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PMID: 17257443 Published · epublish English Journal Article

A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group.

BMC evolutionary biology ·Vol. 7 ·2007-01-29 ·Pages 9

Kawahara Y, Imanishi T

Abstract

Changes in protein evolutionary rates among lineages have been frequently observed during periods of notable phenotypic evolution. It is also known that, following gene duplication and loss, the protein evolutionary rates of genes involved in such events changed because of changes in functional constraints acting on the genes. However, in the evolution of closely related species, excluding the aforementioned situations, the frequency of changes in protein evolutionary rates is still not clear at the genome-wide level. Here we examine the constancy of protein evolutionary rates in the evolution of four closely related species of the Saccharomyces sensu stricto group (S. cerevisiae, S. paradoxus, S. mikatae and S. bayanus). For 2,610 unambiguously defined orthologous genes among the four species, we carried out likelihood ratio tests between constant-rate and variable-rate models and found 344 (13.2%) genes showing significant changes in the protein evolutionary rates in at least one lineage. Of all those genes which experienced rate changes, 139 and 49 genes showed accelerated and decelerated evolution, respectively. Most of the evolutionary rate changes could be attributed to changes in selective constraints acting on nonsynonymous sites, independently of species-specific gene duplication and loss. We estimated that the changes in protein evolutionary rates have appeared with a probability of 2.0 x 10-3 per gene per million years in the evolution of the Saccharomyces species. Furthermore, we found that the genes which experienced rate acceleration have lower expression levels and weaker codon usage bias than those which experienced rate deceleration. Changes in protein evolutionary rates possibly occur frequently in the evolution of closely related Saccharomyces species. Selection for translational accuracy and efficiency may dominantly affect the variability of protein evolutionary rates.

MeSH Terms
Animals Codon Evolution, Molecular Fungal Proteins/chemistry Genes, Fungal Genome, Fungal Likelihood Functions Phylogeny Saccharomyces/genetics
Chemicals
Codon Fungal Proteins
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Kawahara Yoshihiro
Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan. [email protected] <[email protected]>
Imanishi Tadashi
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Article Info
Journal
BMC evolutionary biology
Abbr.
BMC Evol Biol
ISSN
1471-2148
DOI
10.1186/1471-2148-7-9
Email
[email protected]
Published
2007-01-29
Epub
2007-00-29
Pages
9
Language
English
Region
England
NLM ID
100966975
PMCID
PMC1790889
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2148-7-9 PMC Full Text View journal details
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