HomeBest HostingA new way to identify the origin of illegally traded chimpanzees

A new way to identify the origin of illegally traded chimpanzees

Chimpanzee face

A newly created catalog of genomic diversity for endangered wild chimpanzees can help link confiscated chimpanzees to their place of origin, which could help combat illegal animal trafficking.

Using thousands of chimpanzee feces samples, the researchers created the first catalog of genomic diversity for endangered wild chimpanzees. This catalog allows them to bind confiscated chimpanzees from their place of origin in order to reduce the illegal animal trade. People interested in helping to protect endangered chimpanzees can annotate videos for a citizen science project called Chimp & See.

Scientists have produced the first catalog of genomic diversity for endangered wild chimpanzees, as reported today (June 1, 2022) in the journal. Cell genomics. The catalog, which includes 828 samples of chimpanzees in their range, provides a detailed reconstruction of the structure of the chimpanzee population and the fine-scale models of isolation, migration and connection. Researchers are using this information to design a way to link confiscated chimpanzees to their home area within a radius of about 100 kilometers, in order to support efforts to combat the illegal trade in chimpanzees and related products.

“Chimpanzees are an endangered species, with a massive decline in population in recent years,” said Claudia Fontsere, lead author of the study at the Institute for Evolutionary Biology (IBE), a joint center of the CSIC and Pompeu Fabra University. UPF) from Barcelona, ​​Spain. . “Our efforts to describe the current genomic diversity of this species are an attempt to provide a fine-grained map of connectivity between populations, which can be useful to conservationists as a basis and guide to build on their conservation efforts.”

Chimpanzee trap

The PanAf Citizen Science Project is open to anyone who wants to take part in annotating videos with the camera trap in tropical Africa. Credit: MPI-EVA / PanAfChimp & See.org

The effort would not have been possible without the coordinated sampling of thousands of chimpanzee faeces by the Pan-African Program (PanAf) in 48 locations, along with years of efforts to develop methodological strategies to effectively recover and enrich the host.[{” attribute=””>DNA in fecal samples, the researchers say. Fecal samples come with many technical challenges as they contain only small amounts of degraded chimpanzee DNA, but they also have advantages for the study of endangered species as they allow for extensive collection with minimal interference to the animals. These approaches can now be put to work to study many other endangered primates and other species.

“Since we are using sequencing of a whole chromosome with thousands of independent markers, compared to few microsatellite markers, we have a much broader view of the genome [that] it is necessary to refine and describe the very complex evolutionary history of chimpanzees, ”adds Tomas Marques-Bonet, principal investigator at the Institute for Evolutionary Biology (IBE) and co-leader of the study. “Impressively, we do it with non-invasive samples, which are, in a way, the best of all worlds - a valuable source of genomic DNA, but collected in a way that animals should not be contacted or disturbed outside existing researchers in their habitat. “

The wild chimpanzee defecates

The wild chimpanzee defecates. Credit: MPI-EVA / PanAf

Because fossil recordings and ancient DNA for chimpanzees are limited, the only way to reconstruct their past is through studies of living individuals. Scientists recognize four subspecies of chimpanzees, but questions remain about their relationship. There have been long-standing questions about how connected they are and what those subspecies were.

To explore these questions in the new study, Fontsere and colleagues extracted partial genome information from more than 800 non-invasively wild chimpanzee faeces samples collected from their current range. They focused on chromosome 21, the smallest adjacent nuclear sequence in the chimpanzee genome, and a source of a wealth of genomic sequence data to deduce the structure of the chimpanzee population.

Chimpanzee trap room

Photo composition of wild chimpanzees. Credit: MPI-EVA / PanAf ChimpandSee.org

“Only through our sampling method did we discover about 50% more genetic variants on chromosome 21 than previous studies,” Fontsere said. “Our data set was key to understanding recent and past gene flow between populations where previous sampling gaps prevented their study. It also allowed us to describe whether populations were recently isolated or whether there was a historical event that did so. By characterizing the genomic singularities of each community or population, we also created a map that links genomic information to geographic location so that we can devise a strategy to deduce the geographic location of chimpanzee individuals. ”

Claudia Fontserè

Claudia Fontserè is the first author of the study and a researcher at IBE, processing fecal samples in the laboratory. Credit: Claudia Fontsere

Previously, only 59 entire chimpanzee genomes were sequenced with limited information about their origin, the researchers note. There are also large data sets from thousands of geo-referenced fecal samples, but these are only very small fragments of the entire genome. With these new samples and genomic data, they managed to fill the 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 the historical structure of the population, the barriers of genetic continuity between chimpanzee populations, and geographical barriers such as rivers and lakes.

“We have been able to show, using various analyzes that look at very old and newer variations, that the history of chimpanzees is as complex as that of our own species,” says Mimi Arandjelovic, co-leader of the Max study. Planck Institute for Evolutionary Anthropology, iDiv and Leipzig University. “Chimpanzee subspecies have indeed been separated in the past, but since then they have also experienced genetic exchanges between populations. This explains why different studies of the reconstruction of different ancestral periods have come to different conclusions about the evolutionary history of chimpanzees. “

Among many other perspectives, the evidence also reveals extensive connectivity to Western chimpanzees.

“This is so important for their conservation and it is true that the connectivity between the forests of West Africa, especially in the North region, must be maintained for the protection of these populations and subspecies,” said Marques-Bonet.

Anthony Agbor

Anthony Agbor, co-author of the study and field manager at several PanAf sites, prepares samples for field processing. Credit: PanAf

Researchers say they are now beginning to use the methods they have developed for chimpanzees with other large monkeys and primates. Their findings in chimpanzees confirm that fecal samples, although more complex than blood samples, are a good source of host DNA for any species.

PanAf also continues to analyze data collected over 8 years from 18 African countries at more than 40 temporary and long-term research and conservation sites. The aim is to understand the evolutionary and ecological factors of the chimpanzee’s cultural and behavioral diversity. Anyone interested can submit and help by annotating the videos for the citizen science project.

Reference: “Population Dynamics and Genetic Connectivity in the Recent History of Chimpanzees” June 1, 2022, Cell genomics.
DOI: 10.1016 / j.xgen.2022.100133

This work was supported by the La Caixa Foundation, the Vienna Science and Technology Fund, the Vienna project, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program, the Unidad de Excelencia Maria de Maeztu ”funded by AEI, Howard Hughes International Early Career Award, NIH, Secretary of Universities and Research and CERCA Program of the Department of Economics and Knowledge of the Generalitat de Catalunya, UCL’s Wellcome Trust, Generalitat de Catalunya and the Pan-African Program: Cimpanzeul de Culture (PanAf), funded by the Max Planck Society, the Max Planck Society Innovation Fund and the Heinz L. Krekeler Foundation.

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