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A weakly structured stem for human origins in Africa

Nature volume 617, pages 755–763 (2023)Cite this article

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A Publisher Correction to this article was published on 17 July 2023

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Abstract

Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent1. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times1. Here we seek to discriminate among such models by considering linkage disequilibrium and diversity-based statistics, optimized for rapid, complex demographic inference2. We infer detailed demographic models for populations across Africa, including eastern and western representatives, and newly sequenced whole genomes from 44 Nama (Khoe-San) individuals from southern Africa. We infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such weakly structured stem models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa2,3,4,5,6,7. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar, and that only an inferred 1–4% of genetic differentiation among contemporary human populations can be attributed to genetic drift between stem populations. We show that model misspecification explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.

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Fig. 1: Proposed conceptual models of early human history in Africa.
Fig. 2: Genetic diversity across Africa.
Fig. 3: A weakly structured stem best describes two-locus statistics.
Fig. 4: Structure among stems is weak and present-day structure is generally recent.
Fig. 5: Model validation using independent statistics.

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Data availability

Nama sequencing data are available from the European Genome-Phenome Archive (EGA), accession number EGAD00001006198. Data access is permitted for non-commercial, population origins or ancestry research upon application to the South African Data Access Committee with appropriate institutional review board approval. The African Diversity Reference Panel can be found at accession EGAS00001000960.

Code availability

Code for the software used in this paper is found at the following locations: moments-LD (https://bitbucket.org/simongravel/moments), Demes (https://github.com/popsim-consortium/demes-python), Relate (https://myersgroup.github.io/relate/), msprime (https://github.com/tskit-dev/msprime) and tskit (https://github.com/tskit-dev/tskit).

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Acknowledgements

We thank participants for the DNA contributions that enabled this study; in particular, we wish to highlight the generous participation of the Richtersveld Nama community in South Africa and help from local research assistants W. De Klerk and H. Kaimann. Additional assistance and community engagement was conducted by J. Myrick, C. Gignoux, C. Uren and C. Werely. We thank the African Genome Diversity Project for data generation, including T. Carensten, D. Gurdasani and M. Sandhu; L. Anderson-Trocmé and G. Femerling for assistance in creating the map in Fig. 2 and Supplementary Fig. 2, respectively; and N. M. Morales-Garcia for data visualization discussion and designing Figs. 1 and 3. This research was supported by CIHR project grant 437576, Natural Sciences and Engineering Research Council of Canada (NSERC) grant RGPIN-2017-04816, the Canada Research Chair program to S.G. and the Canada Foundation for Innovation, and an NIH grant R35GM133531 to B.M.H.; and E.G.A. was supported by NIH K01 MH121659 and K12 GM102778. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. M.M. and E.H. acknowledge the support of the DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, the South African Medical Research Council Centre for Tuberculosis Research, and the Division of Molecular Biology and Human Genetics at Stellenbosch University, Cape Town, South Africa.

Author information

Authors and Affiliations

  1. Department of Integrative Biology, University of Wisconsin–Madison, Madison, WI, USA

    Aaron P. Ragsdale

  2. Department of Anthropology, University of California, Davis, CA, USA

    Timothy D. Weaver & Brenna M. Henn

  3. Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA

    Elizabeth G. Atkinson

  4. DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Stellenbosch University, Cape Town, South Africa

    Eileen G. Hoal & Marlo Möller

  5. South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Cape Town, South Africa

    Eileen G. Hoal & Marlo Möller

  6. Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa

    Eileen G. Hoal & Marlo Möller

  7. Genome Center, University of California, Davis, CA, USA

    Brenna M. Henn

  8. Department of Human Genetics, McGill University, Montreal, Quebec, Canada

    Simon Gravel

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Contributions

A.P.R., B.M.H. and S.G. designed the study. B.M.H., E.H. and M.M. designed recruitment protocols and recruited participants. B.M.H. and E.G.A. performed data quality control. A.P.R., B.M.H. and S.G. designed the statistical analyses. A.P.R. conducted the statistical analyses. A.P.R., T.D.W., B.M.H. and S.G. interpreted the results and wrote the first draft of the article. All authors read and edited the paper.

Corresponding authors

Correspondence to Brenna M. Henn or Simon Gravel.

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Nature thanks Marta Mirazon Lahr and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Supplementary Information

This file contains further discussion, methods and data, Supplementary Tables S1–S8, Supplementary Figs. S1–S40, and Supplementary References.

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Supplementary Data

This zipped file contains inferred demographic models in Demes format for all models presented in the main text and all alternative models used in validation of our main results that are discussed in the Supplementary Information.

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Ragsdale, A.P., Weaver, T.D., Atkinson, E.G. et al. A weakly structured stem for human origins in Africa. Nature 617, 755–763 (2023). https://doi.org/10.1038/s41586-023-06055-y

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