Signatures of selection were investigated by computing the integrated extended haplotype homozygosity (EHH) score (iHS) and cross-population locus-specific integrated (EHH) score (Rsb) using the R package REHHv3.01 (rehh)51. rehh estimates the probability that a locus, randomly shuffled from any chromosome is identical by descent to a core (focal) locus (ancestral/derived). As this probability breaks down with increasing distance upstream and downstream from the focal locus, the integral of the area under the EHH plot when the focal allele is an ancestral allele to the integral when the focal allele is a derived allele yields the iHS score. Therefore, large negative iHS values would signify selection at the derived allele and vice versa87. In the absence of a focal locus, Rsb is computed using EHH scores for all loci. Replacing the focal and derived alleles with the two populations being compared as popA and popB respectively, Rsb yields selection signatures for pairwise population comparisons. Thus, as above, large negative Rsb values would signify selection in popB and vice versa. iHS and Rsb statistics were computed in our data set using phased haplotypes with MAF ≥ 0.05. First, iHS was computed on the pooled data set (with all the ethnicities), then Rsb was computed with separate pairs of the different ethnicities (SBvsBA, SBvsFO, and BAvsFO). To assess the significance of selection signatures, rehh computes a two-sided p-value from the Gaussian cumulative distribution function of iHS estimates. The p-values were adjusted by the Benjamin–Hochberg (BH) and Bonferroni (BF) methods. Furthermore, rehh generates manhattan plots for visualization of iHS and Rsb results with their corresponding p-values. Genome-wide significance threshold for the manhattan plots was estimated by dividing 0.05 by the effective number of SNPs (those that passed all filters and were used to compute iHS) (Bonferroni method).

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