Targeted conservation genetics of the endangered chimpanzee

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.