First, we extracted the desired regions from the 1000 Genomes dataset. We then selected known SNPs within each region, and extracted a region of plus or minus 2000 SNPs around that SNP, except in the case of CHRNB3-A6 where we selected plus or minus 2500 SNPs. We constructed recombination maps using cM maps provided by the SHAPEIT2 program [37]. Ancestral alleles were determined using the latest version of Seattleseq (http://snp.gs.washington.edu/SeattleSeqAnnotation137/). Phased haplotypes were coded as number of copies of the derived allele. All positions in which the derived allele could not be determined unambiguously (i.e. C/G or A/T SNPs) as well as those without known chimp alleles were removed from further analyses. All analyses were run on each population separately. As iHS is greatly influenced by SNP allele frequency, iHS values from WHAMM were standardized using the average and standard deviation of all SNPs on chromosome 15 and 8 binned by allele frequency such that the average iHS value for each bin after standardization was identical. We excluded SNPs with a minor allele frequency less than 5% because low frequency
