Population genetics and substitution models of adaptive evolution
Mario dos Reis
(Submitted on 26 Nov 2013)

The ratio of non-synonymous to synonymous substitutions ω(=dN/dS) has been widely used as a measure of adaptive evolution in protein coding genes. Omega can be defined in terms of population genetics parameters as the fixation ratio of selected vs. neutral mutants. Here it is argued that approaches based on the infinite sites model are not appropriate to define ω for single codon locations. Simple models of amino acid substitution with reversible mutation and selection are analysed, and used to define ω under several evolutionary scenarios. In most practical cases ω1 can be sometimes expected for single locations at equilibrium. An example with influenza data is discussed.