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In the early 20th century, coffee wilt disease devastated coffee farms across Africa, with catastrophic impacts on production and farmers: millions of dollars were lost, the major coffee variety Coffea excelsa failed commercially, and widespread farm closures occurred. Improved sanitation measures and plant breeding programmes in the 1950s briefly overcame the effects of this first disease outbreak, but just two decades later a second prolific epidemic attacked robusta coffee (C. canephora robusta) in Uganda, Tanzania and the Democratic Republic of Congo. Separately, a third epidemic affected arabica coffee (C. arabica) in Ethiopia. Coffee wilt disease is caused by Fusarium xylarioides, a soil-borne fungal pathogen that induces vascular wilt on coffee trees. Little is understood about coffee wilt disease and F. xylarioides compared with other Fusarium plant pathogens although they all have a similar propensity to cause devastating crop and economic losses. Over the past century, coffee wilt disease is the most significant disease to have affected coffee production, and has caused over US$1 billion in losses to national economies in central Africa. This thesis explores the use of living fungal strains preserved in culture collections to elucidate the evolutionary past of a major disease outbreak. The history of coffee wilt disease highlights the risk of disease re-emergence, and the importance of rapid strategic action in response to outbreaks. The knowledge held in culture collections around the world could help prepare us better for managing future outbreaks. The first experimental chapter of this thesis (chapter two) used genome sequencing of six historical culture collection strains spanning 52 years to identify the evolutionary processes behind repeated outbreaks of coffee wilt disease. Phylogenomic reconstructions and a screen for putative effector genes showed that the host-specific F. xylarioides groups have diverged in gene content and sequence mainly by vertical processes within lineages, and through expansion of certain carbohydrate-active enzyme families. A subset of putative effector genes, however, showed evidence for horizontal acquisition and close homology to genes from F. oxysporum. Subsequently, the next chapter (chapter three) added seven more historic F. xylar- ioides genomes and a long-read sequenced reference genome to test the F. xylarioides host-specific groups found in chapter two and the nature of the putative horizontal transfer. Four genetically differentiated populations were present: arabica, robusta and two populations amongst the strains isolated in the 1950s from the initial 1920s-1950s outbreak. In addition, six other Fusarium strains were sequenced from amongst species that are also found on coffee wilt diseased trees: five F. oxysporum strains and one F. solani. Analyses showed evidence for multiple horizontal transfers of over 20 kilobase long regions between the F. oxysporum mobile chromosomes and the F. xylarioides populations. In addition, F. xylarioides is enriched with miniature impala transposons that are found in F. oxysporum and linked with the horizontal transfer of pathogenicity. These results indicate that horizontal gene transfer occurred repeatedly in the F. xylarioides clade and could be one of the drivers behind the repeated emergence of coffee wilt disease during the last century via the transfer of gene- and repeat-rich genomic regions. The final experimental chapter (chapter four) investigates whether any genes highlighted in the previous chapters were expressed in arabica F. xylarioides strains infecting arabica coffee host plants. RNA sequence data reveals major up-regulation of pectin lyase enzymes, suggesting a key role for them in the onset of vascular wilt infection. It also revealed up-regulation of three F. oxysporum secreted in xylem (SIX ) effectors, which are all less than 1 kilobase from miniature impala transposons. This, combined with the close phylogenetic relationship with F. oxysporum for a subset of several hundred up-regulated genes, highlights the potential role of horizontal gene transfers in the spread of pathogenicity between F. oxysporum and F. xylarioides in shared vascular wilt infections. These results demonstrate how comparative genomics and transcriptomics of historic strains can reveal mechanisms that allow fungal pathogens to keep pace with our efforts to control them. Knowledge of horizontal transfer mechanisms and putative donor taxa could help to design future intercropping strategies that minimize the risk of new and emerging pathogens via effector gene transfers between closely related Fusarium taxa. Open Access

Road traffic is a significant emission source of urban particulate matter (PM). Due to the implementation of exhaust regulatory standards in the UK, PM emissions which arise from the wear of brakes, tyres and the road surface, together with the resuspension of road dust are now predicted to exceed tailpipe emissions. While a growing body of academic literature has developed in recent years, non-exhaust emissions (NEE) remain unregulated and largely understudied, and the impact of powertrain electrification on the vehicle fleet has not been quantified. Thus, the aim of this thesis is to improve our understanding of these important emission sources and to determine the impact of NEE on urban air pollution - both now, and in the future. A series of highly time-resolved atmospheric measurement campaigns has been undertaken at roadside and background locations to determine roadside traffic increments. These measurements provide a comprehensive dataset of traffic emissions in London, Birmingham and Manchester, incorporating locations with different vehicle mix and speed, during summer and winter periods. PM mass and elemental tracers have been used to estimate the contribution of NEE concentrations using a scaling factor approach. A novel CO2 dilution approach has been undertaken to determine average fleet emission factors (EFs), whilst the impact of electric vehicle regenerative braking has also been simulated. The results indicate that NEE concentrations and EFs are highly dependent upon meteorological conditions, traffic speed, traffic volume and vehicle class. Brake wear is the dominant source of road traffic PM emissions in congested environments, whilst for each emission source, heavy duty vehicles (HDVs) contribute an order of magnitude greater than light duty vehicles (LDVs). On the other hand, despite the predicted increase in mass, the regenerative braking simulations suggest that passenger vehicles under electric powertrains will reduce brake wear emissions by 65 – 95%. This reduction depends on the assessed drive cycle and vehicle class, highlighting the importance of driving style on future brake wear emissions. The EFs developed in this thesis have been combined with traffic forecasts to project total national emissions in the UK up to 2035 – and can be used to validate the national atmospheric emission inventory. To conclude, a number of recommendations have been made with respect to air quality measurement strategies and emission policies which are needed to further our understanding of NEE, and to reduce these traffic-related emissions. It is proposed that a multi-disciplinary study should be undertaken encompassing laboratory dynamometer testing, on-vehicle measurements and environmental atmospheric measurements. Open Access

Despite developments in renewable electricity production, space heating and hot-water provision still account for a high proportion of the total greenhouse gas emissions in the world. Decarbonising heating requires an in-depth understanding of the candidate technology options. Should investments in energy systems focus on large-scale/centralised options, or small-scale/distributed ones? How should end-users operate their heating systems to maximise economic and environmental benefits? Should manufacturers design high-performance yet high-cost technologies and reduce the transition cost to the wider electricity system infrastructure, or should they promote more affordable, lower-performance end-use alternatives at a cost to the wider system? In this thesis, technoeconomic models that capture the cost and performance characteristics of heating technologies are developed and used to analyse the design and operation of competing solutions from the perspectives of different stakeholders. An extensive analysis of commercially available air-source and ground-source heat pumps, combined heat and power systems, district heating infrastructure and thermal energy storage systems on the UK market is first conducted. Fitting techniques are used to determine relationships arising from the collected data and quantify the related uncertainty in technology characteristics between the data and fitted relationships. Then, thermodynamic and component-costing models are developed for technologies for which there is a substantial spread in the available data, or for which data are not available. These include electricity- and hydrogen-driven heat pumps and involve dedicated compressor efficiency maps, heat exchanger models, and equipment-costing methods. The resulting technoeconomic models are first used to assess the economic and environmental performance of different centralised and distributed low-carbon heat provision pathways, with a London district as a case study. Centralised gas-fired combined heat and power systems are found to be favourable in terms of annual total cost. However, in recent years, the carbon footprint of grid electricity has reduced significantly, meaning that heat pumps installed at household or community level achieve a higher degree of decarbonisation. Furthermore, an uncertainty propagation analysis reveals the significance of properly accounting for technology performance and cost variations when modelling energy systems. In fact, the use of technoeconomic models is shown to reduce the uncertainty in the results by more than 75% compared to the use of black-box approaches. Two different optimisation studies are then conducted to investigate smart operation strategies of heating technologies in the domestic and commercial sectors. First, thermal network models of a domestic electric heat pump coupled to a hot-water cylinder or to two phase-change material thermal stores are developed and used to optimise heat pump operation for different objective functions. As demonstrated, smart heat pump operation can lead to a decrease in operational costs of more than 20% and an increase in self-sufficiency by up to four times. For the commercial sector, a multi-objective control framework is designed and installed on an existing combined heat and power system that provides heat and electricity to a supermarket. By using a stochastic optimisation approach and considering the uncertainty related to the price of exporting electricity, energy savings higher than 35% can be achieved compared to using a typical gas boiler. The integration of technoeconomic models of technologies within whole-energy system models can be used to extend the capabilities of the latter, so that they can, apart from optimising network infrastructures, provide explicit information about future technology design. Thermodynamic and component-costing models of a domestic electric heat pump, a hydrogen boiler and a hydrogen-driven absorption heat pump, as well an existing whole-energy system model of the UK, are used to compare electrification and hydrogen pathways for the domestic sector. The technologies are compared for different weather conditions and fuel-price scenarios, first from a homeowner’s and then from a whole-energy system perspective. It is shown that, in the UK, hydrogen technologies can be economically favourable only if hydrogen is supplied to domestic end-users at a price below half of the electricity price. From a whole-energy system perspective, electric heat pumps are the least-cost decarbonisation pathway under the investigated scenarios. Lastly, this thesis includes an effort to demonstrate how different component choices when designing domestic electric heat pumps can influence the national energy generation mix and heat-decarbonisation transition cost. Using the developed electric heat pump model, a set of optimal heat pump configurations representing competing components is obtained. The size of heat exchangers and the choice of compressor type and working fluid are shown to have a remarkable influence on the technology’s performance and cost. These configurations are integrated into an existing whole-energy system capacity-expansion and unit-dispatch model, to show that, from a UK energy system perspective, although high-performance heat pumps enable a reduction in the required installed electricity generation capacity by up to 50 GW, low-to-medium performance heat pumps can lead to a reduction of more than 10% in the total system transition cost and end-user investment requirements. Open Access

Sexual conflict arises when the fitness interests of males and females diverge, leading to genes and traits that have antagonistic fitness effects across the sexes. This thesis uses theoretical models to examine the causes and consequences of such conflict, focusing on the roles of population ecology and genetic architecture in shap- ing evolutionary responses to sex-specific selection. Chapter 1 investigates the demographic consequences of selection on males to harm or harass females in order to improve their own mating success. It shows that such male harassment traits readily evolve condition-dependence, whereby individuals in good condition, or of high genetic quality, express more harm. Consequently, intensified sexual conflict can lead high-condition populations to show reduced population size and greater extinction risk, contrary to the commonly held view that individual condition is positively correlated with population viability. Chapter 2 concerns the segregation of sexually antagonistic alleles, genetic variants beneficial to one sex but harmful to the other, in spatially subdivided populations. It shows that a species’ dispersal pattern modulates the evolutionary dynamics of such alleles due to the effects of kin selection. Thus, dispersal ecology can determine which sex is better adapted to its environment, and how much genetic variation is maintained in populations. Finally, Chapter 3 asks how frequently sexually antagonistic alleles arise from sex-specific selection on complex traits (those encoded by many interacting loci). It investigates how antagonism may be resolved through expression modifiers, showing that variation in genetic architecture (such as the number and distribution of fitness effects across trait loci) favours different patterns of sex-specific versus sex-limited gene expression, and that this can drive outbreeding depression in dispersal-limited populations. Together, the chapters of this thesis demonstrate that aspects of trait genetic architecture and a species’ population ecology that have been underappreciated in previous theory, are relevant to the outcomes of sexual conflict. Open Access

Due to the essential role of zoonotic hosts, zoonotic spillover results from a complex system of environmentally-driven ecological and epidemiological processes. Despite being a global public health concern, zoonotic disease epidemiology is rarely viewed through the lens of disease ecology, meaning that the ecological factors driving zoonotic disease risk are typically not quantified. In this thesis I develop mathematical models to understand the zoonotic disease system from a process-based perspective informed by ecology, dependent on environmental variables, and tested using human health data. I focus these methods on a case study of Lassa fever which has historically been a neglected zoonosis but now may have improved opportunities for disease mitigation and surveillance. I present an overview of the topic in Chapter 1, outlining the challenges in zoonotic disease modelling and management. In Chapter 2, I find evidence of a severity bias in Lassa fever case data and estimate that infection incidence is likely on a much greater scale than previously thought. To elucidate environmental and ecological drivers of the Lassa virus system, in Chapter 3 I quantify the climatic dependence of reservoir host demographic processes. Along with strong seasonality, I estimate that year-on-year changes in precipitation can lead to substantial changes in the reservoir host population. In Chapter 4, I extend this population model to include pathogen transmission dynamics. Applying this model to states in Nigeria and linking reservoir host virus dynamics to observed human cases, I find that patterns of Lassa fever are significantly and positively correlated with predicted prevalence of infectious reservoir hosts. Finally, in Chapter 5 I summarise the findings and discuss future directions for the management and mitigation of zoonotic disease, concluding that ecological process-based modelling – facilitated by increased integration of knowledge, methods, and data – is essential for understanding zoonotic disease systems. Open Access

The elemental geochemistry of sediments is studied to understand a wide range of topics in the Earth sciences, e.g., the evolution of the continents, the history of the carbon cycle, and the location of mineral deposits. A challenge underlying all these applications is that sedimentary compositions are affected by a wide range of geochemical processes such as weathering, sorting, and mixing. These competing processes make it hard to extract useful signals from a sediment's elemental geochemistry. In this dissertation I will develop two predictive and invertible models for the elemental composition of a sediment. The first model describes a fine-grained sediment in terms of the composition of its protolith and the intensity of weathering it has experienced. A novel benefit of this model is that it can `unweather' the composition of a sediment to reveal the theoretical protolith from which it derived. Using this unique approach I deduce the composition of the Archean continents from a large compilation of sedimentary rock compositions. I find the Archean exposed continents to be more silica rich than previously considered, comparable to the present day continents. The second model I develop describes fluvial sediments as a conservative mixture of the geochemistry of the sediments in their upstream drainage basin. This model is tested using a uniquely high-resolution geochemical survey covering the Cairngorms, UK, along with 67 new downstream sediment samples gathered for this dissertation. I demonstrate that the composition of these downstream sediments can be reasonably predicted assuming just conservative mixing of the upstream survey dataset. Given the success of this mixing model, I proceeed to invert it. That is, I develop a model to unmix fluvial sediments to generate a geochemical map of their source regions. I find that this unmixing model, when applied to the downstream dataset, generates upstream predictions that compare favourably to the independent survey dataset. The success of both these models suggest that sedimentary elemental chemistry, when considered on appropriate scales, is largely deterministic. Open Access

In order to transition energy use away from fossil fuels, the transformation of renewable lignocellulosic biomass needs to be improved and its supply of sustainable bioenergy into a wider bioeconomy increased. Achieving this will require: (1) renewable, cheap and high-quality lignocellulosic feedstocks, (2) a robust process to transform this feedstock into bioenergy and finally (3) a system to recover and use this bioenergy as well as value-added products. In this PhD, multiple examples were used to explore unconventional feedstocks, novel transformation processes and opportunities for value-added products. Feedstocks ranging from invasive species threatening the UK environment, Rhododendron and Japanese Knotweed (Chapter 3), metal contaminated waste wood (Chapter 4), metal enriched biomass grown on marginal land (Chapter 5), and wastewater irrigated willow, a leading dedicated bioenergy crop (Chapter 6). While conventional bioenergy systems often burn wood pellets for energy co-generation, the innovative transformation process of ionic liquid-based technologies are explored as flexible enough to fractionate unconventional biomass feedstocks and deliver high yields of sustainable bioenergy and bioproducts. This was allowed by the unique and tuneable properties of protic ionic liquids. Here dimethylbutyl-hydrogen sulphate - [DMBA][HSO4], a cheap hydrogen sulphate [HSO4]- based ionic liquid, and 1-methylimidazolium chloride - [C1Him][Cl], were used in the ionic-liquid based ionoSolv process. Key efficiency parameters such as temperature, reaction time, biomass to solvent loading and solvent recycling, were explored. The process was also challenged with the presence of diverse metal contamination to determine the potential to extract the metals and produce a fermentable pulp and lignin in parallel. Bioenergy recovery from the ionoSolv process was explored as well as the potential to recover multiple value-added products. In addition to determination of heating values of isolated lignin as well as hydrolysis and fermentation yields of cellulose rich pulps into bioethanol, interactions of contaminating metals and their impact on yeast fermentation yields were investigated. This investigation highlights the benefits of [C1Him][Cl] ionic liquid pretreatment for the production of clean bioenergy and bioproducts from highly contaminated feedstocks. As an important property of ionic liquids is that they can act as media for electrochemical reactions, electrodeposition of metals from ionic liquid liquor, metal extraction efficiencies and any detrimental interactions with ionic liquid recycling were assessed. To further diversify system outputs beyond bioenergy alone, production of bio-oils, char and gases from pyrolysis of post-hydrolysis residue was determined, as well as the possibility for recovery of phytochemicals as potential complementary value-added products. This research highlights that unconventional feedstocks have the potential to support a developing bioeconomy and that the reallocation of waste and reclamation of contaminated soils and waters could act as a financial, social and environmental levers to improve the sustainability of bioenergy production. The studies also showcase how a versatile engineered ionic-liquid pretreatment has the potential to transform environmental burdens into resources that are compatible with the diversification of multiple product streams. Taken together, these findings can serve as a proof-of-concept for integrated scale-up of sustainable ionic-liquid based biorefinery. Open Access

The extrinsic incubation period (EIP) of malaria is the time required for Plasmodium parasites to undergo sexual reproduction and asexual replication within the mosquito (sporogony). The EIP is long relative to mosquito life expectancy meaning most mosquitoes do not live long enough to transmit malaria and small changes in mosquito survival strongly affect malaria transmission. The EIP is typically estimated in a population of experimentally infected mosquitoes, which are dissected on different days post infection for the presence of infectious, salivary gland sporozoites. I developed a novel mathematical model to estimate the EIP distribution from these data (Chapter 2). This model accounted for heterogeneity in mosquito infection and infection-dependent differences in mosquito survival, which could affect the EIP estimated using historical methods. Existing malaria transmission models that incorporate temperature-dependent changes in the EIP mostly use an existing degree-day model, which was parameterised using the time for the first Anopheles maculipennis mosquitoes (a species complex native to Europe) to be dissected with sporozoites. I therefore estimated the effects of constant temperature on the EIP distribution among Anopheles gambiae sensu stricto mosquitoes (a dominant Plasmodium falciparum vector) (Chapter 3). These EIP estimates were similar to the degree day model except at low temperatures. Theoretically, accounting for the complete EIP distribution marginally affects malaria transmission compared to assuming that all mosquitoes have the mean EIP. If vector control and mosquito mortality are high, however, accounting for heterogeneity in the EIP is important because mosquitoes with a short EIP become more important for transmission (Chapter 4). In the wild, temperature is not constant. I therefore developed a model to predict changes in the EIP of mosquitoes exposed to fine scale diurnal and seasonal fluctuations in temperature using the constant-temperature EIP relationship (Chapter 5). Model performance was assessed using laboratory data from mosquitoes that were exposed to a range of different temperature profiles. Incorporating fluctuations in temperature improved the model performance. Accounting for changes in the mosquito age distribution due to seasonality in mosquito emergence is theoretically important when measuring sporozoite prevalence (Chapter 6). I incorporated seasonality in mosquito emergence and temperature-dependent changes in the EIP into a mechanistic malaria transmission model and assessed the model’s predictive accuracy using seven years of monthly sporozoite prevalence samples from a holoendemic area of Senegal. Seasonality in mosquito emergence caused a small increase in predictive accuracy, and temperature-dependent changes in the EIP had a very small effect if mosquito emergence was allowed to vary and no effect if mosquito emergence was assumed to be constant (Chapter 7). Open Access

With ongoing agricultural land-use intensification and climate change, important functional groups of organisms, including insect pollinators, are being simultaneously and ubiquitously exposed to both pesticides and changing temperatures. Given the notable ongoing declines in insect pollinators, understanding how these stressors affect aspects of key functional behaviours underpinning fitness and pollination service provision is of global ecological and economic importance. Importantly, a critical but understudied step in evaluating pesticide risk is to understand how environmental temperature modulates pesticide effects on these behaviours. Through empirical lab experiments on a key wild pollinator, the bumblebee Bombus terrestris, I quantified the temperature dependent effects of insecticide exposure on individual flight and general mobility. Neonicotinoid exposure dramatically impaired flight motivation and endurance, and these same performance traits were also found to be highly sensitive to environmental temperature. However, the effect of neonicotinoid exposure varied depending on post-exposure temperature, with impacts on flight being enhanced under warmer conditions and impacts on food consumption, walking, and general responsiveness being enhanced under cooler conditions. The hazard posed by insecticides to insect pollinators may therefore vary both temporally and spatially, with impairment to flight and mobility traits likely constraining colony foraging potential and diminishing pollination service capabilities. Interestingly, the same effects were not seen across a different class of insecticide, with the new to market sulfoximine insecticide, sulfoxaflor, showing no detectable effect on any measure of mobility regardless of temperature when applied at comparable concentrations. The findings of this thesis suggest both the choice of insecticide and timing of exposure need to be considered in farming practices. Additionally, my findings provide crucial information for advising insecticide risk assessment protocols, developing mitigative and conservation action, and above all understanding which possible climate regions in the world insect pollinators are most at risk from insecticide exposure. Open Access

This thesis investigates mean field games and related models of dynamic agent behaviour, along with applications to network models. To begin, small time horizon and many--agent limits are taken of stochastic dynamic games. The limits are show to converge to a mean field game and a best reply strategy model. For stationary versions of each model, novel proofs of existence and uniqueness are given. Then the models are simulated for some particular examples that highlight the similarities and differences between the two models. After studying the best reply strategy approximation of mean field games, next an application of mean field games to an economic model of knowledge spillovers is considered. A multi--population mean field game is constructed, with interactions between populations encoded in a network structure. For this model, proofs of existence and uniqueness are given, and simulations are made. The simulations provide some predictions about the effect of the network structure on company productivity, which are then tested using an econometric analysis of patent data. Finally, econometric and network analysis is used to estimate supply network climate risk, through a calculation of company--level embodied emissions. Open Access

There is growing promise that electric vehicles (EVs) may lead to a reduction in the pollution caused by road transport. This thesis begins by assessing the current link between EVs and the electricity system; how EVs are charged. The emissions produced in power plants for charging EVs have significantly decreased over the past decade due to the decarbonation of the electricity system, reaching 41 g CO2, 27 mg NOx and 0.7 mg PM2.5 per kilometre in 2019. But as marginal demand is still met by natural gas power plants there is a small emission increase for NO¬x and CO2 of up to 25%, for new EVs entering the system. In 2020, the COVID-19 pandemic highlighted how additional decarbonisation of the electricity system should continue and will bring additional emission reductions for EVs in the future. This thesis then looks to the future, illustrating a path towards a fully electric fleet and decarbonised electricity system. Emissions from road transport will approach net zero in the 2040s if the current government road transport and power generation targets are met. Under this scenario, air quality may significantly improve over the next decade with exposure to NOx and PM2.5 reducing by 6.7 µgm-3 and 0.5 µgm-3, respectively, but this is only marginally better than without EVs due to the improvements in conventional vehicles. Beyond 2030, a fleet of EVs with a decarbonised electricity system may further reduce NOx and PM2.5 exposure by 1.6 µgm-3 and 0.1 µgm-3 compared to a conventional fleet by 2050. The long-term barrier for improving air quality for EVs is now non-exhaust emissions where exposure to PM2.5 may remain at a significant level (0.4 µgm-3) until 2050. Non-exhaust emissions are highly uncertain and may increase in the future with heavier and cheaper to run EVs. Open Access

The sedimentary record is a crucial archive of past surface processes, including ancient river dynamics, on Earth. Rivers are sensitive to allogenic (external) forcings, such as changes to tectonic and climatic boundary conditions, and can respond to these forcings by propagating environmental signals, such as changes to sediment supply and grain-size, throughout fluvial networks. In theory, environmental signals associated with these allogenic forcings are preserved in depositional stratigraphy. However, rivers are also sensitive to autogenic (internal) forcings, such as channel migration and avulsion, which generates “noise” in depositional stratigraphy. Stratigraphy therefore represents the time-integrated product of the movement of water and sediment, in response to both allogenic and autogenic forcing, across Earth’s surface in the geological past. The ability to reconstruct mass fluxes in time and space from the continents, and to extract these signals from fluvial strata, provides unique insights into the dynamics and behaviour of the Earth system in the geological past. In this thesis, I explore methods to investigate the dynamics and behaviour of ancient fluvial systems from fluvial strata. While qualitative methods (e.g., facies mapping, logging) provide useful insights, these insights are limited in the extent to which they can be used to investigate ancient river dynamics. Here I explore and develop quantitative methods to investigate ancient fluvial systems. Quantitative insights are crucial to constrain total water and sediment discharges, spatial and temporal trends in river dynamics, and the magnitudes and frequencies of river response to forcing. At large spatial and temporal scales, I present a new method to reconstruct water and sediment discharges in palaeo-catchments — this method exploits access to palaeo-digital elevation models and general circulation climate model results, both of which are now becoming increasingly sophisticated. At smaller spatial and temporal scales, I present a framework to reconstruct morphologic (e.g., flow depths, slopes) and hydrodynamic (e.g., flow velocities, water discharges) parameters from fluvial strata, and I present a new method to reconstruct river planform from field-derived observations. These methods and frameworks can provide a range of insights into ancient fluvial systems in general and, in this thesis, I successfully apply them to ancient fluvial systems in the Late Cretaceous North American continent. Beyond the development of new methods and frameworks to investigate the behaviour of ancient fluvial systems, this thesis also presents unambiguous stratigraphic evidence for bedform preservation in non-steady, or disequilibrium, conditions for Upper Cretaceous fluvial deposits in North America. These observations challenge the use of steady-state bedform preservation models in palaeohydraulic reconstructions. My results highlight the importance of making systematic field measurements of cross-set geometries in fluvial strata to determine the nature of bedform preservation, and the importance of considering disequilibrium dynamics for palaeohydraulic reconstructions. Further, these results provide a potentially powerful avenue to quantify flood variability from fluvial strata, and I explore the necessary future work to achieve this research goal. Together, the methods and frameworks that I present in this thesis advance our ability to extract quantitative information from fluvial strata. Further, in exemplifying these methods and frameworks for ancient fluvial systems of the Late Cretaceous North American continent, I highlight the advantages, limitations, and best practices associated with these approaches. These methods and frameworks can be implemented at a variety of spatial and temporal scales and can provide sophisticated insights into the dynamics and behaviour of ancient fluvial systems, both on Earth and other planets. Open Access

The response of coasts to climate change is an uncertain threat to the infrastructure and inhabitants in these areas. Rock coasts are ubiquitous landscapes found along coastlines worldwide and are often sites of important infrastructure, which are vulnerable to coastal erosion and cliff retreat. Furthermore, the stability of rock coasts is threatened by future climate change, particularly the influence of accelerating sea level rise and increased storminess. Constrains need to be placed on past erosion rates at rock coasts across millennial timescales in order to better forecast how future cliff retreat rates will respond to climate change. The ability to quantify coastal cliff retreat rates across millennial timescales has been transformed with the application of exposure dating across shore platforms using cosmogenic radionuclide (CRN) analysis. Previous studies have successfully quantified long-term cliff retreat rates across the Holocene for a range of rock coast sites; however, previous work has been limited by the use of a simplistic geometric-based model to interpret CRN concentrations. Considerable potential remains in the use of CRN analysis along rock coasts. In this thesis, first, I develop a routine that is the first application of a process-based model to interpret CRN concentrations. Next, I apply this technique to a range of rock coast sites across the UK to quantify long-term, transient cliff retreat rates for the past and also make forecasts for the future to better understand the response of rock coasts to climate change. A multi-objective optimisation routine is developed in order to optimise a process-based model to both measured topographic and CRN concentration data for two sandstone sites in the UK. The results highlight that the multi-objective optimisation routine improves model results by reducing equifinality to constrain uncertainties and produce consistent trends in transient long-term cliff retreat rates. This approach is employed to quantify long-term, transient cliff retreat rates for the past 7,000 years at two sandstone rock coast sites. These long-term cliff retreat rates clearly link to the rate of relative sea level rise at both sites. I also use the process-based model to decode insights into the key erosional processes involved in rock coast evolution. Next, I use the optimised parameters from the process-based model results to make forecasts of future cliff retreat rates to the year 2100 using future sea level rise scenarios. At both sandstone sites, cliff retreat forecasts are likely to accelerate by 3–7 times present-day rates, to maximum retreat rates of 22–30 cm yr-1, using the current trajectory of relative sea level rise. Comparisons to cliff retreat rates quantified for the past reveal that these projected cliff retreat rates are unprecedented in the last 3–5 millennia for both sites. These results highlight that even historically stable rock coasts are highly sensitive to sea level rise and need to be included in future planning. Finally, I apply the newly developed optimisation routine to four new chalk rock coast sites on the south coast of England to quantify long-term cliff retreat rates across the late-Holocene. My results identify a recent acceleration in cliff retreat rates, and such rapid cliff retreat rates last occurred 5300–6800 years ago. Furthermore, the optimised, process-based model detects significantly different dominant factors controlling erosion between the sandstone and chalk rock coast sites. Model results for the chalk sites also suggest that heterogeneous lithology and beach material play an important role in the long-term erosion at these sites, and advocates for the inclusion of these factors into future process-based rock coast evolution models. Overall, the results presented in this thesis highlight the knowledge gained from implementing a process-based model to interpret CRN concentrations and quantify transient cliff retreat rates across millennial timescales. Through the methods that I develop, the expected relationship between long-term cliff retreat rates and the rate of sea level rise is supported with empirical data for the first time. Multi-objective optimisation improves model equifinality, which allows for more accurate and well constrained past and future cliff retreat rate forecasts. Results clearly demonstrate the power and utility of these methods to better understand rock coast response to climate change and make more reliable forecasts of cliff retreat rates at coastlines worldwide. Open Access

Effective monitoring and protection of tropical ecosystems has the potential to conserve vast amounts of the earth’s biodiversity. Yet logistical and technical challenges associated with species rarity, large distributions and home ranges, low detectability and inaccessibility of study sites can hinder monitoring efforts. If we are to mitigate against the threats to biodiversity and restore natural ecosystems, then we urgently need rapid and cost-effective methods to evaluate the current state of species, communities, ecosystems and the effectiveness of interventions. Here, we use passive acoustic monitoring (PAM) combined with computational approaches, as a method to effectively measure trends in biodiversity at a wide spatial scale across a biodiverse region in the tropics. In Chapter Two we used soundscape analysis to evaluate changes in acoustic diversity across the diel cycle over a gradient of land use change. We aimed to assess if soundscape indices can reveal changes in the biological community across the diel cycle and whether loss of native forests affect acoustic diversity in tropical ecosystems. In disturbed habitats, we found a loss of the characteristic dawn and dusk peaks in the diel cycle; known as the dawn and dusk chorus. This was especially prominent in palm oil plantations and grasslands, which showed a complete loss of these peaks. This suggests that in disturbed ecosystems there is likely a loss of species diversity, a shift in species composition, where forest specialists are being replaced by disturbance tolerant species, or that there are modifications in species behaviour, reinforcing the value of native old growth forests in maintaining ecosystem functionality. This loss in dawn and dusk peaks was not apparent when analysing acoustic diversity at specific times during the diel cycle, showing that evaluating acoustic diversity at this temporal scale can be misleading, but in assessing trends across the diel cycle, we can gain a much better representation of changes to biotic communities. In Chapter Three we determined if PAM and a newly developed automated detection and classification system was effective at retrieving information on the Geoffroy’s spider monkey at a wide spatial scale. We assessed how this endangered primate responds to habitat loss and human influence across a gradient of disturbance. We found that the Geoffroy’s spider monkey was absent below 80% forest cover and within 1 km of paved roads, yet was found to some extent in areas of secondary forest and near unpaved roads and buildings. The success of this methodology in the study of a vocal rare species suggests that similar rare species could be studied in the same way. Threshold values for percent forest cover and paved roads will be valuable in developing conservation strategies for the protection of this species. In Chapter Four, we investigated the effectiveness of a sustainable use forest reserve in facilitating connectivity for the Geoffroy’s Spider monkey between two National Parks. We specifically evaluated occurrence across the reserve, habitat suitability, barriers to connectivity and potential mitigation strategies to improve connectivity in the region. We found that the Golfo Dulce Forest Reserve is acting as a buffer to Corcovado National Park and is able to support populations of the Geoffroy’s spider monkey, however, as occurrence was limited to the area surrounding Corcovado, it is possible that it is not facilitating connectivity as intended. Primary road and low forest cover were the most important predictors of poor habitat suitability, both acting as barriers to connectivity and potentially impeding the conservation of an endangered species. This is problematic since Piedras Blancas National Park serves as a connection between the Osa Peninsula and populations of the Geoffroy’s spider monkey in other areas of Costa Rica. In summary, we have shown how PAM, combined with computational approaches, can be used to effectively monitor trends at both fine temporal scales and wide spatial scales across a tropical ecosystem. PAM has provided an effective and rapid approach to monitor trends in biological communities across disturbance gradients, to study rare species across a challenging environment and to evaluate the effectiveness of current management interventions, overcoming many of the key logistical and technical challenges associated with biodiversity monitoring. These methods have revealed important information regarding how anthropogenic disturbance, related to land use change and human development, are threatening both species and communities, which can contribute to setting targets and developing conservation strategies for the protection of biodiversity in the Osa region and beyond. Open Access

Non-equilibrium thermodynamics has had a significant historic influence on the development of theoretical ecology, even informing the very concept of an ecosystem. Much of this influence has manifested as proposed extremal principles. These principles hold that systems will tend to maximise certain thermodynamic quantities, subject to the other constraints they operate under. A particularly notable extremal principle is the maximum entropy production principle (MaxEPP); that systems maximise their rate of entropy production. However, these principles are not robustly based in physical theory, and suffer from treating complex ecosystems in an extremely coarse manner. To address this gap, this thesis derives a limited but physically justified extremal principle, as well as carrying out a detailed investigation of the impact of non-equilibrium thermodynamic constraints on the assembly of microbial communities. The extremal principle we obtain pertains to the switching between states in simple bistable systems, with switching paths that generate more entropy being favoured. Our detailed investigation into microbial communities involved developing a novel thermodynamic microbial community model, using which we found the rate of ecosystem development to be set by the availability of free-energy. Further investigation was carried out using this model, demonstrating the way that trade-offs emerging from fundamental thermodynamic constraints impact the dynamics of assembling microbial communities. Taken together our results demonstrate that theory can be developed from non-equilibrium thermodynamics, that is both ecologically relevant and physically well grounded. We find that broad extremal principles are unlikely to be obtained, absent significant advances in the field of stochastic thermodynamics, limiting their applicability to ecology. However, we find that detailed consideration of the non-equilibrium thermodynamic mechanisms that impact microbial communities can broaden our understanding of their assembly and functioning. Open Access

Microbial ecosystems, both on land and in the oceans, are the staging ground for the biogeochemical activity that sustains habitable conditions on Earth. Ocean microbes are of particular importance; the primary producers that drive biogeochemical ocean processes are almost entirely microbial, and are collectively responsible for about half of global net primary production. These ecosystems are extraordinarily complex, by virtue of being driven by very large numbers of living individuals, constantly interacting with each other and their highly dynamic physical environment. Much uncertainty remains about how these dynamics, from micro- to macro-scales, ultimately impact key ecosystem properties such as spatial dynamics and growth rates of populations and communities. In this project I use individual-based modelling (IBM) across a range of spatial and temporal scales, leveraging large, high-resolution physical and biological datasets along with advancements in modelling tools to shed light on spatial and temporal dynamics of microbial populations in inherently fluctuating environments. In doing so I clarify and quantify hitherto unresolved ecological questions relating to interactions between microbes and turbulence, inaccuracies in conventional modelling approaches, and the balance of competition and coexistence between microbes in the marine environment. In the Introductory Chapter, I review our current understanding of microbial ecology in the oceans, and illustrate how complex ecological behaviour emerges from the constant interaction of microbial individuals with each other and with their environment. In the Second Chapter, I begin at the smallest scales directly relevant to ocean microbes, investigating the impact of turbulence on microbial spatial dynamics and patchiness. I adopt an existing mathematical framework for modelling microbes capable of gyrotactic locomotion, with an IBM to reproduce their motion within a fully-resolved 3D simulation of convective turbulence. This work clarifies and extends to more realistic flow regimes the existing theory connecting micro-scale microbe patchiness to a coupling of turbulence and individual motility. Interpreting my results in the context of varying turbulent conditions from the surface to the bottom of the mixed layer, I propose that this turbulence-driven patchiness is ephemeral, non-ubiquitous, and depth-dependent. In the Third Chapter, I transition to larger spatial and temporal scales, and develop an IBM on top of the NEMO-MEDUSA oceanographic model and the global Biotraits database. I use this model to quantify, for the first time, to what degree fluctuating environmental conditions can influence estimates of a microbe's growth rate, due to nonlinear averaging effects similar to the phenomenon known as Jensen's Inequality. In a microbial growth context, such effects predict that growth rate estimates based on mean environmental conditions will differ from realised growth rates in a dynamic environment. I substantiate this prediction by simulating populations of marine phytoplankton following ocean currents, and demonstrating that realised growth differs substantially from mean-environment growth estimates for a clear majority of these simulated populations. I quantify the relative contributions of temperature and nutrient fluctuations to this microbial ``growth gap'' -- the magnitude of the difference between realised and mean-environment growth rates, and discuss the implications of my findings under a warming climate. In the Fourth Chapter, I apply my NEMO-MEDUSA-Biotraits IBM to investigate the ‘Paradox of the Plankton’ -- the puzzling absence of competitive exclusion among ocean microbes. I simulate populations of distinct species with thermal histories which significantly overlap in both space and time within the IBM, which I treat as competitors. I then examine whether the distinct thermal adaptations of these competitors can cause competitive advantage to shift back and forth over time as environmental conditions fluctuate, thus preventing any individual species from permanently outcompeting others. In the Final Chapter, I link my findings to each other and to the bigger picture of microbial ocean ecology, emphasizing how a maturing body of mathematical ecological theory, increasingly large and detailed datasets, and modern computational tools, allow us to shed light on long-standing questions by closely examining interactions between individuals and a dynamic environment. Open Access

Society's dependence on weather systems has broadened to include electricity generation from wind turbines and solar PV systems. Climate change is altering energy flows in the atmosphere, which will affect the economic potential of wind and solar power outputs. This thesis presents a framework to assess the economic impact of climate change on annual average wind and solar power generation. This thesis highlights the knowledge gaps in economic analysis of future wind and solar resource assessments which consider climate change. It presents an interdisciplinarity framework which combines climate model outputs with technoeconomic modelling of financial metrics. This thesis outlines the proof of concept for this framework, exploring the limitations of global climate models for assessing wind and solar resources, and presents a novel bias-adjustment method to create future projected time series. CMIP5 and MERRA(2) datasets are used due to their accessibility and global scale, enabling results to be produced for anywhere on the globe. The framework is demonstrated with three case studies which focus on the cost of wind power in the UK, changing icing related losses in the northern hemisphere, and future impacts of climate change on solar PV in China. In all case studies, climate change impacts are projected under low and extreme climate forcing scenarios from the early to the late 21st century. Results are mixed. The relative change in average-annual capacity factors and levelised cost of energy is between ±2% under low scenarios of climate change and within ±5% for more extreme climate change. The change is also more pronounced later into the 21st century. These results show assessments of future wind and solar power are possible, highlighting that wind and solar power generation remains an attractive investment under all scenarios of climate change. Open Access

This thesis presents the development of a set of practical tools useful for anyone who may want to develop, deploy or estimate the performance of highly efficient multi-junction (MJ) solar cells in concentrator photovoltaic systems (CPV). These tools use open-source datasets and models to estimate the spectral direct normal irradiance (DNI��) for any location and for any period. The estimation schemes developed here differ from existing solutions in that a reliable method for properly treat- ing aerosols is established, which is shown to be essential under clear-sky conditions. In conjunction with a solar cell simulator, the schemes enable the accurate performance prediction of MJ CPV systems, critical to their proliferation and the lowering of cost for solar energy. Amongst the proposed schemes, the Spectral Aerosol Classification Scheme with Circumsolar Factor (SACS + CSF) shows the closest agreement with observations. Under this scheme, the spectral variation of aerosol extinction is represented by an optimally selected aerosol type, whilst the circumsolar irradiance is accounted for using a physics-based look-up table. The simulated broadband DNI carries biases ranging from ���0.27 % to 0.52 % (���2 W m���2 to 3 W m���2 ), averaged at +0.068% (< 1 W m���2 ), when validated across five sites. The average spread of error over the five sites is about 2.5 %. When validating the schemes against spectral observations, the average bias ranges from ���0.6% in the 868 nm channel to +0.3 % in the 500 nm channel. When coupled with an MJ CPV design in a simulator, it is demonstrated that using SACS + CSF statistically significantly reduces the systematic bias in the power output estimation by order of 10 W m���2 (6 %) when compared to the climatological approach. This is important in the context of assessing long-term MJ CPV resources as power outputs are integrated over multidecadal timescales. Although the schemes have been developed with AERONET observations, they are designed to use satellite and reanalysis model inputs. This is necessary to enable the estimation of DNI�� globally based on long-term records. However, retrievals from satellites carry higher uncertainties. This motivated an integrated analysis of the non-linear error propagation chain from aerosol products to DNI��, and to quantities relevant to the performance of MJ CPV cells. It is discovered that factors like surface reflectance and observation zenith, typically thought of as crucial in understanding error in satellite retrievals, become less critical further down the error chain. For MJ CPV resources, it is shown that it is the aerosol typing that primarily dictates the error distribution. This has important implications for the selection of aerosol products for solar resource assessment. For example, products like MODIS and ECMWF MACC may yield better statistics in aerosol optical depth (�� ), but produce less accurate MJ CPV efficiency (��) estimation than, for example, AATSR / ORAC. The error propagation analysis also revealed that high aerosol loading increases the sensitivity of MJ CPV �� to error for coarse aerosols. Continental polluted and urban aerosols with high aerosol loading are also conditions where �� is more susceptible to errors in �� and Angstro ��m exponent (��). �� has minimum sensitivity to error under maritime aerosol conditions. Ultimately, it is concluded that for most climatologies, typical uncertainties of �� and �� in aerosol products propagated into �� produce an error that is less than 10 %, the typical magnitude of the spectral effects for MJ CPV. As such, the use of satellite observations for estimating MJ CPV resources is suitable in most cases. To further illustrate the importance of spectral DNI, the impact of the COVID-19 lockdown and air pollution changes on MJ CPV resources is studied over China using satellite retrievals of NO2 and ��. It is estimated that the combined changes in atmospheric species lead to a 19.8 �� 8.5 % (62 W m���2 ) increase in broadband surface DNI, along with a shift in the spectral distribution towards bluer wavelengths. Feeding these changes into an MJ CPV simulator results in a 29.7��8.5% (29 W m���2) increase in the power output. Around one-third of the increase in power output arises from the improved spectral matching. These results indicate that cleaner atmospheres can have disproportionate co-benefits for MJ CPV technologies, which has important implications for air pollution and climate change policies.

Submarine channels form pronounced morphological features on the seafloor and play an important role in shaping the stratigraphic record. Over the last two decades, their morphology and architectural evolution have been studied in detail using a range of modern and ancient examples. While structural deformation is recognised as a major control, the temporal and spatial complexity associated with these systems means aspects of submarine channel dynamics and how their geomorphic expression translates into time-integrated sedimentary architecture, remain poorly understood. For example, structurally driven changes in slope morphology may locally enhance or diminish a channel’s ability to incise, aggrade and migrate laterally. In this thesis, I explore the sensitivity of submarine channel morphology to structural deformation and evaluate how channel-structure interactions are recorded in seismic stratigraphic architecture. I use novel seismic attribute analysis alongside concepts from landscape dynamics to provide quantitative insights into how the growth of structure on the southern Niger Delta slope has influenced submarine channel morphology and time-integrated stratigraphic architecture. From a 3D, time-migrated seismic reflection volume, I quantify a range of morphometric parameters including, channel gradient, width, depth, sinuosity, curvature, and stratigraphic mobility, on a number of modern and ancient submarine channel systems as they interact with structure. My results show that submarine channel morphology and longitudinal profile are unambiguously linked to the underlying structural template. The modern seafloor expression of submarine channels can be up to an order of magnitude higher aspect ratio and markedly more variable than their ancient, stratigraphic counterpart. Their depositional architectures are composite stratigraphic features that record the morphological response to spatial and temporal variations in structural growth rate. Based on this, three end-member styles of submarine channel architecture are recognised on structured slopes: pre-channel structural bathymetry, coeval positive relief, and coeval negative relief. This thesis quantifies how submarine channel systems integrate kinematic processes at the scale of the fundamental architectural unit, a channel element, and documents the systematic change in channel element kinematics on structured segments of the slope. My observations demonstrate the sensitivity of submarine channels to structural deformation and help us to constrain some of the most important sediment transport systems on planet Earth. Open Access

Mosquitoes are a major global public health concern because they vector pathogens that cause multiple human diseases. Recent reports of local vector-borne disease transmission in temperate suburban and urban populations have raised concerns over how global environmental change will affect the spatiotemporal distribution of vector-borne disease transmission. However, our understanding of the ecological processes that regulate vector population growth and, therefore abundance is incomplete. This limits our capacity to reliably predict and effectively manage any shifts in vector-borne disease risk that may arise from different environmental change scenarios. The life history traits that determine population growth (survival, development, reproduction) in cold-blooded organisms (ectotherms), such as mosquitoes, respond to environmental temperature in predictable ways. This provides a mechanistic basis for predicting how climatic warming will affect vector-borne disease dynamics, partially through the temperature dependence of the abundance dynamics of the vector population. Furthermore, the effects of temperature on abundance should also be affected by other environmental factors; for instance, ecological theory predicts that variation in resource availability should also affect vector traits. However, while this may seem an obvious source of additional variation, this problem remains largely unresolved in vector-borne disease research, and in thermal ecology in general. In this thesis, I address this issue using laboratory experiments to investigate how realistic variation in resource availability in larval environments directly impacts the temperature dependence of life history traits that determine fitness in the mosquito vector, Aedes aegypti. Then, using mathematical population modelling, I use datasets from these experiments to assess how resource variation in the larval environment can affect the temperature dependence of the species’ maximal population growth rate (rm). I also use the results from this experimental and modelling work to assess the ability of a general analytic rm model based on the Euler-Lotka equation to provide reliable estimates of temperature- and resource-dependent rm. I found that resource limitation and larval competition in depleting resource environments can both significantly mediate the shape of rm’s ¬unimodal thermal response. These findings provide compelling evidence that variation in resource availability should be considered when predicting how vector-borne disease dynamics will respond to environmental change. I also show that, except when populations are constrained by resource availability below a certain threshold, analytic rm models based on the Euler-Lotka equation can be used to incorporate the effects of temperature and resource availability on vector fitness into existing vector-borne disease transmission model frameworks. This provides a novel avenue towards improving the reliability of predictions derived from these frameworks. Overall, the strong potential for variation in resource availability in the larval environment to profoundly affect the temperature dependence of population fitness means that future research effort should be invested in developing novel methods to measure effective temperature- and resource-dependent fitness and abundance in the field. Open Access

The effects of aerosols on local and remote climates are myriad and complex. They are incompletely understood, particularly those due to aerosols from tropical regions. The health impacts are poorly constrained, with the future effects uncertain. Prior studies neglected the impacts of African and tropical aerosol perturbations, and the impacts of single continents following different transient emissions scenarios have not been explored. The new generation of climate models simulate the processes which mediate aerosol-driven changes in atmospheric composition and the climate in unprecedented detail. The Shared Socioeconomic Pathway emissions scenarios provide coherent narratives for future anthropogenic emissions and demographics, with much broader projected ranges in aerosol emissions than prior scenarios. To address some of these gaps, this PhD uses the recent UKESM1 model to investigate the climate and health impacts of idealised perturbations to tropical and African aerosol emissions, and scenarios of 21st century African aerosol and CO2 emissions. Tropical carbonaceous aerosol is found to cause overall warming in UKESM1 due to Black Carbon absorption, with surface cooling locally. This cooling persists when including additional CO2 emissions from Africa. The aerosols drive complex responses in precipitation, including significant Inter-Tropical Convergence Zone shifts and rainfall decreases due to atmospheric energy budget changes. Differing African emissions scenarios affect temperature and precipitation extremes, with variations from the mean responses. PM2.5 and O3 decrease globally into the future, remaining more constant in Africa. The human health impacts of air pollution therefore decrease when using present-day populations, but increase when using future projections. O3's impact is currently lower than PM2.5’s, but this switches under strong mitigation. This project contributes to the understanding of the effect of tropical aerosols on the climate, both from idealised experiments and realistic scenarios, and shows the substantial impact of high air pollutant emissions in Africa in the 21st century. Open Access

Since the 90’s, there have been many studies looking at the impact of stratospheric temperature perturbations (STP’s) on the troposphere below, and the mechanisms involved. However, it is not well-understood how these interactions might be modified by atmosphere-ocean coupling. This holds particular relevance to the study of e.g. ozone depletion/recovery in the Southern Ocean region. To investigate this, abrupt uniform, polar, and equatorial STP’s – corresponding to different types of forcings - were applied to the atmosphere of MITgcm in an aquaplanet, double-drake configuration. Each was conducted in three different versions of the model: atmosphere-only, atmosphere + slab-ocean, and fully-coupled atmosphere + ocean. In the atmosphere-only model, atmospheric responses similar to those of previous studies were recorded, underscoring their generic nature. In the coupled models, an initial weakening (~decades), and – in the fully coupled model - subsequent strengthening and poleward-shift (~centuries) of the underlying atmospheric response was produced, in polar/equatorial heating experiments. Uniform heating saw the latter process occur initially too. Sea surface temperature (SST) anomalies were found to drive these changes, with extratropical/tropical anomalies controlling the former/latter process. These were in turn attributable to changes in the zonal winds, causing anomalies in the turbulent and ocean heat fluxes, although uniform STP’s saw SST changes that were more controlled by large, near-uniform anomalous downwelling longwave fluxes. Our results highlight the importance of incorporating atmosphere-ocean coupling when studying the effects of STP’s, especially over longer timescales (&100 years). With respect to ozone depletion in the Southern Ocean, they suggest an amplified poleward jet shift which - as greenhouse gases continue to rise – may continue and amplify further into the 21st/22nd century. Open Access

Large scale (0 ≤ r ≤ 2200 km) and small scale (0 ≤ r ≤ 550 km) infra red satellite imagery of tropical cyclones is examined using a variety of machine learning techniques with varying degrees of complexity. Regarding large scale images, a dipole in outgoing long-wave radiation is revealed through composite analysis. The dipole is composed of low fluxes within the tropical cyclone circulation (r < 500 km) with high fluxes offset (1000 - 2000km) north (poleward) west of the tropical cyclone center. Both the strength and orientation of the dipole are independent of vertical wind shear and cyclone intensity. Using reanalysis data, it is shown that divergence at surface and convergence aloft facilitates subsidence throughout the troposphere over the region of high fluxes. The divergent signal at surface is produced over a region where the cyclone pressure gradient competes with the background meridional pressure gradient, splitting the environmental winds. Aloft the pressure gradients are reversed and environmental winds are impeded by the cyclone outflow producing a convergent signal. Subsidence is induced in both the cyclone outflow and the environmental wind over this region. This is a region, within r ≤ 2200 km from the cyclone center, that consistently accommodates the subsidence of the secondary circulation. Using the ECMWF (European Center for Mid-range Weather Forecasting) ensemble, a significant relationship is identified between the dipole orientation and the cyclone path. The high flux region is positioned north west of the cyclone center for cyclones propagating westward. The high flux region is positioned west of the cyclone center for cyclones propagating eastward. Different environmental flows and pressure regimes, between each case, can explain the anti-clockwise dipole rotation as cyclones recurve towards the east. In this way the dipole configuration is a reflection of some of the vortex environmental interaction that also determines the cyclone track. It is demonstrated that a sub-ensemble can be formed by selecting ensemble members with similar outgoing long-wave radiation (OLR) fields. The strongest improvements (8%) in 24 hour track forecasts are found when sub-ensembles are selected by OLR fields that encompass the dipole. Ensemble members with similar dipole properties demonstrate matching environment interactions, and subsequently, coherent future track paths. Through comparison with other regions of interest in large scale OLR fields, it is demonstrated that the high OLR component of the dipole bears a strong association with future TC tracks. The reductions in track forecast error using sub-ensembles selected by OLR fields are similar to the error reductions found when selecting sub-ensembles by cyclone position. Both of these techniques require accurate cyclone positions. A novel technique to identify the center of tropical storms and tropical cyclones is presented. It is shown that tropical storms demonstrate a highly variable, elliptical, asymmetric cloud structure, typical of mesoscale convective systems. Sequential long and short wave infra red images, encompassing the region r ≤ 550 km, are used to create cyclone videos. Neural networks incorporating both convolutional, and recurrent layers, are trained upon the cyclone videos to identify the cyclone center. A 40% reduction in position error is provided across all intensities over the baseline ARCHER-2 product. Of the networks tested, the best performance was found with networks that initially identify spatial features within each image, and then subsequently identify the temporal evolution of such features. Long-wave infra red channels provide a 25% reduction in position error over short-wave infra red channels. It is proposed that the capacity for long-wave infra red channels to image throughout the troposphere in clear-sky conditions provides this error reduction. 2 Open Access

Tropical forest phenology links with biodiversity and ecosystem process but knowledge gaps remain surrounding the dynamics and drivers of all phenological types, its influence on invertebrate distribution, and how fragmentation may change phenological resources available to higher taxa. Over 1 year, we monitored a 16 ha area of logged tropical forest in Malaysian Borneo. Using UAV imagery within a machine learning pipeline we showed the potential of UAVs to identify individual tree crowns and track their phenology through time but highlighted limitations in classifying spectral outliers into phenological events. In parallel, we ground-truthed the UAV phenology data for 135 of these trees, representing 45 taxa and 17 plant families, demonstrating phenology was taxon specific and highly asynchronous across the landscape, with no one environmental factor determining phenological change. Furthermore, using a grid of canopy-set traps we monitored invertebrate biomass weekly, showing they maintain a low-level, patchy distribution across the landscape but are not influenced by phenology. Finally, in a 10-year spatially explicit simulation of forest fragmentation, we showed that reducing forest area, significantly reduced and de-stabilised temporal phenological resource availability in a 7,200 ha area of forest. The asynchrony displayed by tropical forest phenology demonstrates it is a complex process to monitor and despite leveraging the high spatiotemporal resolution of UAV data and the power of machine learning, there are still challenges that need to be addressed. However, our detailed overview of forest phenology demonstrates it can be susceptible to fragmentation and future climatic change, and even though invertebrates were not affected here, this could have reverberating consequences for higher taxa and ecosystem function. Therefore, we would do well to successfully tackle the challenges of UAV monitoring in the tropics, to rapidly and automatedly assess phenological change and help understand the impacts of these environmental changes on phenology. Open Access

Island arc volcanism is driven by the release of water from the subducting slab. Over time variations in the distribution of chemically bound water in the down-going lithosphere may influence an array of arc processes from rates of seismicity to arc structure. In slow spreading oceanic crust such as the Atlantic strong variations in crustal structure can lead to a pattern of hydration which changes across relatively short wavelengths along the slab front. As one of only two subduction zones to consume slow spreading lithosphere the Lesser Antilles is a key location for understanding the influence that the distribution of subducting fluids may have on potentially hazardous arc processes. However, the tectonics of the Caribbean plate are complex, with a history of arc volcanism which extends over 100 My. As a result it is unclear to what degree along arc variations are result of the influence of recent subduction, and how much is the result of inherited compositional and structural variations in the over-riding plate. The VoiLA (Volatile Recycling in the Lesser Antilles) project collected an array of geophysical and geochemical data across the Lesser Antilles arc system in 2016 and 2017 in order to test the role that subducted volatiles have played in shaping the Lesser Antilles. In this thesis I present marine geophysical data including wide-angle and multichannel seismics, bathymetry and potential field data, collected as part of two research cruises by the R.R.S. James Cook. These data are used to constrain the relative contributions of 1) the Tertiary history of the eastern Caribbean and 2) the degree of alteration in the down-going slab to shaping the modern arc. Results are combined with other key project findings to explain along strike variability in the Lesser Antilles arc. Open Access

Energy consumption in residential buildings is a significant contributor to global climate change. In the United Kingdom, it contributes 14% of national greenhouse gas emissions, and is well behind in the progress needed to achieve climate change targets. To accelerate this progress, a step change in the retrofit of residential buildings and in the uptake of energy efficiency measures is required, and the barriers and drivers to this uptake have been the subject of significant research efforts. This research has highlighted stakeholders’ perceptions of energy efficiency as a central driver of their retrofit decision-making behaviour, and seeks to provide a deeper understanding of these perceptions and behaviours, to accelerate energy efficiency retrofit. However, existing research on residential retrofit decision-making continues to face challenges, including methodological issues and difficulties in translating research findings into practice, such as policymaking and energy systems modelling. This thesis aims to overcome some of these challenges and contributes to the field of retrofit research in several ways, focusing on the United Kingdom. Firstly, it presents 6 original studies which investigate how different stakeholders make retrofit decisions, using 5 distinct methodologies and comparing the usability of the findings for policymaking and energy systems modelling. Secondly, it produces new insights on the retrofit behaviour of various stakeholders, including a little-researched stakeholder group (British private landlords), and highlights the central role of perception in driving this behaviour. Thirdly, where possible it assesses the uptake of specific energy-saving technologies, outlining the differences in perception and behaviour depending on the measure being retrofitted. Fourthly, it empirically grounds qualitative and quantitative research methods in real data, increasing the robustness of the findings generated. Finally, it seeks to close the translational gap between academic research and non-academic stakeholders, such as policymakers, by actively involving these stakeholders in the research design, where possible. Open Access

First appearing in the latest Cretaceous, Crocodylia is a clade of mostly semi-aquatic, predatory reptiles, defined as all of the descendants of the last common ancestor of the extant alligators, caimans, crocodiles, and gharials. Crocodylian phylogeny has been extensively studied using molecular and morphological datasets; however, numerous systematic problems exist, notably the disagreement between these datasets over the affinities of the extant gharials, Gavialis gangeticus and Tomistoma schlegelii. I constructed a new morphological dataset for Crocodylia, through (1) an anatomical reappraisal of a ‘basal’ crocodylian taxon, Diplocynodon hantoniensis; (2) a critical reappraisal of published character data matrices; and (3) extensive, first-hand observations of a global sample of crocodylians. This comprises the most taxonomically comprehensive crocodylian dataset to date (144 OTUs and 330 characters) including a new, illustrated character list, modifications to the construction and scoring of most characters, and 45 novel characters. Nine phylogenetic analyses under maximum parsimony compared the effects of weighting strategies and the treatment of quantitative characters. In agreement with the molecular hypothesis, and for the first time based on morphology alone, Gavialis is recovered as more closely related to Tomistoma than to any other extant crocodylian. This result is recovered in all analyses; however, those using continuous characters and extended implied weighting (with a high k-value) produce the most reliable and stratigraphically congruent topologies. Nevertheless, temporal incongruence between morphological and molecular datasets exists, indicating that several putative gavialids require reappraisal. New interrelationships are discussed along with a comprehensive review of their evolutionary and biogeographic implications, including: (1) support for a North American origin of Caimaninae in the latest Cretaceous; (2) recovery of the early Paleogene South American taxon Eocaiman as a ‘basal’ alligatoroid; and (3) modifications to the taxonomic content of Mekosuchinae, suggesting biogeographic affinities of this Australasian clade with latest Cretaceous–early Paleogene Asian crocodyloids. Open Access

The electrification of the global energy system is cited as necessary to transform economies away from fossil fuel dependence at least-cost because of increasingly cheap intermittent renewable energy sources (iRES). Consequently, power sector decarbonisation is expected to be critical to delivering the Paris Agreement which seeks to limit global warming to "well-below 2°C" by 2100. Integrated Assessment Models that assess global decarbonisation pathways fail to do so at national-scale. This thesis investigates the power system transitions needed to meet the UK and Nigeria’s commitments to the Paris accord. For the UK, we find that the least-cost systems that deliver decarbonisation are dominated by baseload and dispatchable low-carbon generation complemented by carbon dioxide removal (CDR) technologies, with limited expansion of iRES. It was found that CDR deployment could reduce decarbonisation costs by up to 48%. In the long-term, centralised systems consisting of large-scale thermal generation (mostly CCS) and extensive transmission infrastructure are cost-optimal, thus current policies pursuing decentralisation may lead to overbuilt and obsolete systems. For Nigeria, we find that the least-cost systems are dominated by natural gas and hydroelectric generation. Such a system was found to have emissions that were significantly lower than the power sector’s carbon budget. This surplus carbon budget could be traded to offset the emissions of other sectors or countries via carbon offsetting mechanisms. The UK utilises expensive CDR to meet its targets, however the purchase of emissions offsets from developing countries such as Nigeria could prove cheaper, and be a vital source of financing for developing countries. In both countries, iRES were found to play a non-central role in meeting NDCs. Their low availability and variability means that significant capacity coupled with energy storage is required and this proves particularly costly in a context where both power generation and CDR are required. Open Access

Landslide generated waves (LGWs) have many associated uncertainties that need to be ac- counted for during a hazard analysis. The work presented in this thesis developed and applied numerical modelling techniques to investigate and quantify these sources of uncertainty. Firstly, to model the LGW source as a deformable slide, a smoothed particle hydrodynamics (SPH) simulator was improved and adapted. The simulator was tested using lab scale bench- marks and an idealised full scale LGW scenario. The effects of landslide source parameters on the wave at increasing scales were then investigated. In order to make use of the findings regarding complex LGW source models, a probabilistic sensitivity analysis on the full range of source parameters and their effect on the generated wave was performed using the SPH simulator. This showed that the geometric landslide parameters (such as volume and submergence depth) contributed more to uncertainty in the resulting wave characteristics near the source than the rheological parameters. By coupling different wave propagation models to the results from the near-field SPH simulator, it was revealed that the choice of mathematical formulation for propagation made a significant difference to which parameters affected the inundation level the most. These findings have important implications for the design of future LGW modelling studies and which parts of the model workflow should have more computational cost dedicated to them. Near the source the landslide geometry outweighs the complexity of the rheological model in terms of influence on the wave characteristics. During propagation the mathematical formulation chosen can have a large influence on results, so dedicating extra computational cost to this phase would be worthwhile. Open Access

Infectious disease can pose a substantial threat to wildlife populations. While pathogens are generally not thought to drive population extinctions, several factors may increase the risks of pathogen-driven extinction. The African wild dog is an endangered species, living primarily in small populations, potentially making them sensitive to pathogen-driven extinction. African wild dogs are a highly social group-living species, meaning pathogens can spread quickly to entire packs. Rabies and canine distemper virus (CDV) pose particular threats to African wild dogs, each having been implicated in the extinction of important populations. The species' complex population dynamics means responses to pathogens are di cult to predict and are not adequately covered by existing population models. A demographic model can therefore be a useful tool for both understanding African wild dog populations and informing conservation. This thesis describes an individual-based model (IBM) of African wild dog population dynamics, and how it can be used to assess the probability of African wild dog populations persisting under di erent conservation management interventions. This IBM was extended to incorporate rabies epidemiology, including spillover from domestic dogs. The coupled African wild dog and domestic dog models show that, while African wild dogs may be protected effectively through vaccination, vaccinating the local domestic dog population is indicated to be a more effective strategy. The IBM was also used to assess the impact of CDV on African wild dog populations, incorporating the uncertainty surrounding CDV epidemiology. The model highlights important knowledge gaps which constrain assessment of the threat posed by CDV and the potential for managing this threat. This thesis demonstrates the value of combining modelling infectious disease with demographic models to inform conservation, in particular in addressing threats posed by rabies and CDV to African wild dog populations. These insights may also be useful in the context of other threatened wildlife host species. Open Access

Adaptive radiations, the process by which organisms diversify both taxonomically and ecologically, have been attributed to underline the majority of living biodiversity. This type of evolutionary radiation typically transpires following the exploitation of vacant niche space though is not restricted to insular communities as numerous large clades likely diversified in much the same way. There is considerable variation in morphological and ecological diversity both within and between clades at all taxonomic scales. Several near-complete phylogenetic trees and datasets were used to investigate clade disparity in abstract space, trait evolution and the associations between morphology, ecology and diversification rates. These were combined to assess whether imbalances in speciation rates occur among taxa possessing particularly extreme morphologies in beak and body traits. New approaches capturing disparity metrics were used to quantitively analyse the hypervolumes of diverse families and smaller subclades within multidimensional space. These metrics were then employed to assess whether passerine families possess greater disparity in either their beak or body morphospaces. Thraupidae are an incredibly diverse passerine family with its various subclades exhibiting contrasting levels of taxonomic and morphological diversity. Analysis of these two evolutionary aspects revealed speciation rates are often decoupled from trait disparity among the various tanager subclades. Finally, the extreme disparity in form among the nested adaptive radiations within Thraupidae and other passerine families were explored to assess their contrasting trajectories with other endemic taxa to understand how such discrepancy in diversity was achieved and the factors that likely generated it. Open Access

The oceans play a critical role in the climate system, so it is important to understand how ocean circulation is changing with time in order to evaluate the ongoing uptake of anthropogenic heat and carbon from the atmosphere. Ocean tracers can provide valuable insights into such large- scale ocean circulation changes. In this study, I review a new decade of ocean radiocarbon (∆14C) and chlorofluorocarbon (CFC) observations, and describe their recent changes in the context of the last three decades. I compare the observations to a selection of seven ocean models, to evaluate model biases and potentially detect changes in ocean circulation. I also investigate whether the observed changes can be attributed to external forcing, or internal variability. The most recent decade of observations show that average surface ocean ∆14C and CFCs are decreasing, corresponding to their decrease in the atmosphere. Tracers accumulated in the shallow ocean continue to disperse into deeper waters. By comparing the observed tracer changes to modelled tracer changes, I identify regions of enhanced and reduced tracer uptake which could be due to ocean circulation changes, including the Northwest Pacific, the Southern Ocean, the subtropical gyres, the North Atlantic Deep Water and Antarctic Bottom Water. I investigate changes in Southern Ocean circulation in a modelled large ensemble using CFCs, the idealised model tracer Ideal Age (IAGE) and observed changes in CFCs from 1991 to 2005. The ensemble mean change in IAGE is small, suggesting that there has been very little externally forced change in Southern Ocean circulation over this period, in contrast to strong internal variability. My analysis implies that real-world observations of changes in CFCs may not be a robust way to characterize externally driven changes in Southern Ocean circulation because of the large internal variability in CFCs exhibited by the individual ensemble members. Open Access

We have entered the sixth mass extinction in Earth’s history. Our ever-growing extraction of natural resources and conversion of natural habitats is eroding global biodiversity. Averting the loss of biodiversity is essential to maintaining the planet’s ability to support human life. However, given the limited resources available for conservation action, we must prioritise effectively. Biodiversity, in the purest sense, is living variation. One measure of biodiversity, phylogenetic diversity, quantifies the collective contribution of species to the Tree of Life and is linked to the maintenance of future options for humanity. Phylogenetic diversity is increasingly used in conservation prioritisation exercises to capture aspects of biodiversity not represented by species richness alone. In this thesis I will utilise global datasets to explore humanity’s impact on the phylogenetic diversity of the world’s tetrapods. I will then identify priorities for conserving threatened phylogenetic diversity across the world’s amphibians, birds, mammals and reptiles. To facilitate the accurate prioritisation of evolutionarily distinct tetrapod species for conservation, I will develop a novel approach to overcome deficiencies in phylogenetic data for poorly-known species. I will then extend existing approaches to develop a spatially-explicit metric to identify highly irreplaceable regions and species responsible for large amounts of phylogenetic diversity under threat from human encroachment. Finally, I will explore the impacts of major threat types on phylogenetic diversity to determine whether certain extinction drivers pose disproportionately large threats to global biodiversity. The research presented in this thesis will offer new insights into the threats facing phylogenetic diversity and provide advances in global conservation priority setting for the tetrapod Tree of Life. Open Access

Natural habitats are being impacted by human pressures at an alarming rate. Monitoring these ecosystem-level changes often requires labour-intensive surveys that are unable to detect rapid or unanticipated environmental changes. In this thesis, we explore how recording and analysing the sounds of an environment provides a tractable solution to scalable, fully automated ecological monitoring. First, we tackle the problem of autonomous data collection, and develop a device which is able to continuously collect and remotely transmit data from field sites over long time-periods. We then move to the automated analysis of eco-acoustic data, and exploit a learned acoustic feature embedding to achieve accurate monitoring of ecosystem health across multiple spatial and temporal scales. We demonstrate that an unsupervised approach using the same acoustic feature space allows automatic identification of anomalous sounds, including hallmarks of illegal activity such as gunshots and chainsaws. Functional real-time ecological monitoring requires significant computational infrastructure, and we detail the open-source design and implementation of SAFE Acoustics, an eco-acoustic monitoring network in the tropical rainforests of Borneo. Within the ecosystems we study, species movement and behaviour are constrained by habitat structure and connectivity. However, investigating how topology influences a complex network’s behaviour is not a challenge unique to ecology. We investigate the link between structure and function in a model system, the mouse brain, and find that inter-regional axonal connectivity is closely related to the intrinsic dynamics of individual brain areas. Similar studies inspecting the dynamics of data from large-scale ecological monitoring networks may provide a fruitful avenue for further explorations. Open Access

New techniques in exploration geochemistry are required to reduce the increasing amount of time and resources consumed during exploration of porphyry deposits. This can be achieved through developing our understanding of the processes that result in the formation of mineralised systems, and any associated geochemical signatures which could be recorded in mineral indicators. Apatite chemistry can provide a detailed perspective into porphyry system formation. However, the diversity of apatite occurrence and composition, in addition to its susceptibility to metasomatism, presents added complexity in its application as a mineral indicator. Here the La Granja Cu-Mo porphyry was used as a case study in which the occurrence and composition of apatite from porphyry systems could be investigated. The composition of hydrothermal apatite varies greatly between those from least fractionated, magmatic-derived fluids and distinct sericitic-associated apatite. Compositions of magmatic apatite closely reflect the magma evolution including melt differentiation and the behaviour of magmatic volatiles. Apatite inclusions in zircon provide a means to examine the halogen and sulfur content of a melt. At La Granja halogen ratios, together with additional textural and zircon geochemistry evidence, indicate that the late-stage porphyries crystallised rapidly from fractionated, volatile-rich melts, which alludes to the abrupt termination of the system. The highest concentrations of sulfur were observed within apatite inclusions from the mineralised intrusions. The implied increase in sulfur within the melt occurs after the start of porphyry emplacement and may be an important mechanism in the development of mineralisation. Using the conclusions from this study as a framework it has been possible to develop a series of multivariate discrimination tools effective for exploration. These results demonstrate that studies of apatite chemistry can not only help increase our understanding of porphyry formation, but with careful application can be utilised to aid the exploration of mineralised porphyry systems. Open Access

The urban water-energy nexus sits at the intersection of three global challenges: urbanisation, global freshwater scarcity, and climate change caused by energy use. The concept recognises the various interactions between water and energy systems at all stages, as well as the concentration of service demand in cities which drives most of global resource use. Research indicates that end use is the largest component of the nexus, both in terms of energy and of water. However, the interactions on the level of energy and water supply and wastewater have received most attention, part of the reason being the difficulty in characterising end use. There is still a lack of knowledge about the end-use linkages in cities, and about their role in urban dynamics. This research elucidates the urban water-energy nexus with a conceptualisation, a comprehensive appraisal of its components and an investigation of its dynamics. To this end, I developed a system dynamics model for London as a case study, and expanded on it for Mumbai as an example of a city in the Global South for which research of this kind has been thin. The models have at their core a novel end-use structure with bidirectional water-energy interactions by service, and also represent population dynamics, the urban water system, environmental constraints and a tax based climate policy. The results show that end-use interactions play an important role in determining future resource consumption. In London, disregarding them in planning may lock in energy-intensive water supply, while in Mumbai it may perpetuate intermittent water supply. More applications of this kind are needed for global conclusions, and I provide methods for extending the model to the diversity of cities. This work ultimately implies that the end-use water-energy interactions should be more prominent in urban sustainability debates and planning. Open Access

British pollinating insects are vital for their contribution to crop yields as well as maintenance of semi-natural environments across the UK. The Syrphidae family are highly diverse and thought to be an important pollinating group. In order to understand the evolutionary relationships in this family, mitochondrial genomes were used to build the largest tree of the Syrphidae family to date. This tree was used to establish relative ages for divergences within the family, and to explore the evolution of diverse syrphid larval life histories. The recent introduction of a UK pollinator monitoring programme has resulted in a large amount of data with the potential to inform conservation and management, presenting an opportunity for DNA analysis. A CO1 reference database was curated and tested for UK syrphids, resulting in sequences for 70% of UK species and highlighting difficulties in DNA identification. Barcoding of syrphids was then expanded by also metabarcoding pollen from gut samples. This showed the diversity of plant – syrphid interactions at an individual level across three different land use types. It also highlighted the importance of including syrphid larval life histories in analyses of this family, as these appeared to have a larger effect on species composition than pollen composition did. Finally, the reach of this thesis was expanded to include non-bee and non-syrphid pan trap visitors from the pollinator monitoring programme. This highlighted the diversity of non-syrphid Dipterans and allowed species and phylogenetic diversity to be compared in these bulk insect samples. Using DNA methods to analyse monitoring data has the potential to increase our knowledge of cryptic species, phylogenetic diversity and pollinator associations. Alongside this, DNA can be used to analyse large datasets of diverse pollinating insects which otherwise would be overlooked. Open Access

Over the past decades, great progress has been made in understanding the transition of Earth’s climate from the last ice age to the present day, in particular the importance of Southern Ocean processes and their impact on transfer of heat and carbon. This work explores deglacial ocean change through the lens of a new collection of cold-water corals from an understudied region, the southwest Indian Ocean alongside existing palaeo records including two other unpublished cold-water coral collections to form a broader picture of ventilation and structure of the deglacial Southern Ocean. A compelling peak in abundance of solitary scleractinians in the southwest Indian Ocean, as well as at other sites in the Southern Ocean during the late deglacial hints at widespread oceanic controls on habitat suitability. Neodymium isotope analysis reveals maintained Atlantic influence at intermediate depths throughout the record, and particularly strong connectivity at the most southerly sampling site, which records rapid fluctuations in seawater chemistry during the Younger Dryas. Radiocarbon data provides new evidence in support of a Southern Ocean source of atmospheric CO2 early in Heinrich Stadial 1, and potential transfer of old carbon to the upper cell at the end of the Younger Dryas. Overall, regional hydrographic changes appear to have played a significant role in the ventilation and water mass history of the southwest Indian Ocean. Open Access

Freshwater ecosystems are considered hot spots for biodiversity and provide a wide range of ecosystem services for human beings. A variety of natural and anthropogenic stressors are now threatening the stability and prosperity of these ecosystems. In particular, climate change and pollution are the main stressors impacting all freshwater ecosystems on Earth. In this mix of multiple stressors, climate change is already having profound impacts, and is predicted to result in large-scale population collapses, species range shifts, and local species extinctions, as well as altered ecosystem properties. Scientists have spent considerable efforts in recent years investigating how these perturbations might impact food web structures and dynamics to predict potential future scenarios, but much of this work has been hindered by the slow pace of data generation using traditional techniques. Thus, there is a need to adopt and develop new approaches that can answer questions and generate data at a much higher pace. Molecular tools can address this issue by generating millions of DNA sequences in a short period of time with the potential to build food webs in a very reliable way. Therefore, a detailed understanding of food webs and their interactions is critical to predict what effects climate change will have in the near future, and we need to find faster and cheaper ways of building the necessary evidence base. This will ultimately improve our ability to forecast how communities and ecosystems will respond to global change and anticipate which species (and systems) are more likely to deteriorate under these new conditions. In this thesis, I have used a combination of traditional and molecular tools to characterize the diet of a widely distributed generalist predator. DNA sequencing revealed a higher number of links compared to traditional microscopy, but protocols need to be refined to accurately quantify each link. In addition to this, I carried out two sets of laboratory experiments to quantify warming impacts on freshwater invertebrate interactions. Functional response experiments showed increased feeding rates with warming, while qPCR was not able to detect changes in DNA retention time in predator gut contents. Open Access

Dolomitization is a common reaction in carbonate hydrocarbon reservoirs. The volume of hydrocarbons in place and their recovery can be affected by the presence of dolomite bodies that can increase or decrease the reservoir porosity and permeability. At the beginning of the reservoir burial history (< 1 km), dolomitization is likely caused by seawater, that brings Mg into the reservoir. The location and size of the dolomite bodies are challenging to determine because they are controlled by the paleoflow of seawater in the subsurface. The flow pattern depends on unknown parameters, including the seawater temperature and chemistry. The seawater temperature and chemistry are usually inferred from indirect geochemical methods, using proxies measured in dolomites, such as δ18O, δ13C, the Mg/Ca ratio, and recently, clumped isotopes (D47). These proxies can be modified by fluid/rock interactions after dolomitization, a process called diagenesis. If the impact of fluid/rock interactions on the proxies is not well characterized, the reconstruction of ancient seawater temperature and chemistry is biased. The aim of this thesis is to examine the impact of diagenesis on shallow-burial dolomite clumped isotope composition, and therefore evaluate the reliability of D47 in dolomite studies. First, new mass balance models were developed in Matlab in order to quantify the impact of dissolution/precipitation diagenetic processes on D47, as well as δ18O, δ13C, and the Mg/Ca ratio. The outputs of the mass balance models were compared with a real case study, the dolomites of the Marion Plateau (NE Australia). Marion Plateau dolomites were sampled from three IODP holes and the isotopic composition was measured, as well the stoichiometry, ordering, luminescence, crystal size and crystal orientation. The results show that the dominant diagenetic process is rock-buffered recrystallization at low water/rock ratio, evidenced by a correlation between D47 and δ18O. Recrystallization starts from the seafloor and is only associated with an increase of stoichiometry at 700 mbsf. Recrystallization is driven by the dolomite Ca-excess and poor degree of ordering, and enhanced in fine-crystalline dolomites due to their high surface area with the micropores. These findings demonstrate that D47 is the most sensible proxy to diagenesis and that caution must be taken if the aim is to reconstruct the initial conditions of dolomitization. However, clumped isotopes help to gain insight into the diagenetic history of shallow burial dolomites, and potentially many other early diagenetic minerals, for which other temperature proxies such as fluid inclusions are not always available. Open Access

Understanding aqueous uranium VI (UVI) chemistry in alkaline environments (pH >10) is crucial as radioactive waste can be stored and disposed in these conditions. Naturally occurring organic molecules can interact with UVI, modifying its aqueous chemistry and subsequent groundwater facilitated transport. The aim of this research project is to characterise the effect of the (tris)hydroxamate siderophore desferrioxamine B (DFOB) on UVI aqueous chemistry in alkaline solutions. Initially, the physico-chemical properties of UVI precipitates were characterised in solutions containing 42 ��M UVI and 0.1 M NaCl. UVI formed 640 �� 111 and 837 �� 142 nm diameter Na6U7O24 precipitates at pH 10.5 and 11.5 respectively. These were usually physically immobilised in quartz sand columns. When ���130 ��M DFOB was simultaneously added with UVI to pH 11.5, 0.1 M NaCl solutions, UVI quantitatively passes through 0.2 ��m filter membranes. This could be due to the formation of an aqueous UVI-DFOB complex as observed below pH 10. To further explore complex formation, a density functional theory protocol was established. The protocol predicts the stability constants (log ��) of UVI-organic ligand complexes with root mean square deviation of 1.19 log �� units after calibration against experimental data collected in acidic solutions. The relative stability series for UVI complexes with key siderophore functional groups calculated using the fitting equation is: ��-hydroxycarboxylate bound via the ��-hydroxy and carboxylate groups (log ��110 = 17.08), ��-hydroxyimidazolate (log ��110 = 16.55), catecholate (log ��110 = 16.43), hydroxamate (log ��110 = 9.00), hydroxy-phenyloxazolonate (log ��110 = 8.43) and ��-aminocarboxylate (log ��110 = 4.73). Finally the DFT protocol was adapted so that the stability of UVI-hydroxamate complexes can be approximated at pH 11.5. This suggests DFOB complexes in a monodentate fashion via one hydroxamate group. These results highlight the significant effect siderophores can play on aqueous UVI chemistry.

The evolutionary processes that led to the assembly of the diverse Neotropical tree flora are complex and poorly understood. It remains unclear at what pace this superlative diversity was accumulated, as do the causes of poor phylogenetic resolution and gene tree incongruence, which are commonly found when reconstructing the phylogeny of rainforest tree species. In addition, the role that introgression has played in the diversification of Neotropical trees and its effect on phylogeny remains enigmatic. The Brownea clade (Leguminosae) are a group of tree species characteristic of Neotropical rainforests, and so serve as an excellent study group with which to approach questions about the diversification of Neotropical trees. This investigation aimed to infer the rates of diversification and biogeographical history of the Brownea clade following the estimation of a phylogenetic tree for the group. The relationships between species within Brownea were then examined using phylogenomic methods to quantify gene tree incongruence, and phylogenetic model testing was used to ascertain whether this incongruence was better explained by incomplete lineage sorting (ILS) or introgression. Finally, two Brownea species found in sympatry were used to examine the impact of introgression on divergence, and whether species boundaries are maintained despite gene flow. More specifically, this study assessed whether genomic loci differed in the degree to which they introgress when compared to the genome-wide average, which would be expected if species boundaries were being maintained by selection. Furthermore, loci which were candidate regions for selection, and those associated with different aspects of the environment and morphology, were inferred in order to determine possible factors maintaining the divergence between the two species. Open Access

The relationship between offshore subsidence, continental uplift and sedimentary deposition to passive margins is poorly understood. A history of dynamic subsidence, continental uplift and sedimentary deposition to West Africa’s passive margin was synthesised to produce a framework for predicting patterns of sedimentary flux to the Mauritanian basin. Stratigraphy was mapped using seismic/well data and Cretaceous–Recent sedimentary flux was calculated. Clastic sedimentary flux to the centre of the basin increased significantly during Neogene times and accelerated across the basin at ~ 5 Ma. The origins of the Mauritanian basin were explored by backstripping wells from the study area to calculate subsidence histories. Seismic, well, gravity, magmatic and tomographic information was used to show that < 0:8 km of rapid Neogene– Recent subsidence occurred due to the initiation of shallow mantle convection. Neogene–Recent mantle draw-down caused the creation of accommodation within the Mauritanian basin that was subsequently filled by clastic sediments delivered by rivers draining West Africa’s passive margin. The causes of increased Neogene–Recent sedimentary flux were explored by inverting 14700 African longitudinal river profiles using a calibrated stream–power model to calculate a history of continental uplift and to predict the pattern of sedimentary flux to the Mauritanian basin. Results are consistent with independent stratigraphic observations which indicate that from ~ 30 Ma–Recent, sedimentary flux to Africa’s major deltas increased and induced a change from dominantly carbonate to clastic deposition. This pattern of sedimentary flux is consistent with calculations of offshore sedimentary volumes made using seismic and well data. I suggest Neogene clastic flux to the Mauritanian margin was generated by denudation of the uplifting Fouta-Djallon topographic swell and Mauritinides fold-belt, which appears to have accelerated during the last ~ 5 Ma. Results suggest that mantle-driven convective continental uplift exerts an important control on the sedimentary budget to Africa’s passive margins. Open Access

Water is the backbone of human development. However, a major impediment for sustainable development is the limited amount of data available to support evidence-based decision making on water resources and catchment management. Recently, participatory approaches to environmental monitoring have become more popular, and are being promoted as a potential pathway to address long-standing data gaps. I hypothesised that such a participatory approach to monitoring water resources is an efficient way to reduce data scarcity and to support decision making in the context of catchment management. To test this hypothesis, I studied one of the largest bottom-up initiatives of participatory environmental monitoring in the world: The Regional Initiative for Hydrological Monitoring of Andean Ecosystems (iMHEA). iMHEA is a partnership of academic and non-governmental institutions who instrumented a participatory hydrological monitoring network of headwater catchments in the tropical Andes. After a rigorous quality control of the generated data, I used them to analyse the impacts of land-use changes on the hydrological response of different Andean biomes, to develop a statistical model to predict such impacts in ungauged basins, and to evaluate a particular catchment intervention, i.e. pre-Inca artificial infiltration systems. Lastly, I put my findings in a broader context, testing similar approaches in the Ethiopian Highlands, and developing a simple method for the hydro-economic evaluation of nature-based solutions for water. I find that the data generated using such a participatory approach meets quality standards comparable to those of scientific research and, furthermore, stakeholders are more incentivised to provide open access to their data and to participate in a process of knowledge co-creation and its further assimilation. Strengthening the evidence body over which decisions are based can contribute to the improvement of water resources management as well as to the sustainable development of local communities. Open Access

Reservoirs are inherently heterogeneous. The depositional environment, compaction, deformation and cementation can lead to spatial variability in petrophysical properties, over many orders of magnitude and length-scales, with a profound effect on the flow behaviour of the fluids flowing within it. Conventional reservoir modelling workflows have adopted k-orthogonal meshes that are fixed in time and space. Due to the complex geometries found in reservoirs and the multi-scale structure of the governing equations, a more flexible approach is needed. This thesis presents an alternative to conventional grid-based modelling and simulation workflows. SBM is used to capture geological heterogeneity at all scales that impact flow, without reference to an underlying grid. Petrophysical properties within these domains are modelled as internally homogeneous. We show that cell-to-cell variability in reservoir models is not needed to capture multi-phase flow. Instead one can use a small number of larger, internally homogeneous but geometrically complex geological domains. For flow simulations, geomodels are discretised using unstructured tetrahedral meshes and the governing equations are solved using a CVFEM. The proposed simulator incorporates DAMO, designed to tackle the unique challenges of spatially varying petrophysical properties in porous media. Multi-scale features are better captured at lower computational cost by refining the mesh resolution where/when necessary and coarsening elsewhere. Material discontinuities in porous media strongly influence multi-phase flow. Traditional CVFEM smear out jump discontinuities of saturation or concentration. The high aspect ratio elements typically required to discretise the heterogeneous domains in subsurface reservoirs are also very challenging on standard CVFEM. To overcome these issues we develop a new discretisation based on the bubble enriched FEM. This new method is able to accurately represent saturation discontinuities on geologically complex models. Open Access

PhD (Environmental Sciences), North-West University, Potchefstroom Campus The inter- and intraspecific diversity of microbial communities is known to be an important, but difficult to disentangle, factor in pathogen ecology. Conspecific or interspecific microbial interactions may result in competitive suppression, the evolution of pathogens to greater levels of virulence, environmental niche separation and coexistence or even result in the generation of novel recombinant pathogen genotypes. Batrachochytrium dendrobatidis (Bd), the causative agent of chytridiomycosis, is a uniquely destructive pathogen – it is the proximate driver behind the population declines of an unprecedented number of amphibian species and has undergone a global dispersal. It has also become clear that within Bd are multiple phylogenetically deeply diverged lineages. There is evidence that these lineages vary in ecology and virulence, but diagnostic limitations have hampered research assessing the importance of lineage and lineage interactions on Bd epidemiology. I have developed a novel qPCR-based diagnostic to type the Bd lineage present in amphibian skin swabs, museum specimens and experimental animals quickly and economically, to facilitate the collection of baseline data on chytrid lineage distributions globally and to enable experimental work on lineage interactions and ecology. Using this novel diagnostic assay I have delineated Bd lineage distributions over one of the widest areas to date in South Africa and the Lesotho highlands, where both BdGPL and BdCAPE are shown to coexist, but are associated with different environmental conditions and exhibit distinctly different population structures. The data collected from this fieldwork were used to inform experimental work investigating whether the distributions observed in reality may be due to the lineages exhibiting divergent thermal optima. Finally, I considered the role that the wider fungal community may play in modulating pathogen dynamics by investigating whether a novel Malagasy chytrid may be preventing Bd from establishing on Madagascar, a biodiversity hotspot with a diverse endemic amphibian community. Doctoral

Bovine tuberculosis (TB) is recognised as the most important endemic disease affecting the farming industry within the UK. Difficulties in eradicating the disease from the national cattle herd are thought to be in part due to transmission of Mycobacterium bovis (the causative agent of TB) between cattle and wildlife, especially badgers (Meles meles). Whilst it is known that badger-to-cattle and cattle-to-badger transmission of M. bovis is possible, it is less clear when and where these transmissions occur. In the first half of this thesis I investigate two potential locations of interspecific contact; badger activity within cattle grazed pasture fields (Chapter Two) and cattle activity at badger latrines (Chapter Three). I find that badgers preferentially forage in pasture fields that were occupied by cattle 8-14 days previously. Badgers preferred pasture fields occupied by cattle 8-14 days previously, and avoided fields occupied by cattle >35 days previously. These results suggest that badgers preferred to forage on short swards rather than taking advantage of earthworm accumulations under cowpats. This information could be used to ensure cattle do not return to fields during the period when badgers are most likely to be present, and provides a practical way to reduce opportunities for badger-to-cattle transmission of M. bovis. Whilst badger activity in pasture fields gives a broadscale picture of where and when interspecific contact might occur, in Chapter Three I use camera traps to look at badger latrines as a small-scale landscape feature where badger-to-cattle contact might occur. I find that badgers continue to use latrines located in fields occupied by cattle and that cattle graze and sniff at badgers latrines within the environmental survival time of M. bovis. These results suggest that badger latrines are a potential location of cattle infection with M. bovis and that landowners should consider the location and management of badger latrines when cattle are at pasture. The badger population is managed throughout the UK with the aim of reducing badger-to-cattle transmission of M. bovis. Currently, both badger culling and vaccination are used in England, Wales and Northern Ireland. In the second half of this thesis I investigate how effective badger culling might be at a large-scale (Chapter Four) and at a smaller scale (Chapter Five). I find that, under the currently used badger culling protocol in England, culling is associated with an increase in individual badger ranging behaviour. The increased ranging among surviving badgers potentially increases the opportunities for both badger-to-cattle and badger-to-badger contact and therefore increases the potential for the transmission of infection from surviving badgers. Additionally, I find that within a culled area individual badgers are active for less time each night, potentially reducing their accessibility to marksmen. Finally, I investigated the potential effectiveness of badger management programmes (culling or vaccination) conducted at a single-farm level. The results suggest that disease management programmes should target multiple farms in order to be most effective for the target farm. However, the area around the target farm that needs to be included in a management programme is smaller for vaccination than for culling due to the increase in badger ranging behaviour associated with badger culling. Within this thesis I provide new information useful in understanding when and where badger-to-cattle transmission of M. bovis might occur and in designing effective management programmes. The results presented, whilst specific to this system, might also inform management protocols for other diseases transmitted between wildlife and livestock. Open Access

Fracture networks in subsurface rocks significantly impact the mechanical and hydraulic properties of the Earth. Realistic models of fracture networks underpin a variety of important geoscience fields. The physics of how fractures propagate and interact control how networks develop, but such processes are not routinely incorporated into discrete fracture network (DFN) models. This thesis presents a novel approach to model deformation of isotropic, homogeneous, and linear elastic brittle rocks, leading to the development of dense three-dimensional fracture networks. These networks provide realistic representations of subsurface networks that honour the physical process of concurrent fracture growth and interaction. This thesis proposes a number of novel developments that advance the field of discrete fracture modelling, with the aim of growing dense networks in a realistic manner. It presents a number of new validations for fracture growth and interaction, providing benchmarks for the accuracy required to generate realistic networks. Towards the goal of generating realistic fracture networks, several topics are studied numerically. A method for examining fracture interaction in three-dimensions is introduced, which quantifies the change in stress a fracture undergoes due to a neighborhood of nearby fractures. Fracture interaction is examined spatially in novel fracture interaction maps. Realistic fracture growth is demonstrated in both tension and compression. The effect of fracture interaction on mutual fracture growth is demonstrated on fracture arrays. The hydraulic properties of a spent UO\textsubscript{2} fuel pellet are quantified using an effective permeability computation method. The thesis concludes by presenting six geomechanical discrete fracture networks (GDFNs). The primary influences on the geometric and hydraulic properties of these GDFNs are the stresses causing growth and fracture interaction, rather than the random process of initial fracture insertion. GDFNs provide a new way of understanding subsurface processes, and improve our capacity to model hydro-mechanical processes in fractured rock masses. Open Access

In a rapidly changing world, society needs ways to understand the distribution of biodiversity and predict its future trajectory. Mechanistic simulation models provide an alternative to traditional statistical correlative methods in explaining the patterns of biodiversity and their underlying processes. I frame the research in mechanistic models and their potential practical applications in conservation using a computational linguistics approach to assess 35,000 full text publications and their citations. I show that conservation and ecology have been steadily drawing apart in topics they discuss. However, there remains cross-dialogue: conservation maintains a strong interest in trophic interactions, community ecology and macroecology in particular. This motivates my focus on global-scale mechanistic models of complete ecological communities. I first study the predictions of an existing general ecosystem model: the Madingley model and test their relationship to empirical data. I find that general trends – the Bergman cline in average body size and allometric scaling of the pace of life with body size – match fairly well. However I also discover that the pace of life, on the whole, is far too fast and small organisms are far too vulnerable to local extinction, leading to suggestions for further model development. I then present a prototype integrated model which nests the Unified Neutral Theory of Biodiversity in subsets of Madingley model organisms, allowing the model to report on a metric of broad ecological and conservation importance: species diversity and associated patterns in range size and local richness across trophic levels and a body size spectrum. Lastly, I develop an eco-evolutionary simulation showing how varying abundance and speciation rate can cause stable latitudinal gradients. I find that the evolutionary process that affects the relative fitness along this gradient can change the origin of lineages, but not the pattern of richness. Open Access

Using 3D seismic data, the deep-water fold and thrust belt of the southern lobe of the Niger Delta has been investigated over an area of 4500 km2 to document, for the first time, the detailed growth history of a thrust array and how it controlled the distribution and architecture, through time, of the coeval deep-water sedimentary systems. Quantification of the growth of each structure has been achieved using line-length balancing and yielded measures of cumulative shortening and strain, and their evolving rates, along and across strike and through time. This has enabled a new model for thrust growth to be proposed and linked to the observed change in stratigraphic architecture. The results show that all thrusts nucleated coevally in the study area as small segments, deforming at low strain rates, which caused the deflection of early leveed channels. The progressive lateral propagation and linkage of the segments, along with an increase in strain rates, caused the spatial restriction of the slope channels, until it induced the deposition of ponded lobes and the alteration of the channel architectures into erosional forms. The later decrease in strain rates and smoothing of the topography linked to the deposition of channelized sheets within shallow-ponded basins. These observations lead to the development of a predictive facies model where the occurrence of a specific facies (the architecture) is explained depending on when and where (along strike) a channel (or flow) interacts with a given fold. The specific location where channels cross structures, in turn, is dictated by how deformation is partitioned between structures across-strike, and by the particular distribution of strain rates along-strike. Distribution and architecture are effectively two linked variables which depend on a set of evolving parameters during the growth of a thrust array; the cumulative strain, strain rates and degree of fault linkage. Open Access