Genetic restoration of black rhinoceroses in South Africa: conservation implications

Globally, wildlife populations are becoming increasingly small and isolated. Both processes contribute to an elevated risk of extinction, notably due to genetic factors related to inbreeding depression and a loss of adaptive potential. Wildlife translocation is a valuable conservation tool to reintroduce species to previously occupied areas, or augment existing populations with genetically divergent animals, thereby improving the viability of endangered populations. However, understanding the genetic implications of mixing gene pools is key to avoid the risk of outbreeding depression, and to maximise translocation effectiveness. In this study we used mitochondrial and microsatellite DNA collected from 110 black rhinoceroses (Diceros bicornis minor) in Kruger National Park, South Africa, to determine levels of genetic diversity, inbreeding and relatedness. We compared this diversity with the two source populations (KwaZulu-Natal, South Africa and Zambezi River, Zimbabwe) using data from previously published studies, and assessed changes in the relative contribution of source lineages since their reintroduction in the 1970s. Our results show that Kruger’s black rhinoceroses are genetically more diverse than those from KwaZulu-Natal, with levels closer to those from the Zambezi Valley. Furthermore, our findings indicate a relative increase in the Zimbabwean lineage since reintroduction, suggesting a possible selective advantage. From a conservation perspective, our results demonstrate the benefits of mixing multiple source populations to restore gene flow, improve genetic diversity and thereby help protect small, isolated populations from extinction.

Methods
Blood samples (n=110; female = 60, male = 50) were collected from black rhinoceroses in southern Kruger (Fig. 1) from 2014–2019 during various management interventions, performed in accordance with South African National Parks (SANParks) Wildlife Capture Standard Operating Procedures. Sex, date and location were recorded at the time of capture.  DNA was extracted using DNeasy Blood & Tissue Kits (Qiagen, Valencia, CA, USA), following the manufacturer’s instructions. A fragment of the mitochondrial DNA control region was sequenced by ZooOmics™ (Inqaba Biotec, Pretoria) using primers mt15996L (5’-TCCACCATCAGCACCCAAAGC-3’; Campbell et al. 1995) and mt16502H (5’-TTTGATGGCCCTGAAGTAAGAACCA-3’; Moro et al. 1998). Individuals were genotyped by ZooOmics™ using the standard rhinoceros forensic panel in South Africa (Harper et al. 2013) comprised of 23 microsatellite markers.