Research Article

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

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Science  05 Jul 2019:
Vol. 365, Issue 6448, eaaw6275
DOI: 10.1126/science.aaw6275

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East African genetics and pastoralism

The origin and spread of domestic animals across the globe also affected the underlying genetic composition of human populations. In Africa, however, it has been difficult to identify the impact of interactions among migrating food producers and local hunter-gatherers. Prendergast et al. wanted to discern the timing and movement of husbandry and pastoralism and its effects on foraging communities in Africa. They sequenced 41 ancient eastern African human genomes from individuals that lived approximately 100 to 4000 years ago. Surprisingly, relatively little genetic mixture occurred at the same time as the spread of pastoralism.

Science, this issue p. eaaw6275

Structured Abstract


Cattle, sheep, and goats appeared in eastern Africa 5000 years ago, catalyzing the spread of herding throughout sub-Saharan Africa. Archaeologists have long debated the geographic origins of eastern Africa’s first herders, the extent to which people moved with livestock, and relationships among food-producing and foraging communities. In this work, we integrate ancient DNA with archaeological, linguistic, and genetic evidence to explore how pastoralism developed within this region, establishing the roots of one of Africa’s dominant economic strategies.


Research into the spread of herding has been limited by patchy archaeological data and poorly preserved human remains. Ancient DNA has the potential to untangle patterns of movement and interaction underlying this economic and cultural transition. We generated genome-wide ancient DNA data from the remains of 41 individuals (35 directly radiocarbon dated) associated with Later Stone Age (n = 3), early pastoral and Pastoral Neolithic (n = 31), Iron Age (n = 1), and Pastoral Iron Age (n = 6) traditions in what are now Kenya and Tanzania to study how ancient individuals were related to each other and to people living today.


We document a multistep spread of herding and farming into eastern Africa. Ancient individuals genetically correlate with their archaeological associations: Later Stone Age individuals form part of a forager genetic cline, early pastoral and Pastoral Neolithic individuals are most closely related to present-day Afro-Asiatic speakers, and Pastoral Iron Age individuals show affinities to present-day Nilotic speakers. A child buried at an Iron Age agricultural site has shared ancestry with western Africans and Bantu speakers.

We propose a four-stage model that fits the data. First, admixture in northeastern Africa created groups with approximately equal proportions of ancestry related to present-day Sudanese Nilotic speakers and groups from northern Africa and the Levant. Second, descendants of these northeastern Africans mixed with foragers in eastern Africa. Third, an additional component of Sudan-related ancestry contributed to Iron Age pastoralist groups. Fourth, western African–related ancestry, similar to that found in present-day Bantu speakers, appeared with the spread of farming.

We also observe a high frequency of a Y chromosome lineage associated with the spread of pastoralism, as well as a single individual with a genetic variant conferring adult lactase persistence. We do not detect any differentiation among individuals associated with two distinctive Pastoral Neolithic artifact traditions, suggesting that these represent cultural rather than ancestral differences.


Archaeological and now genetic evidence suggest complex spreads of herding and farming in eastern Africa involving multiple movements of ancestrally distinct peoples as well as gene flow among these groups. Models formulated on the basis of ancient DNA are a starting point for further exploration through additional archaeological, linguistic, and genetic research.

Admixture events contributing to ancestry of ancient eastern Africans.

Results were inferred from genome-wide ancient DNA data from 41 individuals from archaeological sites in Kenya and Tanzania, analyzed together with published ancient and present-day genetic data. Black circles represent reported individuals, placed at their median calibrated radiocarbon dates (six individuals, five of whom have forager-related ancestry, had insufficient collagen for dating and thus are not represented here). Ancestry components depicted in green and gray continue to the present day (outside of eastern Africa) but are truncated for readability.


How food production first entered eastern Africa ~5000 years ago and the extent to which people moved with livestock is unclear. We present genome-wide data from 41 individuals associated with Later Stone Age, Pastoral Neolithic (PN), and Iron Age contexts in what are now Kenya and Tanzania to examine the genetic impacts of the spreads of herding and farming. Our results support a multiphase model in which admixture between northeastern African–related peoples and eastern African foragers formed multiple pastoralist groups, including a genetically homogeneous PN cluster. Additional admixture with northeastern and western African–related groups occurred by the Iron Age. These findings support several movements of food producers while rejecting models of minimal admixture with foragers and of genetic differentiation between makers of distinct PN artifacts.

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