Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences

Phylogenetic relationships of mushrooms and their relatives within the orde r Agaricales were addressed by using nuclear large subunit ribosomal DNA se quences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most fa milies within the Agaricales. Several phylogenetic methods were used, inclu ding 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 phylogenet ic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used: however. all Nj trees still supported most o f the same terminal groupings as the Mr anal ML trees did. NJ trees were al ways significantly suboptimal when evaluated against the best MP and ML tre es. by both parsimony and likelihood tests. Our analyses suggest that weigh ted MP and ML provide the best estimates of Agaricales phylogeny. Similar s upport was observed between bootstrapping and jackknifing methods for evalu ation of tree robustness. Phylogenetic analyses revealed many groups of aga ricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Anal yses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singe r). Examples of monophyletic groups include the families Amanitaceae. Copri naceae (excluding Coprinus cumatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pm parte (Stropharia, P holiota. and Hypholoma); the mycorrhizal species of Tricholoma (including L eucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces. Pod abrella, and Lyophyllum: and Pleurotus with Hohenbuehelia. Several groups r evealed by these data to be nonmonophyletic include the families Tricholoma taceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphal ina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular dat a sets.