Figure 3. Decay of LD for SNPs with minor allele frequency <10%.

(A, B) Real data for European Americans and East Asians shows longer range LD when the Neandertal genome has the derived allele (left) than when it has the ancestral allele (right). This is as expected due to gene flow from Neandertal, but is not expected in the absence of gene flow. In other words, the fact that LD conditional on Neandertals having the derived allele is longer than LD when Neandertal does not strongly suggests that the pattern we are observing among ascertained SNPs is reflecting the complex historical relationship between non-African modern humans and Neandertals, the signal we care about here, and not demographic events that solely involve the ancestors of non-Africans. The scale of the LD decay (1/e drop of the fitted exponential curve) is shown in the top right of each panel based on the deCODE genetic distance. (In Figure S8 of Text S1, we show that this signal persists when stratified into narrow allele frequency bins.) (C) In West Africans the pattern is qualitatively different such that when Neandertal is derived at both SNPs, LD decays more quickly than when Neandertal is ancestral at both SNPs, as expected in the absence of gene flow (without gene flow, the derived allele is always expected to be older so LD is expected to have had more time to break down).