Summary We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing ~2/3 of the ancestry of Malawi hunter-gatherers ~8100–2500 years ago, and ~1/3 of Tanzanian hunter-gatherers ~1400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ~3100 year-old pastoralist from Tanzania contributed ancestry to people from northeast to southern Africa, including a ~1200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving long-distance gene flow, or a lineage more deeply diverging than that of the San contributing more to some western Africans than others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

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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Recent excavations in Level 4 at BK (Bed II, Olduvai Gorge, Tanzania) have yielded nine hominin teeth, a distal humerus fragment, a proximal radius with much of its shaft, a femur shaft, and a tibia shaft fragment (cataloged collectively as OH 80). Those elements identified more specifically than to simply Hominidae gen. et sp. indet are attributed to Paranthropus boisei. Before this study, incontrovertible P. boisei partial skeletons, for which postcranial remains occurred in association with taxonomically diagnostic craniodental remains, were unknown. Thus, OH 80 stands as the first unambiguous, dentally associated Paranthropus partial skeleton from East Africa. The morphology and size of its constituent parts suggest that the fossils derived from an extremely robust individual who, at 1.338±0.024 Ma (1 sigma), represents one of the most recent occurrences of Paranthropus before its extinction in East Africa.