Figure 1. Decay of EHH in Simulated Data for an Allele at Frequency 0.5.

(A) Decay of haplotypes in a single region in which a new selected allele (red, center column) is sweeping to fixation, replacing the ancestral allele (blue). Horizontal lines are haplotypes; SNP positions are marked below the haplotype plot using blue for SNPs with intermediate allele frequencies (minor allele >0.2), and red otherwise. For a given SNP, adjacent haplotypes with the same color carry identical genotypes everywhere between that SNP and the central (selected) site. The left- and right-hand sides are sorted separately. Haplotypes are no longer plotted beyond the points at which they become unique.

(B) Decay of haplotype homozygosity for ten replicate simulations. When the core SNP is neutral (s = 0; left side) the haplotype homozygosity decays at similar rates for both ancestral and derived alleles. When the derived alleles are favored (s = 2Ns = 250; right side), the haplotype homozygosity decays much slower for the derived alleles than for the ancestral alleles. The discrepancy in the overall areas spanned by these two curves forms the basis of our text for selection (iHS).