Canada is the fourth largest producer of farmed salmon in the world, with Atlantic salmon being the major species cultivated. Paradoxically British Columbia (BC), which borders the Pacific Ocean, is the major producer province where Atlantic salmon was introduced in the mid-80’s. Escaped salmon may constitute a threat to natural populations of Pacific salmon as they compete for the same resources such as food and spawning territory. A potential solution to the aquaculture industry would be to further develop the aquaculture of native species in the region. The work presented here used semi-natural spawning channels to evaluate the effects of breeding strategies and early-rearing environments on the immune performance of Chinook salmon. Breeding strategy was tested analyzing artificial hatchery practices versus semi-natural propagation in spawning channels. Early-rearing environmental assessment contrasted indoor plastic hatchery tanks with outdoor gravelled-bottom spawning channels. A disease challenge involving over 1400 fish showed interaction effects between breeding strategy and rearing environment. Fish artificially mated presented a disease susceptibility influenced by the rearing environment. The contrary occurred in the offspring of self-breeding brood stock in the spawning channels, as no differences were observed in their susceptibility to the disease regardless of rearing environment. Monitoring of anti-Vibrio anguillarum antibodies during the disease challenge and a follow up of the survivors in sea net pens further confirmed the interaction between breeding strategy and rearing environment. Gene expression in pre- and post-infected artificially propagated fish showed differential gene expression when analyzed with a 695-gene cDNA microarray for Chinook salmon. Genotyping of major histocompatibility (MH) class II β1 alleles showed a tendency of a higher heterozygosity in survivors as expected, as well as a general tendency of a higher heterozygosity in semi-naturally propagated fish. The latter is likely a direct consequence of MH-linked mate choice, which was recently described in Chinook salmon (Neff et al., 2008). To further characterize the mating system of Chinook salmon in the spawning channels, brood stock were genotyped at 12 microsatellite loci. Females and males were found to mate randomly with regards to genetic pairwise relatedness, but they tended to mate with fish of similar condition as revealed by their pairwise differences in Fulton’s condition factor. This work demonstrated that genotype-by-environment interactions can modify the disease resistance of Chinook salmon. More importantly, these effects were seen after just one round of semi-natural spawning of domesticated hatchery fish, suggesting that further studies on spawning channels may highlight other hidden benefits. Therefore, breeding strategy and early-rearing environment should be considered when propagating cultured stocks. The use of more natural propagation methods such as spawning channels could improve the immune performance of Chinook salmon and help to expand the aquaculture of this native species in BC.

Canada is the fourth largest producer of farmed salmon in the world, with Atlantic salmon being the major species cultivated. Paradoxically British Columbia (BC), which borders the Pacific Ocean, is the major producer province where Atlantic salmon was introduced in the mid-80’s. Escaped salmon may constitute a threat to natural populations of Pacific salmon as they compete for the same resources such as food and spawning territory. A potential solution to the aquaculture industry would be to further develop the aquaculture of native species in the region. The work presented here used semi-natural spawning channels to evaluate the effects of breeding strategies and early-rearing environments on the immune performance of Chinook salmon. Breeding strategy was tested analyzing artificial hatchery practices versus semi-natural propagation in spawning channels. Early-rearing environmental assessment contrasted indoor plastic hatchery tanks with outdoor gravelled-bottom spawning channels. A disease challenge involving over 1400 fish showed interaction effects between breeding strategy and rearing environment. Fish artificially mated presented a disease susceptibility influenced by the rearing environment. The contrary occurred in the offspring of self-breeding brood stock in the spawning channels, as no differences were observed in their susceptibility to the disease regardless of rearing environment. Monitoring of anti-Vibrio anguillarum antibodies during the disease challenge and a follow up of the survivors in sea net pens further confirmed the interaction between breeding strategy and rearing environment. Gene expression in pre- and post-infected artificially propagated fish showed differential gene expression when analyzed with a 695-gene cDNA microarray for Chinook salmon. Genotyping of major histocompatibility (MH) class II β1 alleles showed a tendency of a higher heterozygosity in survivors as expected, as well as a general tendency of a higher heterozygosity in semi-naturally propagated fish. The latter is likely a direct consequence of MH-linked mate choice, which was recently described in Chinook salmon (Neff et al., 2008). To further characterize the mating system of Chinook salmon in the spawning channels, brood stock were genotyped at 12 microsatellite loci. Females and males were found to mate randomly with regards to genetic pairwise relatedness, but they tended to mate with fish of similar condition as revealed by their pairwise differences in Fulton’s condition factor. This work demonstrated that genotype-by-environment interactions can modify the disease resistance of Chinook salmon. More importantly, these effects were seen after just one round of semi-natural spawning of domesticated hatchery fish, suggesting that further studies on spawning channels may highlight other hidden benefits. Therefore, breeding strategy and early-rearing environment should be considered when propagating cultured stocks. The use of more natural propagation methods such as spawning channels could improve the immune performance of Chinook salmon and help to expand the aquaculture of this native species in BC.

Les microARN sont des petits ARN non-codant impliqués dans la régulation de multiples fonctions biologiques dont la réponse immunitaire. L'infection par un pathogène induit un changement transcriptomique fort chez l'hôte. Cependant, la variabilité de ces dérégulations reste encore mal décrite. Cette thèse avait pour principaux objectifs de mieux comprendre la spécificité et la variabilité de la réponse des microARN chez l'homme ainsi que mettre en évidence les bases génétiques de cette diversité en utilisant comme modèle l'infection des cellules dendritiques par Mycobacterium tuberculosis (MTB). Nous avons utilisé une approche ex vivo et des techniques à haut débit dans le but de décrire la réponse des microARN suite à l'infection par MTB dans la population générale, et de la comparer à celle induite par d'autres mycobactéries et bactéries intracellulaires. Nous montons que l'infection modifie profondément l'expression des microARN ainsi que la diversité de leurs isoformes, dont un certain nombre de microARN sont impliqués dans une réponse très conservée. Nos résultats soulignent aussi l'effet de l'infection sur les réseaux de régulation de l'expression des gènes impliquant les microARN et montrent que l'expression de 3% de ces transcrits peut-être corrélée à un marqueur génétique. Grâce à l'intégration de ces différentes analyses, nous proposons certains microARN candidats qui pourraient jouer un rôle dans la variabilité de la réponse immunitaire. L'ensemble de nos résultats constitue la première tentative de compréhension de l'architecture génétique de la réponse des microARN et apporte un nouvel éclairage sur le rôle de ces transcrits dans la réponse antibactérienne. / MicroRNAs (miRNAs) are important epigenetic regulators of gene expression that play a key role in many biological processes, including the immune response. Although infection is accompanied by marked changes in the transcriptional profiles of host cells, little is known about the variability of host miRNA responses to infection. In this thesis, we aimed to define the extent and specificity of pathogen-induced miRNA transcriptional responses of host cells, and to characterise the genetic basis of miRNA variability upon infection, using the model of Mycobacterium tuberculosis (MTB) infection of human dendritic cells. To this end, we have combined ex vivo approaches with a range of high-throughput genomic techniques to profile miRNA responses to MTB at the population-level and to compare this response with other mycobacterial and non-mycobacterial infections. We show that miRNAs display marked changes in expression and in isomiR distribution upon infection that are highly consistent across diverse bacteria, demonstrating the presence of a strong core miRNA response to bacterial infection. Our results highlight the impact of infection on miRNA-mediated gene regulatory networks and show that the expression of 3% of miRNAs are controlled by proximate expression quantitative trait loci (eQTLs) and identify a number of candidate miRNAs that may play a role in variability in the immune response to infection. Together, these results provide the first assessment of the impact of genotype-environment interactions on the regulation of miRNA expression, as well as offering novel insights into the specificity of these miRNAs in the response to mycobacterial infections.

In addition to habitat loss and fragmentation, habitat degradation can have important consequences for biodiversity and population persistence, including effects on ecological and genetic processes beyond decreased demographic viability and the loss of genetic variation. Particularly interesting is the potential for evolutionary changes and adaptation to degraded habitats, that can affect population viability even in the short-term. Here, I explore how environmental changes after habitat degradation affect the evolutionary dynamics of populations of the rainforest cycad Zamia fairchildiana, specifically how habitat degradation affects gene dispersal, inbreeding, directional selection, and genotype-by-environment interactions, and the potential for genetic differentiation between populations. Colonies of Z. fairchildiana showed little genetic differentiation in neutral molecular markers across study sites, thus can be considered as subpopulations. Subpopulations in the disturbed habitat are experiencing different environmental conditions when compared to subpopulation in their native habitat. Disturbed-habitat subpopulations showed a faster life-history. This faster life history is associated with a weaker spatial genetic structure and higher levels of inbreeding in the disturbed-habitat subpopulations. In addition, higher light availability in the disturbed habitat seems to be a major agent of selection on traits like leaf production that have the potential to respond to selection in these subpopulations. Different traits were under selection in the native-habitat subpopulations, suggesting the potential for genetic differentiation between native and disturbed-habitat subpopulations. Genotype by environment interactions in seed germination and seedling survival, in response to light and water availability, further suggested that subpopulations can adaptively diverge between habitats, but the relative role of genetic and environmental factors, particularly maternal effects, on the magnitude and rate of genetic differentiation between subpopulations remains to be evaluated. These results suggest that habitat degradation can have important consequences for the evolutionary dynamics of populations of this cycad, not necessarily typical of habitat loss and fragmentation. This study identified factors and processes important for population persistence in degraded habitats, but population responses to habitat degradation are complex. Thus further studies and long-term experiments are required for better understanding the effects of habitat degradation on population viability.

Made available in DSpace on 2015-03-26T13:42:15Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1405747 bytes, checksum: c75e615e150ddd0e86f3240d84082166 (MD5) Previous issue date: 2009-07-17 / The aim was to determine the genetic parameters of progeny tests in Eucalyptus grandis Hill Maiden with 3 years old under competicional effect, as well as to study the genotype x environment interaction and its impact on strategies for direct and indirect selection and analyze different selection strategies like selection among and within, mass, stratified mass selection and combined selection in three different locations of the Company Jari Celulose S/A. The experimental design was a randomized block with 93 half-sib progenies, 10 replications, linear plots of five plants and spacing of 3m x 2m. The evaluated characteristics were height (ALT), in meters, diameter at breast height (DBH) in cm and the volume (VOL) in m3. It were estimated selection gains with a percentage of 20% between half-sib and 40% within, the same being maintained for all selection strategies analyzed. It was detected high plants mortality in the experiments, which interfered with the accuracy of the experiments. The progeny tests showed genetic variability, with greater variability within plots. It was also detected competicional effect observed by the negative intraclass correlation among plants within plots. Its existence interfered in the estimates of phenotypic variance within plots and environmental variance. In the interaction study were found significant effects for genotypes and also for the genotype x environment interaction, showing variability among progenies and differential behavior along these different environments. Regarding to the analised places, local 2 and 3 showed no significant interaction. The site has major direct gain and maximized the gain for the other two locals was the local 2. To analyze the selection gain with different strategies such as selection among and within, mass selection, stratified mass selection and combined selection, the analysis were done only with DAP, because of its high correlation with other variables. The combined selection strategy showed superior results to the selection processes among and within, mass and stratified with percentages estimates ranging from 6.67% to 18.67%. / O objetivo deste trabalho foi a determinação dos parâmetros genéticos de testes de progênies de Eucalyptus grandis Hill Maiden com 3 anos de idade sob efeito competicional, assim como estudar a interação genótipo x ambiente e seus reflexos nas estratégias de seleção direta e indireta e analisar diferentes estratégias de seleção como seleção entre e dentro, massal, massal estratificada e seleção combinada, em três diferentes locais da empresa Jari Celulose S/A. O delineamento experimental utilizado foi de blocos casualizados, com 93 progênies de meios irmãos, 10 repetiçõe, parcelas lineares de 5 plantas e espaçamento de 3m x 2 m. As características avaliadas foram a altura (ALT), em metros, diâmetro à altura do peito (DAP), em cm e o volume (VOL), em m3. Foram estimados os ganhos de seleção com uma percentagem de 20% entre e 40% dentro, sendo as mesmas mantidas para todas as estratégias de seleção analisadas. Foi detectado elevada mortalidade das plantas nos experimentos, que interferiu na precisão dos experimentos. Os testes de progênies apresentaram variabilidade genética, sendo maior variabilidade dentro de parcelas, também foi detectado o efeito competicional, observada pela correlação intraclasse negativa entre plantas dentro de parcelas. Sua existência interferiu nas estimativas de variância fenotípicas dentro de parcelas e variância ambiental. No estudo da interação foram detectados efeitos significativos para genótipos e também para a interação genótipo x ambiente, evidenciando variabilidade entre as progênies avaliadas e comportamento diferencial destas ao longo dos diferentes ambientes. Em relação aos locais analisados, os locais 2 e 3 apresentaram interação não significativa. O local que possui maior ganho direto e maximizou o ganho para os demais locais foi o local 2. Para analisar o ganho de seleção com as diferentes estratégias como seleção entre e dentro, seleção massal, massal estratificada e seleção combinada, as análises foram realizadas somente com a variável DAP, devido sua alta correlação com as demais variáveis. A estratégia de seleção combinada apresentou resultados superiores aos processos de seleção entre e dentro, massal e massal estratificada, com estimativas em percentuais variando de 6,67% a 18,67%.

Prédire les réponses de la biodiversité aux changements climatiques anthropiques est devenu un champ de recherche avec des enjeux scientifiques et sociétaux majeurs. Mon travail de thèse a consisté à évaluer les impacts du réchauffement climatique sur un parasitoïde de drosophiles, Leptopilina boulardi, à une petite échelle géographique, le sud-est de la France. L'objectif était non seulement d'examiner l'évolution de la distribution du parasitoïde en réponse à une hausse des températures qu'il fallait préciser à cette échelle géographique, mais aussi d'appréhender les adaptations mises en place dans la zone de progression de l'espèce. Dans un premier temps, l'analyse de données d'échantillonnages et de données météorologiques m'ont permis de mettre en évidence une rapide expansion de l'aire de répartition du parasitoïde vers le nord, à un taux moyen de 90km/décennie, simultanément à une augmentation moyenne de la température de 1,57°C ces 30 dernières années, dans l'aire d'étude. Après avoir identifié les principaux facteurs environnementaux, structurant la répartition spatiale de L. boulardi, j'ai modélisé sa distribution potentielle dans le sud-est de la France, sous conditions climatiques actuelles et pour 2050, pour deux scénarios d'émission de CO2. En 2050, la distribution géographique de L. boulardi devrait considérablement s'étendre vers le nord sous l'effet des changements climatiques. Ensuite, en mesurant plusieurs traits d'histoire de vie selon 4 régimes thermiques fluctuants, j'ai montré que les populations de L. boulardi situées en limite d'aire de répartition sont génétiquement différenciées de celles situées dans l'aire centrale de répartition. Le fait que les populations marginales aient une valeur sélective plus importante à faible température suggère une adaptation locale des parasitoïdes dans la zone de progression de l'aire de répartition. La dernière partie de ce travail de thèse a pour objectif de mieux comprendre le processus de colonisation de L. boulardi. Pour cela, j'ai entrepris le développement de marqueurs RAD-sequencing sur 15 populations de cette espèce, distribuées le long d'un cline de latitude dans le sud-est de la France. Les nombreuses données issues du séquençage Illumina me permettront de connaître la structuration génétique de ces populations. L'ensemble de ces résultats obtenus au cours de ma thèse révèlent la force avec laquelle les changements climatiques peuvent impacter les espèces, principalement celles de haut niveau trophique, en provoquant des changements très rapide de distribution et des modifications génotypiques et phénotypiques permettant une meilleure adaptation locale / Predicting biodiversity responses to anthropogenic climate change has become a field of research with major scientific and societal issues. The main goal of my thesis was to evaluate the impacts of global warming on a Drosophila parasitoid, Leptopilina boulardi, at a small geographical scale, the South-East of France. The aim was not only to examine the change in the distribution of the parasitoid in response to rising temperatures, but also to understand the adaptations associated with this change. First, the analysis of insect sampling and meteorological data allowed me to demonstrate a rapid expansion of the parasitoid range to the north with an average rate of 90km/decade as well as a simultaneous temperature increase of 1.57°C on average over the past 30 years in the studied area. Following the identification of the main environmental factors structuring the spatial distribution of L. boulardi, I fitted a model predicting its potential distribution in the south-east of France, under the current climate and in 2050, for two CO2 emission scenarios. In 2050, the geographical distribution of L. boulardi should significantly extend northward as a result of climate change. Then, by measuring several life history traits under four fluctuating temperature regimes, I have shown that populations of L. boulardi located on the border of the range are genetically differentiated from those in the central range. The fact that marginal populations have a greater fitness at low temperature suggests local adaptation of parasitoids in the area of progression of range. The last part of this thesis aimed to better understand the process of colonization of L. boulardi. For this, I undertook the development of RAD-sequencing markers to genotype 15 populations of this species distributed along a cline of latitude in the southeast of France. Numerous data from Illumina sequencing will allow me to characterize the genetic structure of the populations. All the results obtained in my thesis highlight the force with which climate change may impact species, in particular those of high trophic level, causing rapid changes in distribution along with genotypic and phenotypic changes underlying local adaptation