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Chimpanzees are likely genetically adapted to their local habitats & to infections such as malaria
17 January 2025
Chimpanzees are, along with bonobos, our closest living relatives. They are also endangered, with numbers continuing to decline. They inhabit diverse habitats in sub-Saharan Africa, from relatively cool and wet rainforest to hot and dry woodland-savannah.
Interestingly, aside from humans, they are the only great ape that can inhabit woodland-savannahs –making them an ideal model to study early human evolution. The diversity of environmental conditions inhabited by chimpanzees provide an opportunity for local genetic adaptations, which could have important implications for our knowledge of the species, their conservation, and our understanding of hominid evolution.
Studies of chimpanzee genetic adaptation had so far been hampered by difficulties associated with accessing genetic samples from endangered wild populations. Chimpanzees are elusive and protected, and as such wild individuals cannot be sampled for DNA. But only such samples allow us to investigate local adaptation to the natural environment. As part of the PanAfr consortium, a large network of collaborators collected hundreds of faecal samples of wild chimpanzees across their geographic and ecological range, together with environmental variables. This information allowed us to conduct the first investigation of local genetic adaptation in chimpanzees.
Capture-sequence was used to generate 828 exomes (and chr21 sequences) from non-invasive samples of wild individuals, of which 388 were analysed post-filtering. SNPs with exceptionally high population allele frequency differentiation that correlate with habitat type provide genome-wide evidence of local adaptation to habitat in chimpanzees, both to forests and to woodland-savannahs. Candidate SNPs inferred to be beneficial in forest habitats are enriched for pathogen-related genes, potentially due to the higher density and diversity of pathogens in the deep rainforests. Most notably, we find evidence for adaptation to malaria in lowland forest chimpanzees, with signatures of positive selection in the same genes that underlie resistance and adaptation to malaria in humans –pointing to a potential case of parallel adaptation in the two species. This work demonstrates the potential of non-invasive population genomics to reveal fine-scale local adaptation in endangered wild populations.