Phylogenetic Relationships of Agaric Fungi Based on Nuclear Large Subunit Ribosomal DNA Sequences

Abstract

Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene 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 the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP 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 values or are consistent with morphology-based classification schemes. Analyses 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 groups revealed by these data to be nonmonophyletic 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.

The evolution of fungus-growing termites and their mutualistic fungal symbionts

“…The fruiting bodies of Termitomyces are always associated with termite nests (8,15,32,33), which implies that within the basidiomycetes there is a single evolutionary origin of mutualistic symbiosis with termites and that there are no known reversals to a nonsymbiotic lifestyle. These results are consistent with earlier findings (18,19,33) based on much less-complete data sets. Additional analyses varying the number of outgroups and using maximum likelihood and maximum parsimony resulted in similar topologies, although the basal relationships between the main clades of fungal symbionts were never strongly supported.…”

A preliminary ITS phylogeny of Melanoleuca (Agaricales), with special reference to European taxa

“…Staude. Sequence analyses by Moncalvo et al (2000Moncalvo et al ( , 2002 place Melanoleuca and Pluteus Fr. as sister to Amanitaceae R. Heim ex Pouzar, while others place the minute uniloculate gasteromycete, Limnoperdon incarnatum G.A.…”

A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota)

“…The six candidate genes were amplified and sequenced using the following primer pairs: ITS1/ITS5 (ITS, White et al 1990), LROR/LR5 (nLSU, Moncalvo et al 2000Moncalvo et al , 2002, EF1-983F/EF1-1567R (tef-1α, Morehouse et al 2003), MS1/MS2 (mtSSU, White et al 1990), RPB1-Ac/RPB1-Cr (rpb1, Stiller and Hall 1997;Matheny et al 2002), and bRPB2-6F/fRPB2-7cR (rpb2, Liu et al 1999;Matheny 2005). PCR was performed in a Techne Prime Thermal Cycler (Cole-Parmer, Staffordshire, UK) using a 50 μL reaction volume composed of 25 μL Biomed 2× Taq Plus PCR MasterMix (Biomed, Beijing, China), 21 μL ddH 2 O, 1.5 μL of each primer (10 μmol/L), and 1 μL DNA template.…”