Figure 3

Intracontinental PCA plot comparing Sowetan genetic variation to other black Africans. To examine African genetic variation in more detail, a PCA plot was generated that incorporated only BSO, SEB, YRI, MKK, LWK, KAR, KHO and NAM populations. PC1 separated populations along a north–south split, whilst the Nilo-Saharan speaking Maasai separated out along PC2. Khoe-San groups (KAR, KHO and NAM) displayed limited clustering in line with previous reports on their unparalleled genetic diversity. Noticeably, BSO clustering was weaker than that seen in northern Africans, suggesting a greater degree of interindividual variation. Plot was based on a panel of 460 568 markers. Refer to Table 1 for sample sizes per population. BSO - Southeastern Bantu-speakers from the Soweto region; KAR - Karretjie in South Africa; KHO - Khomani in South Africa; LWK - Luhya in Webuye, Kenya; MKK - Maasai in Kinyawa, Kenya; NAM - Nama in Namibia; SEB - Southeastern Bantu-speakers; YRI - Yoruba in Ibadan, Nigeria.