A Dissertation submitted to the Faculty of Science in fulfilment of the requirements for the degree: Master of Science In School of Animal, Plants and Environmental Sciences, University of Witwatersrand Johannesburg 2015 / This study aimed to determine the role and relative importance of predator avoidance and nutrition as processes influencing herbivore utilisation of burnt areas, at Satara, Kruger National Park by using variation in fire size and fire season. The driving factors investigated included forage quality, forage quantity, vegetation structure and predation risk. The effect of fire size and season on the landscape was tested by recording grass height, greenness, grass nutrient sampling and visibility. Results showed that fire size and season had a significant impact on the physical environment by decreasing grass/forage quantity post-fire but increasing grass/forage quality. Over time the plots returned to near pre-fire conditions, with forage quantity increasing (grass height and biomass) and forage quality decreasing (nitrogen availability). Visibility increased immediately post-fire, more significantly in regards to herbivores with their heads in a “head-down/grazing” position than in a “head raised/vigilant” position. As with forage quantity and quality, visibility returned to near pre-fire conditions at the end of the study sampling period. The response of animals to these changes in the environment was recorded through dung counts, camera traps and behavioural observations. I found that there was increased use of burnt plots post-fire through comparing herbivore presence on plots burned in different sizes and seasons, day/night utilisation of plots, and using behaviour data I could determine to what extent forage and predation risk were driving the use of burnt areas. I focused on three herbivore species (Aepyceros melampus, Connochaetes taurinus and Equus quagga) which varied in terms of body size digestive systems, forage type, and social behaviour. As expected, I found that predation risk did appear to be more important in driving the behaviour of the smaller-bodied herbivores but both nutrient requirements and susceptibility to predation were shown to play a role in explaining the use of burnt areas for all three herbivore species. Variation between plots in environmental factors such as tree density, forb percentage and distance to water, were found to be not significant and thus did not confound our results

Thesis (Ph. D.)--University of Pretoria, 2005. / Title from PDF t.p. (viewed Mar. 27, 2006). Includes bibliographical references.

M.Sc. / The Olifants- and Luvuvhu rivers both flow through the Kruger National Park (KNP). The Olifants River (OR) is a major tributary of the Limpopo River with water quality being less than desirable due to high concentrations of pollutants as a result of the activities in the upper catchment. The crocodile population of the river declined from 1000 in 2008 to 347 in 2009 due to pansteatitis. Labeobarbus marequensis in the upper catchment also showed symptoms of the disease (Templehoff, 2010). This raised concern about the health of the fish in the OR, particularly in the section flowing through the KNP. The Luvuvhu River (LR) is also a tributary of the Limpopo River with main land uses in the catchment being agriculture, mining and communal lands. Of concern is the finding of DDT residues in water, sediment, and domestic and indigenous biota upstream of the sites sampled in this study (Barnhoorn et al., 2009) which raised concerns about the health of fish in the lower reaches of the river flowing through the KNP. Therefore, the aim of this study was to assess the health status of [9] selected fish species from the OR and LR in the KNP using a histology-based health assessment protocol (HBHA). The species selected for this study included Hydrocynus vittatus, Labeobarbus marequensis, Labeo cylindricus and Labeo rosae. The OR was sampled in September 2009 and May 2010 while the LR was sampled in November 2009 and April 2010. A necropsy was done to determine if there were any internal or external macroscopic alterations with any alterations noted on a score sheet. Blood was taken for haematocrit (Hct), leukocrit (Lct) and total plasma protein (TP) determination. As part of the HBHA, a necropsy-based health assessment index (HAI) was applied using a modified protocol of Adams et al. (1993) where the necropsy and blood parameters were used to calculate the mean and sum HAI for the different species sampled on each sampling trip. Biometric indices including the condition factor, hepatosomatic index, splenosomatic index and the gonadosomatic index were calculated. Age was determined using otoliths for tigerfish and scales for the other species. Samples of selected organs (liver, kidney, gill, testes or ovaries) were taken for histological analysis. Microscope slides were assessed qualitatively to identify any histological alterations present. These results were semi-quantitatively assessed according to the protocol of Van Dyk et al. (2009a) from which an organ index and fish index were calculated. The organ index is an indication of the number and severity of histological alterations in a particular organ of a selected species. The organ indices were classed according to the classes of Van Dyk et al. (2009a) with Class 1 (<10) being tissue with slight histological alterations; Class 2 (10-25) being tissue with moderate histological alterations. The fish index is a sum of all of the organ indices for any given fish sampled.

M.Sc. (Zoology) / The necessity to maintain high water quality standards has become essential not only to man, but also to conserve aquatic life forms. The Olifants, Selati and Letaba Rivers were monitored for water quality variables and metal concentration in water, sediments and muscle, gill, fat, gonads, liver, bile, blood and kidney of the sharp tooth catfish, C. qariepinus. Some of the water quality variables measured were not within the limits of those standards set for the protection of fish and other aquatic life forms. Turbidity seems to be the biggest problem, due to the Phalaborwa barrage. Metal concentrations were found, in descending order, highest in the sediment, fish and water. This pose the problem of metals being reintroduced into the water column when physico-chemical conditions are not favourable. Experimental studies were done with copper on adult C. qariepinus, due to the extensive copper mining activities in the Phalaborwa region. Haematological and enzymatic analyses revealed a interference in metabolic activity after 96 hour copper exposure. Histological studies on the gill morphology, showed an alteration in the structure with a resultant change in respiratory and osmoregulatory function. LC-50 values were determined for adult and juvenile C. qariepinus in order to set new standards for the protection of aquatic lite in a rapidly developing South Africa.

The objectives of this study were(1) to analyse a data-set on cheetah home range size, habitat utilisation, prey selection and hunting behaviour in the Kruger National Park (KNP), and (2) conduct a comparative study on the above aspects of cheetah ecology across a variety of African savanna ecosystems. Cheetah home range sizes in the KNP for territorial male cheetahs were 173 km2, 438 km2 for a nomadic male cheetah coalition, and 193 km2 and 179 km2 for two female cheetahs. Cheetahs preferred open savanna habitat, although females used areas with thicker bush such as drainage lines) more than males, probably because this is the preferred habitat of their main prey. Analysis showed that while females were closely associated with drainage lines, males were closely associated with roads. A male cheetah coalition preferred scent marking along roads rather than in the bush. Impala occurred most frequently in the cheetahs’ diet, although males took larger prey than females. Cheetahs hunted and killed more frequently in open savanna, even though impala densities were higher in adjacent habitats. Mean chase distance for successful hunts was 18l9 m and unsuccessful hunts was 96 m. Cheetah hunting success was 20.7%, kleptoparasitism was 11.8%, mean kill retention time was 165 min, kill rated averaged 1 kill per 4.61 days, and consumption rate of a three-male cheetah coalition was 1,4 kg meat/cheetah/day. Across African savanna ecosystems, female cheetah home range size was determined by the dispersion patterns and biomass of medium-sized prey. Female home range size was larger in areas with migratory (833 km2) than sedentary prey (105 km2) and increase as prey biomass decreased in areas with sedentary prey only. Conversely, male cheetah territory size was smaller in areas with migratory (37 km2) than sedentary prey (108 km2). Although it was predicted that male cheetah territory size would be determined by female cheetah density, no relationship was found here. Across a range of African savannas, cheetahs showed distinct preferences for open habitats that provided some woody cover. Adults (40%) and juveniles (20%) of medium-sized prey made up the largest proportion in the cheetahs’ diet. There were, however, significant variations in the size and age groups of prey taken by cheetahs in different areas. Areas with the least amount of cover appeared to have the longest mean chase distance, and the greatest percentage hunting success and incidents of kleptoparasitism (%). A population viability analysis, using VORTEX, found that cheetah population viability was greater in a woodland savanna than a grassland savanna, particularly at small population sizes. While the grassland savanna population was most affected by changes in juvenile mortality the woodland savanna population with exceptionally high cub mortality may be a sink for cheetahs while the woodland population with lower cub mortality and predicted high dispersal rates may be a source. Maximum annual litter size and female mortality rates had large impacts on population persistence. / Dissertation (MSc (Zoology))--University of Pretoria, 2006. / Zoology and Entomology / unrestricted

Please read the abstract (Uittreksel) in the section, 00front of this document. See also 10summary / Dissertation (MSc (Zoology))--University of Pretoria, 2007. / Zoology and Entomology / MSc / unrestricted

D.Phil. (Nematology) / This was the first study on aquatic nematodes from the Kruger National Park. Samples were taken more or less randomly over a period of two years from the four main rivers in the park, viz. the Crocodile, Sabie, Olifants and Luvuvhu rivers. A total of 33 species representative of 24 genera were found. Dorylaimida seemed to be dominant in most of the sampling sites in the Sabie, Olifants and Luvuvhu Rivers, but there was no dominant group in the Crocodile River. Five new Dorylaimida species are described: Dorylaimus deaconi spec. nov., Laimydorus olifanti spec. nov., Laimydorus africanus spec. nov.; proleptonchus krugeri spec. nov. and Aporcelaimellus glandus spec. nov. Previously known dorylaim species which were redescribed in detail are Mesodorylaimus sp.cf paralitoralis Basson & Heyns, 1974; M. potus Heyns, 1963, M. aegypticus (Andrassy, 1958), Aquatides thornei (Schneider, 1937), Afractinolaimus zairensis (Baqri, Coomans & Van der Heiden, 1975) and Oxydirus gangeticus Siddiqi, 1966. Further dorylaim species recorded are Aporcelaimellus micropunctatus Botha & Heyns, 1990, Discolaimus monoplanus Heyns, 1963, D. major Thorne, 1939, Xiphinema italiae Meyl, 1953, Thornenema baldum (Thorne, 1939), Tyleptus striatus Heyns, 1963 and Dorylaimellus (Axodorylaimellus) caffrae (Kruger, 1965) . The following Tylenchida species were found: Hemicycliophora labiata Colbran, 1969, Helicotylenchus africanus (Micoletzky, 1916) and Scutellonema brachyurum (Steiner, 1939). Three Araeolaimida species were recorded, viz. Chronogaster africana Heyns & Coomans, 1980, Plectus cirratus Bastian, 1865 and Rhabdolaimus terrestris de Man, 1880. The latter species is redescribed in full collected and (de Man, 1979). Only one species of the Cromadorida viz. Achromadora ruricola 1880), Enoplida viz. Eutobrilus annetteae (Joubert & Heyns, Monhysterida viz. Monhystera somereni Allgen, 1952, were Detailed descriptions are given to incorporate additional morphological information obtained. Brief descriptions and new distribution records are also given for Mononchus truncatus Bastian, 1865, M. aquaticus Coetzee, 1968 and Mylonchulus minor (Cobb, 1893) of the Mononchida and Ironus longicaudatus de Man, 1884 and I. ignavus Bastian, 1865 of the Iro~idae.A diagnostic compendium for the Mesodorylaimus species of South Africa and a checklist of the free-living and plant parasitic nematode species from both terrestrial and aquatic habitats in the park are also included. Most of this work has already been published or submitted for publication in scientific journals and is presented in this thesis in the same format as required by the editors of the journals concerned.

No abstract available Copyright / Dissertation (MSc)--University of Pretoria, 2010. / Plant Science / unrestricted

Theileriosis, babesiosis, heartwater and anaplasmosis are considered to be amongst the most important tick-borne diseases of livestock in sub-Saharan Africa‟s tropical and subtropical regions resulting in extensive economic losses to farmers in endemic areas. It is well-known that the African buffalo (Syncerus caffer) is the natural reservoir host of various tick-borne haemoparasites of veterinary importance. In this study, the occurrence of tick-borne haemoprotozoan parasites (Theileria, Babesia, Anaplasma and Ehrlichia species) in buffalo from two geographically isolated national parks in South Africa (Kruger National Park and Hluhluwe-iMfolozi Park) was determined using the reverse line blot (RLB) hybridization assay. The RLB results revealed the presence of Theileria, Babesia and Anaplasma species either as single or as mixed infections. Although not detected with the RLB assay, 5% of the buffalo blood samples from the KNP tested positive for the presence of Ehrlichia ruminantium using the pCS20 real-time PCR assay. Previous studies on the occurrence of haemoparasites in the South African buffalo population have mainly focussed on the prevalence of Theileria species only. The finding on the presence of Anaplasma, Ehrlichia and Babesia species is therefore a novel contribution. This study has confirmed the findings of previous studies that buffalo is the natural reservoir host of both pathogenic and non-pathogenic Theileria species namely, T. parva, Theileria sp. (buffalo), T. mutans, T. velifera and T. buffe1i.In this study, the most frequently occurring Theileria species detected in the KNP were T. mutans (81%), Theileria sp. (sable) (61%), T. parva (40%), Theileria sp. (buffalo) (13%) and T. velifera (11%). Theileria buffeli was not detected in the KNP. In the Hluhluwe-iMfolozi Park, the most occurring Theileria species were T. mutans (55%), T. velifera (54%), T. parva (53%), Theileria sp. (sable) (53%), Theileria sp. (buffalo) (49%) and T. buffeli, (49%). Theileria sp. (sable) causes fatal clinical disease in roan and sable antelope in South Africa and we can only speculate whether the presence of Theileria sp. (sable) DNA in the buffalo population was a true and/or incidental finding. An interesting finding was the presence of Babesia occultans DNA in 50% of the buffalo from the Hluhluwe-iMfolozi Park. Babesia occultans is the causative agent of a benign form of cattle babesiosis in South Africa and, to date; this organism has not been identified in wildlife in South Africa. The significance of this finding warrents further investigation and confirmation using gene cloning, sequencing and phylogenetic analysis. Ehrlichia ruminantium has been reported to infect not only domesticated ruminants but also wild ruminants, however most wildlife species appear to carry the organism asymptomatically. In this study, we were not able to detect E. ruminantium DNA in any of the buffalo samples tested using the RLB hybridization assay. However, using the quantitative pCS20 real-time PCR assay we detected E. ruminantium DNA in 5% of the KNP samples. None of the Hluhluwe-iMfolozi Park samples tested positive for E. ruminantium using the real-time PCR assay. These results suggest that buffalo is not the natural reservoir host of E. ruminantium. However, a subclinical carrier state in buffalo has been experimentally shown to occur after tick transmission from carrier animals and further studies will have to be conducted to confirm whether this finding holds any potential risk to domestic animals. In Southern Africa, two Anaplasma species are known to infect cattle, A. marginale and A. centrale. Clinical bovine anaplasmosis is usually caused by A. marginale; whilst A. centrale generally results in mild disease. Because there is partial cross immunity between the two species, A. centrale is used as a live vaccine for cattle in Israel, South Africa, South America and Australia. Apart from cattle, Anaplasma marginale has been described in wild ruminants which can become persistently infected serving as reservoirs for infection of susceptible hosts; it has been recovered from 10 wild ruminants. Subclinical occurrence of A. marginale, either natural or after artificial infection has been confirmed in the African buffalo and various other wildlife species. In this study, the Anaplasma species detected from HluhluweiMfolozi Park buffalo samples were A. centrale (75%), A. marginale (42%) and Anaplasma (formerly Ehrlichia) sp. Omatjenne (28%). DNA of these species was also detected in buffalo from KNP; A. centrale (49%), A. marginale (24%) and Anaplasma (Ehrlichia) sp. Omatjenne (5%). The presence of A. marginale in the buffalo population suggests that buffalo may be a factor in the epidemiology and spread of bovine anaplasmosis because, as reservoir hosts of A. marginale, they could serve as a source of infective blood for mechanical spread by various routes and biological transmission by ticks. Factors such as climate, host abundance, tick host diversity, and topography have, however, all been shown to also impact on the epidemiology of A. marginale. Subsequently 64 samples were selected that either tested (i) positive for a specific Anaplasma spp. (A. centrale, A. marginale and/or Anaplasma (Ehrlichia) sp. Omatjenne) using the RLB assay, or (ii) in which the PCR products hybridized only with the Anaplasma/Ehrlichia genus-specific probes for molecular characterization by cloning and sequencing of the 16S rRNA gene. Aplification of the full-length and/or partial parasite 16S rRNA gene of any of the selected samples that previously tested positive for the presence of Anaplasma (Ehrlichia)sp. Omatjenne (using the RLB assay) or E. ruminantium (using the pCS20 real-time PCR assay) was unsuccessful. This was most probably due to low rickettsaemia. However, amplification of either the near full-length parasite 16S rRNA gene or a partial 16S rRNA gene from seven samples from the KNP and three from Hluhluwe-iMfolozi Park was successful. Results indicated that the obtained sequences of 12 of the 18 clones were highly similar to published A. centrale 16S rRNA gene sequences, four of the clones were highly similar to the published A. marginale sequences and the sequences of the remaining two clones were closely similar to Anaplasma (Ehrlichia) sp. strain Omatjenne. The observed sequence similarities were confirmed by phylogenetic analyses. An interesting finding was the presence of one full-length parasite 16S rDNA sequence that was 100% identical to that of the published A. centrale vaccine strain sequences. It is well known that A. centrale is widely used as live vaccine for the control of bovine anaplasmosis. The occurrence of A. centrale vaccine strain DNA in the South African buffalo population is therefore of great interest. It can only be speculated whether A. centrale has evolved in the African buffalo, and/or if buffalo act as natural reservoir hosts, or if is it merely being maintained in the buffalo population by in utero transmission. This also serves as the first report of Anaplasma (Ehrlichia) sp. Omatjenne DNA in the African buffalo which warrents further investigation. In conclusion, the findings suggest that buffalo is a natural reservoir of Anaplasma spp. infection and could play an important role in the epidemiology and spread of anaplasmosis and may represent a serious threat to the livestock industry. / Dissertation (MSc)--University of Pretoria, 2012. / Veterinary Tropical Diseases / unrestricted

Methods used to estimate the prey consumption by large carnivores include direct continuous observation, stomach content analysis, carcass observations and scat analysis. Continual observations are widely considered the best approach to estimate large carnivore diets, with lions (Panthera leo) being no exception. Continual observation allows the recording of all prey encounters and biases inherent in the other approaches are minimised. However, continuous observations are not always feasible, and in situations where animals cannot be observed at all times, diets are often estimated from observed carcasses. This often leads to an over-estimation of large kills in the estimated diet. Alternative methods that are free of the constraints placed on continuous observations are needed to provide data of a similar quality to that obtained using these continuous observation bouts. I employed a cluster follow up technique to locate lion kills from remotely accessed Global Positioning System (GPS) data from lions in the Kruger National Park (KNP). I develop Generalized Linear Models (GLMs) that increase the probability of locating kills at GPS cluster events. By increasing the predictive ability of detecting kills I show that this technique can be used to locate kills in a more efficient manner than random searching of GPS clusters, with further advantages in that multiple groups of lions can be monitored simultaneously. By incorporating this technique into an adaptive research framework, the diet of lions (and that of other large carnivores) can be estimated. In addition, I show that the spatial association between lions at kill sites, while feeding on carcasses, provides a further increase in the predictive ability of kill site models. Lionesses were found to be considerably closer together at the start of clusters associated with kills in comparison to clusters where no kill was found. This pattern remained consistent for both small and large kills. This proximity approach could therefore be incorporated into the GLMs that are developed to predict kill sites of large social carnivores. To further reduce the bias (where small kills are often missed) inherent in carcass observations, I combined scats and carcasses collected from known times, locations and lion groups to construct a temporal kill record for each group of lions. By combining scats and carcasses I estimate that at least 50% of the small prey items, namely impala (Aepyceros melampus) and warthog (Phacochoerus africanus) were missed when GPS clusters were investigated for carcasses. Ultimately, I show that a combination of GPS cluster investigations based on models developed using GPS movement data in combination with lion proximity data, augmented with scats collected at GPS clusters, could provide estimates of large carnivore diets that begin to approach estimated diets obtained through continuous monitoring. The resulting diet, estimated from the GPS cluster approach in combination with scat collection, indicated that the dominant prey item in the region was zebra (Equus quagga) followed by wildebeest (Connochaetes taurinus), impala and buffalo (Syncerus caffer). Selection indices for the eight dominant prey items were calculated using prey availability measures obtained from the aerial census data and ground counts of groups. It has been suggested that group level selection is a better approach to calculating predator-prey interactions, and that stability in predator-prey systems is improved if group metrics of prey are used as apposed to individual measures of availability. I show that there is a considerable shift in selection indices, as well as in the order that prey is selected, when using different measures of prey availability. In selection studies, more effort needs to be paid to the assessment and definition of prey availability to ensure results accurately reflect selection patterns in the field, especially when data are used for the development of management practices. Combining buffalo predation data collected from GPS cluster investigations with buffalo mortality data collected over five years prior to the commencement of the GPS cluster investigations, allowed an investigation into patterns of lion predation on buffalo between 2000 and 2007. Buffalo of both sexes were more vulnerable to predation in habitats that gave lions an ambush advantage (i.e. increased grass height and tree density). Despite this similarity in landscape risk, different processes lead to similar fates in dangerous habitats for buffalo of both sexes. Predation pressure by lions on buffalo increased following periods of reduced rainfall; with more buffalo predated on following drier six month periods. Predation on males constituted a significant proportion of all predation and was focused predominantly into the late dry season. The resulting method of locating kills by using GPS clusters and correcting carcass data with scats collected along the movement path represents a robust technique to estimate large carnivore diets. In the concluding chapter I present avenues where future research can build on the current thesis and present a framework that can be employed when attempting to estimate large carnivore diets. / Thesis (PhD)--University of Pretoria, 2010. / Zoology and Entomology / unrestricted