Extended Data Fig. 3: Alternative PCA and allele-sharing analyses.
From: Ancient West African foragers in the context of African population history
a, Broad-scale PCA (differing from Fig. 2a by projecting all present-day Cameroon populations; again using 593,124 Human Origins SNPs). Groups shown in blue were projected onto axes computed using the other populations. HG, hunter-gatherers. The grouping marked W-Cent. HG consists of Aka and Cameroon hunter-gatherers (Baka, Bakola and Bedzan). The majority of the present-day Cameroon individuals fall in a tight cluster near other West Africans and Bantu-speakers. b, Relative allele sharing (mean ± s.e.m., multiplied by 10,000, computed on 538,133 SNPs, as in Fig. 3b) with the Shum Laka individuals versus East Africans (f4(X, Yoruba; Shum Laka, Somali); x axis) and versus Aka (f4(X, Yoruba; Shum Laka, Aka); y axis) for present-day populations from Cameroon (blue points) and southern and eastern Bantu-speakers (Herero in red and Chewa in orange). The Mada and Fulani share more alleles with the Shum Laka individuals than they do with the Aka, but this is probably a secondary consequence of admixture from East or North African sources (as reflected in greater allele sharing with Somali individuals) (Supplementary Information section 3). Bars show one s.e.m. in each direction.
