Figure 2. All Khoisan populations are admixed.

(a) Admixture linkage disequilibrium (LD) in the Ju|'hoan_North. For each pair of SNPs in the Ju|'hoan_North (black) or the Yoruba (grey), we estimate the LD and the product of the differences in allele frequency between the Ju|'hoan_North and the Yoruba. (We use the Yoruba as a proxy for the non-Khoisan, presumably Bantu-speaking ancestral population because there has been very little change in allele frequencies between Niger-Congo-speaking groups.) We then binned pairs of SNPs by the genetic distance between them. For each bin, we plot the regression coefficient (over SNP pairs in the bin) from regressing the level of LD on the product of the allele frequency differences. The rate at which this curve decays is informative about the date of admixture, whereas the amplitude of the curve is informative about the proportion of admixture (Supplementary Methods). In black is the curve if we assume the Ju|'hoan_North are admixed; in grey is the curve if we assume the Yoruba are admixed (which serves as a negative control). The red line is the exponential curve fitted to the black points. (b) Estimates of mixture proportions. We used the modified f₄ ratio19 (Supplementary Methods) to estimate the fraction of non-Khoisan ancestry in each southern African population. (c) Estimates of mixture dates. We used the rate at which admixture LD decays to estimate dates of admixture for all southern African populations (Supplementary Methods). We plot the means, with ranges representing one standard error. Not shown are the Wambo, who have no detectable curve and hence may be unadmixed. The estimates of the mixture proportions and dates are also presented in Supplementary Table S4.