The interaction between the parasite Trichostrongylus tenuis and food quality was investigated in red grouse Lagopus lagopus scoticus, to determine the cause of variation in population cycles between different areas (Scotland and England). Analysis of long-term data, field experiments and population modelling were carried out. Food quality, in terms of nutrient content of heather, was lower on Scottish grouse moors than on English moors. Parasite burdens were also lower in Scottish grouse populations, than in English grouse populations. A three-way interaction, between food, parasites and area (ScotlandlEngland), acting on breeding production, could explain the variation in population cycle period between areas. However, body condition of grouse was not affected by a food-parasite interaction. Experimental manipulation of food quality and parasite burden did not influence the breeding production of female grouse. Modelling the effects of a food-parasite interaction on grouse populations provided evidence that such an interaction could explain variation in cycle period between areas, although other factors are likely to be important in some cases. Red grouse are not unique, as other species also have cycles driven by food and parasites. Other species do not show cyclic population fluctuations because of having shared parasites, and a strong immune response. There is a specialist predator-prey relationship between red grouse and T. tenuis.

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Host-parasite interactions are extremely important drivers of evolutionary change, characterised by co-evolutionary dynamics with strong reciprocal selective pressure on both host and parasite genomes. However, little is known about the genomic basis of host-parasite interactions, particularly which genes may affect parasite susceptibility, parasite burden and the ability to resolve energetic life-history trade-offs under chronic parasite insult. This thesis examines the genomic, epigenomic and transcriptomic basis of an avian host's physiological response to chronic parasite infection. The model system throughout is the red grouse (Lagopus lagopus scotica) and its main parasite, the gastrointestinal nematode Trichostrongylus tenuis. T. tenuis is highly prevalent and imposes substantial fitness costs that affect demography and population dynamics through an impact on territorial behaviour, energy balance, fecundity and mortality. Here, the genomic architecture of variation in individual T. tenuis burden is examined via de novo identified candidate genes, genome-wide SNPs and genome-wide cytosine methylation polymorphisms. Further, molecular signatures of natural selection in identified genomic regions are examined across a landscape in northeast Scotland with heterogeneous parasite pressure. Finally, the transcriptomic response of red grouse to experimental T. tenuis infection and manipulation of testosterone titre is harnessed to identify a transcriptomic component in testosterone-driven physiological trade-offs in a sexual selection context.

State-space modelling is a powerful tool to study ecological systems. The direct inclusion of uncertainty, unification of models and data, and ability to model unobserved, hidden states increases our knowledge about the environment and provides new ecological insights. I extend the state-space framework to create multi-species models, showing that the ability to model ecosystem interactions is limited only by data availability. State-space models are fit using both Bayesian and Frequentist methods, making them independent of a statistical school of thought. Bayesian approaches can have the advantage in their ability to account for missing data and fit hierarchical structures and models with many parameters to limited data; often the case in ecological studies. I have taken a Bayesian model fitting approach in this thesis. The predator-prey interactions between the hen harrier (Circus cyaneus) and red grouse (Lagopus lagopus scoticus) are used to demonstrate state-space modelling’s capabilities. The harrier data are believed to be known without error, while missing data make the cyclic dynamics of the grouse harder to model. The grouse-harrier interactions are modelled in a multi-species state-space model, rather than including one species as a covariate in the other’s model. Finally, models are included for the harriers’ alternate prey. The single- and multi-species state-space models for the predator-prey interactions provide insight into the species’ management. The models investigate aspects of the species’ behaviour, from the mechanisms behind grouse cycles to what motivates harrier immigration. The inferences drawn from these models are applicable to management, suggesting actions to halt grouse cycles or mitigate the grouse-harrier conflict. Overall, the multi-species models suggest that two popular ideas for grouse-harrier management, diversionary feeding and habitat manipulation to reduce alternate prey densities, will not have the desired effect, and in the case of reducing prey densities, may even increase the harriers’ impact on grouse chicks.

Louping ill virus (LIV) is a tick borne disease that causes mortality in red grouse, an economically important game bird of British uplands. The aim of this thesis is to extend previously published models of LIV , to consider the potential impact of different management strategies. In addition a new route of infection and the seasonal biology of both grouse and ticks will be explored. Grouse chicks are known to eat ticks as part of their diet in the first three weeks of life which may contribute to virus persistence if chicks consume infected ticks. This novel route of infection is incorporated in to the model which predicts that ingestion increases the range of host densities for which the virus is able to persist. The ingestion of ticks by grouse also reduces the tick population so that for low host densities the ingestion of ticks by grouse reduces the tick population so virus cannot persist. The model is adapted to take account of the seasonal biology of grouse and ticks. Although the temporal predictions of the seasonal models show some differences the addition of seasonality does not alter the model predictions of when LIV is likely to persist at different grouse and deer densities. Consequently seasonality is felt to be unimportant when considering management strategies. The treatment of sheep with acaricide in an attempt to reduce the tick population on a grouse moor is currently being trialled in Scotland. We use a model to predict the likely effect of this strategy at different deer densities. The number of ticks found attached to sheep varies so we consider the effect of tick attachment rates as well as acaricide efficacy. Although we predict that acaricide treated sheep can reduce the tick population and therefore LIV in grouse in some circumstances the treatment is less effective in the presence of deer. Consequently we use a model to make theoretical predictions of the effectiveness of acaricide treated deer as a control strategy for reducing LIV in red grouse. The effect of culling deer on LIV in grouse is also modelled and contrasted with the effect of acaricide use. It is predicted that acaricide treatment of deer could be highly effective, particularly if the deer density is first reduced by culling. Finally we considered the direct treatment of red grouse with acaricide. Female grouse can be given an acaricidal leg band which protects her directly and indirectly protects her chicks as they acquire some acaricide whilst brooding. Trials have suggested this can reduce tick burdens for individuals. We use the model to determine the potential effect that treating individual broods may have on the whole grouse population. The model predictions suggest that unless acaricide efficacy on chicks is high and long lasting treating individual broods is unlikely to reduce LIV in the whole population but will still provide some benefit for the individuals. The effectiveness of treatment is reduced by higher deer densities. The success of the management strategies considered in this thesis appear to be restricted by the presence of deer. It may therefore be that a combination of treatments including the treatment of deer may be of the greatest benefit to the grouse population.

From an ecological perspective, knowledge of demographic history is highly valuable because population size fluctuations can be matched to known climatic events, thereby revealing great insight into a species’ reaction to past climate change. This in turn enables us to predict how they might respond to future climate scenarios. Prominently, with the advent of high-throughput sequencing it is now becoming possible to assemble genomes of non-model organisms thereby providing unprecedented resolution to the study of demographic history and speciation. This thesis utilises four species of grouse (Aves, subfamily Tetraoninae) in order to explore the demographic history and speciation within this lineage; the willow grouse, red grouse, rock ptarmigan and the black grouse. I, and my co-authors, begin by reviewing the plethora of methods used to estimate contemporary effective population size (Ne) and demographic history that are available to animal conservation practitioners. We find that their underlying assumptions and necessary input data can bias in their application, and thus we provide a summary of their applicability. I then use the whole genomes of the black grouse, willow grouse and rock ptarmigan to infer their population dynamics within the last million years. I find three dominant periods that shape their demographic history: early Pleistocene cooling (3-0.9 Mya), the mid-Brunhes event (430 kya) and the last glacial period (110-10 kya). I also find strong signals of local population history – recolonization and subdivision events – affecting their demography. In the subsequent study, I explore the grouse dynamics within the last glacial period in more detail by including more distant samples and using ecological modelling to track habitat distribution changes. I further uncover strong signals of local population history, with multiple fringe populations undergoing severe bottlenecks. I also determine that future climate change is expected to drastically constrict the distribution of the studied grouse. Lastly, I use whole genome sequencing to uncover 6 highly differentiated regions, containing 7 genes, hinting at their role in adaptation and speciation in three grouse taxa. I also locate a region of low differentiation, containing the Agouti pigmentation gene, indicating its role in the grouse plumage coloration.