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Molecular Biology and Evolution 18:2124-2126 (2001)
© 2001 Society for Molecular Biology and Evolution

Nucleotide Substitution Rate Estimation in Enterobacteria: Approximate and Maximum-Likelihood Methods Lead to Similar Conclusions

Nick G. C. Smith and Adam Eyre-Walker

Centre for the Study of Evolution and School of Biological Sciences, University of Sussex, Brighton, England

Synonymous mutations are "silent" with regard to the amino acid sequence of a protein, but a wealth of evidence indicates that, at least in species with large effective population sizes, synonymous mutations are subject to translational selection (Akashi and Eyre-Walker 1998Citation ). One line of evidence for translational selection has been the perceived negative correlation between codon bias and synonymous substitution rates (KS), reported in both Drosophila (Shields et al. 1988Citation ) and enterobacteria (Sharp and Li 1987aCitation ). The reasoning behind this interpretation of the correlation between KS and codon bias is straightforward. Translational selection means that certain codons are favored over others, so selection causes an increased codon bias with a preponderance of favored codons, which means that most synonymous mutations are selectively disfavored and so selection also reduces KS.

The selective interpretation of the correlation between KS and codon bias in Drosophila has . . . [Full Text of this Article]

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