Article

Reconstructing an African haploid genome from the 18th century

  • Nature Geneticsvolume 50pages199205 (2018)
  • doi:10.1038/s41588-017-0031-6
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Abstract

A genome is a mosaic of chromosome fragments from ancestors who existed some arbitrary number of generations earlier. Here, we reconstruct the genome of Hans Jonatan (HJ), born in the Caribbean in 1784 to an enslaved African mother and European father. HJ migrated to Iceland in 1802, married and had two children. We genotyped 182 of his 788 descendants using single-nucleotide polymorphism (SNP) chips and whole-genome sequenced (WGS) 20 of them. Using these data, we reconstructed 38% of HJ’s maternal genome and inferred that his mother was from the region spanned by Benin, Nigeria and Cameroon.

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Acknowledgements

A.J., H.J. and C.F.-L. were funded by the EUROTAST Marie Curie Framework Programme 7 Initial Training Network 290344). We thank all the members of EUROTAST network for their helpful comments and suggestions. S.S.E. and V.B.G. received grants from The Research Fund of University of Iceland for doctoral studies. M.S.E. received a grant from the Icelandic Research Fund (163428-051).We thank E. Soumonni, a historian whose advice guided the recruitment of Beninese individuals, and J.-P. Chippaux (CERPAGE, Cotonou, Benin) for his help with local authorities.

Author information

Affiliations

  1. deCODE Genetics/Amgen, Reykjavik, Iceland

    • Anuradha Jagadeesan
    • , Ellen D. Gunnarsdóttir
    • , S. Sunna Ebenesersdóttir
    • , Valdis B. Guðmundsdóttir
    • , Elisabet Linda Thordardottir
    • , Margrét S. Einarsdóttir
    • , Hákon Jónsson
    • , Gísli Másson
    • , Augustine Kong
    • , Kári Stefánsson
    •  & Agnar Helgason
  2. Department of Anthropology, University of Iceland, Reykjavik, Iceland

    • Anuradha Jagadeesan
    • , S. Sunna Ebenesersdóttir
    • , Valdis B. Guðmundsdóttir
    • , Margrét S. Einarsdóttir
    •  & Agnar Helgason
  3. Laboratoire d’Eco-Anthropologie et Ethnobiologie, Equipe d’Anthropologie Evolutive, UMR 7206, Centre National de la Recherche Scientifique (CNRS) et Université Diderot Paris 7, Paris, France

    • Jean-Michel Dugoujon
    •  & Cesar Fortes-Lima
  4. Institut de Recherche pour le Développement, UMR D216 MERIT (Mère et enfant face aux infections tropicales), Paris, France

    • Florence Migot-Nabias
  5. COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France

    • Florence Migot-Nabias
  6. Centre d’Etude et de Recherche sur le Paludisme Associé à la Grossesse et l’Enfance (CERPAGE), Cotonou, Benin

    • Achille Massougbodji
  7. Laboratoire de Parasitologie, Faculté des Sciences de la Santé, Université d’Abomey-Calavi, Cotonou, Benin

    • Achille Massougbodji
  8. Institut National d’Etudes Démographiques (INED), Paris, France

    • Gil Bellis
  9. Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal

    • Luisa Pereira
  10. Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal

    • Luisa Pereira
  11. Faculdade de Medicina da Universidade do Porto, Porto, Portugal

    • Luisa Pereira
  12. Faculty of Medicine, University of Iceland, Reykjavik, Iceland

    • Kári Stefánsson

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Contributions

A.J., K.S. and A.H. planned and directed the research. A.J. and A.H. analyzed the data, with A.K., E.D.G., S.S.E., V.B.G., E.L.T., M.S.E., H.J. and G.M. providing assistance with particular tasks. A.J., K.S. and A.H. wrote the paper. J.-M.D., C.F.-L., F.M.-N., A.M., G.B. and L.P. provided data for reference samples from African populations and helped with population structure analysis.

Competing interests

Some authors affiliated with deCODE Genetics are employed by the company, which is owned by Amgen, Inc.: A.J., E.D.G., S.S.E., V.B.G., E.L.T., H.J., G.M., A.K., K.S. and A.H.

Corresponding authors

Correspondence to Kári Stefánsson or Agnar Helgason.

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