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During brewing fermentations, yeast cells are subjected to a range of stress factors including ethanol, osmotic and oxidative stress. These have an impact on population health, affecting fermentation consistency, efficiency, and quality of the product. Typically, the tolerance of a yeast culture to stress is assessed via analysis of the entire population generating mean data, assuming each cell has broadly equivalent characteristics. This can mask detail at the cellular level which can only be obtained by analysing individual cells. In this study, a range of yeast strains significant to the brewing industry were investigated for tolerance to a variety of environmental challenges. This was performed using a novel high throughput assay for investigating 'population heterogeneity', based on cell cytotoxicity. This revealed that some cells within a population were more tolerant to stresses than others. Furthermore, the dynamics of the stress response differed between strains in both the maximum tolerance and degree of heterogeneity. To identify potential sources of variation within populations, key cell organelles were analysed for variation in structural integrity. Yeast cells were also separated according to replicative age, by sorting based on bud scar material, this allowed for the physiological differences between daughter and aged cells to be investigated. Based on this analysis, we provide evidence to suggest that population variation is an innate inheritable characteristic. Subsequently, cell metabolites upregulated under stressed conditions were identified using metabolomics, this data was used this to conduct targeted single cell gene expression analysis, using a highly heterogenous and a less heterogeneous strain. From this, we were able to conclude that genes upregulated in response to stress were heterogenous in nature, matching the phenotypic data observed previously. We also demonstrate that the cause of phenotypic heterogeneity was likely a result of an accumulation of many heterogeneous gene expression events. Clusters were identified in specific groups of cells, implying the presence of population organisation, likely to be a 'division of labour' survival strategy. This data has implications for our understanding of strain specific fermentation limits and the techniques developed here may facilitate screening and prediction of the suitability of yeast strains for specific fermentation types.

Environmental adaptation of a species driven by different agents of natural selection is a major focus of eco-evolutionary research. In this thesis, I aimed to understand the role of selection in shaping phenotypic and genotypic adaptation of a model fish, the three-spined stickleback (Gasterosteus aculeatus) in relation to different environmental factors. Firstly, I found significant associations between the pH of loch water and patterns of morphological diversity when comparing adaptive divergence on two neighbouring islands, North and South Uist. This suggests the influence of an abiotic agent on natural selection which might be responsible for the adaptive divergence of closely-related lineages. Secondly, I observed substantial variation in phenotypic and genotypic traits among hybrids of ancient marine anadromous and newly-adapted freshwater stickleback populations in a natural hybrid zone in North Uist. Phenotypic traits such as standard length of fish, total plate count and parasite abundance showedmosaic patterns, whereas body shape, all spines and pelvic structure exhibited clinal patterns across the hybrid zone due to adaptive divergence between parental populations. Genetic diversity was also observed using adaptive nuclear and mitochondrial markers of specific candidate loci (Eda, PPARA, WNT7B, NLRC5 and Cytochrome b gene) under selection. There was strong genotypic differentiation between marine and freshwater stickleback populations due to strong direct selection across the geographical range from sea to loch. The phenotype-genotype association of selected adaptive traits indicates the evolutionary consequences of adaptation, by identifying signatures of selection on genomic regions underlying phenotypic traits. Third, I found strong genetic links to parasite resistance underlying adaptation to infection, by examining parasitic abundance in stickleback in both natural and experimental environments. The genotypes of selected adaptive loci (Eda, PPARA, WNT7B and NLRC5) varied in relation to the common ectoparasite (Gyrodactylus sp.) and freshwater endoparasite (Diplostomum pseudospathecum), suggesting a role for parasite-mediated selection in the ecological adaptation of stickleback. Finally, I found both environmental and genetic influences on the relative abundance and diversity of bacterial species in the stickleback skin microbiome. In conclusion, the research presented in this thesis provides a significant insight into divergent phenotypic and genotypic adaptation driven by environmental selection to understand the mechanism of ecological speciation in nature.

This PhD study focused on research challenges associated with dependencies of human activities and wellbeing on the functioning of terrestrial ecosystems. It builds on the concepts of ecosystem services (ES) and natural capital accounting, applying a wider scope of actual or potential benefits to people but more specific recognition of the underlying ecological processes, expressed in a single measurement unit of carbon (gCm-2). The aim of the study is to evaluate how carbon sequestration and provisioning services interact and trade-off in spatially-explicit way across the European countries, applying carbon cycle and carbon budget approach. This was carried out through statistical analysis of ecosystems' carbon budget at ground level and spatial modelling at seamless grid-level. Data quality and accuracy issues were encountered at both ground and grid levels and addressed through remote sensing vegetation indices. Because of the high correlation between NDVI (from MODIS) and GPP (from Fluxnet), the former was applied to detect sites with abnormal (outlier) GPP values and inconsistencies with other carbon budget variables. This allowed to ensemble a high quality ground dataset, and consequently to enhance the grid GPP estimates produced with the Vegetation Photosynthesis Model (VPM) of Zhang et al. (2017). Then, the ground carbon budget data was applied to train and validate a new grid estimation method based on VPM-GPP, Corine land cover, soil organic carbon (SOC) and a map of European ecoregions. This method was applied to map comprehensively the key carbon budget components including fluxes, harvests and flows. Finally, consistent NEP and NECB were mapped at 250m x 250m and were assessed against independent ground data from the published studies, which produced statistically significant Pearson correlation r = 0.72 for NECB and r = 0.73 for NEP. Provisioning ESs, including harvests of crops and fodder were mapped and assessed at aggregate regional level against European official statistics from EUROSTAT. The sum of the provisioning services was compared with carbon sequestration in soil and biomass to assess the main ESs trade-offs. The results revealed synergistic supply of services in areas of south and east Europe occupied by forests and other natural vegetation, permanent crops and less productive croplands. Most of the intensively cultivated crops and forestry areas of west and north Europe showed high provisioning ES rates traded-off against carbon sequestration ESs. Highest carbon losses were assessed for crops and pastures on organic soils under intense cultivations.

The aim of the work described in this thesis was to assess the potential sublethal effects of pesticide exposure on buff-tailed bumblebee (Bombus terrestris audax) mobility, navigation, learning and memory through the development of novel bee behavioural assays. The development of such comparative testing platforms adds core tools to our ability to assess sublethal outcomes across a broad behavioural range and provides a sound basis to compare pesticidal impacts across species. This is currently limited, due to a deficit of studies on non-Apis bees. In Chapter 2, core gaps in the existing use of aversive training in bee cognitive studies are highlighted. In Chapter 3, a novel thermal-visual arena was piloted to aversively condition bumblebees to locate a cool reward zone, suggesting ambient temperature as a fruitful avenue for bee aversive learning research. In Chapter 4, this was further confirmed through trials comparing aversive conditioning to other conditioning methodologies, demonstrating that B. terrestris foragers responded best to aversive conditioning elements. In Chapter 5, the thermal-visual arena was used to assess the impact, via oral exposure, of sublethal doses of the neonicotinoid insecticides thiacloprid (500 and 5000ppb) and thiamethoxam (10 and 100ppb) and the sulfoximine insecticide sulfoxaflor (5 and 50ppb) on B. terrestris navigation and learning, demonstrating that thiamethoxam prevents bees from improving in key training parameters. In Chapter 6, new ways of examining behavioural templates were explored utilising power law analyses, uncovering a speed-curvature power law present in the walking trajectories of bees. In Chapter 7, this speed-curvature power law was found to be disrupted under thiamethoxam (10 and 100ppb) exposure. In Chapter 8, potential genetic determinants of individual differences in B. terrestris learning ability were elucidated through RNA-seq analyses of 'good' and 'bad' learners. In Chapter 9, a novel colour learning assay was employed to examine imidacloprid (10ppb) impact on associative and reversal learning in B. terrestris foragers, revealing that foraging behaviours, but not learning, are affected by chronic oral exposure. The results presented in Chapters 5, 7 and 9 clearly demonstrate that low doses of pesticides can have important sublethal effects on buff-tailed bumblebees, and can affect previously unstudied parameters (e.g. power laws governing movement (Chapters 6 and 7)) and that current standard toxicological assessments often miss such subtle (not immediately lethal) impacts.

Ancient, veteran and notable trees are ecologically important keystone organisms and have tangible connections to folklore, history and sociocultural practices. Although found worldwide, few countries have such a rich history of recording and treasuring these trees as the UK, which has resulted in the formation over the past 15 years of a large, comprehensive database of ancient and other noteworthy trees, the Ancient Tree Inventory (ATI). Although the ATI contains over 200,000 recorded trees, there are still thought to be many more that are undiscovered across the UK, and information about their status, condition and distribution is lacking. The primary aim of this thesis is to use the ATI to gain novel and detailed insights into the true distribution of ancient and veteran trees across the UK, important predictors of their presence, and key habitat types in which they are found. The ATI suffers many of the problems of large species databases, including sampling bias, which is a major focus of this thesis. To address this problem, sampling bias is first identified and quantified, and then established and novel bias correction methods are employed to improve predictions of ancient and veteran tree distributions. By combining mathematical models at various scales, from specific habitats to the whole of England, with additional independent data from desk and field surveys, robust accurate distribution maps of ancient and other noteworthy trees are produced and verified. The models suggest that wood-pasture is a particularly important habitat for ancient and veteran trees, and that their distributions are highly influenced by historical features of the environment and human factors. A key result emerging from multiple chapters of this thesis is the potentially large number of undiscovered ancient and veteran trees predicted across England: diverse alternative models produced similar and impressive total estimates of around two million trees. These results can be used to inform the conservation and protection of ancient trees, and highlight the need for more targeted surveying, tree planting and implementation of policy measures to ensure their persistence and survival into the future.

Understanding the limits to species ranges and distributions remains a difficult and long-standing problem in the field of macroecology. This difficulty exists because species’ range limits reflect several complex and interacting processes including; physiological responses to abiotic conditions, biotic interactions and species’ dispersal abilities across geographic space. This complexity is increased further under rapid anthropogenic climate change which is predicted to affect all these processes simultaneously. Nonetheless, recent advances in species distribution modelling—particularly mechanistic species distribution models which can estimate a species’ fundamental niche—have provided novel means to further understand how species distributions manifest across large geographic extents. Despite these methodological breakthroughs, there remain substantial gaps in our knowledge of species’ distributions including: (1) How does climate alter the spatial distribution of ectotherm activity budgets through time and space? (2) What are the relative contributions of biotic interactions, dispersal ability and availability of preferred habitat type in limiting species’ ranges across geographic space? and (3) Does climate generate repeatable and predictable patterns of biodiversity? Here—within a species distribution modelling framework—I use both correlative and mechanistic species distribution models to address these questions. I reveal how climate, biotic interactions and species’ dispersal abilities limit ranges across large spatial extents and that by integrating correlative and mechanistic species distribution models we may tackle questions that have, until very recently, been out of reach. I predict that over the next decade macroecology will witness an increased use of correlative and mechanistic models in tandem to leverage the strengths of both approaches. Despite continued anthropogenic pressures on species across the globe limiting where species can survive, it is nonetheless an exciting time to be working in the field of macroecology and species distribution modelling.

Studying species richness distribution patterns depends on data quality, which imposes challenges for conservation action. Species distribution modelling is a powerful tool to overcome some of these hurdles, and can gives us ecological and biogeographical insights about species distributions patterns and habitat suitability even in poorly sampled habitats. The main objective for this thesis was to model the distribution of 62 terrestrial reptile (lizard and snake) species to obtain the pattern of species richness and habitat suitability across Saudi Arabia. I used both species distribution models (SDMs) built for Egypt (a better-studied area) and then spatially transferred into Saudi conditions, as well as models built with local data. Maxent software was used to interpolate (based on Saudi data) and transfer (based on Egyptian data) models. The accuracies of these models were then evaluated on-the-ground using data from field work conducted in the summer of 2017 and 2018 in Tabuk Province. The detectability and occupancy of each species in the field was estimated using PRESENCE software. I then assessed the conservation value of the proposed and current Protected Area network in Saudi (managed by the Saudi Wildlife Authority) and identified potential new important areas of conservation planning under various different assumptions (socioeconomic and uncertainty analysis) using Zonation software. The maximum species richness of reptiles was predicted to occur in the central plateau, north-western borders, south-western areas, and in the coastal areas of Saudi Arabia. I identified areas across Saudi Arabia that are considered to be under-sampled relative to these predictions. The transferred Egyptian models yielded very effective predictions, analogous to those generated by local independent models based on Saudi data. Some species were predicted better by the transferred Egyptian model than the equivalent Saudi model. Model accuracy across species as estimated using the independent field data varied among species and correlated positively with accuracy estimated using partitioning of the original Saudi data, but validation using independent data gave lower accuracy estimates overall than data partitioning. Ground-truthing validation showed that the transferred Egyptian model was able to predict presences better than the Saudi model built from local data, and that the Saudi model was better at capturing the predicted areas of high species richness. Species detectability in the field was weakly positively correlated with model accuracy calculated from the new independent field data, hinting that models work better for species which are easy to survey. The directed field validation successfully led us to record species within Saudi Arabia that had not been recorded before, and extend the known range for a species that is located completely outside the Protected Areas and had not been recorded for 40 years. I found that the conservation value of current and proposed Saudi’s PAs was significantly better than the areas outside them across all Zonation models. I proposed possible extensions of some PAs to cover top-ranking areas predicted to be suitable for reptile conservation. SDM predictions appear to be a very effective tool for exploring spatial patterns of species diversity, especially when there is a paucity of data. When testing SDMs, using new data, collected independently of the data used to build the models, seems to be the best practice to evaluate model predictive performance, but caveats with such data must be considered as they may not be entirely statistically independent. Incorporating different scenarios in conservation assessments and planning can help increase its reliability in identifying potential important areas for conservation.

Coral reef ecosystems around the world are declining as a result of human impacts including overfishing, pollution and climate change. The coral reefs of South Sinai are significant because of their unique biodiversity, the income that they generate for Egypt through diving tourism and their importance as traditional fishing grounds for the Mzeina Bedu. This PhD takes a multidisciplinary approach to evaluate the status of coral reefs in South Sinai, with particular emphasis on Bedouin fishers and their fisheries. In Chapter 1, I examine the importance of culture and traditional knowledge in the successful management of coral reefs and natural resources in general. In Chapter 2, I focus on the Bedouin tribes of South Sinai to understand their history and socioeconomic status; investigating their fishing techniques and sites as well as their traditional understanding of coral reef biodiversity and ecology. Chapter 3 focusses on the ecological status of finfish populations at sites along the South Sinai coastline, evaluating the status of stocks and potential Bedouin fishery impacts. Chapter 4 examines the invertebrate fishery, which is mainly practised by Bedouin women and targets Tridacna clams. Chapter 5 takes a fishery-dependent approach to assess the catch of Bedouin fishers, to understand important biological and socioeconomic parameters that influence the fishery. In Chapter 6, I use statistical modelling techniques on long-term coral reef ecosystem data sets from the study area to analyse longer-term trends in the ecological status of reefs in South Sinai and likely causes for these trends. Coral reefs provide income, tourism, food and coastal protection to local communities and indigenous people throughout the tropics. The socio-cultural facets of the Mzeina Bedu have been inextricably connected to the reefs and associated fisheries of South Sinai for generations. However, exploited finfish and invertebrate communities have declined in both size and abundance with increased fishing pressure, resulting in ecosystem-wide impacts. The Mzeina themselves should be integral to any proposed fisheries monitoring or management initiatives, and technological approaches may provide useful cost-effective tools. Fisheries ecosystem-level declines have been apparent over at least the last decade and sustained monitoring is essential to ensure that the impact of management initiatives may be measured. If urgent collaborative management and enforcement actions are implemented alongside a programme to develop livelihood opportunities for the Mzeina, the reefs of South Sinai could return to a state that supports both the socioeconomic needs of the Bedu and continues to generate substantial tourism income.

The damage to soils caused by agricultural intensification greatly affects belowground faunal communities, typically via a reduction in population size and diversity in comparison with those in semi-natural habitats. This can cause an imbalance in associated soil functions. The soil mesofauna, including Acari (mites) and Collembola (springtails), fulfil a wide range of these functions and our understanding of soil processes is closely linked to our knowledge of the dynamics of invertebrate communities. In the context of current global change, sustainable food production is a significant challenge that can potentially be better met by improved understanding of the abundance and composition of the soil mesofaunal populations, in order to optimize ecosystem services delivered by agricultural soils. This PhD project addressed this issue by investigating the changes induced by sown grass field margins on the abundance of populations and community structure of soil mesofauna in the context of arable fields. It aimed to understand to what extent field margins affect soil mesofauna communities and whether these effects extend into the adjacent crop. To do so, the project investigated: (i) the nature of the ecological succession of the mesofaunal populations in relation to time since establishment of the margin; (ii) the impact of field operations on the abundance and structure of the invertebrate communities, regarding the effects of the margin; (iii) whether faunal-driven soil processes, such as decomposition, are affected by field management (establishment of field margins) and field operations (traffic; restitution of crop residues); (iv) the impact of historical landscape management on current biodiversity markers. To answer these questions, field margins, on two UK farms which work with BASF to demonstrate sustainability in Agriculture, that had been established for different durations (1, 6 and 10 years) were investigated and changes in structure and population sizes of invertebrate communities associated with these field margins and their adjacent crop areas were studied over two years. Soil mesofauna were sampled, counted and identified from the various field margins of different ages, with differing orientations regarding the field traffic, and their adjacent crop. It was found that population abundances and complexity of the community structures were generally enhanced in the field margins: more invertebrates and complex communities were found in the margins than in the adjacent crops. Likewise, community composition in the margins changed over time toward larger organisms and specialist species. Although it was hypothesised that mesofaunal populations in the crop would be influenced by the presence of the margin (the closer to the margin, the more similar the composition), it was found that field management was also an important driver of the soil mesofaunal communities. In the cropped areas, the heterogenous distribution of species abundances and the differences in community structure reflected the degree of disturbance caused by the different agricultural activities, such as tillage practices, management of crop residues or wheeling from field traffic. The ability of certain groups of soil invertebrates to disperse, and colonise new habitats was revealed; for example, at the margin:crop interface where there are compacted, traffic-related 'tramlines', abundances were particularly low while further into the field in less-disturbed areas, populations were more abundant. The interaction effects between field margins, within-field crops and farm management highlighted the importance of well-designed and integrated agricultural strategies to maximise soil functions contributed-to by the soil fauna, such as litter decomposition and nutrient cycling, which in turn provide ecosystem services, such as maintenance of the soil fertility and structure, essential to sustainable food production.

Tropical peatlands are complex and globally important ecosystems which are increasingly threatened by anthropogenic disturbances such as logging and expansion of oil palm plantations, particularly in South East Asia. Microbes in peatlands play an important role in governing overall functions e.g. carbon and nutrient cycling, yet their characteristics in these habitats are poorly understood. This research aimed to elucidate the response of tropical peatlands to disturbance by quantifying the peat properties, soil microbial community structure, nutrient content and greenhouse gas (GHG) emissions, and the functional interactions between these components under different land uses. Specifically, differences between primary peat swamp forest, secondary peat swamp forest, different land-use types and cropping systems associated with oil palm plantations in Peninsular Malaysia were investigated. Sampling was conducted between November 2014 - October 2018, covering both wet and dry seasons. Bacteria at all depths overwhelmingly dominated all land-use types but microbial phenotypic community structure responded to land-use, depth and changes in season. CO2 emissions were lowest in the primary forest and highest in the secondary forest. CO2 emissions in agricultural plantations were lower than the secondary forest, due to very low autotrophic contribution to net emissions in those habitats. Second generation cropping systems exhibited distinct seasonal variations which were more pronounced in 2nd generation oil palm monocropping, where the CO2 emission was reduced to half in the dry season. CH4 emissions exhibited an opposite trend to that of CO2, with highest CH4 emissions in the primary forest and oxidation in the secondary forest, while the agricultural systems emitted low levels of CH4. However, CH4 emissions were very low in comparison to CO2 emissions. Both CO2 and CH4 emissions were significantly impacted by changes in moisture level, with 2nd generation oil palm exhibiting moisture limitation for CO2 emissions, unlike all the other peat land-use studied. Temperature and pH also significantly influenced microbial community structure and GHG emissions. Gram-positive and Gram-negative relative abundance were positively correlated with CO2 and CH4 emissions, respectively. Almost all the nutrients were substantially lower in the secondary forest to that of the primary forest. Cu and Mo concentration were negatively correlated with CO2 and CH4, respectively. Past drainage in secondary forest reduced nutrient contents, including some with antimicrobial properties, and favoured Grampositive bacteria over Gram-negative bacteria. In agricultural plantations the autotrophic contribution of the vegetation to CO2 emissions was significant only for mature oil palm and yam plants, implying that most of the CO2 emissions from other cropping systems is heterotrophic respiration, resulting in C loss. This is further supported by the 2nd generation mono-cropping having higher bulk density and the lowest organic content, while the 2nd generation intercropping maintained most of the organic content with relatively less change to other peat properties. Overall, the results demonstrate that peat properties, microbial communities and GHG emissions are affected by the land-use changes associated with oil-palm plantations. However, the impact was highest at prolonged oil palm mono-cropping, while the practice of intercropping ameliorated the damage caused by such plantations.

Despite its large volume, Lake Baikal has been experiencing recent changes within its limnological and biological structure, as well as changes within lake water nutrient and dissolved organic carbon concentrations. The biological changes within Lake Baikal include alterations within the distribution and abundance of major phytoplankton and zooplankton groups. These limnological changes are likely to be from both climate warming and anthropogenic impact, particularly over the last few decades. Recent shoreline observations in the South and North regions of Lake Baikal have found large blooms of filamentous green algae, which has been associated with nutrient enrichment from surrounding settlements and growing tourism. This highlights the question as to whether the pelagic regions are similarly showing any signs of anthropogenic driven nutrient enrichment. The aim of this thesis was to examine if pelagic Lake Baikal is showing any evidence of eutrophication and/or response to climate warming. The main themes of the research were to assess the modern-day limnological condition of Lake Baikal in the summer (August 2013) and winter (March 2013) months,and to examine Baikal’s phytoplankton response to nutrient enrichment via the construction of mesocosm experiments. High-resolution limnological change was then reconstructed from sediment cores across the lake. Sites were chosen within pelagic regions, bays and shallow waters nearby river inflows, and palaeolimnological records were used to assess primary production changes and floristic changes over the last few centuries. This timespan enables both natural variability within the system to be explored, and more recent changes pre and post known human influence within the catchment area (c. 1950 AD). The main palaeolimnological techniques applied for primary production proxies were sedimentary algal pigments, stable isotope analysis of bulk organic carbon and diatom valve concentrations. Mercury analyses was also applied to water samples and sediment cores as a pilot study to explore toxic metal pollution at Lake Baikal, due to mining activity along the Selenga River, and examine historic levels of mercury contamination, and examine historic levels of mercury contamination. Both modern-day limnological surveys and palaeolimnological records seem to be showing increasing algal biomass (chlorophyll-aconcentrations) over the last 60 years, with decreasing trends in diatom production (from diatoxanthin pigment concentrations and diatom valve concentrations) in the South basin. Spatial survey data represents a snap shot in Baikal’s limnology in late summer (August 2013), and shows higher than expected concentrations of total phosphorus within the mixing layer, which fall within the meso-eutrophic range. Dissolved organic carbon concentrations seem to now be higher within Lake Baikal’s waters, and both nitrate and silicate concentrations appear to be similar to known previous concentrations at Lake Baikal. A pilot study of mercury concentrations within Lake Baikal waters and sediments, show no signs of mercury contamination from mining activity along the major river inflows, and atmospheric deposition. Experimental results show that within the pelagic regions of Lake Baikal, nitrogen, phosphorus and silicon are influencing algal communities, with Si addition stimulating diatom growth, nitrogen and phosphorus addition stimulating chlorophyte growth, although overall nutrient treatments did not increase chlorophyll-a yield. Interestingly, experimental findings also highlight the potential influence of picocyanobacteria populations on silicon cycling. Concentrations of sedimentary chlorophyll-a concentrations (plus its derivatives) rise prior to major industrial influence within the Baikal catchment region, and stable carbon isotope records show a positive correlation with chlorophyll-a concentrations in the South basin, Selenga and Maloe More sites. Total phosphorus concentrations could be a result of both anthropogenic nutrient pollution, entering into the lake via the Selenga River, and climate driven changes in lake stratification and nutrient utilisation by algae. Results from limnological surveys and palaeolimnological records are thus likely to be reflecting both recent anthropogenic impact and climate change (rising lake water temperatures, declining ice cover thickness and duration and increasing river inflow from permafrost thaw), within the pelagic regions, especially given that recent work provides evidence of toxic cyanobacterial and chlorophyte blooms within the shallow waters of Lake Baikal. For the Maloe Moresite, which is a bay of the Central basin, results show a rise in sedimentary chlorophyte pigments post 1950 AD, suggesting that this bay region of Lake Baikal is currently being affected more than deeper water sites, by human influence, showing signs of eutrophication due to a switch in algal community composition.

Lake Ohrid is a large, deep, ancient lake located on the Balkan Peninsula and has an extraordinary degree of endemic biodiversity. A deep drilling campaign was carried out in 2013 as part of the Scientific Collaboration on Past Speciation Conditions in Lake Ohrid (SCOPSCO) project to better understand the influence of climate and environmental change on evolutionary patterns and endemism. Initial results from a 569 m sediment succession drilled in the centre of the basin indicate continuous lacustrine conditions over the past ca. 1.2 Ma. This thesis presents new stable isotope data from carbonate within the upper 248 m of the composite profile, covering the last ca. 640 ka at a millennial-scale resolution (≈ 0.5 ka). Isotope data are used to provide a long-term palaeoenvironmental reconstruction, which is supported by a quantitative model of modern lake water isotope composition and a detailed multi-proxy investigation of climate evolution since the last glacial period. Water balance calculations confirm Ohrid to be an evaporative system with a complex hydrology. Variations in the isotope composition of modern lake water are suggested to represent long-term fluctuations in water balance. A trend from wetter to drier conditions through the Holocene is consistent with regional and hemispheric processes related to changes in insolation. Over the last ca. 640 ka, endogenic calcite is precipitated in abundance during warm stages, however carbonate is negligible during glacial periods with the exception of discrete horizons comprising early diagenetic authigenic siderite. The oxygen isotope composition of lake water, calculated using calcite and siderite, indicates more evaporated conditions during warm stages and fresher lake water in glacial phases. Low frequency variability shown by calcite isotope data suggests relatively stable conditions before ca. 450 ka, a transition to a wetter climate between ca. 400-250 ka, and a trend to drier climate conditions after ca. 250 ka. Higher frequency millennial-scale oscillations and abrupt climate events observed during warm stages are likely associated with regional climate change as a function of orbital forcing. This study emphasises the potential of Lake Ohrid as a valuable archive of climate change in the central Mediterranean region and demonstrates the efficacy of isotope data for palaeoenvironmental reconstruction at Lake Ohrid.

Lowland tropical peatlands can act as sinks and sources of carbon, interchanging greenhouse gases (GHG) with the atmosphere. Despite the importance of lowland tropical peatlands in the past, present and future global carbon cycle, uncertainties exists about the controls regulating the processes of carbon turnover. Therefore, this study examined different controls of carbon turnover, including abiotic, biotic and anthropogenic. For this purpose, six peatlands with different dominant vegetation were selected in the north western region of the Republic of Panama (9° 4' 16.06" N; 82° 6' 28.98" W). Two phasic communities were used as experimental models; Raphia taedigera palm swamps and mixed forest swamps with Campnosperma panamensis. A combination of in situ and ex situ experiments were performed between March 2010 and November 2012: i) ex situ respirometric assays were used to quantify differences in carbon turnover through the peat profile under different redox regimes, ii) litter bags experiments were used to investigate the effect of plant materials with distinct botanical origins on peat accumulation, iii) the effect of vegetation on greenhouse gases emissions was assessed with in situ and ex situ experiments and iv) land use change (LUC) was monitored to evaluate its consequences on the short term carbon turnover processes. Ex situ respirometric assays suggested that organic matter composition of peat plays a major role in controlling the potential CO2 and CH4 production. Under anaerobic conditions, the potential CO2 and CH4 production decreased with depth. The potential CO2 and CH4 productions in the surface peat layers of the anaerobic assays were 7 and 120 fold higher than those in deeper layers of the peat profile respectively. The change in redox regime affected the carbon turnover; the CO2 potential production in the surface layers (< 50 cm depth) increased 20 fold when exposed to aerobic conditions, whilst the deeper layers (> 50 cm depth) increased 47 fold. In contrast, CH4 production was reduced two orders of magnitude under aerobic conditions. Tissue types of R. taedigera and C. panamensis showed different in situ decomposition rates. Decomposition was significantly slower belowground than at the surface, reflecting the importance of the redox regime on the litter decomposition. Roots presented the lowest in situ decomposition rates among tissues both at the surface (R. taedigera: 0.59 ± 0.04 y-1; C. panamensis: 0.45 ± 0.01 y-1) and belowground (R. taedigera: 0.13 ± 0.01 y-1; C. panamensis: 0.17 ± 0.005 y-1). Macromolecular analyses revealed that roots and stems have similar composition to the peat material accumulated in deeper layers. Vegetation exerted a direct control on GHG fluxes from lowland tropical peatlands. In both ex situ and in situ measurements, fluxes of CO2 and CH4 varied with vegetation activity. In terms of CO2eq (Addition of mass flow of GHG, converted with the global warming potential of each gas), the agricultural LUC increased CO2eq emissions from the R. taedigera swamp at Cricamola by ca. 20 t CO2eq ha-1 y-1. At the pristine site, CO2, CH4 and N2O contributed with ca. 90, 9 and 1 % of the TCO2eq respectively. In contrast, in the anthropogenically impacted plot, CO2, CH4 and N2O contributed with ca. 29, 69 and 2 % of the TCO2eq respectively. Water table strongly influenced the carbon turnover. Under flooded conditions (water table at or above the surface; 0 to 0.15 m), the CH4 emissions were ca. 4 times higher in comparison with those where the water table was below the surface (−0.01 to −0.4 m). In contrast, CO2 emissions were ca. 1.5 times higher when the water table was below the surface. It was concluded that the interdependence of hydrology, peat composition and vegetation activity are the main factors controlling carbon turnover in the lowland peatlands of the north western region of Panama. This thesis has shown that fine scale alterations of these three factors can have large scale consequences, demonstrating sensitivity to perturbations and ease shift of lowland tropical peatlands from carbon sinks to carbon sources.

Nitrogen enrichment in sensitive habitats has become a matter of concern in recent years, and has led to the need to develop a bio-monitoring scheme that could be used by non-specialists to undertake site evaluation across the UK. Epiphytes are ideal candidates for such a project due to their high sensitivity to atmospheric pollutants. Indicator species analysis identified a comprehensive UK-specific list of epiphytic indicators for NH3 pollution in the UK that for the first time also included microlichens. A shortlist of easily identifiable, widely distributed indicator species was produced from these and used to trial the effectiveness of a frequency based scoring system. A simple, un-weighted frequency based scoring system founded on the Lichen Acidophyte Nitrophyte index was found to correlate strongly with NH3 concentrations in air. Assessment of other atmospheric chemistry and climate variables with the scoring system showed that NO2 concentrations in air and bark pH were confounding factors. The influence of pH was further validated by observations in a field experimentation plot where different N forms were applied. In order to address this, a regression equation was formulated that incorporated NH3, NO2 and bark pH to produce a predictive model that could potentially be used to evaluate site condition with respect to atmospheric N pollution, as defined by the combined effect of NH3 and NO2. Investigations into the biochemistry of an indicator species identified that rates of phosphomonoesterase (PME) activity were higher in N-sensitive species than N-tolerant ones. N-sensitive lichen thallus pH measurements for were also consistently more acidic than those of N-tolerant species, and closer to the observed pH optima of PME activity.

Using spatial patterns to infer biotic and abiotic processes underlying plant population dynamics is an important technique in contemporary ecology, with particular utility when investigating and shrub population dynamics, for which experimental and observational methodologies are rarely feasible. Using a novel one-class classification technique, the locations of over 17,000 Spartocytisus supranubius individuals were mapped from aerial imagery generating a spatially extensive (162 ha), yet accurate, dataset. The recent rapid increase in studies using pattern-process inference has not been accompanied by a rigorous assessment of the behaviour of these techniques, nor an appraisal of their utility in addressing ecological research questions. The first part of the thesis addresses these concerns, investigating whether current methodologies are adequate to test hypotheses concerning spatial interactions. A literature review reveals a preponderance of studies of small, little-replicated plots. The results of the research raise concerns about the utility of spatial point pattern analyses as currently applied in the literature. To avoid inaccurate description of fine-scale spatial structures it is recommended that researchers increase plot replication. Furthermore, studies of spatial structure and population dynamics should account for spatial environmental gradients, whatever plot size is used. The second part of the thesis presents a rigorous investigation, incorporating a priori inference and the application of fine-scale spatial statistical and modelling techniques, of the biotic and abiotic mechanisms underlying the spatial structure and population dynamics of S. supranubius, a leguminous shrub species endemic to the Canary Islands. The spatial structure of S. supranubius populations is consistent with the operation of clonal reproduction and intra-specific competition. However, the results indicate that spatial environmental heterogeneity (from small to broad scales), in particular topography, can interact with biotic processes to generate quantitatively different S. Supranubius patterns in different locations. Future research into the spatial and temporal dynamics of interactions between abiotic and biotic processes is recommended.

Knowledge about the distribution of species is limited, with extensive gaps in our knowledge, particularly in tropical areas and in arid environments. Species distribution models offer a potentially very powerful tool for filling these gaps in our knowledge. They relate a set of recorded occurrences of a species to environmental variables thought to be important in determining the distributions of species, in order to predict where species will be found throughout an area of interest. In this thesis, I explore the development, potential applications and possible limitations of distribution models using species from various taxonomic groups in two regions of the world: butterflies, mammals, reptiles and amphibians in Egypt, and butterflies, hoverflies and birds in Great Britain. Specifically I test: 1) which modelling methods produce the best models; 2) which variables correlate best with the distributions of species, and in particular whether interactions among species can explain observed distributions; 3) whether the distributions of some species correlate better with environmental variables than others and whether this variation can be explained by ecological characteristics of the species; 4) whether the same environmental variables that explain species’ occurrence can also explain species richness, and whether distribution models can be combined to produce an accurate model of species richness; 5) whether the apparent accuracy of distribution models is supported by ground-truthing; and 6) whether the models can predict the impact of climate change on the distribution of species. Overall the use of distribution models is supported; my models for species in both Egypt and Britain explained observed occurrence very well. My results shed some light on factors that may be important in determining the distributions of species, particularly on the importance of interactions among species. As they currently stand, distribution models appear unable to predict accurately the impacts of climate change.

Nutrient dynamics of two sub-types of peat swamp forest, mixed swamp forest and low pole forest, in the upper catchment of the Sebangau River in Central Kalimantan, Indonesia were studied. Three permanent study plots, 50 x 50 m, were established in each forest sub-type to facilitate collection of throughfall, stemflow, litterfall, decomposition, above ground and below ground biomass, peat and water samples. Graphical presentation, Wilm's method, and analysis of variance were carried out for both sub-types of forest in order to analyse data to detect any significant differences. Rainfall is slightly acid (pH 5.96+0.35) with a predominance of NH4-N, Ca and K. Throughfall and stemflow are enriched in most elements analysed compared to rainfall and the pH values are lower. Throughfall pH is 4.76±0.33 in mixed swamp forest and 4.37±0.33 in low pole forest. Stemflow pH is 4.03±0.19 in mixed swamp forest and 3.57±0.11 in low pole forest. Greater litter production was obtained in mixed swamp forest (8,411 kg ha-1 yr-1) than in low pole forest (6,534 kg ha-1 yr-1). Dry weight of the different fractions of litterfall (leaves, branches, reproductive parts and other debris) for MSF and LPF were 6216,1246, 460 and 489 kg ha-1 and 4864,1251,169 and 251 kg ha-1, respectively. Decomposition rates (k) in the MSF and LPF are 0.396 yr-1and 0.285 yr-1 respectively. Above ground biomass in MSF and LPF are 313,899 and 252,547 kg ha-1 respectively, while below ground (root biomass) is 26,533 and 14,382 kg ha respectively. Nitrogen is the predominant nutrient in peat soil at 50 cm depth in both MSF and LPF, while manganese is the lowest. Calcium is the element in greatest amount in water run off in MSF and LPF at 8,15 and 7.15 kg ha-1 yr-1 respectively, while manganese was the lowest at 0.01 and 0.02 kg ha-1 yr-1, respectively. Nutrient inputs were higher than nutrient losses during the 1-year study period with the greatest nutrient gain for calcium while manganese was the lowest in both sub-types of forest. Moreover, the results of this study highlight that nutrient concentrations in peat soils are low and the substrates are acidic. These factors are likely to be strongly limiting to agricultural development, including plantations of estate crops and trees. Under such conditions the maintenance of intact forest for natural ecosystem services (e. g. carbon storage, watershed, biodiversity maintenance, timber production in certain time period) is likely to be a far wiser land use from a long-term perspective.

Mathematical models are extensively used to support decision-making in many disciplines. Nevertheless there are not clear standard guidelines to assess models performance. This significantly affects model selection processes, which aim to determine the "best model", among several possible candidates. Model performance is often measured by the accuracy with which models predictions fit independent observations. However this test assesses only a single aspect of a model. A model selection process should establish the similarities between the constructed and the conceptual model. Therefore it should be based on a comprehensive assessment of the models capabilities, which is the objective of the multi-aspect comparison approach proposed in this work. The innovative aspect of this approach is to create a relationship among four conventional tests, i.e. uncertainty and sensitivity analysis, goodness-of-fit prediction-observations, model complexity and level of details, in order to provide a reliable estimation of the differences between the constructed and conceptual models. Although, model complexity is quantified using a standard approach, a novel methodology is proposed in this thesis, intended to be an intuitive and illustrative approach in creating a linkage between model complexity and level of detail. Five radioecological models have been considered: SAVE rural model, TEMAS rural model, SAVE semi-natural model, FORM and RIFE1. The results show that there is a limited resemblance between these models and the respective conceptual models. This is due to low prediction accuracy (RIFE1 and FORM); high level of uncertainty (SAVE rural); sensitivity to parameters which is not consistent with the current understanding of radiocaesium behaviour in the environment (TEMAS and SAVE rural). The SAVE rural model has been revisited in order to increase the similarity between the constructed and conceptual model. The resulting model prediction shows lower degree of uncertainty and there is a significant agreement between the model sensitivity results and the general understanding of the processes affecting Cs soil-to-plant transfer. Nonetheless the revised model does not show higher prediction accuracy than the original model. It is concluded that a reliable methodology for model selection should be based on a comprehensive investigation of each considered model aspect and that there is not a single best approach. The methodology proposed in this work has been successful in the case of the five radioecological models studied.

Habitat fragmentation is widely recognised as a major threat to global biodiversity and by decreasing the size of habitat patches and disrupting important ecological processes through exposure to edge effects, is detrimental to many taxonomic groups, including insects. This research aimed to determine the influence of edge effects on the ecology of the wood ant, Formica rufa L. through an intensive study of a single site in Northamptonshire. The study focused upon the impact of both aspect and distance-related edge effects, measured along three edge to interior transects, a total of 82 sample nests and five control points within four study aspects located around the wood. Nest location and characteristics, density, colony structure, and the phenology of activities were also recorded. Overall, southern transects received more light but lower wind speeds than the other aspects and also supported a greater diversity of tree species. Southern nests also received significantly more light in the early and late parts of the year than nests in other aspects. At the random sampling points, nests received significantly more light and lower wind speeds than the controls. Compared with the controls, nests supported a higher plant species richness, but in terms of abundance, only sycamore (Acer pseudoplatanus) and elder (Sambucus nigra) were found in greater numbers at nest sites than controls. The south also supported significantly higher nest densities and had a higher percentage of polydomous colonies than the other aspects. The results showed that aspect mediated edge effects caused differences in wood ant phenology. Colonies in the south left hibernation earlier, began reproduction earlier, and had completed the reproductive cycle before colonies in the other aspects had begun theirs. Overall, these results are the first to show the impacts of aspect and distance related forest edge effects on F. rufa

This thesis describes PatchMapper, a model combining a population simulator based on individual behaviour, with a spatially explicit representation of a landscape. To investigate the robustness of the technique, representatives of three major taxa were modelled: the nuthatch (Sitta europaea L.), the white-footed mouse (Peromyscus leucopus Rafinesque) and the black hairstreak (Satyrium pruni L.). For the nuthatch and white-footed mouse, the performance of PatchMapper was compared with published models of the same species, but using different approaches, including, for the nuthatch, a comparison against observed numbers in a real landscape. To investigate the behaviour of the model, a sensitivity analysis was also undertaken.;Written in Java, for portability, the model enables the user to select demographic and behavioural parameters via an interactive interface and includes a real-time (computer) display of the position of individuals during the simulation. Novel aspects of the model include perceptual range and field-of-view. Internally generated neutral landscapes can be used for modelling general cases, with imported digitised landscapes enabling specific study areas to be modelled. Habitat area and habitat quality dynamics can also be modelled. Dispersal flow diagrams can be generated, providing a visual explanation of the effects of landscape changes on inter-patch dispersal paths and populations in target patches.;Performance compared well with published models, predicting a feasible match with observed numbers of nuthatches in the real landscape. Revealing predictable and realistic responses, the sensitivity analysis revealed that the model coding was valid. The value of specific case studies was illustrated, along with the dangers of relying on intuition when evaluating the response of species to habitat fragmentation. The individual-based SEPM approach was found to best suited to the modelling of univoltine territorial species (such as nuthatch), with a single dispersal phase between fledging and territorial establishment.

The chemical composition of snow, terricolous lichens and top-soil along with abundance and diversity of lichen communities were assessed in the Pechora and Usa basins, North-Eastern European Russia. Transects were established through the principal industrial towns of Vorkuta, Inta and Usinsk to assess the spatial extent of acid or alkaline and metal deposition. A further eight sites were selected to assess local impacts of oil and gas operations. In the Usa basin decreases of nitrogen concentration in the lichen Cladonia stellaris and winter deposition of non-sea salt sulphate moving northward were attributed to long range transport of oxides of nitrogen and sulphur from lower latitudes. Increased ionic content and pH of snow, along with elevated nitrogen concentrations and modified cation ratios in lichens (Cladonia arbuscula and Flavocetraria cucullata) within 25-40 km of Vorkuta and Inta were attributed to local deposition of alkaline coal ash. Nitrate concentration in snow did not vary with proximity to perceived pollution sources. Trace metal composition of winter snowpack, snow-melt filter residues and top-soils indicated elevated concentrations of elements associated with alkaline combustion ash around coal mining operations in Vorkuta and Inta, adding significantly to the soil metal loading as a result of ash fallout. Around the petrochemical industry near Usinsk there was little evidence of trace metal deposition. Acid deposition was associated with pristine areas, whereas alkaline combustion ash near to emission sources more than compensated for the acidity due to S02 and NOx. There were limited perturbations in the chemical signals in lichens, top-soils and lichen diversity close to an oil and gas industrial complex on the Kolva river. Here, there were elevations of lead and nitrogen concentrations in lichen apices and in the apical : basal nitrogen ratio in Flavocetraria cucullata, with lower lichen diversity of epigeal and epiphytic lichens. Elevated concentrations of Ba and Ca were found in soil-ash, probably as a result of local emissions from construction activity and gas flaring, rather than from long-range transport. Virtually all other sites remained unmodified and reflected background concentrations.The ecological impacts of the measured pollution loads are discussed.

Hoverflies (Diptera: Syrphidae) vary widely in their mimetic associations, comprising wasp-mimetic, bee-mimetic and non-mimetic species. Social wasp mimics are dominated by 'imperfect mimics' which outnumber their supposed models (Hymenoptera: Vespidae) by large factors. The purpose of this thesis is to determine to what degree Batesian mimicry can account for these paradoxes, and to test alternative hypotheses for the evolution of the yellow-and-black patterns. There is little evidence of an effect of wasp abundance on 'imperfect mimic' abundance across 23 years of trapping data, as predicted if mimics are protected from predators through their resemblance to wasps. The seasonal asynchrony and high abundance of 'imperfect mimics' relative to their models is also notable, as well as the possible significance of wasp predation on hoverflies. Predictions concerning the function of the colour patterns of 'imperfect mimics' are tested using the association between similarity to the model and flight agility (indirectly measured assuming a trade-off between reproductive potential and flight agility). There is no strong indication that mimetic protection is the primary function of the colour patterns, but the evidence concurs with an aposematic function, signalling to predators the unprofitability of attempting capture. These conclusions are tentatively supported by direct measures of flight agility, though the small differences among species are difficult to pick up. The data on reproductive morphology of hoverflies show considerable variation across species, especially in males. The existence of giant testes in some species suggests that methods of dealing with sperm competition in hoverflies are diverse and deserve further study. The high ratio of 'imperfect mimics' to both models and good wasp mimics is also partly explained by habitat disturbance; undisturbed habitats show significantly less 'imperfect mimics' as a proportion of the hoverfly population. Current relative abundance in the UK may therefore be very different to when the colour patterns evolved.

The hoverflies (Diptera:Syrphidae) represent an apparently paradoxical visual Batesian mimicry complex, with what appear to be "poor" Mimics outnumbering their more accomplished counterparts. The purpose of this thesis is to determine how far conventional mimicry theory is capable of explaining the apparent paradoxes of mimicry in the hoverflies. It becomes obvious that determining the mimetic status of the supposedly poor Mimics is not a trivial task. Conventional experimental tests of mimicry, using captive predators, seem incapable of predicting the degree of protection enjoyed by a Mimic in the field. The research therefore concentrates on developing some novel empirical approaches to the study of mimicry. This includes developing a method of image analysis which yields an objective, single-value measure of the similarity between Model and Mimic patterns. This index of similarity is used to produce unique descriptions of the structure of mimetic communities in terms of Mimic frequency and similarity to the supposed Model. These profiles indicate that there is an objective basis to the perceived paradox, and suggest that there is not a simple relationship between the actual and perceived similarity of two patterns. The perceived similarity of Model and Mimic will be a key determinant of mimetic success. The index of similarity is also used as a basis for direct comparison of the supposedly mimetic hoverflies with a more established example of mimicry in the butterflies. This exercise demonstrates that an index of pattern similarity enables a unique comparative analysis of mimicry. It is proposed that an index of similarity also provides a unique opportunity to test our theoretical understanding of mimicry, if it is used in conjunction with a mathematical model that possesses some specific attributes. A suitable prototype model is developed and demonstrated. The thesis concludes with an indication that the novel empirical approaches developed here, have been adopted elsewhere. This latter work indicates that those hoverfly species which are apparently "poor" Mimics, may be exploiting some constraint in predator perceptual and cognitive systems to achieve mimetic protection, despite a relatively low degree of actual similarity to the Model species.