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Nearby Chimpanzee Populations Show Greater Genetic Diversity Than Distant Human Populations

March 3, 2012

Chimpanzee populations living in relatively close proximity are substantially more different genetically than humans living on different continents, according to a study published March 2 in PLoS Genetics. The study suggests that genomics can provide a valuable new tool for use in chimpanzee conservation, with the potential to identify the population of origin of an individual chimpanzee or the provenance of a sample of bush meat.

Common chimpanzees in equatorial Africa have long been recognized as falling into three distinct populations, or sub-species: western, central and eastern chimpanzees. A fourth group, the Cameroonian chimpanzee, has been proposed to live in southern Nigeria and western Cameroon, but there has been considerable controversy as to whether it constitutes a distinct group.

Scientists from the Universities of Oxford and Cambridge, the Broad Institute, the Centre Pasteur du Cameroun and the Biomedical Primate Research Centre examined DNA from 54 chimpanzees, measuring the DNA at 818 positions across the genome that varied between individuals. Analysis of patterns in the data showed Cameroonian chimpanzees to be distinct from the other, well-established groups. Intriguingly, previous conclusions based on earlier studies, that Cameroonian and western chimpanzees were most closely related, were shown to be untrue; instead the closest relationships to Cameroonian chimpanzees are with nearby central chimpanzees.

Dr Rory Bowden from the University of Oxford, who led the study, said: “These findings have important consequences for conservation. All great ape populations face unparalleled challenges from habitat loss, hunting and emerging infections, and conservation strategies need to be based on sound understanding of the underlying population structure. The fact that all four recognized populations of chimpanzees are genetically distinct emphasizes the value of conserving them independently.

“Genomics can also provide tools for use in chimpanzee conservation. Genetic tests could cheaply and easily identify the population of origin of an individual chimpanzee or even a sample of bush meat.”

The authors also contrasted the levels of genetic differentiation between the chimpanzees from the different groups with those based on similar data from humans from different populations. Surprisingly, even though all the chimpanzee populations lived in relatively close proximity, with the habitats of two groups separated only by a river, chimpanzees from different populations were substantially more different genetically than humans living on different continents.

Professor Peter Donnelly, Director of the Wellcome Trust Centre for Human Genetics in Oxford and a senior author on the study, said: “Relatively small numbers of humans left Africa 50,000-100,000 years ago. All non-African populations descended from them, and are reasonably similar genetically. That chimpanzees from habitats in the same country, separated only by a river, are more distinct than humans from different continents is really interesting. It speaks to the great genetic similarities between human populations, and to much more stability, and less interbreeding, over hundreds of thousands of years, in the chimpanzee groups.”

The conservation implications of the study extend to other species. New techniques such as next-generation sequencing, which have become available since the study was initiated, will allow a catalogue of genetic variation to be obtained cheaply and easily for any species, simply by sequencing even one or two individuals. Such a catalogue could then be used to perform a study like this one, to identify genetically distinct groups, and subsequently to develop simple and cheap tests of population of origin.

Dr Nick Mundy, from the University of Cambridge, and the paper’s other senior author, said: “Because they are humans’ nearest relatives, the structure and origins of chimpanzee populations have long been of wide interest. Future studies will be able to use genome data to uncover the adaptations that are unique to the Cameroonian chimpanzees.”

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Source: Wellcome Trust