Atlantic salmon (Salmo salar) are found in a range of locations along Sweden's coastline, but Sweden's largest lake, Vänern, also harbors a population of salmon; the rare freshwater migratory form. The majority of the salmon in Lake Vänern migrate upstream in River Klarälven in order to spawn, where they are assisted by humans through the "trap and transport" method to get past Klarälven's eight hydropower dams, which otherwise constitute definite obstacles to upstream migration. When the salmon later migrate downstream to Lake Vänern they receive no assistance and experience a high mortality rate as they are partially forced to swim through the turbines. The wild salmon population today includes over 1000 spawners annually, an increase from <200 in the 196os, but far below historic records of over 10,000 spawners.  This report therefore aimed to investigate the population growth rate and extinction risk for the salmon in Klarälven, both in the current situation and with passages installed past the hydropower plants, and in doing so answer the questions 1) How large is the population growth rate and risk of extinction for today’s population of salmon in Klarälven over the course of 100 years? and 2) How would passage solutions past the hydropower plants in Klarälven affect the population growth rate and risk of extinction for today’s population of salmon in Klarälven over the course of 100 years? These questions were answered by running a population viability analysis in the program Extinction Vortex, which allows the programming of model populations and the manipulation of parameters to test different scenarios. The scenarios that were tested were 1) Scenario 1: Today's method with trap and transport and total lack of passages, 2) Scenario 2: Trap and transport continues, and downstream passages are installed past all eight power plants, and 3) Scenario 3: Upstream and downstream passages are installed past all eight power plants and trap and transport ceases. The results of the vulnerability analysis did not show any risk of extinction for the next 100 years, but a long-term negative trend for the salmon in Klarälven using today's method was seen. However, the development became significantly more positive for the salmon in Klarälven when the installation of downstream passages was simulated, but after that not significantly more positive when the installation of upstream passages was simulated as well. This result provided answers to the research questions and based on them it could be concluded that even though the salmon in Klarälven are not under any acute threat at the moment, and that there may be other fish populations in other regulated streams and rivers that would benefit more from environmental adaptation, measures need to be taken also in Klarälven, to ensure the long-term conservation of the unique freshwater migrating salmon that inhabit the area. / Laxen (Salmo salar) förekommer på flera håll längst Sveriges havskuster, men även Sveriges största insjö Vänern hyser en population av lax; den sällsynta sötvattensvandrande formen. Majoriteten av Vänerlaxarna migrerar upp för att leka i Klarälven, där de assisteras av människan genom metoden ”trap and transport” som tar dem förbi Klarälvens åtta vattenkraftverk vilka annars utgör definitiva vandringshinder. När laxen sedan ska ta sig tillbaka ner till Vänern får de ingen assistans, i stället tvingas de delvis simma genom turbinerna med stor dödlighet som följd. Laxpopulationen idag består av över 1000 lekande fiskar varje år, en ökning från <200 individer på 1960-talet, men långt under historiska siffror på över 10 000 lekande laxar. Detta arbete syftade därför till att undersöka populationsutvecklingen och utdöenderisken för Klarälvslaxen, såväl i nuläget som vid en installation av passager förbi kraftverken, och genom detta besvara frågeställningarna 1) Hur stor är populationsutvecklingen och utdöenderisken för dagens population av Klarälvslax över kommande 100 år? och 2) Hur skulle passagelösningar förbi vattenkraftverken i Klarälven påverka populationsutvecklingen och utdöenderisken för dagens population av Klarälvslax över kommande 100 år? Dessa frågeställningar besvarades med hjälp av en sårbarhetsanalys i programmet Extinction Vortex, som tillåter uppbyggandet av modellpopulationer och manipulation av parametrar för att testa olika scenarier. Scenarierna som testades var 1) Scenario 1: Dagens metod med trap and transport och total avsaknad av passager, 2) Scenario 2: Trap and transport fortsätter samt nedströmspassager installeras förbi alla åtta kraftverk, och 3) Scenario 3: Upp- och nedströmspassager installeras förbi alla åtta kraftverk och trap and transport upphör. Resultatet av sårbarhetsanalysen visade inte på någon utdöenderisk kommande 100 år, men en negativ trend för Klarälvslaxens långsiktiga populationsutveckling med dagens metod. Utvecklingen blev dock signifikant mer positiv för Klarälvslaxen vid den simulerade installationen av nedströmspassager, och ännu något stabilare när även uppströmspassager installerades. Detta resultat gav svar på frågeställningarna, och utifrån detta kunde slutsatsen dras att trots att Klarälvslaxen inte befinner sig under något akut hot för närvarande, och att det kan finnas andra fiskpopulationer i andra vattendrag som är i mer akut behov av miljöanpassning, så behöver åtgärder komma på plats även i Klarälven, för att säkerställa det långsiktiga bevarandet av den unika sötvattensvandrande Klarälvslaxen.

In this study, full coding sequences of Atlantic salmon (Salmo salar L.) muscle genes were cloned, including myogenic regulatory factors (MRFs) (myod1c, myog, mrf4, myf5), inhibitors of Myostatin (fst, decorin), markers of myogenic progenitor cell (MPC) proliferation (sox8) and fusion (calpastatin), a marker of slow muscle fibre differentiation (smlc1) and a novel eukaryotic gene involved in regulating growth (cee). Several of these genes were then characterised using a range of experimental and computational analyses with the aim to better understand their role in myogenesis and their evolution in teleosts. A series of experiments supported previous findings that teleosts have extra copies of many genes relative to tetrapods as a result of a whole genome duplication (WGD) event that occurred some 320-350 Mya. For example, it was shown that genes for myod and fst have duplicated in a common teleost ancestor, but were then specifically lost or retained in different lineages. Furthermore, several characterised Atlantic salmon genes were conserved as paralogues, likely from a later WGD event specific to the salmonid lineage. Phylogenetic reconstruction and comparative genomic approaches were used to characterise the evolution of teleost paralogues within a framework of vertebrate evolution. As a consequence of one experiment, a revised nomenclature for myod genes was proposed that is relevant to all diploid and polyploid vertebrates. The expression patterns of multiple myogenic genes were also established in Atlantic salmon embryos using specific complementary RNA probes and in situ hybridization. For example, co-ordinated embryonic expression patterns were revealed for six salmon MRFs (myod1a, myod1b, myod1c, myog, mrf4, myf5), as well as markers of distinct MPC populations (pax7, smlc1), providing insight into the regulatory networks governing myogenesis in a tetraploid teleost. Furthermore, it was shown that Atlantic salmon fst1 was expressed concurrently to pax7 in a recently characterised MPC population originating from the anterior domain of the epithelial somite, which is functionally analogous to the amniote dermomyotome. In another experiment, the individual expression domains of three Atlantic salmon myod1 paralogues were shown to together recapitulate the expression of the single myod1 gene in zebrafish, consistent with the partitioning of ancestral cis-acting regulatory elements among salmonid myod1 duplicates. Additionally, the in situ expression of cee a novel and highly conserved eukaryotic gene was revealed for the first time in a vertebrate and was consistent with an important role in development including myogenesis. Additionally, Atlantic salmon were reared at 2, 5, 8 or 10 ºC solely to a defined embryonic stage, which was just subsequent to the complete pigmentation of the eye. After this time, animals were provided an equal growth opportunity. Remarkably, changing temperature during this short developmental window programmed the growth trajectory throughout larval and adult stages. While 10 and 8 ºC fish were larger than those reared at 2 and 5 ºC at the point of smoltification, strong compensatory growth was subsequently observed. Consequently, after 18 months of on growing, size differences among 5, 8 and 10 ºC fish were not significant, although each group was heavier than 2 ºC fish. Furthermore, significant embryonic-temperature induced differences were observed in the final muscle fibre phenotype, including the number, size distribution and myonuclear density of muscle fibres. A clear optimum for the final muscle fibre number was observed in 5 ºC fish, which was up to 17% greater than other treatments. In a sub-sample of embryos, temperature induced heterochonies were recorded in the expression of some MRFs (myf5, mrf4) but not others (myod1a, myog). These results allowed the proposition of a potential mechanism explaining how temperature can program the muscle phenotype of adult teleosts through modification of the somitic external cell layer, a source of MPCs throughout teleost ontogeny.

The objective of the work described in the current thesis was to provide a better understanding of some of the key factors associated with sea louse, Lepeophtheirus salmonis, infection of farmed Atlantic salmon. In Chapter 2, initial work focused on establishing the vertical and horizontal distribution of sea lice copepodids and spatial patterns of on-farm infections. The louse distribution was investigated along the main current gradient across adjacent salmon production pens at three commercial sites. A depth profile for the distribution of larval lice was also established for the top 12 m of the water column at three different locations in close proximity to commercial salmon farms. Within all multi-pen sites there were clear patterns of distribution and infection along the main water current gradient with the abundance of lice in end pens at each site appearing to be different from the central pens. The vertical distribution pattern of free swimming L. salmonis larvae (nauplii and copepodids) showed that the surface 6 m harboured 85.5 ± 1.6 % of the lice present in the water body analysed (0 – 12 m depth), irrespective of sampling date and location. In Chapter 3, further environmental effects / influences on attachment success of the copepodids were analysed using controlled infection challenges. A flume with adjustable flow rates, and controlled light conditions was designed for this study. Flume current velocity was observed to be a significant factor in infection success, with higher infection levels observed at lower current velocities, while higher current velocities were demonstrated to reduce settlement success. At fixed velocity, higher copepodid exposure levels gave rise to higher infection levels, this having a linear relationship suggestive of a lack of competitive effects for space on the fish. Light was also shown to play an important role in host settlement. A positive correlation between increasing light intensity and higher louse attachment success was found for all tested light spectra / wavelengths (white - Halogen, blue 455 nm, green 530 nm and red 640 nm). Observation of an infecting cohort of copepodids showed maximal infection at four days post-moulting with a tail-off of infection by six days post-moulting. However, even under the optimal conditions represented by a flume challenge, including linear water flow, the constraint of copepodids to pass close to the salmon host and the very high exposure levels of copepodids per fish, louse attachment success was still relatively low. Chapter 4 examined implementation of a possible management approach based upon some of the environmental influences observed. This chapter described a study in which environmental manipulation of salmon swimming depth was employed on-site in an attempt to reduce farm infection of Atlantic salmon. The effects of submerged artificial lighting in combination with submerged feeding were tested with respect to salmon swimming depth and sea lice infection, following the hypothesis that L. salmonis infection in a commercial salmon population could be reduced through exposure to deep lighting and feeding. The results of the study suggest that swimming depth manipulation can indeed be used at a commercial scale to reduce salmon lice burdens on Atlantic salmon by physically minimising spatial interactions between the two animals. In the final research chapter (Chapter 5), this thesis examines the question of whether ploidy of the host impacts on sea louse infection levels and whether susceptibility of individual fish is consistent between replicate infections. Results showed that triploid salmon are not subject to higher sea louse infection levels under experimental challenge and farm infection conditions compared to diploid hosts. In addition, triploid fish subject to initial infection, did not become more or less resistant to infection compared to diploids when comparing repeated sea louse infections. In summary, this thesis describes work conducted to analyse key infection pathways and factors influencing infection of Atlantic salmon by sea lice and suggestions made as to how findings may be exploited to reduce louse burdens in Atlantic salmon farming. The practical solutions presented to exploit the results found in this work are currently under consideration by the Scottish salmon industry.

Atlantic salmon Salmo salar has a complex life cycle, including long migrations and habitat shifts for both juveniles and adults. As such, salmon populations are vulnerable to habitat degradation and fragmentation along their migratory routes. This makes management and conservation a complex task requiring knowledge of salmon ecology at different temporal and spatial scales. In this thesis I highlight the use of a holistic life-history based approach in the conservation and management of wild and hatchery-reared salmon in regulated rivers and lakes. Small populations of wild-reproducing landlocked salmon and trout Salmo trutta exist in the regulated River Klarälven, Sweden. Since the 1930s, transportation of adult spawners upstream of eight dams has given the fish access to spawning grounds. The number of returning wild spawners became critically low in the 1960s, but stocking of hatchery smolts resulted in an increase in spawners that continues today. My data show that wild smolt may suffer high mortality due to multiple dam passages. To ensure viable populations of wild populations, future management should include both up- and downstream solutions that ensure connectivity in the system. The recreational and commercial salmonid fishery are maintained by compensatory stockings, yielding annual catches of about 75 tons, and a river return rate of hatchery fish of about 1%. As a large portion of the stocked smolts does not survive downstream migration to the lake, there has been discussion about the quality of the stocked smolt and about stocking strategies. Based on my studies, producing hatchery smolts more closely resembling wild-born conspecifics should result in reduced loss rates. I suggest changes in the hatchery and stocking procedures to increase the survival of stocked smolts. The results of my research should be applicable to other regulated systems, particularly those with mixed stocks of wild and hatchery salmonid populations. / Atlantic salmon Salmo salar has a complex life cycle, including long migrations and habitat shifts for both juveniles and adults. As such, salmon populations are vulnerable to habitat degradation and fragmentation along their migratory routes, which make management and conservation a complex task requiring knowledge of salmon ecology at different temporal and spatial scales. In this thesis, I highlight the use of a holistic approach in the conservation and management of wild and hatchery-reared salmon in regulated rivers and lakes. Small populations of wild-reproducing landlocked salmon and trout Salmo trutta exist in the regulated River Klarälven, Sweden. Since 1930, transportation of adult spawners upstream of eight dams has been done to give the fish access to the spawning grounds. My data indicate that a large proportion of the wild smolts are lost due to multiple dam passages, and future management should include both up- and downstream solutions, ensuring connectivity in the system. The fishery in Klarälven and Lake Vänern is maintained by compensatory stockings, yielding catches of about 75 metric tons and a river return rate of stocked fish of about 1%. I suggest changes in the hatchery and stocking procedures to increase the survival of stocked smolts.

Barcode identification is a method that uses genetic information to differentiate species. Because of its general versatility it can be applied to contexts from archaeology to the food industry. Atlantic salmon (Salmo salar) is a fish species commonly hunted in modern times and has been found in archaeological settings. However, barcoding requires enough quality DNA for amplification and abiotic exposure tends to degrade it. High temperatures, such as when boiling, can diminish DNA quality. The extent of DNA degradation between fresh and boiled tissues and whether all tissues retain the same amount of DNA is unclear. In this study DNA was extracted from S. salar tissues fins, muscle, bones and scales without treatment and with boiling treatment. DNA concentrations between fresh and boiled bones were not significantly different, nor were comparisons between samples with the same treatments. Muscles had higher DNA concentrations when boiled and fins had higher when fresh. These findings show that regarding certain tissue types can be expected to better retain DNA concentrations after boiling.

Devido ao consumo predatório e ao risco inerente de extinção de várias espécies de peixes, pesquisadores têm buscado técnicas alternativas de reprodução para viabilizar tanto o cultivo como a conservação ex situ. Os transplantes xenogênicos de gônadas representam uma técnica reprodutiva inovadora e já existem resultados promissores em diversas espécies de mamíferos, aves, insetos e também de peixes. No entanto, a baixa eficiência na geração de gametas alógenos consiste em uma das limitações desta técnica. Um dos possíveis motivos seria o desencadeamento de reações de rejeição por parte do hospedeiro, comum em transplante de órgãos e tecidos humanos. Dentro deste contexto, visamos identificar e avaliar a interferência destes mecanismos durante o processo de enxerto de gônada de truta arco-íris entre linhagens diferentes e salmão do Atlântico, identificando possíveis graus de respostas imunológicas utilizando enxertos autógenos, isógenos, alógenos e xenógenos. Tais avaliações foram feitas pela análise histopatológica dos tecidos transplantados e dos locais dos implantes. Com os resultados obtidos, pudemos avaliar que a resposta imunológica em implantes de tecidos alogênicos e xenogênicos é bem evidente. Já no enxerto de células germinativas dissociadas houve apenas um discreto processo inflamatório em todas as variações dos enxertos, o que pode representar uma adaptação técnica viável e mais eficaz para a obtenção de gametas. / Due the predatory consumption and the inherent risk of extinction of various species of the fish, investigate the alternatives of reproduction to make viable the cultivation as an ex situ. Xenogeneic transplants of gonads represent an innovative reproductive technique and those that can already be found in various species of animals, birds, insects and fish. However, a low efficiency in the range of allogenic gametes is one of the limitation of this technique. A probable cause would be related to an immune response process that would lead to rejection of the transplanted tissue, as observed in organs and tissues transplantation in human. In this context, we aimed to identify and to evaluate the presence of immune rejection mechanisms during the process of gonads tissues transplantation among different rainbow trout lineages and to Atlantic salmon, observing possible response degrees according to the nature of the graft: autogenic, isogenic, allogeneic or xenogeneic transplantations. Histopathological analysis of the transplanted tissues and of the implanted sites were conducted. Results showed a clear evidence of an immune response in allogeneic and xenogeneic implants. Dissociated gonad cells grafts showed a discrete inflammatory process disregarding the graft nature, that may be an indication of a feasible and more efficient technique adaption to obtain viable gametes.

Leptin is a peripheral adiposity signal and a key hormone in energy balance regulation in mammals, acting as a link between nutritional status and the endocrine reproductive axis. If this is also the role of leptin in fish is not fully understood. This thesis investigates how different components of the leptin system are affected by sexual maturation and seasonal changes in energy balance in male Atlantic salmon (Salmo salar L.) parr under fully fed and feed-restricted conditions. Moreover, the role of sex steroids as being one of the possible mechanisms by which sexual maturation interacts with leptin is explored. The salmon leptin-a genes, lepa1 and lepa2, were expressed mainly in liver and the leptin receptor (lepr) in brain and ubiquitously in peripheral tissues. Seasonal characterization of the lepa genes and lepr during the growth and reproductive season in one-year old males showed that hepatic lepa1 and lepa2 mRNA levels and plasma leptin levels were down-regulated concomitantly with an increase in weight and body fat. Feed restriction up-regulated hepatic leptin, and pituitary lepr expression as well as plasma leptin levels. Correlation between leptin levels and body lipid stores were either lacking or negative. These findings show that leptin and lepr are sensitive to changes in energy balance, but that leptin might not reflect adiposity in juvenile salmon. Hepatic lepa1 and lepa2, and testicular lepr expression increased during mid- to late spermatogenesis in early maturing males. This up-regulation was preceded by rapid gonadal growth and elevated pituitary follicle-stimulating hormone gene expression levels, whereas peak leptin levels coincided with peak pituitary luteinizing hormone expression and the presence of running milt in the testes. The sex steroids testosterone (T), 11-ketotestosterone and 17-β estradiol stimulated lepa1 and lepa2 gene expression in Atlantic salmon hepatocytes in vitro differentially depending on developmental stage. T was also able to stimulate hepatic lepa1 and pituitary lepa1 and lepr gene expression in immature male salmon in vivo. These results suggest that leptin plays a role in male fish reproduction during later stages of the maturational process and that the elevation of leptin expression during spermatogenesis could be caused by androgen stimulation.

Diss. (sammanfattning). Umeå : Sveriges lantbruksuniv. / Härtill 5 uppsatser.

Diss. (sammanfattning) Umeå : Sveriges lantbruksuniv. / Härtill 4 uppsatser. I publ. anges Department of Aquaculture som utgivande institution. Med sammanfattning på svenska och franska.

Memoria para optar al Título Profesional de Ingeniero Agrónomo / El afrecho de soya (Glycine max) es una alternativa de reemplazo parcial a la proteína animal producto de la disminución y altos costos de la harina de pescado utilizada como principal materia prima en la elaboración de dietas para salmónidos. En este sentido, el afrecho de soya reúne importantes características nutricionales tales como un elevado contenido de proteínas (48%) y un perfil de aminoácidos adecuado, sin embargo y debido a la presencia de factores anti nutricionales (FAN) sus niveles de inclusión se limitan a 25%, estos componentes están asociados a efectos de disminución de parámetros productivos y de digestibilidad de nutrientes. Dentro de los FAN de mayor concentración se encuentran los carbohidratos indigestibles termo estables, con niveles de 35-45% de la materia seca, dentro de los cuales un 20% corresponden a α-galactósidos (rafinosa y estaquiosa) y polisacáridos no derivados del almidón (celulosa, hemicelulosa y pectinas). En el presente estudio se utilizó un proceso de fermentación en estado sólido utilizando bacterias Streptomyces sp, Cohenella termotolerans y Cellulomicrobium sp., disminuyendo la concentración de α-galactósidos y NSP del afrecho de soya. Con la finalidad de evaluar el efecto de la inclusión de 30% de ingrediente vegetal en dietas para salmón del Atlántico, se realizó un estudio de crecimiento y de digestibilidad de nutrientes.