Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution

PLoS One. 2013;8(3):e59660. doi: 10.1371/journal.pone.0059660. Epub 2013 Mar 27.

Abstract

Bonobos (Pan paniscus) inhabit regions south of the Congo River including all areas between its southerly tributaries. To investigate the genetic diversity and evolutionary relationship among bonobo populations, we sequenced mitochondrial DNA from 376 fecal samples collected in seven study populations located within the eastern and western limits of the species' range. In 136 effective samples from different individuals (range: 7-37 per population), we distinguished 54 haplotypes in six clades (A1, A2, B1, B2, C, D), which included a newly identified clade (D). MtDNA haplotypes were regionally clustered; 83 percent of haplotypes were locality-specific. The distribution of haplotypes across populations and the genetic diversity within populations thus showed highly geographical patterns. Using population distance measures, seven populations were categorized in three clusters: the east, central, and west cohorts. Although further elucidation of historical changes in the geological setting is required, the geographical patterns of genetic diversity seem to be shaped by paleoenvironmental changes during the Pleistocene. The present day riverine barriers appeared to have a weak effect on gene flow among populations, except for the Lomami River, which separates the TL2 population from the others. The central cohort preserves a high genetic diversity, and two unique clades of haplotypes were found in the Wamba/Iyondji populations in the central cohort and in the TL2 population in the eastern cohort respectively. This knowledge may contribute to the planning of bonobo conservation.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Animals, Wild / genetics
  • Congo
  • Conservation of Natural Resources
  • DNA, Mitochondrial / genetics*
  • Genetic Variation*
  • Genetics, Population
  • Geography*
  • Haplotypes / genetics
  • Linear Models
  • Models, Genetic
  • Pan paniscus / genetics*
  • Phylogeny
  • Rivers

Substances

  • DNA, Mitochondrial

Grants and funding

This research was supported by the Environment Research and Technology Development Fund (D-1007) (to TF); the Global Environment Research Fund (F-061) of the Ministry of the Environment, Japan (to Nishida); Japan Society for the Promotion of Science (JSPS) Grants-in-aid for Scientific Research (17255005 and 22255007, to TF); the JSPS Asia-Africa Science Platform Program (2009–2011, 2012–2014 to TF); the JSPS Primate Origins of Human Evolution (HOPE) Project (AS-22-027 and ITP-23-006, to TS); US Fish and Wildlife (2007–2009, 2010–2011, to Lukuru Wildlife Research Foundation); Arcus Foundation (2007–2008, 2010, 2012, to Lukuru Wildlife Research Foundation); Wood Tiger Foundation (2010, 2012, to Lukuru Wildlife Research Foundation); Full Circle Foundation (2011, to Lukuru Wildlife Research Foundation); the US Fish and Wildlife Service Assistance Award (96200-0-G017, to African Wildlife Foundation); Arcus Foundation, the Columbus Zoo and Aquarium, and Barron Wall (to AWF); the L.L. Leakey Foundation (to AKC); the Congo Basin Forest Partnership/USAID-WWF (623-A-00-06-00072-00, to ZSM); Susan McConnell and Richard Scheller (Wildlife Conservation Network) (to ZSM); the AZA Ape TAG Conservation Initiative (to ZSM); WWF Belgium, WWF Netherlands, Belgian Cooperation funding for co-financing, and CARPE program (USAID) for program coordination, for WWF bonobo project in the Lac Tumba Landscape. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.