Figure 3: Relationships among Khoisan and eastern Africans after removing non-Khoisan admixture.

We extended TreeMix to build trees after subtracting out the effect of known admixture (Supplementary Methods) and then applied it to the Khoisan (excluding the Damara, who are genetically close to non-Khoisan). Populations are coloured according to their linguistic affiliation (Khoisan) or geographic location (dark grey=non-Khoisan African, light grey=Eurasian), and the chimpanzee was used as an out-group. The bar chart next to each population shows the estimated ancestry proportions for each population: blue is the proportion of Khoisan ancestry, and red is the proportion of non-Khoisan ancestry. Note that the actual source of these two ancestries may vary among populations. The proportions are not identical to those presented in Fig. 2b because of small differences in how they are estimated. The black dots show splits supported by more than 95% of bootstrap replicates, and the grey dots those supported by more than 80% of bootstrap replicates.