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Genetics. Mar 1996; 142(3): 1033–1036.
PMCID: PMC1207002

Synonymous Nucleotide Divergence: What Is ``saturation''?


The nucleotide divergence at synonymous third sites between two lineages will increase with time since the latest common ancestor, up to some saturation level. The ``null-hypothesis divergence'' is defined as the percentage of difference predicted at synonymous third sites, allowing for amino acid composition and codon bias, but assuming that codon bias is the same at all sites occupied by a given amino acid, when equilibrium has been reached between forward and backward substitutions. For two highly expressed genes, gapA and ompA, in the enterobacteria, the estimated values of the null-hypothesis divergence are 39.3 and 38.15%, respectively, compared to estimated values of saturation divergence of 19.0 and 25.4%. A possible explanation for this discrepancy is that different codons for a given amino acid are favored at different sites in the same gene.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Smith JM. Estimating selection by comparing synonymous and substitutional changes. J Mol Evol. 1994 Aug;39(2):123–128. [PubMed]
  • Sharp PM, Li WH. The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987 Feb 11;15(3):1281–1295. [PMC free article] [PubMed]

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