Reconstructing an African haploid genome from the 18th century

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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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.

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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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