Researchers design a method to identify the origin of illegally traded chimpanzees
Researchers report in the journal Cell genomics on June 1 produced the first catalog of the genomic diversity of endangered chimpanzees in the wild. The catalog, which includes 828 samples of chimpanzees from across their range, offers a detailed reconstruction of chimpanzee population structure and fine-scale patterns of isolation, migration and connection. Researchers are using this information to design a method to link confiscated chimpanzees to their place of origin within a radius of approximately 100 kilometers, with the aim of supporting efforts to combat the illegal trade in chimpanzees and related products.
“Chimpanzees are an endangered species with massive population declines in recent years,” said Claudia Fontsere, first author of the study at the Institute for Evolutionary Biology (IBE), a joint center of CSIC and Pompeu Fabra University (UPF) in Barcelona, Spain. “Our efforts to describe the current genomic diversity of this species are an attempt to provide a fine-scale map of connectivity between populations that can be useful to conservationists as a baseline and guide to build upon in their conservation efforts.”
The effort would not have been possible without the coordinated sampling of thousands of chimpanzee faecal samples by the Pan-African Program (PanAf) at 48 sites, as well as years of effort to develop methodological strategies to efficiently recover and enrich the proportion of host DNA in fecal samples, the researchers say. Fecal samples present many technical challenges because they contain only small amounts of degraded chimpanzee DNA, but they also have advantages for the study of endangered species because they allow extensive collection with minimal interference to animals. These approaches can now be put to work to study many other primates and other endangered species.
“Since we use whole chromosome sequencing with thousands of independent markers, compared to a few microsatellite markers, we have a much broader view of the genome. [that] is necessary to refine and describe the very complex evolutionary history of chimpanzees”, adds Tomas Marques-Bonet, principal investigator of the Institute of Evolutionary Biology (IBE) and co-leader of the study. invasive samples, which in a sense are the best of all worlds – a valuable source of genomic DNA but collected in such a way that the animals never need to be contacted or disturbed beyond the researchers present in their habitat.
Because the fossil record and ancient DNA of chimpanzees is limited, the only way to reconstruct their past is to study living individuals. Scientists recognize four chimpanzee subspecies, but questions remained about their relationships. There have been longstanding questions about how these subspecies are and have been related to each other.
To explore these questions in the new study, Fontsere and his colleagues retrieved partial genome information from more than 800 faecal samples from wild chimpanzees collected noninvasively from their current range. They focused their attention on chromosome 21, the smallest contiguous nuclear sequence in the chimpanzee genome and a source of a wealth of genomic sequence data to be used to infer chimpanzee population structure.
“Just by our sampling method, we discovered about 50% more and new genetic variants on chromosome 21 than previous studies,” Fontsere said. “Our dataset has been essential in understanding recent and past gene flow between populations where previous sampling deficiencies have hampered their study. In addition, it has allowed us to describe whether populations have been isolated recently or there was a historical event that did.By characterizing the genomic singularities of each community or population, we also created a map that relates genomic information to geographic location so that we can design a strategy to infer the geographic location of chimpanzee individuals.
Previously, only 59 whole chimpanzee genomes had been sequenced with limited information about their origin, the researchers note. Large datasets from thousands of georeferenced faecal samples also exist, but they only represent very small fragments of the entire genome. With these new samples and genomic data, they were able to fill in previous gaps in the distribution of eastern and central chimpanzees.
Fontsere says they also provided a more nuanced understanding of the genetic differentiation of the four recognized chimpanzee subspecies. They found a link between historical population structure, genetic continuity barriers between chimpanzee populations, and geographical barriers such as rivers and lakes.
“We were able to show, using different analyzes relating to very old and more recent variations, that the history of chimpanzees is complex, a bit like that of our own species”, explains Mimi Arandjelovic, co-director of the study of the Max Planck Institute for Evolutionary Anthropology, iDiv and University of Leipzig. “Chimpanzee subspecies have indeed been separated in the past but have since also experienced genetic exchange between populations. This explains why different studies aimed at reconstructing different ancestral periods have reached different conclusions about the evolutionary history of chimpanzees.”
Among many other insights, evidence also reveals extensive connectivity in western chimpanzees.
“It is so important for their conservation and it really shows that the connectivity between the forests of West Africa, especially in the northern region, must be preserved for the protection of these populations and subspecies,” said Marques-Bonet.
The researchers say they are now beginning to use the methods they developed for chimpanzees with other great apes and primates. Their findings in chimpanzees confirm that fecal samples, although more complex than blood samples, are an excellent source of host DNA for all species.
PanAf also continues to analyze data collected over 8 years in 18 countries in Africa, at more than 40 temporary and long-term research and conservation sites. The goal is to understand the evolutionary and ecological drivers of cultural and behavioral diversity in chimpanzees. Anyone interested can participate and help by annotating videos on the Citizen Science Project https://www.zooniverse.org/projects/sassydumbledore/chimp-and-see.
This work was supported by “La Caixa” Foundation, Vienna Science and Technology Fund, Vienna City Project, European Research Council (ERC) under the Research and Development Program Innovation Horizon 2020 of the European Union, the “Unidad de Excelencia Maria de Maeztu” funded by the AEI, the Howard Hughes International Early Career Prize, the NIH, the Secretaria d’Universitats i Recerca and the CERCA Program del Departament d’Economia i Together with the Generalitat de Catalunya, the Wellcome Trust of UCL, the Generalitat de Catalunya, and the pan-African program: The Cultured Chimpanzee (PanAf), funded by the Max Planck Society, the Max Planck Society Innovation Fund and the Heinz L. Krekeler Foundation.