We perform a sensitivity analysis to assess whether this type of bias is likely to be problematic. Since strong positive selection is unusual29, we consider a single locus under positive selection. We estimate bias as a function of FSTC at the locus and the variance explained by the locus. The results in Supplementary Table 4 show that only for extreme values of both locus FSTC and heritability will there be significant bias in heritability due to positive selection. As an example we consider the 8q24 locus in prostate cancer, which contains causal SNPs that are highly differentiated SNPs between African and European ancestors, producing an admixture-mapping peak30. However, because this locus explains less than 2% of the heritability of prostate cancer, even exceedingly strong population differentiation at this locus will not substantially bias our overall results.
