Jm. Moncalvo et al., Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences, SYST BIOL, 49(2), 2000, pp. 278-305
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.