We first verified the analytical derivations and examined the properties of the approach under a simple simulation framework. We simulated the genotypes and local ancestry of 4,000 unrelated diploid individuals at 1,000 SNPs from a two-way admixed population with causal variant genetic distance FSTC, and either normally or uniformly distributed ancestry proportion θ. Each local ancestry segment contained exactly one SNP and all segments were generated independently. Phenotypes were simulated under an additive model with heritability h2 in which a proportion r of the 1,000 SNPs was causal (see Online Methods). We applied our method to estimate heritability over a range of values of FSTC, θ, r, and h2. For each parameter setting we estimated heritability from 2,000 independent simulated data sets. The results shown in Table 1 show that our heritability estimates are accurate across a range of parameter settings, confirming our analytical derivation. Results for additional parameter settings are shown in Supplementary Table 1.
