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Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.

Bowden, R; MacFie, TS; Myers, S; Hellenthal, G; Nerrienet, E; Bontrop, RE; Freeman, C; ... Mundy, NI; + view all (2012) Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population. PLoS Genet , 8 (3) , Article e1002504. 10.1371/journal.pgen.1002504. Green open access

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Abstract

In spite of its evolutionary significance and conservation importance, the population structure of the common chimpanzee, Pan troglodytes, is still poorly understood. An issue of particular controversy is whether the proposed fourth subspecies of chimpanzee, Pan troglodytes ellioti, from parts of Nigeria and Cameroon, is genetically distinct. Although modern high-throughput SNP genotyping has had a major impact on our understanding of human population structure and demographic history, its application to ecological, demographic, or conservation questions in non-human species has been extremely limited. Here we apply these tools to chimpanzee population structure, using ∼700 autosomal SNPs derived from chimpanzee genomic data and a further ∼100 SNPs from targeted re-sequencing. We demonstrate conclusively the existence of P. t. ellioti as a genetically distinct subgroup. We show that there is clear differentiation between the verus, troglodytes, and ellioti populations at the SNP and haplotype level, on a scale that is greater than that separating continental human populations. Further, we show that only a small set of SNPs (10-20) is needed to successfully assign individuals to these populations. Tellingly, use of only mitochondrial DNA variation to classify individuals is erroneous in 4 of 54 cases, reinforcing the dangers of basing demographic inference on a single locus and implying that the demographic history of the species is more complicated than that suggested analyses based solely on mtDNA. In this study we demonstrate the feasibility of developing economical and robust tests of individual chimpanzee origin as well as in-depth studies of population structure. These findings have important implications for conservation strategies and our understanding of the evolution of chimpanzees. They also act as a proof-of-principle for the use of cheap high-throughput genomic methods for ecological questions.

Type: Article
Title: Genomic tools for evolution and conservation in the chimpanzee: Pan troglodytes ellioti is a genetically distinct population.
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pgen.1002504
Publisher version: http://dx.doi.org/10.1371/journal.pgen.1002504
Language: English
Additional information: © 2012 Bowden et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: The work was supported in part by a Wellcome Trust Strategic Award, Wellcome Trust Core Award Grant ref. 075491/Z/04/B, and Wellcome Trust WTCCC2 award ref. 084575/Z/08/Z. PD is funded by Wellcome Trust Core Award Grant ref. 090532/Z/09/Z and is supported in part by a Wolfson Royal Society Merit Award. TSM was supported by an MRC Studentship. NIM was supported by the Leverhulme Trust. REB is supported by the NHS NIHR Oxford Biomedical Research Centre and UKCRC (MRC UK Ref G0800778 and Wellcome Trust Ref. 087646/2/08/2). GH was supported in part by Polygene grant LSHC-CT-2005-018827. Part of this work has been supported by EUPRIM-Net under the EU contract RII3-026155 of the 6th Framework Programme. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Keywords: Animals, Biological Evolution, DNA, Mitochondrial, Genetic Speciation, Genetic Variation, Genome, Haplotypes, Pan troglodytes, Polymorphism, Single Nucleotide, Population Dynamics, Sequence Analysis, DNA
UCL classification: UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: http://discovery.ucl.ac.uk/id/eprint/1368659
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