Leveraging population admixture to characterize the heritability of complex traits

Despite recent progress on estimating the heritability explained by genotyped SNPs (h 2 g), a large gap between h 2 g and estimates of total narrow-sense heritability (h 2) remains. Explanations for this gap include rare variants or upward bias in family-based estimates of h 2 due to shared environment or epistasis. We estimate h 2 from unrelated individuals in admixed populations by first estimating the heritability explained by local ancestry (h 2 3). We show that h 2 3 = 2F STC (1 ')h 2, where F STC measures frequency differences between populations at causal loci and is the genome-wide ancestry proportion. Our approach is not susceptible to biases caused by epistasis or shared environment. We applied this approach to the analysis of 13 phenotypes in 21,497 African-American individuals from 3 cohorts. For height and body mass index (BMI), we obtained h 2 estimates of 0.55 ± 0.09 and 0.23 ± 0.06, respectively, which are larger than estimates of h 2 g in these and other data but smaller than family-based estimates of h 2.