iHS is a measure of whether a SNP is on an unusually long haplotype carrying the ancestral or derived allele. It compares the rate of haplotype decay between haplotypes carrying either the ancestral or derived allele at a given site, referred to as the core SNP. Haplotypes whose core SNP is under selection will be unusually long compared to those evolving neutrally. Long haplotypes with derived alleles are indicated by negative iHS values and those with ancestral alleles are indicated by positive iHS values. Under neutrality, extreme scores are distributed throughout the genome, however under selection, they are clustered across the selected region [30]. iHS is a good method for detecting directional selection, especially in a sweep that is in its early phases. We used the program WHAMM to calculate this statistic [30].
