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    Conservation genetics of enclosed black rhinoceros populations in Kenya

    Cain, Bradley (2012) Conservation genetics of enclosed black rhinoceros populations in Kenya. Doctoral thesis (PhD), Manchester Metropolitan University.


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    Population size is a major determinant of extinction risk with small populations experiencing an inherently higher risk of extinction due to genetic threats and stochastic fluctuations in survival, fecundity and environmental conditions. For many species, natural populations are experiencing a dramatic decline in numbers and distribution as a direct result of human activities. The severity of the threats facing some species necessitates the movement of remaining individuals into protected areas or captive breeding programs where resources can be concentrated to promote recovery. Moreover, increasing levels of population fragmentation has led to metapopulation management being regarded as an integral part of many conservation strategies, particularly for large vertebrates. The translocation of individuals between populations across an inhospitable matrix is often needed to offset the detrimental effects of small population size and to maintain natural evolutionary processes. Whilst the benefits of active conservation management involving the mixing of individuals from hitherto isolated populations has been demonstrated in a number of cases, the impact on historic population structure and the potential for outbreeding depression is often poorly understood. Moreover an increasing body of theoretical and empirical work is demonstrating that mate selective choices are mediated not only by additive effects but by non-additive effects, most specifically the amount of genetic similarity between individuals. Recent studies on natural populations have demonstrated that there is a fitness cost associated with choosing maximally dissimilar mates and that even for intrapopulation breeding, individuals exercise a preference for mates of intermediate similarity. Populations subject to active conservation management are typically small admixed populations where individuals are presented with a limited number of potential mates, representing a greater spectrum of genetic divergence than would typically be present in non-managed populations. With many in situ and ex situ conservation programs reporting poor population growth rates linked to low or declining reproduction understanding the genetic influences on mate choice in these populations is potentially of great importance. This thesis examines (1) the effects of active conservation management on levels of genetic diversity and (2) historic population structure in the eastern black rhinoceros (Diceros bicornis michaeli). It also examines the relative influences of additive and non-additive effects on female mate choice in this actively managed conservation priority species. The eastern black rhinoceros (Diceros bicornis michaeli) has been subject to one viii of the severest human induced declines of any mammalian species. The subspecies formally ranged across East Africa from northern Tanzania to Somalia, with its largest populations in Kenya. A significant increase in poaching of rhinoceros for their horn during the 1970s and 1980s eliminated D. b. michaeli from Sudan, Ethiopia, Somalia, Uganda and Rwanda. Extensive populations in Tanzania were reduced to just two small populations and the subspecies was reduced from an estimated Kenyan population of 20,000 in 1970 to just 380 by 1987. In the face of the imminent extinction of the Kenyan population, the Kenya Wildlife Service (KWS) implemented a policy of moving all animals outside protected areas into fenced sanctuaries where resources could be concentrated to counter the poaching threat. The sanctuary system proved successful and as of 2006 Kenya had approximately 540 black rhinoceros protected within 14 separate populations. With the sanctuary system largely successful in countering the continued threat of poaching, emphasis has shifted to metapopulation management to ensure the viability of the small isolated populations within the sanctuary system. To assist in the effective metapopulation management of these isolated populations, data is presented here both on the current levels of genetic diversity and the range of historic genetic diversity captured within five enclosed sanctuary populations. A total of 166 individually identified black rhinoceros were genotyped for 9 microsatellite loci and a 507 bp segment of the mtDNA control region, with the majority of the genotyping conducted on DNA extracted from faeces. To assist in the identification of faecal samples from mixed sex pairings a simple, accurate, single-stage 5′-exonuclease assay for gender determination in the black rhinoceros from low-copy template DNA is presented. Genetic analysis and the examination of translocation records shows that the five sanctuaries are comprised of historic populations from three geographic regions within the country and that significant admixture has occurred between these historically divergent populations. These historically divergent populations are shown by molecular dating to have originated from the south of the country following an expansion which is putatively linked to the contraction of the Pleistocene forests approximately 300 KYA. Examination of mutation bias in the species reveals low levels of mutagenesis in concordance with other studies and evidence of ectopic gene conversion between eutherian sex chromosomes. The current metapopulation retains significant levels of genetic diversity for both nucleic (A = 5.0, HE = 0.689) and organellar (π = 0.007) genomes, with levels of diversity in individual populations related to ix the amount of admixture of former populations. Parentage analysis was undertaken for 107 individuals from three sanctuary populations representing approximately 16 years of successful reproductive activity in these populations. It is demonstrated that in the black rhinoceros male genetic diversity is a significant predictor of reproductive success and that females balance male genetic quality with intermediate levels of genetic similarity in admixed populations. This is the first time these effects have been investigated in a conservation priority species subject to active management and it is anticipated these results will have a profound impact on future management strategies for the species. In particular the overall results of this thesis provide a framework whereby the management of the Kenyan black rhinoceros metapopulation can be guided by the way rhinoceros are shown to manage their own reproductive success.

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