Next we sought to identify candidate selection loci in the new HapMap 3 populations TSI, LWK and MKK (that is, all populations except those likely to be recently admixed). First we identified 54 broad candidate regions for selection using long haplotype tests. Applying CMS to these regions, we localized signals to new and intriguing candidates (Supplementary Table 12). In TSI, pigmentation genes were again identified, including KITLG and MLPH23 (Supplementary Fig. 10e, f). We found other signals, like LAMA3, a gene involved in wound healing, and an olfactory receptor cluster. In the Kenyan populations we identified several immune-related genes, such as CD22624, ITGAE12 and DPP7 (Supplementary Fig. 10g–i). A novel signal identified in MKK localized to the gene ANKH; ANKH has a role in bone growth and susceptibility to arthritis, and has previously been identified as being under positive selection in horses25 (Supplementary Fig. 10j). The complete set of new candidates (Supplementary Table 12) may suggest hypotheses regarding natural selection in these populations.
