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Our knowledge of ancient human population structure in sub-Saharan Africa, particularly prior to the advent of food production, remains limited. Here we report genome-wide DNA data from four children—two of whom were buried approximately 8,000 years ago and two 3,000 years ago—from Shum Laka (Cameroon), one of the earliest known archaeological sites within the probable homeland of the Bantu language group1,2,3,4,5,6,7,8,9,10,11. One individual carried the deeply divergent Y chromosome haplogroup A00, which today is found almost exclusively in the same region12,13. However, the genome-wide ancestry profiles of all four individuals are most similar to those of present-day hunter-gatherers from western Central Africa, which implies that populations in western Cameroon today—as well as speakers of Bantu languages from across the continent—are not descended substantially from the population represented by these four people. We infer an Africa-wide phylogeny that features widespread admixture and three prominent radiations, including one that gave rise to at least four major lineages deep in the history of modern humans., The Shum Laka excavations were supported by the Belgian Fund for Scientific Research (FNRS), the Université Libre de Bruxelles, the Royal Museum for Central Africa and the Leakey Foundation. The collection of samples from present-day individuals in Cameroon was supported by N. Bradman and the Melford Charitable Trust. The genotyping of the present-day individuals sampled from Cameroon was supported by the Biotechnology and Biological Sciences Research Council (grant number BB/L009382/1). I.R. was supported by a Université de Montréal exploration grant (2018-2020). M.G.T. was supported by Wellcome Trust Senior Investigator Award Grant 100719/Z/12/Z. G.H. was supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (grant number 098386/Z/12/Z). C.L-F. was supported by Obra Social La Caixa 328, Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya (GRC 2017 SGR 880), and a FEDER-MINECO grant (PGC2018-095931-B-100). Radiocarbon work was supported by the NSF Archaeometry program (grant BCS-1460369) to D.J.K. and B.J.C. M.E.P. was supported by a fellowship from the Radcliffe Institute for Advanced Study at Harvard University during the development of this project. D.R. was supported by the National Institutes of Health (NIGMS GM100233), by an Allen Discovery Center grant and by grant 61220 from the John Templeton Foundation, and is an Investigator of the Howard Hughes Medical Institute.

Until recently the Grassfields (Western Cameroon), cradle of the Bantu languages, were an unknown zone from an archaeological point of view. The excavations of Shum Laka rock shelter offer the first chrono-cultural sequence for the area. After 20 millenniums of microlithic (Late Stone Age) traditions of hunter-gatherers, a new culture with macrolithic tools, pottery and arboriculture (Stone to Metal Age) slowly developed from 6000 BC onwards. Correlation with palaeo-climatic and historical linguistic data suggests that proto-Benue-Congo and, later, proto-Bantu speakers could have been involved in these industries.

Rock shelters, often containing thick accumulations of cultural debris from repeated occupation, are the most informative archaeological sites in the forest zone of west Africa. They are, however, frequently disturbed by human and natural processes. Extensive excavations at Shum Laka rock shelter yielded a long cultural sequence for the Grassfields in NW Cameroon. The topmost, Late Holocene deposits, are analyzed for natural and cultural spatial patterning through a combination of geomorphic analysis, exhaustive 14C dating, and analysis of spatial distribution of lithic artifacts and pottery refits. we identified post-depositional disturbances and reconstructed for the first time a reliable cultural sequence for the Grassfields during the Late Holocene. Finally, we discuss the transition from the Late Stone Age to the Iron Age in the area along the Gulf of Guinea.