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Examination of the relative frequency of occurrence of alternative synonymous codons for any one amino acid (codon usage) for proteins within and among species suggests that codon usage pattern is a significant component of both genomic expression and expression of individual genes. This generalization implies a functional role of codon usage and that synonymous substitution rates may differ between lineages as a consequence. This could effect models constructed to estimate evolutionary rates, as well as inferences regarding phylogenetic reconstruction. Mouchiroud and Gautier

A shift in the third-codon-position nucleotide frequency in alcohol dehydrogenase genes in the genus Drosophila.