In order to examine the properties of our approach, we first applied our method to data generated under a simple simulation framework for generating genotypes, local ancestries, and phenotypes of individuals from an admixed population. Allele frequencies pA1, pA2, …,pAN of N SNPs from an ancestral population were drawn uniformly from [0.1-0.9]. Allele frequencies of SNPs from P0 were drawn from a beta distribution with parameters p(1- FSTC)/FSTC and (1-p)(1- FSTC)/FSTC for each SNP s, and similarly for P1. The parameter FSTC determines the genetic distance between the two populations. The global proportion of P0 ancestry θ1, θ2, …θM for each of M individuals was drawn either uniformly from [0.4,0.6], from the normal distribution N(0.5,0.1), or fixed at 0.5. Local ancestry for individual i at SNP s (γis), was generated by two draws from binomial distribution with parameter θs. The genotypes from individual i at SNP s(gis) were then generated by drawing from the binomial distributions with allele frequencies specified by the local ancestry for that individual at that SNP. That is, if the individual had two copies of ancestry
