Fig. 1. A population network including four episodes of gene flow, with an embedded gene genealogy.

Upper case letters (X, Y, N, D, and S) represent populations (Africa, Europe, Neanderthal, Denisovan, and superarchaic). Greek letters label episodes of admixture. d and xyn illustrate two nucleotide site patterns, in which 0 and 1 represent the ancestral and derived alleles. A mutation on the red branch would generate site pattern d. One on the blue branch would generate xyn. For simplicity, this figure refers to Neanderthals with a single letter. Elsewhere, we use two letters to distinguish between the Altai and Vindija Neanderthals.