Ancient genomes reveal complex patterns of population movement, interaction and replacement in sub-Saharan Africa

Africa is the source for all human populations, and harbors both deep population structure and significant genetic variation, yet remains only minimally studied from an ancient DNA perspective. While recent studies have revealed insights into population history in eastern Africa, the broader pattern of population changes across sub-Saharan Africa remains to be fully resolved. In particular, understanding of population-level interactions between eastern African pastoralists, southern African foragers and early Bantu-speaking groups has been limited by a scarcity of ancient genomic data. Here, we report genome-wide data from 20 ancient individuals across sub-Saharan Africa, including the first ancient DNA from the Congo, Uganda and Botswana. We demonstrate the potential contraction of once overlapping hunter-gatherer ancestries, showing that millennia ago, eastern Africa witnessed population-level interactions between local foragers and groups whose forager descendants are today restricted to western, southern, and eastern Africa. We also examine the expansion of food-producing populations in sub-Saharan Africa, and suggest that the spread of herding and farming to eastern and southern Africa generally involved multiple dispersing groups with admixture between populations occurring at different rates in different regions. We provide insight into patterns of interaction between pastoralists and foragers, and suggest that delayed-return foragers in stable coastal and lake environments in eastern Africa were resistant to interactions with incoming food producers. We also document the arrival of pastoralist-related ancestry in Congo and Botswana, and show that admixture between pastoralists and foragers precedes later incorporation of Bantu ancestry in Iron Age individuals from northern Botswana, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have dramatically reshaped the genetic map of sub-Saharan Africa in the last few millennia, and highlight the ability of combined archaeological and archaeogenetic approaches to shed light not only on population movements but also social processes in prehistory.