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Selection Signals Uncovered In African Rainforest Hunter-Gatherer Exomes

NEW YORK – A team from France, Denmark, Gabon, and the US has narrowed in on signatures of selection, proposed polygenic adaptations, and other potentially adaptive features in African rainforest hunter-gatherer (RHG) populations from Central Africa.

In particular, the team flagged a selective sweep affecting the TRPS1 gene that appears to be shared across the rainforest hunter-gatherer populations profiled, perhaps explaining some characteristic physical adaptations in the tropical rainforest populations, traditionally known as "Pygmy" populations.

The investigators also uncovered multi-gene contributions to specific physical traits such as height and reproductive age, which appear to be influenced by height-related pleiotropy. Their polygenic analyses and available gene function data also pointed to selective pressures that may be placed on rainforest populations by persistent pathogens, leading to polygenic adaptation involving mast cell, IL-2, and other immune genes.

"Collectively, our analyses uncover height, development, and immune response as iconic adaptive traits of African RHGs," co-senior and co-corresponding authors Lluís Quintana-Murci and Etienne Patin, human evolutionary genetics researchers at the Pasteur Institute, and their colleagues wrote. 

For their study, published online this week in Current Biology, the researchers generated 40 low-coverage genome sequences and 266 new exome sequences for individuals from seven rainforest hunter-gatherer populations in Cameroon, Gabon, and Uganda, and seven farming populations from the same areas, analyzing them alongside 300 available high-coverage exomes from the same populations. Together, the protein-coding sequence collection spanned 298 rainforest hunter-gatherers and 268 Bantu-speaking agriculturalists.

The team also incorporated array-based SNP profiles for the newly sequenced individuals and did SNP imputation to get a look at adaptations affecting regulatory parts of the genome not caught with exome sequencing.

"In doing so," the authors reported, "we found evidence of a unique, strong sweep that is shared by all RHG groups, targeting the regulatory region of TRPS1, mutations in which can cause growth retardation, distinctive craniofacial features, and hypertrichosis."

In a Biorxiv preprint article earlier this year, University of California, Los Angeles researchers highlighted TRPS1 as one of the genes showing signs of introgression from a yet-unidentified archaic hominin. Still, authors of the Current Biology study suggested that further functional studies are needed to dig into possible developmental and immune-related adaptations in that portion of the genome.

The team is not the first to search for genomic clues to characteristic adaptations in hunter-gatherer populations adapted to the rainforest or other distinctive locales.

In a 2012 study in Cell, for example, the University of Pennsylvania's Sarah Tishkoff led a team that sequenced 15 African hunter-gatherers, and delved into possible adaptations related to height, metabolism, immunity, and more in five men from a forest population in Cameroon.

There have also been several past studies exploring population structure in the African hunter-gatherer populations, which point to early divergence and population isolation, followed by more recent mixing with Bantu-speaking farming populations in some parts of central Africa.

With their new exome sequence analysis, the researchers were able to dig into the genomic consequences of such admixture events, particularly in individuals from a BaBongo rainforest hunter-gatherer population with significant ancestry from both rainforest hunter-gatherer and agricultural populations. Results from that analysis indicated that variants involved in adaptation often persist after such population mixing.

"[W]e 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," the authors reported, "suggesting that selection has maintained adaptive variation in the face of recent gene flow from farmers."