Given the high degree of population structure for gene expression, we addressed the possibility that differentiation of eSNP allele frequencies may contribute to the observed associations by calculating FST estimates for each pair-wise comparison of location for the 516,972 SNPs and 16,500 of the genes. No fixed differences were observed and plots of the FST comparisons (Supplementary Fig. 6a online) indicate only moderate overall genetic differentiation, with occasional SNPs having FST values between 0.12 and 0.3. There was no tendency for these outliers to have elevated expression differentiation and in fact almost all of the top 10% most differentially expressed genes are among the least genetically differentiated. Nor was there any correlation between FST and significance of gene expression divergence (Supplementary Fig. 6b online), confirming that the observed expression differences between locations are for the most part not attributable to gene-specific allelic frequency differences between locations.
