Figure 2

Intercontinental PCA plots comparing Sowetan genetic variation to populations worldwide. Sowetan genetic variation was compared to that seen worldwide using principal component analysis. Our data were combined with Omni2.5 data generated as part of the 1000 Genomes Project. We incorporated the main representatives for the European (CEU), Asian (CHB and JPT) and African (LWK, MKK and YRI) continents, as well as Gujarati Indians (GIH) based on reported Indian contributions to the Sowetan gene pool. a) Principal components (PC) 1 and 2 divide populations into broad continental clusters, with the exception of GIH. The BSO overlap well with other Africans of the Niger-Kordofanian linguistic group. Nilo-Saharan speaking Maasai are positioned nearby, reflecting the separate history of this linguistic branch. Several BSO individuals separate out from the cluster, indicating possible admixture. b) PC3 separates Asian, European and Indian populations, whilst PC4 disaggregates Africans along a north–south gradient. BSO and SEB are clearly distinguished from other black Africans and are more loosely clustered. Plots are based on a panel of 460 568 markers. Refer to Table 1 for sample sizes per population.