Genomic Evidence for Local Adaptation of Hunter-Gatherers to the African Rainforest

Curr Biol. 2019 Sep 9;29(17):2926-2935.e4. doi: 10.1016/j.cub.2019.07.013. Epub 2019 Aug 8.


African rainforests support exceptionally high biodiversity and host the world's largest number of active hunter-gatherers [1-3]. The genetic history of African rainforest hunter-gatherers and neighboring farmers is characterized by an ancient divergence more than 100,000 years ago, together with recent population collapses and expansions, respectively [4-12]. While the demographic past of rainforest hunter-gatherers has been deeply characterized, important aspects of their history of genetic adaptation remain unclear. Here, we investigated how these groups have adapted-through classic selective sweeps, polygenic adaptation, and selection since admixture-to the challenging rainforest environments. To do so, we analyzed a combined dataset of 566 high-coverage exomes, including 266 newly generated exomes, from 14 populations of rainforest hunter-gatherers and farmers, together with 40 newly generated, low-coverage genomes. We find evidence for a strong, shared selective sweep among all hunter-gatherer groups in the regulatory region of TRPS1-primarily involved in morphological traits. We detect strong signals of polygenic adaptation for height and life history traits such as reproductive age; however, the latter appear to result from pervasive pleiotropy of height-associated genes. Furthermore, polygenic adaptation signals for functions related to responses of mast cells to allergens and microbes, the IL-2 signaling pathway, and host interactions with viruses support a history of pathogen-driven selection in the rainforest. Finally, we find that genes involved in heart and bone development and immune responses are enriched in both selection signals and local hunter-gatherer ancestry in admixed populations, suggesting that selection has maintained adaptive variation in the face of recent gene flow from farmers.

Keywords: Africa; admixture; genetic adaptation; height; hunter-gatherers; immunity; natural selection; polygenic adaptation; positive selection; rainforest.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Biological*
  • Cameroon
  • Farmers
  • Gabon
  • Gene Flow*
  • Genome, Human
  • Humans
  • Life Style*
  • Multifactorial Inheritance*
  • Rainforest
  • Regulatory Sequences, Nucleic Acid
  • Repressor Proteins / genetics
  • Uganda


  • Repressor Proteins
  • TRPS1 protein, human