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Synonymous nucleotide divergence: what is “saturation”?
journal contribution
posted on 2023-06-07, 20:58 authored by J Maynard Smith, N H SmithThe 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.
History
Publication status
- Published
Journal
GeneticsISSN
0016-6731Publisher
Genetics Society of AmericaPublisher URL
Issue
3Volume
142Page range
1033 - 1036ISBN
0016-6731Department affiliated with
- Biology and Environmental Science Publications
Full text available
- No
Peer reviewed?
- Yes