Journal of Molecular Evolution

, Volume 21, Issue 2, pp 161–167 | Cite as

Interaction of silent and replacement changes in eukaryotic coding sequences

  • David J. Lipman
  • W. John Wilbur


We examined the codon usages in wellconserved and less-well-conserved regions of vertebrate protein genes and found them to be similar. Despite this similarity, there is a statistically significant decrease in codon bias in the less-well-conserved regions. Our analysis suggests that although those codon changes initially fixed under amino acid replacements tend to follow the overall codon usage pattern, they also reduce the bias in codon usage. This decrease in codon bias leads one to predict that the rate of change of synonymous codons should be greater in those regions that are less well conserved at the amino acid level than in the better-conserved regions. Our analysis supports this prediction. Furthermore, we demonstrate a significantly elevated rate of change of synonymous codons among the adjacent codons 5′ to amino acid replacement positions. This provides further support for the idea that there are contextual constraints on the choice of synonymous codons in eukaryotes.

Key words

Amino acid replacements Synonymous codons Codon bias 


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Copyright information

© Springer-Verlag 1985

Authors and Affiliations

  • David J. Lipman
    • 1
  • W. John Wilbur
    • 1
  1. 1.Mathematical Research Branch, National Institute of Arthritis, Diabetes and Digestive and Kidney Diseases, Building 31 Room 4B-54National Institutes of HealthBethesdaUSA

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