To quantify population differentiation with respect to distinct gene expression levels, we calculated the statistic VST for each of 21,800 probes, corresponding to 18,226 unique autosomal Ensembl genes (see Methods), for each pairwise combination of populations. For each pairwise comparison of populations, the distribution of VST values was heavily skewed toward values near 0, with a long narrow tail comprised of values between 0 and 1 (Table S1 and Figure S3). Individual pairwise combinations of populations differ with respect to numbers of genes exhibiting high VST genes (Table S1) such that the amount of VST between a pair of populations is correlated with the degree of genetic distance; For example, the CHB-JPT combination only has 13 genes with VST greater than 0.2, whereas the CHB-MKK combination has 4031 genes with VST greater than 0.2. Together these analyses indicate that the vast majority of genes do not exhibit highly differentiated expression variation between populations, however every pairwise combination of populations has genes with highly structured expression variation. Analysis of the union of probes exhibiting top 5% VST scores from each pairwise
