The epigenomic landscape of African rainforest hunter-gatherers and farmers
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 Heyer, Antoine Gessain, Edouard Betsem, Patrick Mouguiama-Daouda, Jean-Marie Hombert, George H. Perry, Luis B. Barreiro, Michael S. Kobor & Lluis Quintana-Murci
Affiliations Contributions Corresponding author
Nature Communications 6, Article number: 10047 doi:10.1038/ncomms10047
Received 28 April 2015 Accepted 28 October 2015 Published 30 November 2015
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.
Subject terms: Biological sciences Ecology Evolution Genetics
FREE PDF GRATIS: Nature Communications
