Figure B1.

Top, Prior distributions generating base ethnicity probabilities M_i and Poisson crossover rates λ_i for individual i. These parameters are for the autosomes. Similarly, we generate M^X_i and λ^X_i for the X chromosome. The distribution of M^X_i is dependent on the random variable M_i. Bottom, Allele counts, [n^A₀(j),n^A₁(j)], for marker j in sample from population A and similar counts, [n^B₀(j),n^B₁(j)], for population B. We also have parameters τ(A) and τ(B) modeling divergence between our modern samples and the actual parental populations of our admixed sample sample. We generate “true” allele frequencies for the modern populations and then allele frequencies p(j) for the parental populations. M,λ and the allele frequencies p(j) now drive a Lander-Green HMM (Lander and Green 1987) that estimates ancestry at every point of the genome. Ancestries E_ij form a (hidden) Markov chain, and outputs O_ij are observable genotypes generated from the E_ij using the probabilities p^A(j),p^B(j).