Genetic assessment and development of genomic resources for Nubian ibex conservation management in Oman

Al Ghafri, Mataab Khalaf Salim

Abstract

The Nubian ibex (Capra nubiana) is listed as Vulnerable according to IUCN Red List. It is patchily distributed across parts of Africa and Arabia, including Oman where it is present in isolated populations in central and southern region of the country. It is further threatened by habitat degradation, human expansion, poaching, and population fragmentation.

In order to study the impact of these factors and inform future management plans, I investigated the genetic diversity, gene flow and divergence between wild Nubian ibex from Oman, in captivity and from museum samples, using mitochondrial DNA and nuclear DNA using ddRAD. In addition, a hybrid capture technique was performed to analyse nuclear DNA of low-quality samples (faecal and bones) and further investigate the population genetics of ibex in Oman, Yemen and Sudan. Lastly, population viability analysis (PVA) was carried out to assess the effects of different environmental and anthropogenic factors on the isolated ibex population in the central region.

Mitochondrial results showed that the population in the southern region of Oman was more diverse compared to the central region with restricted gene flow. There was a significant divergence between wild and captive populations (FST=0.725). Moreover, a significant differentiation was found between wild ibex from Oman and ibex samples from Sudan (FST=0.971), while results showed no differences between Omani and Yemeni ibex. These results were supported by 5,775 high quality SNP loci across Nubian ibex genome which showed significant genetic differentiation between wild and captive individuals (FST (5,775) = 0.540).

Furthermore, the baits designed from the ddRAD reads generated in this study were successful in targeting DNA of low-quality samples of Nubia ibex populations in Oman, Yemen and Sudan. It generated 1,054 SNPs, which helped in assessment of genetic variation among these different populations.

My results showed a significant divergence between Oman and Sudan populations (FST (1,054) = 0.513). As well as a significant divergence between the Omani population and the captive individuals (FST (1,054) =0.433), while no significant differences were found between Omani and Yemeni populations.

The PVA results indicate that wild ibex in central Oman under the current circumstances are subject to an increased risk of extinction over the next 100 years. High mortality was found to have the strongest influence on the dynamics of the population. Moreover, the analysis showed that the proportion of females played a vital role in population viability, thus they need to be in the central focus of any conservation program.

Synthesising genetic and PVA results, I recommended establishment of a captive breeding population formed from more genetically diverse animals selected from central and southern Omani populations, whilst protecting current populations. This will guarantee sufficient genetic diversity to retain evolutionary resilience to cope with future environmental changes.

My results indicate that captive Nubian ibex did not originate from wild populations in Oman. I advise that captive ibex should not be used for any future re-introduction or reinforcement programs. Nubian ibex in Oman should be treated as a distinct taxonomic unit, potentially at the species level.

Citation

Al Ghafri, M. K. S. Genetic assessment and development of genomic resources for Nubian ibex conservation management in Oman. (Thesis). Edinburgh Napier University

• Thesis Type: Thesis
• Deposit Date: Aug 21, 2024
• Publicly Available Date: Aug 21, 2024
• DOI: https://doi.org/10.17869/enu.2024.3789498
• Award Date: Jul 3, 2024