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.

普通黑猩猩（Pan troglodytes）的野生种群正面临野外灭绝的紧迫风险，其成因包括其自然栖息地遭受的破坏性人为活动干扰，以及非法宠物贸易与丛林肉交易。针对黑猩猩的迁地保护（ex situ）管理计划已在其自然分布范围之外建立，此类计划中的黑猩猩个体有望用于补充未来的野生就地（in situ）保护行动。然而，这类计划往往缺乏关于其奠基个体的地理起源与亚种血统的有效信息。
本研究设计了一款全新的包含60000个祖先信息标记（ancestry informative markers）的基因捕获阵列，用于推断迁地保护种群中黑猩猩个体的血统，并确定被没收收容的庇护所个体的地理起源。我们对167只来源或亚种标识未知的黑猩猩组成的检测队列进行分析，在欧洲动物园与水族馆协会（EAZA）迁地保护计划（EEP）的种群中鉴定出90只合格的纯血统个体。同样重要的是，另有46只个体被鉴定为携带混血亚种血统，因此应逐步将其从繁育种群中淘汰。针对具备野外放归潜力的个体，我们确定了31只源自非法贸易没收行动的黑猩猩的地理起源，并证实了非侵入式采样在未来保护行动计划中的应用前景。总体而言，本研究的基因组学方法为濒危物种的迁地保护管理提供了可借鉴的范例，同时也为未来开展打击非法野生动物贸易的就地保护工作提供了高效工具。