1. The literature has been reviewed with respect to the dietary intake and subsequent metabolism of polyunsaturated fatty acids (PUFA), of both the n-6 and n-3 series, in teleost fish. Particular emphasis has been made to the physiological roles of PUFA with respect to cell membrane function and eicosanoid production. 2. Atlantic salmon post-smolts were fed practical-type diets, based on fish meal, in three separate dietary experiments of 10-16 weeks duration. The first trial compared dietary lipid supplied either as fish oil (FO) or as sunflower oil (SO) with the diets having an n-3/n-6 PUFA ratio of 9.4 and 0.2 respectively. The second trial used diets formulated with blends of FO, SO, grape seed oil and safflower oil to provide linoleic acid at 10, 25 and 45% of total dietary fatty acids. The third trial was similar to the first but with an additional diet in which the lipid component was supplied by linseed oil (LO). All diets satisfied the nutritional requirements of salmonid fish for n-3 PUFA. There were no statistically significant differences in final weights between dietary treatments in the third trial. However, in the second trial fish fed the intermediate level of linoleic acid (25%) attained a significantly higher final weight compared to both other treatments while fish fed the highest level of linoleic acid (45%) had significantly lower final weights compared to both other treatments. In the first trial the effect of diet on growth (weight gain) could not be ascertained as the initial weights of the fish were significantly different. 3. A number of fish fed SO developed severe cardiac lesions which caused thinning of the ventricular wall and heart muscle necrosis. In addition the fish fed diets containing SO were susceptible to a transportation-induced shock syndrome that resulted in 30% mortality. 4. Incorporation of linoleic acid (18:2n-6) into membrane phospholipids increased in response to dietary intake with fish fed SO having increased levels of 18:2n-6 (up to 15-fold), 20:2n-6 (up to 12-fold), 20:3n-6 (up to 25-fold) and arachidonic acid (AA; 20:4n-6) (up to 3-fold), and decreased levels of eicosapentaenoic acid (EPA; 20:5n-3) (up to 3-fold). The ratio of n-3/n-6 PUFA was decreased (up to 4-fold) and the20:4n-6/20:5n-3 ratio increased (up to 9-fold) in membrane phospholipids from fish fed SO compared to those fed fish oil. While the tissue phospholipids from fish fed La had increased levels of 18:2n-6, 20:2n-6 and 20:3n-6, the levels of AA, 22:4n-6 and 22:5n-6 were similar to or significantly reduced compared to fish fed FO. Membrane phospholipids from fish fed LO also had increased 18:3n-3 and 20:4n-3 compared to both other treatments while in some tissues and phospholipid classes EPA was increased compared to fish fed FO. 5. These dietary induced changes in phospholipid eicosanoid precursor ratio were reflected in altered eicosanoid production. In gill cells, stimulated with the calcium ionophore A23187, 12-hydroxy-8, 10, 14, 17-eicosapentaenoic acid (12-HEPE) was the major 12-lipoxygenase product in fish fed Fa. In stimulated gill cells from fish fed SO and LO, 12-HEPE, 12-hydroxy-5, 8, 10, 14-eicosatetraenoic acid (12-HETE), 14- hydroxy-4, 7, 10, 13, 16, 19-docosahexaenoic acid (14-HDHE) and thromboxane B2 (TXB2) were all decreased compared to fish fed FO. However, the ratio of 12- HETE/12-HEPE was significantly elevated in stimulated gill cells from SO-fed fish compared to both other treatments. In stimulated blood leucocytes leukotriene B4 (LTB4)' 12-HETE and TXB2 were significantly increased while LTB5 and 12-HEPE were significantly decreased in fish fed SO compared to those fed FO. Blood leucocytes from fish fed LO produced less TXB2 compared to fish fed SO and prostaglandin E2 was reduced compared to both other treatments. In isolated cardiac myocytes stimulated with A23187, TXB2 production was increased in SO fed fish compared to those fed FO. 6. The activity of cardiac sarcoplasmic reticulum Ca2+-Mg2+ATPase was not affected by dietary treatment. 7. An established cell line derived from chum salmon heart (CHH-1) was utilised to study PUFA metabolism. The CHH-1 cells exhibited considerable A6 desaturase activity but showed no preference towards n-3 over n-6 PUFA. CHH-1 cells did exhibit significant A5 desaturase activity which showed a preference towards n-3 PUFA. No A4 desaturation activity was observed. Elongation of C20 PUFA was especially active in CHH-1 cells with C22 PUFA being specifically incorporated into phosphatidylethanolamine (PE) and phosphatidylserine (PS). CHH-1 cells supplemented with 20:3n-6 showed reduced growth rate, cell death and unusual pycnotic appearance, compared to those supplemented with other PUFA. 8. The lipid compositions of hearts and livers from wild and farmed parr and presmolts were analysed and compared. The fatty acid compositions of triacylglycerols (TAG) and phospholipids from both farmed parr and pre-smolts contained greater amounts of monoenoic fatty acids compared to their wild counterparts. TAG, phosphatidylcholine (PC) and PE from heart and liver of wild fish contained more 18:2n-6 and AA compared to farmed fish. Linolenic acid, EPA and 22:Sn-3 were increased in hearts and livers of wild fish compared to farmed. Docosahexaenoic acid (DHA; 22:6n-3) levels were higher in heart and liver of farmed fish, particularly in heart PC, PS and TAG. The n-3/n-6 PUFA ratio was generally lower in wild compared to farmed fish, largely due to higher n-6 PUFA, in particular AA, in wild fish. 9. The results are discussed with respect to the competitive interactions between PUFA of the n-6 and n-3 series which determine the fatty acid compositions of membrane phospholipids in salmon. The ratio of n-3/n-6 PUFA in membrane phospholipids, and in particular the ratio of AAIEPA, appears important in terms of membrane physiology and biochemistry, eicosanoid production and the development of cardiac histopathological lesions.

Growth plays a key role in regulating ecological and population dynamics. Life history characteristics such as age at maturity, fecundity and age and size at migration are tightly linked to growth rate. In addition, size can often determine survival and individual breeding success. To fully understand the process of growth it is important to understand the mechanisms that drive growth rates. In Atlantic salmon, growth is critical in determining life history pathways. Models to estimate growth could be useful in the broader context of predicting population dynamics. In this dissertation I investigate the growth process in juvenile Atlantic salmon (Salmo salar). I first used basic modeling approaches and data on individually tagged salmon to investigate the assumptions of different growth metrics. I demonstrate the size-dependency in certain growth metrics when assumptions are violated. Next, I assessed the efficacy of linear mixed effects models in modeling length-weight relationships from longitudinal data. I show that combining a random effects approach with third order polynomials can be an effective way to model length-weight relationships with mark-recapture data. I extend this hierarchical modeling approach to develop a Bayesian growth model. With limited assumptions, I derive a relatively simple discrete time model from von Bertalanffy growth that includes a nonparametric seasonal growth function. The linear dynamics of this model allow for efficient estimation of parameters in a Bayesian framework. Finally, I investigated the role of life history in driving compensatory growth patterns in immature Atlantic salmon. This analysis demonstrates the importance of considering life history as a mechanism in compensatory growth. Information provided in this dissertation will help provide ecologists with statistical tools to estimate growth rates, estimate length-weight relationships, and forecast growth from mark-recapture data. In addition, comparisons of seasonal growth within and among life history groups and within and among tributaries should make a valuable contribution to the important literature on growth in Atlantic salmon.

Thesis advisor: Noah P. Snyder / Thesis advisor: Mathias J. Collins / Large wood (used interchangeably with the term “instream wood”), which refers to trees, logs and other wood within a channel, is beneficial to river ecosystems and is being used more frequently as a component of river restoration projects. The process of large wood becoming stable within a river channel, inducing floodplain formation, and eventually providing large wood back to the system is known as the ‘floodplain large-wood cycle’ hypothesis (Collins et al., 2012). In a stream restoration context, this process can be viewed as an indicator of a self-sustaining cycle. The ‘floodplain large-wood cycle’ hypothesis was formulated in the Pacific Northwest. To investigate this process in other regions, I used the Merrimack Village Dam (MVD) study site in southern New Hampshire. The study site provided a location where instream wood was recruited to the river from an adjacent terrace as a consequence of erosion associated with a dam removal. Assessment of wood in this scenario was used to evaluate the ‘floodplain large-wood cycle’ (Collins et al., 2012), and to compare MVD to “passive” large wood restoration and deliberate, and potentially engineered, large wood restoration sites throughout New England. To assess multiple sites, I identified metrics to evaluate the effectiveness of large wood to promote ecological and geomorphic complexity within channels. The metrics were quantified at the MVD site and several other sites in New England with natural or placed large wood. I also collected additional data at the MVD site using methods implemented during previous studies, including cross section surveys and repeat photographs (Collins et al., 2017; Pearson et al., 2011). The study assessed habitat and geomorphic effects of large wood within river systems in the northeastern U.S. and provided information to evaluate the use of large wood during river restoration. Overall, only 33%, 33%, and 20% of surveyed sites are consistent with hypotheses formulated regarding significant differences in depth variability, velocity variability, and median velocity between test and reference reaches, respectively. With evidence for and against each hypothesis at both passive and active sites, large wood structures did not cause the geomorphic and hydraulic changes I expected to see. The availability of sand in a channel and the stream slope influencing sediment transport seem to be important factors in determining whether or not large wood has the ability to impact the geomorphic and hydraulic characteristics of a channel. At the MVD site, where sand is available, up to 0.90 m of sediment deposition is seen on top of the surface eroded by a March 2010 flood, surrounding recruited trees. Evaluation of historical aerial imagery further indicates that evidence of the ‘floodplain large-wood cycle’ hypothesis is present at the MVD06 cross section on the Souhegan River in New Hampshire. / Thesis (MS) — Boston College, 2022. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

The Atlantic salmon (Salmo salar) is an iconic species that dominates the global finfish production sector with increasing market demand. The Scottish industry and government alone aspires for expansion of the sector to 210,000 t by 2020 with 154, 000 t produced in 2013. As such, there are pressures to improve sustainable development in particular to minimise the genetic impact of escapees on wild populations and reduce sea lice infection which are required for the granting of “green licenses” in Norway. The use of triploidy has been tested in the 1980’s with little success owing to suboptimal rearing conditions leading to elevated mortalities, poorer growth and a higher prevalence of deformities, in particular of the skeleton. Collectively: recent success of triploid trout farming, expansion to the salmon production sector and potential resulting pressure on wild stocks through escapee increases have reinstated interest to implement artificially induced triploid Atlantic salmon in commercial production. As diploid Atlantic salmon have undertaken extensive domestication to achieve the high quality production and welfare standards observed to date, triploid conspecifics too require husbandry optimisation to realise potential. In particular, industrialisation requires that higher observations of deformities and inconsistent growth trajectories during seawater ongrowing be resolved through optimisation of rearing regimes and subsequent standardization of husbandry protocols. Triploids possess additional genomic material and increased cell size yet reduced frequency that reflects known differences in physiology and supports that, in effect, triploids should be considered as a new species relative to diploid conspecifics. Therefore, this doctoral thesis aimed to study nutrition and temperature effects on triploid Atlantic salmon traits throughout the production cycle from ‘egg to plate’. Nutrition trials aimed to improve growth potential and mitigate skeletal deformities both in freshwater (FW) and saltwater (SW) whilst attempts were made to define a window of smoltification to ensure optimal ongrowing performance. Finally, impacts of embryonic temperature regimes that are known to impact long term performance and deformity development in triploids, were examined in relation to DNA regulation and yolk composition in an attempt to underpin potential mechanisms for the environmental impact of temperature on developmental phenotype. One of the main restrictions to triploid Atlantic salmon implementation is the increased prevalence and severity of skeletal deformities, particularly after the maring phase. The work performed in this thesis first demonstrated that protein and/or phosphorous (P) supplementation throughout SW ongrowing not only reduced the level of severely deformed (≥ 10 deformed vertebrae observable by x-radiography) individuals by 30 % but also sustained 6.8 % faster growth and improved harvest grade compared to triploids fed a standard grower diet (chapter 2). Comparison of x-radiography and severely deformed individuals between harvest and sea transfer highlighted that protein and P supplementation arrested deformity development whereas prevalence increased in triploids fed a standard grower diet. This implied that severe deformities were of FW origin and strongly suggest requirement for improved nutrition in FW to optimise SW performance. Therefore investigation of higher dietary P inclusion in FW was investigated and results showed significantly reduced number of deformed vertebrae and no severely deformed individuals in those fed 19.7 g total P Kg-1 compared with those fed 13.0 & 16.7 g total P Kg-1 (chapter 3). Most deformities were localised in the central (vertebrae 27 – 31) and caudal (vertebrae 52 – 57) regions for all treatments. However, triploids fed lower dietary P displayed a particular increase in prevalence within the tail region (vertebrae 32- 47) which is consistent with SW ongrowing reports and results from chapter 2, further highlighting FW origin of higher vertebral deformities reported in SW ongrowing in triploids. Higher P supplementation in FW also significantly improved growth in triploid parr compared to diploids and lower supplementation. However, this effect did not transpire in later FW smolt stages where weights were significantly higher in triploids fed lower compared to higher P supplementation. Expression of target genes involved in osteogenesis and bone P homeostasis in vertebrates were then analysed and a ploidy effect of osteogenic genes alp, igf1r and opn as well as a dietary effect on P homeostasis gene fgf23 was apparent in the parr stages but not smolt. In addition, stronger ploidy-diet effects were also observed in parr stages for whole body mineral concentrations. Collectively, growth, gene expression and whole body mineral content results indicate these earlier parr life stages may be more sensitive to P supplementation. This pronounced effect may be a consequence of seasonal accelerated growth associated with this period, where higher temperatures were also observed. The potential for shorter P supplementation windows in commercial production was addressed in chapter 4 with hope to cut economic cost to raw mineral inclusion in feed and also mitigate potential anthropogenic eutrophication on the environment that may be induced by P leached through uneaten feed and faeces. Triploids were fed higher dietary P (17.4 g total P Kg-1) until either early (5 g) or later (20 g) parr stages, or smolt (83 g) and monitored for performance throughout freshwater (FW) development. During later parr development (30 g), x-radiography assessment demonstrated that increased dietary P reduced the number of deformities and severely deformed individuals with no indication that feeding P for shorter windows improved skeletal integrity. Hence, P supplementation may be required throughout FW development for optimal skeletal performance. In addition, no differences in deformities were observed between triploid treatments at smolt. An effect of dietary P supplementation on whole body mineral concentration was observed in the early and later parr stages that was not as pronounced as smolt, which is consistent with results in chapter 3. Together, these results indicate that skeletal assessment during early developmental stages may not reflect smolt performance most likely as a consequence of seasonal effects of improved linear growth in the cooler winter temperatures prior to smolt where reversible deformities observed at parr may also be alleviated. In the same study (chapter 4), the inclusion of the probiotic Pediococcus acidilactici (Bactocell™) was also tested as a means to enhance gut assimilation as suggested in previous studies and therefore reduce the levels of P supplementation. Results clearly indicate superior skeletal performance in parr (30 g) as well as significantly less deformed vertebrae and no severely deformed individuals. However, at smolt (~83g), no effects of the dietary probiotic treatment were observed which may also be attributed to seasonal effects. Overall, nutritional research clearly indicate triploids require higher dietary P for optimal growth and skeletal development, which although is not consistent between life stages, is ultimately required throughout FW for optimal skeletal development at smolt. The use of probiotics offer a promising avenue for reduced P requirement in FW feed and further research should verify results and assess long-term performance. Timing of SW transfer according to correct parr-smolt transformation (PST) is essential for survival and growth performance in ongrowing where feeding and growth rate accelerate post-transfer. So far, SW transfer regimes and in particular the smoltification ‘window’ remains loosely defined in triploid Atlantic salmon and it is crucial that this be addressed to ensure optimal ongrowing survival and performance.

Fish meal (FM) and fish oil (FO) have traditionally been central in aquaculture feed formulation but the finite global supply situation limiting future use along with issues of contaminant levels in these feed ingredients have become critical issues. The objectives of the present study were to investigate alternative feed ingredients as substitutes for both FM and FO in feeds for Atlantic salmon (Salmo salar) to ensure optimal growth, feed efficiency and health of the fish as well as maintaining the nutritional quality of the fish product to the human consumer, especially the levels of n-3 highly unsaturated fatty acid (HUFA), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), in the flesh. The results of the present study revealed that there were no negative effects on growth performance, feed utilisation and apparent digestibility in Atlantic salmon when FO was substituted with vegetable oil (VO) but these parameters were affected when FM was replaced with alternative protein sources from plants and animals at high levels, despite dietary supplementation with crystalline amino acids and lecithin. Reduction in feed intake was a factor affecting growth retardation when FM inclusion decreased. However, replacing FM with alternative plant and animal proteins along with partial replacement of FO had no major effect on nutritional quality, particularly n-3 HUFA content of salmon tissues. Replacing Northern FO with decontaminated FO or blends of southern hemisphere FO and VOs strategies to reduce POP contaminants and retain high nutritional values in flesh were very successful. Dietary treatments and genetic origin of fish both had effects on tissue compositions and gene expression. All fish groups (strain/family), consist of CAL, LEAN and FAT strains, fed a diet containing VO showed significant differential expression of lipid metabolism-related genes compared to fish fed a FO diet with LEAN strain appearing to adapt to VO inclusion better than FAT strain. This thesis has demonstrated dual replacement of FM and FO with alternative raw materials in salmon feeds without a major negative impact on nutritional quality.

Photoperiod manipulations are widely used throughout the Atlantic salmon (Salmo salar) farming industry as a means of producing a product of uniform quality all-year round. However, farmers still remain sceptical over their effectiveness to regulate growth and maturation during the on-growing stage. Furthermore, reports of a characteristic growth-dip following light exposure suggest that light may negatively affect the physiological performance of fish in the short-term. Thus, this thesis investigates the effects of light characteristics (spectral quality, intensity and photoperiod) on growth and maturation of salmonid fish and addresses some of the uncertainties surrounding photoperiod use currently reported within the industry. Rainbow trout (Oncorhynchus mykiss) are seemingly an ideal model species for examining photoperiod effects on growth. Consequently, the application of constant light exposure (LL) at two different intensities (28W and 16W) during two different thermal conditions (summer and winter) was examined on individually tagged fish. Feed intake and growth appeared to be related to the ambient water temperature and did not appear to be affected by intensity or photoperiod, although the onset of constant light did appear to initially affect growth rate. This may indicate that LL has a limiting effect on the growth of trout or that the prevailing water temperature at which light is applied may override the photoperiodic effect. Furthermore, the lack of enhanced growth in trout exposed to LL, unlike that demonstrated for other salmonids, suggest that there may be a species-specific response to environmental variables. Thus, questions regarding photoperiod effects should be limited to the species in question. The main source of variation in results observed under photoperiod manipulations stems from the salmon industry. Atlantic salmon post-smolts were reared in seawater tanks and either maintained under a natural photoperiod (NP) or exposed to a simulated natural photoperiod (SNP), constant light superimposed on the natural light (NPLL) or constant light only (LL). Artificial light onset, irrespective of photoperiod, resulted in an apparent trend for a reduced appetite lasting up to 60 days. Furthermore, the onset of constant light resulted in a significant chronic elevation of plasma cortisol levels and changes to growth and thyroid hormone levels, providing direct evidence that constant light exposure induces stress. In addition, fish exposed to SNP failed to exhibit a stress response despite a low feed intake. However, differences in the plasma melatonin levels during twilight times, as compared to NP, suggest that gradual changes in the natural light intensity throughout the day, particularly around dawn and dusk, may be important for synchronizing daily events. No differences in growth were observed between the NP and NPLL regimes, although fish reared in an enclosed regime (SNP and LL) exhibited a significantly lower weight gain than fish in an open environment (NP and NPLL). This further highlights the impact that the rearing environment has on the growth performances of fish and the need for commercially run trials. Advances in lighting technologies and a greater understanding of how light is transformed through the water column have focussed research on the spectral sensitivity of fish. Therefore the lighting efficiency of novel blue narrow bandwidth LED lighting units through the water column and their effects on growth and maturation performances of salmon reared in commercial production cages were compared against the standard metal halide units currently utilized throughout the industry. LL application, irrespective of intensity or spectrum, reduced the numbers of fish maturing as compared to fish reared under a natural photoperiod. However, this was greatest under the standard metal halide units reflecting a greater light penetration and perception as determined by plasma melatonin levels. The metal halide groups exhibited the greatest relative weight gain over the trial period as compared to control fish. No evidence was observed for a growth-dip under metal halide light, although blue lit treatments exhibited an initial significant reduction in food consumption, suggesting a possible welfare issue. Nevertheless, the prototype blue LED units showed possible potential for commercial application by penetrating the water depth at half the distance of the metal halide units for only one eighth the power and one fifth the brightness. However, further tests of these prototype spectral units are required to examine the potential welfare and physiological growth and reproductive effects. These studies have shown that the efficacy of artificial light regimes is largely dependent upon the effectiveness of the light source through the underwater environment and its perception by fish, providing a sufficient intensity is emitted exceeding the physiological threshold level for the species cultured. Moreover, whilst the onset of artificial light may elicit a stress response and demonstrate a trend for a suppression of appetite for salmon reared in experimental tanks, no compelling evidence for a suppression of appetite or growth was found under normal commercial cage conditions. This suggests that the growth-dip observed within the industry may in part be a combination of a physiological response to the onset of light further exaggerated by the farmer’s perception and altered judgement in feeding. In addition, the results obtained from this study have helped to standardize the use of light regimes within the industry. Nevertheless, further studies are necessary to fully elucidate the underlying mechanisms which may govern growth and maturation in fish following the onset of light exposure.

Pre-harvest sexual maturation in farmed Atlantic salmon, Salmo salar, remains a key biological bottleneck compromising biomass and financial output, production predictability, environmental respect, stock welfare and the overall sustainability of the on-growing industry. The management practices currently in place are not optimized and events of high maturation rate are still sporadically observed. From an ecological perspective, the escape of reproductively competent, domesticated Atlantic salmon constitutes a threat to the integrity of wild stocks. The forecasted expansion of the Scottish salmon industry compels the need for a comprehensive and more reliable control of sexual maturation. The general aim of this research project was to optimize the current management strategy (windows of light-manipulation and quality grading) and test alternative practices (lighting-technologies, selective harvest and triploidization) in the control of pre-harvest sexual maturation within the Atlantic salmon on-growing industry. In that end, a number of trials were performed using stock reared in sea-cages on a full commercial-scale or in tanks on an experimental scale. The results of this project are organized around three experimental chapters dealing consecutively with body-size dimorphism, grading and harvest quality; light manipulations and triploidy. In each chapter, two original manuscripts either published or in review are included. In addition to these experimental results, a literature review chapter composed of two review papers on the photoperiodic synchronization and developmental regulation of maturation in salmonids and on morphological skin colour changes in teleosts (published) are presented. In the first experimental chapters, we aimed at investigating the possibility of detecting and selectively harvesting a high proportion of sexually recruited fish before flesh quality deterioration. Results clearly showed that body-size dimorphisms between maturity cohorts at the end of the anabolic window of reproduction (June/July) are strong and standard predictors of maturation among related populations with the same freshwater history. Dimorphism can therefore be modelled to easily and accurately estimate maturation rate in a number of discrete rearing-units. If required, a high proportion of sexually recruited fish can be selectively harvested as superior quality product while leaving the immature fish for further on-growing. This provides an alternative to visual grilse grading that is not feasible in large-scale aquaculture systems, prevents downgrading and increases production predictability as compared to emergency harvests. Furthermore, our results showed immature males grow faster than immature females which should be further investigated to fully determine gender specific performances and nutritional requirements. Weight-grading performed earlier in the cycle affects the sex-ratio within individual pens and in turn apparent performance. This work also revealed that Atlantic salmon can exhibit significant variations in skin colouration resembling the onset of nuptial display but that are not related to sexual recruitment and do not correlate with reduced flesh quality. This originates from a lack of purine (silver) pigments which was also identified, to a larger extent, as characteristic of the nuptial display. This suggests a degree of desmoltification in these histologically immature fish. The instrumental colouration of the altered phenotype was shown to be improved towards a more silver-like appearance by direct ice-contact. This knowledge could facilitate post-harvest quality grading towards the most appropriate market channel and increase product acceptance and attractiveness. The second experimental chapter investigated the possibility of improving photoperiodic manipulation used to suppress early maturation, currently applied for 6-months during the second winter at sea using wide-spectrum, high-intensity lighting systems. Our results showed that the window of continuous artificial-light (LL) exposure can be reduced to 4-months following its onset in early January without compromising its efficiency in suppressing pre-harvest maturation. In addition, alternative lighting technologies were also highly potent at suppressing sexual maturation. The mean-irradiance (intensity) generated within a commercial sea-cage was inversely proportional to the suppression of nocturnal plasma melatonin (light perception hormone) and negatively correlates with the maturation rate within the commercial sea-pen. Threshold levels of light-intensity required to achieve optimal (total) suppression of sexual maturation are suggested. Alternative, narrow band-width lighting-technologies (cold cathode and light-emitting diodes) present an array of technical, practical, economic and welfare benefits comparing to the system currently in use. Clear improvements of the photoperiod-manipulation strategy were demonstrated and these would reduce economic and environmental costs but also potential impacts on animal welfare. The third experimental chapter showed the strong potential of sterile-triploid Atlantic salmon stocks both in freshwater and seawater. Triploid out-of-season smolts were produced for the first time using a classical accelerated "square-wave" photoperiod. Triploidization affected the smoltification pattern but had no detrimental effects on freshwater and early seawater performances under both a S0+ and S1 regime. This illustrates the need to adapt the timing of seawater transfer for successfully producing triploid Atlantic salmon post-smolts. Following one year of seawater rearing, the prevalence of external deformities was higher in triploids but remained within acceptable levels. Importantly, the incidence of vertebral deformities and ocular cataract was higher in triploids possibly due to their specific requirements. It is suggested that tailoring the diet to the nutritional requirements of triploids holds strong potential for remediation. This must be addressed if the use of sterile-triploid stock is to become a commercial reality. The present research project provides means to optimize the maturation management strategy within the Atlantic salmon on-growing industry through light-manipulation, maturation detection and selective harvest, and quality grading. Proposed improvements have the potential to increase biomass and financial output, production predictability, environmental respect and animal welfare and will allow standardization of the overall control of pre-harvest sexual maturation. Their implementation provides a comprehensive strategy likely to favour a sustainable expansion of the Atlantic salmon industry. From a longer term perspective, the rearing of sterile-triploid stocks is promising and should be actively investigated to isolate domesticated strains from their wild conspecifics. This would also eliminate the need for on-growers to deploy a maturation management strategy that that might still affect stock welfare and remains, despite the strong improvements demonstrated, not 100% reliable, costly, technical and protracted.

The relationships between local and catchment-wide land use patterns and the spatial distribution of stream habitat variables within the Grande Cascapedia drainage basin were investigated using a geographic information system (GIS). Stream habitat variables including substrate composition and channel morphology were sampled at 48 study sites, ranging from highly disturbed to relatively pristine forest conditions in 2nd to 5th order tributaries. Land use and geology-structure variables were extracted for each catchment at four spatial scales using a GIS. The transition between pool-riffle and boulder-rapid morphologies occurred between channel gradients of 1.5% and 1.7%. The surface grainsize distribution is affected by the hydraulic power of the reach, while the subsurface grainsize distribution is associated with the degree of valley incision. The amount of logging within a 1 km radius of a sample site increases the occurrence of fine sediment within the substrate. There was, however, a surprising lack of relationship between the majority of road density metrics and the level of fines within the substrate.

No description available.

The ectoparasitic monogenean fluke, Gyrodactylus salaris, is a parasite known to be highly pathogenic to Atlantic salmon (Salmo salar). Although present in the environment of several neighbouring European countries, the UK is thought to be G. salaris-free, but, if national contingency plans to control this parasite are to be effective, it is vital that we understand the factors underlying its transmission from host to host. This study demonstrates that the majority of parasites transferring to new hosts are mature parasites that have reproduced at least once. Since, exploration and host transfer strategies pose a risk to survival; the parasite will endeavour to pass on its genes before attempting to transfer from one host to another. This study has also shown that when pregnant parasites are forced to leave their hosts, their offspring are aborted prematurely to ensure the survival of the mature parasite. Gyrodactylids do not possess a free-swimming stage in their life cycle, which allows for their migration between hosts. In spite of this, they are able to rapidly colonise naïve hosts, even in non-shoaling populations of fish. This study investigates the transmission strategies employed by detached parasites in the colonisation of new hosts. Observations of gyrodactylids collected from 3-spine sticklebacks, Gasterosteus acuelatus, suggest that their activity increases as a stickleback approaches, alerting the host to its presence. The parasite is then ingested directly by the prospective host. A time series of experimental exposures and specimens prepared for Scanning Electron Microscopy (SEM) suggest that once ingested, the parasites attach to the lining of the buccal cavity and then migrate out to their preferred colonisation site on the outer surface of the fish. It is proposed that this may be an alternative route for host infection. Similarly, direct ingestion by the scavenging on infected hosts by 3-spine sticklebacks suggests another route of infection of new hosts. Although these routes of transmission may be of lesser significance, infections in the buccal cavity may be an important indicator for detection of infection and those personnel involved in screening fish for gyrodactylids should be aware that this is an area in which infections can occur. This study also demonstrated that the use of the anaesthetic 2-phenoxyethanol does not affect the number of gyrodactylids which leave the host to colonise a new host. Additionally, observations of the transmission process suggest that turbulence produced by the movement of the fish’s fins may facilitate the transfer of detached parasites from the substrate. While this hypothesis appears to be supported by video evidence and photographic stills gathered throughout the duration of this study, further work should be conducted using particle tracking techniques to determine the efficacy of using a vortex effect as a means of colonising new hosts. Field sampling processes may have an effect on this type of research, giving rise to problems with the accurate diagnosis, management and control of gyrodactylids in a variety of fish. Gyrodactylus infected specimens of 3-spine stickleback (Gasterosteus aculeatus L.), minnows (Phoxinus phoxinus L.) and stone loach (Barbatula barbatula L.) from one Scottish river were cohabited. The study found that small numbers of Gyrodactylus do transfer to atypical hosts. This study highlights that personnel involved in fish disease surveillance programmes should be aware of the consequences of transporting multiple species in the same transport vessel as gyrodactylids may infect species previously thought to be resistant. Equally, diagnosticians should be aware of the fact that atypical species may act as temporary hosts and that their gyrodactylid fauna should not be assumed. Non-feeding life-cycle stages, such as the dispersal stages of parasites, are dependant for survival upon finite energy reserves gathered during feeding phases. Thus, those individuals with more limited reserves will die sooner and consequently have less time available to find a new host once detached. At this stage, the principal energy reserves in gyrodactylids are stored as large lipids droplets. Confocal laser scanning microscopy (CLSM) has been used to investigate the distribution of lipid droplets in Gyrodactylus, which have migrated off their fish host, testing the hypothesis that these droplets function as a proxy for the nutritional state. This study, demonstrated that the lipid droplets were particularly associated with the gut and that there is a significant variability in the volume of stored lipid carried out by each individual. Transmission Electron Microscopy (TEM) showed that gyrodactylids carry lipid droplets at all stages of their life cycle, including at release from the birth pore. It is likely that transferring worms require stored energy reserves to survive in the event of failure to establish contact with a new host. These reserves could allow the parasite to survive without a host for several days. As gyrodactylids appear to respond to a range of stimuli including vibration and chemicals released from the host, the presence or absence of such cues may have consequences on the rates of Gyrodactylus transmission. If these chemical stimuli can be identified and then mimicked or blocked, then this may offer potential opportunities for the control of gyrodactylid behaviour and for disrupting their transmission to new hosts. Baseline gyrodactylid behaviour, in the absence of a host, was determined under white light and infrared. This was achieved using a specially constructed arena and purpose written image analysis software to analyse parasite movement under different lighting conditions. The study found that gyrodactylids were more active in the dark than in light conditions, typically displaying longer, more sinuous tracks under red light than under white light. To begin investigating the effect of chemical presence on gyrodactylid behaviour, the activity of octopaminergic agonists and antagonist which bind to muscle receptors and alter muscle activity, were assessed. The impact of octopamine hydrochloride, clonidine hydrochloride, amitraz and, a toxic reference, chlordimeform, over a range of concentrations (0.2 to 3.2µM/L) were assessed on gyrodactylid behaviour. All of the four chemicals affected Gyrodactylus and produced muscle tetanus, causing muscle spasms when extension was attempted. Prolonged exposure resulted in death. Only the highest concentration of chlordimeform, the toxic reference, affected 100% of Gyrodactylus after 24 hours. After 48 hours, all of the Gyrodactylus treated with chlordimeform were either affected, moribund or dead. Amitraz was more toxic than chlordimeform with 80% of Gyrodactylus being dead after 24 hours at the highest concentration. After 48 hours 100% of Gyrodactylus exposed to 3.2 µm/L amitraz were dead, and up to 80% were dead in those exposed to lower concentrations; with no parasites being left unaffected. Although these particular compounds are toxic to fish, the effect of these agonistic chemicals on Gyrodactylus behaviour and survival is interesting and suggests that a closely related compound that is safe for use against fish may offer a potential treatment for the control of G. salaris infections in rivers. An ultrastructure study was undertaken to contribute to the current understanding of gyrodactylid ultrastructure. The findings of this research require broad understanding of gyrodactylid behaviour for their interpretation. Photographic evidence was gathered using transmission and electron microscopy. From these results, it is clear that Gyrodactylus gasterostei on a three-spine stickleback host will respond to a range of stimuli (i.e. vibration or chemical cues released from the host) in their assessment of host suitability.