Figure 1:

Illustration of the demographic model and the coalescent hidden Markov model. (a) A sketch of the demographic history relating African, non-African, and the Neanderthal population that contains the key features. (b) The Conditional Sampling Distribution applied to the detection of Neanderthal introgression. At each locus, the ancestral lineage of the focal Non-African (α) haplotype coalesces either with an African lineage (h₁ or h₂), or a lineage in the Neanderthal population (h₃) through the introgression event.