Methods were developed to quantify variation in gill size and microstructure and applied to three fish species: brown trout, Arctic charr and common carp. Measurements of arch length, number and length of gill rakers, number and length of gill filaments and number, length and spacing of the lamellae were taken for each gill arch and combined by principal component analyses to give length-independent scores of gill size. Levels of fluctuating asymmetry in gill arch length were also examined. Buccal and gill cavity volumes were measured from silicon moulds. Standard histological methods were used to examine gill microstructure. Benthic-feeding charr from a sample collected in Loch Awe, Scotland had relatively larger heads and buccal cavities than did sympatric pelagic-feeding fish Allowing for body size, they also had a more extensive respiratory surface, perhaps reflecting exposure to poorly oxygenated water while feeding on the loch bottom and/or a more active life style. Levels of asymmetry in gill arch length were higher in the pelagic-feeding form, which grow faster than the benthic-feeding form (Chapter 2). Gill size and structure were compared in carp (Chapter 3) and trout (Chapter 4) classified by a standard test as having proactive, reactive or intermediate stress copping styles. Proactive carp and trout had more extensive respiratory surfaces and lower levels of hyperplasia than did reactive fish, intermediate fish lying in between. The opposite was the case for density of mucous cells, which was highest in reactive fish and lowest in proactive ones. These data suggest that maintaining a large respiratory surface may represent an unrecognised cost of a proactive coping style. Common carp were held in mixed groups of proactive and reactive fish in one of 6 combinations of temperature (20oC and 25oC) and dissolved oxygen (3-4, 5-6 and 7-8 mg O2 L-¹) for 10 weeks. At the higher temperature fish had relatively larger heads and longer secondary lamellae, but had fewer mucous cells and a lower percentage of hyperplasia. At the lowest oxygen levels fish had relatively larger heads and a higher degree of hyperplasia than those held in normoxic and hyperoxic conditions. These results suggest that, over weeks, carp are able to “remodel” their respiratory structures in response to their current oxygen requirements. Few clear differences in response were found between proactive and reactive fish (Chapter 5). In semi-extensively farmed carp sampled over their final production year. Shortterm, acute husbandry stressors (grading and crowding) produced striking changes in several potential welfare indicators, including reduced body condition, increased in plasma glucose, lactate and cortisol levels and higher level of body damage. Percentage hyperplasia and secondary lamella number and length also increased. Long-term acute stress (pre-harvest crowding in concrete tanks) was associated with increased levels of skin and fin damage and in hyperplasia and mucus cell number, reflecting high stress levels and/or poor water quality. Glucose, lactate and cortisol levels fell, suggesting either habituation to current conditions or differential mortality by physiological stress status (Chapter 6). The results of Chapters 2-6 are synthesised in a general discussion (Chapter 7) and considered in the context of the existing literature on trophic polymorphism, on stress coping strategies, on the effects of environmental conditions of the welfare of cultured fish and on how gill structure and microstructure relate to other indicators of welfare.

Shellfish processing results in the disposal of large quantities of waste to landfill sites. This project sought to deal with the issue of the processing of marine crustacean waste, specifically that of the prawn, Nephrops norvegicus. The exoskeleton of Nephrops norvegicus contains chitin, β-(1→4)-N-acetyl-D-glucosamine. In this study shell waste was demineralised, via lactic acid fermentation, using a commercial silage inoculant. The product contained 11.2% (w/w) ash, 31.1% (w/w) protein and 53.5% (w/w) chitin. Addition of the proteolytic enzyme, bromelain and a nitrogen source to the fermentation system led to deproteinisation and further demineralisation of the shell. The final product contained 4.2% (w/w) ash, 5.3% (w/w) protein and 79.6% (w/w) chitin. Chitin is relatively inert but can be converted to its more reactive derivative, chitosan, by deacetylation. Chitosan, prepared from bioprocessed shell waste, was investigated as a potential coating for urinary catheters. Attempts are currently being made to prevent blockage of these biomedical devices due to mineral ions, via the use of different manufacturing materials. Shell waste that had been demineralised using lactic acid fermentation was deacetylated using 50% (w/v) NaOH at 90oC. Membranes were prepared from the resultant chitosan. After immersion in a bath containing artificial urine, adherence of calcium and magnesium ions to the membranes was measured and compared with adherence of the same ions to polyurethane membranes. Adherence of calcium to the chitosan membranes was not higher than adherence to the polyurethane control membranes. Adherence of magnesium ions was significantly less than to the polyurethane control. The chitosan was hence shown to have potential for use as a coating for urinary catheters.

The appropriate management of visitors to nature reserves is an important conservation concern. In this thesis I briefly review the current literature describing the effects of disturbance on wildlife, concentrating mainly on birds (Chapter 1). Recent literature has provided worrying critiques of the practical and theoretical bases upon which management practice is based. Here, I address a number of questions that seek to clarify the impacts of human disturbance on birds. I started by asking whether behavioural measures of disturbance are accurate indices of the negative effects of disturbance. Through an experimental test of a theoretical model, I showed that animals that respond most to disturbance may in fact be those individuals that face the lowest cost associated with such disturbance (Chapter 2). Turnstones Arenaria interpres provided with extra food over three days showed stronger behavioural responses to a standardised disturbance stimulus than those without extra food. Behavioural measures are therefore not always a good index of disturbance effects. Consequently, the conclusions of some of the studies reviewed in Chapter 1 must be considered doubtful. Although some large declines in breeding success of some species are caused by human disturbance, such effects are obvious, simple to remedy and appear to be rather rare. If human disturbance is a general concern it is therefore necessary to assess whether human disturbance has impacts on species that are not obviously sensitive. To investigate this, I modelled the impact of human disturbance on the nesting success of kittiwakes Rissa tridactyla and guillemots Uria aalge (Chapter 3). By directly measuring a range of nest site parameters as well as those parameters involving human disturbance, I was able to improve the power of the analysis to detect disturbance effects over those of previous, less detailed, studies.

This thesis addressed a central theme in evolutionary biology, namely understanding the process of adaptive radiation, using the three-spined stickleback, which has become a model system in this context. In particular, the work concentrated on sticklebacks from several unique populations in the Outer Hebrides that have lost the body armour after which this species was named, lacking dorsal spines, pelvic girdle and spines and lateral plates. A first specific aim was to examine an existing hypothesis about the selective force responsible for armour loss in these populations, namely that it is an adaptive response to low calcium levels. This is in contrast to the selective force favouring armour loss in North American populations, where predation by piscivorous fish is thought to favour armour development and predation by invertebrates to favour armour loss. This was studied by relating variability in protective body armour to calcium concentration at 10 sites with calcium concentrations ranging from 1.2mgCA2+/L to 50.5mgCa2+/L and spread over a wide geographical range. The results confirmed previous studies, providing partial support for the low-calcium hypothesis for Hebridean populations. Thus armour reduction is only found in sticklebacks from low-calcium sites, although not all fish from such sites are unarmoured. Piscine, avian and invertebrate predators were present at all sites, ruling out the predation regime hypothesis. A second aim was to relate variability in risk-taking to variable armour expression, both within and between populations of stickleback. 180 wild-caught fish from 7 sites across Scotland (but mainly concentrated in the Hebrides) were screened for risk-taking behaviour using a well-established testing protocol (quantifying rates of exploration of and movement in a novel and potentially dangerous environment) that is broadly predictive of some aspects of the sticklebacks’ response to a predator. No significant relationship was found between individual risk-taking score and the extent of body armour, either across populations or among individuals within populations. The risk-taking test (chosen because it is simple and easily controlled) only reflects one aspect of anti-predator behaviour and may have been too focused to identity subtle and individual differences in risk-taking.

This thesis describes a study of a number of aspects of the Nephrops creel fishery. Various aspects have been studied. In particular, work has focused on how the biology of Nephrops affects its catchability in creels, as well as assessing the environmental impacts of the Nephrops creel fishery. A smaller study relating to the physiological effects of the capture and transport of live creel-caught Nephrops, has also been undertaken. Fishery-directed sampling of Nephrops displayed strong seasonal trends in catch composition and catch rate, reflecting patterns in the Nephrops moult and reproductive cycles. Most females were caught in the early spring, following moulting and mating, with catch rates becoming low after spawning in autumn. Catches of males were greatest around February following moulting. Of those animals caught, males were larger than females. These seasonal patterns reflect the exploitation of different components of the stock throughout the year. Fishery sampling also showed there to be considerable stock heterogeneity both among and within creel fisheries. Global positioning system (GPS)-linked data loggers fitted to selected fishing boats provided a more detailed assessment of spatial variability in catch rate. Results showed both effort and landings per unit effort (LPUE) to be patchily distributed in the area studied, further illustrating considerable stock heterogeneity throughout the area. Both approaches illustrated that catch rate varied with sediment type, with high catch rates of small animals on sandy to firm mud and high catch rates of large animals on softer mud. Additionally, population modelling indicated that, in the areas studied, Nephrops are not currently being growth overfished. Behavioural observations in both the field and laboratory indicated a low probability of entry to creels by approaching Nephrops, particularly if other crustacean species were inside the creel. Larger Nephrops appeared to have a greater threshold for disturbances such as and the presence of conspecifics or other species as well as reduced gear avoidance, suggesting that Nephrops creels select larger animals in the population. Using sea pens as an indicator of physical disturbance of the sea bed showed that impacts from creeling were low. The sea pens Virgularia mirabilis and Pennatula phosphorea were caught in moderate quantities in the creel fishery, but were still observed in high densities on creel grounds. Comparison with trawled areas showed some differences in density, the most notable being that the tall sea pen Funiculina quadrangularis was less abundant on trawled grounds, indicating an adverse effect of bottom-towed gear. Bycatch was assessed in two distinct fisheries and varied both between and within areas; however, levels of bycatch (both target and non-target species) in all areas were much lower than previous estimates from the trawl fishery. Additionally, in contrast to the trawl fishery, commercially exploited fish made up a small proportion of the bycatch in the Nephrops creel fisheries studied. The survival of Nephrops discards is considered to be high, although preliminary results suggest that predation by seabirds may cause significant mortality. The effects of ‘ghost fishing’ were investigated experimentally at two sites and it seemed that lost creels do not constitute a serious issue in this fishery. Creels were found to be very selective for their target species, with both target and non-target species being able to escape. Only a few crabs and a small proportion of the captured Nephrops died in the creels, indicating no evidence of a ‘re baiting’ effect from dead animals. Stress associated with the capture, storage and live transport of creel-caught Nephrops was found to be greatest during the transport process, during which Nephrops are kept out of water for long periods of time. Temperature was particularly important, suggesting cooling prior to and during transport was essential in order to ensure their survival. Reduced salinity was found to be a major source of stress. An assessment of the management measures implemented in the Torridon creel fishery show that escape gaps placed in creels are effective in enabling smaller Nephrops and other bycatch species to escape. Limiting effort of individual fishermen has been successful, but this has been followed by an increase in the number of boats fishing within the area, leading to an overall increase in effort. Management measures (both statutory and voluntary) currently applied in the Torridon area are discussed and considered in relation to other areas. It is concluded that creel fishing areas need to be considered on a case-by-case basis, accounting for biological characteristics of individual stocks, as well as management issues at a local scale. The findings of the present study are discussed in the context of providing a detailed description of the characteristics of the Nephrops creel fishery on the west coast of Scotland. Findings are also discussed in relation to other crustacean creel fisheries, enabling issues directly relevant to the specific fishery to be considered in a much broader context. The present study has been particularly valuable in a wider context, as Nephrops are found in a habitat which is very different from the majority of other commercially exploited crustaceans, and their life history characteristics are also different. This study provides an ideal platform to assess what general principles from other creel fisheries apply to the Nephrops creel fishery, as well as what characteristics are unique to this fishery.

In this study I investigated Procellariiformes (albatrosses, petrels and shearwaters) at sea in the southwestern Atlantic Ocean. Fourteen species and 301 individuals were sampled non-destructively using a cast net method described here. A method is described for ageing Atlantic Yellow-nosed (Thalassarche chlororhynchos) and Black-browed (T. melanophris) Albatrosses based on bill colour and moult. Procellariiformes appear to have two distinct moulting strategies: petrels and shearwaters have complete annual moult, start to moult during the breeding period, and replace several primaries and tail feathers at one time, whereas albatrosses undergo long moulting cycles, replace less feathers at once, and suspend the wing moult during breeding periods. Primary moult starting at P2 rather than P1 was demonstrated to be a common feature in this taxon, with important implications for studies of stable isotopes, trace elements and pollutants in feathers. Overlap between moulting and breeding is demonstrated to be common with tail and contour feathers, but limited in wing, which suggests that flight constraint in long distance foragers rather than nutritional and energetic limitations is the ultimate factor determining primary moult timing. Based on molecular sexing and linear measurements, sexual size dimorphism was shown to vary according to species, with females in general smaller than males, more pronounced in bill measurements than in other traits, and more conspicuous in Giant Petrels (Macronectes spp.) and Diomedea albatrosses. Closely related species pairs of Thallassarche albatrosses and Procellaria petrels had differing levels of sexual dimorphism. The pelagic seabird community sampled comprises birds from different ages and breeding status according to species. Skewed Adult Sex Ratio (ASR) has been proposed as a common pattern in birds, frequently biased towards males and with larger biases in globally threatened species. In albatrosses and petrels, differential mortality of one gender in fisheries is suggested to be caused by sexual size dimorphism giving males a competitive advantage, which allows more access of the larger sex to discards and baits, or to at sea segregation of sexes. These hypotheses were tested by sampling birds at sea and reviewing ASR of birds incidentally captured in fisheries. Skewed ASR is common in albatrosses and petrels from the community attending vessels, but there was no correlation between skewed ASR and conservation status, both in terms of population size or global level of threat, or between ASR and sexual size dimorphism. Thus, sexual dimorphism in size does not explain skewed ASR in the community sampled or in incidental captures in fisheries reported in the review. Differential at sea distributions of males and females appear to explain better the patterns found in the community sampled at sea, as well as skewed ASR in seabird fatalities. Kernel density analysis of satellite tracked Spectacled Petrels (Procellaria conspicillata) in 2006 and 2007 demonstrated intense use of waters in the Brazilian Exclusive Economic Zone, from 26 to 31S, mainly over the continental shelf break and offshore waters. The marine habitats used by Spectacled Petrel and described by bathymetry, SST and productivity are remarkably different from those of the sister species White-chinned Petrel (Procellaria aequinoctialis), which occurs in the area during the winter, but remains over the continental shelf, on Sub-Antarctic and oligotrophic waters. A close association between birds and pelagic longline fishery was demonstrated through comparison of the main kernel areas used by Spectacled Petrels and the pelagic longline fleet. Stable isotopes of nitrogen (δ15N) and carbon (δ13C) in blood preserved in different ways and simultaneously growing feathers were analysed in Spectacled Petrel. Mean δ13C and δ15N values in growing feathers were higher than in blood, suggesting tissue-specific fractionation. Different methods of preserving tissues such as blood may bias stable isotope values. Air drying is proposed as a practical and unbiased method for blood preservation in field situations where freezing is not a practical option, and a mathematical approach is suggested to permit comparison between studies using different preservation methods or tissues. By analysing stable isotopes in blood of all species of Procellariiformes sampled it is demonstrated that availability of discard, mainly the preferred shark liver, which is shared among species with contrasting body masses and feeding techniques, is the ultimate cause of overlapping in trophic levels. Carbon isotopic signature overlapped among the species and was typical of subtropical and offshore region. Early migrant individuals from Antarctica and sub-Antarctic (e.g. Cape Petrel Daption capense, White-chinned Petrel, Wilson’s Storm-petrel Oceanites oceanicus) and species still rearing chicks when sampled (Wandering Albatross Diomedea exulans) had clear carbon isotopic signatures from the austral region. All southern latitude species underwent a clear shift in carbon and nitrogen isotope signatures, increasing in trophic level after arriving in the SW Atlantic. Cory’s Shearwater (Calonectris diomedea), the only species not attending vessels, has low nitrogen values resulting from a diet of flyingfish and squids naturally occurring in the area. While some abundant and widespread petrels and shearwaters, particularly those small in size, benefit from discards from pelagic longline vessels, the balance between benefits and the incidental mortality in hooks is negative for albatrosses and some petrels. Information on bycatch rates of seabirds in the Brazilian domestic pelagic longline fishery from 2001 to 2007 in the Exclusive Economic Zone and adjacent international waters of the southwestern Atlantic Ocean is presented, and bycatch rates for the area are reviewed. Overall, seabird capture rate for the Brazilian pelagic longline fleet was 0.229 birds/1000 hooks, varying from zero to 0.542 birds/1000 according to season. Capture rates were higher between June and November (cold season) and affected mainly the Black-browed Albatross (55% of birds captured), the White-chinned Petrel, the Spectacled Petrel and the Atlantic Yellow-nosed Albatross. Capture rates previously reported in the SW Atlantic varied from 0 to 5.03 birds/1000 hooks, with those based on logbooks or fishermen interviews tending to underestimate capture rates, whereas those based on small numbers of hooks or short time periods tend to greatly overestimate rates in both pelagic and demersal longline fisheries. A range of poorly-known hook-and-line commercial fisheries carried out by the Itaipava fleet, southeastern Brazil, composed by 497 vessels, was described with seven fisheries defined. Capture rates were higher for the surface longline for Dolphinfish (0.15 birds/1000 hooks and 1.08 turtles/1000 hooks), slow trolling for Bigeye Tuna (0.41 birds/day) and handlining targeting Yellowfin Tuna (0.61 birds/day). Bycatch of 47 seabirds, mainly the endangered Spectacled Petrel, Atlantic Yellow-nosed, and Black-browed Albatrosses, and 45 turtles of four species were recorded. Longline and other hook-and-line fisheries are the major threat for albatrosses and petrels from different origins when foraging in the SW Atlantic Ocean, and require urgent conservation measures.

This PhD thesis seeks to consider conifer forestry stream corridor design in relation to both in-stream and riparian zone biodiversity and functioning. The contribution, availability and source of basal resources within varying corridor conditions are the focus of this project. This approach is combined with surveys of community diversity on a number of key trophic scales in order to determine how the corridor characteristics and their associated resource availability, affects community structure. The effects of varying design and management of the riparian buffer zones within afforested stream systems on in-stream and overall habitat diversity and functioning remains largely unknown. Although guidelines have been implemented for several years (Forest and Water Guidelines, Forestry Commission), recommendations, although based on sound assumptions, are subjective assessments and tend not based on scientific research or data. As such, the premise of this project is to consider a variety of corridor physical parameters adjacent to low-order streams within two afforested catchments in South-West Scotland, between 2003 and 2005, in order to contribute to the understanding of system functioning within the limitations of forestry land-use and management. A number of different approaches were employed in order to define the proportional contributions of allochthonous and autochthonous material within the benthos of the stream systems. This was done in order to define resource availability, biofilm characteristics, stream functioning and the role of corridor design in influencing resource availability. Yet, despite significant autochthonous productivity, allochthonous organic matter was the primary resource utilised by many taxa. However, conversely, light regime was found to be fundamental in shaping production and community structure within these ecosystems. Consequently, here I explore a number of different trophic scale responses to riparian conditions in order to define the biotic responses to variation of resource availability, with the aim of contributing information which may aid in design and management of afforested riparian zones.