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New Chimpanzee Population Confirmed By High-throughput Genotyping

NEW YORK (GenomeWeb News) – An international research team has used high-throughput SNP genotyping to verify the existence of another genetically distinct chimpanzee population in equatorial Africa — the fourth found so far.

As they reported online last night in PLoS Genetics, researchers from the UK, US, Cameroon, and the Netherlands genotyped 818 SNPs in the genomes of 54 chimpanzees. The individuals tested came from two of the three previously defined chimpanzee sub-species, along with chimpanzees from parts of Nigeria and Cameroon suspected of belonging to another genetically distinguishable population.

From SNP and haplotype patterns in the chimpanzee genomes, the team determined that the latter group is genetically discernable from other chimpanzees living nearby — a finding that is expected to influence future chimpanzee population studies and conservation efforts.

"[C]onservation strategies need to be based on sound understanding of the underlying population structure," co-first author Rory Bowden, a zoology researcher at the University of Oxford, said in a statement. "The fact that all four recognized populations of chimpanzees are genetically distinct emphasizes the value of conserving them independently."

A closer look at chimpanzee populations indicated that there is actually more genetic differentiation between the newly corroborated chimpanzee population and nearby western and central chimpanzee populations than has been reported for human populations living on different continents.

"That chimpanzees from habitats in the same country, separated only by a river, are more distinct than humans from different continents is really interesting," co-senior author Peter Donnelly, director of the University of Oxford's Wellcome Trust Centre for Human Genetics, said in a statement. "It speaks to the great genetic similarities between human populations, and to much more stability, and less inter-breeding, over hundreds of thousands of years, in the chimpanzee groups."

Together, chimpanzees belong to a species called Pan troglodytes. Within that species, though, past studies have delineated at least three sub-species: the western chimpanzee P. t. verus, central chimpanzee P. t. troglodytes, and eastern chimpanzee P. t. schweinfurthii.

Based on mitochondrial DNA patterns, some have argued that chimpanzees in southern Nigeria and western Cameroon belong to yet another sub-species, P. t. ellioti, study authors explained, though autosomal DNA studies have produced conflicting results, with some confirming and others arguing against this designation.

To look at this in more detail, authors of the new PLoS Genetics study turned to some of the same sorts of SNP genotyping strategies that have been applied to human disease and population studies.

The team used Illumina GoldenGate genotyping arrays to genotype 54 chimpanzees at around 700 SNPs identified from Chimpanzee Genome Project data. They also did targeted resequencing of about 1,000 bases of DNA from a dozen autosomal regions of the genome to assess 100 or so more variants.

The chimpanzees tested for the study included 35 wild-born chimpanzee orphans from Cameroon, 15 chimpanzees belonging to the P. t. verus sub-species from Sierra Leone, and four chimps from the Biomedical Primate Research Centre in the Netherlands that were believed to be from the P. t. troglodytes sub-species.

Chimpanzees from the P. t. schweinfurthii population were not included in the study, researchers explained, since they are typically found in a different geographical area from the proposed P. t. ellioti population.

Of the 54 chimpanzees tested, 52 clustered neatly into three groups that corresponded to one western P. t. verus population and two distinct chimpanzee populations within Cameroon: P. t. troglodytes and P. t. ellioti.

The remaining two animals had genetic profiles that fell between the western and central populations, researchers noted, and were found to be the offspring of P. t. verus and P. t. troglodytes chimpanzees that bred in captivity.

Along with SNP-based analyses, authors of the new study noted that haplotype variation patterns also provide information about chimpanzee population structure.

For instance, the team found that the two chimpanzee populations from Cameroon were a bit more closely related to one another than they are to chimpanzees from Sierra Leone.

But their haplotype analyses and follow-up experiments revealed a surprising degree of genetic differentiation between all three populations, which were each more genetically distinct from one another than are human populations in Europe, Africa, and East Asia.

Based on their findings, the researchers cautioned against population analyses based exclusively on information from mitochondrial DNA, explaining, "We compared the classification based on mtDNA with our genome-wide analysis and found that it classified 50 or 52 non-hybrid individuals correctly."

"[T]he two systems generally agree," they added, "but, not surprisingly, single-locus mtDNA is les reliable for classification than genome-wide data."

Instead, they argued that it should be possible to come up with accurate and affordable genetic tests that include information from across the genome, both for determining the population origin of individual chimps or for doing more detailed chimpanzee population studies.

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