For example, polymorphisms that exhibit the greatest divergence in allele frequency among populations (FST outliers) may represent loci subject to divergent selection (Lewontin and Krakauer 1973; Beaumont and Nichols 1996).
The strongest divergence in the frequency of losing OCT1 activity was observed between the populations in America and East Asia (Fig. 7a).
We first develop a simple statistical model based on classical population genetic methods to analyze whole genome divergence in allele frequency.
Second, the genome-wide significance threshold of the present study is quite stringent, requiring high divergence in allele frequency between populations.
The first method examines genotypic data at multiple low-resolution loci, such as chromosomal morphs, allozymes, microsatellites, amplified fragment length polymorphisms (AFLPs) or single nucleotide polymorphisms (SNPs), for heterogeneity of divergence in allele frequency.
When considering the regression r values, which highlight not only departure from colinearity but also local divergence in recombination frequency, 51 out of 84 pair-wise comparisons showed values ≥ 0.99, 25 were comprised between 0.95 and 0.99 and 8 were < 0.95.
Using the theoretical framework of population genetics, phylogeography and phylogenetics, the effects of gene flow and genetic drift on divergence in peak frequencies between divergent lineages has revealed relationships between echolocation divergence and e.g. female philopatry [ 66] geographic distance [ 7, 69], and palaeoclimatic lineage divergence [ 82, 83].
Since heterosis depends on the difference in allele frequencies between the two breeds, these results suggest that selection for CP moves allele frequencies in the two breeds in opposite directions and causes divergence in allele frequencies between both breeds.
To test for geographical divergence in allele frequencies of individual SNPs across the genome, pairwise FST values were calculated for all non-singleton SNPs for each combination of sample sites.
Thus, divergence in allelic frequencies may result from differences in selection pressures not associated with differences in dietary specialization, such as variation in the intensity of predator-prey arms races at different locations.
