score among previously produced MP and NJ trees. A high degree
of consensus was observed between phylogenetic estimates obtained through
MP and ML. NJ trees differed according to the distance model that was
used, however, all NJ trees still supported most of the same terminal
groupings as MP and ML trees. NJ trees were always significantly
suboptimal when evaluated against the best MP and ML trees, using both
parsimony and likelihood tests. Our analyses suggest that weighted
parsimony and ML provide the best estimates of Agaricales phylogeny.
Similar support was observed between bootstrapping and jackknifing methods
for evaluation of tree robustness. Phylogenetic analyses revealed many
groups of agaricoid fungi that are supported by moderate to high bootstrap
or jackknife levels or are consistent with morphology-based classification
schemes. Analyzes also support separate placement of the boletes and
russules, which are basal to the main core group of gilled mushrooms (the
Agaricineae of Singer). Examples of monophyletic groups include the
families Amanitaceae, Coprinaceae (excluding Coprinus comatus and
subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and
Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the
mycorrhizal species of Tricholoma (including Leucopaxillus, also
mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and
Lyophyllum; and Pleurotus with Hohenbuehelia. Several nonmonophyletic
groups revealed by these data include the families Tricholomataceae,
Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina,
and Marasmius. This study provides a framework for future systematics
studies in the Agaricales and suggestions for analyzing large molecular
data sets.