In Scotland, environmental regulation restricts commercial cod culture to the equivalent of 66 % of that granted for commercial Atlantic salmon (Salmo salar L.) farms. This calculation is based on estimations of nitrogen discharge from the difference in protein content between salmon and cod diets, with the higher levels of protein in cod diets suggesting a higher nitrogen discharge compared to that observed for salmon diets. In turn, this could potentially result in increased nitrogen enrichment of a marine ecosystem. The aims of this study (quantifying and modeling of nitrogenous wastes associated with the commercial culture of Atlantic cod (Gadus morhua L.) were achieved through a series of tank and cage investigations, each of which studied juvenile and adult Atlantic cod. The study provided data with respect to nitrogen excretion from juvenile and adult fish in both systems. This would allow the development of dispersion models and the calculation of nitrogen budgets for commercial cod culture, thus providing environmental regulators data independent of salmon models to create regulations that would be specifically applied to cod farming. The tank - based studies investigated three diet formulations produced by EWOS® Innovation in Norway, as a 4 mm pellet (juvenile study) and as a 7 mm pellet (adult study). The three iso -energetic diets varied primarily in protein content (40%, 50% and 60%). Two tank studies, one on juvenile and one on adult cod, investigated growth, condition and tissue composition, and the production of dissolved nitrogenous wastes over a 5 and 7 month period respectively. At the beginning of the acclimation period prior to the adult tank study commencing, the fish had a mean weight of approximately 1275 g. The difference in the final weight promoted by each diet was not significant (with an approximate final weight of 2400g), suggesting that a low protein diet (40 % protein) promoted similar growth to a high protein diet (60 % protein). Other growth and condition parameters were also similar for all diets with the condition improving over the course of the study. As the fish completed spawning immediately prior to the commencement of the study, an increase in condition was not observed until approximately day 90 of the 210-day investigation. Over the course of the 5-month juvenile study, growth was approximately 224g for the 40% protein diet and approximately 275g for the 50% protein and 60% protein diets. This suggests that a higher protein diet is required for optimal growth of juvenile cod and that 50 % and 60% protein diets promote similar growth and condition, potentially reducing the protein requirement of juvenile diets. In the juvenile investigation, condition increased over the full range of the study. In both tank studies, nitrogen digestion was directly related to protein (and associated nitrogen) content of the diets in the juvenile study expressed as a percentage of the nitrogen content of the diet as 59.19% (40% protein), 56.90% (50% protein) and 52.23% (60 % protein) suggesting that nitrogen digestion is more efficient at lower protein content in the diet. When expressed as a percentage of the nitrogen content of the diet, nitrogen digestion observed in the adult study was 60.55%, (40% protein) 60.92% (50% protein) and 60.60% (60% protein) respectively, suggesting protein digestion is similar regardless of protein content in adult cod. In the adult tank study, under a manual feeding regime, a post-prandial-peak is observed at 105 min. following the cessation of feeding. Thereafter, ammonia levels drop over the course of the sampling period. Following the afternoon meal commencing at 420 min., ammonia levels rise at least until the final samples are collected at 450 min. Under an automated regime, a lesser post-prandial-peak is observed but the ammonia concentration is lower over the sampling period compared to the respective profile under a manual regime. The ammonia profile produced throughout the juvenile tank study follows a very similar trend to that observed in the adult study under the manual feeding regime. Two cage - based investigations took place at the No Catch® Ltd. commercial organic cod farm in Vidlin Voe on the east coast of Shetland. Both studies investigated growth, condition and tissue composition, as well as the production of dissolved nitrogenous and particulate wastes associated with the culture of juvenile and adult Atlantic cod in cage systems. Sampling for the adult study occurred over three days during three sampling trips (September 2005, November 2005 and February 2006). Sampling for the juvenile study took place over three days on a single trip to Vidlin in late April 2006. The diets used at No Catch® Ltd. were produced by Biomar® in Grangemouth. A relationship between feeding and ammonia concentration is less evident in the cage studies than in the tank studies, and similarly, the relationship between feeding and ammonia concentration is less evident in juvenile fish than in adult fish. As ammonia values were converted to (µg/L/tonne biomass), the ammonia concentration recorded is largely dependent upon the biomass of the sampled cages at both the nursery site and production site. Deposition rates of organic carbon and nitrogen around the production and nursery cage sites in Vidlin Voe are related to the position of the sediment trap relative to its location and proximity of the trap to the specific cage site. Weather condition also had an impact on deposition rates with calmer weather producing lesser deposition rates. Around the production site, deposition rates of organic carbon and nitrogen are greatest in the direction of the prevailing current. Deposition rates decrease with an increasing distance from the cages. Although sediment trap results were inconsistent, a similar trend is observed for each of the three sampling trips, although actual deposition values were different. Differences between the deposition rates at the highly dynamic production site and the low energy nursery site indicated that sedimentation of waste from cod culture is highly dependent on water currents. Models of particulate waste deposition associated with the production cage site in Vidlin Voe were produced using the spreadsheet - based Cage Aquaculture Particulate Output and Transport (CAPOT) model, developed at the Institute of Aquaculture. The models were parameterised using the data collected and tested against an established regulatory model, DEPOMOD. The similarity in results illustrated the robustness of the highly flexible spreadsheet waste model for cod culture.

To understand the processes affecting the abundance of wild populations is a fundamental goal of ecology and a prerequisite for the management of living resources. Variable abundance, however, makes the investigation of ecological processes challenging. Recruitment, the process whereby new individuals enter a given stage of a ?sh population, is a highly variable entity. I have confronted this issue by developing methodologies speci?cally designed to account for, and ecologically interpret, patterns of variability in recruitment. To provide the necessary context, Chapter 2 begins with a review of the history of recruitment science. I focus on the major achievements as well as present limitations, particularly regarding environmental drivers. Approaches that include explicit environmental information are contrasted with time-varying parameter techniques. In Chapter 3, I ask what patterns of variability in pre-recruit survival can tell us about the strength of density-dependent mortality. I provide methods to investigate the presence of density-dependent mortality where this has previously been hindered by highly variable data. Stochastic density-independent variability is found to be attenuated via density dependence. Sources of recruitment variability are further partitioned in Chapter 4. Using time-varying parameter techniques, signi?cant temporal variation in the annual reproductive rate is found to have occurred in many Atlantic cod populations. Multivariate state space models suggest that populations in close proximity typically have a shared response to environmental change whereas marked differences occur across latitude. Hypotheses that could result in consistent changes in productivity of cod populations are tested in Chapter 5. I focus on a meta-analytical investigation of potential interactions between Atlantic cod and small pelagic species, testing aspects of the cultivation-depensation hypothesis. The ?ndings suggest that predation or competition by herring and mackerel on egg and larval cod could delay recovery of depleted cod populations. Chapter 6 concludes with a critical re?ection on: the suitability of the theories employed, the underlying assumptions of the empirical approaches, and the quality of the data used in my thesis. Application of ecological insights to ?sheries management is critically evaluated. I then propose future work on recruitment processes based on methods presented herein.

Aquaculture is an essential developing sector for world food production, however the attainment of sexual maturity during commercial on-growing is a major bottleneck to industry expansion. Sexual maturation brings a commercial loss due to reduced growth performance as well as reduced immune function. Furthermore, serious concerns exist over potential genetic interaction with native stocks through broadcast spawning or spawning interaction by escapees. In the north Atlantic region, the Atlantic cod (Gadus morhua) and Atlantic halibut (Hippoglossus hippoglossus) are key aquaculture species in which industry expansion is limited by pre-harvest sexual maturation. However, through a species specific combination of modern technologies and refinement in management practices it is possible that this sexual maturation can be controlled and on-growing potential enhanced. Thus the overall aim of this thesis was to conduct novel research that will improve our understanding of the underlying mechanisms that regulate sexual maturation, whilst also advancing the optimisation of technologies for the management of maturation in cod and halibut. In Atlantic cod, owing to the inconsistent inhibition of maturation in commercial conditions, ever increasing intensities of light and in some cases narrow spectrum technologies are being used to try to combat this problem. Firstly, this PhD project investigated the potential welfare impacts of high intensity artificial lighting which have not been studied to date (Chapter 2). The work specifically investigated the effect of traditional metal halide and novel green cathode lighting on the stress response, innate immunity, retina structure, feeding activity and light perception of Atlantic cod. Results indicated that although acute responses to light were observed, there were no clear significant long term effects of any of the lighting treatments on these parameters. Regarding light perception, interestingly even when subjected to high intensity constant lighting (metal halide mean tank intensity: 16.6 watts m-2), cod still demonstrated a day/night rhythm in melatonin release which suggests perception of the overlying ambient photoperiod. The second trial of this PhD project investigated the efficacy of shading of ambient photoperiod in addition to constant lighting to inhibit maturation of cod outdoors (Chapter 3). This aimed at improving the performance of artificial lighting regimes in the open cage system during commercial on-growing by reducing the relative difference between day/night light intensities. The trial was conducted over a one year period where a low and high shade treatment were tested in outdoor tanks. Shading increased the relative night time illumination to 6.6% and 31.3% of daytime levels respectively, compared to <2% in an unshaded set-up. Both shading treatments were effective at suppressing sexual development in cod as confirmed through measurements of gonadosomatic index, histological analysis of gonadal development, oocyte diameter measurements and sex steroid profiles as well as measurements of growth. In addition to research at the applied level in Atlantic cod, this thesis has also extended to the fundamental level and explored one of the potential mechanisms relaying photoperiod signal to the endogenous regulation of sexual maturation in cod, namely the kisspeptin system (Chapter 4). Partial sequences for the signal peptide Kiss2 and its receptor Kissr4 were isolated and described showing similarity to other teleost species such as the medaka, Oryzias latipes and stickleback, Danio rerio. Novel molecular qPCR assays were designed and developed to measure the expression of both genes in male and female cod over a maturation cycle and compared to cod under constant lighting which remained immature. Interestingly, expression patterns of kiss2 and kissr4 did not reveal any clear association with season or photoperiod treatment. However, pituitary expression of gonadotropins (FSH, follicle stimulating hormone; LH, luteinising hormone) did show a differential expression in relation to treatment from early winter approximately 4-6 months after the photoperiod change. These new results are in contradiction with the hypothesis that the kisspeptin system would be involved in the initiation of gametogenesis, as shown in mammals. However, the FSH/LH data defines a window during which time kisspeptin or another GnRH stimulating mechanism must be active, this compels the need further investigation. In Atlantic halibut farming, all-female production removes the concerns of production losses through sexual maturation. Accordingly, this thesis investigated the potential/feasibility of generating monosex populations by FACS (fluorescence activated cell sorting) semen sexing based on cellular DNA content, as proven in terrestrial agriculture. Results however did not show any clear differences between the DNA of sperm in a range of species tested (Atlantic halibut, cod, sea bass, perch) suggesting that this technique may not be applicable in such species. The project also focussed on the production of a population of sex reversed halibut broodstock (neomales) that will generate, in the long term, a basis for traditional monosex population generation in the UK. Two in feed MDHT (17α-methyldihydrotestosterone) treatments were tested with the aim to reduce the use of hormone. Results were very successful with a hormone treatment of 5ppm MDHT generating a 97% phenotypic male population thus suggesting the presence of sex-reversed halibut which can be used for future monosex production. Overall, this work aimed to develop and/or refine potential remediation techniques for sexual maturation in two key commercially important farmed marine fish species, cod and halibut, as well as further our understanding on the regulation of puberty. The knowledge gained from this work provides a means to optimise the techniques employed in the industry and has the potential to increase production and profitability without compromising farmed animal welfare, thus ultimately promoting the sustainable expansion of the Atlantic cod and halibut aquaculture.

<p>An influence at one trophic level can result in dynamic impacts also on other components of a food web. These dynamics are known as trophic cascades, and can be both top-down and bottom-up. After a near-collapse of the Baltic cod <i>Gadus morhua</i> stock in the 1980s, its main prey sprat <i>Sprattus sprattus</i> increased dramatically. The main food of sprat, marine copepods, decreased during the same time period, likely a combined effect of increased predation pressure from sprat and decreasing salinities. This shortage of food for sprat resulted in decreasing quality of sprat as a food source for common guillemots <i>Uria aalge</i>. However, a recent increase in fishing for sprat has again resulted in better feeding conditions for guillemots.</p><p>Human impacts on this simple food web can be complex. In the early 20th century, marine mammals were abundant and nutrient levels were low in the Baltic Sea. This thesis illustrate that this situation corresponded to lower fish biomass. A reduction of seals early in the century led to reduced top-down control, which resulted in increasing fish stocks. Later, in the 1950s, the largest inflow of salt water during the century mobilized accumulated phosphorus from the deep sediments, which stimulated nitrogen fixation. Combined with increasing anthropogenic nutrient loads, this led to increased primary production and a rapid change from an oligotrophic to a eutrophicated state. This change can be termed a regime shift, which also stimulated fish production. Subsequent over-fishing of cod likely caused a second regime shift, from a cod- to a clupeid- dominated state, which led to the described effects on the common guillemots.</p><p>Several factors affect the life-history of this long-lived seabird. Bycatches in gillnet fisheries is one factor directly affecting guillemot survival, and the proportion of bycatches increased during a period of increasing fishing effort. Surprisingly, avian cholera, a previously undocumented disease in common guillemots, was found at times to cause considerable adult mortality. Common guillemot life-history information can communicate the diversity of factors influencing marine ecosystems – hopefully this can increase our understanding of how complex even "simple" food webs are.</p>

An influence at one trophic level can result in dynamic impacts also on other components of a food web. These dynamics are known as trophic cascades, and can be both top-down and bottom-up. After a near-collapse of the Baltic cod Gadus morhua stock in the 1980s, its main prey sprat Sprattus sprattus increased dramatically. The main food of sprat, marine copepods, decreased during the same time period, likely a combined effect of increased predation pressure from sprat and decreasing salinities. This shortage of food for sprat resulted in decreasing quality of sprat as a food source for common guillemots Uria aalge. However, a recent increase in fishing for sprat has again resulted in better feeding conditions for guillemots. Human impacts on this simple food web can be complex. In the early 20th century, marine mammals were abundant and nutrient levels were low in the Baltic Sea. This thesis illustrate that this situation corresponded to lower fish biomass. A reduction of seals early in the century led to reduced top-down control, which resulted in increasing fish stocks. Later, in the 1950s, the largest inflow of salt water during the century mobilized accumulated phosphorus from the deep sediments, which stimulated nitrogen fixation. Combined with increasing anthropogenic nutrient loads, this led to increased primary production and a rapid change from an oligotrophic to a eutrophicated state. This change can be termed a regime shift, which also stimulated fish production. Subsequent over-fishing of cod likely caused a second regime shift, from a cod- to a clupeid- dominated state, which led to the described effects on the common guillemots. Several factors affect the life-history of this long-lived seabird. Bycatches in gillnet fisheries is one factor directly affecting guillemot survival, and the proportion of bycatches increased during a period of increasing fishing effort. Surprisingly, avian cholera, a previously undocumented disease in common guillemots, was found at times to cause considerable adult mortality. Common guillemot life-history information can communicate the diversity of factors influencing marine ecosystems – hopefully this can increase our understanding of how complex even "simple" food webs are.

The recovering harbor seal population along the Swedish west coast has coincided with declining cod stocks. Although the cod stocks were primarily depleted by intense fisheries, some stakeholders argue that reduced seal populations could have direct, positive effects on the cod stocks. The outbreaks of Phocine distemper virus (PDV) in 1988 and 2002 when up to 66% of the harbor seals along the Swedish west coast died, could be viewed as natural experiments allowing for assessment of any positive impacts of reduced mortality from seal predation on cod abundance. I quantified removal from seal predation and fishery landings and analyzed correlations to cod abundance of different length classes. Analyses were conducted for a longer time- series, 1979-2019, reaching back to when removal from fisheries was substantially larger than that from seal consumption. I also analyzed the data with a more recent perspective, 2003-2019, starting after the later PDV outbreak when seal predation relative landing sizes has increased. During this period, fishery discard data is available and included in the models. Methods include graphical presentation, multiple linear regression analyses, and to expand the existing data on seal diet, I collected diet samples of harbor seal feces from two haul-outs in Skagerrak. No statistically significant, negative correlations between seal predation and cod abundance were found in any data set, hence, I cannot support the idea of harbor seals having an impact on cod abundance. Also, the significant correlations between cod abundance and landings were all positive. I argue that culling of seals cannot be motivated as a strategy to help cod recover, as this would jeopardize the persistence of the seal population rather than assuring cod stability.

The thesis combines laboratory experiments and field expeditions to study production, transfer and consumption of non-enzymatic antioxidants and thiamine in an aquatic food web. In particular, I (1) documented spatial and seasonal variation of tocopherols and carotenoids in the Baltic Sea pelagic food web, and (2) examined the effects of abiotic and biotic factors on tocopherol, carotenoid and thiamine concentrations in phytoplankton, zooplankton and fish. Moderate differences in temperature and salinity affected α-tocopherol, β-carotene and thiamine production in microalgae. Furthermore, the results suggest that acute stress favors the expression of non-enzymatic antioxidants rather than enzymatic antioxidants. Because production of α-tocopherol, β-carotene and thiamine differ markedly between microalgae, the availability of non-enzymatic antioxidants and thiamine is likely to be highly variable in the Baltic Sea and is difficult to predict. The transfer of non-enzymatic antioxidants from phytoplankton to zooplankton was biomass dependent. The field expeditions revealed that phytoplankton biomass was negatively associated with α-tocopherol concentration in mesozooplankton. Thus, increased eutrophication of the Baltic Sea followed by an increase in phytoplankton biomass could decrease the transfer of essential biochemicals to higher levels in the pelagic food web. This could lead to deficiency syndromes, of the kind already observed in the Baltic Sea. Astaxanthin is synthesized from precursors provided by the phytoplankton community. Thus biomass dependent transfer of astaxanthin precursors from phytoplankton to zooplankton could be responsible for astaxanthin deficiency in zooplanktivorous herring. Astaxanthin in herring consists mostly of all-Z-isomers, which are characterized by low bioavailability. Therefore, astaxanthin deficiency in salmon could be explained by the low concentration of this substance and its isomeric composition in herring.

Knowledge of offspring production (recruitment) is fundamental to understanding and forecasting the dynamics of a population. In this thesis, I focus on two demographic characteristics of fish stocks that are important to recruitment: population density and age structure. First, populations produce more recruits at low density, but quantifying this response has proven difficult. Using data from hundreds of populations of walleye (Sander vitreus), an economically important freshwater fish, I demonstrate that the growing-degree-day metric (a temperature index) is better than age at explaining variation in density-dependent growth and maturity both within and among populations. I then incorporate multi-lake measures of density-dependent life history change into a temperature-based biphasic model of growth and reproduction to predict sustainable rates of mortality for walleye throughout most of their range. Second, the age (or size) structure of a population may also affect recruitment because of positive effects of maternal age on offspring production and survival; however, evidence for these ‘maternal influences’ on recruitment is limited. Using both an analytical model and a meta-analysis of stock-recruitment data from 25 species of exploited marine fish, I show that (i) maximum reproductive rate increased with the mean age of adults in a population, and (ii) the importance of age structure increased with a species’ longevity. I then demonstrate a similar effect of maternal influences on reproductive rate in a detailed study of Lake Erie walleye. By highlighting the importance of fisheries-induced demographic change to recruitment, this thesis provides insight into past and present failures. However, it also demonstrates clearly the benefits of proactive management strategies that (i) identify and respect the limits of exploitation, (ii) protect from exploitation reproductively valuable individuals—principles that apply generally to any freshwater, marine, or terrestrial species that is of recreational, commercial, or conservation value.

Knowledge of offspring production (recruitment) is fundamental to understanding and forecasting the dynamics of a population. In this thesis, I focus on two demographic characteristics of fish stocks that are important to recruitment: population density and age structure. First, populations produce more recruits at low density, but quantifying this response has proven difficult. Using data from hundreds of populations of walleye (Sander vitreus), an economically important freshwater fish, I demonstrate that the growing-degree-day metric (a temperature index) is better than age at explaining variation in density-dependent growth and maturity both within and among populations. I then incorporate multi-lake measures of density-dependent life history change into a temperature-based biphasic model of growth and reproduction to predict sustainable rates of mortality for walleye throughout most of their range. Second, the age (or size) structure of a population may also affect recruitment because of positive effects of maternal age on offspring production and survival; however, evidence for these ‘maternal influences’ on recruitment is limited. Using both an analytical model and a meta-analysis of stock-recruitment data from 25 species of exploited marine fish, I show that (i) maximum reproductive rate increased with the mean age of adults in a population, and (ii) the importance of age structure increased with a species’ longevity. I then demonstrate a similar effect of maternal influences on reproductive rate in a detailed study of Lake Erie walleye. By highlighting the importance of fisheries-induced demographic change to recruitment, this thesis provides insight into past and present failures. However, it also demonstrates clearly the benefits of proactive management strategies that (i) identify and respect the limits of exploitation, (ii) protect from exploitation reproductively valuable individuals—principles that apply generally to any freshwater, marine, or terrestrial species that is of recreational, commercial, or conservation value.