Extended Data Fig. 6: Comparison of different selection statistics for rs200342067 and other variants with a similar DAF and recombination rate.

a, Distribution of iHS for 2,062 independent variants (that are at least 1 Mb apart) matched in DAF and local recombination rate to rs200342067. iHS values are calculated for Peruvian individuals in the 1000 Genomes Project (n = 85 individuals) and were obtained from a previously published study¹⁹. Red line, iHS of rs200342067 (iHS = −1.5; 4.7th percentile); green and blue lines, fifth and first percentile of the iHS distribution. b, EHH decay curves for rs200342067 (red line) as well as haplotypes that carry 2,062 independent variants (at least 1 Mb apart) matched in DAF and local recombination rate to rs200342067 in our cohort (n = 6,268 haplotypes (grey lines)). c, Distribution of integrated EHH for haplotypes shown in b, haplotypes carrying the rs200342067*C allele are longer than 97.5% of haplotypes that carry similar variants. The x axis shows the integrated EHH; the red line indicates the integrated EHH of the rs200342067*C allele (integrated EHH = 0.115). d, Histogram of Fisher’s exact test results comparing the extent of allele frequency differences between coastal (n = 46 individuals) and non-coastal (n = 104 individuals) regions in Peru for 2,062 independent variants that were matched in DAF and local recombination rate to rs200342067. the x axis shows the −log₁₀-transformed P values from the two-sided Fisher’s exact test; the dashed blue and green vertical lines show the 99th and 95th percentiles, respectively; the solid red line indicates the −log₁₀-transformed P value of the two-sided Fisher’s exact test (P= 0.0005) for rs200342067 (1.1% percentile). e, Bayenv2 XTX statistics, a measure of deviation from neutral patterns of population structure, for 2,062 independent variants that were matched in DAF and local recombination rate to rs200342067. The x axis shows the XTX statistics; the red line indicates the XTX value for rs200342067 (XTX = 2.13; 8.3th percentile); the green and blue lines show the fifth and first percentile of the XTX distribution, respectively.