Chimpanzees bear genetic adaptations that help them thrive in their different forest and savannah habitats, some of which may protect against malaria, according to a study by an international team led by UCL researchers.
Chimpanzees are our closest living relatives, sharing over 98% of their DNA with humans, and the scientists say that their findings, published in Science, can not only teach us about our own evolutionary history, but also about the biology of malaria infection in humans.
Chimpanzees are endangered due to habitat destruction, poaching and infectious disease. The results of this study could also inform conservation as they suggest that climate and land use changes will likely have different impacts on different chimpanzee groups.
Lead author Professor Aida Andrés (UCL Genetics Institute) said: "There are just a few hundred thousand chimpanzees alive, but they are found across very different landscapes from east Africa to the far west of the continent, including dense tropical rainforests and open areas of woodland and savannah. This makes them quite unique, because except for humans, all other apes live exclusively in forests.
"Here we have shown that besides acquiring behavioural adaptations, different chimpanzee populations have evolved genetic differences to survive in their different local habitats.
"As chimpanzees are facing threats across their range, including environmental changes to the climate and displacement due to human pressures, it is important that their genetic diversity is conserved to maintain their resilience and ensure the long-term survival of this intelligent and fascinating species."
To study genetic adaptation, the international team of researchers, from institutions across Africa, Europe and North America, needed to obtain DNA from the endangered and highly elusive wild chimpanzees without disturbing them. To do so, they used faecal samples that were collected as part of the Pan African Programme: The Cultured Chimpanzee (PanAf). State-of-the-art laboratory and computational methods enabled the scientists to study the chimpanzee DNA in these samples and perform the largest study of local adaptation in wild endangered mammals to date.
The researchers analysed the exomes (the protein-coding part of the genome) from 828 wild chimpanzees, 388 of which were included in the final analysis, representing 30 different populations of chimpanzees across the geographic and ecological range of the four chimpanzee subspecies. The scientists compared the genetic information to data about the local environment each chimpanzee population lives in, identifying genetic variants that stand out as being much more frequent in certain regions than others, and that likely confer a benefit to those carrying the genetic variant in particular habitats.
The scientists found evidence of genetic adaptation in genes related to certain pathogens (disease-causing microorganisms) among the chimpanzees living in forests, where there is a high concentration of pathogens, with the strongest evidence found in genes linked to malaria. This includes two genes that are also known to be responsible for adaptation and resistance to malaria in humans: GYPA and HBB, the latter being responsible for sickle cell anaemia in humans.
The findings suggest that malaria is likely a significant disease for wild forest chimpanzees and that adaptation to the malaria parasite has happened, independently, through changes in the very same genes in chimpanzees and humans.
First author Dr Harrison Ostridge (UCL Genetics Institute) said: "The close genetic similarities between the great apes have resulted in diseases jumping from apes to humans, such as with malaria and HIV/AIDS, so studying wild chimpanzees is extremely useful to understand these and other shared infectious diseases in humans, and could help to develop new treatments or vaccines.
"Finding evidence of adaptation to malaria in chimpanzees linked to the same genes that affect malaria resistance in humans is striking from an evolutionary point of view, as it suggests there may be limited ways that we can evolve resistance to the malaria parasite."
The study suggests that chimpanzees have also adapted to their savannah habitats, which have higher temperatures, lower rainfall and less food availability. This shows that studying savannah chimpanzees may shed light on how human ancestors adapted to similar habitats millions of years ago, when they first moved from the African forest to the savannah.
Co-author and PanAf co-director Dr Hjalmar Kuehl (Senckenberg Museum of Natural History, Germany) commented: "This ground-breaking study on chimpanzee local adaptations could not be accomplished without the extraordinary collaboration of an international team of scientists who worked tirelessly to collect non-invasive data, including faecal samples, from countries across the chimpanzee range."
Co-author and PanAf co-director Dr Mimi Arandjelovic (Max Planck Institute for Evolutionary Anthropology, Germany) added: "We further welcome everyone interested in our research to contribute as community scientists at ChimpandSee.org, where one can help annotate videos collected alongside the genetic samples from across the chimpanzee range."
