Mitochondrial DNA Phylogenetics of Black Rhinoceros in Kenya in relation to Southern Africa Population

Abstract

Black rhinoceros (Diceros bicornis) are highly endangered due to poaching and other anthropological reasons and their protection to rebound the numbers and genetic improvement are necessary remedial measures defined by Rhino International Union of Conservation for the Nature Red List (IUCN). In Kenya black rhino numbers declined from approximately 20,000 in the 1970s to fewer than 400 in 1982. Wildlife conservation managers effected strategies to manage/breed the remaining rhinoceros populations in Eastern and Southern Africa within regional sanctuaries. This study analyzes the genetic variability of these remnant rhinoceros using Mitochondrial DNA (mtDNA). Majority of the rhinoceros in both Kenyan and Southern Africa group are monophyletic clusters with insignificant genetic variations while some lineages are underrepresented. The Eastern Africa rhinoceros forms a distinct clade from the Sothern Africa counterpart while Tanzania population has admixtures. Tajima-D test showed that these two populations are under different selection pressure possibly due to different history of adverse anthropologic activities. Similarly, the Southern Africa rhinoceros have low genetic diversity compared to the Eastern African population due to extended periods of game hunting during Africa colonization. This study suggests that managed translocations of individual rhinoceros across the separated fragments can be applied to improve their genetic diversity.

Research Article Genetic assessment of a breeding population of black rhinoceros in Kenya using mitochondrial DNA D-loop sequencing

“…Our finding showed moderate bootstrap values of the maximum likelihood tree ( Figure 1); this may be because of the overall high degree of relationship among Kenyan black rhinos (Moodley et al, 2017). The low to moderate bootstrap values are consistent with those reported in a previous mitochondrial DNA D-Loop study of black rhinos (Githui et al, 2017). Although some bootstrap values were low, the populations consistently clustered into the same grouping in the tree.…”

“…DNA extraction, amplification and sequencing procedures were similar to those in our previous study; for details see Githui et al (2017).…”

“…As a result, the remaining small populations are now restricted to protected areas (Hilborn et al, 2006). In an effort to restore the black rhinoceros population in Kenya, a sanctuary approach was adopted whereby some subpopulations under high security comprise a nucleus breeding population to breed rhinos for subsequent translocations to their previously known historic habitats (Brett, 1990;Thuo, 2015;Githui et al, 2017) or to repopulate dwindling populations.…”

Genetic diversity of the eastern black rhinoceros (Diceros bicornis michaeli) in Tanzania; implications for future conservation

“…Based on a search of Genbank, no additional Tanzanian samples were available other than those described in Moodley et al (2017); all six of the Tanzanian haplotypes identified here had been found in other East African populations in that study. However, two additional studies reported samples from Kenya (Muya et al 2011;Githui et al 2017) but without the date of sampling, so these were considered as "unclassified" . This allowed a more extensive assessment of the relative frequency of East African haplotypes in a broader context (Supplementary Table S1; Figure 5).…”

“…In previous years , a total of 23 black rhinoceroses were translocated to Tanzania from areas outside East Africa but this was done without consideration of genetic variation (Fyumagwa & Nyahongo 2010). Only three haplotypes (haplotypes 3, 5 and 6) were found Githui et al 2017;Moodley et al 2017). However, the three introduced haplotypes were closely related and clustered together on the tree, suggesting that the previous translocations achieved limited augmentation of genetic diversity in the extant populations.…”