Analyzes of bat echolocation calls enable to investigate diverse patterns of bat communities without the need for contact manipulation with individuals. The continuous all-night acoustic recordings provide standardised data open to quantitative comparisons and testing effects of diverse contextual factors upon bat community structure. The multidisciplinary project MOSAIK (Monitoring Savanna Biodiversity in Kruger NP) mapping patterns of variation in savanna communities under different spatial and temporal influences includes bats as one of the model groups. At standardized monitoring points of the project (covering 20 different areas, each containing triplet points differing in access to the water surface: permanent, seasonal and the crests without a water source), all-night acoustic recordings of bats were undertaken over two seasons (using Song Meter recorders SM4BAT). All records were analyzed with aid of Kaleidoscope Pro software and cluster identification technique (with an input database developed by Weier et al. 2018 and Taylor et al. 2020) controlled by manual checking. Multiple comparisons of diverse coenologic variables of the particular samples were performed together with testing effects of associated contextual variables (geographic setting and climatic currents, seasons, vegetation,...

S.J.P. Kruger, four times president of the Zuid-Afrikaansche Republiek (ZAR), played a central role in the Afrikaners' struggle for independence both in the 19th and 20th centuries. His significance as a leader also becomes apparent when considering the plethora of literature written on him both during his lifetime and after. Not only is his own life story intertwined with the history and development of the ZAR and rise of Afrikanerdom, but as a leading figure he was also subject to much criticism. This was particularly evident in the years leading up to and during the South African War (1899-1902) when the ZAR forces clashed with Britain. Against this dualistic background a stereotypical and binary portrayal of Kruger emerged. Some of these have been perpetuated into the literature of the 21st century. However, despite the array of works published on Kruger, it remains remarkable why his involvement in the South African War has not received extensive scrutiny, principally his "behind-the-scenes" contribution. It is to this prominent event in the life of Kruger that this study turns with particular reference to the year 1900 which has been identified as a so-called "crisis period". Using the War telegrams dispatched by Kruger during the said period, this study endeavours to not only investigate Kruger's War-time contribution and motives, but also to reassess his character in the context hereof. Although much of the evidence suggests that the Kruger persona is somewhat entrenched, the War telegrams however point to additional representations of Kruger and call thus for further reappraisal. / Dissertation (MHCS)--University of Pretoria, 2016. / Historical and Heritage Studies / MHCS / Unrestricted

Black rhinoceroses (Diceros bicornis) have been extirpated from most of their historic range with the remaining individuals (ca. 5200) living in geographically isolated populations. Management priorities include creating new populations whilst maintaining genetic diversity and promoting gene flow between existing isolated populations. Such objectives are however currently hindered by a lack of comparative/reference data on levels of diversity, relatedness and inbreeding in a large, free-ranging black rhinoceros population. Here I attempt to address this gap in our knowledge by investigating the genetic diversity of the black rhinoceros Diceros bicornis minor within Kruger National Park (the largest free-ranging population of this subspecies) using nuclear and mitochondrial DNA. I compared the diversity of this founded population with the two source populations (KwaZulu-Natal, South Africa and Zimbabwe) using published studies, and evaluate the relative contribution of source lineages relative to the proportion of original founders. Analysis of the mtDNA control region revealed four haplotypes, with moderate haplotype and nucleotide diversity (h=0.48 (± 0.05 SD); π= 0.29%). Data from 13 microsatellite loci revealed moderate to high levels of genetic variation (number of alleles = 4.92 ± 0.90, effective number of alleles = 2.26 ± 0.25, observed heterozygosity = 0.50 ± 0.04, expected heterozygosity = 0.51 ± 0.04), low mean pairwise relatedness (r = -0.03), a low inbreeding coefficient (Fis = 0.04) and no evidence of genetic structuring. Diversity levels within the Kruger black rhinoceros population were high compared to levels reported in black rhinoceroses originating in KwaZulu-Natal and similar to those reported in individuals originating in Zimbabwe. Results show that 40-60% of the Zimbabwean lineages are represented in the Kruger population which is a noticeable increase in the relative contribution of the Zimbabwe founder population. The data provided by this study can be used to guide management and conservation decisions regarding maximising genetic variability across the subspecies. Furthermore, given the encouraging levels of genetic diversity observed, the Kruger black rhinoceros population would be an ideal source population for supplementation of genetically depauperate populations or creating new populations. Finally, these findings demonstrate a positive outcome in mixing the KwaZulu-Natal and Zimbabwe gene pools, with evidence that the founder Kruger black rhinoceros population has been genetically rescued from the low diversity seen in the KwaZulu-Natal black rhinoceroses in South Africa.

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

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

As part of the larger survey to map the geographical distribution of Babesia and Theileria parasites in the Southern African rhinoceros population, white rhinoceroses were sampled during routine immobilizations in the Kruger National Park. Polymerase Chain Reaction (PCR) and Reverse Line Blot (RLB) hybridization assays were used to screen for the presence of haemoprotozoa and complete blood counts were used to assess associated changes in clinical parameters. Of the 195 rhinoceroses sampled, 36.4% tested positive for the presence of Theileria bicornis, with no significant change in the haematological parameters measured. None of the rhinoceroses sampled tested positive for Babesia bicornis, the parasite linked to mortalities in black rhinoceroses. Copyright / Dissertation (MSc)--University of Pretoria, 2009. / Veterinary Tropical Diseases / unrestricted