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MBE Advance Access originally published online on October 14, 2008
Molecular Biology and Evolution 2009 26(1):27-34; doi:10.1093/molbev/msn221
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© The Author 2008. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Phylogenomic Analyses Support the Monophyly of Taphrinomycotina, including Schizosaccharomyces Fission Yeasts

Yu Liu*, Jessica W. Leigh{dagger}, Henner Brinkmann*, Melanie T. Cushion{ddagger}, Naiara Rodriguez-Ezpeleta*, Hervé Philippe* and B. Franz Lang*

* Robert Cedergren Centre, Département de Biochimie, Université de Montréal, Montréal, Québec, Canada
{dagger} Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
{ddagger} Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati College of Medicine

E-mail: franz.lang{at}umontreal.ca.

Accepted for publication September 13, 2008.

Several morphologically dissimilar ascomycete fungi including Schizosaccharomyces, Taphrina, Saitoella, Pneumocystis, and Neolecta have been grouped into the taxon Taphrinomycotina (Archiascomycota or Archiascomycotina), originally based on rRNA phylogeny. These analyses lack statistically significant support for the monophyly of this grouping, and although confirmed by more recent multigene analyses, this topology is contradicted by mitochondrial phylogenies. To resolve this inconsistency, we have assembled phylogenomic mitochondrial and nuclear data sets from four distantly related taphrinomycotina taxa: Schizosaccharomyces pombe, Pneumocystis carinii, Saitoella complicata, and Taphrina deformans. Our phylogenomic analyses based on nuclear data (113 proteins) conclusively support the monophyly of Taphrinomycotina, diverging as a sister group to Saccharomycotina + Pezizomycotina. However, despite the improved taxon sampling, Taphrinomycotina continue to be paraphyletic with the mitochondrial data set (13 proteins): Schizosaccharomyces species associate with budding yeasts (Saccharomycotina) and the other Taphrinomycotina group as a sister group to Saccharomycotina + Pezizomycotina. Yet, as Schizosaccharomyces and Saccharomycotina species are fast evolving, the mitochondrial phylogeny may be influenced by a long-branch attraction (LBA) artifact. After removal of fast-evolving sequence positions from the mitochondrial data set, we recover the monophyly of Taphrinomycotina. Our combined results suggest that Taphrinomycotina is a legitimate taxon, that this group of species diverges as a sister group to Saccharomycotina + Pezizomycotina, and that phylogenetic positioning of yeasts and fission yeasts with mitochondrial data is plagued by a strong LBA artifact.

Key Words: Fungi • Taphrinomycotina • Schizosaccharomyces • Pneumocystis • phylogeny • mitochondria • long-branch attraction artifact

Laura Katz, Associate Editor


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