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Marine protected areas (MP As) are increasingly viewed as an important management tool within a suite of policy alternatives to reduce, prevent and/or reverse on-going declines in marine biodiversity. The overall aim of this thesis was to test the efficacy of MP As as a conservation measure, particularly focusing on partially protected areas which have received less attention than fully protected areas. An evidence-based approach, combining a rigorous assessment of the literature through 'systematic review' methodology, with field studies of fishing gear restriction areas in the UK was undertaken to examine the biological effects of partially protected areas on biota relative to fully protected areas and open access fished areas. The syntheses of available evidence included in the systematic review suggested that while partially protected areas significantly enhanced density and biomass of fish relative to open access areas, fully protected areas yielded significantly higher biomass of fish within their boundaries relative to partially protected areas. The positive response to protection was primarily driven by target species. The effects of life history and ecological traits on the response of fish species to fully and partially protected areas were further examined using mixed effects modelling. Fish maximum body size, adult habitat preference and the exploitation status of the species were significantly related to the magnitude of response to full and partial protection. These results highlighted the importance of incorporating species information in the design of new MP As, which ensures that protection is provided at spatial scales relevant to the species in need of conservation. Fishery closed areas, where fishing with bottom-towed gear is prohibited but fishing with static gear is permitted are amongst the commonest examples of MP As in the UK. Underwater camera surveys were conducted at Cardigan Bay Special Area of Conservation (SAC), the Modiolus Box within the Pen Llyn a'r Sarnau SAC, Skomer Marine Nature Reserve and the Port Erin closed area in the Isle of Man to examine the response of epibenthic invertebrate communities to protection from bottom fishing. Benefits from protection were observed for three of these MP As and the magnitude of response was generally higher for the target species such as scallops and for sessile, fragile taxa such as hydroids, bryozoans and sponges. Two key environmental characteristics that influenced the effect of protection were the intensity of fishing at the control unprotected areas and the level of natural disturbance from waves and tides. Overall, the results showed that partially protected areas are a valuable spatial management tool particularly in areas where exclusion of all extractive activities is not a socio- economically and politically viable option. The findings also highlight the importance of considering the physical nature and dynamics of the environment, the nature of the species concerned and past and present level of fishing intensity throughout the designation process of MP As, so as to avoid negative impacts on fisheries and limited conservation benefits.

With an increase in demand on deep-sea resources comes a need for appropriate and effective management of this ecosystem. The establishment of a representative network of deep-sea Marine Protected Areas offers one tool with which to address the conservation needs of the deep sea. While a number of deep-sea habitats have been identified as vulnerable to anthropogenic activities (e.g. cold-water coral reefs and sponge aggregations), poor knowledge of the distribution of these habitats hinders conservation efforts and network planning, and thus we need habitat maps. With improvements in acoustic data resolution acquired from the deep sea, and the ability to cover large areas rapidly, the use of acoustic techniques in mapping biological habitats is growing. Multibeam bathymetry and its derived terrain variables can potentially provide important information that can aid in the delineation and characterisation of biological communities. A necessary prelude to mapping is therefore the definition of biological assemblages for use as mapping units. Two megahabitat features (seamount and submarine canyons) were sampled using acoustic and ground-truthing to characterise and map the distribution of benthic assemblages. Species were identified as distinct morpho-types and catalogued, and still images quantitatively analysed. Standard multivariate community analysis was undertaken to define distinct faunal assemblage that may act as mapping units. Those clusters identified by the SIMPROF routine were taken against a set of criteria to reject/accept as robust assemblages that may be used as mapping units. Twenty two benthic assemblages or biotopes were defined from multivariate analysis of quantitative species data, 11 from the SW Approaches and 11 from Anton Dohrn Seamount, and a further one from video observations (SW Approaches). Taken against current definitions, 11 of these were considered as Vulnerable Marine Ecosystems (VME). Diversity was measured to compliment the comprehensive description of biotopes. The use of multivariate diversity indices proved better for comparing diversity of biotopes as it captures a more than one aspect of diversity of the community. Two biotopes were common to both megahabitat features, cold-water coral reef habitats, and those from Anton Dohrn Seamount were more diverse than from the SW Approaches. Modelling techniques were employed to test the relationship between biotopes and environmental and geophysical parameters, which may be used as surrogates to map VME. Generalised Additive Models of Vulnerable Marine Ecosystems revealed multibeam bathymetry and its derived parameters to be significant surrogate for mapping the distribution of some assemblages, particularly those that appear to be influenced by current regime; whilst not so well for those whose distribution is not so strongly current driven e.g. soft sediment communities. In terms of deep-sea mapping, the use of multibeam can prove a useful mapping tool if the resolution of the data is at an appropriate scale that will identify meso-scale geomorphological features, such as cliff-top mounds, that may act as proxies for occurrence of biotopes, but this relationship is still unclear. Surrogates were used to map VME across the seamount and submarine canyons, and full coverage maps were produced for all biotopes occurring on these megahabitat features.