Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Ke Wang¹, Steven Goldstein², Madeleine Bleasdale², Bernard Clist^{3

4}, Koen Bostoen³, Paul Bakwa-Lufu⁵, Laura T Buck^{6

7}, Alison Crowther^{2

8}, Alioune Dème⁹, Roderick J McIntosh¹⁰, Julio Mercader^{11

2}, Christine Ogola¹², Robert C Power^{2

13}, Elizabeth Sawchuk^{2

14}, Peter Robertshaw¹⁵, Edwin N Wilmsen^{16

17}, Michael Petraglia^{2

8

18}, Emmanuel Ndiema¹², Fredrick K Manthi¹², Johannes Krause¹, Patrick Roberts^{2

8}, Nicole Boivin^{2

8

11

18}, Stephan Schiffels¹

Affiliations

¹ Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
² Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
³ UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Ghent, Belgium.
⁴ Institut des Mondes Africains, Paris, France.
⁵ Institut des Musées Nationaux du Congo, Kinshasa, Democratic Republic of Congo.
⁶ Department of Archaeology, University of Cambridge, Cambridge, UK.
⁷ Department of Anthropology, University of California, Davis, Davis, CA, USA.
⁸ School of Social Science, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
⁹ Department of History, Cheikh Anta Diop University, Dakar, Senegal.
¹⁰ Department of Anthropology, Yale University, New Haven, CT, USA.
¹¹ Department of Archaeology and Anthropology, University of Calgary, Calgary, Alberta, Canada.
¹² Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya.
¹³ Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany.
¹⁴ Department of Anthropology, Stony Brook University, Stony Brook, NY, USA.
¹⁵ Department of Anthropology, California State University, San Bernardino, San Bernardino, CA, USA.
¹⁶ University of Texas-Austin, Austin, TX, USA.
¹⁷ Witwatersrand University, Johannesburg, Republic of South Africa.
¹⁸ Department of Anthropology, Smithsonian Institution, Washington, DC, USA.

PMID: 32582847
PMCID: PMC7292641
DOI: 10.1126/sciadv.aaz0183

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Ke Wang et al. Sci Adv. 2020.

. 2020 Jun 12;6(24):eaaz0183.

doi: 10.1126/sciadv.aaz0183. eCollection 2020 Jun.

Authors

Affiliations

¹ Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
² Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
³ UGent Centre for Bantu Studies, Department of Languages and Cultures, Ghent University, Ghent, Belgium.
⁴ Institut des Mondes Africains, Paris, France.
⁵ Institut des Musées Nationaux du Congo, Kinshasa, Democratic Republic of Congo.
⁶ Department of Archaeology, University of Cambridge, Cambridge, UK.
⁷ Department of Anthropology, University of California, Davis, Davis, CA, USA.
⁸ School of Social Science, University of Queensland, St Lucia, Brisbane, QLD 4072, Australia.
⁹ Department of History, Cheikh Anta Diop University, Dakar, Senegal.
¹⁰ Department of Anthropology, Yale University, New Haven, CT, USA.
¹¹ Department of Archaeology and Anthropology, University of Calgary, Calgary, Alberta, Canada.
¹² Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya.
¹³ Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany.
¹⁴ Department of Anthropology, Stony Brook University, Stony Brook, NY, USA.
¹⁵ Department of Anthropology, California State University, San Bernardino, San Bernardino, CA, USA.
¹⁶ University of Texas-Austin, Austin, TX, USA.
¹⁷ Witwatersrand University, Johannesburg, Republic of South Africa.
¹⁸ Department of Anthropology, Smithsonian Institution, Washington, DC, USA.

PMID: 32582847
PMCID: PMC7292641
DOI: 10.1126/sciadv.aaz0183

Abstract

Africa hosts the greatest human genetic diversity globally, but legacies of ancient population interactions and dispersals across the continent remain understudied. Here, we report genome-wide data from 20 ancient sub-Saharan African individuals, including the first reported ancient DNA from the DRC, Uganda, and Botswana. These data demonstrate the contraction of diverse, once contiguous hunter-gatherer populations, and suggest the resistance to interaction with incoming pastoralists of delayed-return foragers in aquatic environments. We refine models for the spread of food producers into eastern and southern Africa, demonstrating more complex trajectories of admixture than previously suggested. In Botswana, we show that Bantu ancestry post-dates admixture between pastoralists and foragers, suggesting an earlier spread of pastoralism than farming to southern Africa. Our findings demonstrate how processes of migration and admixture have markedly reshaped the genetic map of sub-Saharan Africa in the past few millennia and highlight the utility of combined archaeological and archaeogenetic approaches.

Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

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Figures

**Fig. 1. Basic information of newly reported ancient genomes.**
(A) Approximate locations of new samples and published present-day modern African populations. Same legend scheme applies to the principal components analysis (PCA) plot in Fig. 2. (B) C14 dates after calibration. Samples from Botswana (green) and Uganda (orange) are based on archaeological context dates rather than accelerator mass spectrometry (AMS) measurements.

**Fig. 2. PCA of ancient genomic data analyzed in this and previous studies, together with published modern genetic data.**
Modern populations shown are detailed in the legend of Fig. 1 and fig. S1. A separate PCA with only present-day populations is shown in fig. S1A. Color circles highlight the key groups discussed in this paper and summarized in Fig. 3A.

**Fig. 3. Admixture history of ancient African populations.**
(A) Overview of coexistence of distinct African ancestries through time drawing on currently available ancient genomes. (B) Ancestral components of ancient African groups/individuals according to qpAdm. We order ancient groups in the same order shown in (A) and highlight newly reported genetic groups/individuals in bold. P values and estimated ancestral proportions can be found in table S3.

See this image and copyright information in PMC

References

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Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Affiliations

Ancient genomes reveal complex patterns of population movement, interaction, and replacement in sub-Saharan Africa

Authors

Affiliations

Abstract

Figures

References

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Miscellaneous