Fig 1.

A) Schematic of two-population modeling framework: at each site, derived and ancestral fragments (a, d) are binomially sampled from the true genotype of the archaic individual, with some amount of contamination and error. In turn, the true genotype depends on a demographic model, which can include the contaminant population. B) Schematic of three-population modeling framework, incorporating admixture between the archaic population and one of two anchor populations.