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High-depth African genomes inform human migration and health

Author

Listed:
  • Ananyo Choudhury

    (University of the Witwatersrand)

  • Shaun Aron

    (University of the Witwatersrand)

  • Laura R. Botigué

    (Plant and Animal Genomics Program, CSIC-IRTA-UAB-UB)

  • Dhriti Sengupta

    (University of the Witwatersrand)

  • Gerrit Botha

    (IDM, University of Cape Town)

  • Taoufik Bensellak

    (Abdelmalek Essaadi University, ENSA)

  • Gordon Wells

    (Centre for Proteomic and Genomic Research (CPGR)
    University of the Western Cape
    Africa Health Research Institute)

  • Judit Kumuthini

    (Centre for Proteomic and Genomic Research (CPGR)
    University of the Western Cape)

  • Daniel Shriner

    (National Human Genome Research Institute, National Institutes of Health)

  • Yasmina J. Fakim

    (University of Mauritius
    University of Mauritius)

  • Anisah W. Ghoorah

    (University of Mauritius)

  • Eileen Dareng

    (University of Cambridge
    Institute of Human Virology Nigeria)

  • Trust Odia

    (Covenant University)

  • Oluwadamilare Falola

    (Covenant University)

  • Ezekiel Adebiyi

    (Covenant University
    Covenant University)

  • Scott Hazelhurst

    (University of the Witwatersrand
    University of the Witwatersrand)

  • Gaston Mazandu

    (IDM, University of Cape Town)

  • Oscar A. Nyangiri

    (Makerere University)

  • Mamana Mbiyavanga

    (IDM, University of Cape Town)

  • Alia Benkahla

    (Institute Pasteur of Tunis)

  • Samar K. Kassim

    (Ain Shams University, Abbaseya)

  • Nicola Mulder

    (IDM, University of Cape Town)

  • Sally N. Adebamowo

    (University of Maryland Baltimore
    University of Maryland Baltimore)

  • Emile R. Chimusa

    (University of Cape Town)

  • Donna Muzny

    (Baylor College of Medicine)

  • Ginger Metcalf

    (Baylor College of Medicine)

  • Richard A. Gibbs

    (Baylor College of Medicine
    Baylor College of Medicine)

  • Charles Rotimi

    (National Human Genome Research Institute, National Institutes of Health)

  • Michèle Ramsay

    (University of the Witwatersrand
    University of the Witwatersrand)

  • Adebowale A. Adeyemo

    (National Human Genome Research Institute, National Institutes of Health)

  • Zané Lombard

    (University of the Witwatersrand)

  • Neil A. Hanchard

    (Baylor College of Medicine)

Abstract

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals—comprising 50 ethnolinguistic groups, including previously unsampled populations—to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that population from Zambia were a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.

Suggested Citation

  • Ananyo Choudhury & Shaun Aron & Laura R. Botigué & Dhriti Sengupta & Gerrit Botha & Taoufik Bensellak & Gordon Wells & Judit Kumuthini & Daniel Shriner & Yasmina J. Fakim & Anisah W. Ghoorah & Eileen , 2020. "High-depth African genomes inform human migration and health," Nature, Nature, vol. 586(7831), pages 741-748, October.
  • Handle: RePEc:nat:nature:v:586:y:2020:i:7831:d:10.1038_s41586-020-2859-7
    DOI: 10.1038/s41586-020-2859-7
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    Citations

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    Cited by:

    1. Sam Tallman & Maria das Dores Sungo & Sílvio Saranga & Sandra Beleza, 2023. "Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Tracey Hurrell & Jerolen Naidoo & Tiro Ntlhafu & Janine Scholefield, 2024. "An African perspective on genetically diverse human induced pluripotent stem cell lines," Nature Communications, Nature, vol. 15(1), pages 1-5, December.
    3. Fiona B. Tamburini & Dylan Maghini & Ovokeraye H. Oduaran & Ryan Brewster & Michaella R. Hulley & Venesa Sahibdeen & Shane A. Norris & Stephen Tollman & Kathleen Kahn & Ryan G. Wagner & Alisha N. Wade, 2022. "Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa," Nature Communications, Nature, vol. 13(1), pages 1-18, December.
    4. Sulagna Ghosh & Ralda Nehme & Lindy E. Barrett, 2022. "Greater genetic diversity is needed in human pluripotent stem cell models," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    5. Surina Singh & Ananyo Choudhury & Scott Hazelhurst & Nigel J. Crowther & Palwendé R. Boua & Hermann Sorgho & Godfred Agongo & Engelbert A. Nonterah & Lisa K. Micklesfield & Shane A. Norris & Isaac Kis, 2023. "Genome-wide association study meta-analysis of blood pressure traits and hypertension in sub-Saharan African populations: an AWI-Gen study," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    6. Pamela X. Y. Soh & Naledi Mmekwa & Desiree C. Petersen & Kazzem Gheybi & Smit van Zyl & Jue Jiang & Sean M. Patrick & Raymond Campbell & Weerachai Jaratlerdseri & Shingai B. A. Mutambirwa & M. S. Rian, 2023. "Prostate cancer genetic risk and associated aggressive disease in men of African ancestry," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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