Thesis (PhD)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: Fleas (Siphonaptera) are obligate ectoparasites of mammals and birds. Due to their economic importance as disease vectors, most contemporary studies on macroparasites now also consider the spatial variation of parasite communities and the underlying mechanisms involved in shaping current distribution patterns. Fleas differ in life history traits, such as the level of host specificity and microhabitat preferences, which can result in differential evolutionary responses to similar abiotic events. The main objectives of this study are to investigate: (1) the influence of vicariance and host association on the genetic structure of two generalist flea species, Listropsylla agrippinae, and Chiastopsylla rossi. The taxa differ in the time spent on the host (fur vs. nest) and the level of host specificity; (2) the taxonomy of Dinopsyllus ellobius to determine whether more than one species exist and if so to then elucidate the mechanisms of speciation; and (3) the influence of flea life history on species distribution model performance and see if the relative importance of predictor variables differ between species with different life histories. A total of 1423 small mammals were brushed to collect 2906 flea individuals originating from 31 geographically distinct localities throughout South Africa (SA). Phylogeographic structure of L. agrippinae and C. rossi were determined by making use of 315 mitochondrial COII (mtDNA) and 174 nuclear EF1-α (nDNA) sequences. The more host specific fur flea, L. agrippinae, displayed pronounced spatial phylogeographic structure, based on mtDNA, which was congruent with host vicariance in the region. In contrast, the more generalist nest flea, C. rossi, showed a higher level of inter-populational divergence, based on mtDNA and nDNA, and this may be attributed to comparatively higher restrictions to dispersal when compared to the more specific fur flea. In an attempt to resolve the taxonomy of D. ellobius, 151 mtDNA and 68 nDNA alleles were generated from individuals meeting the morphological description of D. ellobius. Two distinct D. ellobius lineages that corresponded to previously described species (D. ellobius and D. abaris) were recorded. The results indicate that the two species indeed differ morphologically and based on the distribution of the two species it was concluded that the diversification could be a result of climate driven vicariance and subsequent ecological segregation according to habitat use. Locality records from Segerman (1995) were digitized and used as background data in species distribution modelling. Sufficient information was obtained for 21 flea species. A total of 68 climatic and landscape feature predictor variables were obtained and through a process of elimination, 19 variables were ultimately used. Model performance was good to excellent on average and the contribution of climate and landscape feature variables differed between fleas with different life histories. Historical and contemporary climate has the most prominent effect on flea distribution at the regional scale, but the level of host association influences the phylogeographic pattern of fleas. This study provides the first evidence of congruent phylogeographic patterns between a generalist temporary parasite and its hosts. Our findings provide further support for the notion that more than one species exist within the D. ellobius complex and that speciation is a result of complex interactions. The study also provides novel data on the role of environmental variables in shaping the geographic distribution of flea species with different life histories. With the anticipated rise in flea-borne diseases worldwide, due to changes in vector distribution, the study further emphasize the need for studying the mechanisms involved in shaping flea distribution patterns. / AFRIKAANSE OPSOMMING: Vlooie (Siphonaptera) is verpligte ektoparasiete van soogdiere en voëls. As gevolg van hul ekonomiese belangrikheid as vektore van oordraagbare siektes, neem meeste kontemporêre studies oor makroparasiete nou die ruimtelike variasie (vikariansie) van parasiet gemeenskappe en die onderliggende meganismes betrokke by die vorming van die huidige verspreiding patrone in ag. Vlooie verskil in lewensgeskiedenis eienskappe, soos die graad van gasheer spesifisiteit en mikrohabitat voorkeur, wat kan lei tot differensiële evolusionêre patrone tot soortgelyke abiotiese gebeure. Die belangrikste doelwitte van hierdie studie is om ondersoek in te stel na: (1) die invloed van vikariansie en gasheer assosiasie op die genetiese struktuur van twee algemene vlooi spesies, Listropsylla agrippinae en Chiastopsylla rossi. Die taxa verskil in die hoeveelheid tyd wat gespandeer word op die gasheer (pels vs. nes) en die graad van gasheer spesifisiteit; (2) die taksonomie van Dinopsyllus ellobius om te bepaal of daar meer as een spesie bestaan, en indien wel, die meganismes van spesiasie voortbring; en (3) die invloed van vlooi lewensgeskiedenis op die prestasie van die spesies verspreidings model en kyk of die relatiewe belangrikheid van omgewingsvoorspellers verskil tussen spesies met verskillende lewensgeskiedenisse. 'n Totaal van 1423 klein soogdiere is geborsel om 2906 vlooi individue afkomstig van 31 geografies verskillende plekke in Suid-Afrika in te samel. Filogeografiese struktuur van L. agrippinae en C. rossi is bepaal deur gebruik te maak van 315 mitochondriale COII (mtDNA) en 174 kern EF1-α (nDNA) volgorde bepalings. Die meer gasheer spesifieke pels vlooi, L. agrippinae, het ruimtelike filogeografiese struktuur aangetoon, gebaseer op mtDNA, wat ooreenstem met gasheer vikariansie in die streek. In teenstelling hiermee het die minder gasheer spesifieke nes vlooi, C. rossi, 'n hoër vlak van inter-populasie divergensie getoon, gebaseer op mtDNA en nDNA, wat toegeskryf kan word aan relatief hoër beperkings op verspreiding teenoor die meer gasheer spesifieke pels vlooi. In 'n poging om die taksonomie van D. ellobius op te los is 151 mtDNA en 68 nDNA allele gegenereer uit individue wat voldoen aan die morfologiese beskrywing van D. ellobius. Twee afsonderlike D. ellobius afstammelinge wat ooreengestem het met voorheen beskryfde spesies (D. ellobius en D. abaris) is aangeteken. Die resultate dui daarop dat die twee spesies inderdaad morfologies verskil en gebaseer op die verspreiding van die twee spesies is daar tot die gevolgtrekking gekom dat die diversifikasie moontlik toegeskryf kan word aan klimaat gedryfde vikariansie en daaropvolgende ekologiese segregasie volgens habitat gebruik. Geografiese verspreidings rekords van Segerman (1995) was gedigitaliseerd en gebruik as agtergrond data in die spesie verspreidings modelle. 'n Totaal van 68 klimaat en landskap kenmerk voorspeller veranderlikes is verkry, en deur 'n proses van eliminasie, is 19 veranderlikes gebruik. Model prestasie was oor die algemeen goed tot uitstekend en die bydrae van klimaat en landskaps veranderlikes het verskil tussen vlooie met verskille in lewensgeskiedenis. Historiese en kontemporêre klimaat het die mees prominente effek op vlooi verspreiding by die plaaslike skaal, maar die vlak van die gasheer assosiasie beïnvloed die filogeografiese patroon van vlooie. Hierdie studie bied die eerste getuienis van ooreenstemmende filogeografiese patrone tussen 'n minder gasheer spesifieke, tydelike parasiet en sy gashere. Ons bevindinge bied verdere ondersteuning vir die idee dat meer as een spesie bestaan binne die D. ellobius kompleks en dat spesiasie 'n gevolg is van komplekse interaksies. Die studie bied ook nuwe data oor die bydrae van die omgewingsveranderlikes in die vorming van die geografiese verspreiding van vlooi spesies met verskillende lewensgeskiedenisse. Met die verwagte styging in vlooi-oordraagbare siektes wêreldwyd, as gevolg van veranderinge in vektor verspreiding, beklemtoon die studie verder die noodsaaklikheid vir die bestudering van die meganismes betrokke in die vorming van vlooi verspreiding patrone. / National Research Foundation (NRF)

This study examines, from a modelling point of view, the dynamics of infectious diseases in wildlife caused by macroparasites and by tick-borne infections. The overall aim was to investigate the important role played by parasite aggregation in the dynamics of both systems. For macroparasites we first developed some deterministic models that incorporate explicit mechanisms for generating aggregation in parasite distribution, specifically multiple infections and host heterogeneity. We explored the role of aggregation in host regulation and in determining a threshold value for parasite establishment. A large aggregation makes it more difficult for parasites both to regulate hosts, and to get established in a population at carrying capacity. Furthermore, the stabilization yielded by aggregation strongly depends on the mechanism that produces the aggregation. We then introduced some uncertainties into the host-macroparasite system, presenting an individual-based stochastic model that incorporated the same assumptions as the deterministic model. Stochastic simulations, using parameter values based on some real case studies, preserved many features of the deterministic model, like the average value of the variables and the approximate length of the cycles. An important difference is that, even when deterministic models yield damped oscillations, stochastic simulations yield apparently sustained oscillations. The amplitude of such oscillations may be so large as to threaten the parasites’ persistence. With respect to tick-borne diseases we presented a general model framework that incorporated both viraemic and non-viraemic routes of infections. We compute the threshold for disease persistence and study its dependence on the parameters and on host densities. The effects of tick aggregation and correlation between different tick stages on the host have both an important effect on infection persistence, if non-viraemic transmission occurred. In the case of Lyme Disease and Tick-borne Encephalitis (TBE) in Trentino (northern Italy) we showed some numerical results, using parameter estimates based on a detailed field study, and explored the effects of uncertainty on the endemic equilibrium of both diseases assuming only viraemic transmission for Lyme Disease while for TBE we permitted only non-viraemic transmission through co-feeding ticks. In conclusion we have examined the patterns and changes of aggregation in a number of contrasting systems and believe that these studies highlight both the importance of considering heterogeneities in modelling host-parasite interactions and, more specifically, modelling the biological mechanisms that produce aggregation in parasite distributions.

Species of Argulus are macro-, ecto-parasites known to infect a wide variety of fish, but in the UK mainly cause problems in rainbow (Oncorhynchus mykiss) and brown trout (Salmo trutta). Argulus foliaceus is estimated to have caused problems in over 25% of stillwater trout fisheries in the UK. While A. foliaceus does not usually cause high levels of mortality, the parasite affects fish welfare, and also makes fish harder to catch due to morbidity and reduced appetite. This can cause severe economic problems for the fishery, resulting in reduced angler attendance due to poor capture rates and the reduced aesthetic appearance of fish; in the worst-case scenario this can result in the closure of the fishery. Current methods of control include chemical treatment with chemotherapeutant emamectin benzoate (Slice), physical intervention with egg-laying boards which are removed periodically and cleaned in order to reduce the number of parasites hatching into the environment, and the complete draining and liming of the lake to remove all free-living and egg stages of the parasite. While these treatments have all been shown to reduce parasite numbers, none are known to have resulted in permament eradication of the parasite. There is evidence to suggest that A. foliaceus will eventually develop resistance to Slice - the only currently available chemical treatment against the infection - and egg-laying boards and the draining and liming of the lake are both time- and labour-intensive. Previous studies have shown that slow fish turnover is a risk factor with respect to A. foliaceus infections, and with a wide variety of stocking practices occurring in the UK one of the first aims of this project was to determine their impact on the host-parasite dynamics. Mathematical models provide a cost-effective way of examining the impact of such practices, and after a literature review (chapter one), in chapter two a three-compartment mathematical model was adapted for use in the A. foliaceus-trout system. Four generalised stocking methods were then incorporated and analysed, and a minimum threshold host density was found to be necessary to sustain the parasite. Including a function which reduced the capture rate as the parasite burden increased allowed the parasite to survive at a lower host density, as susceptible fish were removed from the water at a slower rate, and attached parasites also remained in the water for longer. This resulted in hysteresis in the model, as the invasion threshold for the parasite remained the same, but once established the parasite became harder to eradicate, requiring significant reductions in the host density. In chapter three the model was further developed in order to improve its biological real- ism. Several features were added and these included: natural host mortalities, a separate compartment for the parasite egg population, and parasite survival after the natural or parasite-induced mortality of its host. In chapter four seasonality was added by incorporating temperature-dependent egg-laying rates and an over-wintering period during which the parasite was unable to reproduce. The model was then fit to the available data, and estimates for the rate of parasite-induced host mortalities and the parasite’s rate of attachment to a host were found. In chapter five we returned to stocking methods, this time looking at the frequency and timing of stocking events and the impact of imposing a rod limit (whereby anglers are only permitted to capture four fish per visit); it was concluded that while current guidelines suggest that very frequent trickle stocking is recommended when dealing with Argulus spp. infections, monthly stocking does not appear to worsen the infection, and if the fish capture rate is high then less-frequent stocking may also be permissable - particularly if stocking occurs towards the end of the year when the parasite is no longer active. This practice may, however, be detrimental to the fishery due to low fish densities in the summer months. In chapter six treatment with Slice was included in the model, and it was demonstrated that with constant treatment, and in the absence of reservoir hosts and a withdrawal period from the drug prior to stocking treated fish into the fishery, the parasite was eradicated. Under current veterinary cascade guidelines, however, trout are required to undergo a withdrawal period of 500 degree days prior to being made available for human consumption. When this was included in the model the drug still decreased parasite abundance, but did not eradicate it - this is in agreement with results reported by communications with fishery managers currently treating fish with Slice. A reduction in the withdrawal period of 25% was shown to further decrease parasite abundance, but still did not result in parasite extinction. As constant treatment with Slice is not advisable due to the potential for resistance build-up, we then sought to find time at which to apply a single treatment of Slice, and found that this was in August when the temperature was highest and the parasite was reproducing and attaching to hosts quickly. Egg-laying boards were also incorporated into the model and similarly to findings by Fenton et al. [11] the success of this treatment was mostly dependent on the proportion of eggs being laid on the boards (as opposed to natural substrates). In contrast with the A. coregoni system, however, the boards would have to be cleaned and replaced more frequently that once per year, as several cohorts of A. foliaceus emerge during a single year.

Mandated by the Sikes Act of 1960, natural resource managers work to manage the habitats and wildlife that are found on military installations in the United States and Territories. At Camp Edwards Military Training Reservation (hereby abbreviated to Camp Edwards), (Bourne, MA), such wildlife includes the state-protected eastern box turtle (Terrapene carolina carolina) and the declining prairie warbler (Setophaga discolor), which both occupy pine barrens. In 2020, natural resource managers at Camp Edwards noticed that eastern box turtles were being infected by myiasis, which occurs when flesh flies deposit larvae into the living tissue of a vertebrate host. In the literature, it has been documented that several ectothermic hosts respond to disease or parasite infection through a phenomenon referred to as ‘behavioral fever’ by moving to warmer locations to raise their internal temperature. Behavioral fever may clear the infection faster because higher body temperatures can induce parasite mortality or prevent secondary infections. However, it is unclear if myiasis induces behavioral fever in eastern box turtles or impacts other aspects of their behavior, such as habitat use. In Chapter 1, I compare behavior and habitat characteristics of myiasis infected and noninfected eastern box turtles at Camp Edwards. I radio-tracked 48 turtles weekly from May to August 2022. Upon capture, I recorded their infection status, shell surface temperature, and capture location habitat characteristics: understory vegetation, basal area, and canopy closure. I used generalized linear models and linear models to compare body condition indexes, shell temperatures, habitat use, and movement distances between infection statuses, sexes, and age classes. I found that myiasis infection had no significant effect on any variable other than shell surface temperature, which suggests infected turtles may be exhibiting behavioral fever. A second species of great concern at Camp Edwards are prairie warblers. Prairie warblers occupy early successional forests, which means that habitat management could have a direct impact on the distribution and abundance of this species. Despite declining populations regionally, prairie warbler populations at Camp Edwards have increased in the last few years. In Chapter 2, I analyze the effect of management projects (i.e., prescribed fire and mechanical projects) on prairie warbler colonization, extinction, and detection probabilities at Camp Edwards. I found that colonization was significantly predicted by the number of years since management and the proportion of the following vegetation cover types at a site: grassland, disturbed land, pitch pine – oak forest, and pitch pine – scrub oak community. I also found that extinction was significantly predicted by the proportion of pitch pine – scrub oak community at a site. Lastly, I found that detection probability was significantly predicted by the year of observation and the proportion of the following vegetation cover types: grassland, pitch pine – oak forest, and pitch pine – scrub oak community. These results can help managers predict how prairie warbler populations respond to management projects at Camp Edwards.

Die Einschleppung gebietsfremder Parasiten durch den Menschen ist einer der Hauptgründe für das Auftreten neuer Krankheiten in the letzten Jahrzehnten. Neue Wirte sind oftmals anfälliger für diese invasiven Parasiten als die ursprünglichen Wirte. In schwerwiegenden Fällen können invasive Parasiten zu Massensterben und zum Aussterben ihrer neuen Wirte führen. Der ursprüngliche Wirt des Aalparasiten Anguillicola crassus ist der Japanische Aal. In den frühen 1980er Jahren wurde der Parasit in die Population des Europäischen Aals eingeschleppt. Er ist einer der Faktoren, die für den Populationsrückgang des Europäischen Aals verantwortlich sind. Die molekularen Prozesse, die zur stärkeren Anfälligkeit des Europäischen Aals im Vergleich zum Japanischen Aal führen, sind noch nicht zureichend bekannt. Die Analyse transkriptomweiter differenzieller Genexpression von Immungewebe ergab, dass im Europäischen Aal sowohl Immun- als auch Nichtimmungene differenziell exprimiert waren. Dies war im Japanischen Aal nicht der Fall und deutet darauf hin, dass der Europäische Aal eine ineffiziente und kostspielige Immunantwort auslöst. Die Resultate ensprechen jenen die schon in anderen Wirbeltierwirt-invasiven Parasiten-Systemen beobachtet wurden. Ausserdem stützen diese Resultate die Hypothese, dass neuen Wirten eine wirksame Immunantwort fehlt und sie deuten darauf hin, dass Nichtimmunprozesse wesentlich zur höheren Anfälligkeit von neuen Wirten beitragen. Als Reaktion of die negativen Fitnesseffekte können neue Wirte Abwehrmechanismen entwickeln. Im Europäischen Aal entspricht das der Einkapselung von A. crassus. Einkapselung führte zu eine niedrigere Abundanz adulter A. crassus. Dies deutet darauf hin, dass das Einkapseln sich positiv auf die Gesundheit infizierter Aale auswirkt. Jedoch war die Abundanz zweier nativer Parasiten höher in Aalen, die A. crassus einkapselten. Eine verbesserte Abwehr des eingeschleppten Parasiten könnte daher die Abwehr nativer Parasiten beeinträchtigen. / The human-mediated translocation of non-native parasites into foreign regions is one of the primary factors for the emergence of new diseases in recent decades. Novel hosts are often more susceptible to these invasive parasites than the native host. In severe cases, invasive parasites can lead to population declines and extinctions of their novel hosts. The eel parasite Anguillicola crassus is native to the Japanese eel. In the early 1980s it was introduced into the European eel population and is now considered to be one factor contributing to the population decline of its novel host. The underlying molecular processes determining higher susceptibility in the European eel compared to the Japanese eel are not well understood. Using whole-transcriptome differential gene expression analysis of immune organs, I found that genes involved in both immune and non-immune processes were differentially expressed in the European eel but not the Japanese eel, suggestive of an ineffective and costly immune response in the former. These results are in line with those observed between susceptible and resistant hosts in other vertebrate host-invasive parasite systems. Furthermore, the results support the hypothesis that novel hosts lack an effective immune response. The results also suggest that alteration of non-immune processes contributes substantially higher susceptibilities of novel hosts. In response to the negative fitness effects of invasive parasites, novel hosts can evolve coping mechanisms. The European eel has the capacity to encapsulate and kill A. crassus. Using natural infections, I found a lower abundance of adult A. crassus, the most costly parasitic stage in those eels encapsulating the parasite, suggesting that encapsulation can potentially improve health of infected eels. At the same time, the abundance of two native parasites was higher in those eels encapsulating A. crassus. Thus, coping with A. crassus may come at the expense of coping with native parasites.