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BIOLOGICAL SCIENCES / EVOLUTION
Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes

Yeong-Shin Lin^*,, Jake K. Byrnes^*, Jenn-Kang Hwang, and Wen-Hsiung Li^*,

*Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637; and Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 300, Taiwan

Contributed by Wen-Hsiung Li, July 28, 2006

Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (K_S), a higher sequence similarity to each other than to orthologues in Saccharomyces bayanus, or slow evolution compared with the orthologue in Kluyveromyces waltii, a non-WGD species. This decelerated evolution was attributed to gene conversion between duplicates. Using 300 WGD gene pairs in four species and their orthologues in non-WGD species, we show that codon-usage bias and protein-sequence conservation are two important causes for decelerated evolution of duplicate genes, whereas gene conversion is effective only in the presence of strong codon-usage bias or protein-sequence conservation. Furthermore, we find that change in mutation pattern or in tDNA copy number changed codon-usage bias and increased the K_S distance between K. waltii and S. cerevisiae. Intriguingly, some proteins showed fast evolution before the radiation of WGD species but little or no sequence divergence between orthologues and paralogues thereafter, indicating that functional conservation after the radiation may also be responsible for decelerated evolution in duplicates.

selective constraints | whole-genome duplication | concerted evolution | decelerated evolution

The authors declare no conflict of interest.

To whom correspondence should be addressed. E-mail: whli{at}uchicago.edu

© 2006 by The National Academy of Sciences of the USA

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