The Atlantic cod (Gadus morhua L.) fishery is of great economic importance to the Faroese economy. There are two separately managed cod stocks around the Faroe Islands, the Faroe Plateau and the Faroe Bank cod. Both have experienced dramatic decreases in size and informed management decisions are vital for both stock viability and exploitation. The stocks are geographically isolated by an 800 m deep channel and water temperatures are on average 1 – 2 ºC higher on the Faroe Bank than on the Faroe Plateau. There are clear phenotypic differences between the stocks; in particular, the markedly higher growth rate for the Faroe Bank cod has caught public and scientific attention. There is continuing debate regarding the relative importance of genetics and environmental contributions to the contrasting phenotypes. Analyses of reproductive parameters (field data and experimental captive spawnings) as well as analyses of microsatellite and single nucleotide polymorphism (SNP) markers were undertaken to better resolve the issue. Field data as well as data from experimental captive spawnings provided evidence of reproductive differences between Faroe Plateau and Faroe Bank cod. Peak spawning occurred earlier on the Faroe Plateau than on the Faroe Bank and this difference in timing of spawning was maintained in captivity. In particular, differences in sizes of eggs (average diameters of 1.40 and 1.30 mm for Faroe Plateau and Faroe Bank cod eggs, respectively) and indirect evidence of greater volumes spawned by the Faroe Bank females suggested stock differences with respect to egg size – egg number trade-off. It was hypothesised that the strategy adopted by cod on the Faroe Bank, with a higher number of smaller eggs, evolved in response to a more hostile environment (bare seabed and higher exposure to predators) experienced by early life stages in this area. Experimental captive spawnings with Faroe Bank cod showed a large interfamily skew in survival rates of cod eggs and fry. Egg size was identified as a useful indicator of survival rates in the egg stage, but egg survival rates could not be used to predict viability in later developmental stages, thus highlighting the importance of employing some sort of genetic monitoring of cod fry to ensure sufficient family representation in the progeny. While no tank effect was evident concerning fry survival, a significant tank effect was identified concerning body sizes of fry. Microsatellite data were analysed using large sample sizes of Faroe Plateau and Faroe Bank cod with the Faroe Plateau divided into two locations, Faroe Plateau North-East and Faroe Plateau West (cod from each of the two were known to belong to separate spawning grounds). Two Norwegian coastal cod samples were included as outlier populations. While no genetic differentiation was detected between the two Faroe Plateau locations, these analyses revealed a detectable, albeit relatively modest, degree of genetic differentiation between cod from the Faroe Plateau and the Faroe Bank (FST = 0.0014 and 0.0018; DJost_EST = 0.0027 and 0.0048; P < 0.0001 and P < 0.001 for the Faroe Plateau North-East – Faroe Bank and the Faroe Plateau West – Faroe Bank comparisons). These values were several times smaller than those between Faroese and Norwegian coastal cod (pairwise FST and DJost_EST values in the range of 0.0061 – 0.0137 and 0.0158 – 0.0386, respectively). Despite recent reductions in census population sizes for Faroe Plateau and, particularly, Faroe Bank cod, genetic diversity estimates were comparable to the ones observed for Norwegian coastal cod and there was no evidence of significant genetic bottlenecks. Lastly, data for one of the markers (Gmo132) indicated genotype-dependent vertical distribution of cod (as investigated for Faroe Plateau North-East cod). Contrary to some previously published studies, analysis of SNPs of two candidate genes for adaptive divergence, the hemoglobin gene Hb-ß1 and the transferrin gene Tf1, failed to detect differentiation between samples of Faroe Plateau and Faroe Bank cod analysed in this thesis. Of 3533 novel SNPs simultaneously discovered and genotyped by restriction-site associated DNA (RAD) sequencing, 58 showed evidence of genetic differentiation between Faroe Plateau North-East and Faroe Bank cod (P < 0.05). No single locus was fixed for different alleles between Faroe Plateau and Faroe Bank cod. A set of eight informative SNPs (FST values between Faroe Plateau and Faroe Bank samples > 0.25; P < 0.0005) were selected for validation in larger samples, that included cod from both Faroe Plateau areas and the Faroe Bank as well as Norwegian coastal and White Sea cod. Six out of the eight loci amplified successfully with a PCR-based method and there was 100 % concordance between genotypes of individuals screened by both techniques. Due to ascertainment bias, the SNPs should only be applied with caution in a broader geographical context. Nonetheless, these SNPs did confirm the genetic substructure suggested for Faroese cod by microsatellite analyses. While no genetic differentiation was evident between the two Faroe Plateau locations, significant genetic differentiation was evident between Faroe Plateau and Faroe Bank cod at five of the SNPs (FST values in the range of 0.0383 – 0.1914). This panel of five SNPs could confidently be used to trace groups of Faroe Plateau and Faroe Bank cod to their population of origin. In conclusion, multiple lines of evidence demonstrate that Faroe Plateau and Faroe Bank cod are truly two genetically distinct populations. While the findings contribute to a broader understanding of the biology and the genetics of Faroe Plateau and Faroe Bank cod, the novel SNPs developed may provide a valuable resource for potential future demands of i.e. genetic stock identification methods.

Traditionally, fish meal (FM) and fish oil (FO) have been used extensively in aquafeeds, mainly due to their excellent nutritional properties. However, various reasons dictate the use of sustainable alternatives and the reduction of the dependence on these commodities in fish feeds. Hence, the aim of the present thesis was to investigate the effects of the replacement of FM and FO with two vegetable oils (VO) and an oilseed meal on the growth performance, feed utilization, nutrient and fatty acids (FA) digestibility and tissue FA composition and metabolism in three commercially important European fish species. Specifically, in Experiment I crude palm oil (PO) was used to replace FO in diets for rainbow trout. In Experiments II and III FO was replaced with rapeseed oil (RO) in diets for Atlantic salmon at various dietary protein/lipid levels aiming also at further reductions of FM by using low protein (high lipid) diet formulations. In Experiments II and III the fish were reared at low and high water temperatures, respectively, in order to elucidate, also, the potential effects of temperature. Lastly, the effects of the replacement of FM with full fat soya meal (FFS) in Atlantic cod were investigated in Experiment IV. The results of the present thesis showed no negative effects on growth performance and feed utilization in rainbow trout when FO was replaced with PO. The dietary inclusion of RO improved the growth of Atlantic salmon, possibly, due to changes in the nutrient and FA digestibilities and FA catabolism while, the growth and feed utilization were unaffected by the dietary protein/lipid level. However, the growth of Atlantic cod was affected negatively by the replacement of FM with FFS. The proximate composition of the fish whole body was in most cases unaffected by dietary treatments. The changes in dietary formulations affected the dietary FA compositions and resulted in significant changes in the fish tissue FA compositions. It was clearly shown that the fish tissue total lipid FA composition reflects the FA composition of the diet, although specific FA were selectively utilized or retained in the tissues by the fish. These may have serious implications not only for fish metabolism and growth but also for the quality of the final product, especially in terms of possible reductions of n-3 HUFA.

In this thesis I assessed the causes of long-term changes in two large, commercially important decapod crustacean populations, American lobster (Homarus americanus) and snow crab (Chionoecetes opilio), in the northwest (NW) Atlantic Ocean. By combining available time-series data, including commercial landings, research surveys, and local ecological knowledge (LEK), I explored the causes of an observed ecosystem shift in the NW Atlantic (~1950–2009) which entailed a region-wide decline of groundfish and an increase in benthic invertebrates, including these decapods. Three hypotheses were examined to explain the increase in decapod abundance: (1) the predation hypothesis, whereby a decrease in predatory groundfish led to an increase in their decapod prey (top-down effects); (2) the climate hypothesis, whereby changes in temperature or other climatic variables helped to increase decapod numbers (bottom-up effects); and (3) the anthropogenic hypothesis, whereby changes in fishing pressure drove decapod population dynamics. I explored these hypotheses separately for lobster and snow crab, which may experience different ecological and commercial pressures. First, I investigated the interactions between predatory groundfish and lobster in the inshore region of southwest Nova Scotia. Long-term fisheries-independent abundance indices for lobsters and their predators are available for Gulf of Maine (GOM) waters in the USA, but not in Canada. To address research gaps I designed and executed a survey to collect the LEK of lobster fishermen fishing in the Canadian GOM. Forty-two fishermen were interviewed. Corresponding survey results from the USA were compared to the LEK results. Both sources provided evidence for a top-down effect (predation release), contributing to observed increases in GOM lobster abundance and landings. Second, I explored relationships between lobster abundance and landings in the NW Atlantic as they may relate to temporal changes in predators, temperature, climate (North Atlantic Oscillation Index, NAOI), and fishing. Available landings data and fisheries-independent abundance estimates were collated to investigate trends in lobster abundance and catch. Links between lobster, groundfish, temperature and climate indices were explored using mixed effects models. Results offered partial support for the predation hypothesis, namely in the waters off Newfoundland, Nova Scotia, and southern New England as well as broad support for a climate effect on early life stages. This effect appeared related to a region-wide climate signal, the NAOI, but was independent of changes in water temperature. Fishing effort appeared to be following lobster abundance, rather than regulating abundance in a consistent way. Third, variation in snow crab abundance was examined through meta-analysis of time-series data of cod and crab abundance and temperature. Temperature had opposing effects on the two species: snow crab abundance was negatively correlated with temperature whereas cod and temperature were positively related. Controlling for the effect of temperature, the analysis revealed significant negative interactions between snow crab and cod abundance, with cod leading snow crab up to a five-year lag. Results indicate that snow crab is largely influenced by temperature during early post-settlement years and becomes increasingly regulated by top-down mechanisms as they approach fishery recruitment. Overall, I conclude that both climate and predation can act as population controls on large decapod populations, but these variables affect decapods at different life stages.