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The epigenomic landscape of African rainforest hunter-gatherers and farmers

Author

Listed:
  • Maud Fagny

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique
    Université Pierre et Marie Curie, Cellule Pasteur UPMC)

  • Etienne Patin

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique)

  • Julia L. MacIsaac

    (Centre for Molecular Medicine and Therapeutics, University of British Columbia)

  • Maxime Rotival

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique)

  • Timothée Flutre

    (INRA, UMR AGAP)

  • Meaghan J. Jones

    (Centre for Molecular Medicine and Therapeutics, University of British Columbia)

  • Katherine J. Siddle

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique)

  • Hélène Quach

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique)

  • Christine Harmant

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique)

  • Lisa M. McEwen

    (Centre for Molecular Medicine and Therapeutics, University of British Columbia)

  • Alain Froment

    (IRD-MNHN, Sorbonne Universités)

  • Evelyne Heyer

    (CNRS, MNHN, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Université)

  • Antoine Gessain

    (Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes)

  • Edouard Betsem

    (Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes
    Faculty of Medicine and Biomedical Sciences, University of Yaoundé I)

  • Patrick Mouguiama-Daouda

    (Laboratoire Langue, Culture et Cognition (LCC), Université Omar Bongo)

  • Jean-Marie Hombert

    (CNRS UMR 5596, Université Lumière-Lyon 2)

  • George H. Perry

    (Pennsylvania State University)

  • Luis B. Barreiro

    (Université de Montréal, Centre de Recherche CHU Sainte-Justine)

  • Michael S. Kobor

    (Centre for Molecular Medicine and Therapeutics, University of British Columbia)

  • Lluis Quintana-Murci

    (Institut Pasteur, Unit of Human Evolutionary Genetics
    Centre National de la Recherche Scientifique)

Abstract

The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.

Suggested Citation

  • Maud Fagny & Etienne Patin & Julia L. MacIsaac & Maxime Rotival & Timothée Flutre & Meaghan J. Jones & Katherine J. Siddle & Hélène Quach & Christine Harmant & Lisa M. McEwen & Alain Froment & Evelyne, 2015. "The epigenomic landscape of African rainforest hunter-gatherers and farmers," Nature Communications, Nature, vol. 6(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms10047
    DOI: 10.1038/ncomms10047
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    Cited by:

    1. Ampumuza, Christine & Duineveld, Martijn & van der Duim, René, 2020. "The most marginalized people in Uganda? Alternative realities of Batwa at Bwindi Impenetrable National Park," World Development Perspectives, Elsevier, vol. 20(C).

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