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MBE Advance Access published online on October 14, 2008
Molecular Biology and Evolution, 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 Article

Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts

Yu Liu1, Jessica W. Leigh2, Henner Brinkmann1, Melanie T. Cushion3, Naiara Rodriguez-Ezpeleta1, Hervé Philippe1 and B. Franz Lang1,*

1 Robert Cedergren Centre, Département de Biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, C.P. 6128, Montréal (Québec), H3T 1J4, Canada
2 Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, (Nova Scotia) B3H 4H7, Canada
3 Department of Internal Medicine, Division of Infectious Diseases, University of Cincinnati College of Medicine, Cincinnati, Ohio 45220, US A

Corresponding author: B. Franz Lang (Franz.Lang{at}Umontreal.ca)

Received for publication May 19, 2008. Revision received August 13, 2008. 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 multi-gene analyses, this topology is contradicted by mitochondrial phylogenies. To resolve this inconsistency, we have assembled phylogenomic mitochondrial and nuclear datasets 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 dataset (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 dataset, 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


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