Ancient West African foragers in the context of African population history

Abstract

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.

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Fig. 1: Y chromosome phylogeny.
Fig. 2: PCA results.
Fig. 3: Allele-sharing statistics.
Fig. 4: Admixture graph results.

Data availability

The aligned sequences are available through the European Nucleotide Archive under accession number PRJEB32086. Genotype data used in analysis are available at https://reich.hms.harvard.edu/datasets. Any other relevant data are available from the corresponding author upon reasonable request.

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Acknowledgements

We thank I. Lazaridis, V. Narasimhan and K. Sirak for discussions and comments; M. Karmin for help with Y chromosome data; L. Eccles for help with radiocarbon dating; B. Erkkila for help with isotopic analysis; R. Bernardos, M. Mah and Z. Zhang for other technical assistance; J.-P. Warnier for his role in locating the site of Shum Laka; and O. Graf for proofreading, photograph editing and other figure assistance for the Supplementary Information. 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.

Author information

N.R., G.H., M.E.P. and D.R. supervised the study. I.R., R.N.A., H.B., E.C., I.C., P.d.M., P.L., C.M.M., R.O., E.S., P.S., W.V.N., C.L.-F., S. MacEachern and M.E.P. provided samples and assembled archaeological and anthropological materials and information. S.L., N. Bradman, F.L.M.F., M.G.T., K.R.V. and G.H. provided data from present-day populations. S. Mallick, N.R., N.A., N. Broomandkhoshbacht, A.M.L., J.O., K.S. and D.R. performed ancient DNA laboratory and data-processing work. B.J.C. and D.J.K. performed radiocarbon analysis. M.L., S. Mallick, I.O., N.P. and D.R. analysed genetic data. M.L., I.R., H.B., E.S., C.L.-F., S. MacEachern, M.E.P. and D.R. wrote the manuscript.

Correspondence to Mark Lipson.

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Extended data figures and tables

Extended Data Fig. 1 Overview of the site of Shum Laka.

The left column represents generalized stratigraphy, with radiocarbon dates (uncalibrated years before present) shown as red dots on the y axis, and deposits indicated by their archaeological nomenclature. P, S/Si, Pleistocene; T, A, Holocene; Ao, Holocene ochre ashy layer; Ag, Holocene grey ashy layer (after ref. 76). Columns 1–6 display the chronological extents of technological traditions: 1, microlithic quartz industry; 2, macrolithic flake and blade industry on basalt; 3, bifaces of the axe–hoe type; 4, pecked grounded adze and arrow heads; 5, pottery; and 6, iron objects. Column 7 indicates the two burial phases. Column 8 shows climatic reconstructions based on carbon stable isotopes and pollen from organic matter extracted from sediment cores at Lake Barombi Mbo in western Cameroon (more arid conditions to the left and more humid conditions to the right60,76), along with archaeological eras. IA, Iron Age; LSA, Later Stone Age; SMA, Stone to Metal Age. RMCA Collection; drawings by Y. Paquay, composition © RMCA, Tervuren; modified by E. Cornelissen77.

Extended Data Fig. 2 Kinship analysis.

Mean genome-wide allelic mismatch rates for each pair of individuals (blue), as well as intra-individual comparisons (red), are shown. We selected one read per individual at random at each targeted SNP (using all 1,233,013 targeted sites). Monozygotic twins (or intra-individual comparisons) are expected to have a value one-half as large as unrelated individuals; first-degree relatives, halfway between monozygotic twins and unrelated individuals; second-degree relatives, halfway between first-degree relatives and unrelated individuals; and so on. The presence of inbreeding also serves to reduce the rate of mismatches. For 4/A and 5/B, we can eliminate a grandparent–grandchild relationship because both died as children, and the lack of long segments with IBD sharing on both homologous chromosomes implies that they are not double cousins (the few ostensible double-IBD stretches are probably a result of inbreeding (Supplementary Information section 2)). Thus, we can conclude that they were either uncle and niece (or aunt and nephew) or half-siblings. Bars show 99% confidence intervals (computed by block jackknife).

Extended Data Fig. 3 Alternative PCA and allele-sharing analyses.

a, Broad-scale PCA (differing from Fig. 2a by projecting all present-day Cameroon populations; again using 593,124 Human Origins SNPs). Groups shown in blue were projected onto axes computed using the other populations. HG, hunter-gatherers. The grouping marked W-Cent. HG consists of Aka and Cameroon hunter-gatherers (Baka, Bakola and Bedzan). The majority of the present-day Cameroon individuals fall in a tight cluster near other West Africans and Bantu-speakers. b, Relative allele sharing (mean ± s.e.m., multiplied by 10,000, computed on 538,133 SNPs, as in Fig. 3b) with the Shum Laka individuals versus East Africans (f4(X, Yoruba; Shum Laka, Somali); x axis) and versus Aka (f4(X, Yoruba; Shum Laka, Aka); y axis) for present-day populations from Cameroon (blue points) and southern and eastern Bantu-speakers (Herero in red and Chewa in orange). The Mada and Fulani share more alleles with the Shum Laka individuals than they do with the Aka, but this is probably a secondary consequence of admixture from East or North African sources (as reflected in greater allele sharing with Somali individuals) (Supplementary Information section 3). Bars show one s.e.m. in each direction.

Extended Data Fig. 4 Primary inferred admixture graph with full parameters.

Of the approximately 1,200,000 targeted SNPs, 932,000 are used for fitting (that is, are covered by all populations in the model). Branch lengths (in units of squared allele frequency divergence) are rounded to the nearest integer. All f-statistics relating the populations are predicted to within 2.3 standard errors of their observed values.

Extended Data Fig. 5 Schematic of first alternative admixture graph.

Results are shown including ancient individuals from Taforalt in Morocco associated with the Iberomaurusian culture, with the Shum Laka individuals modelled as having a mixture of ancestry related to western Central African hunter-gatherers plus two additional components: one from within the main portion of the West African clade, and one that splits at nearly the same point as one of the sources that contributes ancestry to the Taforalt individuals. Branch lengths are not drawn to scale. Points at which multiple lineages are shown diverging simultaneously indicate splits that occur in short succession (the order of which we cannot confidently assess) but are not meant to represent exact multifurcations. *Proportion not well-constrained (for Mbuti, the sum of the two indicated proportions is well-constrained but not the separate values). Supplementary Information section 3 provides the full parameters of the inferred model.

Extended Data Fig. 6 Deep ancestry correlation from the West African clade.

An allele-sharing statistic sensitive to ancestry that splits more deeply than southern African hunter-gatherers (f4(X, Mursi; chimpanzee, ancient South African hunter-gatherers), mean ± 2 s.e.m. from block jackknife, computed on 1,121,119 SNPs, as in Fig. 3a) is shown as a function of ancestry related to the West African clade (from admixture graph results; the Mota individual, Yoruba and Lemande are shifted slightly away from the boundaries for legibility). The (relative) allele-sharing rate for Mursi is zero according to the definition of the statistic.

Extended Data Fig. 7 Schematic of the second alternative admixture graph.

Results are shown with a single-component deep source for West Africans. Branch lengths are not drawn to scale. Points at which multiple lineages are shown diverging simultaneously indicate splits that occur in short succession (the order of which we cannot confidently assess) but are not meant to represent exact multifurcations. *Proportion is not well-constrained (for Mbuti, the sum of the two indicated proportions is well-constrained but not the separate values). Supplementary Information section 3 provides the full parameters of the inferred model.

Extended Data Table 1 Populations in the study
Extended Data Table 2 Allele-sharing statistics for deep ancestry
Extended Data Table 3 Admixture graph parameter estimates

Supplementary information

Supplementary Information

This file contains supplementary information sections 1-3.

Reporting Summary

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Lipson, M., Ribot, I., Mallick, S. et al. Ancient West African foragers in the context of African population history. Nature 577, 665–670 (2020). https://doi.org/10.1038/s41586-020-1929-1

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