The largest genomic catalogue of wild chimpanzees

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The researchers used faecal samples as a non-invasive method to obtain genetic m

The researchers used faecal samples as a non-invasive method to obtain genetic material without disturbing the chimpanzees. Photo: MPI-EVA PanAf

New genomic tools shed light on the evolutionary history of chimpanzees and contribute to their conservation An international research team led by the Institute of Evolutionary Biology (IBE), the German Centre for Integrative Biodiversity Research (iDiv), the Max Planck Institute for Evolutionary Anthropology (MPI EVA) and Leipzig University has compiled the largest genomic catalogue of wild chimpanzee populations in Africa. For the first time, genomic information, obtained from hundreds of faecal samples of chimpanzees from across their range, has been sequenced, clarifying their evolutionary history and contributing to the conservation of these great apes. The new genomic atlas, published in the journal Cell Genomics, has the potential to map routes and sources of illegal trafficking that could be used to protect this endangered species.

Chimpanzees inhabit the tropical African savannah woodlands and forests. In contrast to the hominid sites preserved to this day - mainly in caves and temperate climates - the areas that chimpanzees have inhabited have resulted in few specimens preserved or detected in the archaeological record. Given the almost complete absence of chimpanzee fossils, the genetic information from current populations is crucial for describing their evolutionary history and their genetic diversity and contributing to their conservation.

An international research team led by IBE in Barcelona, iDiv and MPI EVA in Leipzig, has built the most extensive catalogue of genomic diversity in wild chimpanzee populations to date. Genetic information has been retrieved using new technologies, from hundreds of non-invasively collected chimpanzee faecal samples. For the first time, methods applied to analyse ancient DNA in human populations have been used to retrieve genetic information from great apes’ faecal samples. Further, the genomic database developed by the team can be used in practice for the conservation of chimpanzees, such as identifying illegal trafficking routes of wildlife products and orphans.

The first genomic atlas for chimpanzees with non-invasive samples The research team retrieved partial genome information from more than 800 chimpanzee faecal samples to create the largest and most detailed genomic diversity atlas of this African great ape.

"Using methods designed to study ancient DNA, as in the case of Neanderthals, we have been able to retrieve genomic information from faecal samples, which are very difficult to work with. We have applied that approach to an unprecedented number of chimpanzee samples from the field," points out Professor Tomàs Marquès-Bonet, principal investigator from IBE and co-author of the study.

"We have seen that faecal samples, while posing technical difficulties, provide very valuable genomic information for the study of wild chimpanzee populations, and also allow us the possibility to geo-reference them and track contacts between populations without affecting their well-being," adds Dr Clàudia Fontserè , a researcher at the IBE Comparative Genomics group and first author of the study.

Reconstructing the evolutionary history of chimpanzees to promote their conservation With this extensive data set, the authors shed light on the demographic past of chimpanzees and provide further evidence of the genetic differentiation of, and exchanges between, the four recognized subspecies.

The research team identified that geographical features, such as rivers, constitute permeable barriers to gene flow between chimpanzee subspecies, but also between communities. In addition, researchers proposed patterns of migration, connectivity, and isolation between groups of chimpanzees that have shaped the variation in the genomic landscape of these populations over the past 100,000 years.

"We’ve noticed that sometimes, even though two communities are geographically very close, they may live on two different sides of a river and have only had very limited and sporadic contact. Our approach is very helpful in identifying barriers and natural corridors between populations and may have implications for their conservation," says Clàudia Fontserè .

"Chimpanzees, like humans, have a complex evolutionary history. Their dynamics and areas of past and current population contact must be clearly identified in order to contribute to the protection of this endangered species," points out co-author Dr Mimi Arandjelovic, a researcher at iDiv, MPI EVA and Leipzig University. Arandjelovic is co-director of the Pan African Programme: The Cultured Chimpanzee (PanAf) , a consortium of researchers and conservationists from Africa, Europe and North America who spent eight years collecting behavioural, ecological and organic data from across the entire chimpanzee range.

Genomics to fight chimpanzee illegal trafficking The new genomic tool has allowed the team to reliably identify from where individuals originate; a task not feasible until now. The ability to accurately determine the origin of chimpanzees has direct applications for their conservation, such as detecting the places where their poaching might be concentrated and identifying the routes and origins of illegal chimpanzee trafficking. "The tool developed can infer the origin of the confiscated chimpanzees, which are usually found just a few hundred kilometres from their real origin, and thus provide reliable information on the regions most in need of protection," adds Marquès-Bonet. The developed methodology is already being applied in conservation projects for other primate and mammal species.

Original publication in Cell Genomics:
Population dynamics and genetic connectivity in recent chimpanzee history , DOI: 10.1016/j.xgen.2022.100133

Sebastian Tilch, based on a press release by IBE in Barcelona

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