Biodeterioration is the least understood decay mechanisms of outdoor stone monuments. Microbial colonisation is largely determined by the properties of the stone and environmental conditions. The literature on microorganisms on outdoor stone monuments and their decay mechanisms was reviewed. For the assessment and quantification of microbial deterioration, methods that can be carried out by cultural heritage conservators with limited microbiological skills were selected and adjusted for the application on outdoor stone monuments. To this end, the total biomass was quantified by a protein assay (Folin-Lowry method), its phototrophic contribution through chlorophyll a absorbance and the amount of extracellular substances (EPS) were assessed by carbohydrate quantification (phenol method). Microbial activity was measured through two different enzyme assays: fluorescein diacetate cleavage and dehydrogenase activity (INT reduction). In order to develop a long-term monitoring strategy, these parameters were tested in the morning (8 am) and in the afternoon (4 pm) on biofilms from a sunny and a shady sampling site on a limestone wall in the south of Mexico. The experiments were performed in the dry season and the rainy season. Changes in biofilm composition and activity during the day were very small, while seasonal changes were more pronounced. The largest differences could be seen in samples from the different sampling sites (sun and shade), where the microbial population had established over years of distinct environmental conditions. Variations in biofilm composition and activity exceeding such natural variation may indicate the necessity for an antimicrobial treatment. The choice of an antimicrobial agent is difficult and the ideal treatment does not exist. Of the various chemical antimicrobial agents tested (Mergal K14, Parmetol DF12, Troysan S97, Preventol R50 hydrogen peroxide and ethanol) on microbial biofilms on stone, ethanol (70%) was the most effective, as revealed by ATP measurements. A flexible, non-invasive in vivo system, employing the bioluminescent bacterium Vibrio fischeri, was developed to assess sub-lethal effects of antimicrobial treatments and to test combined treatments for synergy. Various biocides and ultrasound (267 kHz, 20 kHz), alone and in combination, were tested for their effect on V. fischeri (Mergal K14, Parmetol DF12, Troysan S97, Preventol R50 hydrogen peroxide and ethanol) and a microbial biofilm on stone (Troysan S97, Preventol R50 and ethanol). The tests did not reveal synergistic effects however, a systematic, comprehensive study on chemical and/or physical methods might reveal an innovative approach towards a more environmentally friendly microbial eradication method for outdoor stone monuments. Long-term monitoring of the composition and activity of a microbial biofilm may provide data to determine if an antimicrobial treatment is necessary. If an antimicrobial intervention cannot be avoided, low-toxic substances, such as ethanol, should be considered first. For the evaluation of the success of an antimicrobial treatment, ATP measurement has proven to be a reliable and simple method that does not require specialised skills.

Sphaerothecum destruens is a multi-host parasite which can infect and cause mortality in a number of fish species including Chinook salmon Oncorhynchus tshawytscha, Atlantic salmon S. salar and the sunbleak Leucaspius delineatus. It has been hypothesised that S. destruens has been introduced to the UK with its invasive hosts L. delineatus and topmouth gudgeon Pseudorasbora parva. As the effects of a novel parasite to naive populations could be detrimental, this thesis aimed to better elucidate the life cycle of S. destruens, its prevalence in wild populations and the susceptibility of cyprinid species. S. destruens was able to infect multiple organs (kidney, liver, gill, gonad and intestine) with similar histopathology between L. delineatus, a cyprinid species, and the histopathology reported for salmonid species. Its spore and zoospore life stages displayed a wide temperature tolerance and zoosporulation occurred at temperatures between 4-30 C. A survey of one UK location detected S. destruens in a wild L. delineatus population. A quantitative polymerase chain reaction was developed in order to quantify S. destruens' infection levels. Reproductive L. delineatus were more susceptible to S. destruens and experienced higher S. destruens prevalence and infection levels. The presence of a second host, P. parva, had no influence on S. destruens' prevalence and infection levels. However, presence of P. parva resulted in significantly lower somatic condition in parasitized female L. delineatus. Exposure to S. destruens through immersion in water containing S. destruens spores revealed that bream Abramis brama and carp Cyprinus carpio were susceptible to S. destruens. A. brama experienced high (53 %) mortalities when exposed to S. destruens whilst C. carpio experienced low (8 %) mortalities. The susceptibility of roach Rutilus rutilus and rudd Scardinius erythrophthalmus could not be excluded and needs to be further investigated.

Southeast Asia is experiencing unprecedented biodiversity declines brought about by human population growth and economic development leading to unsustainable use of natural resources and loss of natural habitat. The scientific community has emphasized this biodiversity crisis in the past decade, calling for immediate action. In this context, I set my research as a case study in Nakai-­‐Nam Theun National Protected Area (NNT NPA), central eastern Laos where wildlife hunting has been rampant and management strategy failing to prevent wildlife declines. This research aimed (1) to re-­‐assess and bring forward the importance of NNT NPA for wildlife conservation, (2) to identify the key species for which NNT NPA is a priority for their conservation, (3) to use the data collected to develop a long-­‐term project in the area for research and conservation. In addition to this local-­‐level case study, I aimed (4) to identify the National near-­‐future priorities for research and conservation of Lao non-­‐ human primates (primates). For the latter, I reviewed the literature for the most reliable occurrence localities of Lao primate species across the country to model their potential distribution. I used the models to re-­‐assess their current status and identify the remaining gaps in our knowledge that need to be addressed. For the research in NNT NPA, I collected baseline data on key species occurrence and threats within the area. From January 2011 to March 2012, I conducted transect surveys in 10 different sites in the area. At each site, I set four to 20 transects, each replicated up to three times. During the transect walks I recorded all diurnal primate species sighted. In addition, I used the camera-­‐trap database of 2006 management staff. Using modelling softwares (MAXENT, ENFA, DISTANCE) to provide baseline predictions, I analysed both my transect survey and the camera-­‐trap survey data to assess the current status and distribution of red-­‐shanked doucs (Pygathrix nemaeus), four macaque species (Macaca arctoides, M. assamensis, M. leonina, M. mulatta), small-­‐carnivores (i.e. Viveridae, Prionodontidae, Herpestidae and Mustelidae), small medium-­‐sized cat species and muntjacs species (Muntiacus spp.) occurring in the area. My analysis of Lao primates distribution models at the National level reveals that (1) so-­‐far unvisited regions of northestern Laos may hold populations of highly-­‐ threatened colobines. Future research should focus on the taxonomy and distribution range limit between taxa of Nomascus, Pygathrix, T. francoisi s.l. and T. germaini s.l. The modelling results emphasise the need for more research on primate species in Laos, a country of high priority for primate conservation. My case-­‐study research in NNT NPA reveals that (2) based on a MAXENT analysis, I predicted a conservative suitable habitat of ca. 1600 km2 in NNT NPA and through a distance analysis, I estimated an average group density of 2.8 groups/km2, yielding a potential for ca. 4900 groups in the area. The population of red-­‐shanked doucs in NNT NPA likely -­‐term global survival. (3) Based on a MAXENT analysis using records from both transects and camera-­‐traps, the four resident macaque species were predicted to occupy a different geographical range and niche within NNT NPA. Macaca arctoides, M. assemensis, M. leonina and M. mulatta, respectively were predicted along a general environmental gradient: from low to high temperature and precipitation, and high to low elevation and slopes. The potential distribution of these four co-­‐existing, and morphologically similar species will have important implication for their management and future research. (4) Of 20259 camera trap-­‐days, from March 2006 to January 2011 only 21 images taken were of these four cat species. All these species were found with much lower survey efforts in NNT NPA in the 1990s. These species are readily camera-­‐ trapped in other evergreen forest sites in South-­‐east Asia. In combination, these factors indicate that the present low encounter rate is likely to represent their induced low density in NNT NPA due to high hunting pressure. This indicates that protected large forest blocks or mainly primary forests do not ensure the long-­‐term survival of hunting-­‐sensitive species. (5) Of the at least 21 small-­‐carnivore species (Viverridae, Prionodontidae, Mustelidae, and Herpestidae) confirmed in Laos, 15 occur in Nakai-­‐Nam Theun NPA of which ten were photographed during this survey: common palm civet Paradoxurus hermaphroditus, masked palm civet Paguma larvata, large Indian civet Viverra zibetha Chrotogale owstoni, spotted linsang Prionodon pardicolor, binturong Arctictis binturong, yellow-­‐throated marten, ferret badger sp(p). Melogale sp(p)., hog badger Arctonyx collaris and crab-­‐ eating mongoose Herpestes urva. The high rate of hunting with ground snares in the 5 area put some of these species at high risk of local extinction; however, NNT NPA remains one of the most important areas in Laos for small-­‐carnivore species, in (6) Based on an ENFA and MAXENT analysis, Critically Endangered large-­‐antlered muntjac M. vuquangensis and other resident muntjac species differ in their predicted potential distribution. The former is predicted at lower elevation range, in the western part of the NPA. NNT NPA represents the core habitat of M. vuquangensis and its conservation should be a priority in the area (7) Over my field work in NNT NPA I counted over 3000 ground snares (active or about to be set). Despite a management strategy in place and funding available, wildlife conservation in NNT NPA has not been successful. The major threat to wildlife is unsustainable hunting, using ground snares, by both Lao and Vietnamese hunters driven by a lucrative wildlife trade between the two countries. This indicates the urgent need for wildlife management improvement in the area, to be targeted on illegal hunting activities and the need for a long-­‐term research and conservation project to improve our knowledge of this rich wildlife, ensure its long-­‐term conservation and empower and educate local communities towards an integrated conservation strategy.

Biodiversity is in global decline and around 19% of the world's vertebrate species are listed as threatened on the IUCN Red List (Baillie et al. 2010; IUCN 2013). Linguistic diversity is also in decline and it is believed that as many as 90% of the world's 7,000 languages are threatened with extinction this century (Krauss 1992; Nettle and Romaine 2000). It has also been noted that there is a strong similarity in the distributions of terrestrial species diversity and linguistic diversity at the global scale, with the greatest richness found in the humid tropics and the lowest richness in the cold temperate zones (Mace and Pagel 1995; Sutherland 2003; Gavin et al. 2013). The term biocultural diversity has come into use to describe the collective diversity of species, languages and cultures around the world and their ongoing declines (Maffi 2001b; Harmon 2002). One of the papers presented here develops the first national index of biocultural diversity, which confirms the pattern of greatest richness in the tropics, particularly in Southeast Asia (Loh and Harmon 2005). However, measures of the state of biological, linguistic and biocultural diversity based on richness alone simply record the number of species or languages present and ignore underlying trends in abundance or populations of species or speakers of languages. Extinction risk has been the most widely-used measure of the status of both species and languages, but indicators based on time-series population data offer an alternative and more responsive measure of status and trends. The other papers presented here describe the development of Living Planet Index (Loh et al. 2005; Collen et al. 2009), an indicator which aggregates trends in populations of several thousand vertebrate species worldwide and shows an overall decline of about 30% over four decades since 1970, and the Index of Linguistic Diversity (Harmon and Loh 2010; Loh and Harmon 2014), a closely-related indicator based on trends in speaker numbers of around a thousand languages worldwide, and which also shows a decline of about 30% over the same period. At the regional level, the respective trends diverge. For biodiversity, there was a greater rate of decline in the tropics compared with temperate regions, whereas for linguistic diversity, there was a far higher rate of decline in the Americas, Australia and the Pacific compared with Africa, Asia and Europe. An analysis of the threat status of 1,500 languages using the IUCN Red List criteria reveals that 27% languages are threatened with extinction and confirms the regional pattern in the status of languages apparent in the Index of Linguistic Diversity. The differing regional patterns between the declines in languages and species reflect differences in the proximate drivers of diversity loss, where habitat loss or degradation are the major causes of species population declines (Millennium Ecosystem Assessment 2005), while linguistic diversity is lost primarily through language shift, a process whereby a politically, socially or economically dominant language displaces local or indigenous languages either as a result of colonialization, industrialization or migration (Nettle 1999).

The Sundarbans is a Tiger Conservation Landscape of global priority that supports one of the most important tiger populations across their current range. In Bangladesh, Sundarbans is the last stronghold of the critically endangered tiger, therefore conserving this flagship species will help to ensure the long-term future of the Sundarbans which has been providing significant economic and ecosystem services to human communities for centuries. However, scientific information is lacking on many aspects of the Sundarbans tigers, including population and genetic status, and detailed patterns of tiger and prey poaching. The objectives of this study were therefore to improve the knowledge base to help design better management strategies for long-term persistence of the Sundarbans tigers. As a consequence of challenges faced in applying conventional census methods in the Sundarbans mangrove habitat, a non-invasive genetic approach was applied to collect samples that were then screened using polymorphic microsatellite markers to estimate density and population size of tigers within the spatially explicit capture-recapture model. DNA analyses provided reasonable population estimates, indicating that a non-invasive genetic approach is a viable method for monitoring tigers and can be applied to monitor tiger populations elsewhere. Bayesian and Maximum likelihood inferences using mitochondrial DNA sequences supported a polyphyletic relationship between tiger population in the Sundarbans and the populations in central India. Together, microsatellite and mitochondrial DNA analyses revealed a signal of fine-scale genetic structure and significant genetic differentiation on a spatial scale which is probably the consequence of limited tiger dispersal due to the presence of wide rivers in the Sundarbans landscape. Systematic field survey across sample areas detected a range of snaring methods used to catch tiger prey and evidence of killing tigers by poisoning prey carcasses with the Carbofuran pesticide. Spatial analysis showed that poachers selected sites that tended to be further away from guard posts, and close to river banks. Based on these results, a range of future management interventions were recommended including the reduction of water-based commercial and resource collection activities to allow tiger dispersal, and regulation of Carbofuran and snare materials to better tackle tiger and prey poaching in the Sundarbans.

Disturbance of wildlife is inevitable in a world with a rapidly increasing human population. Whilst improving engagement with the natural world can have the benefit of encouraging people to help protect it, there is also the issue of increased potential for damaging effects of disturbance. A better understanding is needed of the circumstances under which disturbance would be expected to be a conservation problem, either alone or in combination with the impacts of other human activities. The aim of this thesis is therefore to address these questions: using wintering waders in estuarine habitats as the study system and taking a joint fieldwork and simulation modelling approach. Fieldwork was centred on Poole Harbour; an estuary and wetland of international importance located on the south coast of the UK. Disturbance experiments and observations showed that bird responses to disturbance are highly variable and related to factors including body mass, environmental conditions, site quality, and disturbance type. The energetic and lost-feeding-opportunity costs of responding to individual disturbance events were relatively small and therefore considered unlikely to cause major reductions in individual body condition or significantly limit overwintering population size, given observations of present-day spatial and temporal patterns of human activities. Simulation modelling using two types of individual-based model (IBM) supported this conclusion. Although high levels of disturbance can have a significant impact on wintering bird populations, current frequencies of human activities in Poole Harbour were not found to be reducing the carrying capacity of the site. Increased disturbance frequencies were predicted to be problematic, however, in combination with environmental change that reduced bird ability to meet their daily energy requirements: such as loss of foraging habitat through sea level rise, or reductions in prey availability due to over-exploitation. This has important implications for identifying the most effective conservation management methods. As well as site-specific management recommendations, this research contributes to understanding of the mechanisms by which disturbance may or may not have a significant impact on wintering wader populations; along with applications to other systems; and tools and general principles that conservation managers and decision makers can use to prioritise further investigation and action.

Climate and socio-economic change impacts interact in complex ways. These are likely to cross traditional sectoral and regional boundaries with cascading indirect and potentially far reaching repercussions. This is particularly important for the food-water-land-ecosystems (FWLE) nexus. A holistic understanding of these interactions is central for devising appropriate adaptation strategies. This thesis presents a systematic methodological framework that provides new insights into understanding key sensitivities and uncertainties of these possible cross-sectoral impacts for informing future adaptation policies. The research is based on: (1) appraisal of integrated assessment models (IAMs), and (2) investigation of the direct and indirect implications of a wide range of climate and socio-economic scenarios taking into account important cross-sectoral linkages and interactions between six key European land- and water-based sectors/sub-systems (agriculture, biodiversity, coasts, forests, urban, and water). This is achieved through (1) a review of existing integrated approaches and tools, and (2) assessment and extensive application of one European IAM – the CLIMSAVE* Integrated Assessment Platform (IAP). The IAP application uses a combined approach drawing on a systematic: (i) Sensitivity analysis based on a One-Driver-at-a-Time (ODAT) approach, (ii) Scenario and uncertainty analysis based on Multiple-Drivers-at-a-Time (MDAT) approach, and (iii) Robustness Assessment of Adaptation Policies (RAAP). The key outputs include: (i) new quantitative insights into the complex interactions of the FWLE nexus and associated synergies, conflicts and trade-offs in Europe, (ii) identifying key sensitivities and uncertainties of the potential cross-sectoral impacts and adaptation policies under various scenarios of future changes in climate as well as social, technological, economic, environmental, and policy governance settings, (iii) development of a new nexus-based conceptual framework for a long-term, multi- and cross-sectoral adaptation planning, and (iv) identification of potential areas of improvement of the IAP to inform development of the next generation of IAMs to assess the FWLE nexus. The ODAT analysis demonstrates that while a large number of drivers (20 out of 25) affect most sectors/sub-systems either directly or indirectly, eight drivers are key parameters at the European scale, with important cross-sectoral implications (i.e., ‘strong’ and ‘non-linear’ impacts on more than one sector/sub-system). These include: four climatic (temperature, summer and winter precipitation, and CO2 concentration) and four socio-economic (population, GDP, food imports, and agricultural yields) factors. Considering a wide range of scenario combinations of these drivers (taking into account the ‘full’ and ‘plausible sample’ scenario ranges), the MDAT analysis demonstrates that: (i) food production is likely to be the main driver of Europe’s future landscape change dynamics (even without climate change), (ii) agriculture and land use allocation in general is often driven by complex interactions between various sectors/sub-systems, (iii) there are no clear trends/patterns in future food production under most climate scenarios, (iv) agricultural changes have significant cascading effects on other sectors/sub-systems such as forestry, biodiversity, and water and (v) there are consistent trends for biodiversity, water and flood impacts with regional variations. The results also demonstrate that the combined effects of socio-economic and climatic factors are not always additive, highlighting the complexity of understanding impacts across sectors/sub-systems and regions. As a result, adaptation policy choices are complicated and difficult, even without climate change. A better understanding of the critical trade-offs across sectors/sub-systems and regions under various adaptation options is required. Such systematic analysis provides important insights for decision-makers to devise robust adaptation policies that maximise benefits and minimise unintended consequences across sectors/sub-systems and scales. *CLIMSAVE (Climate change integrated assessment methodology for cross-sectoral adaptation and vulnerability in Europe) is an FP7 project (2010–2013) funded by the European Commission. The CLIMSAVE IAP is an interactive exploratory web-based integrated landscape change assessment model that allows stakeholders to investigate climate and socio-economic change impacts, adaptation and vulnerabilities for six key sectors/sub-systems (agriculture, biodiversity, coasts, forests, urban areas and water resources) (Harrison et al. 2013; 2015a).

There is increasing emphasis to consider ecosystem services in natural resource policy and management, which has the potential to provide win-wins for species and habitat conservation and human use of resources. Inland freshwater fisheries provide over 33% of the world’s small scale fish catch and employ over 60 million people. However inland waters are the most threatened ecosystem in the world, which in turn threatens thelivelihoods and sustenance of millions globally. This thesis assesses the role of freshwater species in providing food as an ecosystem service, particularly to poor and vulnerable groups, and how the needs of fisheries align and contrast with threatened species inhabiting the waterways. In Chapter 2 the value of fisheries was assessed alongside other ecosystem services provided by inland water systems, where it was shown that monetary and nonmonetary valuations suggest very different priorities across a suite of services. Disaggregation of beneficiaries also showed a mismatch in prioritisation between different stakeholders, and in particular that fishermen and women, who rely most directly on the water resources, value resources incompatibly from a standard monetary valuation. In Chapter 3 I examined the effect of biodiversity on fishery yields and variability to determine if there is a potential for a win-win for conservation and ecosystem service delivery, and showed that increased species richness provides a significant positive contribution. The study of inland water systems and fisheries is hampered by a lack of data and in order to map the benefits from fisheries a model was created for Chapter 4 to spatially predict the relative importance of inland waterways to fishery yields. Example output from this model was used in Chapter 5 to explore how fisheries and freshwater species hotspots overlap spatially, and how this information can be used to determine potential areas of synergy where improved management could ensure benefits to humans while protecting wetland species, but equally to examine where there is potential conflict. With an increased understanding of freshwater ecosystems and their link to the resources they provide, there is potential for inland waters to be managed to benefit both people relying on food provision and the species living within.

Southeast Asian rainforests have, in recent decades, experienced the highest rates of deforestation and logging across the major tropical regions. This has left a vast estate of degraded forest in the region, which is under threat from further degradation and conversion to agriculture, principally for the expansion of oil palm (Elaeis guineensis) plantations. However, knowledge of the relative conservation value of different land-uses in the region is still limited, and a robust quantitative basis for resolving land-use tradeoffs, in particular between agricultural yield and biodiversity, is lacking. I aimed to assess terrestrial mammal species richness, abundance and β-diversity across a gradient of land-use intensity (old-growth forest, logged forest and oil palm) in Sabah, Malaysian Borneo. Overall mammal species richness was conserved even in the intensively-logged forests that I sampled, as were the majority of apparent old-growth specialists. Oil palm, on the other hand, harboured a highly depauperate mammal community. These broad patterns were echoed for overall mammal abundance, as well as in the potential ecosystem functions of mammals that I examined. However, I found evidence that the fundamental drivers of community assembly were altered across the land-use gradient and so, consequently, were patterns of β-diversity. Fine-grained β-diversity, in particular, was highest across the land-uses in logged forest, reflecting the increased environmental heterogeneity in this habitat. In addition, community composition and species abundance were not stable across land-uses. Omnivores and herbivores were more abundant in logged forest compared to old-growth forest, and only a limited number of carnivore species persisted in oil palm. Invasive species increased in abundance with land-use intensity. My findings underline the conservation importance of the large areas of degraded forest in Southeast Asia, and the extremely limited value offered by oil palm. If sustainability of the palm oil industry is to be achieved, new plantations should be diverted away from all remaining unfragmented forests, both old-growth and degraded forests alike.

The financial importance of the south Devon crab fishery was highlight by landings of 17,800 tonnes in 2010 (£18.9 million), approximately 59% of total UK crab landings. In recent years crab landings have increased and as such Bannister (2009) recommended ‘a precautionary approach to future crab fishing’ and ‘the setting of management objectives to prevent any further increase in fishing mortality’. It is the responsibility of the MMO to achieve this as part of the EU target of setting catch limits to accomplish Maximum Sustainable Yield (MSY) in all fisheries by 2020. Despite this aims the authorities responsible for the enforcement measures to achieve MSY are grossly under-resourced. Thus an innovative and inexpensive method to create sustainable small-scale fisheries is a necessity. Therefore the aim of this thesis, as part of the GAP1 and 2 Projects, was to devise a bottom up approach to create a sustainable fishery in south Devon using a fisher-directed stock assessment method and quota system, whilst working collaboratively with local fishers. To achieve this aim we carried out the following objectives. We collected fine-scale data on catch, landings and discards gathered onboard fishing vessels over most of a year and 10 years worth of fisheries diaries this produced spatiotemporal mapping of crab distribution within the IPA. We performed semi-structured interviews answered by a subset of fishers to gather their Fisher Local Ecological Knowledge (FLEK). The results were then compared with empirical data and the scientific literature, which revealed that the FLEK was accurate and valid enabling its use in future management measures. Further we evaluated our approach of collaborative working, identifying the strengths and weaknesses of the style of research. We established guidelines for future researchers and fishers to work collaboratively. The aforementioned data and knowledge was synthesised and evaluated as inputs to the Individual Based Model (IBM) of the fishery that was independently developed by P. J. B. Hart. The IBM currently enables its users to explore how the crab population and the fishery interact, as well as a tool that can be used to better understand the abiotic factors that affect the fluctuations in the fishery. In the future we hope the model will be able to output a sustainable quota of landings for the fishery. Finally, we produced a comprehensive plan of action to implement the future fisher-directed stock assessment and quota system into local management.