Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes

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

*Corresponding author for this work

Research output: Contribution to journalArticle

27 Scopus citations


Many Saccharomyces cerevisiae duplicate genes that were derived from an ancient whole-genome duplication (WGD) unexpectedly show a small synonymous divergence (Ks), 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 Ks 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.

Original languageEnglish
Pages (from-to)14412-14416
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number39
StatePublished - 26 Sep 2006


  • Concerted evolution
  • Decelerated evolution
  • Selective constraints
  • Whole-genome duplication

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