Figure 1.
Allele frequency dependence of FST under different ascertainment schemes. This shows FST for CEU and CHB as a function of allele frequency when ascertaining in either CEU, CHB, or YRI. The increased FST for rare variants is consistent with bottlenecks being a stronger force on FST for CEU and CHB than recent expansion. In fact, this is consistent with a stronger bottleneck in the population history of CHB. We note that this frequency dependence disappears when ascertaining in YRI, suggesting that YRI is a reasonable outgroup for the comparison of CEU and CHB.
