Worldwide, bats are in decline with populations under threat from many pressures, including habitat loss, disease and climate change. A detailed understanding of bat social structure and population dynamics is needed to understand and tackle this decline. Yet despite bats representing around twenty percent of all mammalian diversity, they are underrepresented in life history studies, restricting our understanding of social associations, spatial patterns and mating systems for many species. This, in turn, inhibits efforts to conserve species and restricts interpretation of their population dynamics. This study, therefore, aimed to analyse the ecology of social structure and population dynamics using long-term ringing data from several British bat species: Natterer’s bats (Myotis nattereri), brown long-eared bats (Plecotus auritus), Pipistrellus spp. (P. pipistrellus and P. pygmaeus) and Bechstein’s bats (Myotis bechsteinii). Analysis of long-term data of M. nattereri and P. auritus revealed that bats maintain long-term associations persisting over several years. Spatial patterns revealed high fidelity to roost sites. However, on occasions when bats were disturbed during ringing, their dispersal patterns suggested that bats possess a wide knowledge of alternative roost sites which may facilitate relocation following habitat or climate change. Analysis of population dynamics and social structure of three sympatric species (M. nattereri, P. auritus and Pipistrellus spp.) revealed that social systems vary between species and seasons. Large roosting groups were reported for M. nattereri and P. auritus. Males were found to roost with females both pre- and post-parturition, however populations were female-biased for both species. Solitary male Pipistrellus spp. found pre-parturition were joined by an influx of predominantly new adult females for the formation of mating groups post-parturition. There was no preference for roosting in boxes facing North, South-east or South-west for any species. Roosting groups of M. nattereri persisted from pre- to post-parturition whilst the abundance of P. auritus found in boxes post-parturition was low, suggesting alternative roosting behaviour for this species post-parturition perhaps due to increased activity at swarming sites. Increasing population trends were reported for M. nattereri and Pipistrellus spp. whereas the pre-parturition population of P. auritus showed a moderate decline, the cause of which requires further investigation. Survival analysis revealed female-biased survival rates for M. nattereri and P. auritus. Cohort variation in juvenile survival was found in female M. bechsteinii whereby high rainfall during the lactation period and an additive effect of high population density resulted in lower survival. Age of first reproduction varied between one and five years for this species, but did not vary between cohorts with the majority of females reproducing for the first time aged two years. Furthermore, an ecophysiological field study revealed no effect of social structure or roost microclimate on the metabolic rates of free-ranging M. nattereri. However, low metabolic rates indicated torpor was frequently used both pre-and post-parturition. The results of this study suggest that future studies on population biology should take an integrated approach incorporating aspects of both ecology and ecophysiology for the conservation of a species, especially in the face of climate change.

Understanding physiological processes is key to answering the questions of why organisms behave in the way they do, and how they interact with each other, and their environment. Despite technological innovations in recent decades, assessment of physiological state in free-living animals still generally requires subjects to be trapped and handled, so tissues or blood can be sampled, or so measurement devices can be attached or implanted. Such methods limit research to species and individuals that can be caught, potentially restricting the generalisability of findings, and introducing bias. Additionally, natural behaviours are interrupted, and subsequent physiology, behaviour or performance may be altered as a result of the stress of capture, the burden of attached apparatus, or the effects of surgery. Consequently, alternative techniques such as inferring physiological state from traits that do not require invasive sampling would be a valuable development. Body temperature is a particularly promising candidate trait, linked with an array of physiological functions, and having previously been used as a proxy for metabolic activity, stress state and immune challenge. With the advent of low cost, highly portable thermal imaging cameras, physiological ecologists are now presented with unprecedented opportunities to measure body surface temperature non-invasively, and at high frequencies from free-living animals. In this thesis, I investigated relationships between body surface temperatures, measured using thermal imaging from free-living blue tits or captive zebra finches, with physiological measures or situations relevant to the assessment of physiological state. I developed reliable thermal imaging techniques to take non-invasive measurements of body surface temperatures in a variety of contexts, allowing characterisation of physiological responses in real time. My studies of captive birds revealed that activity levels influence body surface temperatures measured from free moving animals, and so should be accounted for in experimental designs. I also successfully acquired body surface temperatures from overwintering blue tits visiting food-baited traps, and from breeding blue tits entering and leaving their nest. Using this data, I showed that body surface temperature exhibits a characteristic response to acute stress, which differs with stressor type. While the mechanisms require explanation, much potentially useful information appears to be stored within body surface temperature dynamics during acute stress. Additionally, I established links between body surface temperature and longer term physiological processes in free-living blue tits. I observed near identical correlations between body surface temperature and body condition across differing seasons and life history stages. Also, I found evidence suggesting both that repeated acute stressors (predation risk and human disturbance) had a chronic effect on body condition breeding blue tits, and that surface temperature in those birds was linked to body condition. If confirmed, these results would be particularly interesting in a conservation physiology context, as it may prove possible to detect a signal of persistent physiological effect(s) relating to human disturbance, non-invasively. Furthermore, my discovery of a further correlation between baseline plasma glucocorticoids and body surface temperature in overwintering birds implies links with the hypothalamic-pituitary-adrenal axis. All of these results combined suggest that body surface temperatures measured using thermal imaging are highly likely to prove useful in determining aspects of physiological state non-invasively from free-living animals. While further investigation and validations are necessary, this work has laid the foundations for an exciting new methodology that could help solve many questions that remain unanswerable using current techniques.

Global biodiversity is under threat from multiple fronts. The Millennium Ecosystem Assessment predicts that climate change (CC) will be the “dominant direct driver of biodiversity loss” by the end of the 21st century. This project studies the impact of CC on the distribution and conservation status of antelopes found in Africa. Africa is an area of high climate variability and high vulnerability to CC, and most of the world’s antelope species are native to the continent. Various threats are already causing the decline in 63% of antelope species with 26% being classified as threatened. Antelopes are a speciose and biologically diverse group and therefore provide an ideal opportunity to reveal more general patterns of the effect of CC across taxa. To assess the impact of climate change on Africa’s antelopes I use species distribution models (SDMs), based on climatic variables, to produce ensemble predictions of species distributions for 2080. Using the SDMs I also establish links between biological traits and the optimal climatic conditions for species. The ensemble predictions incorporate three climate models for three climate scenarios, and I predict the future distributions using three approaches. The first is a pessimistic representation of species’ distributions in a future where they are unable to disperse from their current range to track CC. The second, optimistic approach, permits species to disperse at a given rate based on body mass. Finally, the envelope approach presents a comparison of suitable climatic conditions, which are connected to the existing distribution, between now and the end of the century (i.e. not restricted by current distribution or dispersal). The results indicate that 81-85% of species (59-62 of 73) will exhibit a contraction in range based on suitable climatic conditions, and that the average contraction of those species is 39.4-50.1%. Up to six of 73 species are predicted to be without any climatically suitable areas in 2080 depending on the modelling and forecasting approach taken. Worryingly, there is also a disproportionate reduction in the predicted distribution of threatened antelope, whereas species with broader climatic niche and a preference for warmer temperatures typically perform better. Using Marxan conservation planning software, I produce protected area network solutions that protect Africa’s antelopes based on their predicted distributions in 2080. High and low protection options are presented which require 8.7 and 8.1% respectively of Africa’s land mass in order to protect Africa’s antelopes. These solutions, that are based around the existing IUCN protected area network (categories I-VI), reveal key new areas are required in Somalia, while expansion of existing protected areas (PAs) are required continent-wide, particularly in Liberia, Cameroon, Kenya, Tanzania, and the Central African Republic. I also find that the contribution of community led PAs, and other non-IUCN PAs, to these solutions is currently limited, but in some areas they play an important role in bridging gaps between existing IUCN PAs. Finally, 14 species are either identified to qualify as threatened due to climate change based on IUCN Red List criteria, or can be considered threatened due to having no protected area coverage within their predicted range in 2080. Based on predicted species distributions under the A1B climate scenario, the hirola (Beatragus hunteri) and Aders’ duiker (Cephalophus adersi) have no suitable climatic conditions within, or connected to, their existing range in 2080. However, for all species, climatically suitable conditions are present in Africa in the future, and protected areas are found within those regions. For the species most at risk I provide recommendations for translocation options taking into account the potential for interspecific competition by assessing the number of novel antelope species and interspecific niche overlap in the climatically suitable areas.

A breeding population of Redshanks was studied by trapping adults at the nest and individually marking them, over a period of nine years, on part of the extensive Ribble saltmarshes. Other aspects of breeding biology were investigated over three years. The capture-recapture analysis of the breeding adults revealed an overall annual survival rate, of both sexes, of 0.77, and a population of approximately 200 pairs in 1.04km? Mate fidelity was very high, with 71% of surviving pairs remaining faithful. Nest site fidelity was extremely strong for faithful pairs and males with new mates, but significantly weaker for females with new mates. A lower nest site fidelity of young birds was regarded as a major contributing factor to their lower recapture rates. The timing of both the onset and ending of the breeding seasons varied greatly, and was determined mainly by the rainfall. High rainfall delayed onset and hastened ending of breeding. Mithin a breeding season the older birds bred throughout, while the young ones were mostly not able to breed early. The substantial losses of nests due to cattle grazing on the marsh (45%) could easily be controlled by preventing the access of cattle to the main breeding area until after the end of the nesting season. Nest predation was rare (less than 4%) in most years, but increased in a year of short vegetation (to 25%). The production of pulli was estimated under varying environmental influences and ranged from 0.73 to 2.28 pulli. pair": The variation of egg size within the population was investigated and the significant influences of laying order (within a clutch) and maternal size demonstrated. Pullus size at hatching was positively correlated with egg size and also with maternal size. The growth and development of pulli were described for weight, bill length, tarsus length and postnatal moult. For three days after hatching the weight remained below the hatching value and then rapidly increased, whereas the bill and tarsus showed a linear increase in length A tentative model of the population dynamics was produced, despite the lack of good estimates of pre- and post-fledging mortality. This model indicated a high pre-fledging mortality of 0.67 and also further highlighted the impact on the population of cattle grazing during the nesting season.

This study develops a fractographic method to diagnose hammerstone- and carnivore induced fracture. This is important because interpretations of hominin entry into the carnivore guild and evolution of meat-eating are based on rare tool and tooth marks in Oldowan (2.5-1.8mya) fossil assemblages. Consequently, estimating hominin and carnivore involvement is difficult, and questions remain about Oldowan hominin’s position in the carnivore guild and socioecology. One aspect of bone damage, fracture surfaces, is ubiquitous, but largely unstudied. The fractographic (study of fracture surfaces) method is based on fracture principals, particularly how differences in static- and impact-loading affect material response and fracture features resulting from loading extremes. The method is applied to analysis of fracture features in a) the Amboseli Hyaena Den assemblage, b) an experimental hammerstone-broken assemblage, c) a Plio-Pleistocene assemblage previously interpreted as a carnivore accumulation, FLK-NN2 (Olduvai Gorge), and d) the zooarchaeological assemblage from FLK-Zinj, (Olduvai Gorge). This is the first zooarchaeological/taphonomic study to demonstrate that a) static and impact fracture differ fundamentally in applied load size and material responses to loading extremes, b) impact-forces are significantly greater than the maximum carnivore bite-force, c) cones, incipient flakes, radiating cracks, and lateral stress features are characteristic of impact fracture, and e) Oldowan hominins at FLK-Zinj were responsible for breakage of 54% of the limb assemblage (a 37% – 40% increase over estimates based on percussion marks). The socioecological implications of the habitual transport of food from death and/or kill sites to secondary locations are explored by examining reasons why social carnivores transport food. Aspects of modern carnivore behaviour suggest general mammalian constraints that may have predicated food transport by early Homo. Early Homo food transport behaviour was structured by anti-predator defense strategies associated with a) foraging in an open habitat rich with competing predators, b) the lack of masticatory and digestive apparatus to quickly consume animal tissue, and c) the presence of altricial young in the hominin group.

Infectious diseases pose a significant threat to animal and human health across the globe, with much of the burden falling on low-income countries. Despite efforts to control many of these diseases, very few have ever been eradicated. Their dynamics are often embedded in complex, heterogeneous landscapes defined by interacting population and landscape level processes. As such, landscape heterogeneity plays a key role in driving disease transmission and persistence. Incorporating landscape heterogeneity in studies of pathogen dynamics is challenging but the accessibility of data, particularly next generation sequencing data, has opened new avenues of research. Landscape epidemiology involves using an integrated approach to understand spatial patterns of disease, using methods that combine landscape genetics, ecology and epidemiology. in this thesis I use these integrative methods to determine the underlying mechanisms facilitating the spread and persistence of canine rabies virus in Tanzania. Whole genome level characterisation of rabies virus samples was achieved and used in combination with cutting-edge inference techniques to explore spatial patterns of rabies at different spatial scales. Phylogeographic patterns were able to characterise spatial scales of endemic rabies transmission in Tanzania, uncovering strong viral population structure at sub-continental levels with evidence of a more fluid dispersal dynamic at local ( less than 100km2 area) spatial scales . Within-country phylogeographic patterns revealed large regional movements within Tanzania that could be attributed to human-mediated movements and revealed the presence of multiple co-circulating lineages within a single administrative district. Finely resolved incidence data from the Serengeti District complemented with whole genome sequences enabled the exploration of local scales of transmission in more detail. By extending phylogeographic diffusion models to incorporate landscape heterogeneity I was able to uncover evidence supporting landscape predictors of rabies diffusion. While much of the spatial structure was attributable to the effects of isolation by distance, landscape predictors had discernible effects on diffusion. In particular, rivers appeared to act as a barrier to dispersal and road networks facilitated diffusion and I found evidence to support vaccination as an effective control measure for canine rabies in the Serengeti District. Importantly, I also found evidence to support vaccination as resistance to diffusion and therefore an effective control measure for dog rabies. As a complementary approach a space-time-genetic algorithm was used to determine who-infected-whom in the Serengeti District. The model explicitly accounted for the possibility of exogenous sources of infection and how to incorporate genetic data available for only a proportion of samples. Direct transmission events were estimated between 42% of observed cases and highlighted the co-circulation of two major lineages in both time and space. Direct transmission events predominantly occurred over very small distances, less than 1km, but a large proportion of cases had unobserved sources that could represent transmission from dogs in neighbouring regions or larger indirect transmission events. A future development of the model is to delineate between these possibilities to assess the true contribution of exogenous sources to the system dynamic. Ultimately these integrative models are at an early stage of development but highlight the power of genetic data to delineate fine-scale transmission patterns. The results from this thesis suggest that landscape features such as rivers could be exploited as barriers in step-wise vaccination campaigns and highlight the utility of genetic surveillance to monitor control and elimination as rabies management progresses.

The research presented here constitutes the latest advances in the use of the Antarctic bivalve mollusc Aequiyoldia eightsii as a sclerochronological proxy for Antarctic coastal waters. A. eightsii has the potential to provide annually-resolved records for the Antarctic shallow waters beyond the beginning of the instrumental record. A comprehensive study of A. eightsii shell growth was carried out, which highlighted two ontogenetic trends: i) negative exponential and ii) a quasi-cyclic trend of a period of nine years, which may relate to allocation of energetic resources. Using crossmatching techniques, four chronologies from adjacent locations near Rothera Station (West Antarctic Peninsula, WAP) and an additional chronology from historical samples collected near Signy Station (South Orkney Islands, SOIs) were developed. Additionally further work on a pre-existing chronology from the SOIs is presented. Instrumental records and climatic indices were analysed to determine environmental variability and the factors controlling shell growth. Seawater temperature and fast-ice duration seem to be the main environmental drivers of A. eightsii shell growth. Shell growth of South Cove (WAP) specimens seem to better reflect to environmental conditions recorded in the Rothera Biological Time Series. Stable oxygen and carbon isotope (δ18O and δ13C) records were developed from shell carbonate material; these showed sub- and inter-annual variability and all specimens showed similar trends in δ18Oshell and δ13Cshell, with the exception of a deep-collected specimen of the SOIs, which showed much reduced interannual variability and a stronger δ13Cshell negative trend with ontogenetic age. Additionally, stable isotope fractionation depending anatomical part of the shell (anterior, ventral and posterior) was studied, which showed intra-increment variability in δ18Oshell and δ13Cshell. The present work constitutes a comprehensive calibration of A. eightsii as a sclerochronological proxy for Antarctic shallow coastal waters, which will help to expand our understanding of climate trends in the region.

Assessment of disease status in fish is used as an indicator of the biological effects of contaminants in the marine environment. At some UK offshore sites the prevalence of liver tumours in Limanda limanda (dab) exceeds 20%. However, the molecular mechanisms of tumour formation and the causative agents are not known. The contribution of epigenetic mechanisms, although well-established in human tumourigenesis, is under-studied in tumours of aquatic species. In this thesis, alteration in the DNA methylation patterns in tumours of two fish species, the model species zebrafish (Danio rerio) and the un-sequenced marine flatfish dab, were investigated. The data presented provided a comprehensive characterisation of DNA methylation pattern in zebrafish liver and the first evidence of alterations in DNA methylation profiles of key genes in tumourigenesis pathways in any aquatic species. A statistically significant lower level of global DNA methylation was demonstrated in hepatocellular adenoma (HCA) and non-cancerous surrounding liver tissue (ST) compared to liver of non-cancer bearing dab. The evidence presented in this thesis suggests that chronic exposure to a mixture of pollutants contribute to global DNA hypomethylation followed by further epigenetic and genomic changes, leading to the development of tumours in dab. These findings suggest a link between the environment, epigenome and cancer in fish tumours in the wild.

Phenotypic differences within a species significantly contribute to the variation we see among plants and animals. Plasticity as a concept helps us to understand some of this variation. Phenotypic plasticity plays a significant role in multiple ecological and evolutionary processes. Because plasticity can be driven by the environment it is more likely to produce beneficial alternative phenotypes than rare and often deleterious genetic mutations. Furthermore, differences in phenotypes that arise in response to the environment can affect multiple individuals from the same population (or entire populations) simultaneously and are therefore of greater evolutionary significance. This allows similar, beneficial alternative phenotypes to increase quickly within a single generation and allow new environments to produce and select for new phenotypes instantly. The direction of the present thesis is to increase our understanding of how phenotypic plasticity, coupled with contrasting environmental conditions, can produce alternative phenotypes within a population. Plasticity provides a source of variation for natural selection to act upon, and may lead to genetic isolation as a by-product. For example, there are multiple cases of polymorphic populations of fish, where groups belonging to multiple isolated gene pools, have arisen in sympatry. Here it is shown that although plasticity is important in sympatric speciation events, plasticity alone is not responsible for the frequency in which sympatric polymorphic populations occur. The most frequently observed differences among sympatric polymorphic populations are morphological differences associated with parts of the anatomy used in the detection, handling and capture of prey. Moreover, it is shown here that there are physiological effects associated with foraging on alternative prey that may significantly contribute towards ecological speciation. It is also shown in this study that anthropogenic abiotic factors can disrupt developmental processes during early ontogeny, significantly influencing morphology, and therefore having ecological consequences. Phenotypic structuring in postglacial fish is most frequently based around a divergence towards either pelagic or littoral benthic foraging specialisms. Divergences that deviate from this pattern are of greater scientific interest as they increase our understanding of how evolutionary processes and selection pressures work. Here we describe a rare divergence not based around the typical pelagic/littoral benthic foraging specialisms. Finally, in this study, the effectiveness of local level conservation policy shows that species of fish which are highly variable in their life history strategies are harder to effectively manage and often poorly represented at a local level.

Predators can have both direct and indirect effects on how their prey interact with parasites. This thesis explores these effects using observational and experimental approaches. A behavioural experiment suggested that the direct effects of predators are size- and sex-biased, with small and male guppies, Poecilia reticulata Peters 1859, more prone to Gyrodactylus turnbulli Harris 1986 parasite-induced vulnerability to predation (Chapter 2). Trait-mediated indirect effects of predators also appear important to this host-parasite interaction, as revealed by surveys of natural Trinidadian populations under different predation regimes. First, predator-driven life history evolution predicts an apparent population divergence in parasite tolerance (Chapter 3). Similar divergence in a second trait, social behaviour, may drive sex- and age-biased parasitism: the guppies most liable to shoal have the highest infection probability (Chapter 4). Social behaviour is thus an important driver of parasite transmission, but how parasites affect social interactions remains poorly understood. The second part of this thesis investigates how guppies may use sensory information to mitigate this cost of sociality. Many fishes rely on chemical and visual information and the interaction between sensory modalities to behave appropriately; for example, chemical cues change how guppies respond to visual cues (Chapter 5). In a social context, guppies use both chemical and visual cues to detect infection in conspecifics, but only avoid those in the later stages of infection (Chapter 6). Infection avoidance behaviour is not innate, but likely results from juvenile guppies imprinting on cues of conspecifics, and associating with these cues in adulthood (Chapter 7). This imprinting-mediated avoidance appears to be adaptive: a transmission experiment showed that the onset of avoidance behaviour coincides with the stage of infection at which conspecifics are most infectious (Chapter 8). The sensory ecology of the host and the community in which it lives therefore have important implications for disease dynamics.