Understanding the extent and cause of small mammal diversity and movement in an area is one of the major challenges in modern ecology. Rodents are a very successful group forming the largest Order of mammals, but monitoring trends in populations remains complicated, especially when populations are influenced by changes in vegetation structure, seasonal climate fluctuations and different management practices. This project aims to determine the biodiversity of rodent populations in the northern plains of the Kruger National Park and to investigate the possible role they may play as bio-indicators for different management practices. Movement of rodents from one area to the next is expected to be restricted due to changes in the habitat structure. This study describes the results of small mammal trapping in, surrounding and outside the N’washitshumbe enclosure site, an area enclosed since 1968 for the protection of endangered antelope species in the northern plains of the Kruger National Park, South Africa. The study refers to plant association, seasonal change, management practices (e.g. presence or absence of fire and elephant impact) and community dynamics of rodents. It is argued that progress in estimating rodent diversity to develop an understanding of small mammal community dynamics will be enhanced by building local inventories of fluctuations of species diversity and abundance, and in descriptive and experimental studies of the structure of the communities. / Dissertation (MSc)--University of Pretoria, 2009. / Zoology and Entomology / unrestricted

The African wild dog Lycaon pictus is Africa’s second most endangered carnivore. Only 14 out of 39 countries in Africa still have wild dogs present. This makes the populations of wild dogs in South Africa very valuable with respect to the entire species. Kruger National Park (Kruger) has the only self-sustaining and viable population of wild dogs in South Africa, making Kruger the core area of conservation for South African wild dogs. It is of vital importance to know the numbers of wild dogs present in Kruger. In chapter 2 of this dissertation I monitored and gathered demographic information from as many southern Kruger wild dog packs and individuals as possible over a three month period. I used real time text messaging to collect the information. A wild dog hotline number was used for tourists to contact immediately after they sighted a pack, noting location, time and number of wild dogs sighted. This new technique resulted in more than 300 reported wild dog sightings in three months enabling a count of individuals and packs. This also created an opportunity to take identification photographs and to collect DNA samples. In 1997 it was decided to establish and manage several small wild dog populations in various geographically isolated reserves in South Africa as one large managed metapopulation. In order to simulate the natural dispersal patterns of wild dogs, individuals are translocated between the managed metapopulation reserves, imitating natural gene flow and hopefully preventing inbreeding. To date, all decisions have been made using demographic data only. This in time is likely to result in a loss of genetic diversity and subsequent inbreeding. The aim of chapter 3 was to obtain genetic information from wild dogs in the managed metapopulation and Kruger (chapter 2) to provide a basis for sound population management including monitoring of inbreeding and maintaining levels of genetic diversity similar to those found in large self-sustaining populations (such as Kruger). This study included both mitochondrial DNA (mtDNA) and nuclear microsatellite loci to determine the genetic structure of South Africa’s wild dogs specifically with regards to genetic diversity, population structure and relatedness. The results showed a difference in historical and recent diversity between the managed metapopulation and Kruger. Two genetic clusters were evident in South Africa, however one was due to wild dogs from Botswana being translocated into the managed metapopulation. After the Botswana influence was removed from the analysis, three genetic clusters were observed in the South African wild dogs. These three genetic clusters comprise too few wild dogs to manage them as separate units. Relatedness between and within populations, reserves and packs were estimated and can in future be used to guide translocations of wild dogs to maximise their genetic variability. It is suggested that due to the low numbers, and historical and recent trends in genetic structure of South Africa’s wild dogs, they should be managed as one unit, allowing movements to and from neighbouring countries. All translocations should follow an isolation-by-distance pattern. / Dissertation (MSc)--University of Pretoria, 2010. / Animal and Wildlife Sciences / unrestricted

Mycobaterium bovis is the causative agent of bovine tuberculosis (BTB) and it is a member of the Mycobacterium tuberculosis complex (MTBC). This bacterium has a wide host range of which, cattle is considered as the maintenance host. Humans, goats, wildlife, cats, dogs and lions are also susceptible to the bacterium and are considered putative spillover hosts as infection is not confined in these hosts. Mycobacterium bovis is prevalent in developing countries especially in farmed animals. This presents a problem since BTB is a zoonosis. People living in close contact with infected cattle or those who drink unpasteurized milk are at risk of infection. About 10% of cases of human tuberculosis are thought to be caused by M. bovis. In some instances, wildlife provides a reservoir for the pathogen and transmits it to cattle in farms and poses further risk to humans at the wildlife/livestock/human interface. Certain countries like the United Kingdom where BTB was previously eradicated are experiencing substantial increase in BTB infection. This is thought to be a result of wildlife reservoirs that infect farmed animals, especially cattle. Such reservoirs make eradication of the disease extremely difficult and require programmes to be put in place to control spread of the disease. This makes M. bovis a pathogen of economic importance since the programmes may be costly. In addition, wildlife that is infected cannot be exported and this further affects the economy negatively. In order to control the spread of the pathogen, it is essential to determine the source of infection. However, it is difficult to determine the source or to track the spread of BTB especially in wildlife where animals have unrestricted movement. The inability to conduct epidemiological studies of BTB may be a result of the lack of molecular typing methods that allow bacteria to be identified to strain level rapidly and fairly simpler than culture, thus providing much needed information about the pathogen. In recent years, typing of M. bovis isolates to strain level has been made possible by the development of PCR-based technologies such as IS6110 typing and spoligotyping. These technologies were however, found to be unsuitable for differentiating certain species in the MTBC. Newer technologies based on the variable number of tandem repeats (VNTRs) in organisms have been developed and allow for the differentiation of members in the MTBC, which have a high level of genome homology. These technologies include multiple-locus variable number tandem repeat analysis (MLVA) and mycobacterial interspersed repetitive unit (MIRU)-VNTR analysis. It was also discovered that mycobacteria have genomic regions of difference (RD) that could be used to identify the different species of bacteria in the MTBC. Retrospective studies may play a key role in tracing the source of diseases and following the pattern of transmission. However, in most instances, no fresh samples are available for such studies. For this reason, formalin-fixed paraffin-embedded (FFPE) tissue from wildlife in the Kruger National Park (KNP) was used for conducting a retrospective study aimed at determining the epidemiology of M. bovis in the KNP. However, amplification of DNA derived from FFPE tissue for PCR based techniques has been found to be a difficult exercise and not many standard protocols have been developed and validated for the use of such DNA. In this study, different methods of extraction were used to obtain DNA from FFPE tissue since it is difficult to obtain high quality DNA from such tissue, which is degraded. Formaldehyde, the main component of formalin which is used to fix tissue samples, causes degradation and cross-linking of DNA. In addition, previous studies are inconsistent with regards to the best method to use when extracting DNA from FFPE tissue. Three PCR-based techniques were used to type or identify the isolates in order to standardize a protocol for use in typing isolates from FFPE tissue. These techniques included analysis of the RDs, VNTR based methods i.e. MLVA and MIRU-VNTR and spoligotyping. Since there are many factors that influence the quality of FFPE tissue, samples confirmed BTB positive by VNTR analysis, spoligotyping and IS6110 analysis were used in order to optimize a PCR for FFPE tissue. Furthermore, in order to serve as control samples for spoligotyping and analysis of the RDs, DNA obtained from fresh tissue was also used in the study. Despite the various methods used to extract and to type DNA, the DNA from FFPE tissue provided unspecific results that did not allow for an informative retrospective study of M. bovis. This may be due to the fact that the DNA used had a high degree of degradation from prolonged fixation in formalin. Although M. bovis could not be typed in FFPE tissues, it could be identified by analysis of the regions of difference, more specifically the RD9 region. Amplification of RD9 is thus recommended for use in retrospective studies for diagnostic purposes, especially in cases where highly degraded DNA is used. This region (RD9) should however, only be used as a presumptive diagnosis since RD9 also identifies M. africanum, M. microti, M. pinnipedii, M. caprrae and M. bovis BCG. However, RD9 specifically excludes M. tuberculosis. In the SA context, particularly in the KNP, this allows for some sound inferences since the animals are likely to be infected with M. bovis as opposed to M. tuberculosis. This study highlighted statements in previous studies where it was stated that fixation of tissue in formalin should be done in such a way to reduce degradation of DNA in FFPE tissue in order to allow for its use in retrospective molecular studies which may be very insightful in determining the epidemiology of diseases that are difficult to track and/or control. Copyright / Dissertation (MSc)--University of Pretoria, 2012. / Veterinary Tropical Diseases / unrestricted

Thesis (M.A. (Sociology)) -- University of Limpopo, 2000 / Please refer to the document

Thesis (M.Sc. (Statistics)) - Rhodes University, 2007. / A thesis submitted in partial fulfilment of the requirements for the degree of Master of Science.

The status, distribution and ecology of klipspringer were studied in the Kruger National Park. For the status and distribution, the Kruger National Park south of the Olifants River was used as the study area. Data on the status and distribution were gathered from all the ranger sections in the study area with the use of a non-sampling method, namely a systematic search. The results showed that the klipspringer population in the Kruger National Park is secure with a patchy distribution consisting of 773 individuals in the study area and a sex ratio of one male per 1.1 female. The ecology of the klipspringer was studied in a specific study area on the Nwatindlopfu spruit between Skukuza and Tshokwane where five klipspringer individuals were radio collared. The aspects covered in the study on the ecology of klipspringer, were the activities associated with environmental and vegetation related variables as well as scent-marking. It was found that vegetation is the determining factor in the habitat selection of klipspringer in the Kruger National Park, in that it provides both shelter and food. The ideal klipspringer habitat can be described as an area that has limited access to other ungulates that can attract predators. The vegetation should consist of palatable plant species that could be utilized by klipspringer, and must also provide sufficient shelter against possible danger. Klipspringer scent marks were surveyed in a specific klipspringer range in the Kruger National Park with the use of a strip transect method. Both the male and the female klipspringer scent-mark their ranges. A pair of pre-orbital glands below the eyes produces the scent. The secretion produced is a sticky milky substance that is deposited on a suitable twig. The results showed that klipspringer in the Kruger National Park scent-¬mark more frequently on the boundaries of their ranges and also more on those sides where there is another resident klipspringer group. / Dissertation (MSc (Wildlife Management))--University of Pretoria, 2005. / Animal and Wildlife Sciences / unrestricted

Genetic variation, structure and dispersal among Cape buffalo populations from the Hluhluwe-Imfolozi and Kruger National Parks of South Africa Barend Jacobus (Ben) Greyling Doctor of Philosophy (Zoology) Department of Zoology and Entomology Supervisor: Prof. Armanda Slager-Bastos Co-supervisor: Dr. Pim van Hooft 2007 The research reported on in this thesis is aimed at quantifying and qualifying, using a molecular genetics approach, some of the factors that influence the population dynamics of Cape buffalo (Syncerus caffer caffer) from the Kruger National Park (KNP) and Hluhluwe-imFolozi park (HiP) in South Africa. Prior to large-scale genotyping of animals sampled from these parks, a high-throughput, cost- and time-effective profiling system was developed. The system, based on a panel of 17 microsatellites (Msats), was found to be quite suitable for the intended application, since it uncovered substantial genetic variation, while exclusion probabilities were in excess of 0.999 and a random match probability of 6.5 x 10-17 was obtained. Inter-population level analyses revealed that the two populations were significantly differentiated (Msat data: FST = 0.159; mtDNA data: FST = 0.275), while little or no differentiation could be demonstrated among most herds and subpopulations. It seems that while drift has played a major role in divergence of the two populations, gene flow is the primary driving force behind the maintenance of genetic variation among herds and subpopulations. A striking feature was that HiP exhibited significant lower levels of genetic variation than KNP, which is reflected by the fact that a mere 4 haplotypes could be found in HiP compared to 34 identified in KNP. The absence of geographic partitioning and small genetic distances separating the haplotypes may be attributed to genetic contact between the respective populations in the distant past. The reduced levels of genetic variation in HiP may be the remnants of the rinderpest bottleneck. HiP also displayed signals of a population contraction, while KNP is in equilibrium and seems to have retained substantial levels of genetic variation. HiP also experienced a steady decline in genetic variation from 1986 to 2004, while sex-biased dispersal was less pronounced in HiP than in KNP, possibly due to the lack of mtDNA diversity and the small size of the park. The results presented here provide valuable baseline information for making conservation management decisions from a genetic point of view. / Thesis (PhD (Zoology))--University of Pretoria, 2007. / Zoology and Entomology / unrestricted

This thesis reports on the number of individuals in Macrotermes natalensis (Hav.) colonies, their biomass and food consumption in the northern Kruger National Park (KNP). The ecology of M. natalensis is largely undocumented despite the abundance of colonies in southern African savannas. New approaches to mound excavation, sub-sampling and data management are introduced. Via the intracolonial demography of colonies the contribution of each caste in number or proportion is determined. Using this information in combination with body mass and mound density data, biomass per unit area has been computed indicating the importance of this termite in synecology. The measurement of food consumption gives further insight as to how much litter is removed, fragmented and redistributed as nutrients in the ecosystem. Mounds were completely excavated, termites collected by means of vacuuming, and colony size estimated by sub-sampling. It was estimated that, on average, small mounds contain more than 5 000, medium mounds more than 45 000, and large mounds more than 200 000 individual termites. A highly significant relationship between total number of individuals (N ) and mound height (h ) was found, given by lnN = 7.893 + 1.093h (r = 0.92). The proportion of soldiers was found to change as colonies grew larger. In order to derive biomass estimates, a statistical bootstrap procedure was carried out using three databases: body mass, colony population sizes and mound density. Live biomass for small, medium and large mounds was found to be 0.17, 1.40 and 4.16 kg. Dry/wet body mass ratios were established for workers (23.7 %), major soldiers (20.3 %), minor soldiers (35.3 %), nymphs (17.1 %), king (35.4 %) and queen (20.8 %). Average live and dry biomass was calculated to be 0.51 kg/ha (0.051 g/m2) and 0.11 kg/ha (0.011 g/m2). Geology, geomorphology, elevation, local relief, soil patterns and annual rainfall were the abiotic factors shown to be most influential in determining termite biomass, either directly or indirectly. Termite biomass is high in undulating areas where the elevation is 250-400 m, where granitic and rhyolitic soils occur, and where annual rainfall is high (650-700 mm) in the context of the region. Major workers fetch woody litter outside the nest through ingestion into the section of the crop and gizzard. Gut contents were dried, weighed, ashed and reweighed. The ash mainly represents soil particles. The ash-free mass of food that is consumed during a single foraging trip by a foraging individual is 0.166 ± 0.009 mg (CI). Frequency of foraging trips between the mound and food source was observed using translucent tubing. The annual food consumption is given by the formula 365mnp/t , where m = individual mass of ashed crop-gizzard contents, n = number of foraging major workers, p = daily foraging period, and t = individual time spent between nest and food source. Food consumption of this termite in the northern KNP is calculated to be 20.2 kg/ha/yr. It is shown that termites are primary decomposers and contribute to litter fragmentation and the recycling of nutrients into the soil. This thesis gives greater insight into aspects such as colony development, biomass investment and resource utilization of M. natalensis in the northern KNP. / Dissertation (PhD)--University of Pretoria, 2003. / Zoology and Entomology / unrestricted

MaxEnt modelling uses only the known locations of a species to predict the overall distribution of a species. Large trees are important for the functioning of savanna ecosystems, bringing nutrients to the surface, providing shelter to animals and providing a number of ecological functions. Large trees have been identified as declining in density in many southern African reserves, making the conservation of large trees within reserves an issue in park management, such as in Kruger National Park (KNP) and Hluhluwe iMfolzi Parks (HiP). Two species of primary concern are Acacia nigrescens and Sclerocarya birrea, which have similar distributions in Southern Africa. Effective management of large trees requires understanding their distribution within reserves and any potential distribution changes. By determining the current locations of a species, and using GIS layers of environmental variables to predict the extent of habitats that could support the species, niche models can predict species distribution. Maximum Entropy techniques evaluate the probability of finding the species in raster squares, with values for environmental factors controlling distribution. For this study, the locations of A. nigrescens and S. birrea trees higher than 5 m were recorded in KNP and HiP, and were used in conjunction with MaxEnt to produce distribution probability maps for both species in each reserve. In HiP, the distribution map was compared with an independent existing data set to determine if the predicted distributions were accurate. The factors effecting their distribution were compared between HiP and KNP to determine why the species were found together in KNP but not in HiP. MaxEnt could predict the locations of the species within HiP, but predictions were better for A. nigrescens than S. birrea. In both Reserves, rainfall was the best predictor of tree location, along with elevation. The niche overlap was higher in KNP, where both species are well within their total species range, than in HiP where A. nigrescens was at the edge of its distribution. These variables that are limiting distribution at a reserve scale will have an influence on the overall distribution of the species. Niche models can be used to inform the establishment of botanical reserves or other management strategies that can help preserve large trees within reserves. / Thesis (M.Sc.)-University of KwaZulu-Natal, Westville, 2011.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of requirements for the degree of Master of Science. / Central to the study of animal ecology is the usage an animal makes of its environment. In arid and semi-arid environments worldwide, the availability of surface water largely determines the behaviour, distribution and abundance of animals. As a consequence, the distribution and quality of water are factors that influence carrying capacities of protected areas in environments such as the Kruger National Park, South Africa. Just as wildlife may select water sources according to water quality, they may also select drinking locations according to perceived predation risk. Predation risk can therefore strongly influence the patch use and resource selection of animals. Similarly, human traffic and activity in natural areas can also have an effect on the behaviour and resource use of resident wildlife. This research investigates mammal usage patterns at selected water sources within the Makuleke Wetland System in Kruger National Park to contribute towards management planning for this important Ramsar Wetland Site. The research examines daily and seasonal trends in usage as well as possible links to water quality, land cover and human disturbance. Camera traps were set up seasonally at perennial pans and rivers within the Makuleke Wetland system to determine mammal species’ usage patterns. Environmental characteristics associated with each water source, such as water quality, vegetation cover and extent of human activity were also determined. A cluster analysis and Canonical Correspondence Analysis (CCA) were run in order to determine how environmental variables may influence mammal species’ seasonal drinking site selection. Overall, mammals appear to be selecting for drinking sites with increased distances to ground cover where they are more likely to see predators in advance. Mammal species appear to be avoiding the Zimbabwean border as a result of human activity in the Zimbabwean side of the Great Limpopo Transfrontier Park. The perennial pans and rivers appear to be a significant water source during the dry months to large herbivore and large carnivore species, which display the greatest seasonal fluctuations. Elephants show the greatest demand for water during the dry season and access the perennial water sources throughout the day and night. The Makuleke wetland system, and in particular the perennial water sources, provide an important dry season refuge for the northern Kruger National Park’s and the Greater Limpopo Transfrontier Park’s elephant population. The Luvuvhu River and its associated pan (Nwambe), within its floodplain, are sources of water for the greatest diversity and richness of species when compared to the water sources associated with the Limpopo floodplain, within the Makuleke Wetland System. Information from this study may aid South African National Parks management with their “adaptive management” strategy for Kruger National Park, to manage the park in an ever changing environment. It is widely accepted that emphasis be placed on the major role river systems play in biodiversity, and hence their high priority in conservation.