@article{1530b2354f9c4c89a4e6e9b8e2f795e9,
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.",
author = "Maud Fagny and Etienne Patin and Macisaac, {Julia L.} and Maxime Rotival and Timoth{\'e}e Flutre and Jones, {Meaghan J.} and Siddle, {Katherine J.} and H{\'e}l{\`e}ne Quach and Christine Harmant and McEwen, {Lisa M.} and Alain Froment and Evelyne Heyer and Antoine Gessain and Edouard Betsem and Patrick Mouguiama-Daouda and Hombert, {Jean Marie} and Perry, {George H.} and Barreiro, {Luis B.} and Kobor, {Michael S.} and Lluis Quintana-Murci",
note = "Funding Information: We thank Vincent Colot, Etienne Danchin, Jean-Philippe Fortin, Tatiana Giraud, Aur{\'e}lie Labbe, Guillaume Laval and Carla Saleh for feedback on data analyses and reading of the manuscript. We also thank Martin Sikora and Carlos Bustamante for providing the variant calling of whole-genome sequencing data. We are grateful to all the study participants for their generous contributions of DNA. This study was funded by the Institut Pasteur, the CNRS, a CNRS {\textquoteleft}MIE{\textquoteright} (Maladies Infectieuses et Environnement) Grant, and a Foundation Simone & Cino del Duca Research Grant (L.Q.-M.), and the Canadian Institute for Advanced Research (CIFAR) (M.S.K.). M.J.J. was supported by a Mininig for Miracles post-doctoral fellowship from the Child and Family Research Institute. L.B.B is supported by the Canada Research Chairs Program. M.S.K. is the Canada Research Chair in Social Epigenetics and a Senior Fellow of CIFAR.",
year = "2015",
month = nov,
day = "30",
doi = "10.1038/ncomms10047",
language = "English (US)",
volume = "6",
journal = "Nature communications",
issn = "2041-1723",
publisher = "Nature Research",
}