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We speculate that residual differentiation between Ethiopian and other SSA populations after masking Eurasian ancestry (pairwise F, confirmed widespread Eurasian and HG admixture in SSA (Supplementary Tables 2 and 3). Our finding of ancient Eurasian admixture corroborates findings of non-zero Neanderthal ancestry in Yoruba, which is likely to have been introduced through Eurasian admixture and back migration, possibly facilitated by greening of the Sahara desert during this period9,000 years ago) among Igbo and more recent admixture in East and South Africa (multiple events ranging from 100 years ago to 3,000 years ago), broadly consistent with historical movements reflecting the Bantu expansion.

Quantification of admixture (Supplementary Table 4, Supplementary Methods and Supplementary Notes 3 and 4) indicated substantial Eurasian ancestry in many African populations (ranging from 0% to 50%), with the greatest proportion in East Africa (Fig. Similarly, HG admixture ranged from 0% to 23%, being greatest among Zulu and Sotho (Fig. The proportion and distribution of Eurasian and HG admixture among different populations across Africa, with approximate dating of admixture using MALDER (code was provided by J. We found evidence for historically complex and regionally distinct admixture with multiple HG and Eurasian populations across SSA (Fig. Specifically, ancient Eurasian admixture was observed in central West African populations (Yoruba; 150–1,500 years ago) (Fig. An exploration of the likeliest sources of admixture in our data suggested that HG admixture in Igbo was most closely represented by modern day Khoe-San populations rather than by rainforest HG populations (Supplementary Note 5).

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Additionally, we found no evidence for background selection as the primary driver of differentiation among these loci (Supplementary Note 7).

K = 6 and K = 18 were the most likely clusters on ADMIXTURE analysis.

ADMIXTURE analysis suggests substructure between North, East, West and South Africa.

To account for confounding due to Eurasian admixture, we also conducted analyses after masking Eurasian ancestry (Supplementary Methods and Supplementary Note 6).

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On examining locus-specific Europe–Africa differentiation, enrichment of loci known to be under positive selection was observed among the most differentiated sites (P = 1.4 × 10).‘Unsupervised’ (that is, without including known information on individual ancestry) ADMIXTURE (https:// analysis including the 1000 Genomes Project and Human Origins data sets (Fig. To assess the effect of gene flow on population differentiation in SSA, we masked Eurasian ancestry across the genome (Supplementary Methods and Supplementary Note 6).



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