The epigenomic landscape of African rainforest hunter-gatherers and farmers.

Maud Fagny,Alain Froment,Luis B Barreiro,Christine Harmant,George H Perry,Lisa M Mcewen,Julia L Macisaac,Meaghan J Jones,Maxime Rotival,Hélène Quach,Timothée Flutre,Patrick Mouguiama-Daouda,Katherine J Siddle,Edouard Betsem,Antoine Gessain,Michæl S Kobor ,Évelyne Heyer ,Étienne Patin ,Jean Marie Hombert ,Lluís Quintana‐Murci

doi:10.1038/ncomms10047

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.

Highlights

The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized
We show that DNA methylation variation that correlates with historical lifestyle shows strong associations with nearby genetic variants that, are enriched in signals of natural selection
We investigated genome-wide genotype and DNA methylation data from a total of 362 individuals, including a group of RHGs (w-RHG, n 1⁄4 112), agrarian lifestyle (AGRs) groups occupying nearby urban deforested habitats (w-AGR, n 1⁄4 94), and an AGR group that lives and regularly practices hunting in a forested region (f-AGR, n 1⁄4 61) of the Gabon/Cameroon area (Fig. 1a; Table 1)

Summary

Introduction

The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. The increasing amounts of genomic data available have provided significant insight into African evolutionary history, including the origins of huntergatherers, population structure, and patterns of migration and admixture[2,3,4,5,6,7,8,9,10] These studies have reported evidence of selection targeting gene functions related to the changes in environment, diet and exposure to infectious disease[11]. Recent studies have shown that DNA methylation differences exist between major ethnic groups[20,23,24,25], highlighting the potential contribution of epigenetic modifications to human phenotypic variation These studies have mostly compared urban populations of different continental ancestries, so the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human DNA methylome remain unknown. We assess the contribution of genetic variation to the DNA methylation levels observed, and search for signals of positive selection targeting genetic variants associated with methylation variation

Methods

Results

Conclusion