One possible explanation for the increase sharing of caQTLs between closely related population (
Figure 2A) is that since the allele frequency can affect power to detect QTLs, more similar allele frequencies could lead to greater levels of sharing. To test this possibility, for each SNP, we calculated the sharing as in
Figure 2A after excluding any population that had a pre-ATAC allele frequency >5% away from the mean frequency across all 10 populations. Although this excluded 75% of pairwise comparisons, we still observed a similar pattern of sharing, suggesting that patterns of sharing are unlikely to be driven solely by allele frequency differences.