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La perchaude (Perca flavescens) constitue une ressource socioéconomique de grande importance dans le Lac Saint-Pierre (Québec, Canada). Bien que ce lac fluvial soit désigné réserve de la biosphère par l’UNESCO, le statut de la perchaude est préoccupant. Afin de permettre à l’espèce de persister en fonction des diverses pressions anthropiques, il est important de comprendre sa dynamique populationnelle et les mécanismes qui en sont responsables. La perchaude est connue pour sa philopatrie ; le fait de toujours se reproduire à son site de naissance peut entraîner la subdivision d’une espèce en de multiples populations, où chacune pourra être pourvue d’adaptations locales distinctes. Il est possible d’étudier ces processus à l’aide des signaux génétiques associés à la reproduction des individus. Toutefois, une faible différentiation génétique entre les populations du Lac Saint-Pierre est envisagée en raison de la colonisation récente du système (moins de 8000 ans). L’objectif de cette étude est de déterminer s’il existe plusieurs populations de perchaude dans le Lac Saint-Pierre. Les simulations réalisées ont révélé que l’utilisation de marqueurs AFLP (amplified fragment length polymorphism), permettant une analyse globale du génome, affiche une meilleure détection de la différentiation des populations que celle des marqueurs microsatellites. Afin d’associer les individus à leur site de naissance, la méthode d’AFLP et des microsatellites ont été utilisées sur des larves capturées suite à l’éclosion des oeufs. Trois analyses distinctes d’AFLP ont indiqué une corrélation entre la composition génétique des individus et des sites géographiques, confirmant ainsi la présence de plusieurs populations sympatriques dans le Lac Saint-Pierre, découlant vraisemblablement de la philopatrie de l’espèce. L’absence de différentiation génétique relatée par les marqueurs microsatellites vient confirmer l’importance du choix des marqueurs génétiques. Bien que la différentiation génétique observée soit relativement faible, la gestion de la perchaude devrait tenir compte de la dynamique des populations distinctes dans ce système. / Yellow perch (Perca flavescens) is a commercially-exploited freshwater fish species in Lake Saint-Pierre (Quebec, Canada). Even if this fluvial lake is designated as a biosphere reserve by UNESCO, the yellow perch status is of concern. To ensure the persistence of species facing to anthropogenic pressures, understanding dynamics and mechanism that structure populations are of major importance. Because the habitat characteristics are spatially structured and this species is known to display natal site fidelity, a subdivision of the species in multiple populations and local adaptations may occur. It is possible to detect these processes according to genetic signal associated with individuals’ reproduction. However, low genetic differentiation is hypothesised due to the recent colonization of the system (< 8 K years). This study aims at determining if there are multiple populations of yellow perch in Lake Saint-Pierre. Simulations was first performed to confirm that population differentiation is better depicted by amplified fragment length polymorphism (AFLP) than microsatellite markers. In order to associate individuals to their site of birth, larvae captured after hatching were used. A survey of the variation throughout the entire genome was then performed by using the AFLP approach and variations at microsatellite loci were used to further investigate the organization of these populations. Three distinct AFLP analyses indicated a correlation between genetic composition of individuals and spawning sites, and thus confirmed the presence of multiple sympatric populations in Lake Saint-Pierre, resulting likely from natal site fidelity. At the opposite, the lack of genetic differentiation reported by microsatellites markers confirms the importance of the choice of genetic markers. While the genetic differentiation is very low, the management of this species should take into account the existence of distinct population structures in this system.

The thesis was focused on the microevolutionary mechanisms that contribute to morphological diversity in selected members of the sedge family (Cyperaceae). Natural hybridization, evidenced from both morphological characters and molecular markers, was revealed to be a potentially important source of diversification in the tropical spikerushes of Eleocharis subgenus Limnochloa. High levels of phenotypic plasticity of clonal growth but rare genetic (ecotypic) differentiation among contrasting morphotypes were found in the polymorphic species Carex nigra, which implied that taxonomic splitting of the species was unreasonable.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Apomixis is an asexual mechanism of reproduction through seed formation with clonal embryos. The high rate of polyembryonic seeds is usually an indicative for the occurrence of sporophytic apomixis and in Bignoniaceae the expression of sporophytic apomixis seems to be related to polyploidy. Handroanthus ochraceus and H. chrysotrichus are two tree species of Bignoniaceae that area morphologically related, which usually leads to identification problems. Handroanthus ochraceus has self-incompatible non-apomictic and monoembryonic populations and self-fertile sporophytic apomictic and polyembryonic populations. H. chrysotrichus has only self-fertile, sporophytic apomictic and polyembryonic populations recognized until now. To understand the genetic and phenotypic consequences of this reproductive mosaic in these populations it were conducted molecular and morphological analysis in the present study. The aims of molecular analyzes were to verify the genetic variability of H. ochraceus populations, compare the genetic diversity parameters investigating the propose of a possible relationship between the reproductive systems and genetic diversity in this species and still understand the possible relationships between apomictic and non-apomictic populations. The ten primers resulted in 104 fragments and the genetic diversity parameters showed a high mean for the populations (P = 66.35%, I = 0.341 and He = 0.227). In this study no clones were detected. The AMOVA analysis showed the higher variation within populations (61%), like allogamous populations. Cluster analysis and Bayesian analysis of genetic assignment determined two distinct groups, one consisting of two non-apomictic populations, Pires do Rio and Biribiri, and other gathering the apomictic populations and the non-apomictic from Uberlândia. The strong relationship between the self-incompatible population of Uberlândia and the apomictic populations indicates separate origins for non-apomictic populations of H. ochraceus. This relationship between self-incompatible population of Uberlândia and self-fertile populations suggest that these non-apomictic individuals may have the same genetic constitution of a possible ancestral population of self-fertile populations. The morphological analysis aimed to find differences between monoembryonic and polyembryonic populations of H. and morphological traits to separate the H. chrysotrichus and H. ochraceus. With this purpose non-apomictic monoembryonic populations and apomictic polyembryonic populations of H. ochraceus and an apomictic polyembryonic population of H. chrysotrichus were analyzed. Qualitative and quantitative morphological characteristics of leaf, flower and fruit were evaluated through univariate and multivariate analyzes. The pollen grain area, the length of peduncles, the width of stigma and the number of extrafloral nectaries in the calyx showed higher values for polyembryonic populations of H. ochraceus so they could be an evidence of polyploidy in H. ochraceus, since these larger measures may be associated with the cell volume increase usually entailed by polyploidy. Several morphological characters separated H. ochraceus from H. chrysotrichus, which can support the identification of individuals and the distinction between the two species. Therefore, the morphometric analysis determined that morphological features can make a distinction between mono and polyembryonic populations of H. ochraceus and the association of this methodology with reproductive biology analysis can be a complement for the determination of ploidies and reproductive system in both species. / A apomixia é um mecanismo de reprodução assexuada através da formação de sementes com embriões clonais. A elevada taxa de sementes poliembriônicas é um indicativo da ocorrência da apomixia esporofítica e, em Bignoniaceae a expressão da apomixia esporofítica parece estar vinculada à poliploidia. Handroanthus ochraceus e H. chrysotrichus são duas espécies arbóreas de Bignoniaceae morfologicamente semelhantes, o que normalmente ocasiona problemas de identificação. Handroanthus ochraceus apresenta populações autoincompatíveis, não apomíticas e monoembriônicas, e populações autoférteis, apomíticas esporofíticas e poliembriônicas. Já H. chrysotrichus apresenta apenas populações autoférteis, apomíticas esporofíticas e poliembriônicas conhecidas. Para compreender as consequências genéticas e fenotípicas deste mosaico reprodutivo foram realizadas análises moleculares e morfológicas. As análises moleculares tiveram por objetivos determinar a variabilidade genética de populações de H. ochraceus, comparar os parâmetros de diversidade genética, averiguar a possível relação entre os sistemas reprodutivos e a diversidade genética na espécie e ainda compreender as possíveis relações entre populações apomíticas e não apomíticas. Os dez primers ISSR utilizados resultaram em 104 bandas e os parâmetros de diversidade genética apresentaram uma média elevada para as populações (P = 66,35%, I = 0,341 e He = 0,227). Não foram detectados clones nas amostras populacionais. O cálculo da AMOVA demonstrou alta variação genética dentro das populações (61%), semelhante a populações alógamas. A análise de agrupamento e a análise Bayesiana de atribuição genética determinaram a formação de dois grupos distintos, um constituído por duas populações não apomíticas, Pires do Rio e Biribiri, e o outro reunindo as populações apomíticas e a não apomítica de Uberlândia. A forte relação entre a população autoincompatível de Uberlândia e as apomíticas indica origens distintas para as populações não apomíticas de H. ochraceus. Esta relação entre a população autoincompatível de Uberlândia e as populações autoférteis permite supor que os indivíduos não apomíticos dessa população apresentem a mesma constituição genética de uma possível população ancestral das populações autoférteis. As análises morfológicas tiveram por objetivo buscar diferenças entre populações mono e poliembriônicas de H. ochraceus e determinar características morfológicas que auxiliam na separação de H. ochraceus e H. chrysotrichus, para isso populações reconhecidamente monoembriônicas não apomíticas e poliembriônicas apomíticas de H. ochraceus e uma população poliembriônica apomítica de H. chrysotrichus foram analisadas. Características qualitativas e quantitativas de folha, flor e fruto foram avaliadas utilizando análises estatísticas univariadas e multivariadas. As características área do grão de pólen, comprimento do pedicelo, largura do estigma e número de nectários extraflorais no cálice apresentaram maiores valores para populações poliembriônicas de H. ochraceus e poderiam ser uma evidencia de poliploidia em H. ochraceus, pois, podem estar associadas ao aumento do volume celular geralmente acarretado pela poliploidia. Diferentes características morfológicas separaram as populações de H. ochraceus da população de H. chrysotrichus, as quais podem auxiliar na identificação de indivíduos e na distinção das espécies. Assim as análises morfométricas determinaram que características morfológicas de alguma forma podem distinguir populações mono e poliembriônicas de H. ochraceus, e em conjunto com análises de biologia reprodutiva podem ser uma metodologia auxiliar na determinação da ploidia e sistema reprodutivo. / Mestre em Genética e Bioquímica

Examiner les liens existant entre la variabilité environnementale, les traits d'histoire de vie, la dispersion et les décisions d'accouplement est un enjeu central en Ecologie et en Evolution. J'ai exploré ces questions chez un amphibien, le sonneur à ventre jaune (Bombina variegata). Dans le premier volet de ma thèse, je me suis intéressé à l'influence des variations spatiotemporelles de l'environnement sur les patrons de covariation entre les traits d'histoire de vie, la dispersion et les types comportementaux à l'échelle inter-populationnelle. J'ai examiné comment le degré de stochasticité interannuel de l'habitat de reproduction régule le positionnement des populations le long du slow-fast continuum et génère des syndromes de dispersion parmi les populations. J'ai ensuite analysé les conséquences de ces syndromes sur les patrons de différenciation génétique au sein des populations. Dans le second volet de ma thèse, je me suis intéressé au rôle de la canalisation environnementale dans la stratégie d'histoire de vie de B. variegata et j'ai évalué comment diverses formes de variations météorologiques pouvaient affecter la dynamique de différentes populations. Dans chacune d'elles, j'ai mesuré l'impact de facteurs météorologiques sur des paramètres démographiques tels que la survie, le recrutement et les probabilités de reproduction. Dans le troisième et dernier volet de ma thèse, je me suis intéressé au choix d'accouplement des femelles, en examinant successivement les hypothèses de bons gènes et de gènes compatibles puis en me focalisant sur le rôle de la qualité et de la disponibilité des sites de reproduction sur les décisions d'accouplement des femelles / Investigating the links between environmental variability and life history traits, dispersal and breeding decisions is critical challenge for ecologists. I have examined this issue in anuran, the yellow-bellied toad (Bombina variegata). In the first part of my thesis, I have examined the influence of spatio-temporal variation of the environment on the covariation patterns between life history traits, dispersal and behavioral types at inter-population scale. I have investigated how the level of breeding habitat stochasticity may regulate the position of B. variegata populations along the slow-fast continuum and may promote dispersal syndromes among populations. Then I have analyzed the consequence of such dispersal syndromes on population genetic differentiation. In the second part of my thesis, I have focused on the role of the environmental canalization in the life history strategy of B. variegata and I have evaluated how various forms of weather variation (mean and extreme events) could affect the dynamics of different populations. In each studied populations, I have quantified the impacts of weather variation on various demographic parameters as survival, recruitment and breeding probabilities. In the third part of my thesis, I have investigated female mate choice in B. variegata by successively examining good genes and compatible gene hypotheses, and then by evaluating the role of breeding habitat quality and availability on mating decisions

The Atlantic cod (Gadus morhua L.) fishery is of great economic importance to the Faroese economy. There are two separately managed cod stocks around the Faroe Islands, the Faroe Plateau and the Faroe Bank cod. Both have experienced dramatic decreases in size and informed management decisions are vital for both stock viability and exploitation. The stocks are geographically isolated by an 800 m deep channel and water temperatures are on average 1 – 2 ºC higher on the Faroe Bank than on the Faroe Plateau. There are clear phenotypic differences between the stocks; in particular, the markedly higher growth rate for the Faroe Bank cod has caught public and scientific attention. There is continuing debate regarding the relative importance of genetics and environmental contributions to the contrasting phenotypes. Analyses of reproductive parameters (field data and experimental captive spawnings) as well as analyses of microsatellite and single nucleotide polymorphism (SNP) markers were undertaken to better resolve the issue. Field data as well as data from experimental captive spawnings provided evidence of reproductive differences between Faroe Plateau and Faroe Bank cod. Peak spawning occurred earlier on the Faroe Plateau than on the Faroe Bank and this difference in timing of spawning was maintained in captivity. In particular, differences in sizes of eggs (average diameters of 1.40 and 1.30 mm for Faroe Plateau and Faroe Bank cod eggs, respectively) and indirect evidence of greater volumes spawned by the Faroe Bank females suggested stock differences with respect to egg size – egg number trade-off. It was hypothesised that the strategy adopted by cod on the Faroe Bank, with a higher number of smaller eggs, evolved in response to a more hostile environment (bare seabed and higher exposure to predators) experienced by early life stages in this area. Experimental captive spawnings with Faroe Bank cod showed a large interfamily skew in survival rates of cod eggs and fry. Egg size was identified as a useful indicator of survival rates in the egg stage, but egg survival rates could not be used to predict viability in later developmental stages, thus highlighting the importance of employing some sort of genetic monitoring of cod fry to ensure sufficient family representation in the progeny. While no tank effect was evident concerning fry survival, a significant tank effect was identified concerning body sizes of fry. Microsatellite data were analysed using large sample sizes of Faroe Plateau and Faroe Bank cod with the Faroe Plateau divided into two locations, Faroe Plateau North-East and Faroe Plateau West (cod from each of the two were known to belong to separate spawning grounds). Two Norwegian coastal cod samples were included as outlier populations. While no genetic differentiation was detected between the two Faroe Plateau locations, these analyses revealed a detectable, albeit relatively modest, degree of genetic differentiation between cod from the Faroe Plateau and the Faroe Bank (FST = 0.0014 and 0.0018; DJost_EST = 0.0027 and 0.0048; P < 0.0001 and P < 0.001 for the Faroe Plateau North-East – Faroe Bank and the Faroe Plateau West – Faroe Bank comparisons). These values were several times smaller than those between Faroese and Norwegian coastal cod (pairwise FST and DJost_EST values in the range of 0.0061 – 0.0137 and 0.0158 – 0.0386, respectively). Despite recent reductions in census population sizes for Faroe Plateau and, particularly, Faroe Bank cod, genetic diversity estimates were comparable to the ones observed for Norwegian coastal cod and there was no evidence of significant genetic bottlenecks. Lastly, data for one of the markers (Gmo132) indicated genotype-dependent vertical distribution of cod (as investigated for Faroe Plateau North-East cod). Contrary to some previously published studies, analysis of SNPs of two candidate genes for adaptive divergence, the hemoglobin gene Hb-ß1 and the transferrin gene Tf1, failed to detect differentiation between samples of Faroe Plateau and Faroe Bank cod analysed in this thesis. Of 3533 novel SNPs simultaneously discovered and genotyped by restriction-site associated DNA (RAD) sequencing, 58 showed evidence of genetic differentiation between Faroe Plateau North-East and Faroe Bank cod (P < 0.05). No single locus was fixed for different alleles between Faroe Plateau and Faroe Bank cod. A set of eight informative SNPs (FST values between Faroe Plateau and Faroe Bank samples > 0.25; P < 0.0005) were selected for validation in larger samples, that included cod from both Faroe Plateau areas and the Faroe Bank as well as Norwegian coastal and White Sea cod. Six out of the eight loci amplified successfully with a PCR-based method and there was 100 % concordance between genotypes of individuals screened by both techniques. Due to ascertainment bias, the SNPs should only be applied with caution in a broader geographical context. Nonetheless, these SNPs did confirm the genetic substructure suggested for Faroese cod by microsatellite analyses. While no genetic differentiation was evident between the two Faroe Plateau locations, significant genetic differentiation was evident between Faroe Plateau and Faroe Bank cod at five of the SNPs (FST values in the range of 0.0383 – 0.1914). This panel of five SNPs could confidently be used to trace groups of Faroe Plateau and Faroe Bank cod to their population of origin. In conclusion, multiple lines of evidence demonstrate that Faroe Plateau and Faroe Bank cod are truly two genetically distinct populations. While the findings contribute to a broader understanding of the biology and the genetics of Faroe Plateau and Faroe Bank cod, the novel SNPs developed may provide a valuable resource for potential future demands of i.e. genetic stock identification methods.

Tous les individus ne répondent pas de la même façon à un même traitement médicamenteux, tant sur le plan pharmacologique (efficacité) que sur le plan toxicologique (effets indésirables). Des facteurs génétiques affectant la pharmacocinétique et la pharmacodynamie des médicaments jouent un rôle déterminant dans cette variabilité interindividuelle de réponse. Certains de ces facteurs sont distribués de manière hétérogène entre les populations humaines. Ces différences s’expliquent en partie par des phénomènes d’adaptation locale des populations à leur environnement. Au cours de son histoire, l’homme a dû en effet faire face à des changements de son environnement chimique, qui ont entraîné des pressions de sélection naturelle sur les gènes intervenant dans la réponse de l’organisme aux xénobiotiques. Ce sont ces mêmes gènes qui, aujourd’hui, influencent la réponse aux médicaments.La formidable accélération des progrès de la génétique donne accès aujourd’hui à la variabilité génétique des populations humaines sur l’ensemble du génome, facilitant la découverte et la compréhension des mécanismes génétiques à l’origine des traits complexes comme la réponse aux médicaments. Les outils de la génétique des populations permettent notamment d’identifier des variants affichant un niveau de différenciation génétique inhabituel entre les populations humaines et de déterminer dans quelle mesure la sélection naturelle a joué un rôle dans les profils atypiques observés.Dans cette thèse, nous avons appliqué ces outils à des données de génotypage et de séquençage pour analyser les profils de différenciation génétique des populations humaines pour les gènes de la réponse aux médicaments. Nous avons ainsi démontré qu’une sélection positive récente en Asie de l’Est dans la région génomique du gène VKORC1 était responsable d’une hétérogénéité de distribution du variant fonctionnel de VKORC1, à l’origine des différences de sensibilité génétique aux anticoagulant oraux de type antivitamine K entre les populations humaines. Puis, en étendant notre analyse à l’ensemble des pharmacogènes majeurs, nous avons identifié de nouveaux variants potentiellement intéressants en pharmacogénétique pour expliquer les différences de réponse aux médicaments entre les populations humaines et les individus. Enfin, l’étude approfondie du gène NAT2 nous a permis de révéler un processus de sélection homogénéisante ciblant un variant fonctionnel associé à un phénotype d’acétylation très lent. Ces résultats soulignent l’influence déterminante de la sélection naturelle dans la variabilité de réponse aux médicaments entre les populations et les individus. Ils montrent l’apport de la génétique des populations pour une meilleure compréhension de la composante génétique de la réponse aux médicaments et des traits complexes. / Response to drug treatment can be highly variable between individuals, both in terms of therapeutic effect (efficacy) and of adverse reactions (toxicity).Genetic factors affecting drug pharmacodynamics and pharmacokinetics play a major role in this inter-individual variability. Some of these factors are heterogeneously distributed among human populations. Local adaptation of populations to their environment partly explained those differences. Indeed,during human evolution, populations had to cope with changes in their chemical environment that triggered selective pressures on genes involved in xenobiotic response. Those genes are the same ones that influence drug response today.The tremendous recent advances in genotyping and sequencing technologies now provide access to the genome-wide patterns of genetic variation in a growing number of human populations, facilitating our understanding of the genetic mechanisms underlying complex traits such as drug response. Population genetic tools allow the identification of variants showing an unusual pattern of genetic differentiation among human populations and the determination of the role played by natural selection in shaping the atypical patterns observed.In this thesis, we have applied these tools on both SNP-chip genotyping data and Next Generation Sequencing data to analyze the genetic differentiation patterns of human populations for genes involved in drug response. We show that a nearly complete selective sweep in East Asia in the genomic region of the VKORC1 gene is responsible for an heterogeneous distribution of theVKORC1 functional variant and can explain the inter-population genetic differences in response to oral anti-vitamin K anticoagulants. Extending the analysis to all major pharmacogenes, we have identified new variants of potential relevance to pharmacogenetics which could explain inter-population and inter-individual differences in drug response. Finally, by a comprehensive analysis of the NAT2 gene, we evidence a homogenizing selection process targeting a functional variant associated with a very slow acetylation phenotype. These results emphasize the crucial role of natural selection in the inter-population and inter-individual drug response variability.They also illustrate the relevance of population genetics studies for a better understanding of the genetic component underlying drug response and complex traits.

No description available.