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The prevention and control of infectious disease continues to be a central priority for human public health. Two infectious agents, the bacterium Yersinia pestis and the filarial nematode Onchocerca volvulus have been responsible for significant public health burden in many populations, and challenges remain in the control and prevention of them both. With known environmental and climatic drivers, vector based transmission and in the case of Y. pestis, zoonotic reservoirs, fully characterising the ecological context of both diseases is vital to properly understanding their epidemiology. In the present study, ecological field data is utilised to investigate this, towards improving predictions and designing control strategies. Despite being contrasting infectious agents, the role of spatial scale and resolution are identified to be vital aspects of both investigations. Ultimately, the importance of a holistic approach to infectious disease epidemiology is highlighted across both systems. In humans and some other animals, infection with Yersina pestis causes the disease plague. Although human infections are now limited to the hundreds annually, they disproportionately affect individuals in lower income settings and as such are still of public health concern. A number of wild rodent species tolerant to infection with Y. pestis act as reservoirs for the bacterium, from which it can transmit into less tolerant susceptible populations. To this end, much research has focused on predicting periods of high infection prevalence (epizootic outbreaks) in the reservoir species in order to predict and prevent transmission events into less tolerant populations. One such reservoir species is the great gerbil, Rhombomys opimus, residing across the pre Balkhash desert in Kazakhstan. Y. pestis prevalence in this population is known to be strongly associated with the gerbil population size. The present study aims to resolve current ability to predict the gerbil population. Burrow level environmental properties are identified to be predictors of gerbil presence at, and long term occupancy of burrows. Gerbil occupancy of burrows could not be replicated using standard metapopulation approaches, nor related to the connectivity of the burrow. Atypical strains of Y. pestis lacking the fraction 1 (F1) surface antigen are isolated and found to be common in the gerbil population. This antigen is highly immunogenic and has a role in virulence determinance. However, no significant hetereogeneities in their distribution or associations with epidemiological outputs could be identified. In several African countries with endemic levels of infection with Onchocerca volvulus, an unusually high prevalence of epilepsy has been observed in the population. Here cross sectional data from a population in the Democratic Republic of Congo is used to build a picture of epilepsy prevalence and to explore a possible functional relationship between epilepsy and O. volvulus. The relationship between O. volvulus and epilepsy is strengthened, and spatial and ecological data lead to the suggestion that responsible drivers have local, rather than global relationships with epilepsy.

In urban slums, residents often live in close proximity to reservoirs of zoonotic pathogens. Leptospirosis is a zoonosis that humans can contract via contact with animal reservoirs directly or with water contaminated with their urine. The recent population increase in Salvador, a coastal city in North East Brazil, led to the creation of slums, which are overcrowded and lack basic sanitation. The conditions of the slums favour rodent borne transmission of leptospirosis. The Norway rat (Rattus norvegicus) is asymptomatic and can transmit the infection for the entirety of its life. It is the main reservoir host for leptospirosis in Salvador. Motivated by the annual outbreaks of human leptospirosis in Pau da Lima, an urban slum community in Salvador, the within population infection dynamics of the Norway rat were investigated. A mechanistic model of the dynamics of leptospire infection was developed and explored analytically. A global sensitivity analysis of the basic reproduction number to its components was performed. Using newly obtained age-prevalence data from the field, we sought evidence that would indicate which transmission routes actually occur in the wild. By considering the survival from infection, we created risk curves of infection over time and looked for differences in risk for different demographic factors that were a proxy for transmission. There are some model parameters which we were unable to estimate and some which we expected not to vary by system. To confirm that proposed values of demographic parameters were sufficient to describe population dynamics in wild Norway rats we present a Bayesian analysis of a mathematical population dynamics model. These analyses were used to parameterise an age-structured mechanistic model for leptospire infection in the rodent population. Using the age-structured model, optimal control measures were found that would reduce the total (and infected) rat population. Costs of the controls as well as the cost of human infection were included in the analysis. We conclude that vertical and environmental transmission occurs in the wild, and that environmental transmission is the most important route for the maintenance of infection in Norway rats. To control wild Norway rats, combinations of controls are recommended but environmental control should also be investigated to reduce prevalence of infection in rats.

There is increasing interest regarding the impacts of human activities on the functioning of marine systems. A primary driver of change to marine systems is through the impacts of fishing. Biomass-dominant target species have the potential to mediate a number of ecosystem functions, either directly or indirectly, through the influences that taxa have on ecological processes and/or other biotic or abiotic components of the system. This thesis investigates the roles of the cockle, Cerastoderma edule on ecosystem functioning within intertidal sedimentary systems. A series of investigations revealed that cockles have the potential to mediate benthic primary productivity through their roles in the recycling of nutrients and effects of sediment structure and have impacts upon assemblage biomass and functional diversity. However, the roles of cockles on other aspects of ecological functioning were less apparent. An investigation also assessed the suitability of the use of assigning taxa to functional groups when assessing functional diversity. Taxa were shown to have the potential to change their feeding activity following disturbance, with evidence suggesting a change to benthic-pelagic coupling. This change however, would not have been observed with investigations of functional traits alone and thus supports the use of direct measures of functions to support functional trait diversity measures. It is imperative for ecological investigations to consider long-term changes to population dynamics. However, particularly in marine systems, such data are generally lacking. This thesis presents a novel approach, using information from sea fisheries reports to gain a semi-quantitative 30-year data set on cockle landings within Morecambe Bay, north-west England. This technique revealed evidence of temporal changes to the functional processes at a large scale. This thesis provides evidence for cockles acting as key contributors to ecological functioning. The functional role of cockles is tempered by the high degree of redundancy within these assemblages, highlighting a number of issues relating to the use of field studies and encouraging a move towards increased use of traditional ecology in future studies.