Climate-change has the potential to affect migratory birds by altering prey availability across their annual cycle. Observational and experimental approaches were used to understand the causes and consequences of these changes on the breeding productivity, mass regulation and survival of a wetland bird; the Eurasian reed warbler Acrocephalus scirpaceus. Climatic influences on wetland invertebrate populations were assessed by monitoring natural and experimentally-induced variations in temperature. Further increases in early spring temperatures are likely to result in earlier availability of prey resources. The responses of breeding birds to changes in their prey were tested with food supplementations, which advanced egg-laying dates, reduced the laying interval and incubation duration, and increased nestling growth rate. These effects enable earlier first fledglings and increase the opportunity for second breeding attempts within the peak invertebrate prey window. The consequences of prey availability on wintering body condition were tested by comparing resources and energy reserves in contrasting habitats in West Africa during the non-breeding period. Birds occupying prey-rich habitats maintained lower body reserves than conspecifics occupying prey-poor dry-scrub habitats, consistent with strategic buffering of reserves against starvation in food-poor habitat. These results suggest how reed warblers are able to survive in lower quality habitats and potentially avoid density-dependent mortality associated with drought as observed in other wetland migrants. Analysis of long term (>30 year) weather effects on survival revealed measurable but minor impacts, suggesting reed warblers are very adaptive to environmental change. Overall, this study provides strong support for climate-driven advance in spring invertebrate availability and identifies the reed warbler breeding and survival parameters most affected by increases to prey availability. This study provides an integrated and original understanding of the mechanisms which may underlie current levels of population growth in what appears to be one of the few long-distance migratory European songbird species currently benefiting from climate-change.

The Imperial Dock Lock Special Protection Area (SPA) in Leith Docks on the Firth of Forth currently supports the largest common tern (Sterna hirundo) colony in Scotland. The nest site, a former lock wall in an operational port, was designated as an SPA for the species in 2004 but very little is known about the ecology of common terns in this man-made environment. This thesis examined their ecology using a combination of long-term data for the Firth of Forth region and field research at the colony. The dynamics of the Firth of Forth breeding population of common terns was linked both to local influences of predators and the regional status of their main food source, the Firth of Forth sprat stock. Colonisation of Leith Docks resulted from relocation of birds from natural islands in the Firth of Forth which were abandoned due to unsustainable levels of predation by gulls. Herring gulls (Larus argentatus) and lesser black-backed gulls (L. fuscus) are active predators in Leith Docks but at relatively low levels. Predation attempts by mink present a serious threat and could be highly detrimental to the colony. Foraging studies revealed that terns are feeding primarily in the Forth of Forth rather than within the docks, and that their diet consists mostly of sprat, but also sandeels and gadoids. The importance of sprat in the diet is discussed in relation to the potential reopening of the sprat fishery. Surveys of birds commuting between the colony and the feeding grounds showed that a range of flight lines are used but to different extents, and found no evidence of collisions with buildings or other man-made structures. Terns were well-habituated to regular human activity but were sensitive to unusual or high-level human disturbance factors. Gulls and crows, rather than humans, were the greatest disturbance factors for nesting birds overall. Currently the Imperial Dock Lock SPA is the only site in the region that could support common terns breeding in considerable numbers, and so the future of the Firth of Forth population of common terns is now dependent on this one site. There are a number of management options available, and the future persistence of the population relies on the continued monitoring of breeding numbers of terns, of predation levels and further assessment of the sprat stock.

At the St Kilda archipelago, Outer Hebrides, declines have been recorded in the Leach's Storm-petrel breeding population, the largest in Britain and Ireland, and rapid increases in the population of Great Skuas. Leach's Storm-petrels have frequently been found in the diet of Great Skuas at St Kilda, where storm-petrels are active on land only at night and, unusually, skuas often hunt after dark. Apparent severe skua predation of Leach's Storm-petrels has raised conservation concerns regarding the sustainability of the St Kilda Leach's Storm-petrel population. However, it was recognised that this particular predator-prey relationship is a globally rare phenomenon, had not previously been studied for long at St Kilda (and never elsewhere), and warranted further research before conservation management interventions could be considered. Additionally, research on Leach's Storm-petrels was desirable in its own right, because the species had rarely been studied in the UK, due to its highly pelagic lifestyle and very remote breeding locations. The aim of this study was to increase our understanding of the ecology, behaviour and predator-prey interactions of Great Skuas and Leach's Storm-petrels at St Kilda. Results showed that Great Skua predation of Leach's Storm-petrels was considerable and sustained. Estimated numbers of Leach's Storm-petrels consumed annually by skuas were variable but averaged approximately 21,000 individuals per year. There was strong evidence from storm-petrel ringing and behavioural observations conducted at night that skuas fed predominantly on non-breeding Leach's Storm-petrels, which likely visit the archipelago in very large numbers each year, from huge colonies elsewhere, and probably play and important role in reducing impacts on the breeding population at St Kilda. It was found that Leach's Storm-petrels did not exhibit any specialised counter-predator adaptations to Great Skuas, and were very easily captured at night on the surface of the breeding colonies by skuas on foot. However, prey specialisation by skuas on nocturnally active seabirds (predominantly storm-petrels) did not create fitness advantages over prey specialisation on diurnally active seabirds or fish. Leach's Storm-petrel specialist skua pairs were very few and all pairs exhibited a tendency to feed on a diversity of prey and to switch prey-types between years. Adult and juvenile Leach's Storm-petrels were highly sensitive to light, and artificial light reduction measures in autumn helped prevent storm-petrel attractions and mortality in the village on Hirta. The St Kilda Great Skua population was found to be declining slightly, in contrast to the exponential growth recorded between 1990 and 2000, and Leach's Storm-petrel conservation issues now appear less severe than had been expected.

Conservation of phenotypically variable taxa such as the European whitefish (Coregonus lavaretus) can be particularly challenging. In this thesis it is argued that the recent designation of seven native C. lavaretus populations as three endemic species (C. clupeoides, C. stigmaticus and C. pennantii) by Kottelat & Freyhof (2007) are incorrect and cannot be substantiated with the results presented here. However, evidence for important infra-specific variation between populations has been found. Two native Scottish populations of C. lavaretus show considerable variation in morphology, trophic ecology and life history. The variation in these populations warrants protection, one conservation action becoming more commonly utilised in Britain is conservation translocation. It was found that there were significant differences between source and refuge populations in Scotland. The wisdom of using this conservation measure on a phenotypically plastic organism is discussed. Nevertheless the establishment of further refuge populations are considered to be a viable conservation action. Sub-structuring within the largest native Scottish population of C. lavaretus was not found. However, evidence of residence within certain basins of Loch Lomond was found through significant differences in muscle stable isotope signatures. Investigation was also made into the trophic ecology of other fish in Loch Lomond. It was found that brown trout (Salmo trutta) in Loch Lomond have a non-typical migration pattern and invasive ruffe (Gymnocephalus cernuus) now form an important part of the trophic ecology of this site. In Britain several whitefish populations have been invaded by ruffe, a species native to Britain, but not to these sites. An experiment is conducted into the protective ability against ruffe predation on C. lavaretus ova of substrates typical on spawning grounds. It was found that pebbles and gravel form the best spawning substrate. The impact this mortality may have on the life history of Loch Lomond C. lavaretus is discussed. Using information gathered in this study, recommendations for the management of Coregonus spp. are summerised. There is the potential for these recommendations to apply to other phenotypically plastic species that vary between sites such as Arctic charr (Salvelinus alpinus) and brown trout.

This thesis examines visual anti-predator strategies employed by the Lepidoptera. I examine key aspects of pattern and behaviour and how they relate to the reduction of an individual’s predation risk. Symmetrical patterns have been found to be easier to remember and pick out, suggesting that symmetry is beneficial to aposematic displays. This suggests that symmetry may be maladaptive in cryptic patterning and asymmetry beneficial. In Chapter one, I report the results of a field experiment using artificial prey and wild birds to investigate how asymmetry and symmetry affect the efficiency of cryptic patterning to reduce predation. I found that asymmetry does not affect predation rate, in agreement with previous work. Yet, there is still the problem of how to mesh this with the potentially conflicting conclusions of symmetry studies. Chapter two examines aspects of the intimidation hypotheses of Lepidopteran eyespots. These address the generally larger and more centrally placed spots found on Lepidopteran wings and state that they startle or intimidate predators, providing time for escape. While it is agreed that eyespots intimidate or startle predators, the mechanism has not been agreed. There are two competing lines of thought 1) that ‘eyespots’ intimidate because they resemble the eyes of the predators’ own predators and 2) that it is the conspicuous colouration of the pattern that induces the startle or avoidance behaviour. The first experiment utilised artificial prey with differing ‘directions of gaze’ in a field setting. If purely conspicuous patterns direction of gaze should have no influence on prey survival. The results indicate that patterns imitating staring or upward gazes provide the greatest protection, suggesting that in some cases eyespots may be being perceived as eyes and not simply as conspicuous patterns. I wanted to see if it would be possible to find a way in which to measure or quantify the reaction of an animal to ‘real’ eyes, in order to compare it to the reaction to eyespots. Recent trials investigating human reactions to eye contact suggested a computer based method may be possible. In this second experiment we examined whether the direct gaze of a predator might produce a measurable effect in human subjects. I was not able find any effect, but it is unclear as to whether this is due to problems with the experimental set up. In Chapter three I investigate a factor often over looked in the study of crypsis, that of the behavioural adaptations that can enhance its efficiency. The larvae of the early thorn moth (Selenia dentaria) masquerade as twigs, using both colouration and behaviour adaptations. I compared the angle at which the larvae rested, to the angle at which real twigs deviate from the main stem. The results found that the larvae showed variation in their angle of rest and do not appear to match the angle of real twigs on the host tree. This result suggests that perfectly matching the angles of real twigs is not necessary to twig mimicry. While carrying out this experiment it was noticed that a breeze appeared to increase larval activity and induced a ‘swaying’ behaviour. This led me to examine whether mimic species may utilise the visual ‘noise’ produced by windy conditions to camouflage movement. Firstly, a small ‘proof of concept’ pilot was carried out, followed by a larger study using 2 different twig mimic species. The study involved measuring movement and swaying behaviour in 3 conditions (still air, wind setting 1 and 2). The results suggest that cryptic and mimetic lepidopteran species may use windy conditions to camouflage their movements and that some species may employ specialised ‘swaying’ behaviours. Cryptic species are limited in opportunities to move between foraging sites without increasing detection by predators, therefore, any adaptation that might reduce detection is extremely advantageous. In Chapter four I examine how conspicuousness and colouration are affected by living in a group, particularly in relation to other group members. A field experiment using groups of artificial prey, with differing densities and group sizes was used to explore the effect of group size and density on the predation risk and detectibility of cryptic prey. My results show that, as expected, larger groups are more likely to be detected, but that the increase is much slower than a linear increase. This suggests that groups must increase considerably in size before any individual group member will suffer increased predation risk. The second experiment examines the ‘oddity effect’ and how it affects predation. This hypothesises that when confronted by grouped prey, predators can increase their kill rate by concentrating their efforts on capturing unusual or ‘odd’ prey, a strategy that reduces the ‘confusion effect’. A field experiment was conducted with groups composed of differing proportions of two artificial cryptic prey types. Groups with odd individuals did not suffer an increase in conspicuousness and were not attacked more often. However, once located and attacked the groups did suffer a greater predation rate. Odd individuals were predated at a greater rate than normal individuals and the rate did not change as more or less odd individuals were added to the group. A computer based ‘game’ was used to further investigate the oddity effect. The results from the initial run of the game appeared to show strong evidence for the oddity effect, with a further significant increase in this effect when attention is split between foraging for prey and scanning for predators. To be confident of this result the experiment was repeated with the ‘odd’ and ‘normal’ seed patterns reversed. The new data set strongly suggested that much of the effect seen in the previous experiment was due to a difference in pattern visibility between the two seed patterns. Nevertheless, the results indicated that selecting odd seeds is quicker than selecting normal seeds. The results from both the field and computer trials suggest that preference for odd prey may improve predator foraging speed and efficiency. Chapter five investigates whether cryptic and non-defended prey could reduce their predation risk by grouping with aposematic and defended prey. This was tested using artificial prey in a field setting. My results show that undefended non-aposematic prey can benefit by grouping with aposematic prey with no evidence that predation rates for aposematic prey were adversely affected by this association. If confirmed this might illuminate the origins of Batesian mimicry. I have investigated a range of anti-predator adaptations and strategies in the Lepidoptera and in particular pattern elements and use of crypsis and aposematic displays. These anti-predator strategies are important in that they modify predation rate and so directly influence the evolution of species. While I have been able to provide evidence for some current hypotheses, in many respects my results demonstrate that there is still a lot to learn about visual anti-predatory strategies.

Mussels (Mytilus edulis) are able to bioaccumulatc many chemicals including potential genotoxicants in their soft tissues. Certain genotoxicants damage DNA and other macromolecules via production of reactive oxygen species. Genotoxicants can also interfere with DNA repair processes in the cell. This project examined the potential of such agents to produce oxidative damage in gill of mussels both under laboratory and field exposures. Indigenous mussels from a polluted (New Brighton) and a reference (Llandudno) estuary were collected in 2005-2006 and were examined for DNA damage, lipid peroxidation, glutathione depletion and effects on repair of DNA damage (8-oxo-deoxyguanosine). From the parameters tested, 8-oxodeoxyguanosine levels (assessed using the formamidopyrimidine glycosyJasemodified comet assay) were higher in mussels from the polluted site only during summer whereas repair (cutting) of 8-oxo-deoxyguanosine in DNA was lower in the polluted site at most collection times. Lipid peroxidation varied according to season. Subsequent maintenance of mussels under clean laboratory conditions for one month abolished the differences between sites in most cases for all the parameters. In vivo exposure of mussels to the metals hexavalent chromium and cadmium also verified DNA damage via reactive oxygen species and the suppression of DNA repair mechanisms (towards either 8-oxo-deoxyguanosine or ethenoadenosine) was shown to be a potential contributor to genotoxicity. Overall, mussels were shown to be sensitive to the genotoxic potential of different aquatic pollutants. The study emphasises the need to measure specific oxidative DNA lesions rather than a simple measurement of frank DNA strand breaks and supports the strategy of "recovery" experiments to determine recoverable, field-induced damage to DNA and other macromolecules.

Climate change is altering the phenology of bumblebees in parts of the UK, with worker activity recorded during winter. This presents a unique set of physiological challenges to bumblebees, as they are typically exposed to exclusively summer conditions. The aim of this thesis was to assess the capacity for winter activity and survival in the UK-native bumblebee Bombus terrestris audax (Harris, 1780) (Hymenoptera: Apidae) and the commercially imported B. t. dalmatinus Dalla Torre, 1882 (Hymenoptera: Apidae). Cold tolerance assessments indicated that both subspecies were physiologically ill-adapted to winter temperatures. However, both species were found to undergo Rapid Cold Hardening (RCH); the first evidence of RCH in Hymenoptera. Thermal activity thresholds (CTmin, chill coma and chill coma recovery) were significantly lower in B. t. audax than B. t. dalmatinus. However, only B. t. dalmatinus was able to lower these thresholds as a result of acclimation. This highlights the potential for competition between the subspecies. Field experiments showed a lack of winter-active bumblebees in Birmingham, and an inability of commercial colonies to survive winter. Finally, this thesis presents the first evidence to suggest that sublethal neonicotinoid exposures impair bumblebee activity at low temperatures. Results are discussed in the light of climate change, pesticide use and the bumblebee pollinators in future climate scenarios.

Understanding what environmental factors influence species’ responses is crucial for adequate conservation management and prediction of responses to climate change. My study focused on a widespread aquatic migratory bird in Brazil; the Black Skimmer (Rynchops niger). Throughout the thesis I investigated the reliability of using photographs, citizen data, and visual observation to assess biological data such as moult score, occurrence, and identification of sexes. I also used stable isotopes and counts to assess changes in Black Skimmer’s resource use and abundance according to ENSO. I found photographs can be used to score moult in primary feathers, and that sexes in this species can be identified by visual observation from skins and photographs with Black Skimmer males being significantly larger than females. Using citizen photographs from nature enthusiasts web platforms, I found Black Skimmers moult during austral spring to summer in Brazil. Individuals select areas mostly in southern and southeastern Brazil to perform moult. Both sub-species (Amazonian and South American Black Skimmers) and sexes in Brazil selected estuaries while moulting yet coastal built-up areas could also be used. The South American Black Skimmers also selected more dunes and less mudflats than the Amazonian ones. There were differences in timing or duration of moult between sub-species or sexes with males taking more time and starting to moult earlier than females. I found Black Skimmers changed resource and had a higher diet input from estuarine habitats during the El Niño. Not only the foraging use during moult changed but also the abundance. The number of individuals overstaging (staying longer at the non-breeding site during the breeding season) at the study site was higher during the El Niño and lower during the La Niña than in regular years. Abundance was higher during eastern and northern winds but negatively affected by an interaction of temperature and ENSO. This study provided affordable non-invasive methods to studies in ornithology, fulfilled gaps in Black Skimmer’s life-history annual cycle, and was one of the first studies addressing how ENSO affects aquatic species in the South American Atlantic coast. Lessons learned from this study might underpin more effective conservation plans.

Despite that the life histories of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) are very well studied, there are still gaps in our knowledge which have consequences for management and conservation of these species. This is of particular importance now that wild populations of Atlantic salmon and anadromous brown trout are decreasing throughout their distribution range. This thesis aims to address some of these gaps in knowledge in life stage specific habitat use and mortality of these two species by bringing together five separate studies. Regular assessment of stock size is one of the most important aspects of fisheries management. Electrofishing techniques are widely used for the estimation of the size of stream dwelling fish populations for both fishery management and scientific study. In contrast to multiple pass, population depletion methods, single pass catch-per-unit-effort (CPUE) methods are less time consuming and labour intensive. A possible issue with the commonly used, fixed total time CPUE protocol is that it does not differentiate between the time spent actively fishing and the time incurred while not actively fishing, leading to handling error which is likely related to fish density. This was tested in a comparative field study. I showed that this commonly used technique is systematically underestimating juvenile salmonid numbers at higher densities. In addition this technique is failing to adequately determine fish community structure at low population densities. This work indicates a simple modification to the methodology that will reduce systematic error. Knowledge of the species’ biology and habitat requirements can be linked with habitat data to create a model that predicts the distribution of that species. As salmonids, such as Atlantic salmon, have fairly strict habitat requirements, knowledge of habitat use by salmon can then be used to estimate the potential salmonid production in a given area of certain quality. The accuracy of a habitat grading system currently used by the Loughs Agency was tested. The results suggest that in its current format, the habitat grading system does not accurately describe the abundance of juvenile salmonids. When data was analysed to see which habitat variables best described salmonid density, for 0+ salmon important variables were flow and substrate and for older juveniles the important variables were flow, substrate, depth and percentage of undercut banks. All populations are controlled by density-dependent and density –independent factors. For a species such as Atlantic salmon that has life stages differing in habitat requirements, the relative contributions of these two factors for population regulation on each life stage are likely to vary. Using a long-term data-set on Atlantic salmon migrants returning to the Foyle catchment, Ireland, the role of density-dependent and life-stage specific environmental factors regulating population size was determined. A Ricker density-dependent model showed that the spawning adult population size significantly predicted variation in the resultant filial generation, however a large amount of variation remained unexplained. It was shown that environmental factors were significant in explaining some of the remaining variance and that these influences were linked to specific life stages. Three life stages – spawning and incubation, fry emergence, and marine survival – were shown to be sensitive to environmental effects resulting in changes to the returning cohort strength. It is concluded that these life stage specific environmental effects are likely to contribute to the stochastic variation in population size resulting from the application of traditional stock-recruitment models. Atlantic salmon undertake extensive migrations between freshwater and marine habitats. Smolt migration is associated with high mortality and is thus considered a critical life stage in the Atlantic salmon life history. Smolt migration through standing waters is still mostly an unknown process and it is not known what guides migration during lake migration. Using acoustic telemetry, three hypotheses derived from known principles of migration in rivers were tested: i.) smolts will take the shortest possible route, ii.) smolts will display unidirectional movement and iii.) smolts will be continuously moving. None of these three expectations were supported by the results of this study. Instead evidence was found of smolts moving in a seemingly random fashion, displaying counter intuitive migration patterns and spending relatively long periods effectively static during their lake migration. Brown trout display a great range of life history variation ranging from river residency to anadromy. Unlike Atlantic salmon that migrate hundreds of kilometres to the open ocean to feed, anadromous brown trout often stay within 80-100 km from their natal river in coastal areas. Despite this, very little is still known about their behaviour during this coastal feeding part of the life cycle. It was found that brown trout in the Clyde estuary use a fairly small part of the estuary and seem to move fairly actively. Fish size did not explain any of the movement or residency patterns. The five separate studies presented in this thesis combine field empirical studies from rivers, lakes and the coastal marine environments and historical data analysis studies on two salmonid species. The results presented in this thesis provide tools for managers of anadromous salmonids.

Collective movements are ubiquitous in biological systems, occurring at all scales; from the sub-organismal movements of groups of cells, to the far-ranging movements of bird flocks and herds of large herbivores. Movement patterns at these vastly different scales often exhibit surprisingly similar patterns, suggesting that mathematically similar mechanisms may drive collective movements across many systems. The aims of this study were three-fold. First, to develop mechanistic movement models capable of producing the observed wealth of spatial patterns. Second, to tailor statistical inference approaches to these models that are capable of identifying drivers of collective movement that could be applied to a wide range of study systems. Third, to validate the approaches by fitting the mechanistic models to data from diverse biological systems. These study systems included two small-scale in vitro cellular systems, involving movement of groups of human melanoma cells and Dictyostelium discoideum (slime mould) cells, and a third much larger-scale system, involving wildebeest in the Serengeti ecosystem. I developed a series of mechanistic movement models, based on advection-diffusion partial differential equations and integro-differential equations, that describe changes in the spatio-temporal distribution of the study population as a consequence of various movement drivers, including environmental gradients, environmental depletion, social behaviour, and spatial and temporal heterogeneity in the response of the individuals to these drivers. I also developed a number of approaches to statistical inference (comprising both parameter estimation and model comparison) for these models that ranged from frequentist, to pseudo-Bayesian, to fully Bayesian. These inference approaches also varied in whether they required numerical solutions of the models, or whether the need for numerical solutions was bypassed by using gradient matching methods. The inference methods were specifically designed to be effective in the face of the many difficulties presented by advection-diffusion models, particularly high computational costs and instabilities in numerical model solutions, which have previously prevented these models from being fitted to data. It was also necessary for these inference methods to be able to cope with data of different qualities; the cellular data provided accurate information on the locations of all individuals through time, while the wildebeest data consisted of coarse ordinal abundance categories on a spatial grid at monthly intervals. By applying the developed models and inference methods to data from each study system, I drew a number of conclusions about the mechanisms driving movement in these systems. In all three systems, for example, there was evidence of a saturating response to an environmental gradient in a resource or chemical attractant that the individuals could deplete locally. I also found evidence of temporal dependence in the movement parameters for all systems. This indicates that the simplifying assumption that behaviour is constant, which has been made by many previous studies that have modelled movement, is unlikely to be justified. Differences between the systems were also demonstrated, such as overcrowding affecting the movements of melanoma and wildebeest, but not Dictyostelium, and wildebeest having a much greater range of perception than cells, and thus being able to respond to environmental conditions tens of kilometres away. The toolbox of methods developed in this thesis could be applied to increase understanding of the mechanisms underlying collective movement in a wide range of systems. In their current form, these methods are capable of producing very close matches between models and data for our simple cell systems, and also produce a relatively good model fit in the more complex wildebeest system, where there is, however, still some room for improvement. While more work is required to make the models generalisable to all taxa, particularly through the addition of memory-driven movement, inter-individual differences in behaviour, and more complex social dynamics, the advection-diffusion modelling framework is flexible enough for these additional behaviours to be incorporated in the future. A greater understanding of what drives collective movements in different systems could allow management of these movements to prevent the collapse of important migrations, control pest species, or prevent the spread of cancer.