The seeming lack of barriers to gene flow in the northwest Atlantic ocean has led to the general assumption that the population of the American lobster (Homarus americanus) is largely panmictic. However, morphological and genetic data presented in this dissertation suggest that lobster populations are less homogenous than once believed with potential for behavioral barriers to mating and selection of locally adaptive traits. Additionally, both long-term fishing pressures and the recent spread of a destructive epizootic shell disease may have impacted population structure. We developed a novel photographic technique to rapidly collect accurate morphological data with the ability to maintain a database of images for the purposes of re-sampling and testing additional hypotheses. During this study, we found significant morphometric differences between samples of lobsters from collection sites as close as 25km apart. Morphological differences may have originated due to differential selection or plastic responses to environmental variation. To analyze population genetic structure, I surveyed genetic variation using RADseq. Analysis of 1614 putatively neutral SNPs found little genetic difference (Average F¬ST=0.00137) between sample sites suggesting a high level of gene flow between regions. Several additional markers appeared to be under divergent selection between sample sites. A genome scan analysis of both neutral SNPs and SNPs under selection found several selected SNPs associated with principal components of morphological characters. A subsequent BLAST analysis identified a number of the selected SNPs lying in the H. americanus transcriptome, suggesting functional importance. Further experimentation is required to quantify the impacts of plasticity or local adaption in the origin of morphological differences between lobster populations, although the significant differences identified in this research are likely due to a combination of the two. The overarching conclusion is that lobster populations are, in fact, more differentiated than previously predicted and, as such, the findings presented here may have significant management implications.

Les deux sous-espèces annuelles de téosinte qui sont les plus proches parents sauvages du maïs sont d’excellents systèmes pour étudier l’adaptation locale car leur distribution couvre un large éventail de conditions environnementales. Zea mays ssp. parviglumis est distribuée dans un habitat chaud et mésique en dessous de 1800 m d’altitude, tandis que Zea mays ssp. mexicana prospère dans des conditions sèches et fraîches à des altitudes plus élevées. Nous avons combiné des approches d’écologie inverse et de génétique association afin d’identifier les déterminants de l'adaptation locale chez ces téosintes. A partir de données de séquençage haut débit (HTS) de six populations comprenant des populations de basses et hautes altitudes, une étude précédente a identifié un sous-ensemble de 171 polymorphismes nucléotidiques (SNP candidats) présentant des signaux de sélection. Nous avons utilisé ces SNP candidats pour tester l'association entre la variation génotypique et phénotypique de 18 caractères. Notre panel d’association était constitué de 1663 plantes provenant de graines de 11 populations échantillonnées le long de deux gradients d’altitude. Il a été évalué deux années consécutives dans deux jardins communs. Nous avons contrôlé sa structure neutre en utilisant 18 marqueurs microsatellites. La variation phénotypique a révélé l’existence d'un syndrome altitudinal composé de dix caractères. Nous avons ainsi observé une augmentation de la précocité de floraison, une diminution de la production de talles et de la densité en stomates des feuilles ainsi qu’une augmentation de la taille, de la longueur et du poids des grains avec l’élévation croissante du site de collecte des populations. Ce syndrome a évolué malgré des flux de gènes détectables entre populations. Nous avons montré que le pourcentage de SNP candidats associés aux différents caractères dépend de la prise en compte de la structure neutre soit en cinq groupes génétiques (71,7%), soit en onze populations (11,5%), indiquant une stratification complexe. Nous avons testé les corrélations entre les variables environnementales et les fréquences alléliques des SNP candidats sur 28 populations. Nous avons trouvé un enrichissement à la fois pour les SNP présentant des associations phénotypiques et les SNP présentant des corrélations environnementales dans trois larges inversions chromosomiques, confirmant leur rôle dans l'adaptation locale. Pour explorer la contribution de la variation structurale à l'évolution adaptative, nous nous sommes concentrés sur le contenu en éléments transposables (ET) des six populations séquencées (HTS). Ces éléments constituent environ 85% du génome du maïs et contribuent à sa variabilité fonctionnelle. Nous avons effectué la première description populationnelle des ET chez les téosintes pour deux catégories d'insertions, celles présentes et celles absentes du génome de référence du maïs. Nous avons ensuite recherché des polymorphismes liés aux ET présentant des fréquences alléliques contrastées entre populations de basse et de haute altitude. Nous avons identifié un sous-ensemble d'insertions candidates. Enfin, nous avons génotypé, dans un panel d'association, des insertions d’ET connues pour avoir contribué à l'évolution phénotypique du maïs. Contrairement à ce qui a été observé chez le maïs, certaines de ces insertions n'ont montré aucun effet phénotypique chez les téosintes, ce qui suggère que leur effet dépend du fond génétique. Notre étude apporte de nouvelles connaissances sur l’adaptation altitudinale chez les plantes. Elle ouvre la discussion sur les défis soulevés par l'utilisation (1) d'outils de génomique des populations pour identifier la variation adaptative, (2) de populations naturelles en génétique d’association, et (1) de ressources génétiques sauvages pour l'amélioration des espèces cultivées. / Annual teosintes, the closest wild relatives of maize, are ideal systems to study local adaptation because their distribution spans a wide range of environmental conditions. Zea mays ssp. parviglumis is distributed in warm and mesic conditions below 1800 m, while Zea mays ssp. mexicana thrives in dry and cool conditions at higher altitudes. We combined reverse ecology and association mapping to mine the determinants of local adaptation in annual teosintes. Based on high throughput sequencing (HTS) data from six populations encompassing lowland and highland populations growing along two elevation gradients, a previous study has identified candidate regions displaying signals of selection. Within those regions a subset of 171 candidate single nucleotide polymorphisms (SNPs) was selected to test their association to phenotypic variation at 18 traits. Our association panel encompassed 1663 plants from seeds collected from eleven populations sampled along the elevation gradients. We benefit from phenotypic characterization of all the plants in two common gardens located at mid-altitude for two years. In addition, we controlled for neutral structure of the association panel using 18 microsatellite markers. Phenotypic variation revealed the components of an altitudinal “syndrome” constituted of ten traits evolving under spatially-varying selection. Plants flowered earlier, produced less tillers, displayed lower stomata density and carried larger, longer and heavier grains with increasing elevation of population collection site. This syndrome evolved in spite of detectable gene flow among populations. The percentage of candidate SNPs associated with traits largely depended on whether we corrected for five genetic groups (71.7%) or eleven populations (11.5%), thereby indicating a complex stratification in our association panel. We analyzed correlations between environmental variables and allele frequencies of candidate SNPs on a larger set of 28 populations. We found enrichment for SNPs displaying phenotypic associations and environmental correlations in three Mb-scale chromosomal inversions, confirming the role of these inversions in local adaptation. To further explore the contribution of structural variation to adaptive evolution, we focused on transposable element (TE) content of the HTS populations. TEs constitute ~85% of the maize genome and contribute to its functional variability via gene inactivation and modulation of gene expression. We performed the first population-level description of TEs in teosintes for two categories of insertions, those present and those absent from the maize reference genome. We next searched for TE polymorphisms with contrasted allele frequencies between lowland and highland populations. We pinpointed a subset of adaptive candidate insertions. Finally, we genotyped in our association panel TE insertions known to have contributed to maize phenotypic evolution. In contrast to what was found in maize, some of these insertions displayed no measurable phenotypic effects in teosintes, suggesting that their effect depends on the genetic background. Altogether our study brings new insights into plant altitudinal adaptation. It opens discussions on the challenges raised by the use (1) of population genomic tools to discover adaptive variation, (2) of natural populations in association mapping, and (1) of wild genetic resources in crop breeding.

There is repeated evidence that hybridization is a major contributor to the production of adaptive diversity; however, the evolutionary fate of hybrids in natural populations remains poorly understood. In Heliconius butterflies, hybridization is common and responsible for generating a variety of warning color patterns across the genus. Predator avoidance of warning colorations appears to largely be learned, which drives strong positive frequency-dependent selection. This creates a paradox for hybrid lineages: how do novel hybrid forms manage to establish and persist under such strong selection? In this dissertation, I present a series of studies centered on the selection dynamics of Heliconius hybrid zones, to elucidate how novel adaptive traits establish in nature. Clines across hybrid zones have often been analyzed to estimate selection on ecologically important loci. Here, warning color clines were characterized and compared across multiple transects along a Heliconius hybrid zone in the Guiana Shield. Furthermore, a mark-resight experiment and communal roost observations were completed near the center of this hybrid zone to determine the survival and likelihood of establishment of native and foreign forms. These studies reveal similar survivorship of hybrid and pure color patterns, and specifically demonstrate that a rare putative hybrid form can survive and establish within a hybrid zone. Both hybrids and pure color patterns showed comparable life expectancies in the mark-resight experiment and similar patterns of presence at nocturnal roosts. These results suggest that selection on warning color pattern is relatively weak within the hybrid zone. Analyses of color pattern clines uncovered strong selection bounding the hybrid zone in bi-race areas, while weaker selection was estimated for a tri-race area. In fact, the tri-race area was three times wider than the bi-race areas. Collectively, these studies suggest that the selection dynamics across hybrid zones may play an integral role in the establishment of new adaptive traits, and offers a route by which a reputed hybrid race may have arisen. The investigations within this dissertation also provide a new view of hybrid zone dynamics, and improve our understanding of how hybridization and selection shapes the evolution of biodiversity.

Forests are among the most important repositories of terrestrial biodiversity and provide a broad range of ecosystem services. During millennia, forests have changed, adapted and evolved under changing conditions. However, in the present century, forests are facing environmental changes at rates with no precedents. A major concern is the risk of declining forest genetic diversity, since genetic variation as the raw material underpinning adaptation is key in maintaining the resilience of forest ecosystems against environmental changes. Understanding the different processes responsible for developing and maintaining the genetic diversity of tree species is essential to better predict tree responses under new conditions. Therefore, this thesis aimed to determine how different forces interact to shape and maintain within and among population genetic diversity of Scots pine and what the implications are for conservation and management under forthcoming environmental conditions. From local to continental scales, I followed a multilevel approach, and found that (i) historic climate changes and geographical barriers have played an important role in shaping the extent and spatial distribution of current genetic diversity of Scots pine. Despite contemporary habitat reduction and fragmentation we found that (ii) high levels of neutral genetic diversity remain in the Scottish populations of Scots pine, with gene flow and specifically wind-driven gene flow dominating over genetic drift and preventing differentiation among the Scottish populations. However, (iii) considerable impacts in the spatial distribution of genetic variation have occurred as a consequence of intensive historical forest management practices. Furthermore, we found that (iv) substantial levels of adaptive genetic variation are present in the Scottish populations of Scots pine, likely a result of selective processes resulting from the different environments they live in, with highly heritable traits, although similar capacity for response through phenotypic plasticity to warming. The results of this thesis help to further disentangle the forces maintaining genetic diversity in one of most widespread conifers in the world, and improving predictions of likely range shifts and adaptation of the species in response to contemporary changes. The thesis provides some recommendations to conservation and management practices.