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A time transect of exomes from a Native American population before and after European contact

Author

Listed:
  • John Lindo

    (University of Chicago)

  • Emilia Huerta-Sánchez

    (University of California)

  • Shigeki Nakagome

    (University of Chicago)

  • Morten Rasmussen

    (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
    School of Medicine, Stanford University)

  • Barbara Petzelt

    (Metlakatla Treaty Office)

  • Joycelynn Mitchell

    (Metlakatla Treaty Office)

  • Jerome S. Cybulski

    (Canadian Museum of History
    University of Western Ontario
    Simon Fraser University)

  • Eske Willerslev

    (Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen
    University of Cambridge, Downing St.
    Wellcome Trust Sanger Institute, Wellcome Genome Campus)

  • Michael DeGiorgio

    (Pennsylvania State University, 502 Wartik Laboratory
    Institute for CyberScience, Pennsylvania State University)

  • Ripan S. Malhi

    (Carl R. Woese Institute for Genomic Biology, University of Illinois
    University of Illinois)

Abstract

A major factor for the population decline of Native Americans after European contact has been attributed to infectious disease susceptibility. To investigate whether a pre-existing genetic component contributed to this phenomenon, here we analyse 50 exomes of a continuous population from the Northwest Coast of North America, dating from before and after European contact. We model the population collapse after European contact, inferring a 57% reduction in effective population size. We also identify signatures of positive selection on immune-related genes in the ancient but not the modern group, with the strongest signal deriving from the human leucocyte antigen (HLA) gene HLA-DQA1. The modern individuals show a marked frequency decrease in the same alleles, likely due to the environmental change associated with European colonization, whereby negative selection may have acted on the same gene after contact. The evident shift in selection pressures correlates to the regional European-borne epidemics of the 1800s.

Suggested Citation

  • John Lindo & Emilia Huerta-Sánchez & Shigeki Nakagome & Morten Rasmussen & Barbara Petzelt & Joycelynn Mitchell & Jerome S. Cybulski & Eske Willerslev & Michael DeGiorgio & Ripan S. Malhi, 2016. "A time transect of exomes from a Native American population before and after European contact," Nature Communications, Nature, vol. 7(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms13175
    DOI: 10.1038/ncomms13175
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    Cited by:

    1. Gabriela Montejo-Kovacevich & Joana I. Meier & Caroline N. Bacquet & Ian A. Warren & Yingguang Frank Chan & Marek Kucka & Camilo Salazar & Nicol Rueda-M & Stephen H. Montgomery & W. Owen McMillan & Kr, 2022. "Repeated genetic adaptation to altitude in two tropical butterflies," Nature Communications, Nature, vol. 13(1), pages 1-16, December.

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