The first catalog of genetic diversity for endangered chimpanzees in the wild was published in the journal Cell Genomics on June 1st. The catalog, which has 828 chimp samples from all over the world, provides a thorough reconstruction of chimp population structure as well as fine-scale patterns of isolation, migration, and connectivity.
The researchers will utilize this information to develop a mechanism for linking confiscated chimps to their origins within a 100-kilometer radius, in order to aid efforts to prevent the illegal traffic in chimps and associated 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.”
According to the researchers, the effort would not have been possible without the Pan African Program’s (PanAf) coordinated sampling of thousands of chimp fecal samples at 48 locations, as well as years of effort to develop methodological strategies to efficiently retrieve and enrich the proportion of host DNA in fecal samples.
Fecal samples pose a number of technical hurdles since they contain only minute amounts of degraded chimp DNA, but they also have advantages for endangered species research because they allow for extended collection with minimal animal involvement. These methods can now be used to investigate a variety of other endangered primates and 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 are sparse, examinations of current individuals are the only means to reconstruct their past. Scientists have identified four chimp subspecies, but their links have remained a mystery. There have long been doubts about how closely those subspecies are and have been related to one another.
Fontsere and colleagues used partial genome information from more than 800 non-invasively collected wild chimpanzee fecal samples from across their present range to answer these concerns in the new study.
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.
Claudia Fontsere
They concentrated their efforts on chromosome 21, the chimp genome’s smallest continuous nuclear sequence and a source of a plethora of genomic sequence data for inferring 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.”
Only 59 entire chimpanzee genomes had previously been sequenced, with little information on their origins, according to the researchers. There are also large datasets based on thousands of geo-referenced fecal samples, but they only represent a small portion of the complete genome. They were able to fill in prior gaps in the distribution of Eastern and Central chimps using these additional samples and genomic data.
They’ve also supplied a more sophisticated knowledge of the genetic differentiation between the four known chimp subspecies, according to Fontsere. They discovered a relationship between historical population structure, genetic continuity barriers among chimp groups, and geographic barriers like 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.”
The evidence also demonstrates considerable connection in Western chimps, among other things.
“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’re now experimenting with other great apes and primates using the approaches they’ve established for chimps. Their findings in chimps demonstrate that, albeit more complex than blood samples, feces are an excellent source of host DNA for any species.
The PanAf is also still analyzing data obtained over the last eight years in 18 African countries at over 40 short and long-term research and conservation sites. The goal is to figure out what drives chimp cultural and behavioral diversity, both evolutionarily and ecologically.
Anyone interested can pitch in and help by annotating videos at the citizen science project https://www.zooniverse.org/projects/sassydumbledore/chimp-and-see.
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.
