SYNONYMOUS NUCLEOTIDE DIVERGENCE - WHAT IS SATURATION

The nucleotide divergence at synonymous third sites between two lineag es will increase with time since the latest common ancestor, up to som e saturation level. The ''null-hypothesis divergence'' is defined as t he percentage of difference predicted at synonymous third sites, allow ing 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 eq uilibrium 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 3 8.15%, respectively, compared to estimated values of saturation diverg ence 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.