This thesis presents models applicable for aquatic ecosystems. Geographical Information Systems (GIS) form an important part of the thesis. The dynamic mass balance models focus on nutrient fluxes, biotic/abiotic interactions and operate on different temporal and spatial scales (site, local, regional and international). The relevance and role of scale in mass balance modelling is a focal point of the thesis. A mesocosm experiment was used to construct a model to estimate the nutrient load of phosphorus and nitrogen from net cage fish farming (i.e., the site scale). The model was used to estimate what feeding conditions that are required for a sustainable aquaculture scenario, i.e., a zero nutrient load situation (a linkage between the site scale and the regional scale). A dynamic model was constructed for suspended particulate matter (SPM) and sedimentation in coastal areas (i.e., the local scale) with different morphometric characteristics and distances to the Sea. The results demonstrate that the conditions in the Sea (the regional and international scale) are of fundamental importance, also for the most enclosed coastal areas. A foodweb model for lakes was transformed and recalibrated for Baltic Sea conditions (i.e., the international scale). The model also includes a mass balance model for phosphorus and accounts for key environmental factors that regulate the presuppositions for production and biomasses of key functional groups of organisms. The potential use of the new model for setting fish quotas of cod was examined. For the intermittent (i.e., regional) scale, topographically complex areas can be difficult to define and model. Therefore, an attempt was made to construct a waterscape subbasin identification program (WASUBI). The method was tested for the Finnish Archipelago Sea and the Okavango Delta in Botswana. A comparison to results from a semi-random delineation method showed that more enclosed basins was created with the WASUBI method.

A introdução de espécies exóticas é uma prática que acompanha a história da humanidade, sendo as espécies introduzidas a base da nutrição e economia em vários países. Porém, esse processo contínuo tem levado a uma homogeneização da flora e fauna global. Os ecossistemas aquáticos, que têm recebido menor atenção que os terrestres, têm sofrido perda de diversidade, hibridação, introdução de patógenos, degradação do habitat além da necessidade e alto custo de controle das espécies introduzidas. O desenvolvimento da aqüicultura tem acelerado a introdução de peixes exóticos, que são a base dessa produção em países como o Brasil. Além desta, entre as razões para a introdução citam-se o esporte, a manipulação ecológica com controle de organismos indesejáveis, o melhoramento dos estoques, a ornamentação ou ainda introduções acidentais. No Rio Grande do Sul, nos rios dos Campos de Cima da Serra estão ocorrendo introduções da espécie exótica truta arco- íris (Oncorhynchus mykiss) desde meados da década de 90 como forma de estímulo ao turismo rural. O objetivo dessa prática é a pesca esportiva, que atrai turistas de várias regiões. Porém, os rios da região possuem várias espécies de peixes endêmicas e as conseqüências dessa prática sobre a biota aquática são desconhecidas. O objetivo do presente trabalho é avaliar o efeito da introdução da truta arco-íris sobre o ecossistema de rios de baixa ordem no município de São José dos Ausentes – RS, Brasil. Para tanto foi descrita a biologia da truta arco- íris no novo ambiente, verificando sua alimentação, movimentação, presença e viabilidade da reprodução. A ictiofauna autóctone dos rios com ausência e presença de trutas foi comparada, bem como o efeito da predação sobre a macrofauna bentônica. A ictiofauna foi amostrada com o uso da pesca elétrica, sendo o conteúdo estomacal das trutas avaliado sazonalmente. Três trutas foram marcadas e acompanhadas por ii biotelemetria para determinação da sua área de vida. Um experimento com ninhos artificiais foi conduzido para verificação da sobrevivência de ovos de trutas nas condições dos rios de São José dos Ausentes. O experimento de exclusão de peixes foi feito a fim de avaliar o efeito da predação sobre a macrofauna bentônica, comparando a macrofauna em rios com e sem trutas. Os resultados indicaram que a truta arco- íris tem como alimento principal os invertebrados bentônicos, porém as maiores classes de tamanho incluem peixes em seus alimentos principais. Logo após sua introdução a movimentação é restrita, porém alguns exemplares foram capturados em um rio onde não foi feita introdução dessa espécie. Apesar de baixa, a sobrevivência dos adultos ocorre, assim como a reprodução. A sobrevivência dos ovos também é baixa, porém, uma pós-larva foi encontrada. A ictiofauna autóctone é diferenciada nos rios com presença de truta, apresentando menor riqueza e diversidade e uma tendência a diminuição da biomassa. A macrofauna bentônica também é diferenciada, apesar de não ser possível atribuir essa diferença somente à presença das trutas. / The introduction of exotic species is a practice that accompanies the humanity's history, being the introduced species the base of the nutrition and economy in several countries. Even so, that continuous process has been taking to a homogenization of the global flora and fauna. The aquatic ecosystems, that have been receiving smaller attention than the terrestrial ones, have been suffering diversity loss, hybridization, pathogens introduction, degradation of the habitat and costs of control of the introduced species. The development of aquaculture has been accelerating the introduction of exotic fish, that are the base of that production in countries as Brazil. Among the reasons for the introduction are the sporting fishing, the ecological manipulation with control of undesirable organisms, the improvement of the stocks, the ornamentation or still accidental introductions. In Rio Grande do Sul, in the rivers of Campos de Cima da Serra are occurring introductions of the species exotic rainbow trout (Oncorhynchus mykiss) from middles of the decade of 90 as incentive form to the rural tourism. The objective of that practice is the sporting fishing, which attracts tourists of several areas. Even so, the rivers of the area possess several endemic species of fish and the consequences of that practice on the aquatic biota have been ignored. The objective of the present work is to evaluate the effect of the introduction of the rainbow trout on rivers of low order in the municipal district of São José dos Ausentes - RS, Brazil. Thus the biology of the rainbow trout was described in the new environment, verifying its feeding, movement, presence and viability of reproduction. The autochthonous ictiofauna of the rivers with absence and presence of trouts was compared, as well as the effect of the predation on the benthic macrofauna. The ictiofauna was collected with the use of the electric fishing, being the stomacal content of the trouts evaluated seasonally. Three trouts were marked and accompanied by biotelemetry for determination of its life iv area. An experiment with artificial nests was driven for verification of the survival of eggs of trouts in the conditions of the rivers of São José dos Ausentes. The experiment of exclusion of fish was made in order to evaluate the effect of the predation on the benthic macrofauna, comparing the macrofauna in rivers with and without trouts. The results indicated that the rainbow trout has as main food benthic invertebrates, even so, in larger size classes it include fishes as main food. After its introduction the movement is restricted, even so trout s were found in a river where they were not introduced. Although low, have survival, as well as reproduction. The survival of the eggs is low, but it is happening in Silveira River, a post larvae being found. The autochthonous ictiofauna is differentiated in the rivers with trout presence, presenting smaller richness and diversity. The benthic macrofauna is also differentiated, in spite of not being possible to attribute that difference only to the presence of trouts.

Current literature suggests that little, if any, research has been conducted in South Africa to determine the impact of alien invasive trout on indigenous amphibian biodiversity. The primary aim of the research project was to establish whether waterfalls are seasonally important in protecting the indigenous Natal Cascade Frog Hadromophryne natalensis tadpole populations from predation by alien rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta at two sampling areas located at Injesuthi and Monk‟s Cowl Nature Reserve within the uKhahlamba Drakensberg Park World Heritage Site (UDPWHS). The dissertation argues in favour of a biotic rationale, namely trout predation, as being the primary cause for the decline of H. natalensis tadpoles below the waterfalls and systematically negates the influence of geo-physical (abiotic) environmental factors on tadpole abundance. Habitat isolation and fragmentation is identified as a latent threat to the continued persistence of H. natalensis populations in the UDPWHS. / Environmental Sciences / M. Sc. (Environmental Science)

A introdução de espécies exóticas é uma prática que acompanha a história da humanidade, sendo as espécies introduzidas a base da nutrição e economia em vários países. Porém, esse processo contínuo tem levado a uma homogeneização da flora e fauna global. Os ecossistemas aquáticos, que têm recebido menor atenção que os terrestres, têm sofrido perda de diversidade, hibridação, introdução de patógenos, degradação do habitat além da necessidade e alto custo de controle das espécies introduzidas. O desenvolvimento da aqüicultura tem acelerado a introdução de peixes exóticos, que são a base dessa produção em países como o Brasil. Além desta, entre as razões para a introdução citam-se o esporte, a manipulação ecológica com controle de organismos indesejáveis, o melhoramento dos estoques, a ornamentação ou ainda introduções acidentais. No Rio Grande do Sul, nos rios dos Campos de Cima da Serra estão ocorrendo introduções da espécie exótica truta arco- íris (Oncorhynchus mykiss) desde meados da década de 90 como forma de estímulo ao turismo rural. O objetivo dessa prática é a pesca esportiva, que atrai turistas de várias regiões. Porém, os rios da região possuem várias espécies de peixes endêmicas e as conseqüências dessa prática sobre a biota aquática são desconhecidas. O objetivo do presente trabalho é avaliar o efeito da introdução da truta arco-íris sobre o ecossistema de rios de baixa ordem no município de São José dos Ausentes – RS, Brasil. Para tanto foi descrita a biologia da truta arco- íris no novo ambiente, verificando sua alimentação, movimentação, presença e viabilidade da reprodução. A ictiofauna autóctone dos rios com ausência e presença de trutas foi comparada, bem como o efeito da predação sobre a macrofauna bentônica. A ictiofauna foi amostrada com o uso da pesca elétrica, sendo o conteúdo estomacal das trutas avaliado sazonalmente. Três trutas foram marcadas e acompanhadas por ii biotelemetria para determinação da sua área de vida. Um experimento com ninhos artificiais foi conduzido para verificação da sobrevivência de ovos de trutas nas condições dos rios de São José dos Ausentes. O experimento de exclusão de peixes foi feito a fim de avaliar o efeito da predação sobre a macrofauna bentônica, comparando a macrofauna em rios com e sem trutas. Os resultados indicaram que a truta arco- íris tem como alimento principal os invertebrados bentônicos, porém as maiores classes de tamanho incluem peixes em seus alimentos principais. Logo após sua introdução a movimentação é restrita, porém alguns exemplares foram capturados em um rio onde não foi feita introdução dessa espécie. Apesar de baixa, a sobrevivência dos adultos ocorre, assim como a reprodução. A sobrevivência dos ovos também é baixa, porém, uma pós-larva foi encontrada. A ictiofauna autóctone é diferenciada nos rios com presença de truta, apresentando menor riqueza e diversidade e uma tendência a diminuição da biomassa. A macrofauna bentônica também é diferenciada, apesar de não ser possível atribuir essa diferença somente à presença das trutas. / The introduction of exotic species is a practice that accompanies the humanity's history, being the introduced species the base of the nutrition and economy in several countries. Even so, that continuous process has been taking to a homogenization of the global flora and fauna. The aquatic ecosystems, that have been receiving smaller attention than the terrestrial ones, have been suffering diversity loss, hybridization, pathogens introduction, degradation of the habitat and costs of control of the introduced species. The development of aquaculture has been accelerating the introduction of exotic fish, that are the base of that production in countries as Brazil. Among the reasons for the introduction are the sporting fishing, the ecological manipulation with control of undesirable organisms, the improvement of the stocks, the ornamentation or still accidental introductions. In Rio Grande do Sul, in the rivers of Campos de Cima da Serra are occurring introductions of the species exotic rainbow trout (Oncorhynchus mykiss) from middles of the decade of 90 as incentive form to the rural tourism. The objective of that practice is the sporting fishing, which attracts tourists of several areas. Even so, the rivers of the area possess several endemic species of fish and the consequences of that practice on the aquatic biota have been ignored. The objective of the present work is to evaluate the effect of the introduction of the rainbow trout on rivers of low order in the municipal district of São José dos Ausentes - RS, Brazil. Thus the biology of the rainbow trout was described in the new environment, verifying its feeding, movement, presence and viability of reproduction. The autochthonous ictiofauna of the rivers with absence and presence of trouts was compared, as well as the effect of the predation on the benthic macrofauna. The ictiofauna was collected with the use of the electric fishing, being the stomacal content of the trouts evaluated seasonally. Three trouts were marked and accompanied by biotelemetry for determination of its life iv area. An experiment with artificial nests was driven for verification of the survival of eggs of trouts in the conditions of the rivers of São José dos Ausentes. The experiment of exclusion of fish was made in order to evaluate the effect of the predation on the benthic macrofauna, comparing the macrofauna in rivers with and without trouts. The results indicated that the rainbow trout has as main food benthic invertebrates, even so, in larger size classes it include fishes as main food. After its introduction the movement is restricted, even so trout s were found in a river where they were not introduced. Although low, have survival, as well as reproduction. The survival of the eggs is low, but it is happening in Silveira River, a post larvae being found. The autochthonous ictiofauna is differentiated in the rivers with trout presence, presenting smaller richness and diversity. The benthic macrofauna is also differentiated, in spite of not being possible to attribute that difference only to the presence of trouts.

A introdução de espécies exóticas é uma prática que acompanha a história da humanidade, sendo as espécies introduzidas a base da nutrição e economia em vários países. Porém, esse processo contínuo tem levado a uma homogeneização da flora e fauna global. Os ecossistemas aquáticos, que têm recebido menor atenção que os terrestres, têm sofrido perda de diversidade, hibridação, introdução de patógenos, degradação do habitat além da necessidade e alto custo de controle das espécies introduzidas. O desenvolvimento da aqüicultura tem acelerado a introdução de peixes exóticos, que são a base dessa produção em países como o Brasil. Além desta, entre as razões para a introdução citam-se o esporte, a manipulação ecológica com controle de organismos indesejáveis, o melhoramento dos estoques, a ornamentação ou ainda introduções acidentais. No Rio Grande do Sul, nos rios dos Campos de Cima da Serra estão ocorrendo introduções da espécie exótica truta arco- íris (Oncorhynchus mykiss) desde meados da década de 90 como forma de estímulo ao turismo rural. O objetivo dessa prática é a pesca esportiva, que atrai turistas de várias regiões. Porém, os rios da região possuem várias espécies de peixes endêmicas e as conseqüências dessa prática sobre a biota aquática são desconhecidas. O objetivo do presente trabalho é avaliar o efeito da introdução da truta arco-íris sobre o ecossistema de rios de baixa ordem no município de São José dos Ausentes – RS, Brasil. Para tanto foi descrita a biologia da truta arco- íris no novo ambiente, verificando sua alimentação, movimentação, presença e viabilidade da reprodução. A ictiofauna autóctone dos rios com ausência e presença de trutas foi comparada, bem como o efeito da predação sobre a macrofauna bentônica. A ictiofauna foi amostrada com o uso da pesca elétrica, sendo o conteúdo estomacal das trutas avaliado sazonalmente. Três trutas foram marcadas e acompanhadas por ii biotelemetria para determinação da sua área de vida. Um experimento com ninhos artificiais foi conduzido para verificação da sobrevivência de ovos de trutas nas condições dos rios de São José dos Ausentes. O experimento de exclusão de peixes foi feito a fim de avaliar o efeito da predação sobre a macrofauna bentônica, comparando a macrofauna em rios com e sem trutas. Os resultados indicaram que a truta arco- íris tem como alimento principal os invertebrados bentônicos, porém as maiores classes de tamanho incluem peixes em seus alimentos principais. Logo após sua introdução a movimentação é restrita, porém alguns exemplares foram capturados em um rio onde não foi feita introdução dessa espécie. Apesar de baixa, a sobrevivência dos adultos ocorre, assim como a reprodução. A sobrevivência dos ovos também é baixa, porém, uma pós-larva foi encontrada. A ictiofauna autóctone é diferenciada nos rios com presença de truta, apresentando menor riqueza e diversidade e uma tendência a diminuição da biomassa. A macrofauna bentônica também é diferenciada, apesar de não ser possível atribuir essa diferença somente à presença das trutas. / The introduction of exotic species is a practice that accompanies the humanity's history, being the introduced species the base of the nutrition and economy in several countries. Even so, that continuous process has been taking to a homogenization of the global flora and fauna. The aquatic ecosystems, that have been receiving smaller attention than the terrestrial ones, have been suffering diversity loss, hybridization, pathogens introduction, degradation of the habitat and costs of control of the introduced species. The development of aquaculture has been accelerating the introduction of exotic fish, that are the base of that production in countries as Brazil. Among the reasons for the introduction are the sporting fishing, the ecological manipulation with control of undesirable organisms, the improvement of the stocks, the ornamentation or still accidental introductions. In Rio Grande do Sul, in the rivers of Campos de Cima da Serra are occurring introductions of the species exotic rainbow trout (Oncorhynchus mykiss) from middles of the decade of 90 as incentive form to the rural tourism. The objective of that practice is the sporting fishing, which attracts tourists of several areas. Even so, the rivers of the area possess several endemic species of fish and the consequences of that practice on the aquatic biota have been ignored. The objective of the present work is to evaluate the effect of the introduction of the rainbow trout on rivers of low order in the municipal district of São José dos Ausentes - RS, Brazil. Thus the biology of the rainbow trout was described in the new environment, verifying its feeding, movement, presence and viability of reproduction. The autochthonous ictiofauna of the rivers with absence and presence of trouts was compared, as well as the effect of the predation on the benthic macrofauna. The ictiofauna was collected with the use of the electric fishing, being the stomacal content of the trouts evaluated seasonally. Three trouts were marked and accompanied by biotelemetry for determination of its life iv area. An experiment with artificial nests was driven for verification of the survival of eggs of trouts in the conditions of the rivers of São José dos Ausentes. The experiment of exclusion of fish was made in order to evaluate the effect of the predation on the benthic macrofauna, comparing the macrofauna in rivers with and without trouts. The results indicated that the rainbow trout has as main food benthic invertebrates, even so, in larger size classes it include fishes as main food. After its introduction the movement is restricted, even so trout s were found in a river where they were not introduced. Although low, have survival, as well as reproduction. The survival of the eggs is low, but it is happening in Silveira River, a post larvae being found. The autochthonous ictiofauna is differentiated in the rivers with trout presence, presenting smaller richness and diversity. The benthic macrofauna is also differentiated, in spite of not being possible to attribute that difference only to the presence of trouts.

Au cours des dernières années, l'augmentation de la production aquacole a nécessité un changement dans la composition des aliments pour poissons, pour remplacer la farine (FP) et l’huile de poisson (HP) par des sources végétales plus disponibles. Dans ce contexte, le travail de ma thèse avait pour but d'analyser les effets d’une substitution totale et concomitante de la FP et HP par des ingrédients végétaux dans les aliments distribués pendant tout le cycle de vie de la truite arc-en-ciel, de la première alimentation jusqu’à la reproduction. Ce travail a montré pour la première fois que la truite peut survivre, se développer et avoir une descendance viable, lorsqu’elle est nourrie tout au long de son cycle de vie avec un régime 100% végétal. Un tel remplacement alimentaire a entraîné des changements radicaux dans le profil en acides gras des tissus des femelles. Cependant, nous avons constaté que la truite était capable de synthétiser des acides gras polyinsaturés à longue chaîne n-3 (AGPI-LC n-3) à partir de précurseurs présents dans l'aliment, et de stocker dans les ovules une partie de ces acides gras néosynthétisés dans le foie , permettant ainsi une reproduction efficace. Nous avons également étudié les possibles effets trans-générationnels d’une alimentation 100% végétale des géniteurs, sur la survie et la croissance de la descendance et sur sa réponse à différents régimes aux stades précoces, en nous appuyant sur des analyses du transcriptome des alevins entiers. Aucun effet significatif de l’alimentation maternelle avec des régimes à base de végétaux n’a été observé sur les descendants avant leur première alimentation, à l'exception d'un poids corporel légèrement inférieur (-13%) à celui des descendants de femelles nourries avec un aliment contenant des FP et HP. En revanche, des effets significatifs de l'alimentation maternelle sur le transcriptome des alevins sont apparus après 3 semaines d'alimentation. L'histoire nutritionnelle de la mère a affecté principalement des gènes impliqués dans la croissance/contraction musculaire et dans les métabolismes énergétique et glucidique. Quelle que soit l'origine maternelle, l’alimentation des alevins avec des aliments contenant des ingrédients végétaux conduit à une régulation positive des gènes impliqués dans le métabolisme des AA/protéines et le métabolisme du cholestérol, ainsi qu’à des changements dans l'expression des gènes impliqués dans le métabolisme glucidique. Enfin, les effets à long-terme de régimes à base de matières premières végétales chez la truite arc-en-ciel ont également été étudiés chez les juvéniles (10g) et les poissons «en croissance» (250-350g), en se focalisant principalement sur l’expression des gènes dans l’intestin et le foie. Cette étude à long-terme a mis en évidence chez les juvéniles des effets subtils sur des gènes intestinaux et hépatiques (transcriptome), avec principalement une augmentation de l’expression des gènes impliqués dans les voies de synthèse des AGPI-LC et du cholestérol chez les poissons nourris avec des régimes à base de plantes. Ces changements d’expression ont été maintenus chez les poissons «en croissance». L'expression de gènes impliqués dans le catabolisme des protéines, le métabolisme des glucides et dans le transport intracellulaire a également été modifiée par les régimes à base de plantes chez les juvéniles, mais ces résultats ne sont pas entièrement confirmés chez les poissons «en croissance». L'ensemble des résultats de cette thèse fournissent des informations originales sur l'utilisation de régimes alimentaires avec des taux de remplacement élevés de FP et d’HP pendant l'ensemble du cycle de vie des poissons, y compris les reproducteurs et les stades précoces, car la majorité des études précédentes avaient concerné la phase de grossissement. Des ajustements de la formule alimentaire sont encore nécessaires pour continuer à optimiser les performances de reproduction et la croissance des poissons d’élevage. / In the last years, the increase in aquaculture production has forced a change in fish feed composition, with increasing substitution of fish meal and fish oil by more available plant sources. In this context, the present PhD work aimed at analyzing the effects of different levels of concomitant dietary replacement of fish meal and fish oil by plant ingredients during the whole life cycle of rainbow trout (from first feeding to reproduction). This work showed for the first time that rainbow trout was able to survive, grow and produce viable offsprings, when fed a totally plant-based diet throughout the whole life cycle. Such dietary replacement resulted in drastic changes in tissues fatty acid profile of broodstock females. However, we found that trout was capable to synthetize n-3 long chain- polyunsaturated fatty acids (LC-PUFA) from dietary precursors and to transfer large amounts of these fatty acids in ova, so that an efficient reproduction can occur. We also studied the potential carry over generation effects of feeding broodstock a totally plant-based diet on progeny and their response to different diets at early stages, using molecular approaches, including the study of the whole body transcriptome. Considering the effects on progeny, the present study confirmed the capability of trout to survive and grow on a plant-based diet, but with slight differences in terms of weight. While no effects of maternal dietary background were observed before first feeding, except slightly lower body weight (-13%), significant effects on the transcriptome of whole body alevins appeared after 3 weeks of feeding. These effects of maternal nutritional history were mainly related to muscle growth/contraction and carbohydrate and energy metabolism. Irrespective of the maternal origin of progeny, first feeding diets containing plant ingredients resulted in up-regulation of genes involved in AA/protein and cholesterol metabolism, as well as in changes in the expression of genes involved in carbohydrate metabolism. Finally, the effects of long-term feeding trout plant-based diets were also studied in juveniles (10g) and ongrowing fish (250-350g), mainly focusing on intestine and liver gene expression. The long term trial in juveniles highlighted subtle effects on both intestinal and hepatic gene expression (transcriptome), mainly related to LC-PUFA and cholesterol biosynthetic pathways, which were enhanced in fish fed the plant based diets. This transcriptional pattern was maintained in ongrowing fish. Genes involved in protein catabolism, carbohydrate metabolism and trafficking were also affected by plant-based diets in juveniles, but these results were not fully confirmed in ongrowing fish. Overall, the results of the present thesis allowed extending the use of diets with high replacement rates of fish meal and fish oil to the whole life cycle of fish, including broodstock and early stages. Adjustments of the feed-formula are still needed to further optimize reproductive and growth performance.

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

La génomique des populations rend possible la mise en évidence de traces de sélection dans le génome. Les travaux effectués considèrent en général une échelle de temps longue (~ 10³ générations). En comparaison, peu d’intérêt a été porté aux études expérimentales de court terme (~ 10 générations). De telles expériences sont pourtant susceptibles de nous renseigner sur la base génétique de caractères complexes. Nous proposons une méthode de vraisemblance basée sur un modèle de Wright-Fisher pour détecter la sélection à partir d’échantillons génétiques temporels acquis sur une période de dix générations. Nous montrons par simulation que notre méthode permet de différencier les signaux dus à la combinaison de la sélection et de la dérive génétique de ceux dus à la dérive seule. Nous montrons également par simulation qu’il est possible d’estimer le coefficient de sélection appliqué à un locus testé. De plus, nous illustrons l’intérêt de notre méthode pour la détection de marqueurs candidats à la sélection au travers de deux études génomiques sur données réelles, chez le diable de Tasmanie (Sarcophilus harrisii) et chez la truite arc-en-ciel (Oncorhynchus mykiss). Ces applications mettent en évidence des régions génomiques candidates pour des phénotypes complexes dans des contextes différents. Dans l’ensemble, nos résultats montrent qu’il est possible de détecter des gènes sujets à une sélection directionnelle intense à partir d’échantillons génétiques temporels, même si la sélection est de courte durée et si les populations examinées ont un faible effectif. / Population genomics makes it possible to detect traces of selection in the genome. Studies in this field have mainly focused on long time scale (~ 10³ generations). In comparison, short-term experimental studies (~ 10 generations) have attracted much less interest. Such experiments are, however, likely to inform us about the genetic basis of complex characters. We propose a likelihood method based on a Wright-Fisher model to detect selection from genetic temporal samples collected over ten generations. We show through simulation that our method can disentangle signals due to the combination of genetic drift and selection to those due to drift alone. We also show through simulation that it is possible to estimate the selection coefficient applied to a tested locus. In addition, we illustrate the interest of our method for the detection of candidate markers for selection through two genome scans performed on real data, in the Tasmanian devil (Sarcophilus harrisii) and in the rainbow trout (Oncorhynchus mykiss). These practical applications highlight candidate genomic regions for complex phenotypes in different contexts. Collectively, our results show the possibility of detecting genes submitted to strong directional selection from genetic time-series, even if selection is applied on a short time period and if the examined populations are small.

Det kommer ske en stor utbyggnad av elektrolys för produktion av vätgas i Sverigeoch övriga världen. För att sänka produktionskostnaden och därmed göra vätgasenbilligare analyserar denna rapport vilket behov av syrgas och värme som en landbaserad fiskodling har, samt hur mycket syrgas och värme fiskodlingen skulle behövaköpa från en elektrolysör. Analysen visar att de arter som används i studien - tilapia(Oreochromis, Oreochromis,. Alcolapia), regnbåge (Oncorhynchus mykiss) och lax(Salmo salar) - i en odling som producerar 40 ton fisk om året skulle förbruka cirka1,16 procent av syrgasen och cirka 0,35 procent av värmen från en 3 MW PEMelektrolysör. Försäljningsvärdet av syrgasen och värmen från en 3 MW elektrolysörberäknas till cirka 695 000 SEK/år för syrgasen och cirka 1 830 000 SEK/år för värmen. Den genomsnittliga kostnaden för syrgas och värme för arterna i studien i enodling på 40 ton/år beräknas till 8900 SEK/år för syrgasen och 6400 SEK/år förvärmen i en landbaserad fiskodling. / There will be a major expansion of electrolysis for production of hydrogen in Sweden and the rest of the world. To reduce production costs and thus make hydrogencheaper, this report analyzes how much oxygen and heat a fish farm consumes andtherefore would need to buy from an electrolyser. The analysis shows that the species used in the study - tilapia (Oreochromis, Oreochromis, Alcolapia), rainbow(Oncorhynchus mykiss) and salmon (Salmo salar) - in a farm that produces 40 tonsof fish per year would consume 1.16 percent of the oxygen and 0,35 percent of theheat produced from a 3 MW PEM electrolyzer. The value of the oxygen and theheat from a 3 MW electrolyser is calculated at SEK 694,939/year for the oxygenand SEK 1,829,813/year for the heat. The average cost for the species in the studyin a 40 tonne/year fish farm is calculated at SEK 8,900/year for the oxygen and SEK6,400/year for the heat in a land-based fish farm.

Tesis por compendio / [ES] La presente tesis doctoral presentaba como principal objetivo contribuir al conocimiento sobre estrategias de alimentación y técnicas de producción que puedan mejorar la sostenibilidad del sector acuícola a través de un enfoque multidisciplinar, evaluando el crecimiento, la salud y la calidad sensorial de los peces, así como la producción de especies vegetales. También se evaluó El impacto ambiental de las diferentes propuestas mediante el análisis del Ciclo de Vida (LCA) como parte de la discusión general de la tesis. El primer estudio evaluó el efecto de la sustitución de diferentes niveles de aceite de pescado (FO) por aceites vegetales en piensos para la seriola mediterránea (Seriola dumerili, Risso, 1810) en el perfil de ácidos grasos (FA) de diferentes tejidos. El perfíl de FA de la grasa visceral, hígado, músculo rojo y blanco cambiaron cuando se modificó la fuente lipídica en el pienso, mientras que el perfíl de FA del tejido cerebro fue bastante resistente a su alteración por los cambios en la dieta. Estos nuevos datos podrían ayudar a evaluar si las funciones fisiológicas claves se conservan cuando los peces son alimentan con dietas con niveles bajos de FO, así como para definir las necesidades de FA en la dieta de la S. dumerili para mejorar la sostenibilidad de la producción y el bienestar de los peces. El segundo estudio evaluó los efectos de un periodo de realimentación en la composición de ácidos grasos en el músculo de la seriola mediterránea. Después de 109 días durante los cuales los peces fueron alimentados con un pienso a base de aceite de pescado (FO 100) o un pienso (FO 0) en la que el FO fue sustituido completamente por aceites vegetales, todos los peces alimentados con la dieta FO 0 fueron sometidos a una realimentamentación con un pienso FO 100, durante 90 días. Un recebo de 90 días puede mejorar parcialmente el perfil de FA en los músculos de la seriola mediterránea previamente alimentada con dietas a base de aceite vegetal.El tercero estudio analizó los efectos de dos densidades de producción (baja - ALD, 3,81 kg m¿3 frente a alta - AHD, 7,26 kg m¿3) sobre el crecimiento, la salud y la calidad de la carne de la trucha arco iris (Oncorhynchus mykiss, Walbaum 1792) así como el rendimiento y calidad microbiológica de la lechuga (Lactuca sativa, L.) producida en un sistema acuapónico de baja tecnología en comparación con el cultivo hidropónico (HYP). Las producciones de trucha arco iris y lechuga fueron exitosas en el sistema acuapónico probado, mientras que la densidad de población no afectó el crecimiento de los peces ni a la calidad de la carne. En el cuarto estudio se evaluó el efecto de la sustitución dietaria de la harina de pescado (FM) por harina de Hermetia illucens (Linnaeus, 1758), parcialmente desgrasada (HI) sobre el crecimiento, la digestibilidad del alimento, la morfología intestinal y la calidad del filete de la trucha arco iris producida en un sistema acuapónico de baja tecnología. El crecimiento de los peces y la calidad del filete no se vieron esencialmente afectados por la sustitución de harina de pescado al 25% con HI. Sin embargo, con una sustitución del 50%, se detectó ciertos efectos sobre la histología intestinal y el color del filete y las características nutricionales, que justifican una mayor investigación. en base a los resultados de esta tesis, los aceites vegetales y la harina de insecto son ingredientes alternativos prometedores para ser incluidos en las dietas de especies marinas y de agua dulce de alto valor económico. Sin embargo, las formulaciones futuras deberán centrarse no solo en las características nutricionales y el coste de los ingredientes, sino también en su impacto ambiental. La acuaponía es una técnica prometedora para la cría de especies de agua dulce de alto valor como la trucha arco iris. Además, la optimización de la densidad de producción de peces en acuaponía es un aspecto clave para obtener altos rendimientos y una buena calidad del producto. / [CA] La present tesi doctoral va tenir com a objectiu contribuir al coneixement sobre estratègies d'alimentació i tècniques de producció que puguin millorar la sostenibilitat del sector aqüícola a través d'un enfocament multidisciplinari, avaluant el creixement, la salut i la qualitat sensorial dels peixos, així com la producció de espècies vegetals. El impacte ambiental de les diferents propostes també es va avaluar mitjançant l'anàlisi de l'Cicle de Vida (LCA) com a part de la discussió general de la tesi. En el primer estudi es va avaluar la substitució de diferents nivells d'oli de peix per olis vegetals en pinsos per a la seriola Mediterrània (Seriola dumerili, Risso, 1810) en el perfil d'àcids grassos (FA) de diferents teixits. El segon estudi es van avaluar els efectes d'un període de realimentació en la composició d'àcids grassos en el múscul de la seriola mediterrània. Un rentat de 90 dies pot millorar parcialment el perfil de FA en els músculs de la seriola mediterrània prèviament alimentada amb dietes a base d'oli vegetal. El tercer estudi va estudiar els efectes de dues densitats de producció (baixa - ALD, 3,81 kg m-3 enfront de alta - AHD, 7,26 kg m-3) sobre el creixement, la salut i la qualitat de la carn de la truita (Oncorhynchus mykiss, Walbaum 1792) i el rendiment i qualitat microbiològica de l'enciam (Lactuca sativa, L.) produïda en un sistema aquapònic de baixa tecnologia en comparació amb el cultiu hidropònic (HYP). En conclusió, les produccions de truita i enciam van tindre èxit en el sistema aquapònic provat, mentre que la densitat de població no va afectar al creixement dels peixos ni a la qualitat de la carn. En el quart estudi es va avaluar l'efecte de la substitució dietària de la farina de peix amb farina de Hermetia illucens (Linnaeus, 1758), parcialment desgreixada (HI) sobre el creixement, la digestibilitat de l'aliment, la morfologia intestinal i la qualitat del filet de la truita produïda en un sistema aquapònic de baixa tecnologia, el creixement dels peixos i la qualitat de l'filet no es van veure essencialment afectats per la substitució de farina de peix al 25% amb HI, mentre que amb una substitució del 50%, es va detectar certs efectes sobre la histologia intestinal i el color del filet i les característiques nutricionals, que justifiquen una major investigació. En conclusió, en base als resultats d'aquesta tesi, els olis vegetals i la farina d'insecte són ingredients alternatius prometedors per a ser inclosos en les dietes d'espècies marines i d'aigua dolça d'alt valor econòmic. No obstant això, les formulacions futures hauran de centrar no només en les característiques nutricionals i el cost dels ingredients, sinó també en el seu impacte ambiental. La aquaponia és una tècnica prometedora per a la cria d'espècies d'aigua dolça d'alt valor com la truita. A més, l'optimització de la densitat de producció de peixos en aquaponia és un aspecte clau per obtenir alts rendiments i una bona qualitat del producte, al temps que es redueix l'impacte ambiental, assegurant la salut i el benestar dels peixos. / [EN] The present PhD thesis aimed at improving the knowledge on feeding strategies and rearing techniques that might improve the sustainability of the aquaculture sector through a multidisciplinary approach, evaluating fish growth performance, health and quality, and vegetable production. The environmental impact of the different solutions was also assessed using a Life Cycle Assessment (LCA) analysis as a part of thesis general discussion. The first contribution evaluated how replacing different levels of fish oil by vegetable oils in the diet of Mediterranean yellowtail, Seriola dumerili (Risso, 1810), affects the fatty acids (FA) signature, i.e. overall FA profile, in different tissues. The FA signatures of red and white muscle, liver, and visceral fat tissues changed when the dietary FA source changed, whereas FA signatures in the brain were rather robust to such dietary changes. The second contribution assessed the effects of a wash-out on the fatty acid composition in the muscles of Mediterranean yellowtail. A 90-d wash-out can partially improve the FA profile in muscles of Mediterranean yellowtail previously fed vegetable oil-based diets. The third contribution investigated the effects of two stocking densities (low - ALD, 3.81 kg m¿3 vs. high - AHD, 7.26 kg m¿3) on the growth, health, and flesh quality of rainbow trout (Oncorhynchus mykiss, Walbaum 1792) and the yield and microbiological quality of lettuce (Lactuca sativa, L.) produced in a low-tech aquaponic system compared to hydroponic cultivation (HYP). Rainbow trout and lettuce productions were successful in the tested aquaponic system, whereas stocking density did not affect fish growth or flesh quality. The fourth contribution evaluated the effects of dietary substitution of fishmeal with partially defatted (Hermetia illucens, Linnaeus, 1758,) meal (HI) on the growth, feed digestibility, gut morphology, and fillet quality of rainbow trout reared in a low-tech aquaponic system fish growth and fillet quality were essentially unaffected by a 25% fish meal replacement with HI, whereas at a replacement rate of 50%, certain effects on gut histology and fillet colour and nutritional characteristics were detected, which warrant further investigation. In conclusion, based on the results of the present thesis, vegetable oils and insect meal are promising alternative ingredients to be included in diets for high-value marine and freshwater carnivorous species. Nevertheless, future aquafeed formulations will be required to focus not only on the nutritional characteristics and costs of the ingredients but also on their environmental impact. Aquaponics is a promising technique to be used for rearing high-value freshwater species such as rainbow trout. Furthermore, the optimization of fish stocking density in aquaponics is a key aspect to obtain high product yields and quality, reducing the environmental impact as well as assuring fish health and welfare. / Thesis written with the financial contribution of ECCEAQUA project (MIUR; CUP: C26C18000030004) / Bordignon, F. (2022). Feeding Strategies and Rearing Techniques for a Sustainable Aquaculture [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/180851 / Compendio