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.

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1–4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80–20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

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Changing perspectives on concepts of personhood are explored by deconstructing mortuary customs from 10 Tucson Basin (Arizona) Hohokam archaeological sites dating from the Preclassic (A.D. 700–1150) and Classic (A.D. 1150–145011500) periods. Results indicate that certain aspects of personhood did not change across time and space at these sites. However, by analyzing changes through time in cremation rituals, it was possible to infer that some aspects of personhood did change. In the Preclassic period, after bodies were burned, the remains were distributed as inalienable possessions within social networks. This behavior suggests a relational social construction of self where burning transformed the deceased and the remains were considered part-person and part-object. Later in the Classic period, a higher frequency of cremated remains were not divided but instead transferred as a unit to secondary deposits. Perceptions of personhood during this period appear to have defined self as a complete, bounded unit, even after transformation by fire. This change possibly occurred as a result of a general decrease in remembrance networks. These changes in cremation parallel broader sociopolitical changes where increases in social differentiation and complexity are proposed for the Classic period Hohokam.