Development of genome-wide SNPs for Nubian ibex (Capra nubiana) to support conservation of wild populations in Oman

The Nubian ibex (Capra nubiana) is a desert-adapted ungulate, and the remaining free-roaming populations within Oman are small and fragmented. The appropriateness of captive insurance populations for reinforcing existing, or establishing new, wild populations remains uncertain for Oman due to uncertainties regarding taxonomy and genetic provenance. For effective management of this Vulnerable species, it is essential to assess the genetic relationships between the wild and captive animals, and investigate hybridisation with domestic goats (Capra hircus). To facilitate this, we developed genetic resources for Nubian ibex using double digest restriction-associated DNA, identifying 32,461 SNPs which will be invaluable for future development of marker systems to assess wild populations using low-quality DNA from non-invasive sampling. After applying stringent filters, we used 5775 high quality SNPs, to assess genetic structure, gene flow and divergence between wild and captive populations of Nubian ibex. We detected hybridisation within captivity between Nubian ibex and goats, which will require careful attention in future from the captive management authorities and recommend that genetic assessment of captive individuals is routinely used to evaluate their suitability for reintroduction or reinforcement programs. Substantial population structure and significant genetic differentiation was found between wild and captive individuals (FST = 0.540). Our results support a previous mitochondrial study, showing a divergence between the wild Nubian ibex in Oman and those in captivity. These data support the need for further research into Nubian ibex taxonomy to determine whether this species is at greater conservation risk than currently known.