The derived allele frequency distribution shows substantial divergence between populations below a frequency of 40% (Fig. 2c), such that individuals from populations with substantial African ancestry (YRI, LWK, ASW) carry up to three times as many low-frequency variants (0.5-5% frequency) as those of European or East Asian origin, reflecting ancestral bottlenecks in non-African populations15. However, individuals from all populations show an enrichment of rare (<0.5%) variants, reflecting recent explosive increases in population size and the effects of geographic differentiation6,16. Compared to the expectations from a model of constant population size, individuals from all populations show a substantial excess of high-frequency derived variants (>80% frequency).
