This is apparent in the plots of Ks against both Ka and K16S, in which those bacteria subject to higher levels of drift have elevated divergence at slightly deleterious sites (Ka and K16S) relative to neutral sites (Ks).
Furthermore, the theory of drift, mutation, and selection in subdivided populations implies that purifying selection against deleterious mutations leads to lower divergence among populations connected by migration than for neutral sites (Charlesworth B and Charlesworth D 2010, p. 355).
We measured the rate of adaptive evolution using the statistic ωa, which is the rate of adaptive substitution at nonsynonymous sites relative to the rate of synonymous substitution, using a method that takes into account the contribution of slightly deleterious mutations to polymorphism and divergence (Eyre-Walker and Keightley 2009; Keightley and Eyre-Walker 2012).
This is likely due to the fact that we estimate fewer nearly neutral mutations (fig. 2) and more recent growth in D. melanogaster (supplementary S2, Supplementary Material online), implying a smaller proportion of neutral and slightly deleterious nonsynonymous substitutions to nonsynonymous divergence.
One population contains a significant amount of non-neutral variation; this could be indicative of adaptive divergence or the accumulation of deleterious mutations due to small population processes.
Previous studies have demonstrated a positive relationship between tissue specificity of expression and evolutionary rate, presumably due to selection against the deleterious pleiotropic effect of mutation restricting the divergence of broadly expressed genes [ 40- 42].
To substantially underestimate the fraction of protein divergence due to accumulating slightly deleterious mutations, the past population sizes of both species would have to have been considerably smaller than estimated for an appreciable amount of time.
Thus, if adaptation is mutation limited, rates of adaptation are expected to be higher in species with larger N e, and given the higher efficacy of selection against mildly deleterious mutations, so is the proportion of divergence attributable to positive selection relative to mildly deleterious or neutral mutations.
Polymorphism in mtDNA often shows an excess of slightly deleterious mutation in comparisons of polymorphism within and divergence within and between species [ 67].
As slightly deleterious mutations contribute more to polymorphisms than to divergence, the SNPs were then classified by the frequency of their rarer allele into low frequency SNPs (< 5%), moderate frequency SNPs (5-15%), and common SNPs 15-500%) following Fay et al.[ 88].
