Salmonids are a diverse group of fishes whose common ancestor experienced an evolutionarily important whole genome duplication (WGD) event approximately 90 MYA. This event has shaped the evolutionary trajectory of salmonids, and may have contributed to a proliferation of the repeated DNA sequences known as transposable elements (TEs). In this work I characterized repeated DNA in five salmonid genomes. I found that over half of the DNA within each of these genomes was derived from repeats, a value which is amongst the highest of all vertebrates. I investigated repeats of the most abundant TE superfamily, Tc1-Mariner, and found that large proliferative bursts of this element occurred shortly after the WGD and continued during salmonid speciation, where they have produced dramatic differences in TE content among extant salmonid lineages. This work provides important resources for future studies of salmonids, and advances the understanding of two important evolutionary forces: TEs and WGDs. / Graduate / 2019-04-19

Le saumon atlantique (Salmo salar) est une espèce tant emblématique que menacée à l’échelle internationale, au même titre que la plupart des espèces de poissons diadromes. La présence de barrages, en entraînant une rupture de la continuité écologique des cours d’eau, participe à ce déclin. Le remplacement du barrage en porte à flot sur l’estuaire du Couesnon (Normandie, France) par un barrage procédant à des lâchers d’eau à l’étale de basse mer, est susceptible d’impacter l’abondance et la dynamique migratoire des saumons. Pour étudier les remontées de saumons adultes sur ce fleuve, un échosondeur à faisceau partagé a été installé en amont du barrage et a enregistré en continu tous les passages de saumons lors des périodes estivales de 2010 à 2014. L’hydroacoustique, méthode non intrusive et indépendante des conditions de turbidité de l’eau, permet l’acquisition d’informations difficilement accessibles par d’autres techniques. Pour évaluer la réelle influence du barrage sur les migraticours d’eau voisin dont l’estuaire est libre, à l’aide d’un outil hydroacoustique bénéficiant de larges innovations technologiques, une caméra acoustique DIDSON. Les méthodologies développées soulignent les avantages et les limites des deux outils, mettant en lumière le gain d’information apporté par les caméras acoustiques. L’interprétation des résultats met en évidence que si le fonctionnement du barrage n’impacte pas le maintien de la population sur ce fleuve, la dynamique migratoire des saumons y est modifiée. Cette étude souligne les grandes capacités d’adaptation des saumons atlantique / The Atlantic salmon (Salmo salar) is as emblematic as in a global decline, as most of the diadromous fish species. Dams have direct consequences on the river ecological continuity and indirect effects, such as the modification of the hydrological and hydrosedimentary dynamics which affects these populations. In Normandy (France), the Couesnon River’s estuary flood-gate dam has recently been replaced by a new dam proceeding to water releases at low tide stall. This functioning may decrease the salmon abundance or disturb their migration dynamic on this river. To study the dam influence, a split-beam echosounder has been settled upstream the dam and has recorded Philippe BOëTpermanently the salmon migrations during the summer period from 2010 to 2014. The hydroacoustic methods, non-intrusive and independent from the turbidity conditions, provide useful information, neither available nor quantifiable with other existing monitoring technics. To evaluate the disturbance of the estuarine damthe migration dynamic of the same species has also been monitored on a nearby river, the Sélune River, whose estuary is free-flowing. The hydroacoustic tool settled on this river, a DIDSON, belongs to the acoustic camera generation and benefits from recent technological improvements. The defined methodologies highlight the advantages and limits of both tools, revealing the information gain brought by the acoustic cameras. A dam functioning influence on the Atlantic salmon migration has been revealed, but no negative impact has been described on the salmon annual recruitment level. This study

En général, le métabolisme des poissons est estimé à des valeurs de température constantes, mais les effets de fluctuations journalières de température similaires à celles retrouvées en milieu naturel semblent peu connus. Les objectifs du présent mémoire sont de quantifier les effets de la température moyenne d’acclimatation et d’évaluer les effets de l’historique thermique des individus, sur les réponses métaboliques de tacons de saumon Atlantique (Salmo salar) aux fluctuations journalières de la température. Des tacons provenant de deux rivières, une fraîche et une chaude, ont été acclimatés à un maximum de quatre régimes thermiques (constant 15 °C ou 20 °C, fluctuant 15 °C ± 2.5 °C ou 20 °C ± 2.5 °C) et leur taux métabolique standard estimés par respirométrie par débit-intermittent. Les fluctuations journalières de température (15 °C ± 2.5 °C) près de l’optimum thermique pour cette espèce (16 °C) n’affectent pas le taux métabolique standard. À l’opposé, les fluctuations journalières de température plus chaudes (20 °C ± 2.5 °C) augmentent de 35.4% le taux métabolique standard des tacons de la rivière plus chaude, mais pas ceux des poissons de la rivière fraîche. Ainsi, la température moyenne à laquelle sont acclimatés les poissons peut affecter leur réponse métabolique aux fluctuations journalières de température, mais cette réponse peut varier entre populations provenant de rivières présentant des régimes thermiques différents. Enfin, grâce aux données de métabolisme précédemment estimées, un modèle de métabolisme standard a été développé pour des tacons de saumon Atlantique soumis à des fluctuations journalières de température. / Usually, fish metabolism is evaluated under constant values of temperature, but the effects of daily temperature fluctuations similar to those found in natural environment on metabolism seems to be much less understood. The goals of this study are to quantify the effects of the mean acclimation temperature and to assess the effects of the thermal history on the metabolic response of Atlantic salmon (Salmo salar) parr to daily fluctuations of water temperature. Atlantic salmon parr originating from two rivers, one cool and one relatively warm, were acclimated to up to four thermal regimes (constant 15 °C or 20 °C, daily fluctuating 15 °C ± 2.5 °C or 20 °C ± 2.5 °C) and their standard metabolic rate was estimated using intermittent-flow respirometry. Daily temperature fluctuations (15 °C ± 2.5 °C) near this species’ thermal optimum (16 °C) do not influence standard metabolic rate. In contrast, daily fluctuations of higher temperature (20 °C ± 2.5 °C) do increase standard metabolic rate by 35.4% for fish from the warmer river, but not for fish from the cooler river. Therefore, the mean temperature to which fish are acclimated may affect their responses to daily fluctuations of water temperature, but this response may vary between populations originating from rivers having different thermal regimes. Using standard metabolic rates previously estimated, a standard metabolic rate model was developed for Atlantic salmon parr exposed to daily fluctuations of temperature.

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.