We searched the larger and more diverse HapMap 3 genotype data for genomic regions showing signals of positive natural selection using a recently published method, the composite of multiple signals (CMS)19. In the three original HapMap populations, CEU, CHB+JPT and YRI, comparing the regions identified in HapMap 3 with published results from HapMap Phase II (Supplementary Methods), we replicated 83% (147 out of 178) of the previous HapMap Phase II candidate regions (Supplementary Fig. 10a–d). Of the 17% of regions that did not replicate, most had lower SNP density in HapMap 3 than in HapMap Phase II; in 20 regions, none of the high-scoring HapMap Phase II SNPs was genotyped in HapMap 3.
