The haplotype decay is calculated until the extended haplotype homozygosity (EHH) reaches 0.05. EHH is defined as “the probability that two randomly chosen chromosomes carrying the core haplotype of interest are identical by descent for the entire interval from the core region to point x” [36] (p. 833). 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].
