Models and measures of codon usage bias

<p><em>Second term paper for my Biol L533 class (evolution of genes and genomes) with Mike Lynch, Winter term 2013.</em></p> <p>Bias in the usage of synonymous codons has been observed in all major taxa. Various mechanistic models have been proposed to explain this bias, some motivated by adaptive selection on features such as translational eciency, and some motivated by the nonadaptive stochastic dynamics of population genetics. A variety of quantitative measures of codon usage bias have also been proposed, but interpretation of these measures is confounded by considerable gaps that remain in our understanding of the fundamental mechanisms driving codon usage. This review discusses proposed theories and quantitative measures of codon usage bias, and provides a critical assessment of each.