Complex Patterns of Genomic Admixture within Southern Africa
(A) Circular Neighbor Joining phylogenetic tree for 24,402 LD-pruned autosomal markers after merging our data with global population data for a total of 521 samples from 14 populations, with the Pan genome as the outgroup. We confirm early divergence of the Ju/'hoan and report independent branching of the Angolan !Xun. (B) Plot of total length of ROH against number of ROH (>500 kb) for each study sample against European and Yoruba using 716,734 markers (367 samples). Our foraging groups show smaller overall ROH lengths than the Europeans, yet longer than the Yoruba, suggesting small effective population sizes of a likely ancient population with minimal to no impact from a dramatic bottleneck.