Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Ancient West African foragers in the context of African population history

Nature volume 577, pages 665–670 (2020)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

Prices may be subject to local taxes which are calculated during checkout

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.

References

  1. de Maret, P. in Aspects of African Archaeology: Papers from the 10th Congress of the Pan-African Association of Prehistory and Related Studies (eds Pwiti, G. & Soper, R.) 274–279 (Univ. of Zimbabwe Publications, Harare, 1996).

  2. Ribot, I., Orban, R. & de Maret, P. The Prehistoric Burials of Shum Laka Rockshelter (North-West Cameroon) (Annales du Musée Royal de l’Afrique Centrale vol. 164) (Musée Royal de l’Afrique Centrale, Tervuren, 2001).

  3. Lavachery, P. The Holocene archaeological sequence of Shum Laka rock shelter (Grassfields, western Cameroon). Afr. Archaeol. Rev. 18, 213–247 (2001).

    Article  Google Scholar 

  4. de Maret, P. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.) 627–643 (Oxford Univ. Press, 2013).

  5. Cornelissen, E. in The Oxford Handbook of African Archaeology (eds Mitchell, P. & Lane, P.) 403–417 (Oxford Univ. Press, 2013).

  6. Vansina, J. New linguistic evidence and ‘the Bantu expansion’. J. Afr. Hist. 36, 173–195 (1995).

    Article  Google Scholar 

  7. Tishkoff, S. A. et al. The genetic structure and history of Africans and African Americans. Science 324, 1035–1044 (2009).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  8. Berniell-Lee, G. et al. Genetic and demographic implications of the Bantu expansion: insights from human paternal lineages. Mol. Biol. Evol. 26, 1581–1589 (2009).

    Article  CAS  PubMed  Google Scholar 

  9. Bostoen, K. et al. Middle to late Holocene Paleoclimatic change and the early Bantu expansion in the rain forests of Western Central Africa. Curr. Anthropol. 56, 354–384 (2015).

    Article  Google Scholar 

  10. Patin, E. et al. Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America. Science 356, 543–546 (2017).

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Bostoen, K. in Oxford Research Encyclopedia of African History (ed. Spear, T.) https://oxfordre.com/africanhistory/view/10.1093/acrefore/9780190277734.001.0001/acrefore-9780190277734-e-191 (Oxford Univ. Press, 2018).

  12. Mendez, F. L. et al. An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am. J. Hum. Genet. 92, 454–459 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Krahn, T., Schrack, B., Fomine, F. L. M. & Krahn, A.-M. Searching for our most distant (paternal) cousins in Cameroon. Institute for Genetic Genealogy 2016 Conference, San Diego (2016).

  14. Rohland, N., Harney, E., Mallick, S., Nordenfelt, S. & Reich, D. Partial uracil-DNA-glycosylase treatment for screening of ancient DNA. Phil. Trans. R. Soc. Lond. B 370, 20130624 (2015).

    Article  CAS  Google Scholar 

  15. Gonder, M. K., Mortensen, H. M., Reed, F. A., de Sousa, A. & Tishkoff, S. A. Whole-mtDNA genome sequence analysis of ancient African lineages. Mol. Biol. Evol. 24, 757–768 (2007).

    Article  CAS  PubMed  Google Scholar 

  16. Batini, C. et al. Phylogeography of the human mitochondrial L1c haplogroup: genetic signatures of the prehistory of Central Africa. Mol. Phylogenet. Evol. 43, 635–644 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Wood, E. T. et al. Contrasting patterns of Y chromosome and mtDNA variation in Africa: evidence for sex-biased demographic processes. Eur. J. Hum. Genet. 13, 867–876 (2005).

    Article  CAS  PubMed  Google Scholar 

  18. Karmin, M. et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 25, 459–466 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Mendez, F. L., Poznik, G. D., Castellano, S. & Bustamante, C. D. The divergence of Neandertal and modern human Y chromosomes. Am. J. Hum. Genet. 98, 728–734 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Fan, S. et al. African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Genome Biol. 20, 82 (2019).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. Schlebusch, C. M. et al. Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago. Science 358, 652–655 (2017).

    Article  ADS  CAS  PubMed  Google Scholar 

  22. Skoglund, P. et al. Reconstructing prehistoric African population structure. Cell 171, 59–71 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Gallego Llorente, M. et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350, 820–822 (2015).

    Article  ADS  CAS  PubMed  Google Scholar 

  24. Gronau, I., Hubisz, M. J., Gulko, B., Danko, C. G. & Siepel, A. Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet. 43, 1031–1034 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Mallick, S. et al. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature 538, 201–206 (2016).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  26. van de Loosdrecht, M. et al. Pleistocene North African genomes link Near Eastern and sub-Saharan African human populations. Science 360, 548–552 (2018).

    Article  ADS  PubMed  CAS  Google Scholar 

  27. Plagnol, V. & Wall, J. D. Possible ancestral structure in human populations. PLoS Genet. 2, e105 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  28. Hammer, M. F., Woerner, A. E., Mendez, F. L., Watkins, J. C. & Wall, J. D. Genetic evidence for archaic admixture in Africa. Proc. Natl Acad. Sci. USA 108, 15123–15128 (2011).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  29. Durvasula, A. & Sankararaman, S. Recovering signals of ghost archaic admixture in the genomes of present-day Africans. Preprint at bioRxiv https://doi.org/10.1101/285734 (2018).

  30. Hey, J. et al. Phylogeny estimation by integration over isolation with migration models. Mol. Biol. Evol. 35, 2805–2818 (2018).

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Ragsdale, A. P. & Gravel, S. Models of archaic admixture and recent history from two-locus statistics. PLoS Genet. 15, e1008204 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Huysecom, E. et al. The emergence of pottery in Africa during the 10th millennium calBC: new evidence from Ounjougou (Mali). Antiquity 83, 905–917 (2009).

    Article  Google Scholar 

  33. Gasse, F. Hydrological changes in the African tropics since the Last Glacial Maximum. Quat. Sci. Rev. 19, 189–211 (2000).

    Article  ADS  Google Scholar 

  34. Triska, P. et al. Extensive admixture and selective pressure across the Sahel belt. Genome Biol. Evol. 7, 3484–3495 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Laval, G., Patin, E., Barreiro, L. B. & Quintana-Murci, L. Formulating a historical and demographic model of recent human evolution based on resequencing data from noncoding regions. PLoS ONE 5, e10284 (2010).

    Article  ADS  PubMed  PubMed Central  CAS  Google Scholar 

  36. Soares, P. et al. The expansion of mtDNA haplogroup L3 within and out of Africa. Mol. Biol. Evol. 29, 915–927 (2012).

    Article  CAS  PubMed  Google Scholar 

  37. Behar, D. M. et al. A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675–684 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Poznik, G. D. et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nat. Genet. 48, 593–599 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Pickrell, J. et al. The genetic prehistory of southern Africa. Nat. Commun. 3, 1143 (2012).

    Article  ADS  PubMed  CAS  Google Scholar 

  40. Scerri, E. in Oxford Research Encyclopedia of African History (ed. Spear, T.) https://oxfordre.com/africanhistory/view/10.1093/acrefore/9780190277734.001.0001/acrefore-9780190277734-e-137 (Oxford University Press, 2017).

  41. Hublin, J.-J. et al. New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens. Nature 546, 289–292 (2017).

    Article  ADS  CAS  PubMed  Google Scholar 

  42. Harvati, K. et al. The later Stone Age calvaria from Iwo Eleru, Nigeria: morphology and chronology. PLoS ONE 6, e24024 (2011).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  43. Scerri, E. M., Blinkhorn, J., Niang, K., Bateman, M. D. & Groucutt, H. S. Persistence of Middle Stone Age technology to the Pleistocene/Holocene transition supports a complex hominin evolutionary scenario in West Africa. J Archaeol. Sci. Rep. 11, 639–646 (2017).

    Google Scholar 

  44. Scerri, E. M. L. et al. Did our species evolve in subdivided populations across Africa, and why does it matter? Trends Ecol. Evol. 33, 582–594 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  45. Henn, B. M., Steele, T. E. & Weaver, T. D. Clarifying distinct models of modern human origins in Africa. Curr. Opin. Genet. Dev. 53, 148–156 (2018).

    Article  CAS  PubMed  Google Scholar 

  46. Dabney, J. et al. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc. Natl Acad. Sci. USA 110, 15758–15763 (2013).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  47. Korlević, P. et al. Reducing microbial and human contamination in DNA extractions from ancient bones and teeth. Biotechniques 59, 87–93 (2015).

    Article  PubMed  CAS  Google Scholar 

  48. Briggs, A. W. et al. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 38, e87 (2010).

    Article  PubMed  CAS  Google Scholar 

  49. Lipson, M. et al. Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science 361, 92–95 (2018).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  50. Fu, Q. et al. DNA analysis of an early modern human from Tianyuan Cave, China. Proc. Natl Acad. Sci. USA 110, 2223–2227 (2013).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  51. Haak, W. et al. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature 522, 207–211 (2015).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  52. Fu, Q. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  53. Mathieson, I. et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528, 499–503 (2015).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  54. Lazaridis, I. et al. Genomic insights into the origin of farming in the ancient Near East. Nature 536, 419–424 (2016).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  55. Kircher, M., Sawyer, S. & Meyer, M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 40, e3 (2012).

    Article  CAS  PubMed  Google Scholar 

  56. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Weissensteiner, H. et al. HaploGrep 2: mitochondrial haplogroup classification in the era of high-throughput sequencing. Nucleic Acids Res. 44, W58–W63 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Skoglund, P., Storå, J., Götherström, A. & Jakobsson, M. Accurate sex identification of ancient human remains using DNA shotgun sequencing. J. Archaeol. Sci. 40, 4477–4482 (2013).

    Article  CAS  Google Scholar 

  59. Korneliussen, T. S., Albrechtsen, A. & Nielsen, R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics 15, 356 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Giresse, P., Maley, J. & Brenac, P. Late Quaternary palaeoenvironments in the Lake Barombi Mbo (West Cameroon) deduced from pollen and carbon isotopes of organic matter. Palaeogeogr. Palaeoclimatol. Palaeoecol. 107, 65–78 (1994).

    Article  Google Scholar 

  61. Lohse, J. C., Culleton, B. J., Black, S. L. & Kennett, D. J. A precise chronology of middle to late Holocene bison exploitation in the far southern Great Plains. J. Texas Archeol. Hist. 1, 94–126 (2014).

    Google Scholar 

  62. van Klinken, G. J. Bone collagen quality indicators for palaeodietary and radiocarbon measurements. J. Archaeol. Sci. 26, 687–695 (1999).

    Article  Google Scholar 

  63. Lavachery, P. De la Pierre au Métal: Archéologie des Dépôts Holocènes de l’Abri de Shum Laka (Cameroun). PhD thesis, Université Libre de Bruxelles (1997).

  64. Bronk Ramsey, C., Higham, T. F., Owen, D., Pike, A. & Hedges, R. E. Radiocarbon dates from the Oxford AMS system: archaeometry datelist 31. Archaeometry 44, 1–150 (2002).

    Article  Google Scholar 

  65. Ward, G. K. & Wilson, S. R. Procedures for comparing and combining radiocarbon age determinations: a critique. Archaeometry 20, 19–31 (1978).

    Article  CAS  Google Scholar 

  66. Ramsey, C. B. & Lee, S. Recent and planned developments of the program OxCal. Radiocarbon 55, 720–730 (2013).

    Article  CAS  Google Scholar 

  67. Reimer, P. J. et al. IntCal13 and Marine13 radiocarbon age calibration curves 0–50,000 years cal bp. Radiocarbon 55, 1869–1887 (2013).

    Article  CAS  Google Scholar 

  68. Hogg, A. G. et al. SHCal13 Southern Hemisphere calibration, 0–50,000 years cal BP. Radiocarbon 55, 1889–1903 (2013).

    Article  CAS  Google Scholar 

  69. Marsh, E. J. et al. IntCal, SHCal, or a mixed curve? Choosing a 14C calibration curve for archaeological and paleoenvironmental records from tropical South America. Radiocarbon 60, 925–940 (2018).

    Article  CAS  Google Scholar 

  70. Jobling, M. A. & Tyler-Smith, C. Human Y-chromosome variation in the genome-sequencing era. Nat. Rev. Genet. 18, 485–497 (2017).

    Article  CAS  PubMed  Google Scholar 

  71. Patterson, N., Price, A. L. & Reich, D. Population structure and eigenanalysis. PLoS Genet. 2, e190 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  72. Liu, L. T., Dobriban, E. & Singer, A. ePCA: high dimensional exponential family PCA. Preprint at https://arxiv.org/abs/1611.05550 (2016).

  73. Patterson, N. et al. Ancient admixture in human history. Genetics 192, 1065–1093 (2012).

    Article  PubMed  PubMed Central  Google Scholar 

  74. Lipson, M. & Reich, D. A working model of the deep relationships of diverse modern human genetic lineages outside of Africa. Mol. Biol. Evol. 34, 889–902 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Lipson, M. et al. Parallel palaeogenomic transects reveal complex genetic history of early European farmers. Nature 551, 368–372 (2017).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  76. Moeyersons, J., Cornelissen, E., Lavachery, P. & Doutrelepont, H. L’abri sous-roche de Shum Laka (Cameroun Occidental): données climatologiques et occupation humaine depuis 30.000 ans. Geo. Eco. Trop. 20, 39–60 (1996).

    Google Scholar 

  77. Cornelissen, E. in Field Manual for African Archaeology (eds Smith, A. L. et al.) 168–173 (Royal Museum for Central Africa, 2017).

  78. Prüfer, K. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014).

    Article  ADS  PubMed  CAS  Google Scholar 

Download references

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

Author notes

  1. Iñigo Olalde

    Present address: Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain

  2. Nasreen Broomandkhoshbacht

    Present address: Department of Anthropology, University of California, Santa Cruz, CA, USA

  3. Jonas Oppenheimer

    Present address: Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA

  4. Neil Bradman

    Present address: The Henry Stewart Group, London, UK

  5. These authors jointly supervised this work: Mary E. Prendergast, David Reich

Authors and Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, MA, USA

    Mark Lipson, Swapan Mallick, Nadin Rohland, Iñigo Olalde, Nicole Adamski, Nasreen Broomandkhoshbacht, Ann Marie Lawson, Jonas Oppenheimer, Kristin Stewardson, Nick Patterson, Mary E. Prendergast & David Reich

  2. Département d’Anthropologie, Université de Montréal, Montreal, Quebec, Canada

    Isabelle Ribot

  3. Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Swapan Mallick & David Reich

  4. Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA

    Swapan Mallick, Nicole Adamski, Nasreen Broomandkhoshbacht, Ann Marie Lawson, Jonas Oppenheimer, Kristin Stewardson & David Reich

  5. UCL Genetics Institute, University College London, London, UK

    Saioa López, Neil Bradman, Mark G. Thomas & Garrett Hellenthal

  6. Department of Arts and Archaeology, University of Yaoundé I, Yaoundé, Cameroon

    Raymond Neba’ane Asombang

  7. Department of Geosciences, Biogeology, University of Tübingen, Tübingen, Germany

    Hervé Bocherens

  8. Senckenberg Research Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany

    Hervé Bocherens

  9. Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA, USA

    Brendan J. Culleton

  10. Department of Cultural Anthropology and History, Royal Museum for Central Africa, Tervuren, Belgium

    Els Cornelissen

  11. CNRS, UMR 5199-PACEA, Université de Bordeaux, Bordeaux, France

    Isabelle Crevecoeur

  12. Faculté de Philosophie et Sciences Sociales, Université Libre de Bruxelles, Brussels, Belgium

    Pierre de Maret

  13. Department of History and African Civilization, University of Buea, Buea, Cameroon

    Forka Leypey Mathew Fomine

  14. Agence Wallonne du Patrimoine, Service Public de Wallonie, Namur, Belgium

    Philippe Lavachery

  15. Department of Arts and Archaeology, University of Yaoundé I, Yaoundé, Cameroon

    Christophe Mbida Mindzie

  16. Royal Belgian Institute of Natural Sciences, Brussels, Belgium

    Rosine Orban, Patrick Semal & Wim Van Neer

  17. Department of Anthropology, Stony Brook University, Stony Brook, NY, USA

    Elizabeth Sawchuk

  18. Department of Genetics, Evolution and Environment, University College London, London, UK

    Mark G. Thomas & Garrett Hellenthal

  19. Department of Biology, University of Leuven, Leuven, Belgium

    Wim Van Neer

  20. Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA

    Krishna R. Veeramah

  21. Department of Anthropology, University of California, Santa Barbara, CA, USA

    Douglas J. Kennett

  22. Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA

    Nick Patterson & David Reich

  23. Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain

    Carles Lalueza-Fox

  24. Division of Social Science, Duke Kunshan University, Kunshan, China

    Scott MacEachern

  25. Department of Sociology and Anthropology, Saint Louis University, Madrid, Spain

    Mary E. Prendergast

Authors
  1. Mark Lipson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Isabelle Ribot
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Swapan Mallick
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Nadin Rohland
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Iñigo Olalde
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nicole Adamski
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Nasreen Broomandkhoshbacht
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Ann Marie Lawson
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Saioa López
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jonas Oppenheimer
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Kristin Stewardson
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Raymond Neba’ane Asombang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Hervé Bocherens
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Neil Bradman
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Brendan J. Culleton
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Els Cornelissen
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Isabelle Crevecoeur
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Pierre de Maret
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Forka Leypey Mathew Fomine
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Philippe Lavachery
    View author publications

    You can also search for this author in PubMed Google Scholar

  21. Christophe Mbida Mindzie
    View author publications

    You can also search for this author in PubMed Google Scholar

  22. Rosine Orban
    View author publications

    You can also search for this author in PubMed Google Scholar

  23. Elizabeth Sawchuk
    View author publications

    You can also search for this author in PubMed Google Scholar

  24. Patrick Semal
    View author publications

    You can also search for this author in PubMed Google Scholar

  25. Mark G. Thomas
    View author publications

    You can also search for this author in PubMed Google Scholar

  26. Wim Van Neer
    View author publications

    You can also search for this author in PubMed Google Scholar

  27. Krishna R. Veeramah
    View author publications

    You can also search for this author in PubMed Google Scholar

  28. Douglas J. Kennett
    View author publications

    You can also search for this author in PubMed Google Scholar

  29. Nick Patterson
    View author publications

    You can also search for this author in PubMed Google Scholar

  30. Garrett Hellenthal
    View author publications

    You can also search for this author in PubMed Google Scholar

  31. Carles Lalueza-Fox
    View author publications

    You can also search for this author in PubMed Google Scholar

  32. Scott MacEachern
    View author publications

    You can also search for this author in PubMed Google Scholar

  33. Mary E. Prendergast
    View author publications

    You can also search for this author in PubMed Google Scholar

  34. David Reich
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

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.

Corresponding author

Correspondence to Mark Lipson.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature thanks George Busby, Katerina Harvati, Stephan Schiffels, Lluis Quintana-Murci and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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
Full size table
Extended Data Table 2 Allele-sharing statistics for deep ancestry
Full size table
Extended Data Table 3 Admixture graph parameter estimates
Full size table

Supplementary information

Supplementary Information

This file contains supplementary information sections 1-3.

Reporting Summary

Supplementary Tables

This file contains Supplementary Tables 1-5.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41586-020-1929-1

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing