Chimpanzees are humans' closest living relatives, sharing over 98% of our DNA. They are endangered, with fewer than 250,000 left and an annual decline of between 1.5% and 6%. This is due to habitat destruction, hunting and infectious diseases, among other threats.
Understanding how chimpanzees have adapted to survive in the wild can shed light on key questions in human biology and evolution. It can also inform their conservation. However, we know very little about genetic adaptation in chimpanzees, because obtaining high-quality DNA samples from wild individuals is extremely challenging.
We attempted to address this knowledge gap by collecting faecal samples from hundreds of wild chimpanzees across 17 African countries as part of the Pan African Programme: The Cultured Chimpanzee. This is an international consortium of scientists including geneticists, primatologists and ecologists.
Getting enough good-quality DNA from faecal samples is difficult and has never been done on this scale for chimpanzees. However, using cutting-edge techniques, we overcame these challenges.
We found evidence that different populations have evolved genetic differences to adapt to their local habitats. In particular, forest-dwelling populations have adaptations in genes associated with infectious diseases. These include the same genes involved in resistance and adaptation to malaria in humans.
The evidence of local genetic adaptation identified here has important implications for chimpanzee conservation, and, potentially, our understanding of human evolution and medicine. More generally, this work demonstrates how faecal samples can be used to investigate local adaptation. It opens the door for future studies to shed light on adaptation in wild, endangered populations.
Chimpanzee habitats
Chimpanzees live across 2.6 million km² of west, central and east Africa. They span a variety of habitats, from dense forests to open woodland-savannahs. Different habitats present unique challenges to chimpanzees' survival. Forests have consistently high rainfall and stable temperatures year-round, but they also have a great abundance and diversity of disease-causing microorganisms. In contrast, woodland-savannahs on the edge of the chimpanzee geographic range are more seasonal, with dry seasons characterised by high temperatures and less food and water.
Chimpanzees have developed behavioural adaptations to these different habitats. For example, some populations in woodland-savannahs shelter in caves, bathe in water and are more active at night to avoid overheating. However, until this study, it was not known whether genetic changes also helped chimpanzees adapt to their local habitats. This phenomenon is known as local adaptation.
Read more: Why humans walk on two legs: a close look at chimpanzees puts some old theories to the test
DNA samples
Answering this question requires obtaining DNA from wild chimpanzees. But collecting traditional DNA sources, such as blood samples, is not an option because darting or trapping wild individuals is far too disruptive. This has limited the study of wild populations of many endangered species.
The only options are "non-invasive" samples, such as faeces. These samples are hard to work with because faecal DNA is degraded and contaminated by DNA from bacteria, dietary material and the environment. However, recent technological advancements are now allowing enough good-quality DNA to be obtained from them.
Using faecal samples collected as part of the Pan African Programme: The Cultured Chimpanzee, we generated genetic data for 828 chimpanzees from 52 locations spanning all four chimpanzee subspecies. This allowed us to perform the largest study of local adaptation in a wild endangered mammal to date.
Genetic adaptations to local conditions
By comparing the DNA of different chimpanzee populations, we identified genetic variants that are much more frequent in certain locations than others. This is likely because they help individuals to survive particular local conditions. This pattern indicates that genetic differences help explain how chimpanzees inhabit such a range of habitats.
We found evidence of adaptation to woodland-savannahs, but it is challenging to pinpoint exactly what these adaptations may be to.
In forests, however, we found clear evidence for the evolution of genetic adaptations to infectious diseases. This is likely due to the higher prevalence of infectious diseases in these habitats. This mimics previously observed patterns of genetic adaptation in human populations living in these same forests.
Intriguingly, some of the strongest evidence of adaptation in chimpanzees is found in genes that are involved in adaptation to malaria in humans: GYPA and HBB. GYPA encodes a protein that the malaria parasite uses to enter blood cells. HBB is the gene responsible for sickle cell anaemia in humans. This suggests that both chimpanzees and humans have independently evolved similar adaptations in response to the same disease.
The malaria parasites that infect wild chimpanzees are closely related to Plasmodium falciparum, which is responsible for 90% of malaria deaths in humans. The fact that the same genes have signatures of adaptation in chimpanzees and humans suggests that there may be only a few ways in which hosts can adapt to the parasite. Therefore, studying wild chimpanzees may improve our understanding of this disease in humans.
These results also have implications for chimpanzee conservation. Specifically, they indicate that malaria may be or may have been a strong selective pressure for chimpanzees living in forests. Furthermore, the presence of important genetic differences between chimpanzee populations suggests that they are not interchangeable. Instead, ecological shifts driven by climate change are likely to have different effects on different populations.
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Further work
Future work is required to demonstrate that the genetic variants identified in this study truly are protective against malaria. Also, that they are adaptive in the particular habitats where we find them at unusually high frequencies.
Studying more woodland-savannah populations could increase our power to interpret adaptations to such habitats. Understanding these adaptations may provide clues as to how our own ancestors adapted to similar habitats millions of years ago when they moved from forests to woodland-savannahs. This is considered a key step in human evolution.
Our work is part of a continuing international effort to deepen our understanding of the evolution of our closest relatives, including the work of the Pan African Programme: The Cultured Chimpanzee and the community-science project Chimp&See.
Harrison J. Ostridge, Scientist, UCL Genetics Institute, UCL
Aida Andres, Professor of Population and Evolutionary Genomics, UCL
Mimi Arandjelovic, Staff Scientist, Max Planck Institute for Evolutionary Anthropology
