Supplementary Figure 11: Levels of nucleotide diversity around SNPs conditional on FST.
Neutral diversity (Watterson’s theta, θw) in the African bees was measured in 1-kb windows up to a distance of 250 kb on either side of every SNP detected between African and European bees and grouped into FST intervals (size = 0.05; the last interval contains the fixed SNPs). The mean diversity close to a SNP of a particular FST class (1–20 kb away) was compared to the diversity of all SNPs (at 100–250 kb away, matching the average diversity computed across the whole genome). (a) All SNPs. Diversity is reduced by ∼8% around SNPs with FST = 0.95–1.00 and by ∼23% around fixed SNPs with FST = 1 (pink, FST = 0.9–0.95; green, FST = 0.95–1.00; blue, FST = 1; 95% bootstrap confidence intervals are shown; average diversities computed for all lower FST classes shown in dark blue). (b) Coding SNPs. SNPs in coding regions are associated with the greatest reduction in diversity (FST(1) = 31%; FST(0.95–1.00) = 32%; FST(0.9–0.95) = 16%; FST(0.85–0.90) = 15%). (c) Intronic SNPs. It is mainly the fixed SNPs in introns that show reduced levels of variation (23%). (d) Intergenic SNPs. These SNPs are only weakly associated with reduced variation (FST(1) = 6%).
