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

Research output: Contribution to journalArticlepeer-review

54 Scopus citations


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.

Original languageEnglish (US)
Article number10047
JournalNature communications
StatePublished - Nov 30 2015

All Science Journal Classification (ASJC) codes

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


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