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Chimpanzee Genetics Offer Clues to Population History, Conservation


NEW YORK – An international team led by investigators in Spain and Germany has characterized genetic features in chimpanzees (Pan troglodytes) from dozens of sites in Africa, uncovering clues to the primates' evolutionary history, population structure, and geography-related genetic differences that may help to nab those involved in illegal wildlife trading.

Using chromosome 21 capture and sequencing on more than 800 fecal samples collected noninvasively by Pan African Program investigators at 48 sampling sites across the chimpanzee range, the researchers assessed genetic profiles in chimpanzee populations representing the Western, Nigeria-Cameroon, Central, and Eastern subspecies — work outlined in a study published in Cell Genomics on Wednesday.

"Our study represents a step forward in the study of chimpanzees genomic diversity," first and co-corresponding author Clàudia Fontserè, a post-doctoral researcher at the Institute of Evolutionary Biology in Barcelona, explained in an email, adding that "large datasets from thousands of geo-referenced fecal samples also existed before, but they represent only very small fragments of the entire genome (a few microsatellites)."

The new sequence collection provides an opportunity for more detailed analyses of chimpanzees' complex demographic history, the authors noted, while filling in prior gaps in population representation across the full distribution of eastern and central chimpanzees.

"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," co-senior and co-corresponding author Tomas Marques-Bonet, a researcher affiliated with the Institute of Evolutionary Biology, the Barcelona Institute of Science and Technology, the Autonomous University of Barcelona, and the Catalan Institution of Research and Advanced Studies, said in a statement.

Along with analyses that placed the chimpanzees within the four previously defined subspecies, the team used the chromosome 21 sequence data to interrogate chimpanzee population dynamics, retracing past and current population connections at geographic sites across the chimp's range going back to the Middle Pleistocene — a time period previously linked to splits between chimp subspecies and related migrations.

"The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale," the authors reported. "We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus)."

By highlighting relationships between chimpanzee populations on different parts of the continent, the work may help conservationists come up with ecology-informed strategies for managing and preserving chimpanzee habitat. In particular, she explained, the work pointed to extensive connections between chimpanzee populations found in Western Africa's forests, suggesting that the populations will benefit from efforts to retain and boost forest connectivity.

Because the chimpanzees' genomic diversity tracked with their geographic origin, meanwhile, the investigators were able to come up with a geolocalization method for genetically tracing chimps within around 62 miles of their origin, noting that such advances are expected to support efforts to combat illegal trade in wildlife or wildlife products.

"We hope that the resources we have generated here (both the genomic dataset and the geolocalization strategy) can be applied in the future to help the conservation of this endangered species," Fontserè explained, adding that the same strategy may be used to more fully characterize conservation-related features found in other great ape or primate populations in the future.

Together, the authors suggested, the chromosome 21 sequence dataset "allows for the determination of fine-scale population structure, past and recent gene flow, and migration events, and the construction of a geo-genetic map for the geolocalization of orphaned chimpanzees and confiscated bushmeat."