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.

Modern Homo sapiens engage in substantial ecosystem modification, but it is difficult to detect the origins or early consequences of these behaviors. Archaeological, geochronological, geomorphological, and paleoenvironmental data from northern Malawi document a changing relationship between forager presence, ecosystem organization, and alluvial fan formation in the Late Pleistocene. Dense concentrations of Middle Stone Age artifacts and alluvial fan systems formed after ca. 92 thousand years ago, within a paleoecological context with no analog in the preceding half-million-year record. Archaeological data and principal coordinates analysis indicate that early anthropogenic fire relaxed seasonal constraints on ignitions, influencing vegetation composition and erosion. This operated in tandem with climate-driven changes in precipitation to culminate in an ecological transition to an early, pre-agricultural anthropogenic landscape.

The landscape of northern Malawi is defined by several river catchments that drain from the highlands at the west into Lake Malawi at the east. Many thousands of Middle Stone Age (MSA) artefacts are present on the surface, in particular in areas where sedimentary units assigned to the Chitimwe Beds are exposed. The unique configuration of the region and its exposures makes it possible to address landscape-scale questions about MSA behaviour that augment information derived from excavated assemblages. In this study, data are derived from initial results of surveys conducted in 2012 which focussed on how lithic raw materials (in the form of cobbles) and core technology (in the form of mapped and analysed cores) are distributed across the landscape relative to different landforms, geologies, and one another. These data are used to examine if differences in core reduction technology occur in different catchment areas with different raw material quantities and qualities, and to test hypotheses about lithic provisioning scenarios. This allows for examination of core reduction technologies in relation to raw material sources via surface finds on a larger regional scale than usually is possible from excavations. Different catchments show differences in the type and quality of the raw material, with higher-quality quartzites occurring in the North Rukuru catchment and declining to the south. This is reflected in the types of materials MSA people chose to use for the production of stone tools. However, differences in raw material selection and distance from cobbles did not influence preferred core reduction strategies, and most cores cluster together near cobble sources. This suggests that throughout the MSA in the study area core reduction strategies were highly conserved even while raw material use remained flexible, and cores were not regularly transported as part of a provisioning strategy.Resumé Le paysage du nord du Malawi est caractérisé par la présence de divers bassins hydrographiques des rivières qui s'écoulent des régions montagneuses de l'ouest vers le Lake Malawi, à l'est. Des milliers d'artefacts de l'Âge de la pierre moyen (MSA) sont dispersés dans ce paysage, en particulier dans les zones où les sédiments de Chitimwe Beds sont exposés. La richesse et le caractère unique de ce paysage, permettent de soulever de nouvelles questions concernant le mode de vie des hommes de MSA. Ces nouvelles questions enrichissent les informations apportées par les fouilles. Dans cette recherche, des données, sur lesquelles celle-ci a été basée, proviennent de 'surveys' effectuées en 2012 qui avaient pour objectif de découvrir la manière dont la matière première lithique (sous forme de pavés) et les industries lithiques (sous la forme de nucléus) sont réparties à travers le paysage. Ces données ont été tout d'abord utilisées pour examiner s'il existe des différences dans le débitage sur nucléus dans diverses zones à bassins hydrographiques ayant des quantités et des qualités de matière première diverses et ensuite pour vérifier...

The site of Mwanganda's Village, located along a paleochannel in northern Malawi, is one of only a few sites that have characterized the Middle Stone Age (MSA) of Malawi for decades (Clark & Haynes, ; Clark et al., ; Kaufulu, ). The Malawi Earlier‐Middle Stone Age Project has re‐examined the site using new mapping and chronometric tools in order to reinterpret the site's significance within the context of current debates surrounding human origins and the potential role the environment played in shaping human behavior. The new data do not support the previous hypothesis that the site was an elephant butchery location (contra Clark & Haynes, ; Clark et al., ; Kaufulu, ). Instead, the evidence shows successive colonization of riparian corridors by MSA hunter‐gatherers focused on exploiting localized resources during periods of generally humid climates while other lakes desiccated across Africa. We challenge the hypothesis that stable and intermediately high lake levels within the African Rift Valley System (sensu Trauth et al., ) catalyzed the evolution of regional interaction networks between 42 and 22 ka. Instead, we interpret the evidence to suggest that regional variants of technology persist into the late MSA as foragers focused on exploiting resources from local catchments.

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