An analogy between the extended haplotype homozygosity (EHH) test and a multimarker test of unusual allele frequency differentiation. (A) In the EHH test, one searches for sites where the change in allele frequency since a putative selection event began (as assessed by its derived allele frequency) occurred too quickly (as assessed by the extent of LD around the tested allele) due to random genetic drift. The open circles show the expectation under neutrality, while the filled circles shows a selection signal (adapted from Fig. 3 of Sabeti et al. 2002). (B) In the multilocus test of allele frequency differentiation (XP-CLR) the idea is to search for regions in the genome where the change in allele frequency at the locus occurred too quickly (as assessed by the size of the affected region) due to random drift. A large region with moderate differentiation can easily stand out as genome-wide significant (filled circle).
