Researchers design a method to pinpoint the origin of illegally traded chimpanzees
IMAGE: THE PANAF CITIZEN SCIENCE PROJECT IS OPEN TO ANYONE WILLING TO TAKE PART IN ANNOTATING CAMERA TRAP VIDEOS FROM ACROSS TROPICAL AFRICA view more
CREDIT: MPI-EVA/PANAFCHIMP&SEE.ORG
Researchers reporting in the journal Cell Genomics on June 1 have produced the first catalogue of genomic diversity for endangered chimpanzees in the wild. The catalogue, which includes 828 chimp samples from across their range, offers a detailed reconstruction of chimp population structure and fine-scale patterns of isolation, migration, and connection. The researchers use this information to design a method to link confiscated chimpanzees to their place of origin within about 100 kilometers, with the goal to support efforts to combat the illegal trade of 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 of Evolutionary Biology (IBE), a joint centre of CSIC and Universitat Pompeu Fabra (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 of service to conservationists as a baseline and guide to build upon their conservation efforts.”
The effort would not have been possible without coordinated sampling of thousands of chimp fecal samples by the Pan African Program (PanAf) at 48 locations together with years of effort to develop methodological strategies to efficiently retrieve and enrich the proportion of host 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] is needed to refine and describe the very complex evolutionary history of chimpanzees,” adds Tomas Marques-Bonet, principal investigator from the Institute of Evolutionary Biology (IBE) and co-lead of the study. “Impressively, we are doing it with non-invasive samples, which, in a sense, are the best of all worlds—a valuable source of genomic DNA but collected in a way that animals never need to be contacted or disturbed beyond researchers existing in their habitat.”
Because the fossil record and ancient DNA for chimps is limited, the only way to reconstruct their past is through studies of living individuals. Scientists recognize four chimp subspecies, but questions had remained about their relationships. There have been long-standing questions about how connected those subspecies are and have been to each other.
To explore these questions in the new study, Fontsere and colleagues retrieved partial genome information from more than 800 non-invasively-collected wild chimpanzee fecal samples from across their current range. They focused their attention on chromosome 21, the smallest contiguous nuclear sequence in the chimpanzee genome and a source for a wealth of genomic sequence data for use in inferring chimpanzee population structure.
“Just by our sampling method, we have discovered around 50% more, and new, genetic variants on chromosome 21 than previous studies,” Fontsere said. “Our dataset has been key in understanding recent and past gene flow between populations where previous sampling gaps impeded their study. Also, it has allowed us to describe if populations have been isolated recently 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 were able to devise a strategy to infer the geographic location of chimpanzee individuals.”
Previously, only 59 whole chimpanzee genomes had been sequenced with limited information on their origin, the researchers note. Large datasets from thousands of geo-referenced fecal samples also exist, but they represent only very small fragments of the entire genome. With these new samples and genomic data, they’ve been able to fill the previous gaps in the distribution of Eastern and Central chimpanzees.
CAPTION
Wild chimpanzee defecating
CREDIT
MPI-EVA/PanAf
Fontsere says they’ve also provided a more nuanced understanding of the genetic differentiation of the four recognized chimpanzee subspecies. They found a link between historical population structure, barriers of genetic continuity between chimpanzee populations, and geographical barriers such as rivers and lakes.
“We were able to show, using different analyses that look at very old and more recent variation, that the history of chimpanzees is complex, much like that of our own species,” says Mimi Arandjelovic, co-lead of the study from the Max Planck Institute for Evolutionary Anthropology, iDiv, and Leipzig University. “Chimpanzee subspecies were indeed separated in the past but have since also experienced genetic exchange between populations. This nicely explains why different studies aiming at reconstructing different ancestral periods have come to different conclusions about the evolutionary history of chimpanzees.”
Among many other insights, the evidence also reveals extensive connectivity in Western chimpanzees.
“This is so critically important to their conservation and really argues that connectivity between forests across Western Africa, especially in the northern region, needs to be preserved for the protection of these populations and the subspecies,” said Marques-Bonet.
The researchers say they are now beginning to use the methods they’ve developed for chimpanzees with other great apes and primates. Their findings in chimpanzees confirm that fecal samples, although more complex than blood samples, are a fine source of host DNA for any species.
The PanAf also continues to analyze data collected over 8 years from 18 countries across Africa, at over 40 temporary and long-term research and conservation sites. The goal is to understand the evolutionary and ecological drivers of chimpanzee cultural and behavioral diversity. Anyone interested can pitch in and help by annotating videos at the citizen science project https://www.zooniverse.org/projects/sassydumbledore/chimp-and-see.
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This work was supported by “La Caixa” Foundation, the Vienna Science and Technology Fund, the City of Vienna project, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, the “Unidad de Excelencia Maria de Maeztu” funded by the AEI, the Howard Hughes International Early Career award, the NIH, the Secretaria d’Universitats i Recerca and CERCA Programme del Departament d’Economia i Coneixement de la Generalitat de Catalunya, UCL’s Wellcome Trust, the Generalitat de Catalunya, and the Pan African Programme: The Cultured Chimpanzee (PanAf), funded by the Max Planck Society, the Max Planck Society Innovation Fund, and the Heinz L. Krekeler Foundation.
Cell Genomics, Fontsere et al. “Population dynamics and genetic connectivity in recent chimpanzee history” https://www.cell.com/cell-genomics/fulltext/S2666-979X(22)00062-3
Cell Genomics (@CellGenomics) is a new gold open access journal from Cell Press publishing multidisciplinary research at the forefront of genetics and genomics. The journal aims to bring together diverse communities to advance genomics and its impact on biomedical science, precision medicine, and global and ecological health. Visit https://www.cell.com/cell-genomics/home. To receive Cell Press media alerts, please contact press@cell.com.
JOURNAL
Cell Genomics
METHOD OF RESEARCH
Experimental study
SUBJECT OF RESEARCH
Animals
ARTICLE TITLE
Population dynamics and genetic connectivity in recent chimpanzee history
ARTICLE PUBLICATION DATE
1-Jun-2022
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) in Barcelona, the Max Planck Institute for Evolutionary Anthropology (MPI-EVA), the German Centre for Integrative Biodiversity Research (iDiv) and Leipzig University
Peer-Reviewed PublicationIMAGE: GRAPHIC ABSTRACT OF THE STUDY view more
CREDIT: MARINA ÁLVAREZ-ESTAPÉ
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 absence of chimpanzee fossils, the genetic information from current populations is crucial for describing their evolutionary history, their genetic diversity and to contribute to their conservation.
An international research team led by the Institute of Evolutionary Biology (IBE), a joint centre of the CSIC and the Pompeu Fabra University (UPF) in Barcelona, the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) and the German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, has built the most extensive catalogue of genomic diversity in wild chimpanzee populations to date. Genetic information has been retrieved non-invasively using new technologies, from hundreds of 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 they have developed has direct applications for the conservation of chimpanzees, such as identifying illegal trafficking routes of wildlife products and orphans.
CAPTION
Photo composition of wild chimpanzees. Credit: MPI-EVA PanAf/ChimpandSee.org
CREDIT
MPI-EVA PanAf/ChimpandSee.org
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 Prof. Tomàs Marquès-Bonet, principal investigator of the Institute of Evolutionary Biology (IBE) and co-lead of the study.
Collecting geo-referenced non-invasive samples from nature is an effective way to obtain genomic information from wild chimpanzees when many factors limit the collection of high-quality samples, such as blood or tissues.
“We have seen that faecal samples, while imposing 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, researcher at 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, 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 Fontserè.
"Chimpanzees, like humans, have had 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 Dr. Mimi Arandjelovic, co-lead of the study and researcher at the Max Planck Institute for Evolutionary Anthropology, iDiv and Leipzig University. Dr. 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 8 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, usually at a few hundred kilometres from the real origin, and thus provide reliable information on the priority regions to be protected,” adds Marquès-Bonet. The developed methodology is already being applied in global conservation projects for the other great apes, bonobos, orangutans and gorillas, as part of collaboration with the Illumina iConserve program and currently being sequenced at the CNAG-CRG in Barcelona.
This study is part of the PanAf, hosted at the Max Planck Institute for Evolutionary Anthropology and the German Centre for Integrative Biodiversity Research (iDiv) in Leipzig, as well as the European ERC Consolidator grant ApeGenomeDiversity, awarded to Tomàs Marquès-Bonet.
Reference article: Fontsere et al., Population dynamics and genetic connectivity in recent chimpanzee history, Cell Genomics (2022); https://www.cell.com/cell-genomics/fulltext/S2666-979X(22)00062-3; DOI: https://doi.org/10.1016/j.xgen.2022.100133
JOURNAL
Cell Genomics
METHOD OF RESEARCH
Experimental study
ARTICLE TITLE
Population dynamics and genetic connectivity in recent chimpanzee history
ARTICLE PUBLICATION DATE
1-Jun-2022
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