Fig. 2.
SWIF(r) localizes canonical adaptive mutations and provides additional evidence for suspected sweeps in YRI, CHB and JPT, and CEU63. Plotted points indicate the calibrated posterior sweep probability calculated by SWIF(r) at each site, using prior sweep probability π = 10−5. Plots were made with LocusZoom64. Where available, functionally verified adaptive SNPs are depicted as filled diamonds and labeled with rsids. a, b In YRI, two loci where SWIF(r) reports high sweep probabilities are DARC and DOCK3. DARC encodes the Duffy antigen, located on the surface of red blood cells, and is the receptor for malaria parasites. The derived allele of the causal SNP shown has been determined to be protective against Plasmodium vivax malaria infection25. DOCK3, along with neighboring genes MAPKAPK3 and CISH, are all associated with variation in height, and have previously been shown to harbor signals of selection in Pygmy populations65. CISH may also play a role in susceptibility to infectious diseases, including malaria66. c, d In CEU, we uncover multiple loci in genes involved in pigmentation, including rs1426654 in SLC24A5, which is involved in light skin color24, and rs12913832 in the promoter region of OCA2, which is functionally linked with eye color and correlates with skin and hair pigmentation26. rs1426654 has the highest sweep probability reported by SWIF(r) in SLC24A5 (0.9992 after smoothed calibration; see Supplementary Data 1); note each panel depicts genomic windows containing multiple genes. e, f In CHB and JPT, SWIF(r) recovers a strong adaptive signal in the vicinity of EDAR; multiple GWA studies have shown rs3827760 to be associated with hair and tooth morphology67,68. SWIF(r) also identifies variants with high sweep probability in ADAM17, which is involved in pigmentation69, and has been identified in other positive selection scans in East Asian individuals70,71