Benefits and pitfalls of captive conservation genetic management: Evaluating diversity in scimitar-horned oryx to support reintroduction planning

Abstract

The reintroduction of the scimitar-horned oryx to Chad is a multi-disciplinary endeavour, planned and implemented over the past decade, utilizing a wide range of conservation science applications to maximise the chances of long-term population sustainability. The principle of incorporating genetic diversity information into founder selection for species reintroductions is widely recognized; however, in practice, a full assessment of available ex-situ genetic variation is rarely attempted prior to identifying individuals for release.In this study we present the results of over ten years of research analyzing and interpreting the genetic diversity present in the key source populations for the Chad scimitarhorned oryx reintroduction. Three empirical genetic datasets (mitochondrial DNA sequence, nuclear DNA microsatellite and SNP markers) comprising over 500 individuals sampled from public and private institutions were analysed, accompanied by simulation studies to address applied questions relating to management of the reintroduction.The results strongly demonstrate the importance of conservation genetic analysis in ensuring that founders represent the greatest breadth of evolutionary diversity available. The inclusion of both intensively and lightly managed collections allowed us to bridge the gap between studbook and group managed populations, enabling the inclusion of individuals from populations that lack historic data on their origins, but which may hold unique diversity of significant conservation value. Importantly, however, our study also reveals the potential risks of applying standard population genetic approaches to multiple captive populations, for which small founder sizes are likely to strongly bias results, with potentially serious consequences for the genetic management of conservation breeding programmes.

Integrating genomics into conservation management

“…(2020) reveal surprisingly high levels of genetic diversity in scimitar‐horned oryx populations, attributable to successful husbandry leading to rapid population growth in captivity. This result confirms earlier work using molecular markers with less resolution (Iyengar et al., 2007; Ogden et al., 2020). Humble et al.’s (2020) results also uncover the possibility that the semicaptive private collection was founded with a larger number of animals than previously thought, especially encouraging news for conservation.…”

Chromosomal‐level genome assembly of the scimitar‐horned oryx: Insights into diversity and demography of a species extinct in the wild

“…Sequence similarity and haplotype frequencies were calculated using the R package pegas (Paradis, 2010). To place the mitochondrial data into a broader geographic context, the six control region sequences were aligned to 43 previously described haplotypes (NCBI accession numbers DQ159406–DQ159445 and MN689133–MN689138, Iyengar et al., 2007; Ogden et al., 2020) using Geneious Prime . A median‐joining haplotype network was generated using popart v1.7 (Leigh & Bryant, 2015).…”

“…To date, ~200 individuals have been released into Chad, and more animals are due to be reintroduced in the coming years until a self‐sustaining population is reached. To facilitate an assessment of ex situ genetic variation and inform the selection of suitable founder individuals, SNP genotyping using reduced representation sequencing (ddRAD) has been carried out across multiple populations (Ogden et al., 2020). However, to carry out analyses that rely on markers with known genomic coordinates, such as demographic inference (Li & Durbin, 2011) or characterising runs of homozygosity (Kardos, Luikart, & Allendorf, 2015), a genome assembly for the SHO is required.…”

“…However, an early study using mitochondrial DNA reported considerably high levels of variation in captive SHO populations (Iyengar et al., 2007). Furthermore, a recent analysis using both microsatellites and a small panel of SNPs found support for higher levels of genetic diversity in studbook managed populations, implying that diversity is not spread evenly across the globe (Ogden et al., 2020).…”

Global Commitments to Conserving and Monitoring Genetic Diversity Are Now Necessary and Feasible

“…Zoos and botanic gardens increasingly incorporate molecular genetic data to carefully select breeding individuals (Wood et al 2020 ), whereas other programs aim to conserve genetic variation through rapid population size increase (Wildt et al 2019 ). Ideally genetic diversity may be best conserved via integrated management of wild and captive populations, informed by genetic data of in situ and ex situ populations, following the One Plan approach (Byers et al 2013 , Ogden et al 2020 ).…”