O entendimento da contribuição diferencial de processos neutros e adaptativos envolvidos na diferenciação genética entre populações, assim como sua relação com varáveis físicas e ambientais da área de distribuição das espécies, é fundamental para melhorar o conhecimento da história evolutiva, mas também para fazer um manejo e conservação mais adequados da diversidade genética das espécies. O surgimento da Planície Costeira do Atlântico Sul foi um processo relativamente recente, que conduziu a processos de colonização e expansão dos organismos para um ambiente costeiro. Os padrões de estrutura genética gerados em processos de colonização e expansão podem ser difíceis de interpretar devido ao fato de que podem apresentar sinais sobrepostos de efeito fundador em série, isolamento por distância e isolamento por ambiente quando envolvem gradientes ecológicos na área de estudo. No presente trabalho foram conduzidas caracterizações da diversidade e estrutura genética de dois taxa predominantemente costeiros co-distribuídos, Calibrachoa heterophylla e Petunia integrifolia ssp. depauperata, em toda a amplitude da distribuição. Também foram inferidas as dinâmicas de fluxo gênico entre populações e sua relação com variáveis topográficas e climáticas reconstruídas pelo meio de um levantamento exaustivo e modelamento para a área de estudo. Processos de diferenciação genética promovidos pelo regime diferencial de chuvas nos extremos da distribuição foram inferidos para as duas espécies. Também foram identificadas populações das duas espécies apresentando alto nível de mistura de identidade genética nas localidades ao redor da Lagoa dos Patos. Isso foi associado a alta instabilidade na história geomorfológica recente desta região e dinâmicas atuais do vento que favorecem a dispersão secundária de sementes a maiores distâncias. Adicionalmente foram identificados processos espécie-específicos que se relacionaram principalmente a fatores históricos de cada táxon. Em P. depauperata o efeito fundador relacionado a um processo único de colonização do ambiente costeiro determinou o nível superior de estrutura genética, enquanto que em C. heterophylla foi a história filogeográfica da espécie na qual a diferenciação intraespecífica é anterior à colonização da região costeira atual o fator preponderante. As diferenças de duração do ciclo de vida entre as espécies também influenciaram as dinâmicas contrastantes de fluxo gênico dos dois taxa, sugerindo que a colonização e adaptação local de C. heterophylla nas bordas da distribuição poderia ser condizente com um processo de monopolização. Em vista dos resultados obtidos neste trabalho, propõem-se o desenvolvimento de experimentos de transplante recíproco para confirmar o processo de adaptação local nas duas espécies e abordagens genômicas para identificar regiões do genoma responsáveis pelos processos de adaptação ao ambiente costeiro e de adaptação local nas margens da distribuição. / The understanding of differential contribution of neutral and adaptive processes to the genetic differentiation among populations, as well as its relationship to physical and environmental variables of species’ distribution area, is essential to improve the knowledge of species evolutionary history, but also to direct appropriate management and conservation policies for the genetic diversity. The emergence of the South Atlantic Coastal Plain was a relatively recent event that led to colonization and expansion processes to the coastal environment. Genetic structure patterns generated in colonization and expansion processes can be difficult to interpret because the overlapping signals, which can present the founder effect in series, isolation by distance, and isolation by environment in the presence of ecological gradients in the study area. In this work characterization diversity and genetic structure were conducted to two co-distributed and predominantly coastal taxa, Calibrachoa heterophylla and Petunia integrifolia ssp. depauperata alongside their complete geographical range. Moreover, we also inferred dynamic of gene flow among populations and investigated the relation between topographical and climatic variables reconstructed by means of an exhaustive survey and modeling for the study area and the gene flow. Shared genetic differentiation processes promoted by differential rainfall conditions at the distribution edges were inferred. In addition, we identified populations from both species with high level of mixed genetic membership in locations around the Patos Lagoon. This was associated with a high instability in recent geomorphological history of coastal region and current wind dynamics that favor the secondary seed dispersal over longer distances. Additionally, specific species processes were identified mainly related to historical factors of each taxon. In P. depauperata founder effects associated with unique colonization process to coastal environment determined the upper level of genetic structure, while in C. heterophylla the upper level of genetic structure was related to the phylogeographical history wherein the intra-specific differentiation preceded colonization to the current coastal region. The differences of the life span length of the species were also related to contrasting gene flow dynamics indicating that the colonization and local adaptation of C. heterophylla at the edges of the distribution could lead to monopolization process. In view of the results we propose the development of reciprocal transplant experiments to confirm the local adaptation process in both species and genomic approaches to identify regions of the genome responsible for the processes of adaptation to the coastal environment and local adaptation in distribution margins.

Genetically structured populations arise when gene flow between groups of individuals is hindered by geographical, behavioural or temporal barriers. The identification of such groups is important for understanding evolution and has large implications for conservation concern. The field of population subdivision has received a lot of interest throughout the years and gained empirical support from a number of species. However, very little is known about population structure at small spatial scales, especially in a highly mobile species such as fish. The main object for my thesis was to further investigate population differentiation, explicitly at small spatial scales in the Eurasian perch. My results show that in this species, genetic differentiation occurs, even at very small spatial scales, both within lakes and in the Baltic Sea. Additionally, the differentiation can be stable over years and thus have a large impact in the evolution of adaptation to different environments. I also found barriers to gene flow that overlapped with the largest change in spring temperature, suggesting a temporal difference in spawning. Morphological differences were found at these small scales as well which indicates that a difference in food resources might be an underlying cause of change. My thesis work shows that the aquatic environment might not be as homogenous as widely thought and that there could be barriers or adaptations to different environments that hinder the fish from genetic panmixia. Slight patterns of isolation by distance (IBD) were found in the Baltic Sea, implying that the distance (i.e. currents) effect the level of differentiation via drifting of larvae and/or small fish. However, I have also theoretically investigated the IBD model of and seen that it is no longer correct when differences in population sizes are introduced. The pattern of IBD can mean high levels of gene flow or no gene flow at all, solely dependent on population size differences and fluctuations. My thesis has resulted in new and important findings regarding the existence and cause of genetic differentiation at very small spatial scales and thus added new knowledge into the field of evolution and speciation. In addition, my results also give insights into the contemporary state of the Eurasian perch and future evolutionary potential.

Understanding the events and processes responsible for patterns of within species diversity, provides insight into major evolutionary themes like adaptation, species distributions, and ultimately speciation itself. Here, I combine ecological, genetic and spatial perspectives to evaluate the roles that both historical and contemporary factors have played in shaping the population structure and genetic variation of foxsnakes (Pantherophis gloydi). First, I determine the likely impact of habitat loss on population distribution, through radio-telemetry (32 individuals) at two locations varying in habitat patch size. As predicted, individuals had similar habitat use patterns, but restricted movements to patches of suitable habitat at the more disturbed site. Also, occurrence records spread across a fragmented region were non-randomly distributed and located close to patches of usable habitat, suggesting habitat distribution limits population distribution. Next, I combined habitat suitability modeling with population genetics (589 individuals, 12 microsatellite loci) to infer how foxsnakes disperse through a mosaic of natural and altered landscape features. Boundary regions between genetic clusters were comprised of low suitability habitat (e.g. agricultural fields). Island populations were grouped into a single genetic cluster suggesting open water presents less of a barrier than non-suitable terrestrial habitat. Isolation by distance models had a stronger correlation with genetic data when including resistance values derived from habitat suitability maps, suggesting habitat degradation limits dispersal for foxsnakes. At larger temporal and spatial scales I quantified patterns of genetic diversity and population structure using mitochondrial (101 cytochrome b sequences) and microsatellite (816 individuals, 12 loci) DNA and used Approximate Bayesian computation to test competing models of demographic history. Supporting my predictions, I found models with populations which have undergone population size drops and splitting events continually had more support than models with small founding populations expanding to stable populations. Based on timing, the most likely cause was the cooling of temperatures and infilling of deciduous forest since the Hypisthermal. On a smaller scale, evidence suggested anthropogenic habitat loss has caused further decline and fragmentation. Mitochondrial DNA structure did not correspond to fragmented populations and the majority of foxsnakes had an identical haplotype, suggesting a past bottleneck or selective sweep. / Thesis (Ph.D, Biology) -- Queen's University, 2011-01-11 10:40:52.476

The genetic diversity and genetic structure of populations, and the processes shaping gene flow within and between populations, are influenced by the landscapes they occur within. Within terrestrial landscapes, rivers and their riparian habitat are among the most dynamic, diverse and complex of landscapes and their linear structure appears as an interlinking feature across large landscapes. This thesis took a landscape genetics approach to examine the influence of river landscape features on Alnus glutinosa populations, a widespread keystone tree species of European riparian ecosystems. By accounting for the differing dispersal mechanisms of A. glutinosa (wind and water), landscape effects on seed- and pollen-mediated gene flow, genetic diversity, demographic and genetic structure were identified at different spatial scales of a large UK river catchment. Widespread gene flow within and between A. glutinosa populations was identified with no apparent limitation of wind-mediated pollen dispersal. Hydrochorous dispersal of seed between populations was evident, and found to increase genetic connectivity between riparian populations; however an isolation by distance effect was identified between populations located further apart from each other. No pattern of genetic diversity was found, with high levels of genetic diversity identified at all spatial and temporal scales. At the river-catchment scale no genetic clustering was observed, either within or between the six rivers studied. Demographic structuring within A. glutinosa populations was evident, and correlated with distance from the main river channel. Interactions between seed dispersal, hydrological disturbance, colonisation, and historical influences are discussed in relation to fine-scale spatial genetic structure between A. glutinosa sapling and adult generations. Central to the landscape genetics approach taken in this thesis was the incorporation of key A. glutinosa life history attributes. By incorporating gene flow analyses, species ecology and landscape features, the research presented here furthers our understanding of riverine landscape influences on their riparian populations at different spatial scales and can be used to inform management principles.

Les invasions biologiques dans les agroécosystèmes engendrent de lourdes pertes économiques. Parmi les nombreuses espèces en cause, on retrouve les nématodes phytoparasites, vers microscopiques s’attaquant principalement aux racines. Présent dans tous les principaux pays producteurs de soya, le nématode à kyste du soya (NKS), Heterodera glycines, serait à lui seul responsable annuellement de plusieurs milliards de dollars de pertes. La rotation avec des cultivars résistants est le moyen le plus efficace de contrôler les populations de NKS, mais la surutilisation des mêmes lignées a conduit à la sélection d’individus virulents et mené à leur inefficacité. À ce jour, les mécanismes ainsi que les gènes de virulence associés au contournement de la résistance continuent de mystifier les scientifiques. Dans cette thèse, les effets des changements climatiques sur la reproduction et l’établissement du NKS ainsi que sur la phénologie de son hôte, le soya, ont été étudiés. Le premier modèle bioclimatique simulant le cycle de vie du NKS et du soya a été développé. Il a démontré que le nématode peut déjà se reproduire dans toutes les régions du Québec et que la hausse attendue des températures dans le futur proche (2041-2070) permettrait au NKS de pratiquement doubler le nombre de générations produites par saison de croissance dans toutes les régions. De plus, la production de soya issu du groupe de maturité I pourrait s’étendre à toutes les régions du Québec d’ici 2070. Une étude sur la distribution de la variabilité génétique entre 64 populations américaines et ontariennes et les gènes associés à diverses composantes bioclimatiques et leur rôle dans l’adaptation a également été réalisée. Celle-ci a révélé que la diversité génétique était très élevée entre les populations et qu’un flux de gène continu aurait facilité l’adaptation du NKS à diverses conditions bioclimatiques et son établissement dans toutes les régions nord-américaines où l’on produit du soya. Finalement, cette thèse présente l’analyse des génotypes du NKS et des gènes différentiellement exprimés sur des plants de soya résistant (Peking et PI88788) et sensible (Essex). En plus d’identifier plusieurs protéines liées à la virulence, cette étude a permis de mettre en évidence une région génomique sous forte pression évolutive. Cet îlot génique contient plusieurs répétitions en tandem qui ont divergé et dont certaines sont maintenant utilisées de façon sélective pour le contournement de différents types de résistance. / Biological invasions in agroecosystems are a major cause of economic losses. Plant parasitic nematodes are among the many species causing significant crop damages. The soybean cyst nematode (SCN) is causing billions of dollars of losses in all areas where soybean is produced. Rotation with resistant cultivars is the most effective mean of controlling SCN populations, but the overuse of the same lines has led to the selection of virulent individuals and the ineffectiveness of resistance. To this day, the virulence genes and mecanisms associated with the circumvention of resistance continue to mystify scientists. In this thesis, I explored the effects of climate change on the reproduction and establishment of SCN as well as on the phenology of its host, soybean. I have demonstrated that the nematode can already reproduce in all regions of Québec and that the expected rise in temperatures in the near future (2041-2070) will allow the development of more generations per growing season in all regions. In addition, I have demonstrated that the area suitable for the production of soybean from maturity group I will expand toward the north by 2070, further facilitating the expansion of SCN. I have also explored the genetic variability among more than 64 SCN populations from North America and analyzed the genes associated with various bioclimatic components and their role in adaptation. These analyses revealed that the genetic diversity was very high among SCN populations. This diversity associated with a continuous gene flow between populations has facilitated the adaptation of SCN to various bioclimatic conditions and its establishment in all US and Canadian soybean producing regions. Finaly, this thesis presents an analysis of the SCN genotypes and the differentially expressed genes associated with virulence in two resistant soybean lines (Peking and PI88788) and susceptible Essex. This work has identified several proteins associated with virulence and allowed the discovery of a genomic region under strong evolutionary pressure. This island contains several genes in tandem duplications that have diverged and are now used selectively for overcoming different sources of resistance.