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The distributions of the three blue-eye associated alleles and the haplotypes associated with blue eyes are relatively consistent across all populations (Figs. 2 and 3), which indicates that blue-eye associations are ancient and have been shaped by ancient selection. The distributions of the different genotypes of each of the blue-eye associated haplotypes in the populations are similar to one another, which indicates that these associations are recent and reflect recent selection on the populations. For example, the distribution of the haplotype TG is similar to that of BEH2, which implies that the G allele of the two haplotypes are very similar, and the DG allele of BEH2 is most similar to the AG allele of BEH3. This is to be expected if these haplotypes reflect ancient selection pressures as the G, A, and D alleles of the three haplotypes are very ancient and the only alleles that are present outside of Europe are the derived alleles.
We investigated this hypothesis by analyzing the relationship of BEH2 and skin pigmentation in Europe (Supplemental Fig. 12). There is a significant negative relationship between the BEH2 allele and skin pigmentation in Europe. This is to be expected since the blue-eye associated allele of BEH2 is not present in Africa, a region that has the lowest skin pigmentation in the world. If there are two phenotypes being selected for at BEH2, it seems more likely that skin pigmentation would be chosen over eye color. Further investigation should be done to determine the significance of this relationship. The evidence from Europe is consistent with the alternative hypothesis that the blue-eye phenotype is not under selection.
The distribution of the haplotypes associated with blue eyes only in Europe is not consistent with the distribution of the haplotypes in the HGDP populations (Supplemental Fig. 13). This is because these populations have experienced a much higher degree of population growth and differentiation, and a higher degree of admixture, than European populations. Since the time since the onset of selection on these haplotypes, which is the same for all populations, can vary by hundreds of thousands of years, the haplotypes are no longer in equilibrium. Therefore, the allele frequencies in the HGDP populations cannot be used to infer selection pressures on these phenotypes.
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