Thesis (Ph.D.) (Zoology)--University of Pretoria, 2005. / Abstract in English. Includes bibliographical references. Available on the Internet via the World Wide Web.

Please read the abstract in the section front of this document / Thesis (PhD (Zoology))--University of Pretoria, 2007. / Zoology and Entomology / unrestricted

Calow (1983) realized that differences between parasites and their free-living relatives can be explained by the differences in nutrient richness. I propose a model that is based on Calow's idea which identifies the relative position of different trophic strategies (e.g. predation, grazing, parasitism and others) based on (1) the differences by which consumers arrive at their intrinsic rate of growth, and (2) the ecological impact they inflict on their hosts. I hypothesize that trophic interactions can be clarified if a parameter is included that takes into account the host's/prey's fate in the interaction. Moreover, this model suggests specific trophic evolutionary pathways (TEPs) between each strategy, and suggests that some pathways are more likely than others. In particular, parasitoidism is believed to be a highly derived strategy, and the TEPs presented in the model suggest parasitoidism could have arisen from either a predator-like or a typical-parasitic ancestor. Though the trophic categories determined by the model seem intuitive, this approach does provide, apparently for the first time, an objective, mathematically and ecologically useful basis for classifying animal trophic relationships. / Graduation date: 1998

Malaria is a serious and life-threatening mosquito-borne disease that every year affects over 200 million individuals and causes 400,00 deaths. An additional 0.5 billion people globally are at risk of malaria infection. The unique role of climate in influencing malaria transmission outcomes across individual communities by acting on multiple dimensions of the malaria vector and parasite ecology has been long recognized. This recognition has led to the development of explicit and implicit climate-driven models of malaria transmission designed to better understand and predict patterns of population vulnerability and uncover potential challenges to malaria control. However, existing implicitly-forced process-based models of malaria have relied on indirectly correlated predictors of malaria transmission, instead of direct relationships among climate, vector entomology and parasite ecology. The lack of biologically-motivated modulation of malaria transmission compromises meaningful interpretation of the ecological role played by climate in malaria transmission. Similarly, the specific influence of climate on vector and parasite dynamics is obscured, limiting the utility of these simple and powerful model forms. This dissertation focuses on elaborating the direct ecological relationships between climate, the malaria vector and parasite to enhance the ecological utility of lower dimensional mathematical models of malaria transmission. In the 2nd chapter of this thesis, a climate-driven entomological modeling framework is developed, consisting of a simple dynamic model that explicitly tracks malaria transmission in human populations and implicitly represents the malaria force of infection through climate-regulation of multiple aspects of the Entomological Inoculation Rate (EIR). The EIR-model construct is found to accurately capture seasonal malaria dynamics under free-simulation, when coupled to local rainfall and temperature climatology across multiple local regions in Rwanda. Furthermore, local rainfall modulation of sub-adult survivorship is found to be a more critical driver of seasonal malaria dynamics than other environmentally-regulated components of EIR. In chapter 3, the model framework is paired with data assimilation methods to dynamically simulate interannual malaria incidence in Rwanda, infer parameters of malaria transmission and validate the malaria model. Results indicate that the implicitly-forced transmission model is able to reproduce interannual and seasonal malaria incidence at regional and local scales. However, accuracy of model description of malaria incidence is more varied at the more resolved local level. Intensified malaria control efforts during the later years of the study are suspected to increase the discrepancy between the vector and parasite dynamics dictated by climate and the observed widespread decline in malaria activity in the region. Nonetheless, the parameters of transmission identified across populations in Rwanda were comparable to existing estimates of malaria, further validating the transmission model and data assimilation approach. For the 4th chapter, a state-of-the-art Bayesian inference forecasting system for the EIR-model framework is developed, as well as a multi-model forecasting system consisting of weighted-average predictions from the dynamic malaria model and historical expectance predictions. Retrospective forecasts of four years of malaria data from 42 regions in Rwanda indicate that the model-inference forecasting system predicts malaria incidence more accurately than historical expectance alone, particularly for predictions with 1-6 weeks lead times. Although slightly less skillful, the multi-model system was found to substantively enhance forecast reliability of the EIR-model system, bolstering the utility of the malaria model as a robust forecaster of malaria in the region. The concluding chapter describes areas for improving the specification of the parsimonious model construct. The need to include malaria control coverage data as exogenous forces of transmission, non-climate drivers and alternate sources of climate exposure that support transmission are highlighted. Future works on forecast calibration needed to improve model performance for real-time prediction are also detailed. In addition, areas for application within information systems for evaluating malaria risk and for advising malaria control efforts, specifically relating to local variability in malaria burden and characterization of entomological drivers of local malaria, are identified and further discussed. The model systems developed in this thesis advance the capabilities of lower dimension dynamic models to connect the ecological drivers of malaria transmission to climate variation. Such process-based formulations could provide better climate-driven descriptions of malaria, while limiting model complexity, without compromising representation of entomological relationships that are potentially valuable for improved understanding and control of malaria transmission.

In South Africa, 2 primate species, Chacma baboons (Papio ursinus) and vervet monkeys (Chlorocebus pygerythrus), and 2 nocturnal mammals, Cape porcupine (Hystrix africaeaustralis) and bushbuck (Tragelaphus scriptus), are among many species of crop raiders. Currently, cost-effective, non-lethal solutions are lacking. From June through December 2012, I installed novel electronic scarecrows on two commercial citrus orchards and a private reserve and used video-recording remote cameras to assess cropraiders’ reactions to them in Limpopo Province, South Africa. I used focal animal sampling data from treatment and control group animals to examine differences in activity budgets and behaviors of interest between groups. Compared to animals at sites with an inactive or no scarecrow, I hypothesized that animals in the treatment group would have altered activity budgets and rates of behaviors; that they would forage or feed less, run more (as a result of being frightened), be more vigilant and thus scan their surroundings more often, and display a visible startle in response to stimuli from scarecrows. Bushbuck at treatment sites spent a larger proportion of their activity budget running, and were more often startled. However, foraging was never observed, and bushbuck in the control group scanned their surroundings more often. Porcupines at treatment sites spent a larger portion of their activity budget running, though foraging was only observed in 1 control group animal and looking was never observed. For primates, treatment (control, scarecrow) was meaningful in explaining differences in focal animal activity budgets of baboons (F = 5.49, P = 0.001) and vervet monkeys (F = 7.09, P = 0.001) as indicated by a permutational MANOVA in R. In baboons, treatment was positively correlated with running; ratios of baboons that ran to baboons that did not run differed between treatment groups (G = 15.78, P < 0.001). Treatment was negatively correlated with feeding; ratios of baboons that fed or foraged to baboons that did not feed or forage differed (G = 5.39, P = 0.02). Significant differences between groups of vervet monkeys were not found with G-tests for the same behaviors of interest. Electronic scarecrows are promising tools for human-wildlife conflict mitigation, particularly for nocturnal antelopes. For primates, further innovation in design of scarecrows to incorporate a visual stimulus is recommended.

This project represents the first comprehensive study applying molecular and genetic methods to study historical contexts such as migration and trade based on human parasites. Using specially developed techniques, the study focused on parasites with minor symptoms which allowed the infected person to go about their daily business. The combination of state of the art techniques in archaeology, molecular methods and phylogenetic analysis enabled us to develop a novel powerful tool to study historic events. Diseases have a considerable impact on societies. Various publications indicate that human intestinal parasites are commonly found in a variety of archaeological contexts, including latrines, graves and mummies. These parasites can be detected by microscopy which focuses the work on samples which do close association to humans; widespread prevalence and the possibility for reliable microscopic diagnostics suggest that these parasites are an attractive study system for human activities. Infectious diseases have a much short generation time which offers greater opportunity to track historical events at higher resolution. Looking at a range of human parasites, their different life-cycles allowed insight into various aspects of human culture, comparing different origins of the samples allows an estimation of the epidemiological burden of ancient populations. Application of a parallel sequencing approach (MiSeq) enabled building a comprehensive database of sequences from various archaeological sites dating as far back as 3630 BCE. Indepth phylogenetic analysis reveals patterns in the genetic signatures of both coding and non-coding genetic regions, taking various levels of selective pressure into account. This project has produced the oldest pathogen sequence and the most comprehensive database of ancient pathogen sequences.

M.Sc. / There are 39 known species of Lamproglena to date. A review of all species including the species name, the author, as well as an accompanying sketch and information regarding the distribution, pathology and host preference is given. Lamproglena clariae is a copepod gill parasite found on Clarias gariepinus. It has been observed that they cause extensive gill tissue proliferation, which may interfere with respiration. It is uncertain on which tissue type Lamproglena feeds, as red blood is never apparent in the gut of Lamproglena monodi, whereas in the cases of both L. clariae and L. barbicola they undoubtedly feed on blood, proven by the frequently blood-filled gut. Even thought the mouthparts are not fully understood as yet, it is deduced that feeding involves only the maxillae and maxillipedes. Many poecilostomes lacks mandibles. Also, in the lernaeids the mandible is appendage is the smallest and from the 39 known Lamproglena species, the mandibles are described in only eight species. This study examines the digestive tract and the structure of the mouthparts using both light and scanning electron microscopy and tracts the nerves to establish if L. clariae does possess mandibles. Specimens were collected from Clarias gariepinus in the Vaal Dam after the fish were euthanised and the gills removed. The samples were fixed in an aceto formaldehyde alcohol solution and preserved in 70% ethanol prior to dehydration and embedding in resin. Serial section were made at 5 pm and stained with a trichrome stain. A schematic as well as graphic reconstruction of the digestive system is presented. The digestive system consist of three predominant parts, the fore, mid and hindguts. The foregut has a cuticularised epithelium. The oesophagus has a muscle layer iv which stretched and contracts in order to aid feeding and it extends into the midgut via a funnel-like structure. There are four designated zones within the midgut. The hindgut is a simple, cuticle lined tube. Cell structures are discussed. The bilobed protocerebrum in L. clariae is present. The deutocerebrum innervates the antennules. The tritocerebrum consist of two lobed parts and innervates the antennules. The ventral nerve cord is situated posterior to the cephalon. It protrudes dorsally, from where the posterior commissures innervates. The anterior commissures innervates closer to the tritocerebrum. The nerves leading to the mandibles are innervated from the anterior commissure. The more posteriorly located commissure innervates the nerve to the seta located between the antennae and the maxillae. Both the nerves to the maxillae and the endopodite to the maxillae are innervated from this commissure. Mandibles were left out of previous species descriptions of L. clariae. Other Lamproglena species descriptions, showing the mandibles, revealed slender looking mandibles located in close proximity to the mouth opening. This is contrary to the stout mandibles of L. clariae. Future research topics are highlighted and discussed