Marine Protected Areas (MPAs) have been widely advocated as a tool to protect marine species and habitats and also as a precautionary measure to prevent overfishing. This thesis attempts to do two things: 1) explain the emergence of MPAs in international and national polices by applying three policy network models – the epistemic community, advocacy coalition, and discourse coalition; and 2) discuss the scientific and normative debates surrounding the designation of MPAs in England. In essence it is a critical analysis of how the natural science of MPAs has been produced, interpreted and applied to inform marine planning. The recurring argument throughout this thesis is that advocacy from scientists for MPAs, particularly no-take marine reserves (NMRs) on the basis of their benefits to fisheries, has caused the science-policy boundary to blur. Chapters 3 and 4 examine the social context in which science on MPAs has been produced. Chapter 3 applies social network analysis to study co-author relationships in the MPA literature, and also examines paper citation networks between different research fields. The main findings were that 90% of scientists leading research on MPAs are marine ecologists and that MPA studies dominate the wider marine literature in terms of the number of publications and number of citations. It is speculated that the popularity of MPAs with marine environmental organisations has meant that a disproportionate amount of money has been spent on MPA research compared to other types of marine management intervention. Chapter 4 examines the publication practices of scientists, and also their experiences of having articles rejected in the peer-review process. Ten percent of scientists who responded did indicate that they thought their manuscript had been rejected because of ideological bias (pro-MPA or anti-MPA) held by a peer-reviewer or editor, though no scientists admitted to self- censorship. Interestingly, a bias towards studies showing stronger effect sizes is likely to exist in the wider ecology literature due to the way that research is incentivised and how researchers prioritise their time; it is easier to get larger effect sizes published in higher impact journals, and it takes more time for a researcher to publish non- significant effects in lower impact journals. The ramification of this finding is that claims made by meta-analyses on the ecological effects of MPAs are likely to be exaggerated. Chapter 5 systematically reviewes the literature showing the ecological effects of MPAs. The main finding was that the majority of studies have focused on the measurement of fish biomass within no-take marine reserves (NMRs), and that measurements have been mainly made on fish assemblages residing over reef type habitats. The evidence for the effect of MPAs on the recovery of temperate fin-fish species residing in soft sediment systems is less clear, thus it is problematic if scientists over-generalise claims on the benefits of MPAs, particularly NMRs, to commercial fin- fish fisheries found around England. In chapter 6 key-informant interviews were carried out with leading members of the English policy community to examine competing worldviews on Marine Conservation Zones (MCZs). A discourse analysis was undertaken on the interview transcripts, and also relevant policy literature that has informed the planning of MCZs in England. Two general discourses were identified, one emphasising the establishment of MPA networks driven by ecological theory whose adherents consist mainly of conservationists, and another, whose adherents consist mainly of members of the fishing industry, emphasised the establishment of MPAs on a case-by case basis to protect habitats vulnerable to damage by mobile fishing gears. This study found that debates preceding the introduction of MCZs were heavily influenced by a popular discourse that documented the decline of English marine ecosystems and emphasised the use of MCZs as a fisheries management tool to rebuild fish stocks. This subsequently caused confusion amongst stakeholders over what objectives MCZs are being designated to achieve, and in the confusion, important normative areas of debate such as equity and fairness issues were overlooked. The concluding chapter focuses on the role of the scientist in the policy process, and discusses how the linear transfer of information from scientist to policy maker is undesirable. It argues that scientists need to be more reflexive in how their underlying worldview affects how they conduct their research, and also affects how they interpret the meaning of their research findings for policy makers. The thesis argues that institutions that encourage a two-way dialogue between scientists, managers, fishermen, and wider civil society need to form, thereby increasing the salience, credibility and legitimacy of scientific knowledge for policy.

A central question in evolutionary biology is how do new species evolve? Recent advances stem from studies of ecological speciation, where reproductive isolation among incipient species is promoted by divergent adaptation to local habitats. The cichlid fish Telmatochromis temporalis from Lake Tanganyika has evolved two ecologically distinct ecomorphs that occupy different habitats, with large bodied fish on rock habitat, and small bodied fish on shell-bed habitat. It has been suggested that the diversification of these two ecomorphs has taken place repeatedly and has been driven by ecological processes. In this thesis population genetic and phylogenetic analyses are presented of geographically-distinct populations. The results provide evidence for a repeatedly and independently-derived adaptation from rock to shell bed habitat, consistent with parallel evolution. Demographic expansions of most populations and splitting time estimates indicate that the age of habitat and hence habitat availability is vital in shaping population dynamics and evolutionary trajectories. A series of behavioural studies on wild caught fish demonstrated that body-size dependent competition is a fundamental mechanism that determines habitat use and mediates assortative mating in laboratory conditions. The extent of phenotypic plasticity in ecomorph-specific trait evolution was studied under controlled laboratory conditions on first generation offspring. The results suggest that absolute body size is subject to plasticity in both ecomorphs but size at sexual maturity is strongly heritable, with the shell ecomorph maturing at smaller body size. Overall these findings demonstrate how extrinsic factors and divergent selection continue to shape the evolution of novel phenotypes and genotypes in T. temporalis, despite ongoing genetic exchange between diverging lineages.

Dimethylsulphide (DMS) is a climate-relevant trace gas derived from the algal secondary metabolite dimethylsulphoniopropionate (DMSP). DMS and DMSP have been shown to act as infochemicals (information-conveying chemicals) for a variety of organisms over a wide range of spatial and temporal scales. Grazing by microzooplankton increases the production of DMS, which in turn may act as an infochemical cue to attract carnivorous copepods that preferentially prey on herbivorous microzooplankton. This extra copepod predation on microzooplankton could release excessive grazing pressure on phytoplankton. Such infochemical-mediated multitrophic interactions are poorly understood in pelagic systems, but may be important for the structuring and functioning of marine food webs. Experimenting with several trophic levels of plankton in laboratory microcosms is challenging and, as a result, empirical data confirming the roles of DMS and DMSP in trophic interactions is lacking. Mathematical models provide a suitable tool to gain insight into such complex interactions. The mathematical models analysed in this thesis show DMS-mediated interactions to have a stabilising effect on food web dynamics and to promote the formation of phytoplankton blooms. Food web models with two species of phytoplankton constituting the first trophic level were analysed. The key result of this analysis was that chemoattractants, which increase the susceptibility of the producer to grazing, enhance the persistence of the producing phytoplankton species by attracting carnivorous copepods to consume microzooplankton grazers. Analysis of a Nutrient-Phytoplankton-Microzooplankton-Zooplankton (NPMZ) model showed the ability of phytoplankton to bloom to be a combination of both top-down (DMS-mediated predation) and bottom-up (nutrient limitation) processes. Analysis of a model simulating these interactions in a vertically heterogeneous environment showed foraging through chemodetection to provide fitness benefits to copepods and to enhance copepod persistence. Overall the results presented indicate that infochemicals have important consequences for the dynamics of marine food webs

Phosphorus plays a crucial role in biology, and so microorganisms have developed many ways of obtaining phosphorus including the catabolism of aminoalkylphosphonates. Previous studies have led to a model of phosphonate use only as a phosphorus source by phosphorus starved marine microorganisms. However, a small number of terrestrial bacteria can use specific phosphonates as a carbon or nitrogen source when not phosphorus starved, but this possibility has not been investigated in marine organisms. Enrichment cultures confirmed that phosphonates are bioavailable phosphorus sources for marine bacteria and also that AMPA, 2AEP, OH2AEP and PnAI can support growth as nitrogen sources even in the presence of phosphate. Twelve isolates from these cultures grew using 2AEP as the sole nitrogen source despite exogenous phosphate addition. Cell-free extracts showed that four isolates catabolised PnAcHyde to produce Pi and an aldehyde, characteristic of a PhnX enzyme. The remaining isolates catabolised PnAc to release Pi and acetate, characteristic of a PhnA enzyme. While these enzymes are known to be involved the degradation of 2AEP under phosphorus starvation this is the first demonstration of marine bacteria capable of phosphate-insensitive 2AEP catabolism by these enzymes. Another isolate used OH2AEP and 2AEP as nitrogen sources even with exogenous phosphate addition. OH2AEP degradation enzymes, induced by OH2AEP, produce an aldehyde, Pi and ammonium, consistent with the proposed HpnWX pathway. The aldehyde could not be identified. A collection of inhibition, product and cofactor studies showed that 2AEP catabolism is carried out by an unusual PhnWA pathway. Therefore marine microorganisms can use some aminoalkylphosphonates as nitrogen sources regardless of Pi concentrations, despite the current model of marine phosphonate catabolism excluding this possibility. This is achieved using a mixture of characterised and previously undescribed C-P cleavage pathways. As such we need to reconsider the importance of aminoalkylphosphonates to microbial nutrition and marine biogeochemistry.

The oceanic uptake of anthropogenic CO2 emissions is leading to an alteration of seawater carbonate chemistry, manifested as increasing [H+], falling [CO32-] and a drop in seawater pH. Over the coming centuries this process, termed “ocean acidification”, is expected to negatively impact marine biota, with implications for marine biological and biogeochemical processes. In this thesis, the impact that such changes may have on the net production of a range of climatically- and atmospherically-important marine biogenic trace gases, including halocarbons and dimethyl sulphide (DMS), is assessed through a mesocosm phytoplankton bloom CO2 perturbation experiment, two laboratory CO2 incubation experiments on natural seawater samples, and at a volcanically-acidified shallow marine fieldsite in Italy. Large and significant reductions in DMS and DMSP concentrations under future high CO2 conditions were observed during the mesocosm experiment (mean decreases of 57 percent and 24 percent, respectively), a finding in strong support of a previous study (Avgoustidi 2007). Furthermore, concentrations of iodocarbons showed large decreases, with mean decreases under high CO2 ranging from 59 to 93 percent. Results for the laboratory incubation experiments also showed a reduction in iodocarbon concentrations (when normalised to chlorophyll a) under high CO2. These changes may be the result of shifts in plankton community composition in response to the high CO2 conditions, and/or impacts on dissolved organic matter and the bacterial communities involved in the formation of these compounds. The response of bromocarbons was less clear cut during the experimental studies. Following investigations at a naturally-acidified fieldsite in Italy, it was concluded that this site was a poor natural analogue to the impact of future ocean acidification on marine trace gas production. Taking the results of the mesocosm and laboratory incubations into consideration, a combined decrease in both DMS and iodocarbons in response to ocean acidification may have considerable impacts on future atmospheric chemistry and global climate.

Corals, sessile as adults, disperse by releasing a pelagic larval stage into the water, which drifts with the ocean currents over potentially thousands of kilometres between reef habitats. Determining patterns of dispersal is an important but difficult task for reef conservation science; coral larvae are impossible to track directly in the marine environment. Biophysical models provide an essential tool to explore the patterns and drivers of dispersal. However, they have previously been utilised at regional scales, excluding the potential for long-distance transport events of particular importance to coral biogeography. In light of recent computational advances, I develop the first high-resolution global model of coral larval dispersal. The model provides critical evidence regarding the influence of dispersal on coral biogeography, highlighting vulnerable isolated areas as well as important sources and stepping stones for dispersal. For example, eastern Pacific reefs emerge as some of the most isolated globally. Contrary to hypotheses of increased dispersal into this region during El Nino events, I find only westward dispersal out of the eastern Pacific over a 10 year period, including the extreme 1997-98 El Nino. The Galapagos Islands act as the sole source for dispersal across the 6000 km separating eastern from central Pacific reefs. The model is the first to incorporate the effects of environmental factors (temperature and ocean pH) on larval physiology, predicted to result in alterations to patterns of dispersal with climate change. I find that dispersal patterns are especially sensitive to the effect of temperature on larval mortality, although the response varies geographically. Increases in temperatures predicted for 2060 reduce long-distance dispersal and increase local retention in the model, potentially reducing the scale over which /management efforts will be effective. Future work will aim to incorporate various other factors likely to influence future dispersal, informing management of reefs under climate change.

This study attempts to understand some aspects of ecological invasions from the perspective of consumer-resource interactions. Two successful Ponto-Caspian invaders of Irish lacustrine habitats, Hemimysis anomala and Chelicorophium curvispinum, are considered here. I establish that the invasive H. anomala has a higher per capita functional response towards cladoceran prey than does a native analogue, Mysis salemaai, whether consumption occurs alone, in conspecific groups, or in conspecific groups in the presence of a higher fish predator. In addition, the presence of this higher predator reduces the consumption of cladocerans by the natives, but not by the invaders. In situ experiments designed to track the vertical migrations of both mysids further reveal that the functional response of the invader is both higher and. more variable over diurnal periods than that of the native. Thus, the impacts of invaders - or natives - on prey can depend on per capita effects, how these vary spatiotemporally and modulation by con specifics and predators. Where invaders are potential resources for native species, as is the case with C. curvispinum, I demonstrate how two defensive characteristics - the propensity to construct protective tubes and to associate with complex habitat architecture - can systematically dampen interactions with a range of vertebrate and invertebrate predators. I highlight how associating with habitat architecture collapses predator capture rates across body mass distributions and, using artificial manipulations of habitat architecture, I demonstrate how increases in the availability of predator-free space can reduce the magnitude and alter the shape of predatory functional responses. These findings allude to the importance of defensive characteristics in mediating the persistence of C. curvispinum. Altogether, this work demonstrates: (i) the utility of functional responses as impact assessment tools; (ii) the importance of quantifying both top-down and bottom-up contributions to interactions; and (iii) the need to consider the context in which interactions occur.

This thesis addresses the need to involve all members of society in marine environmental education, policy-making and stakeholder processes. Several strategies are considered. Firstly, marine environmental citizenship and the concept of joint responsibility as a way of enabling people to contribute meaningfully to marine environmental management processes. This incorporates the implementation of programmes that enable adults to participate in local environmental projects and the importance of using skilled volunteers in wildlife recording programmes. Chapter two outlines ‘A Citizens’ Day’ between school pupils and environmentalists that enables participants to take part in debates and environmental planning in real life situations. The thesis examines the effects of links between universities, industries and schools were pupils surveyed a coastal area and made 15 recommendations for its sustainable management which were implemented by industry employees. Intergenerational learning as a means of encouraging transfer of knowledge between generations was tested in depth during one study. The methods proved effective, the majority of the adults in the project claimed that their knowledge of their areas maritime heritage had increased significantly. ‘The Tale of the Herring’ project looked at the concept of sense of place education as a tool for promoting environmental citizenship and connecting young people to their marine environment. The results of the study concluded that this approach did encourage a feeling of belonging and a sense of responsibly for one’s local environs. Global marine citizenship was assessed through International Schools Partnership in Ghana and the UK. Schools carried out independent surveys of local coastal habitats and made recommendations to managers. Despite many differences in their lives, pupils’ recommendations had many similarities. Innovative methods of giving children who have Special Education Needs a voice in marine environmental citizenry were also investigated. The focus had special emphasis on fieldwork, enquiry-based and cross-curricula approaches to learning. Pupils’ believed that their work motivated their interest in science and gave them a sense of pride in their work. Finally the thesis explored the potential use of the creative arts as an effective means of communicating marine environmental messages.

By fixing nutrients into biomass, marine phytoplankton influence ecosystem function, ocean biogeochemical cycles and the earth system. Thus, quantitative representations of phytoplankton activity are essential if we are to understand the current, and project the future, state of the earth . The last century has seen huge advances in the scale of observation, theory and experimentation concerning marine phytoplankton. Yet: large scale projections of earth system processes usually rely heavily on empirical parameterisations. The manner in which individuals, populations and communities adapt to climate change depends on a suite of biological mechanisms that may not be fully accounted for with purely empirical parameterisations. The overarching aim of this thesis is to develop a theoretical modelling framework for the estimation of phytoplankton growth and photosynthesis by accounting for organism adaptation to its environment, and mechanistic biological constraints. The thesis starts with an introduction to the science area (chapter 1) and a review of quantitative systems approaches to ecosystem modelling developed in the second half of the previous century (chapter 2) , with emphasis on representations of phytoplankton growth and photosynthesis. The third chapter presents a model that assumes organisms optimally partition resources to a suite of components involved in resource acquisition and growth, subject to a set of physiological constraints. The model is used to predict the manner in which resources are (re)distributed to suit an environment in which the abiotic conditions do not vary with time. The model is found to be a poor predictor of observed stoichiometry and rates of photosynthesis observed in diatom species thought to occupy more variable environments. In the fourth chapter, the theoretical environment in which hypothetical cells must balance resource allocation is refined to represent more dynamic ocean regimes. Results indicate that resource allocation can differ substantially when organisms are adapted to either a static, or a dynamic environment. Furthermore, comparison with observations from different ocean regimes indicates that the degree of environmental variability profoundly influences the ability of the model to predict plasticity of photosynthesis-irradiance relationships and cellular chlorophyll. The manner in which observed biological rates vary with organism size is of interest to earth systems scientists, in part because sin king of particles to the deep ocean depends on community size distribution. However, reliable represent at ions of the size dependence of growth and photosynthesis have long eluded ecosystem modellers. In the final theory chapter, the model is altered to account for a size related constraint on the capacity to store carbon. Using optimality arguments similar to early chapters, the model is used to generate predictions of growth and photosynthesis of phytoplankton size classes exposed to variable conditions. Results indicate that enhanced storage capacity can raise the daily average growth rate of large phytoplankton in environments that involve prolonged light limitation. Furthermore, optimal resource allocation to components of the cell responsible for carbon fixation can be higher in large organisms with greater storage capacity. Comparison of model predictions of photosynthetic rate in different size classes agree with observations from a eutrophic ecosystem. The overarching conclusions of this thesis are two fold. First, organism adapation to its environment is likely to depend on the degree of spatio-temporal variability in environmental variables, not just daily averaged values. To the best of my knowledge, this has not before been shown in a quantitative framework that links subcellular biological constraints with environmental variability and observations made both in 'vitro and in situ. Second, constraints on carbon storage that in some cases are related to organism size are likely to interact with changes in the environment in a manner that influences the size dependence of biological rates. This may be the first time that carbon storage limitations have been linked with organism growth and photosynthetic rates in variable light environments. The thesis finishes with a discussion of the significance of the results to large scale simulations of ocean biogeochemistry.

Monitoring the response of upper trophic level animals to ecological change is important to understanding the state and stability of ecosystems. Marine predators integrate information over large geographical scales and are relatively long-lived; furthermore, many of these organisms are restricted to terrestrial or freshwater habitats at certain times during their life history and are accessible to researchers. This thesis investigated the response of marine predators to ecological change at a variety of spatial and temporal scales using stable isotope ratio methods with the aims of developing meaningful proxies, or indices, of variability in marine ecosystems. The first study explored the intrinsic (i.e. ontogenetic) and extrinsic (i.e. environmental) factors important to modulating variation in the stable isotope ratios of C and N in tooth dentin of male Antarctic fur seals (Arctocephalus gazella) in the Southern Ocean. In the second study, long-term records of variation in δ15N δ13C values of Atlantic salmon (Salmo salar) scales and grey seal (Halichoerus grypus) tooth dentin provided evidence for large-scale climate forcing across the eastern North Atlantic. In the following study, a more detailed examination of intra- and inter-individual stable isotope variation in Atlantic salmon within a single year was undertaken in an attempt to better understand recent declines in somatic condition of these fish. The last two studies were concerned with the development of high resolution sampling of fish otoliths using secondary mass spectrometry (SIMS) and the application of this technique to reconstructing the thermal and metabolic histories of individual Atlantic salmon from intra-otolith δ13C and δ18O values. Stable isotope proxies can be used to document shifts in trophic dynamics and animal movement that may be associated with ecological change. Using multiple tissues, elements and species, such studies provide unique monitoring tools at a range of spatial and temporal scales.