We utilized the LCT gene region as a positive control. LCT encodes the protein lactase and mutations in the region give rise to lactase persistence. The lactase persistence phenotype is due to changes in a regulatory region that enhances the expression of LCT located in intron 13 of the neighboring gene, MCM6 [27]. Fig 1A shows the distribution of Tajima’s D values in the sliding windows in the LCT region in AFR, ASN and EUR. As expected, both the Asian and European populations show many windows above 2 but very few exist in the African population. All p-values are derived using permutations of 10,000 regions of the same size from across the genome. For Europeans and Asians, the proportion of windows with extreme values was 8.6% and 6.5%, respectively (Table 1). This is highly significant in EUR, when compared to the negative control regions, and modestly significant in ASN (<p = 2x10-7 and p = 0.01 for EUR and ASN, respectively) and appears inconsistent with the null hypothesis of neutral evolution and demography at the LCT locus especially in the
