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Reconstructing an African haploid genome from the 18th century

Nature Genetics volume 50, pages 199–205 (2018)Cite this article

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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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Fig. 1: Genealogical reconstruction of HJ’s maternal chromosome 3.
Fig. 2: HJ’s reconstructed genome.
Fig. 3: HJ singleton alleles in descendants with WGS data.
Fig. 4: Multidimensional scaling (MDS) using worldwide reference populations.
Fig. 5: wIBS using worldwide reference populations.
Fig. 6: wIBS and IBD with African reference populations.

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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.

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Authors and 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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  1. Anuradha Jagadeesan
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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.

Corresponding authors

Correspondence to Kári Stefánsson or Agnar Helgason.

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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.

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Jagadeesan, A., Gunnarsdóttir, E.D., Ebenesersdóttir, S.S. et al. Reconstructing an African haploid genome from the 18th century. Nat Genet 50, 199–205 (2018). https://doi.org/10.1038/s41588-017-0031-6

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