Little has been described of the Holocene populations of South-Central Africa, despite the region demonstrating major subsistence shifts relating to dispersals of agriculturalists at least 2,000 years ago. Seven sites with associated human skeletal remains were selected. Hora, Chencherere, Fingura, and Mtuzi represent the Middle Holocene (2,000-5,000 years ago), and Phwadze, Mtemankhokwe, and Nkudzi Bay represent the Late Holocene and the arrival of agriculturalists between 500-2,000 years ago. Focusing on the identity of Hora and Chencherere specimens, two questions were addressed: are the various Holocene Malawians similar to each other, or do they suggest morphological change over time? What modern populations are closest to the prehistoric specimens? The archaeological sample was compared to modern sub-Saharan Africans from four regions, plus a historic Khoi-San foraging group. Factor analyses were performed in order to identify complex patterns of variation in metric traits of the skull. According to the results, prehistoric Malawians showed only slight differences between the Late and Middle Holocene, suggesting a population change without any major discontinuity. Later Stone Age skulls did not exclusively show similarities with the Khoi-San, as they frequently fit well within the variation of modern Bantu-speaking groups, especially West-Central Africa. Therefore, we reject the hypothesis that Middle Holocene South-Central Africans have an exclusively Khoi-San ancestry, and support an alternative hypothesis that both Middle and Late Holocene groups share a common biological heritage originating in West-Central Africa in earlier times.
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