1. Rivers are highly structured ecosystems in which habitat complexity and heterogeneity are postulated to affect species diversity and abundance. However, the exact links between habitat structure and organisms such as macro-invertebrates remain poorly understood. 2. Field surveys at the patch and reach scale were combined with a field experiment in the Rivers Wye and Usk, Wales, to: i) quantify variations in habitat complexity and heterogeneity among habitats and river sections, ii) assess their influence on macro-invertebrates, iii) separate the ecological effects of confounding physical factors and iv) determine whether habitat type and heterogeneity promote nestedness of assemblages. 3. At the patch scale, surface complexity but not habitat heterogeneity increased macro-invertebrate diversity, richness and abundance independently of surface area, but only when habitat type was ignored. Surface complexity and heterogeneity were minor determinants of variations in macro-invertebrates among habitat types. 4. A field experiment involving baskets containing cobbles, pebbles, gravel or 50:50 mixtures revealed that flow type explained significant variations in macro-invertebrate richness, abundance and composition, and appeared to filter organisms based on their body size. Surface complexity and interstitial volume had no ecological effect, implying that differences in assemblages among mineral habitats may result from flow-related effects. 5. Macro-invertebrate assemblages occurring in some mineral habitats, typically with lower macro-invertebrate diversity, richness, abundance and trait diversity, appeared to be nested sub-sets of those occurring in some organic habitats. Nested assemblages had reduced trait diversity and altered trait representation. River sections containing fewer habitats supported assemblages of lower abundance, which appeared to be weakly nested sub-sets of those in heterogeneous sections. 6. Habitat complexity and heterogeneity are concluded to have consistently weak effects on macro-invertebrates at the scales studied. In contrast, habitat type and flow type affected macro-invertebrate assemblage composition, structure, and traits, with important implications for river management and conservation.

Avian eggshell colouration fulfills multiple adaptive functions, including egg camouflage. The potential role of the two main eggshell pigments in oxidative stress, biliverdin and protoporphyrin, may be behind a relationship between female immunocompetence and eggshell pigment investment strategies. In this study, environmental conditions were manipulated during different life cycle stages, via a variety of methods, including food-restriction and stress hormone exposure in female Japanese quails (Coturnix coturnix japonica), in order to experimentally test the condition-dependence of eggshell pigmentation, and to give first insights into the possible implications for egg crypsis. I demonstrated that eggshell pigmentation strategy is not only affected by female current body condition, but is also shaped by its early life experience such as exposure to stress, and that eggshell colouration is a key factor involved in egg crypsis in Japanese quail. Eggshell colour and maculation were both independently affected by breeding conditions; which stresses the complexity of the relationship between eggshell pigment concentrations and its appearance. My findings imply that eggshell appearance is a female extended phenotypic trait, and that trade-offs between eggshell pigmentation and immune-functions may lead to inter-females differences in their ability to maximise egg crypsis.

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.

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).

A study into the role of secreted CLIC3 in tumour cell invasion The initiation and progression of cancers is thought to be linked to their relationship with a population of activated fibroblasts, which are associated with tumours. I have used an organotypic approach, in which plugs of collagen I are preconditioned with fibroblastic cells, to characterise the mechanisms through which carcinoma-associated fibroblasts (CAFs) influence the invasive behaviour of tumour cells. I have found that immortalised cancer-associated fibroblasts (iCAFs) support increased invasiveness of cancer cells, and that this is associated with the ability of CAFs to increase the fibrillar collagen content of the extracellular matrix (ECM). To gain mechanistic insight into this phenomenon, an in-depth SILAC-based mass proteomic analysis was conducted, which allowed quantitative comparison of the proteomes of iCAFs and immortalised normal fibroblast (iNFs) controls. Chloride Intracellular Channel Protein 3 (CLIC3) was one of the most significantly upregulated components of the iCAF proteome. Knockdown of CLIC3 in iCAFs reduced the ability of these cells to remodel the ECM and to support tumour cell invasion through organotypic plugs. A series of experiments, including proteomic analysis of cell culture medium that had been preconditioned by iCAFs, indicated that CLIC3 itself was a component of the iCAF secretome that was responsible for the ability of iCAFs to drive tumour cell invasiveness. Moreover, addition of soluble recombinant CLIC3 (rCLIC3) was sufficient to drive the extension of invasive pseudopods in cancer cell lines, and to promote disruption of the basement membrane in a 3D in vitro model of the ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC) transition. My investigation into the mechanism through which extracellular CLIC3 drives tumour cell invasiveness led me to focus on the relationship between CLIC3 and the ECM modifying enzyme, transglutaminase-2 (TG2). Through this, I have found that TG2 physically associates with CLIC3 and that TG2 is necessary for CLIC3 to drive tumour cell invasiveness. These data identifying CLIC3 as a key pro-invasive factor, which is secreted by CAFs, provides an unprecedented mechanism through which the stroma may drive cancer progression.

Farmland birds in Europe have declined as agriculture has intensified, with granivorous specialists disproportionately affected. Despite grassland based farming being widespread, farmland bird research to date has focussed on mixed and arable farms. Yellowhammers are a red-listed species in the UK. This study investigated year round habitat requirements, diet, and movements of yellowhammers at four grassland dominated farms in Ayrshire, Scotland. Data were obtained via field surveys and trials, radio-tracking and faecal analysis. Fine scale breeding season foraging habitat requirements were studied by comparing invertebrate and vegetation communities at foraging sites with paired controls across all four farms. A small scale winter supplementary feeding trial was conducted on one farm. Breeding yellowhammers were distributed throughout the study sites; average density was low at 0.11 pairs per hectare (range 0.06 to 0.15), half the densities reported in arable and mixed regions. Yellowhammers preferentially foraged within 10m of field margins. Grassland summer foraging sites contained significantly higher invertebrate diversity and more large invertebrates than control sites. Faecal analysis revealed that adults ate significantly more cereal than nestlings, with both including more invertebrate material than observed in previous studies. Diptera, Coleoptera and Araneae were key orders, with Lepidoptera larvae additionally important for nestlings. A low proportion of cereal was found in nestling diet, suggesting that the invertebrate dominated diet provided was of high quality. In contrast to summer diet, and despite grassland being the dominant habitat, cereal dominated winter diet; grass seeds and invertebrates accounted for <1% of diet in winter. Winter yellowhammer density at each farm was positively correlated with stubble availability. Radio-tracking found yellowhammers significantly selected stubble in early winter and game managed habitat in late winter. Supplementary feeding attracted an estimated 247 to 267 yellowhammers at a site where the previous year’s winter surveys recorded only 5 birds despite holding a good breeding population. Survival rates of 1st years at the supplementary fed site appeared higher than elsewhere in the landscape, and a small increase in breeding density was observed post feeding. As winter progressed, the use of the grain provided increased, suggesting that the late winter period was the most crucial time for the birds regarding food supply. Providing supplementary food represents a cheap and easy solution that could be utilised by agri-environment schemes to tackle late winter farmland bird food shortages. Alternatively, increasing winter stubble in grassland dominated regions should provide additional biodiversity benefits associated with increased landscape heterogeneity as well as increased winter food availability. This study highlights differences in breeding density, habitat selection, movements and diet of yellowhammers on grassland farms compared to arable and mixed farm populations. Restricted winter stubble habitat limits winter food availability, and hence the likely overall size of the population able to subsist in this habitat.

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.