The closure of the Cardiff Bay Barrage in November 1999 signified the end of a period of slow estuarine maturation, and the beginning of a period of more rapid freshwater succession. Such a marked ecological change has rarely been studied, and provides an opportunity to gain insights into the consequences of both natural and anthropogenic changes in the wetland environment. The current thesis describes the results of a study into the changes in habitats, plants, invertebrates and birds which have occurred as a result of Barrage closure. It includes overviews of the background to the Cardiff Bay Barrage project, the pre-Barrage estuary, and the post-Barrage ecological succession. Four main chapters are dedicated to outlining the changes in habitats, macrophytes, macro invertebrates and birds. The overall habitat diversity of Cardiff Bay increased as a result of Barrage closure, mainly because of the establishment of clear habitat zones in formerly uniform inter-tidal areas. Macrophytes were found to have increased from less than 30 species to over 80 in the same post-Barrage area. Macro invertebrate diversity also increased significantly - although this was countered by a reduction in overall abundance - a result of the generally lower productivity of freshwater versus estuarine habitats. Birds likewise showed an overall increase in diversity at the expense of a loss in abundance, especially of wading birds. Most of the increase in diversity was due to an increase in herbivorous and piscivorous species. Birds of the Gwent Levels Wetland Reserve (part of the compensation package for the loss of the Taff7Ely SSSI in Cardiff Bay), were also subject to a brief analysis. This area now attracts a wide diversity and abundance of wetland birds, and has fulfilled one of its primary objectives by attracting Nationally Important numbers of Shovelers <italic>Anas clypeata,</italic> Pintails <italic>Anas acuta</italic> and Black-Tailed Godwits <italic>Limosa limosa.</italic>.

Rod catches of Atlantic salmon (Salmo salar) from the River Wye were previously the greatest in England and Wales. However, a 30-year decline in catches of salmon and brown trout (S. trutta ) prompted management action. Since 1996, the Wye and Usk Foundation have excluded livestock, managed riparian trees, protected banks, cleared migratory barriers and limed selected tributaries. The aim was to enhance salmon habitat and extend spawning opportunities. The outcomes of such activities in Britain are still poorly understood. This thesis i) identified variations in the water quality, aquatic invertebrates and salmonids of the Wye catchment ii) evaluated the impact of recent management on habitats and aquatic organisms iii) assessed whether any larger-scale factors could explain management effects. Because no suitable project-specific data were collected, routine monitoring data and surveys were applied in the most applicable post-hoc experimental designs. Ecological quality varied widely among the Wye's tributaries. Combined biotic indices supported the need to mitigate acidification in some upland streams and reduce diffuse nutrients in the lower catchment. Riparian management appeared to reduce bank poaching and increase algae by comparison with reference streams. Post-treatment invertebrate communities were richer in recently managed streams than in controls. However, there was no evidence that management reversed the decline in salmonid populations. The typical life-cycle of salmonids in the Wye might delay response to management, but this effect cannot be evaluated with only six years' post-treatment data. Alternatively, local effects could be masked by larger-scale trends. In particular, salmonid abundance in the Wye declines significantly with increasing summer temperatures, decreasing summer rainfall and discharge. I conclude that riparian management has had some of the desired outcomes at the reach or tributary scale. However, salmonid numbers in the Wye potentially reflect climatic effects, implying a need to consider climate-change in future management action.

Changes in agricultural management have caused massive declines across many taxa associated with the farmed landscape including many of conservation value. Population declines of farmland birds have been particularly rapid, massive and widespread. Although currently under utilised, particularly in Wales, short rotation willow coppice (SRC) could provide a sustainable fuel that offers a significant reduction in net carbon emissions compared with fossil fuels. This anticipated change to the Welsh agricultural landscape warrants investigation in terms of the impact it is likely to have on biodiversity. This study aimed to investigate the biodiversity of SRC in the Welsh agricultural landscape, concentrating on likely effects to bird populations. Weed floral diversity and species richness was found to increase significantly when SRC was planted compared to the previous landuse. This in turn provided substantial amounts of weed seeds in young SRC easily utilised by many bird species during the winter. As the crop matured the bird community changed but mainly, provided valuable habitat for diverse bird communities during the breeding season. SRC was found to be a highly beneficial breeding bird habitat chiefly for migrant warblers. The increased production of SRC in Wales could significantly increase the productivity of the Willow Warbler in particularly. Planting SRC in Wales could be of significant benefit to biodiversity including those bird species contributing to the UK government's Wild Bird Index. By making it financially beneficial for farmers to be less aggressive in their control of weeds, for instance through Tir Gofal or equivalent agri-environment scheme, SRC could realize its biodiversity potential. This could enable the government to reach both its carbon emissions and biodiversity targets.

Line transect data obtained from 'platforms of opportunity' are useful for the monitoring of long term trends in dolphin populations which occur over vast areas, yet analyses of such data axe problematic due to violation of fundamental assumptions of line transect methodology. In this thesis we develop methods which allow estimates of dolphin relative abundance to be obtained when certain assumptions of line transect sampling are violated. Generalised additive models are used to model encounter rate and mean school size as a function of spatially and temporally referenced covariates. The estimated relationship between the response and the environmental and locational covariates is then used to obtain a predicted surface for the response over the entire survey region. Given those predicted surfaces, a density surface can then be obtained and an estimate of abundance computed by numerically integrating over the entire survey region. This approach is particularly useful when search effort is not random, in which case standard line transect methods would yield biased estimates. Estimates of f (0) (the inverse of the effective strip (half-)width), an essential component of the line transect estimator, may also be biased due to heterogeneity in detection probabilities. We developed a conditional likelihood approach in which covariate effects are directly incorporated into the estimation procedure. Simulation results indicated that the method performs well in the presence of size-bias. When multiple covariates are used, it is important that covariate selection be carried out. As an example we applied the methods described above to eastern tropical Pacific dolphin stocks. However, uncertainty in stock identification has never been directly incorporated into methods used to obtain estimates of relative or absolute abundance. Therefore we illustrate an approach in which trends in dolphin relative abundance axe monitored by small areas, rather than stocks.

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Aim: This thesis aims to investigate the potential impacts of climatic change on Afro-Palaearctic migratory birds by investigating simulated changes in breeding and non-breeding distribution. Methods: Generalised Additive Models were used to determine those climatic variables that produced the most robust species distribution models. Tests on the performance of three regression-based techniques were undertaken and consensus modelling framework was subsequently chosen. This framework was used in conjunction with three general circulation models and two emission scenarios to model the future distributions of Afro-Palaearctic migratory birds. Changes in both breeding and non-breeding range and migratory distance were examined for groups of species. A vulnerability index was created to indicate those species that were most vulnerable to climate change. Finally, changes in recent population trends observed on the European breeding grounds were related to simulated climatic suitability to investigate the role of climate in recent population changes and determine the vulnerability of populations to climate change. This analysis also enabled a partial validation of species distribution models. Results: The results indicate differential change on the breeding and non-breeding grounds for many species. For many migratory birds a progressive separation of the two ranges is projected, potentially increasing migratory distances in future. However, for some species newly suitable climatic areas may provide non-breeding areas closer to the breeding range, enabling species to adapt to climatic change. Trans-Saharan migrants, species residing in dry environments as well as montane and coastal species are projected to be most vulnerable to climatic change. Although a link between population trends and climatic suitability could be found, the results indicated, as might be expected, that climate is only one of a number of factors potentially contributing to population changes Conclusion: This thesis gives the first broad analysis of the likely direction and magnitude of change of the distribution of migratory birds to climate change, when only climate is considered. The challenge ahead is to refine these coarse scale models to include habitat and demographic data so as to provide more realistic estimates of change and improve conservation strategies that aim to support species under climate change.

In this study the molecular ecology and fitness of two Delphinidae species, the striped dolphin (Stenella coeruleoalba) and the common dolphin (Delphinus delphis), were investigated in the Mediterranean Sea and Atlantic Ocean. This thesis provides a comparative assessment of the striped and the common dolphin, using molecular methods regarding the genomic diversity and parasite resistance. The striped and the common dolphin have a world-wide distribution, inhabiting pelagic waters and differ with respect to population structure within the study area. The aim is to reveal different patterns of genetic diversity and fitness in the species that shows greater populations structure. In order to test this, my analyses structure was a) to analyse the population structure of the striped dolphin in the Mediterranean Sea and Atlantic Ocean and compare structuring patterns with previous published studies, b) to examine the heterozygosity fitness correlation for both species, using neutral and non-neutral markers and specific parasites that are important of animal’s health. In this context this study tests that local populations show stronger relationship between genetic diversity and fitness. This study suggested that different methods regarding to power and studied subareas show a fine-scale structure beyond that reported previously in striped dolphin populations. A key new finding is the structuring pattern in the Atlantic Ocean, where populations from Scotland and the Biscay Gulf were isolated from the one in Ireland. Also, the Ionian Sea samples grouped with the western Mediterranean, which could either be an effect of the small sample size from the Ionian Sea, or reflect a boundary closer to Greece, dividing the basins of the Mediterranean for this species. In this study I found differences between the two hosts with respect their genetic diversity and parasite loads for both nuclear and functional loci. I also found that evidence for a heterozygosity fitness correlation was strongest for females, and this was true both for the correlation with genomic diversity as assessed using neutral markers, and for the functional immune system gene. This observable association suggests that parasites may act as an energetic stress, and may reflect the non-identical pathogenesis of parasites and their ability to inflict damage through the hormone profiles. Results illustrate potentially important interactions between genetic drift and selection, and provide specific information that will be valuable towards the conservation and management of diversity in these species.

A new approach to the assessment of relationships between habitat controlling processes and salmon and trout abundance is presented and applied to the River Eden, Cumbria, UK. The potential of Geographical Information Systems (GIS), remote sensing, aerial photography, risk- based environmental modelling and electrofishing is demonstrated for the collection and integration of habitat and species abundance data at the scale of large catchments (˃1000km2). Based on this data, a key output of the research is the development of a spatially-structured, hierarchical database that allows hypotheses regarding the relationship between habitat controls and salmon and trout abundance to be tested at multiple scales. In particular, assessment has been made at the whole catchment-scale (2,300km2) and then at a series of sub-catchment scales (10-100s km2). Analyses at these two scales revealed contrasting results, emphasising that the scale of observation and analysis is crucial in determining the relationships identified. In the catchment-scale analysis, salmon and trout abundance were significantly correlated with the catchment-scale process of surface hydrological connectivity, both weighted and un-weighted by land cover. However, as the scale of analysis contracted, the spatial variance exhibited by catchment-scale processes declined and more local-scale riparian and in-stream habitat controlling processes such as cover and bank erosion became important. These results provide evidence in support of theories which suggest a hierarchical structuring of catchments where large scale processes provide the structure within which riparian and in-stream habitat controls operate. Results are also presented showing that fish abundance responds and maps onto to this hierarchical structuring in different ways depending on the potential for mobility at different life- stages and the location of habitat utilised within the landscape. Based on these results it is concluded that effective habitat restoration strategies must adopt a multi-scale approach in which in-stream and riparian scale actions are situated within the context of their controlling catchment-scale processes. The concept of hydrological connectivity is also recommended as an effective tool by which to assess the influence of landscape factors such as land cover on in-stream condition and salmon and trout abundance.

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