Targeted conservation genetics of the endangered chimpanzee

Abstract

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). Importantly, 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.

Insights from the rescue and breeding management of Cuvier’s gazelle (Gazella cuvieri) through whole‐genome sequencing

“…Overall, our results suggest that mixing the SPA‐ALM and SPA‐CAN gazelles, which had no gene flow for two generations, has avoided the loss of genetic diversity and even resulted in a slight increase in genome‐wide heterozygosity in the F1 Offspring cohort. Our findings are in line with previous publications stating that genetic diversity in several endangered species can be increased, by including individuals from different populations (Biebach & Keller, 2012 ; Frankham, 2008 ; Rick et al, 2019 ).…”

New developments in the field of genomic technologies and their relevance to conservation management

“…Genomic techniques allow us to detect DNA sequence variation at single nucleotides (i.e. single-nucleotide polymorphism: SNP, see glossary) that can be used to evaluate the effects of historic founder selection (Gomes Viana et al 2018;Frandsen et al 2020;Ogden et al 2020;Wei and Jiang 2021) and set guidance on how to increase levels of genetic diversity and minimise genetic similarity (Bragg et al 2020) via selective addition of unrepresented lines (Wildt et al 2019;Galla et al 2020;Miller et al 2010). The efficiency of ex situ management partly relies on the profound knowledge of a species' taxonomic status and recent demographic history.…”

“…For many species of conservation concern, such information is either missing or incomplete, and genomics has proven key in filling knowledge gaps (e.g. Frandsen et al 2020;Robinson et al 2021a) and delineating management units (Barbosa et al 2018) starting from almost any type of sample (e.g. museum collections and biobanks; Baveja et al 2020).…”

The Diversity of Primates: From Biomedicine to Conservation Genomics

“…However, this represents a vanishingly small proportion of primate species diversity and an exceptionally small number of individuals per species. Most zoos only house a subset of charismatic primates, and little verifiable information about the biogeographic origin and pedigree of the animals is often known (126). Collecting blood or tissue samples from free ranging primates is challenging.…”