To quantify population differentiation with respect to gene expression levels, we calculated the statistic VST for each of the 21,800 probes for each pairwise combination of populations. VST is a measure of the proportion of expression level variance explained by between-population divergence, and is analogous to the population genetics parameter FST, but for a quantitative trait [28]. For a single probe measured in two populations, VST is calculated as: (VT−VS)/VT, where VT is equal to the total variance across all individuals of the pair of populations and VS is the average within-population variance weighted by each population sample size. VS = (V1*n1+V2*n2)/(n1+n2), where V1 is the within-population variance of population 1, V2 is the within population variance of population 2, and n1 and n2 are the numbers of individuals sampled from population 1 and 2, respectively. VST values range from 0 to 1, with values near 1 signifying that the majority of gene expression variance for a probe segregates between populations rather than within populations.
