Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation

Abstract

Kenya's black rhinoceros population declined by more than 98% from 20,000 individuals in the 1970s to around 400 individuals in 1990 due to the effects of poaching, at which time the surviving individuals were isolated in a series of demographically inviable subpopulations. An initial management exercise translocated the survivors into four high security sanctuaries to control poaching and enhance breeding, and this measure successfully arrested the decline. Subsequently, new sanctuaries were established and the metapopulation size reached 650 animals by 2008. However, translocations and the current management strategy that partitions the metapopulation into 'montane' and 'lowland' rhinoceros may have substantial consequences at the population level and their impact on population genetic diversity has not been investigated. In this study, 12 of the 16 extant subpopulations were analysed using 408 bp of mitochondrial control region sequence (n = 170) and nine microsatellite loci (n = 145). Both markers detected moderate to high genetic diversity (h = 0.78 ± 0.027, n = 170; H O = 0.70 ± 0.087, n = 145) consistent with previous studies on Diceros bicornis michaeli. However, mtDNA and nDNA diversity varied substantially between subpopulations. The results suggest that the Masai Mara is more differentiated, inbred and isolated than other subpopulations. It also suggests that there are neither distinct montane and lowland groups nor other detectable historical barriers to gene flow. Instead the large majority of genetic diversity was partitioned at the level of individuals; highlighting the need to conserve as many individuals as possible. Future translocations should consider the genetic profile of individuals and the demographic history of both the donor and recipient subpopulations.

Genetic structure of the black rhinoceros (Diceros bicornis) in south-eastern Africa

“…Although a direct comparison is not possible given the differing number of loci used in previous studies, our finding is consistent with studies showing particularly low microsatellite diversity in South African populations (Harley et al 2005;Karsten et al 2011). Considering variation within the subspecies D. b. minor in southern Africa, we detected an average of over five alleles per locus, comparable to levels among Kenyan black rhinoceros (Harley et al 2005;Muya et al 2011), but higher than populations in Namibia (Harley et al 2005;van Coeverden de Groot et al 2011).…”

“…This suggests that the mtDNA diversity in South Africa must, in reality, be higher than the single haplotype reported by Anderson-Lederer et al (2012). The extant mtDNA diversity in Zimbabwe (Zambezi Valley and Sebungwe) as well as the combined extant diversity of Zimbabwe and South Africa is comparable to average levels reported for the same locus in Kenya (HD = 0.73, p = 0.7, Muya et al 2011), although it should be noted that levels for some Kenyan populations such as the Maasai Mara and Tsavo East were much higher (HD C 0.9, p C 0.8).…”

Limited mitochondrial DNA variation within South Africa's black rhino (Diceros bicornis minor) population and implications for management

“…With no historical records of migration and the extent of gene flow between the subspecies unknown, some authors have speculated that each subspecies may have genetic or behavioural adaptations to their local environments (Emslie & Brooks, ; Harley et al ., ). Their suggestion regarding genetic differences was confirmed through recent mtDNA and autosomal DNA analyses (Merenlender et al ., ; Ashley, Melnick & Western, ; O'Ryan & Harley, ; O'Ryan, Flamand & Harley, ; Swart & Ferguson, ; Brown & Houlden, , ; Nielsen et al ., ; Karsten et al ., ; Muya et al ., ). Thus, current black rhino management policy is for each subspecies to be managed separately in order to maintain possible local adaptive traits and minimize the risk of outbreeding depression (Templeton, ; O'Ryan, Flamand & Harley, ; Brown & Houlden, ; Harley et al ., ).…”

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

“…Between 1960s and 1980s wanton illegal poaching and loss of habitat due to increased human developments in areas that were formerly wilderness resulted in approximately 96% decline (65,000 to 3,800 individuals) in population black rhinoceros across their range in Africa [3,4]. In recent years, conservation measures have resulted in increase of in situ black rhino numbers from of 2475 individuals in 1993 to approximately 4880 in 2010 [2,5,6].…”