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

Publication ,  Journal Article
Moncalvo, JM; Lutzoni, FM; Rehner, SA; Johnson, J; Vilgalys, R
Published in: Systematic biology
June 2000

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.

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Published In

Systematic biology

DOI

EISSN

1076-836X

ISSN

1063-5157

Publication Date

June 2000

Volume

49

Issue

2

Start / End Page

278 / 305

Related Subject Headings

  • Phylogeny
  • Genetic Variation
  • Evolutionary Biology
  • DNA, Ribosomal
  • DNA, Fungal
  • Classification
  • Biological Evolution
  • Base Sequence
  • Agaricales
  • 3105 Genetics
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Moncalvo, J. M., Lutzoni, F. M., Rehner, S. A., Johnson, J., & Vilgalys, R. (2000). Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Systematic Biology, 49(2), 278–305. https://doi.org/10.1093/sysbio/49.2.278
Moncalvo, J. M., F. M. Lutzoni, S. A. Rehner, J. Johnson, and R. Vilgalys. “Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.Systematic Biology 49, no. 2 (June 2000): 278–305. https://doi.org/10.1093/sysbio/49.2.278.
Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Systematic biology. 2000 Jun;49(2):278–305.
Moncalvo, J. M., et al. “Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences.Systematic Biology, vol. 49, no. 2, June 2000, pp. 278–305. Epmc, doi:10.1093/sysbio/49.2.278.
Moncalvo JM, Lutzoni FM, Rehner SA, Johnson J, Vilgalys R. Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences. Systematic biology. 2000 Jun;49(2):278–305.
Journal cover image

Published In

Systematic biology

DOI

EISSN

1076-836X

ISSN

1063-5157

Publication Date

June 2000

Volume

49

Issue

2

Start / End Page

278 / 305

Related Subject Headings

  • Phylogeny
  • Genetic Variation
  • Evolutionary Biology
  • DNA, Ribosomal
  • DNA, Fungal
  • Classification
  • Biological Evolution
  • Base Sequence
  • Agaricales
  • 3105 Genetics