The Kruger black rhino population offered a unique opportunity to evaluate the outcome of mixing the two remnant south-central black rhino source populations. Using mtDNA and microsatellite markers, we found that mixing gene pools substantially enhanced both the mitochondrial and nuclear diversity of the founded Kruger population relative to the source D. b. minor population in South Africa. Together with the low levels of relatedness and no evidence of non-random mating, our results confirm that the Kruger black rhino population is a diverse, outbred, panmictic population. This study provides a baseline for informing black rhino metapopulation management strategies and indicates that Kruger black rhinos would be ideal candidates for translocation and reintroduction efforts aimed at improving diversity in other D. b. minor black rhino populations.
Maintaining adequate levels of genetic diversity is essential for ensuring both the short-term health and long-term survival of isolated populations of endangered species. Small population numbers, genetic drift and/or inbreeding may all contribute to a substantial loss in genetic diversity of such populations, and consequently may negatively impact their viability. For example, the small, reintroduced population of black rhinos in Addo Elephant National Park, South Africa has comparatively low genetic diversity and high relatedness relative to their source populations, resulting in low fitness, manifesting as low population growth rate and reduced male survival (le Roex et al. 2018).
Our results are consistent with several other studies across taxa that have reported improved genetic diversity, and ultimately genetic rescue, in bottlenecked populations through translocation, including Australia’s mountain pygmy possum (Burramys parvus; Weeks et al. 2017), adders (Vipera berus; Madsen et al. 1999), Scandinavian wolves (Canis lupis; Åkesson et al. 2016) and New Zealand’s South Island robins (Petrioica australis; Heber et al. 2013). Similarly, Poirier et al. (2019) reported that outbreeding with a few translocated individuals significantly increased the low genetic diversity observed in a post-bottleneck population of bighorn sheep (Ovis canadensis). Following this recovery in genetic diversity, first-generation (F1) admixed lamb survival rates improved and population size consequently increased, i.e. genetic restoration resulted in genetic and evolutionary rescue.
The reconstructed mtDNA haplotype network in this study demonstrates that the Zimbabwean mitochondrial lineages are well established in the Kruger black rhino population. Genetic analyses of museum specimens identified at least four mtDNA haplotypes historically found in South African black rhinos (Moodley et al. 2017). Thus our results suggest that mixing the two source populations has restored a comparable level of mtDNA diversity to South African black rhinos. The single haplotype (H2) found in all KwaZulu-Natal black rhino (Anderson-Lederer et al. 2012; Kotzé et al. 2014) was the most common haplotype present in the Kruger population (67.96%). We also found two Zambezi River haplotypes (H1 and H5) within the Kruger population; the remaining Kruger haplotype (H3) was reported in a single captive Zimbabwean black rhino (Fernando et al. 2006). Thus at least two (or three, if including H3) of the six known Zimbabwean haplotypes (33-50%) have been retained in the Kruger black rhino population. It is also possible that with more extensive sampling, additional Zimbabwean haplotypes would be detected. Future studies that directly compare the nuclear contributions of the two source populations within the current Kruger population would also provide further insight into this genetic admixture.
While mixing individuals from different source populations may increase genetic diversity and reduce the likelihood of inbreeding depression, it may increase the risk of outbreeding depression (Edmands 2007). For example, if source populations are under unique environmental pressures (e.g., different climates or habitats), local adaptations may arise, especially in long-isolated populations. Thus, outbreeding with genetically diverse individuals is counterproductive if the hybrid offspring face lowered fitness due to the loss of locally adapted genetic variants (Edmands 1999). A classic case of outbreeding depression occurred when two subspecies populations of Alpine ibex (Capra ibex) were translocated from the Sinai Peninsula and Turkey into the European Alps. Unfortunately, the introduced Ibex bred earlier in the season than their European counterparts, resulting in hybrid offspring born in midwinter, reducing survival and ultimately leading to the hybridised herd’s extinction (Templeton 1986). However, this is example is an exceptional case, and outbreeding depression is seldom seen in practice (Frankham et al. 2011; Ralls et al. 2018).
Outbreeding depression from mixing KwaZulu-Natal and Zambezi River black rhinos is unlikely when considering primary risk factors, such as chromosomal differences, lack of gene flow for more than 500 years, and substantial environmental differences between populations (Frankham et al. 2011). The Zambezi River and KwaZulu-Natal black rhino populations were historically connected (Kotzé et al. 2014) and a healthy population of translocated KwaZulu-Natal black rhino in Malilangwe, Zimbabwe suggests that the different environment between populations is unlikely to contribute to outbreeding depression. Furthermore, the increase in Zimbabwean lineage proportion seen in the extant Kruger population (relative to the ratio of founder females) contradicts any potential loss of local adaptation; if anything, selection over the generations may have favoured the more diverse Zambezi River black rhino. Further research, however, is required to test whether a selective advantage or stochastic events are responsible for the lineage proportion increase seen in this study.
In conclusion, this study indicates that the admixture of black rhinos from different gene pools substantially enhanced both the nuclear and mitochondrial diversity of the founded Kruger population relative to the source D. b. minor population in South Africa. In the absence of threat alleviation, metapopulation management strategies (such as population supplementation through translocation) aimed at increasing the range and securing the genetic health of black rhino are critical. The improved genetic diversity found in the Kruger population is encouraging for the long-term survival of this subspecies as a managed metapopulation within South Africa, possibly improving its adaptive potential to respond to environmental change. Given the encouraging levels of diversity observed, this also makes the Kruger black rhino population an ideal source candidate for founding new populations or improving the genetic variation (and thus reducing extinction risk) for genetically depauperate D. b. minor populations in South Africa.