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Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation

Nature Genetics volume 48, pages 1066–1070 (2016)Cite this article

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Abstract

To shed light on the peopling of South Asia and the origins of the morphological adaptations found there, we analyzed whole-genome sequences from 10 Andamanese individuals and compared them with sequences for 60 individuals from mainland Indian populations with different ethnic histories and with publicly available data from other populations. We show that all Asian and Pacific populations share a single origin and expansion out of Africa, contradicting an earlier proposal of two independent waves of migration1,2,3,4. We also show that populations from South and Southeast Asia harbor a small proportion of ancestry from an unknown extinct hominin, and this ancestry is absent from Europeans and East Asians. The footprints of adaptive selection in the genomes of the Andamanese show that the characteristic distinctive phenotypes of this population (including very short stature) do not reflect an ancient African origin but instead result from strong natural selection on genes related to human body size.

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Figure 1: Ancestry of Indian populations.
Figure 2: Fewer African-derived alleles in Indians, Andamanese, Papuans and Aboriginal Australians than in Europeans and East Asians.
Figure 3: Model of gene flow in Asia.

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Acknowledgements

J. Nye and C. Tyler-Smith kindly corrected the manuscript in depth. Thanks are given to R.A. Foley for discussion and inspiring input for Figure 3. Our main funding was provided by the joint Spain–India bilateral grant PRI-PIBIN-2011-0942 from the Ministerio de Economía y Competitividad (Spain). Complementary funding was provided by grant BFU2013-43726-P from the Ministerio de Economía y Competitividad (Spain), with the support of Secretaria d'Universitats i Recerca, Departament d'Economia i Coneixement de la Generalitat de Catalunya (GRC 2014 SGR866).

Author information

Author notes

  1. Mayukh Mondal, Ferran Casals and Tina Xu: These authors contributed equally to this work.

  2. Qibin Li, Partha P Majumder and Jaume Bertranpetit: These authors jointly directed this work.

Authors and Affiliations

  1. Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Barcelona, Spain

    Mayukh Mondal, Marc Pybus, David Comas, Hafid Laayouni & Jaume Bertranpetit

  2. Servei de Genòmica, Universitat Pompeu Fabra, Barcelona, Spain

    Ferran Casals

  3. BGI Shenzhen, Shenzhen, China

    Tina Xu & Qibin Li

  4. Computational Biology, Target Sciences, GSK R&D, GlaxoSmithKline, Stevenage, UK

    Giovanni M Dall'Olio

  5. Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands

    Mihai G Netea

  6. Departament de Genètica i de Microbiologia, Universitat Autonòma de Barcelona, Bellaterra, Spain

    Hafid Laayouni

  7. National Institute of BioMedical Genomics, Kalyani, India

    Partha P Majumder

  8. Department of Archaeology and Anthropology, Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge, UK

    Jaume Bertranpetit

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  1. Mayukh Mondal
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Contributions

M.M., F.C., P.P.M. and J.B. conceived and designed the project. P.P.M. provided the samples. P.P.M., T.X. and Q.L. sequenced samples and carried out initial analyses. M.M. performed the remaining genetic data analyses. F.C., G.M.D., M.P., M.G.N., D.C., H.L., P.P.M. and J.B. participated in and discussed analyses. M.M., F.C., P.P.M. and J.B. wrote the manuscript.

Corresponding authors

Correspondence to Partha P Majumder or Jaume Bertranpetit.

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The authors declare no competing financial interests.

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Supplementary Figures 1–38, Supplementary Tables 1–17 and Supplementary Note. (PDF 6962 kb)

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Mondal, M., Casals, F., Xu, T. et al. Genomic analysis of Andamanese provides insights into ancient human migration into Asia and adaptation. Nat Genet 48, 1066–1070 (2016). https://doi.org/10.1038/ng.3621

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