In the limit as the number of divergence points d increases and the proportion of diverging sites θ decreases, the model approaches the covarion model.
These analyses revealed that dominant morphs are associated with highly divergent haplotypes of this gene in P. dardanus, with a large proportion of the divergence occurring at non-synonymous sites, but not in other species.
Third, the proportion of nucleotide divergence attributable to the presence of an indel decreases over time, indicating that indels cause a short burst of nucleotide diversity but only transiently (McDonald et al. 2011).
We used those counts and the maximum likelihood framework developed by Welch and implemented in the software MKTest (Welch 2006; see also Obbard et al. 2009) to infer from MK tables counts the proportion (1 − f) of amino acid (AA) changing mutation undergoing strong purifying selection and the proportion of nonsynonymous divergence that was driven by positive selection.
Given the general observation that a substantial proportion of protein divergence is adaptive in Drosophila (Smith and Eyre-Walker 2002; Fay et al. 2002; Begun et al. 2007; Langley et al. 2012), one interpretation of increased dN/ dS ratio on the X is more adaptive protein evolution on the X chromosome.
In each region we compare the proportion of divergent TFBS/miRNA target sites with the amount expected given the over-all sequence divergence of the opsin BACs and introns (a measure of neutral evolutionary divergence [ 42, 43]).
Trans-effects correlated more highly than cis with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared with nonadditive inheritance patterns.
Although the fraction of elements that are fixed is proportionally lower in elements that have a low divergence from the family consensus, a significant proportion of those low divergence elements are also fixed.
Finally, we considered the proportion of the mean divergence value of the coding regions to the nonsynonymous substitutions (see supplementary table S2, Supplementary Material online).
Toll 1 had the highest proportion of non-synonymous divergence due to adaptive evolution (α=0.91), as well as the highest number of adaptive substitutions per site (a = 0.058).
