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Targeted conservation genetics of the endangered chimpanzee

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  • Peter Frandsen, Copenhagen Zoo, University of Copenhagen
  • ,
  • Claudia Fontsere, Pompeu Fabra University
  • ,
  • Svend Vendelbo Nielsen
  • ,
  • Kristian Hanghøj, University of Copenhagen
  • ,
  • Natalia Castejon-Fernandez, Aarhus University
  • ,
  • Esther Lizano, Pompeu Fabra University, Autonomous University of Barcelona
  • ,
  • David Hughes, MRC Integrative Epidemiology Unit at University of Bristol
  • ,
  • Jessica Hernandez-Rodriguez, Pompeu Fabra University
  • ,
  • Thorfinn Sand Korneliussen, GLOBE, Higher School of Economics
  • ,
  • Frands Carlsen, Copenhagen Zoo
  • ,
  • Hans Redlef Siegismund, University of Copenhagen
  • ,
  • Thomas Mailund
  • Tomas Marques-Bonet, Pompeu Fabra University, Autonomous University of Barcelona, ICREA, Centre for Genomic Regulation
  • ,
  • Christina Hvilsom, Copenhagen Zoo

Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. Here, we present a newly designed capture array with ~60,000 ancestry informative markers used to infer ancestry of individual chimpanzees in ex situ populations and determine geographical origin of confiscated sanctuary individuals. From a test panel of 167 chimpanzees with unknown origins or subspecies labels, we identify 90 suitable non-admixed individuals in the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (EEP). Equally important, another 46 individuals have been identified with admixed subspecies ancestries, which therefore over time, should be naturally phased out of the breeding populations. With potential for future re-introduction to the wild, we determine the geographical origin of 31 individuals that were confiscated from the illegal trade and demonstrate the promises of using non-invasive sampling in future conservation action plans. Collectively, our genomic approach provides an exemplar for ex situ management of endangered species and offers an efficient tool in future in situ efforts to combat the illegal wildlife trade.

Original languageEnglish
JournalHeredity
Volume125
Issue1-2
Pages (from-to)15-27
ISSN0018-067X
DOIs
Publication statusPublished - Aug 2020

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