Lake trout (Salvelinus namaycush) have a broad distribution across Canada’s north, yet most studies that describe reproductive habitat and behaviour have been conducted in the southern extent of their range. Northern regions are experiencing unprecedented changes from climate and industrial development, and thus there is a pressing need to understand the reproductive habitat and behaviour of this species. I examined a dozen sites around Alexie Lake, Northwest Territories, to test if physical habitat and wind exposure were important determinants of spawning site use and embryonic survival. Spawning was found to occur in ~2 m water depth, on 3–15 cm diameter clean substrate on the leading edge of shoals that ended in a rock crib rising abruptly in nearshore regions around the lake. Wind direction was predominantly from the west, although it was highly variable within and among spawning seasons. I found evidence of lake trout spawning at each site examined, which was not limited to shoals facing a predominant wind direction. High variation in embryonic survival (2–83%) from incubation trays was observed among spawning sites, demonstrating a large gradient in habitat quality exists within a given lake. However, modelled wind exposure did not predict embryonic survival, nor did physical characteristics - including shoal depth and slope, as well as cobble size and shape - that may influence interstitial water flow on spawning shoals. Using an acoustic telemetry monitoring system and novel spatial temporal clustering analysis, I was able to quantify lake trout spawning movements and behaviours over the course of an entire spawning season. Lake trout formed clusters on spawning shoals around the entire nearshore region, as well as around several islands, confirming that suitable spawning habitat is abundant in Alexie Lake. Males arrived on spawning shoals earlier than females and remained longer for a maximum of 25 consecutive days; females occupied spawning shoals for a maximum of 8 consecutive days over the course of the spawning season. Males formed over four times as many spawning clusters and visited twice as many sites than females. Spawning clusters were predominantly formed at night but were also observed during daylight hours, especially during the peak spawning season (September 9–19). I found males had higher activity rates, and spent longer periods on spawning shoals, than females, in spite of similar daily travel distances between sexes. Overall, my findings challenge the conventional role of wind as a predominant predictor of lake trout spawning site quality. I propose that the unpredictable nature of wind and abundance of suitable habitat may favour lake-wide spawning by lake trout as a bet-hedging strategy in northern lakes with limited fetch. / May 2016

Genetic diversity of two salmonid species, Dolly Varden (Salvelinus malma) and coastal cutthroat trout (Oncorhynchus clarki clarki) in Prince William Sound, Alaska were examined at multiple spatial scales with three molecular markers. Pleistocene glaciers covered what is now Prince William Sound 8,000- 12,000 years ago and both species colonized the region subsequently. Because these species have different migratory behavior and historic ranges I expected to see different patterns of genetic diversity within Prince William Sound. Haplotype frequency and nucleotide diversity in sixteen mitochondrial DNA (mtDNA) restriction fragment enzymes combinations in Prince William Sound were higher in Dolly Varden than in coastal cutthroat trout, which were close to fixation. Low estimates of these measures in coastal cutthroat trout may reflect a founder effect resulting from colonization of this region from a single glacial refuge (Cascadia) and low dispersal capacity. To examine if genetic diversity in coastal cutthroat trout was higher in areas of glacial refuge, three additional locations from throughout their distributional range were examined with the same restriction enzymes. Haplotype frequency and nucleotide diversity were lower in areas that were glaciated than estimates of the same measures in a glacial refuge. Again, founder effects during colonization of the three glaciated sites may account for these results. Genetic variation of Dolly Varden and coastal cutthroat trout was also examined within and among populations in Prince William Sound with microsatellites and allozymes. The pattern of genetic variation in coastal cutthroat trout was complex. There was lower genetic diversity within populations that were recently colonized following recent de-glaciation (150-350 ybp). Genetic diversity among some coastal cutthroat trout populations was high, which possibly reflects restricted migration. In other trout populations there was low diversity among populations, possible reflecting historic gene flow. In Dolly Varden, genetic variation among anadromous populations in Prince William Sound was low. There were large differences among resident and anadromous populations. These data provide information for the management for both species, which may reduce the risk of the loss of genetic diversity within local populations. / Graduation date: 2003

No description available.

Thesis (MSc)--Stellenbosch University, 2012. / ENGLISH ABSTRACT: A 2010 Food and Agriculture Organization (FAO) report indicated that 85% of the world´s fish stocks overexploited. This highlights the importance of commercial aquaculture as a sustainable alternative to capture fisheries. Growth rates for international aquaculture production are slowing, although an average annual increase of 12.6% occurred in Africa between 1970 and 2008. Sub-Saharan Africa accounted for 0.50% of the total world aquaculture production in 2008. The South African aquafeed industry recognized the need for aquaculture research in alternative feed ingredients to ensure a more sustainable future. With routine use of antibiotics in aquaculture, antibiotic resistance have emerged, and novel strategies are needed. Currently, alternative feed ingredients and practical substitution of antibiotics are two of the major challenges faced in aquaculture. The use of plant proteins is preferred over animal proteins such as fish meal. By developing sustainable aquafeeds, that have both nutritional and health benefits, the gastrointestinal tract (GIT) microbiota of the host should be considered. The fish GIT is an open system and acts as a route of infection for pathogenic bacteria. A comparative study was done to determine the structure of the GIT microbiota in Mozambique tilapia (Oreochromis mossambicus) and rainbow trout (Oncorhynchus mykiss). Tilapia and trout are important freshwater aquaculture species in South Africa. Tilapia is a warmwater herbivorous fish with a long coiled GIT, whereas trout is a coldwater carnivore and its GIT is short and compartmentalized. Tilapia was reared in recirculation systems with lower water pH and trout in flow-through systems with higher water pH. Tilapia diets consisted of plant-based protein, whereas trout diets contained animal-based proteins. To understand the role of the autochthonous bacteria in the GITs of these fish, we determined community structure along the length of the respective GITs. A highly reproducible DNA fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used that targeted the intergenic spacer region (ITS) in bacteria. Community analysis based on operational taxonomic units (OTUs) was used to statistically compare the microbiota in different segments. The different GIT compartments in trout also showed distinct bacterial community structures. However, the degree of variation between identical segments between different fish was shown, and consequently, individual microbiotas was not seen. ARISA was further used to determine if formulations containing dietary phytogenics will modify the GIT microbiota. The GIT of fish plays a role in food digestion, while the resident GIT bacteria are important contributors to disease control and nutrient utilization. During two feeding trials tilapia was fed 16 and trout six different diets. Microbial diversity was lower in the GIT of tilapia as compared to trout and no significant shifts in community structure were detected in both species. With a high-throughput DNA sequencing technique, we followed a metagenomic approach to classify the autochthonous microbiota of tilapia and trout on a phylogenetic level. Pyrosequencing was used to define a core microbiota that would enable comparative feeding studies to be carried out. The proposed microbiota of tilapia consisted of genera from the Proteobacteria (5), Firmicutes (1), Actinobacteria (1), Fusobacteria (1) and Cyanobacteria (2). The microbiota of trout comprised genera of the Proteobacteria (3), Firmicutes (3) and Actinobacteria (1). Three genera from the Proteobacteria were common in tilapia and trout, confirming the dominance of this group in the GIT of freshwater fish. The variability and distribution of Lactobacillus in the GITs of both species was determined. Culturing of lactic acid bacteria (LAB) from the GIT of tilapia proves to be difficult and this was confirmed by the low-abundance of particularly Lactobacillus. A number of other LAB genera were identified that confirmed LAB as part of the autochthonous microbiota in freshwater cultured fish. The detection of secondary bacterial fish pathogens as part of the resident microbiota was also established. The use of 454 pyrosequencing in this study, gave a deeper insight into the structure of bacterial communities in the GITs of tilapia and trout. This research is novel and based on our knowledge, the first study to determine the core microbiota in two South African aquaculture species. Data based on community diversity and structure can be used as a basis for further studies. One important study would be to determine the effect environmental stressors would have on the core microbiota. / AFRIKAANSE OPSOMMING: Volgens `n 2010-verslag van die FAO (Food and Agriculture Organization) is 85% van die wêreld se visbronne oorbenut. Dit beklemtoon die belangrikheid van kommersiële akwakultuur as `n alternatief tot visvangste. Internasionaal neem die groeitempo van akwakultuur produksie af, alhoewel groei in Afrika tussen 1970 en 2008 jaarliks met `n gemiddeld van 12.6% toegeneem het. In 2008 was lande suid van die Sahara verantwoordelik vir 0.50% van die wêreld se akwakultuur produksie. Die Suid-Afrikaanse akwavoer industrie het die behoefte raakgesien vir akwakultuur navorsing in alternatiewe voerbestanddele om 'n meer volhoubare toekoms te verseker. Die roetine gebruik van antibiotika in visboerderye het bygedra tot die ontstaan van weerstandbiedende organismes, en daarom is nuwe strategieë nodig. Tans is alternatiewe voeding en die praktiese vervanging van antibiotiese stowwe belangrike uitdagings in akwakultuur. Die gebruik van plantaardige proteïne in viskos word verkies bo dierlike proteïene soos vismeel. Deur die ontwikkeling van volhoubare viskos, wat beide voedingswaarde en voordele vir die gesondheid van visse inhou, moet die mikrobiota in die spysverteringskanaal (SVK) van die gasheer oorweeg word. Die SVK van visse is `n oop sisteem en dien sodoende as `n infeksie kanaal vir patogeniese bakterieë. `n Vergelykende studie is uitgevoer om SVK mikrobiota struktuur te bepaal in Mosambiek tilapia (Oreochromis mossambicus) en reënboogforêl (Oncorhynchus mykiss). Tilapia en forêl is twee belangrike varswater spesies in Suid-Afrikaanse akwakultuur. Tilapia is `n warmwater herbivoor met `n lang, gekronkelde SVK. In teenstelling is forêl `n kouewater vis met `n kort SVK, wat uit verskillende segmente bestaan. Tilapia is in hersirkulasie waterstelsels met `n lae pH gekweek terwyl forêl in deurvloei waterstelsels met `n hoër pH gekweek is. Tilapia diëte het plantaardige proteïne bevat tewyl forêl diëte proteïne vanaf dier-afkoms bevat het. Om die rol van SVK bakterieë beter te verstaan is populasie struktuur bepaal langs die lengte van die SVK. Geoutomatiseerde ribosomale intergeniese spasie analise (ARISA) is `n herhaalbare DNS vingerafdruk tegniek wat die intergeniese spasies gebied (ITS) in bakterieë teiken. Analise gebaseer op operasionele taksonomiese eenhede (OTEs) is gebruik om die mikrobiota van SVK segmente statisties te vergelyk. Die SVK kompartemente in forêl het ook duidelike bakteriële populasie strukture getoon. `n Groot variasie tussen identiese segmente van verskillende vise is waargeneem en individuele mikrobiota kon nie uitgesonder word nie. ARISA is gebruik om die effek van plantaardige dieet formulasies op die SVK mikrobiota te toets. Die SVK van visse speel `n rol in voedselvertering, terwyl die natuurlike SVK bakterieë `n belangrike rol speel in siektebeheer en die benutting van voedingstowwe. Twee voedingsproewe is op tilapia en forêl uitgevoer, met onderskeidelik 16 en 6 verskillende diëte,. Mikrobiese diversiteit was laer in die tilapia SVK in vergeleke met die SVK van forêl en geen beduidende verskuiwings in populasie struktuur is in beide visse waargeneem nie. `n Hoë deurvloei DNS-volgorde bepalings tegniek, gekombineer met `n metagenomiese benadering is gebruik om die mikrobiota van tilapia en forêl op `n taksonomiese vlak te bepaal. “Pyrosequencing” is gebruik om `n kern microbe populasie te identifiseer ten einde vergelykende studies te vergemaklik. Die voorgestelde kern mikrobiota in tilapia het bestaan uit genera van die Proteobakterieë (5), Firmikute (1), Aktinobakterieë (1), Fusobakterieë (1) en Sianobakterieë (2). Die voorgestelde kern mikrobiota van forêl het bestaan uit genera van die Proteobakterieë (3), Firmikutes (3) en Aktinobakterieë (1). Drie genera van die Proteobakterieë het algemeen in tilapia en forêl voorgekom, wat die oorheersing van hierdie groep in die SVK van varswatervisse bevestig. Die veranderlikheid en verspreiding van Lactobacillus in die SVKs van beide visse is bepaal. Dit is moelik om melksuurbakterieë (MSB) uit die SVK van tilapia te isoleer en `n lae voorkoms van Lactobacillus is waargeneem. Ander MSB genera is ook geïdentifiseer wat MSB as deel van die plaaslike mikrobiota in varswater gekweekte visse bevestig. Verder is daar ook vasgestel dat sekondêre patogene deel uitmaak van die plaaslike mikrobiota. In hierdie studie het 454 “pyrosequencing” `n dieper insig gegee oor die struktuur van bakterie-populasies in die SVK van tilapia en forêl. Hierdie navorsing is oorspronklik en volgens die literatuur die eerste studie wat `n kern mikrobe populasie in twee Suid-Afrikaanse akwakultuur spesies waargeneem het. Data wat gebasseer is op populasie diversiteit en struktuur kan gebruik word as basis vir verdere studies. Een so `n studie kan die effek van omgewings stresfaktore op die kern mikrobiota in hierdie vise bepaal.

The brown trout, Salmo trutta L., displays one of the most variable and polymorphic life-history strategies of all the salmonids. In some populations, individuals spend their whole life-cycle in the river (freshwater-resident) whereas in others, a varying proportion migrates to sea for variable amounts of time to better feeding conditions before returning to spawn (anadromous). The ‘decision’ if an individual will migrate or not will be determined by the balance of the costs and benefits of following a particular life-history strategy. The balance of these, which do not affect males and females equally, will determine the future success (measured by fitness) of each strategy. This research addresses the influences of parental contribution, mainly maternal effect, of anadromous and freshwater-resident brown trout on offspring performance and subsequent life-history. A partial migratory population of brown trout was studied in the Tadnoll Brook, one of the seven major tributaries on the River Frome. The tributary is classified as a circum-neutral chalk stream, 9.9 km long with a catchment approximately 50 km2. Carbon and nitrogen stable isotope analysis (SIA) was used to quantify maternal reproductive contribution of anadromous and freshwater-resident brown trout to offspring and determine the future success (measured by fitness) in terms of size and time of emergence. A panel of 12 microsatellite loci was used to assign parentage to 0+ parr. Using field data collected over 1.5 years on individual fish, this study tested parental influence on offspring performance in terms of size and growth rate and calculate the reproductive contribution of maternal/paternal anadromous and freshwater-residents. Adult life-history strategy was identified using a combination of results from SIA, PIT tag data and ecological data (body size, temperature). Parr life-history strategy (1+) was inferred using PIT tag detection data. The results of the SIA indicated fry of anadromous females emerged earlier and at a larger size than fry of freshwater-resident females. Parentage assignment of parr was low (28 %), with 8 parr assigned to both parents and 43 assigned to only a single parent. There was no detectable effect of parental life-history on parr size and growth rate, however the raw data may suggest offspring of anadromous parents have an early size advantage but a slower growth compared to offspring of freshwater-resident parents during the first year of the parr stage. Twenty-four percent of the offspring were identified as putative smolts at 2+ and both forms interbred and could produce offspring of each life-history. Estimates of reproductive contribution (SIA and growth) show a higher proportion of anadromous females and males (growth only) contributed to offspring production. The results of this research indicate that the maternal anadromous contribution is higher in the Tadnoll Brook population, affording fitness benefits to their offspring during early ontogeny such as size advantages and emerging at a more profitable time to establish feeding territories. Adult life-history does not appear to influence juvenile (0+ parr) life-history but may have an effect on offspring performance. The presence of both forms in the population suggests the anadromous fitness benefits to offspring may only have an affect during ontogeny and early stages of growth. Then after juveniles reach a size threshold environmental factors influence offspring life-history, resulting in the largest parr with the fastest growth adopting an anadromous life-history.

Lake trout (Salvelinus namaycush) were extirpated from Lake Champlain around 1900 and from the lower four Great Lakes by 1960. Their ecological, commercial and recreational importance has prompted extensive restoration efforts. Despite widespread evidence of natural reproduction by stocked lake trout, there is minimal evidence of survival of wild progeny beyond age-0. Various abiotic and biotic impediments may be preventing self-sustaining lake trout populations from becoming established. Unsuccessful restoration in shallow areas has recently prompted a shift to restoration efforts to offshore, deep reefs in the Great Lakes. The first objective of this study was to develop, test, and implement methods for evaluating lake trout reproduction in deep water, where previously established techniques were ineffective. The second objective addressed the recruitment bottleneck between the emergent fry and juvenile life stages in Lake Champlain, by assessing the severity of predation on lake trout fry by epi-benthic fish. In order to quantify egg density on deep-water habitats (>18 m), we paired a deep-water egg trap with egg bags to establish a relationship between the two types of gear in Lake Champlain. There was no significant difference between densities in the egg bags and deep-water traps, but there was a positive correlation of their ranks (correlation coefficient = 0.514, p<0.0001). The deep-water traps were then used in Lake Michigan to successfully acquire the first egg density data from two sites on the deep Mid Lake Reef Complex. A drop electroshocker was developed to detect fry presence and tested in Lake Champlain in conjunction with emergent fry traps. Both types of gear exhibited similar patterns of fry relative abundance. To assess fry predation in Lake Champlain, two-hour gillnet sets during the period of fry emergence to identify fry predators and to describe how predation patterns changed diurnally and temporally. Seven species of epi-benthic fry predators were identified, including five species that had not been previously identified as fry predators. Yellow perch and rock bass dominated the predator community at two study sites (83% of total catch, N=1179, 77% of all fry predators, N=57). Predator presence and fry consumption was almost entirely nocturnal. There was a linear aggregational response in predator CPUE (fish/hr) to increasing fry relative abundance (p<0.033) but confirmed predators did not exhibit a functional response. There was evidence of a threshold of fry relative abundance at 1 fry/trap/day for the onset and conclusion of fry predation. Temperature was a driving factor in the timing of fry emergence and predator abundance, allowing us to predict the relative impact of predators based on temperature scenarios. Only 5% of the potential predators consumed fry. We used empirical probabilities of consumption to model loss of fry due to predation. This consumption model revealed that predator abundances would have to be extremely high for predation to significantly reduce the population of fry. However, given the relatively high species richness of predators observed at the shallow water study sites, lake trout fry survival is likely to be higher at deep, offshore reefs. These results support the recent shift in restoration efforts to focus on deep reefs.

In order to develop a system that could provide fish farmers with information to monitor stock performance and plan for a timely production, a computerised recording system was designed and tested on a trout hatchery in Scotland. It facilitated routine data capture on site with a small hand-held computer, programmed in BASIC language, which subsequently downloaded the data to a central desk-top microcomputer for further processing. Both direct and long-distance transmission via the telephone network using modems were possible. The LOTUS 1-2-3 general purpose software package, running on the microcomputer, was customised using 'macro' commands to accept the transmitted data and create files for storage on 'floppy' or 'hard' magnetic disks. Further information could be calculated and graphs and summary reports for stock control could be generated at will. Other customised LOTUS worksheets were developed to allow identification and access of specific historical data in order to calibrate regression equations and provide growth predictions for particular fish types. This information combined with cost and pricing details was further utilised by a linear programming package. Guidelines on optimum policies were formulated and sensitivity analyses could be performed. This production information system was implemented on the IBM-PC and the OLIVETTI M24 desk-top microcomputers and as field devices the SHARP PC 1500A and the HUSKY HUNTER were used. Since existing technology and 'off-the-shelf' software were utilised, the developed information system can be easily adjusted to suit the individual needs of different fish farms. However, the most important requirement for successful implementation would be the commitment and enthusiasm of the fish farm manager.

La truite arc-en-ciel (Oncorhynchus mykiss), espèce d'élevage majeure en Europe et notamment en France, est l'une des espèces de poisson les mieux connues dans un grand nombre de domaines, y compris l'immunologie. Les virus qui l'infectent ont aussi été bien caractérisés, en particulier deux Novirhabdovirus, le virus de la septicémie hémorragique virale (VSHV) et le virus de la nécrose hématopoïétique infectieuse (VNHI), tous deux connus pour provoquer des pertes importantes dans les élevages aquacoles. Quelques travaux, conduits notamment à l'INRA, ont mis en évidence l'existence d'une variabilité génétique de la résistance à ces infections chez la truite (Quillet et al., 2007). Une approche combinant analyse génétique et étude des réponses cellulaires a été développée pour tenter de mieux caractériser la réponse de la truite contre le VSHV. L'objectif est de développer des outils d'amélioration de la santé dans les élevages piscicoles et de mieux comprendre les mécanismes de résistance antivirale chez les vertébrés. Tout d'abord, une démarche de cartographie de QTL (quantitative trait locus) a permis de détecter un QTL majeur de résistance au VSHV dans la région télomérique du groupe de liaison 31 de la truite arc-en-ciel. Ce QTL contrôle la survie des poissons et la croissance in vitro du virus sur explants de nageoire (VREFT), ce qui suggère fortement l'implication de mécanismes innés dans la résistance. Le QTL est retrouvé dans des croisements impliquant des reproducteurs de résistance variée, et peut expliquer jusqu'à 65% (survie) et 49% (VREFT) de la variance phénotypique observée. Enfin, l'effet du QTL est conservé quel que soit le mode d'infection employé (balnéation ou injection intrapéritonéale), suggérant que la résistance n'est pas liée à des particularités des tissus superficiels (peau, mucus), premiers sites de contact entre le virus et son hôte. En parallèle, des lignées cellulaires ont été dérivées à partir d'ovaires de truites appartenant à des lignées isogéniques présentant des niveaux de résistance variable à l'infection par le VSHV. Une corrélation remarquable est observée entre la résistance à l'infection des lignées cellulaires et la survie des poissons dont elles sont issues, confirmant définitivement le rôle déterminant de mécanismes innés dans la résistance. Ce modèle cellulaire a également permis de montrer que le contrôle précoce de la prolifération virale était une étape clé de la résistance. Le parallélisme entre résistance in vitro et in vivo semble conservé lors de l'infection par un second rhabdovirus, le VNHI, bien qu'aucune corrélation dans la résistance à ces deux infections n'ait été observée dans cette étude. Par ailleurs, le QTL à effet fort identifié pour la résistance au VSHV ne joue pas un rôle majeur dans la variabilité de résistance au VNHI. Ceci suggère que, même si ils concourent à l'activation de voies de signalisation communes, les facteurs clés de la résistance aux deux virus sont différents, et leur expression contrôlée par des zones génomiques distinctes. Les résultats obtenus dans cette étude ont permis de démontrer sans équivoque le rôle clé des mécanismes innés dans la résistance de la truite à l'un de ses principaux virus, et l'existence d'une forte variabilité génétique sous-tendant l'expression des facteurs impliqués. En proposant des bases nouvelles pour aborder l'analyse des interactions hôte-virus chez la truite, ils ouvrent la voie à la découverte de mécanismes potentiellement nouveaux dans la réponse des poissons à ces infections et à une meilleure compréhension de ces mécanismes chez les vertébrés. / The rainbow trout (Oncorhynchus mykiss) is one of most significant fish model in many scientific fields, including immunology. Due to its importance in aquaculture, viruses that can infect this species have been well characterized. Two well-known Novirhabdoviruses, the viral haemorrhagic septicemia virus (VHSV) and the infectious hematopoietic necrosis virus (IHNV) cause serious damage in fish farms and represent a significant threat for aquaculture in a number of countries. Our laboratories have previously reported a wide range of susceptibility to these infections in rainbow trout depending on the host genetic background (Quillet et al., 2007). In this work, we undertook a dual approach to better characterize the antiviral response in fish. A without a priori approach led to the detection of a major QTL (quantitative trait locus) for resistance to VHSV in the telomeric region of the rainbow trout linkage group 31. This QTL controls both fish survival and viral replication in excised fin tissue (VREFT), suggesting the involvement of innate mechanisms in the resistance, and can explain up to 65% (survival) and 49% (VREFT) of the observed phenotypic variation. Additionally, this major locus was retrieved in a number of genetic backgrounds, and regardless of the infection route (waterborne infection or injection), suggesting that the virus entry in fish is not the main factor of resistance. In parallel, cell lines were derived from ovaries of several rainbow trout isogenic lines with various levels of susceptibility to infection with VHSV. Resistance of cell lines to infection by the virus was remarkably correlated with the survival of fish from which they were derived, confirming the importance of innate factors for the resistance. This model also showed that the early stage response is critical for the cellular fate after infection. The parallelism between resistance in vitro and in vivo has finally been observed after infection by a second rhabdovirus, IHNV, although no correlation in resistance to these two viruses could be detected. Moreover, no major QTL for IHNV resistance was found in the region of the VHSV QTL. This observation suggests that the key factors of resistance are different, even if they contribute to the activation of common signaling pathways. The expression of these factors is in any case controlled by distinct regions of the genome. Our work demonstrates a strong genetic determinism of resistance to a major virus in rainbow trout, based on innate mechanisms. We believe that these results pave the way for the discovery of new host response mechanisms against viruses, leading to a better understanding of antiviral immunity in vertebrates.

In many cases in the past fish bones recovered during archaeological excavations at Upper Palaeolithic sites were often assumed to result from human activity without any consideration for alternate accumulation processes. Many of these assemblages had not been analysed in a scientifically rigorous manner, with some receiving no consideration at all. A review of current evidence and results of new analyses indicate that salmonids (salmon and trout) are the most frequently recorded fish at the European Palaeolithic cave sites. Two potential accumulation agents for fish remains were explored: brown bears (Ursus arctos) and eagle owls (Bubo bubo). Controlled feeding experiments integrated with ecological studies indicate that salmonid remains survive the digestive systems of both species and result in distinctive patterning in assemblage characteristics. Post-depositional taphonomic processes, such as trampling, also produce distinct taphonomic signatures and are an agent of differential inter-species preservation. A thorough consideration of depositional and post-depositional processes of archaeological assemblages in central Italy (Grotta di Pozzo, Maritza, La Punta and Ortucchio) and Spain (El Juyo, Altamira, Salitre, Castillo and Rascaño) shows that the fish remains from these sites result from human activity. The overrepresentation of cranial elements at the Italian sites suggest that fish were processed by removing the head to perhaps smoke or dry before transportation to other locations for consumption. This research lead to improved methods of analysis, and thus enhanced understanding of the role of fishing and fish consumption in Upper Palaeolithic hunter-gatherer societies.

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.