As judged by this measure, informativeness varied greatly for different population pairs. Consistent with the observation that non-African diversity is largely a subset of African diversity14, African samples provided a more complete discovery resource for variant sites in non-African samples than the converse (Fig. 2a). Focusing only on low-frequency variants in the original sample of 30 A individuals (one or two copies, corresponding to allele frequencies of 3.3% or less), even African samples were highly incomplete for diversity outside of Africa, with informativeness ratios dropping to 40–60% in LWK and YRI (Fig. 2b). In general, for low-frequency variants only closely related populations did an adequate job of capturing variation (Fig. 2b), probably reflecting the recent origins of low-frequency variants. Two populations, LWK and GIH, stand out as being poorly captured by any of our other populations, the result of admixture with an ancestral population not closely related to any in our regional sequencing data (Supplementary Methods). (Although the MKK captures similar East African ancestry to that of LWK (Supplementary Fig. 2), it had not been included in the regional sequencing.)
