title: The epigenomic landscape of African rainforest hunter-gatherers and farmers.
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.
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.|Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris 75015, France.
authors.forename: Maud
authors.initials: M
authors.lastname: Fagny
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.
authors.forename: Etienne
authors.initials: E
authors.lastname: Patin
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4.
authors.forename: Julia L
authors.initials: JL
authors.lastname: MacIsaac
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.
authors.forename: Maxime
authors.initials: M
authors.lastname: Rotival
authors.affiliation: INRA, UMR AGAP, Montpellier 34060, France.
authors.forename: Timothée
authors.initials: T
authors.lastname: Flutre
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4.
authors.forename: Meaghan J
authors.initials: MJ
authors.lastname: Jones
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.
authors.forename: Katherine J
authors.initials: KJ
authors.lastname: Siddle
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Quach
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.
authors.forename: Christine
authors.initials: C
authors.lastname: Harmant
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4.
authors.forename: Lisa M
authors.initials: LM
authors.lastname: McEwen
authors.affiliation: IRD-MNHN, Sorbonne Universités, UMR208, Paris 75005, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Froment
authors.affiliation: CNRS, MNHN, Université Paris Diderot, Sorbonne Paris Cité, Sorbonne Université, UMR7206, Paris 75005, France.
authors.forename: Evelyne
authors.initials: E
authors.lastname: Heyer
authors.affiliation: Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Paris 75015, France.
authors.forename: Antoine
authors.initials: A
authors.lastname: Gessain
authors.affiliation: Institut Pasteur, Unité d'Epidémiologie et Physiopathologie des Virus Oncogènes, Paris 75015, France.|Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, BP1364 Yaoundé, Cameroon.
authors.forename: Edouard
authors.initials: E
authors.lastname: Betsem
authors.affiliation: Laboratoire Langue, Culture et Cognition (LCC), Université Omar Bongo, BP 13131 Libreville, Gabon.
authors.forename: Patrick
authors.initials: P
authors.lastname: Mouguiama-Daouda
authors.affiliation: CNRS UMR 5596, Université Lumière-Lyon 2, Lyon 69007, France.
authors.forename: Jean-Marie
authors.initials: JM
authors.lastname: Hombert
authors.affiliation: Departments of Anthropology and Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: George H
authors.initials: GH
authors.lastname: Perry
authors.affiliation: Université de Montréal, Centre de Recherche CHU Sainte-Justine, Montréal, Canada H3T 1C5.
authors.forename: Luis B
authors.initials: LB
authors.lastname: Barreiro
authors.affiliation: Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics, University of British Columbia, Vancouver, Canada BC V5Z 4H4.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Kobor
authors.affiliation: Institut Pasteur, Unit of Human Evolutionary Genetics, Paris 75015, France.|Centre National de la Recherche Scientifique, URA3012, Paris 75015, France.
authors.forename: Lluis
authors.initials: L
authors.lastname: Quintana-Murci
mesh_terms: D044383:Black People / Q000235:genetics*; D019175:DNA Methylation; D017753:Ecosystem; D057890:Epigenomics; D000067565:Farmers; D005260:Female; D014644:Genetic Variation; D005828:Genetics, Population; D006801:Humans; D008297:Male; D065947:Rainforest