4.6 Article

Genomic Tools for Evolution and Conservation in the Chimpanzee: Pan troglodytes ellioti Is a Genetically Distinct Population

Journal

PLOS GENETICS
Volume 8, Issue 3, Pages -

Publisher

PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pgen.1002504

Keywords

-

Funding

  1. Wellcome Trust [075491/Z/04/B, 084575/Z/08/Z, 090532/Z/09/Z, 087646/2/08/2]
  2. Wolfson Royal Society
  3. MRC
  4. Leverhulme Trust
  5. NHS NIHR Oxford Biomedical Research Centre
  6. UKCRC (MRC UK) [G0800778]
  7. Polygene grant [LSHC-CT-2005-018827]
  8. EUPRIM-Net under EU [RII3-026155]
  9. MRC [G0800778] Funding Source: UKRI
  10. Wellcome Trust [075491/Z/04/B] Funding Source: Wellcome Trust
  11. Medical Research Council [G0800778] Funding Source: researchfish

Ask authors/readers for more resources

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.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.6
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available