MBE Advance Access originally published online on March 19, 2004
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Mol. Biol. Evol. 21(7):1340-1349. 2004
DOI: 10.1093/molbev/msh130
© 2004 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038
Research Article |
Covarion Shifts Cause a Long-Branch Attraction Artifact That Unites Microsporidia and Archaebacteria in EF-1
Phylogenies
,,
* Program in Evolutionary Biology, Canadian Institute for Advanced Research and Genome Atlantic, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
Department of Bioscience, Nagahama Institute of Bioscience and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
Department ofMathematics and Statistics and Genome Atlantic, Dalhousie University, Halifax, Nova Scotia, Canada
Departmentof Botany, University of British Columbia, Vancouver, British Columbia, Canada
E-mail: yinagai{at}dal.ca.
Abstract
Microsporidia branch at the base of eukaryotic phylogenies inferred from translation elongation factor 1
(EF-1) sequences. Because these parasitic eukaryotes are fungi (or close relatives of fungi), it is widely accepted that fast-evolving microsporidian sequences are artifactually "attracted" to the long branch leading to the archaebacterial (outgroup) sequences ("long-branch attraction," or "LBA"). However, no previous studies have explicitly determined the reason(s) why the artifactual allegiance of microsporidia and archaebacteria ("M + A") is recovered by all phylogenetic methods, including maximum likelihood, a method that is supposed to be resistant to classical LBA. Here we show that the M + A affinity can be attributed to those alignment sites associated with large differences in evolutionary site rates between the eukaryotic and archaebacterial subtrees. Therefore, failure to model the significant evolutionary rate distribution differences (covarion shifts) between the ingroup and outgroup sequences is apparently responsible for the artifactual basal position of microsporidia in phylogenetic analyses of EF-1 sequences. Currently, no evolutionary model that accounts for discrete changes in the site rate distribution on particular branches is available for either protein or nucleotide level phylogenetic analysis, so the same artifacts may affect many other "deep" phylogenies. Furthermore, given the relative similarity of the site rate patterns of microsporidian and archaebacterial EF-1 proteins ("parallel site rate variation"), we suggest that the microsporidian orthologs may have lost some eukaryotic EF-1–specific nontranslational functions, exemplifying the extreme degree of reduction in this parasitic lineage.
Key Words: phylogenetic artifact • long-branch attraction • EF-1 • microsporidia • covarion model • parallel site rate variation
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