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Understanding how migration, genetic drift, and natural selection interact to maintain the genetic and phenotypic variation we observe in natural populations is a central goal of population genetics. Amphibians provide excellent model organisms for investigating the interplay between these evolutionary forces because amphibians are generally characterized by limited dispersal abilities, high philopatry, and are obligately associated with the areas around suitable habitats (e.g. breeding ponds). Thus, on relatively small geographic scales, the relative effects of all of these evolutionary forces can be studied together. Here, we study the interaction of migration, genetic drift, natural selection, and historical process in the ornate chorus frog (Pseudacris ornata). We report the development and characterization of 10 polymorphic microsatellite genetic markers. Number of alleles per locus ranged from 2 to 21 averaging 9.2 and expected heterozygosities ranged from 0.10 to 0.97 averaging 0.52. However, in an analysis of two populations, three locus-by-population comparisons exhibited significant heterozygote deficiencies and indicated that null alleles may be present some loci. Furthermore, we characterized genetic structure and historical biogeographic patterns in P. ornata using these microsatellite markers along with mitochondrial DNA sequence data. Our data indicate that in these frogs, migration may play a large role in determining population structure as pairwise estimates of FST were relatively small ranging from 0.04 to 0.12 (global FST = 0.083). Additionally, we observed an overall pattern of isolation-by-distance in neutral genetic markers across the species range. Moreover, our data suggest that the Apalachicola River basin does not impede gene flow in P. ornata as it does in many vertebrate taxa. Interestingly, we identified significant genetic structure between populations separated by only 6 km. However, this fine scale genetic structure was only present in the more urbanized of two widespread sampling localities. Finally, in this study, we demonstrated that there was a significant correlation between the frequency of green frogs and latitude. There was a higher frequency of green frogs in southern samples and a lower frequency of green frogs in northern samples. However, when we interpreted this phenotypic cline in light of the overall pattern of isolation-by-distance, it was apparent that the neutral evolutionary forces of genetic drift and migration could explain the cline, and the invocation of natural selection was not necessary.

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The accurate assessment of forest persistence under environmental change is dependent on the fundamental understanding of the genetic consequences of human intervention and its comparison to that of natural processes, as declines in genetic diversity and changes in its structuring can compromise the adaptive ability of a population. The European beech, Fagus sylvatica, has experienced prolonged human impact over its 14 million ha range with contemporary forests harbouring high ecological, economic, and cultural value. Historical traditional management practices, such as coppicing and pollarding, have impacted a large portion of Europe’s forests. This form of management encouraged vegetative regeneration, prolonging the longevity of individual trees. In several cases, the structure and function of managed trees and their associated ecosystems were significantly altered. Specifically, coppiced beech forests in Europe displayed significantly larger extents of spatial genetic structuring compared to their natural counterparts, revealing a change in the genetic composition of the population due to decades of management. Humans have also aided in the dispersal of beech within and outside of its natural range. In Great Britain, the putative native range retained signals of past colonisation dynamics. However, these signals were obscured by the wide-spread translocation of the species throughout the country. Evidence of post-glacial colonisation dynamics can be found in Sweden as well. In contrast to Britain, the structure of this natural leading range edge displays a gradual reduction in population size where isolation was found to have acted as an effective barrier to gene flow reducing the genetic diversity of populations.

The ranging behaviour, habitat preferences, genetic structure, and demographic parameters of bottlenose dolphins living in the Azores were studied using data collected from 1999 to 2004. Only 44 dolphins out of 966 identified were frequently sighted within and between years and showed strong site fidelity. The remaining individuals were either temporary migrants from within or outside the archipelago, or transients. Estimates of home range size were three times larger than previously reported for this species, possibly as a result of the lower availability of food resources. Mitochondrial DNA sequences showed very high gene and nucleotide diversity. There was no evidence of population structuring within the Azores. The Azorean population was not differentiated from the pelagic population of the Northwest Atlantic, suggesting the "unproductive" waters of the Atlantic do not constitute a barrier to dispersal. Population size, survival and temporary emigration rates were estimated using open-population models and Pollock's robust design. A few hundreds of dolphins occur in the area on a given year, though the majority should use it temporarily, as suggested by the high emigration rates. Bottlenose dolphins preferentially used shallow areas with high bottom relief. Temporal and spatial persistence of dolphin-habitat associations documented in this study further supports the idea of a close relationship between certain bathymetric features and important hydrographic processes and suggests the occurrence of prey aggregations over these areas may be, to some extent, predictable. Several results of this study suggest there are no reasons for concern about the status of this population. Yet, the resident group may be negatively affected by increasing pressure from the whale watching activity. Although the proposed Marine Park constitutes important habitat for resident dolphins, at present, the area is clearly insufficient to satisfy their spatial requirements and its conservation value may be limited.

Mon étude vise à évaluer la propagation d’une zoonose en émergence au Québec, la maladie de Lyme, en conséquence du réchauffement climatique. Le pathogène responsable de cette infection, Borrelia burgdorferi, est transmis par l’intermédiaire d’une tique parasite, Ixodes scapularis, de plus en plus commune au Québec en raison de l’augmentation de la température moyenne du climat depuis les dernières décennies. Puisque la tique a une capacité de déplacement très restreinte, on s'attend à ce que sa dispersion soit liée à celle de son hôte primaire, soit la souris à pattes blanches (Peromyscus leucopus). Je décrirai donc d’abord les espèces impliquées, leur écologie et leur rôle dans ce système à trois niveaux (hôte/pathogène/vecteur). Puis, à l’aide de séquences d’ADN mitochondrial, je comparerai la phylogéographie des deux principales espèces de souris au Québec, la souris à pattes blanches et la souris sylvestre (P. maniculatus). Des analyses d’arbres et de réseaux d’haplotypes ont révélé des différences significatives dans la structure génétique et ainsi montré que les populations de P. leucopus seraient en expansion dans le sud du Québec. Cette étude nous a finalement permis d’émettre des hypothèses sur le patron d’établissement de la maladie de Lyme au Québec. / My study aims to assess the spread of an emerging zoonosis in Québec, Lyme disease, as a consequence of global warming. The pathogen responsible for this infection, Borrelia burgdorferi, is transmitted through a tick parasite, Ixodes scapularis, increasingly common in Québec due to the elevation of the average temperature of the atmosphere over the past decades. Since the tick has a very limited dispersal capacity, it is expected that its dispersion is linked to that of its primary host, the white-footed mouse (Peromyscus leucopus). I first described the species involved, their ecology and role in this three-level system (host / pathogen / vector). Then, using mitochondrial DNA sequences, I compared the phylogeography of the two main mouse species in Québec, the white-footed mouse and the deer mouse (P. maniculatus). Analyses of trees and haplotype networks revealed significant differences in the genetic structure, and thus showed that populations of P. leucopus are expanding in southern Québec. This study finally allowed making assumptions on the pattern of establishment of Lyme disease in Québec.

Les communautés microbiennes du sol peuvent améliorer la croissance de la plante en augmentant la disponibilité en nutriments du sol, favorisant ainsi leur prélèvement par la plante. Dans le contexte d’une production agricole à bas niveau d’intrants, la nutrition de la plante est susceptible de reposer de plus en plus sur les interactions plante-communautés microbiennes de la rhizosphère, qui peuvent être modulées par le génotype de la plante. Pourtant, très peu d’études se sont intéressées aux modifications des communautés microbiennes de la rhizosphère dans leur globalité et ce en relation avec à la fois le génotype et le phénotype de la plante. Ces travaux de thèse ont été consacrés à étudier l’effet du génotype de la plante sur la structure génétique des communautés microbiennes de la rhizosphère en relation avec les stratégies nutritionnelles de la plante.L’interaction plante-communautés microbiennes de la rhizosphère a été évaluée par une approche multidisciplinaire alliant écophysiologie et écologie microbienne. L’effet du génotype de la plante sur la structure génétique des communautés microbiennes de la rhizosphère qui lui sont associées a été analysé par DNA fingerprint. Les différentes stratégies nutritionnelles de la plante ont été analysées par une approche de type structure/fonction prenant en compte la mise en place des structures (feuilles, racines) et leur fonctionnement (photosynthèse, rhizodéposition, prélèvement spécifique d’azote).Dans une première expérimentation réalisée sur sept génotypes de Medicago truncatula, nous avons montré qu’à un stade précoce du développement de la plante, le génotype de Medicago truncatula affectait la structure génétique des communautés bactériennes du sol. En revanche, à ce stade précoce, peu de différences de croissance ont été observées entre les différents génotypes étudiés. Ces derniers ont par contre présenté des stratégies nutritionnelles contrastées. Les descripteurs fonctionnels sont donc plus efficaces que les descripteurs structurels pour discriminer les génotypes de plantes à un stade précoce du développement de la plante. De plus, nous avons montré un lien entre les stratégies nutritionnelles de la plante et la sélection des communautés bactériennes associées. Cette étude nous a également permis de développer un cadre d’analyse écophysiologique appliqué à l’étude des interactions plante-communautés microbiennes de la rhizosphère.Outre l’effet majeur du génotype de la plante dans les interactions plante-communautés bactériennes de la rhizosphère, nous avons également montré qu’il y avait un effet important de l’environnement, comme la disponibilité en azote minéral du sol. En effet, la disponibilité en azote minéral du sol a affecté la structure génétique des communautés bactériennes rhizosphériques via un effet indirect de la plante dépendant du génotype considéré. Les effets des différents génotypes de Medicago truncatula et de leurs stratégies de réponses à des contraintes environnementales, comme la disponibilité de l’azote du sol, se sont révélées être des composantes majeures de la sélection des communautés microbiennes. [...] / The soil microbial communities can improve plant growth by increasing soil nutrient availability, thereby promoting their uptake by the plant. In an overall context of input reduction, the plant nutrition should be increasingly based on plant- rhizosphere microbial communities’ interactions. Yet, very few studies have examined the entire rhizosphere microbial communities in relationship with both plant genotype and phenotype. The aim of this thesis was to study the plant genotype effect on the rhizosphere microbial communities in relationship with the plant nutritional strategies.To do so, the plant-rhizosphere microbial communities’ interaction was assessed by a multidisciplinary approach combining ecophysiology and microbial ecology. The plant genotype effect on the genetic structure of the associated rhizosphere microbial communities was analyzed by DNA fingerprinting. The different plant nutritional strategies were analyzed by a structural/functional approach taking into account both structure establishment e.g. leaves and functions e.g. photosynthesis.In a first experiment carried out on seven genotypes of Medicago truncatula, we showed that the Medicago truncatula genotype affected the genetic structure of the rhizosphere bacterial communities very early relatively to the plant development stages. However, at this early stage, few growth differences could be observed among the different genotypes. Yet, those genotypes presented contrasted nutritional strategies. Therefore, the functional descriptors were more efficient than the structural ones to discriminate plant genotypes at an early developmental stage. In addition, we showed that a link existed between the plant nutritional strategies and the rhizosphere bacterial communities selection. Finally, this study enabled to develop a multidisciplinary framework applied to the study of the plant- rhizosphere microbial communities’ interactions.In addition to the plant genotype effect, we showed that there is an environmental effect e.g. soil mineral nitrogen availability on the rhizosphere bacterial communities. Indeed, the soil mineral nitrogen availability affected the genetic structure of the rhizosphere bacterial communities via an indirect effect of the plant depending on its genotype. The effects of the different Medicago truncatula genotypes and their response strategies to environmental constraints (soil mineral nitrogen availability), proved to be a major component of the selection of the rhizosphere microbial communities.In order to identify the genetic determinisms of the interaction between the plant and the rhizosphere microbial communities, a second experiment was conducted on a core collection of 184 genotypes of Medicago truncatula. Initial results enabled to identify and characterize four groups of genotypes with contrasted phenotypes for their growth and their specific nitrogen uptake. Thanks to high-throughput sequencing, we will analyze the rhizosphere microbial communities’ diversity associated with the different Medicago truncatula genotypes. These results should determine if the plant genotype influences the selection of beneficial rhizosphere microbial communities. Moreover, when the whole genome sequencing data would be available for the 184 genotypes of the Medicago truncatula core collection, a genome-wide association study will be proceed. The creation of plant ideotypes, which will promote beneficial interactions with rhizosphere microbial communities, will be possible. Plant growth and yield will be improved without the concomitant increase of agricultural inputs.

En plus des facteurs environnementaux et démographiques, les propriétés génétiques des populations sont devenues une préoccupation majeure pour préserver les populations en déclin de l'extinction. Afin d’acquérir des informations pertinentes pour la planification et la mise en œuvre des stratégies de conservation, les biologistes de la conservation ont réalisé le besoin d’avoir des connaissances en génétique des populations. Grace à l'acquisition de plus en plus rapide et de moins en moins chère d'une large gamme de marqueurs moléculaires, le recours a l’usage de l’outil moléculaire se répand de plus en plus. Ainsi, la génétique de la conservation se confirme comme une discipline à part entière qui est donc l’utilisation de la génétique dans la préservation des espèces comme entités dynamiques capables d'évoluer pour faire face aux changements environnementaux et afin de minimiser leur risque d'extinction. Par le biais de l’utilisation d’un large panel de marqueurs moléculaires (gènes mitochondriaux et nucléaires, microsatellites et SNPs), nous nous sommes intéresse à l’histoire évolutive à différentes échelles spatio-temporelles de la sous-espèce ouest méditerranéenne Testudo. hermanni hermanni (THH), qui présente une distribution insulaire et continentale très fragmentée. Le but de ce travail consiste à 1) comprendre les processus qui expliqueraient la distribution actuelle de la diversité génétique des populations et leur structure, 2) identifier l'origine des populations introduites (à Minorque et au Delta de l’Ebre), et 3) dater l’origine de la sous espèce THH. A l’échelle des populations, il s’agit d’identifier le nombre de groupes génétiques homogènes chez la tortue d’Hermann et le degré de différentiation génétique entre ces groupes afin de définir des unités de conservation évolutivement significatives (ESU) et des unités de gestion (MU). Enfin, nous nous sommes intéresses à l’étude des derniers noyaux de populations de THH dans le Var par des approches de génétique du paysage. Nos résultats ont révélé qu’une divergence par vicariance est à l’ origine de l’apparition de la sous-espèce T.h. hermanni. Ce scenario biogéographique s’expliquerait par les successions d’évènements glaciaires et interglaciaires qu’a connu le Pléistocène depuis plus de 2 MA provoquant un mouvement de retrait de l’espèce vers des zones refuges sur la frange côtière nord-méditerranéenne. Par ailleurs, le patron de différentiation mitochondriale Ile-continent observe et confirme par les microsatellites est très original par rapport à ce qui est connu chez d’autres espèces de reptiles partageant la même aire de distribution. Au vue de l’analyse phylogénétique confirmée par les microsatellites, on peut affirmer que la tortue d’Hermann n’est pas native sur Minorque et qu’elle a une double origine : la première, résultant d’une introduction à partir d’une seule source, probablement d’une population continentale génétiquement proche des Albères. La seconde d'origine insulaire, serait le résultat d’apports multiples, à partir de la Corse, de la Sardaigne ou de la Sicile. Enfin, l’isolement des populations de THH au sein de chaque région géographique reflète une structure génétique très forte. Par conséquent, six unités de gestion (MUs) sont proposées comme unités de conservation et de suivi sur le terrain. / In addition to environmental and demographic factors, the study of genetic properties of populations became inevitable issues in the conservation of declining populations. To acquire relevant information for conservation planning and implementing conservation strategies, conservationists have realized the need of population genetics tools. Moreover, this discipline has become more efficient with the development of a wide range of effective and relatively cheap methods for the characterization of a huge number of molecular markers. This led to define the conservation genetics as a separate discipline, which is the use of genetics in species preservation as dynamic entities evolving to cope with environmental changes and to minimize their extinction risk. Using a broad panel of molecular markers (mitochondrial and nuclear genes, microsatellites and SNPs), we interested in the evolutionary history at different spatial and temporal scales of the Mediterranean western subspecies Testudo hermanni hermanni (THH), which presents a very fragmented insular and continental distribution. The aim of this study is to 1) understand the processes that explain the current distribution of the structure and genetic diversity of populations, 2) identify the origin of introduced populations (Menorca and Ebro Delta) and 3) Dating the origin of the subspecies THH. At the population level, our study aimed to identify the number of homogeneous genetic groups of THH tortoise and the degree of genetic differentiation between these groups in order to identify evolutionarily significant units (ESU) and management units (MU). Finally, we were interested in the study of the last core populations of THH in the Var by landscape genetics approach. Our results revealed that a divergence by vicariance pattern explains the origin of the appearance of the subspecies THH. This biogeographic scenario is explained by the succession of glacial and interglacial events of the Pleistocene causing a withdrawal of the species toward refugia on the northern Mediterranean fringe. Moreover, the observed differentiation pattern (island vs continent) is very original compared to the reported diversity patterns of other reptiles sharing the same distribution range. According to our results, we may conclude that the Hermann’s tortoise is not native in Menorca and has a double origin: the first, is an introduction resulting from a unique source, probably from a continental lineage genetically close to Albera. The second, from an island origin, is the result of multiple contributions, from Corsica, Sardinia or Sicily. Lastly,the isolation of THH populations within each geographic region reflects a very strong genetic structure, therefor the six most relevant management units forconservation purposes are proposed on the basis that they represent a significant part of the evolutionary legacy of the species.