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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.

Rocky shore microphytobenthic biofilms are areas of high biodiversity, and are protected under UK and European Union legislation. Despite this, little is known about the photophysiology of these biofilms. This study aimed to provide a new contribution to microphytobenthic research with the addition of photophysiological knowledge focussing on the rocky intertidal to add to the extensive photophysiological research which has focussed on mudflats. More specifically the photoregulatory mechanisms of rocky shore biofilms had not been studied prior to this work. This study aimed to determine the effects of ambient environmental conditions, community structure and grazing on the photophysiology of the biofilms and elucidate the complex relationships between the abiotic and biotic factors which influence the biofilm. The community structure of the biofilm changed seasonally, with larger species (> 40 μm valve length and > 25 μm diameter) such as Parlibellus delognei being dominant during the winter months (December, January and February) and smaller ones (<40 μm valve length and < 25 μm diameter) such as Navicula bottnica during the spring months (March, April and May) indicating an environmental influence on the community structure of the biofilm. The biofilms were found to die-off (biomass below detection levels) in April and May and grow back in the November and December during a ‘reproductive phase’. An observed photophysiological ‘seasonality’ was primarily the result of the timing of the‘reproductive phase’ of the biofilm, with higher maximum relative electron transport rates (rETRmax) being recorded during November and December (on average 85 compared to 60 relative units), when these biofilms were growing after the spring die-off. High temperature and light dose had a negative effect on the rETRmax, particularly for biofilms on the upper shore sites. It was concluded that the combination of increased temperature and light dose, reducing rETRmax, and so productivity, and increased grazing contributed significantly to the spring dieoff with cells unable to replicate rapidly enough to compensate for increased grazing. By exposing biofilms to different temperatures ex-situ it was found that the lower shore biofilms ii were more resilient to high (> 25 °C) and low (< 10 °C) temperature with a smaller reduction in rETRmax, and ΔF/Fm’ observed in comparison to upper shore. Temperature was found to induce movement in the tube-forming upper shore species Navicula bottnica. This was likely to act as a secondary photoregulation strategy as it was found that high temperatures resulted in a reduced ability to induce non-photochemical quenching (NPQ). Biofilms were also treated with Latrunculin A (LAT-A) and DL- Dithiothreitol (DTT) in situ, and by comparing the photosynthetic patterns of response over an exposure period it was found that the upper shore biofilms utilised NPQ as the primary means of photoregulation whereas the lower shore biofilms utilised cell movement as the primary photoregulatory mechanisms. The upper and lower shore biofilms also utilised secondary mechanisms, migration in the upper shore samples, and NPQ in the lower shore samples, of downregulation, which allowed the cells to persist on the rocky shore where the rapid changes in environmental conditions result in a high stress environment. The overarching conclusion from this study is that rocky shore biofilms utilise a combination of photoregulatory mechanisms dependent upon life form in order to survive in an environment where many rapidly changing biotic and abiotic factors affect the community structure and photosynthesis of the biofilms.

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.

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.

The leishmaniases are neglected tropical diseases with an urgent need for effective drugs. Better understanding of the metabolism of the causative parasites will hopefully lead to development of new compounds targeted at critical points of the parasite’s biochemical pathways. In my work I focused on the pentose phosphate pathway of Leishmania, specifically on transketolase, sugar utilisation, and comparison between insect and mammalian infective stages of the parasites. The pentose phosphate pathway (PPP) is the major cellular source of NADPH, an agent critical for oxidative stress defence. The PPP uses glucose, reduces the NADP+ cofactor and produces various sugar phosphates by mutual interconversions. One of the enzymes involved in this latter part is transketolase (TKT). A Leishmania mexicana cell line deleted in transketolase (Δtkt) was assessed regarding viability, sensitivity to a range of drugs, changes in metabolism, and infectivity. The Δtkt cell line had no obvious growth defect in the promastigote stage, but it was more sensitive to an oxidative stress inducing agent and most of the drugs tested. Most importantly, the Δtkt cells were not infective to mice, establishing TKT as a new potential drug target. Metabolomic analyses revealed multiple changes as a consequence of TKT deletion. Levels of the PPP intermediates upstream of TKT increased substantially, and were diverted into additional reactions. The perturbation triggered further changes in metabolism, resembling the ‘stringent metabolic response’ of amastigotes. The Δtkt cells consumed less glucose and glycolytic intermediates were decreased indicating a decrease in flux, and metabolic end products were diminished in production. The decrease in glycolysis was possibly caused by inhibition of fructose-1,6-bisphosphate aldolase by accumulation of the PPP intermediates 6-phosphogluconate and ribose 5-phosphate. The TCA cycle was fuelled by alternative carbon sources, most likely amino acids, instead of glucose. It remains unclear why deletion of TKT is lethal for amastigotes, increased sensitivity to oxidative stress or drop in mannogen levels may contribute, but no definite conclusions can be made. TKT localisation indicated interesting trends too. The WT enzyme is present in the cytosol and glycosomes, whereas a mutant version, truncated by ten amino acids, but retaining a C-terminal targeting sequence, localised solely to glycosomes. Surprisingly, cells expressing purely cytosolic or glycosomal TKT did not have different phenotypes regarding growth, oxidative stress sensitivity or any detected changes in metabolism. Hence, control of the subcellular localisation remains unclear as well as its function. However, these data are in agreement with the presumed semipermeable nature of the glycosome. Further, L. mexicana promastigote cultures were grown in media with different combinations of labelled glucose and ribose and their incorporation into metabolism was followed. Glucose was the preferred carbon source, but when not available, it could be fully replaced with ribose. I also compared metabolic profiles from splenic amastigotes, axenic amastigotes and promastigotes of L. donovani. Metabolomic analysis revealed a substantial drop in amino acids and other indications coherent with a stringent metabolic response in amastigotes. Despite some notable differences, axenic and splenic amastigotes demonstrated fairly similar results both regarding the total metabolic profile and specific metabolites of interest.

The Earth’s climate is changing at an unprecedented rate due to increasing use of fossil fuels and widespread deforestation. This means that the concentration of atmospheric carbon dioxide is increasing, elevating mean global temperatures. In addition, the oceans act as a huge carbon sink and are absorbing more carbon dioxide than they have in the last 650, 000 years causing the oceans to become more acidic. At the beginning of this study the guidelines stated that the control pCO2 concentration for laboratory studies should be 380 µatm (Meehl et al., 2007), concordant with the then current atmospheric pCO2. Four years later, the most recent literature reports that current concentrations of atmospheric pCO2 have now risen to 400 µatm (IPCC, 2013). This demonstrates the unprecedented speed at which our climate is changing and highlights the urgency for research into the potential implications that this change may have on marine systems. In many coastal marine systems calcifying organisms construct biogenic formations that can underpin the ecosystem and form biodiversity hotspots. Calcifying algae and cold water corals are two such organisms. These habitats are economically, politically and socially important. However our knowledge of how these keystone marine organisms may respond in the future is still ambiguous. In general marine calcifiers are likely to be negatively affected, although within some taxa there is considerable variability in their response during climate change studies (e.g. coralline algae and corals). Furthermore, natural variability will overlay the environmental changes associated with anthropogenic global climate change, and as such is likely to significantly influence the response of marine biota to the projected environmental changes. Currently, there are few studies that consider global climate change in the context of natural variability and/ or run long enough to assess acclimatisation potential. Thus, this research aims to provide a better understanding of the impact global climate change may have on key marine calcifiers in the context of natural variability and acclimatisation. This was achieved through a number of laboratory- and field-based studies, utilising well established and adapted techniques. This research focused primarily on red coralline algae. Projected changes in seawater carbonate chemistry mean that marine organisms that utilise dissolved inorganic carbon species as a substrate for multiple physiological processes (i.e. photosynthesis and calcification) are likely to be amongst those most greatly impacted by environmental change. Chapter 3 is the longest laboratory study (24 months), to date, investigating the effects of global climate change on a marine calcifier. Results suggest that seasonal variability in environmental conditions will greatly impact the response of coralline algae to elevated temperature and pCO2. In addition, while calcification may be maintained or increase in response to elevated temperature and/ or pCO2 (chapter 3 and 5) and despite evidence of acclimatisation potential, overall growth was significantly hampered by elevated temperature in the long term. This supports the hypothesis that dissolution may in fact be the primary threat to marine calcifiers, as opposed to impaired calcification. Irradiance is key in coralline algal photosynthesis yet the role of light availability on mediating coralline algal responses to multiple stressors remains scant. The present study examined net photosynthesis and photosynthetic characteristics in the free-living coralline algae, Lithothamnion glaciale in response to sub-diel changes in irradiance in algae exposed to elevated temperature and pCO2 (chapter 4). Observations suggest that light availability will mediate the response of coralline algae to global climate change in the future, as optimal light for photosynthesis increases with increasing temperature and pCO2 (chapter 3, 4 and 5). Cold-water corals make up some of the most heterogeneous, biologically diverse, three-dimensional ecosystems known in the deep sea. However, due to the difficulty in accessing these habitats, to date there is little information about how these organisms may respond to global climate change. The present study provides evidence of intraspecific variability in the response of cold water corals to global climate change that may be dependent upon their prior environmental experience (chapter 7). In situ acclimatisation to variable and low pH may provide cold water corals with the physiological flexibility to acclimatise and adapt to global climate change in the future. Evidence of intraspecific differences in physiology and morphology were also observed in situ in the brown partially calcifying alga, Padina gymnospora between algae located on the reef crest and more environmentally variable reef flat (chapter 6).

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.