Figure 1. Linkage disequilibrium patterns expected due to recent gene flow and ancient structure.

(A) In the case of recent gene flow from Neandertals (NEA) into the ancestors of non-Africans (CEU) but not into the ancestors of Africans (YRI), we expect long range LD at sites where Neandertal has the derived allele, and this expectation of admixture generated LD is verified by computer simulation as shown in the right of the panel along with a fitted exponential decay curve. (B) In the case of ancient structure, we expect short range LD, reflecting the time since Neandertals and non-Africans derived from a shared ancestral population, and this expectation is also verified by simulation.