![]() Yet, most recent attempts based on microsatellite markers (Hvilsom et al. Early attempts to add a genetic layer to the EEP management has confirmed that knowledge of subspecies ancestries, inbreeding and relatedness estimates are instrumental to preserve genetic diversity in captive populations (Hvilsom et al. However, in times before high resolution genetic technologies were available and even in its early development, knowledge of subspecies labels and relatedness between founders were inaccurate and has led to admixture of subspecies in the captive population (Hvilsom et al. The extant EEP populations consist of wild founders and descendants thereof. ![]() The primary aim of the EEP is to safeguard the survival of healthy self-sustaining populations targeting the taxonomical level of subspecies (Carlsen and de Jongh 2019). troglodytes) have been established (Carlsen and de Jongh 2019). The EEP targets the subspecies level and today, breeding programmes for two of the four recognised subspecies, the western chimpanzee ( P. Outside Africa, several regional chimpanzee conservation programmes exist, with the largest being the European Association of Zoos and Aquaria (EAZA) Ex situ Programme (henceforth EEP). 2019) to prevent the predicted extinction of chimpanzees within the current century (Estrada et al. Together, these threats emphasise the importance of a ‘ One Plan Approach’ conservation programme linking in situ and ex situ efforts (Traylor-Holzer et al. Besides wildlife trade, other continuous threats including habitat destruction, poaching for local consumption, and human linked disease outbreaks has led to a drastic decline in the wild chimpanzee populations (Humle et al. ![]() One by-product of the human wildlife conflicts has been a rise in opportunistic trafficking of chimpanzees, which, in recent years has become more organised and systematic (Stiles et al. Human encroachment on the natural range of the chimpanzee has further caused an intensified conflict between humans and chimpanzees (Hockings et al. verus) being listed as ‘Critically Endangered’ in the latest assessment (Humle et al. In the last two decades, chimpanzees have been listed as ‘Endangered’ at the species level on the IUCN Red List, with one of the four recognised subspecies, the western chimpanzee ( P. ![]() Despite our fascination, human activities have led to a drastic decline in the population size of the chimpanzee. Since the discovery of the common chimpanzee ( Pan troglodytes), humans have been drawn to this charismatic species. 2015), conservation efforts to save endangered species are calling for novel approaches to mitigate the ongoing extinction crisis. In an era of human-induced acceleration of species loss, often referred to as the sixth mass extinction era (Ceballos et al. 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. 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. 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. 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). 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. However, these programmes have often suffered from inadequate information about the geographical origin and subspecies ancestry of the founders. 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). 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.
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