We used the coalescent model (msprime v.7.311) to simulate European (CEU) and African (YRI) genotypes, based on whole-genome sequencing of HapMap populations, for chromosome 20 as described previously by Martin et al.2 Genotypes were modeled after the demographic history of human expansion out of Africa,12 assuming a mutation rate of 2 × 10−8. We simulated 200,000 Europeans and 200,000 Africans for each simulation trial, for a total of 50 independent simulations (20 million total individuals). We generated founders from an additional 1,000 Europeans and 1,000 Africans (10,000 total across the 50 simulations) to simulate 5,000 admixed individuals (250,000 total across the 50 simulations) with RFMIX v.2,13 assuming two-way admixture between Europeans and Africans with random mating and 8 generations of admixture.
