New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Jolanta Miadlikowska, Frank Kauff, Valérie Hofstetter, Emily Fraker, Martin Grube, Josef Hafellner, Valérie Reeb, Brendan P. Hodkinson, Martin Kukwa, Robert Lücking, Geir Hestmark, Monica Garcia Otalora, Alexandra Rauhut, Burkhard Büdel, Christoph Scheidegger, Einar Timdal, Soili Stenroos, Irwin Brodo, Gary B. Perlmutter, Damien ErtzPaul Diederich, James C. Lendemer, Philip May, Conrad L. Schoch, A. Elizabeth Arnold, Cécile Gueidan, Erin Tripp, Rebecca Yahr, Connie Robertson, François Lutzoni

Research output: Contribution to journalArticle

196 Scopus citations

Abstract

The Lecanoromycetes includes most of the lichen-forming fungal species (>13 500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota - 2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.

Original languageEnglish (US)
Pages (from-to)1088-1103
Number of pages16
JournalMycologia
Volume98
Issue number6
DOIs
StatePublished - Nov 2006

Keywords

  • Bayesian inference
  • Lecanoromycetes
  • Lichen-forming ascomycetes
  • Maximum likelihood
  • Missing data
  • Mitochondrial ribosomal small subunit (mitSSU)
  • Molecular phylogenetic classification
  • Nuclear ribosomal large subunit (nucLSU)

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • Molecular Biology
  • Genetics
  • Cell Biology

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    Miadlikowska, J., Kauff, F., Hofstetter, V., Fraker, E., Grube, M., Hafellner, J., Reeb, V., Hodkinson, B. P., Kukwa, M., Lücking, R., Hestmark, G., Otalora, M. G., Rauhut, A., Büdel, B., Scheidegger, C., Timdal, E., Stenroos, S., Brodo, I., Perlmutter, G. B., ... Lutzoni, F. (2006). New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia, 98(6), 1088-1103. https://doi.org/10.3852/mycologia.98.6.1088