Systematic Biology 49(2):278-305 (2000)

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

Jean-Marc Moncalvo, Francois M. Lutzoni1, Stephen A. Rehner2, Jacqui Johnson3, and Rytas Vilgalys

Department of Botany, Duke University, Durham, North carolina 27708, USA

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Present addresses: 1 Department of Botany, The Field Museum of Natural History, Chicago, Illinois 60605, USA; 2 Department of Biology, University of Puerto Rico, Box 23360, San Juan, Puerto Rico 00931; 3 Louis Calder Biological Field Station, Fordham University, Armonk, New York 10504, USA

It is particularly hoped ... that DNA analysis can be methodically extended to generic taxonomy and that ways will be discovered to add new approaches to the solution of problems(Singer, 1986).Whence cometh the Agarics?(Miller and Watling, 1987).

Abstract.-  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 comatusand subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota,and Hypholoma);the mycorrhizal species of Tricholoma(including Leucopaxillus,also mycorrhizal); Mycenaand Resinomycena;Termitomyces, Podabrella,and Lyophyllum;and Pleurotuswith 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.  [Fungal evolution; higher phylogeny; homobasidiomycete; large scale molecular phylogeny; tree support.]

Figure 2:  Agaricales phylogeny based on maximum parsimony analysis of large nuclear subunit rDNA sequences.  The figure shows one most-parsimonious tree found in both equally weighted parsimony (UP) and weighted parsimony (WP) searches.  Bold lines indicate branches present in the strict consensus of all most-parsimonious UP and WP trees.  UP searches yielded 312 equally parsimonious trees of length 3100 (CI = 0.207, RI = 0.555) located in three different tree-islands.  WP searches yielded four equally parsimonious trees of score 12655.9 (CI = 0.220, RI = 0.563).  Branch lengths were estimated using ACCTRAN with character-state changes having equal weight.  Bootstrap values * 50% are shown above each branch (bootstrap values based on 100 replicates with MAXTREE set to 100 in each replicate, random addition sequence, TBR branch swapping, and character-state changes having equal weight).  Groups that are paraphyletic in Fig. 2 or 5 are labeled in quotation.

Figure 5: Agaricales phylogeny estimated using maximum likelihood.  Tree score = 15689.295.  Groups labelled A to BB are the same as in Fig 2.  Groups that are paraphyletic in Fig. 2 or 5 are labeled in quotation.

View the data matrix in a new window, or download the agaric154.PAUP file

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