Ancient DNA reveals a multistep spread of the first herders into sub-Saharan Africa

Abstract

been inhibited by several factors. A spatial and chronological gap exists between the earliest evidence of pastoralism in the Turkana Basin and the later PN expansion, with few material culture similarities between them. Additionally, relationships among PN and diverse Iron Age groups remain poorly understood. Human skeletal material from relevant contexts tends to be fragmentary, limiting bioarchaeological analysis, and reliable radiocarbon dates are rare. Finally, the persistence of foraging groups raises questions about interaction networks during this period (12, 15), and whether food production spread primarily via demic expansion or via local adoption of novel practices and livestock. To address these debates, we generated genome-wide ancient DNA data from individuals buried at sites associated with LSA (n = 3), early pastoral and PN (n = 31), IA (n = 1), and PIA (n = 6) archaeological traditions in what are now Kenya and Tanzania (Fig. 1, Table 1, and table S1). We extracted DNA from a combination of tooth and bone samples and enriched for a targeted set of ~1.2 million single nucleotide polymorphisms (SNPs; (21)). Surprisingly, given the tropical climate and variable curatorial conditions, we obtained excellent data quality, with a median of approximately 0.51× coverage, or 440,000 SNPs covered by at least one sequence, for the 41 newly reported individuals (from a total of 67 sequencing libraries; table S2). The data scored well in standard ancient DNA authenticity metrics for all but two individuals (I12391 and I13970, whom we excluded from genome-wide analyses but for whom we obtained Y chromosome and mitochondrial DNA [mtDNA] haplogroups; (21)). We also generated direct radiocarbon dates for 35 individuals (tables S3 and S4 and fig. S1). We analyze these data jointly with sequences from published ancient African individuals (22–27), as well as from people living in eastern Africa today (28–31). Overview of genetic affinities of ancient eastern Africans We visualized the genetic structure of the ancient individuals using principal component analysis (PCA) of the genomewide data (Fig. 2 and table S5). We defined PCs using a small set of present-day groups (southern Africans, northeastern Africans, and non-Africans; (21)) and projected a large number of diverse individuals onto these axes. An alternative analysis with western Africans additionally used to compute the axes yielded almost identical results (fig. S2). Present-day groups from Sudan mostly lie along a cline extending from Copts (upper right, near individuals from northern Africa and the Levant) to Nilotic speakers such as Dinka and Nuer (bottom left). Afro-Asiatic speakers (mostly from Ethiopia) form a second cline, with the right end near Sudanese Beja and Nubians, and the left end extending toward eastern African foragers (who themselves form a south-to-north gradient; cf.