Extended Data Fig. 5: Simulation of haplotypes under the neutral demographic model.

a, PCA plot of principal component (PC)2 versus PC1 for simulated individuals (n = 1,000 simulated individuals and 2,000 simulated haplotypes). Individuals were simulated using a demographic model matching the population history of Peru and under neutral selection. Red dots, simulated individuals; other dots, reference populations from the 1000 Genomes Project. b, PCA plot of PC3 versus PC1 as described for a. c, We compared the integrated EHH of rs200342067*C with the integrated EHH of 1,000 variants that had a similar DAF to rs200342067 (DAF = 4.7 ± 1%) and that overlapped the same genomic region as rs200342067 on a simulated chromosome 15 (physical position, 48,773,926 ± 20 kb). The integrated EHH of rs200342067 is more extreme than the integrated EHH observed for any of the variants in the simulated data. The x axis shows the integrated EHH; the distribution is the integrated EHH of variants in simulated haplotypes (n = 2,000 haplotypes); the vertical red line shows the integrated EHH value of rs200342067 in our cohort (n = 6,628 haplotypes, integrated EHH = 0.115). d, e, Similar to c for two different neutral regions on chromosome 15. Vertical red lines, integrated EHH of rs17580697 (d, integrated EHH = 0.012, 76th percentile) and rs305008 (e; integrated EHH = 0.010, 74th percentile) in our cohort (n = 6,628 haplotypes).