The epigenomic landscape of African rainforest hunter-gatherers and farmers

Maud Fagny (1) , Etienne Patin (1) , Maxime Rotival (1) , Julia L. Macisaac (2) , Timothée Flutre (3) , Meaghan J. Jones (2) , Katherine J. Siddle (1) , Hélène Quach (1) , Christine Harmant (1) , Lisa M. Mcewen (2) , Alain Froment (4) , Evelyne Heyer (4) , Antoine Gessain (5) , Edouard Betsem (6, 5) , Patrick Mouguiama-Daouda (7) , Jean-Marie Hombert (8) , Luis B. Barreiro (9) , Michael S. Kobor (2) , George H. Perry (10) , Lluis Quintana-Murci (1)

1 Génétique Evolutive Humaine - Human Evolutionary Genetics
2 Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute and Department of Medical Genetics
3 UMR AGAP - Amélioration génétique et adaptation des plantes méditerranéennes et tropicales
4 Département des Jardins botaniques et zoologiques
5 EPVO (UMR_3569 / U-Pasteur_3) - Epidémiologie et Physiopathologie des Virus Oncogènes
6 Faculty of Medicine and Biomedical Sciences
7 LCC - Laboratoire Langue, Culture et Cognition [Libreville, Gabon]
8 EMC - Laboratoire d'Etude des Mécanismes Cognitifs
9 Centre de recherche du CHU Sainte-Justine / Research Center of the Sainte-Justine University Hospital [Montreal, Canada]
10 Departments of Anthropology and Biology

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.

Domains: Life Sciences [q-bio]; Genetics; Populations and Evolution [q-bio.PE]

Maud Fagny, Etienne Patin, Maxime Rotival, Julia L. Macisaac, Timothée Flutre, et al.. The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nature Communications, 2015, 6, 11 p. ⟨10.1038/ncomms10047⟩. ⟨pasteur-01238387⟩