Ocean acidification is a consequence of rapidly increasing atmospheric levels of carbon dioxide and, in tandem with increasing sea temperature, poses a significant threat to marine life. A series of mesocosm experiments have been conducted at the Plymouth Marine Laboratory (Plymouth, UK) and the Kings Bay Marine Laboratory (Ny-Alesund, Svalbard) where ophiuroid brittlestars were used as a model to investigate the physiological response of marine organisms to ocean acidification and ocean warming. A 'whole organism' approach was adopted to elucidate the primary physiological responses, trade offs and conflicts that occurred. Three ophiuroid species of differing lifestyle and habitats were chosen to give an insight into how such factors influenced a species' response to ocean acidification and warming; the infaunal Amphiura filiformis, the epibenthic Ophiura ophiura, both temperate, and the Arctic epibenthic Ophiocten sericeum. There was a similar physiological response of metabolic upregulation across all three species. All species survived the lowest pH exposures (6.8 for A. filiformis, 7.3 for 0. ophiura and 0. sericeum) and showed signs of synergy between increasing water temperature and ocean acidification with the effects of lowered pH amplified as temperature increased. Beyond this, whilst specific responses differed between species, some similarity was observed between the epibenthic species 0. ophiura and 0. sericeum which both reduced arm regeneration and motility at lowered pH. In contrast, A. filiformis increased arm regeneration and suffered arm muscle wastage that appeared unsustainable. Differences in response and long term vulnerability to ocean acidification related to lifestyle (infaunal versus epibenthic) were consolidated by the Energy Limitation Model whereby the response of a species to ocean acidification is based on the increased cost of maintaining the acid-base balance of extracellular fluids. The ability to do this, and where the energy is taken from to do so, rationalises the variety of physiological responses seen between species. The results of the investigations described in this thesis indicate that even species with low regulatory capacity may survive ocean acidification. However, lifestyle may have a determining role in where energy trade offs are made to maintain acid-base balance and this may ultimately determine species survival.

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Low-intensity tropical agro-ecosystems may be of high conservation value. However, identifying appropriate strategies for managing tropical ~ountryside for biodiversity is contentious. Bengal Florican Houbaropsis bengalensis is a globally threatened bustard restricted to the Indian subcontinent and Indochina. Within Indochina floricans are characteristic of low-intensity grassland agro-ecosystems typified by rice cultivation and burning. Surveys during 2005/06 and 2006/07 showed the importance ofgrasslands surrounding the Tonie Sap lake, Cambodia, for Bengal Florican, producing estimates of approximately 830 adult birds, at least 60% ofthe global population. However, analysis of remotely-sensed habitat classifications show that grassland cover declined by 53-66% between 1995/96 and 2006 owing to agricultural abandonment and, more recently, intensification of rice cultivation. Both processes reduce habitat suitability for Bengal Florican. Predictive models (using multi-model inference techniques applied to field survey data) suggest that florican distribution is limited by human activity outside areas targeted by conservation-outreach schemes, where florican abundance is now highest. This reduces model transferability between regions and I suggest such variation in species density can limit transferability of predictive distribution models generally. Comparing habitat between male display locations and random points showed agricultural activity in grasslands, particularly annual burning, provides suitable habitat for males within leks. Such tolerance of low-intensity human activity provides support for recent community-conservation initiatives. Radio telemetry studies indicate that burning also maintains the heterogeneity essential for the contrasting breeding-season requirements of male and female florican resulting from the species's polygynous breeding biology. However, less than one-third of t~gged females appeared to nest within leks, suggesting that other areas may be important for breeding and that conservation activities should not be restricted to leks. Further research must focus on female autecology and how best to maintain suitable grassland structure, for nesting female and displaying male florican, without alienating existing low-intensity users of the grasslands.

1. Distribution models are used as management tools to predict species' distributions and quantify their habitat preferences. Numerous methodological issues require further development, which are explored using the distribution of birds along rivers as a model system in which there is a need to i) develop the quantification and analysis of variation in river habitat features and ii) better quantify species' habitat preferences for conservation and prediction. These themes were linked using a combination of the British Trust for Ornithology's Waterways Breeding Bird Survey (WBBS) and the Environment Agency's River Habitat Survey (RHS), along with similar data from upland Wales and the Himalayan mountains. 2. Training data are the starting point for distribution models and their properties can have profound effects. These issues were investigated via a literature review, which identified key factors including the type of predictors chosen, the approach to environmental sampling and spatial autocorrelation in distribution patterns. Recommendations are made that should optimise model quality, whilst making the most efficient use of available resources. 3. Testing the performance of distribution models is vital. Using a review of the available literature, highlighting weaknesses in current practice, and a case study using a Himalayan river bird, recommendations are made for improved practice. Bootstrapping and independent data should be used to assess overfitting and transportability, respectively. Accuracy statistics should facilitate inter-model comparisons, examining both discrimination and calibration. Nominal presence/absence predictions are problematic: information-theoretic methods may be the most useful approach. 4. Complex habitat data, such as RHS, may create a range of problems during statistical analyses unless the sample size is large. Data reduction, using methods such as principal components analysis (PCA), is an effective solution, but the resulting axes may be difficult to interpret. Using models built with Welsh river bird-RHS data, I compared the interpretability and predictive efficacy of PCA used in its conventional form against PCA preceded by the clustering of RHS variables that referred to the same ecological factors. The two approaches produced similar predictive performance but habitat indices produced by the latter were easier to interpret. A variant of PCA devised for qualitative data was also examined, and benefited RHS analyses involving ordinal variables. 5. Predictive models for 28 river birds, built with the WBBS, represent the first quantitative study linking detailed river habitat data with river bird distributions across the UK. Accuracy varied widely, with better performance for species associated with the river channel, rather than floodplain habitats, reflecting the relative coverage of these river features in RHS. By using variable clustering, the likelihood of species occurrences could be easily related to the observed habitat. 6. By utilising important methodological developments, this project provides important evidence that RHS forms an effective basis for relating many river birds to their habitats, and that when used in conjunction with the WBBS, could bring valuable benefits to river bird conservation. More generally, the work illustrates how RHS can describe variations in river structure and anthropogenic modification in a manner that is relevant to riverine organisms, along with transferable methods for describing and modelling the resulting relationships.

i) Acid deposition has declined across Europe and North America but chemical and biological recovery in streams is slow. Mitigation techniques such as liming are still being considered, but they have seldom been evaluated across whole catchments. ii) At 42 stream sites in the upper catchment of the River Wye, macroinvertebrates and diatoms were evaluated as bio-indicators of water quality. Both groups indicated continued acidification in headwaters. iii) Chemical and biological responses to catchment liming in the upper Wye were assessed through a Before-Afler-Control-Impact (BACI) experiment across multiple limed, acid control and circumneutral reference sites. Liming did not change pH, alkalinity, calcium or aluminium at limed sites relative to acid controls because effects were small or masked by marked inter-annual variations in discharge. iv) There was no significant change in the abundance or richness of macroinvertebrate assemblages at treated sites in the first two post-liming years. Acid-sensitive species (e.g. Baetis rhodani) colonised some limed sites, but not at a significantly increased frequency. v) In-situ survival experiments revealed increased mortality in Baetis rhodani in limed and acid streams relative to circumneutral reference streams even following brief exposures. vi) These data illustrate that recent liming of streams in the Wye catchment has not yet changed stream chemistry sufficiently to support acid-sensitive macroinvertebrate assemblages similar to those found at circumneutral sites. Further lime applications and continued evaluation is recommended.

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Locations in southern Iberia were sampled to assess patterns in the distributions and diversities of land molluscs and to determine the effects of habitat structure on diversity at differing scales. In Part One of the study 91 sites, each 1km , were sampled. Species with higher abundances were present at more sites than those with lower abundances. Low levels of similarity were found between the land mollusc communities. The monthly mean of sunshine hours per day during the wet period and the annual mean absolute humidity provided the best explanation of the species data. The results suggest that the heterogeneous habitats from the region allow a large number of mollusc species to co-exist in varied communities possibly controlled by historical and regional factors including climate and geology. In Part Two of the study 60 sites, each 1600m2, were sampled. Twenty sites were located in each of three habitat types (sand, steppe and garigue), and for each habitat type ten sites were sampled in both the wet period and dry period. Diversities and habitat structure were assessed at 1m , 5m and 20m . There were differences in the number of species, abundances and diversities between habitats, and between the wet and dry periods at each habitat. Increasing heterogeneity and complexity increased the number of species, but not their abundances. Components of habitat structure affected the number of species and abundances independently of the total complexity. Relationships between heterogeneity, complexity, number of species and species diversity were scale-dependent with most of the statistically significant relationships between these occurring at lm2. Increases in abundances and number of species with increasing area support the passive sampling model and the area per se hypothesis.

This study investigates the genetic and parasite diversity of two primate species living in the Lower Kinabatangan Wildlife Sanctuary (LKWS), Sabah, Malaysia. Based on non-invasive samples (faeces), the effects of forest fragmentation and geographical barriers, especially the Kinabatangan River, on these two species of primates with different social systems and dispersal abilities were examined. While the proboscis monkey is an endangered primate, the long-tailed macaque is considered one of the most successful invasive alien species. The genetic diversity and the potential effect of the Kinabatangan River on the population structure were examined using microsatellites and a microsatellite library specific for the proboscis monkey was developed during this study. High and moderate levels of genetic diversity were found for the long-tailed macaque and the proboscis monkey respectively. As predicted from the dispersal pattern of these primates, microsatellite analysis revealed low genetic differentiation among sites, suggesting high levels of gene flow as well as regional admixture with one genetically-based cluster inferred from Bayesian analyses. In addition to the neutral genetic marker, as a preliminary approach to study adaptive genetic variation in these populations, Mhc-DRB loci were identified in both species using generalist -DRB primers. High levels of diversity and evidence of positive selection were found in the long-tailed macaque sequences, which included representatives of several -DRB loci/lineages according to phylogenetic analyses. In contrast, only five -DRB sequences were detected in the proboscis monkey, all belonging to a single -DRB locus although few, these are the first MHC reported sequences for this species. MHC variability is believed to be maintained by pathogen-driven selection, mediated either through heterozygote advantage or frequency- dependent selection. Using the same samples as for the genetic analysis, a survey of the gastrointestinal parasite fauna of both primates revealed 14 taxa. Parasite richness was higher in proboscis monkeys, and prevalence of particular parasites differed between the primates. Potential effects of natural and anthropomorphic mediated habitat fragmentation on parasite species richness, proportion of individuals with mixed infections and the prevalence of particular parasites between the two primate species were explored. Natural fragmentation (the Kinabatangan River) did not affect parasite distribution. Although it was expected that areas with high rates of human-non-human primate contact would have a positive correlation with the assessed parameters this was not always the case as host-parasite dynamics are likely to be affected by complex interactions between environmental, and host demographic, behavioural and genetic factors. The results of this study can be used as a baseline for conservation and management measures for the proboscis monkeys and long-tailed macaques of the LKWS.