Le changement climatique rapide auquel nous assistons actuellement est déjà en train de modifier le cycle de vie d’un grand nombre d’organismes. Des études basées sur des modèles d’enveloppe bioclimatique apportent des réponses mais ces prédictions de nouvelles aires de répartition ne tiennent pas compte d’une part de l’adaptation rapide des espèces (plasticité phénotypique et diversité génétique non neutre), et d’autre part des interactions interspécifiques ou de la dynamique des populations. Ce travail de recherche est centré sur les mécanismes permettant la persistance des individus dans un environnement changeant.Nous avons travaillé dans les Pyrénées françaises sur deux espèces à large répartition européenne (chêne sessile et hêtre commun) sur un gradient altitudinal de 1500 m de dénivelé correspondant en moyenne à 8°C d’amplitude thermique. Ce gradient a été répété dans deux vallées parallèles, distantes de 30 km. Basée sur l’étude de traits fonctionnels, nous avons caractérisé les variations altitudinales de traits morphologiques et physiologiques de ces caractères dans des conditions naturelles. Les capacités écophysiologiques apparaissent plus élevée pour le chêne et pour les populations de haute altitude, suggérant une adaptation locale à un environnement stressant. Dans une étude préliminaire, nous avons établi qu’il était nécessaire d’intégrer les variations de pression partielle de dioxyde de carbone et non se concentration dans les mesures d’échanges gazeux. Tous les traits fonctionnels mesurés en populations naturelles varient avec l’altitude. Ainsi la taille des feuilles diminue avec l’altitude tandis que les autres traits augmentent, avec des valeurs de 1.3 à 3.9 fois supérieures entre le haut et le bas du gradient tous traits confondus. Nous avons ensuite cherché à déterminer l’origine de ces variations phénotypiques. Une expérimentation en test de provenance a ainsi permis de déterminer les traits dont la variation in situ était en partie sous contrôle génétique. Les résultats de notre étude montrent que le gradient altitudinal a induit une différenciation génétique au niveau de la croissance, de la phénologie et de traits fonctionnels foliaires pour ces espèces, malgré la proximité des populations étudiées dans leur milieu naturel. Néanmoins, les capacités photosynthétiques pour le hêtre et la surface spécifique foliaire pour le chêne ne montre aucune différentiation génétique, ainsi que la densité stomatique pour les deux espèces. D’autre part, l’expérimentation de transplantations réciproques le long du gradient, a mis en évidence une forte plasticité phénotypique pour les deux espèces, ce qui suggère que les populations peuvent dans une certaine mesure répondre immédiatement aux variations climatiques rencontrées le long de ce gradient. Cependant, tandis que la température optimale pour la longueur de saison de végétation ne semble pas encore atteinte, les populations pourraient réagir négativement à une élévation de la température en terme de croissance. En conclusion, les mécanismes adaptatifs mis en évidence le long d’un gradient climatique naturel, pourraient permettre aux populations de faire face au changement climatique actuel. / The rapid climate change, which we are currently witnessing, is already modifying the physiology and distribution of species. Predictions of changes in species distributions do not take evolutionary mechanisms and biotic interactions into account. Our main objective was to assess the inherent adaptive capacities of tree populations by i) quantifying the phenotypic variations of functional traits with altitude and ii) studying the extent to which these variations are environmentally driven (phenotypic plasticity) and/or genetically fixed (adaptation). The study took place in the French Pyrenees along an altitudinal gradient range of 1500 m corresponding on average to 8°C of thermal amplitude. We focused on two broadleaved species with a wide European distribution (sessile oak and common beech). This gradient was repeated in two parallel valleys, distant from 30 km. Altitudinal trends were investigated for several morphological, physiological and phenological traits in natural conditions (in situ), in a common garden experiment and in reciprocal transplant experiments (RTEs). The phenotypic variability observed in situ showed significant altitudinal trends for all the studied traits and followed similar patterns for both species. We established that together with temperature, it was also necessary to integrate the variations of atmospheric gas partial pressure along the altitudinal gradient. In the common garden experiment, our results showed that the altitudinal gradient induced genetic differentiations for growth, leaf phenology and several morphological and physiological traits. This experiment made it possible to demonstrate, for both species, a weaker effect of genetic variations than in situ observed variations, suggesting a strong effect of the environment on leaf functional traits. A higher intrapopulation than interpopulation genetic variability was also observed for all traits. Finally, the reciprocal transplant experiments highlighted a high magnitude of phenotypic plasticity whatever the trait and the species.

The distribution of the expressed genotype is moved around in the population over time byevolution. Natural selection is one of the forces that act on the phenotype to change the patterns ofnucleotide variation underlying those distributions. How the phenotype changes over aheterogeneous environment describes the type of evolutionary force acting on this trait and thisshould be reflected in the variation at loci underlying this trait. While the variation in phenotypesand at the nucleotide level in a population indicates the same evolutionary force, it does notnecessarily mean that they are connected. In natural populations the continuous shifting of geneticmaterial through recombination events break down possible associations between loci facilitates theexamination of possible causal loci to single base pair differences in DNA-sequences. Connecting thegenotype and the phenotype thus provides an important step in the understanding the geneticarchitecture of complex traits and the forces that shape the observed patterns.This thesis examines the European aspen, Populus tremula, sampled from subpopulations overan extensive latitudinal gradient covering most of Sweden. Results show a clear geneticdifferentiation in the timing of bud set, a measure of the autumnal cessation of growth, betweendifferent parts of Sweden pointing at local adaptation. In the search for candidate genes thatunderlie the local adaptation found, most genes (25) in the photoperiodic gene network wereexamined for signals of selection. Genes in the photoperiodic network show an increase in theheterogeneity of differentiation between sampled subpopulations in Sweden. Almost half (12) of theexamined genes are under some form of selection. Eight of these genes show positive directionalselection on protein evolution and the gene that code for a photoreceptor, responsible for mediatingchanging light conditions to downstream targets in the network, has the hallmarks of a selectivesweep. The negative correlation between positive directional selection and synonymous diversityindicates that the majority of the photoperiod gene network has undergone recurrent selectivesweeps. A phenomenon that likely has occurred when P. tremula has readapted to the northern lightregimes during population expansion following retracting ice between periods of glaciations. Two ofthe genes under selection also have single nucleotide polymorphisms (SNP) that associate with budset, two in the PHYB2 gene and one in the LHY2 gene. Furthermore, there is an additional SNP inLHY1 that explain part of the variation in timing of bud set, despite the lack of a signal of selection atthe LHY1 gene. Together these SNPs explain 10-15% of the variation in the timing of bud set and 20-30% more if accounting for the positive co-variances between SNPs. There is thus rather extensiveevidence that genes in the photoperiod gene network control the timing of bud set, and reflect localadaptation in this trait.

Host-Associated Differentiation (HAD) is the formation of genetically divergent hostassociated lineages maintained by ecological isolation. HAD is potentially an important route to ecological speciation in parasites including many insects. While HAD case studies are accumulating, there is a dearth of negative results in the literature making it difficult to know how common the phenomenon really is or whether there are specific traits of parasites which promote HAD. To address these two problems, studies are needed which both publish negative results (i.e., parasites not showing HAD) and test for HAD in multiple parasite species on the same pair of host species (i.e., control for host plant effects). In this study, HAD was tested in three species of herbivorous insects and one parasitoid species on the same two host tree species: pecan and water hickory. The insects were selected based on the presence or absence of two traits, parthenogenesis and endophagy. A test for HAD was considered “positive” when population substructure was explained by host-association. To test for the presence of HAD, insects were sampled sympatrically to eliminate geographical isolation as a confounding factor, sampling was replicated spatially to assure that HAD persisted, and multiple loci were sampled from each individual. Genetic data was analyzed using cluster analyses. HAD was found in both pecan leaf phylloxera and yellow pecan aphid but not in pecan bud moth or in the parasitoid of the yellow pecan aphid, Aphelinus perpallidus. Interestingly, both taxa showing HAD are parthenogenetic and both taxa not showing HAD reproduce sexually. Species showing HAD were tested for the presence of a pre-mating reproductive isolating mechanism (RIM) which could be maintaining HAD despite the potential for gene flow. Selection against migrants to the alternative host was tested in yellow pecan aphid using a no-choice fitness experiment. The overall contribution of this RIM to total isolation was positive and ranged from 0.614 to 0.850. The RIM of “habitat preference” was tested in pecan leaf phylloxera using a dual-choice preference experiment. In this species, preference was only detected for phylloxera originating from water hickory suggesting that host discrimination ability may be a less important factor promoting differentiation in phylloxera.

Habitat fragmentation can have an impact on a wide variety of biological processes including abundance, life history strategies, mating system, inbreeding and genetic diversity levels of individual species. Although fragmented populations have received much attention, ecological and genetic responses of species to fragmentation have still not been fully resolved. The current study investigated the ecological factors that may influence the demographic and genetic structure of the giant white-tailed rat (Uromys caudimaculatus) within fragmented tropical rainforests. It is the first study to examine relationships between food resources, vegetation attributes and Uromys demography in a quantitative manner. Giant white-tailed rat densities were strongly correlated with specific suites of food resources rather than forest structure or other factors linked to fragmentation (i.e. fragment size). Several demographic parameters including the density of resident adults and juvenile recruitment showed similar patterns. Although data were limited, high quality food resources appear to initiate breeding in female Uromys. Where data were sufficient, influx of juveniles was significantly related to the density of high quality food resources that had fallen in the previous three months. Thus, availability of high quality food resources appear to be more important than either vegetation structure or fragment size in influencing giant white-tailed rat demography. These results support the suggestion that a species’ response to fragmentation can be related to their specific habitat requirements and can vary in response to local ecological conditions. In contrast to demographic data, genetic data revealed a significant negative effect of habitat fragmentation on genetic diversity and effective population size in U. caudimaculatus. All three fragments showed lower levels of allelic richness, number of private alleles and expected heterozygosity compared with the unfragmented continuous rainforest site. Populations at all sites were significantly differentiated, suggesting restricted among population gene flow. The combined effects of reduced genetic diversity, lower effective population size and restricted gene flow suggest that long-term viability of small fragmented populations may be at risk, unless effective management is employed in the future. A diverse range of genetic reproductive behaviours and sex-biased dispersal patterns were evident within U. caudimaculatus populations. Genetic paternity analyses revealed that the major mating system in U. caudimaculatus appeared to be polygyny at sites P1, P3 and C1. Evidence of genetic monogamy, however, was also found in the three fragmented sites, and was the dominant mating system in the remaining low density, small fragment (P2). High variability in reproductive skew and reproductive success was also found but was less pronounced when only resident Uromys were considered. Male body condition predicted which males sired offspring, however, neither body condition nor heterozygosity levels were accurate predictors of the number of offspring assigned to individual males or females. Genetic spatial autocorrelation analyses provided evidence for increased philopatry among females at site P1, but increased philopatry among males at site P3. This suggests that male-biased dispersal occurs at site P1 and female-biased dispersal at site P3, implying that in addition to mating systems, Uromys may also be able to adjust their dispersal behaviour to suit local ecological conditions. This study highlights the importance of examining the mechanisms that underlie population-level responses to habitat fragmentation using a combined ecological and genetic approach. The ecological data suggested that habitat quality (i.e. high quality food resources) rather than habitat quantity (i.e. fragment size) was relatively more important in influencing giant white-tailed rat demographics, at least for the populations studied here . Conversely, genetic data showed strong evidence that Uromys populations were affected adversely by habitat fragmentation and that management of isolated populations may be required for long-term viability of populations within isolated rainforest fragments.

Made available in DSpace on 2014-06-11T19:26:07Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-10-15Bitstream added on 2014-06-13T20:33:51Z : No. of bitstreams: 1 silva_pvc_me_jabo.pdf: 474489 bytes, checksum: 1d66e81d39696776d2b564803c77e0a8 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Universidade Estadual Paulista (UNESP) / A ocorrência de híbridos entre javalis e suínos, tanto na natureza como em cativeiro, é bastante comum. Assim, tem-se detectado polimorfismo em javalis, variando o número de cromossomos de 36 a 38. Nesse sentido, objetivou-se, com este trabalho, caracterizar geneticamente javalis (Sus scrofa scrofa) puros e híbridos criados no Brasil, por meio de loci de microssatélites (STRs) do suíno doméstico (Sus scrofa domestica). Para efeito de classificação, os animais foram agrupados, segundo análise de pedigree e número diplóide (2n), em 5 grupos genéticos: grupo I, constituído de 59 suínos domésticos; grupo II, formado por 46 javalis puros de origem; grupo III, constituído de 3 híbridos, com 2n=36, provenientes de acasalamentos entre híbridos e retrocruzamentos; grupo IV, representando 30 híbridos com suíno doméstico de ploidia igual a 37 cromossomos; e grupo V, constituídos de 10 híbridos também com o doméstico, porém com 2n=38, conhecidos popularmente como Javaporcos, devido à similaridade cariotípica e fenotípica com o suíno doméstico. O DNA genômico foi extraído e, posteriormente, amplificou-se, pela técnica de PCR, os fragmentos desses microssatélites - IGF1, ACTG2, TNFB -, os quais foram desenvolvidos para a subespécie Sus scrofa domestica. As condições de amplificação foram padronizadas para as amostras de javali realizadas em um termociclador, com as temperaturas de anelamento variando para cada primer. Ao final das amplificações, os produtos dos microssatélites foram colocados em um seqüenciador capilar modelo ABI 3100 Avant (Applied Biosystems). A partir dos resultados obtidos no presente trabalho, concluiu-se que os microssatélites IGF1, ACTG2 e TNFB, usados em suínos, são eficiente na amplificação heteróloga e podem ser aplicados em javali. Os javalis puros se diferenciam geneticamente dos suínos e dos híbridos... / The occurrence of crossbred animals between wild boar and pigs, both in nature and in captivity, is quite common. Thus, polymorphism has been detected among wild boar, varying chromosomes from 36 to 38. Considering this, the objective of the present work was to perform a genetic characterization of wild boar and crossbred boars raised in Brazil, through. the microsatellites loci (STRs) of the domestic pig (Sus scrofa domestica). For classification purposes, the animals were grouped according to pedigree analysis and diploid number (2n) into 5 genetic groups: group I, composed of 59 domestic pigs with 2n = 38; group II, composed of 46 wild boar with 2n = 36 imported from France in 1997; group III, composed of 3 crossbred animals with 2n = 36 from the crossing between crossbred and backcrossing animals; group IV, composed of 30 crossbred animals with domestic pig with ploidy equal to 37 chromosomes and group V, composed of 10 crossbred animals also with domestic pig, but with 2n = 38, popularly known as “Boarpigs” due to their karyotypic and phenotypic similarity with the domestic pig. The genomic DNA was extracted and, after that, the fragments of these microsatellites - IGF1, ACTG2, TNFB - were amplified through the PCR technique, which were developed for the Sus scrofa domestica species. The amplification conditions were standardized for wild boar samples and performed in a thermocycler with the annealing temperatures varying for each primer. At the end of amplifications, the products of microsatellites were placed in a genetic analyzer model ABI 3100 Avant (Applied Biosystems). Considering the results of this research, the microsatellites IGF1, ACTG2 and TNFB used for pigs, were considered to be efficient on the heterologous amplifications and can also be applied on wild boar. The wild boar differs genetically from pigs and crossbreds... (Complete abstract, click electronic access below)

Submitted by Cássia Santos (cassia.bcufg@gmail.com) on 2016-12-20T11:26:24Z No. of bitstreams: 2 Dissertação - Ramilla dos Santos Braga - 2015.pdf: 3958526 bytes, checksum: 5fd3bdc31a219fa6ad48dc842f1f6cb3 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-12-27T12:54:04Z (GMT) No. of bitstreams: 2 Dissertação - Ramilla dos Santos Braga - 2015.pdf: 3958526 bytes, checksum: 5fd3bdc31a219fa6ad48dc842f1f6cb3 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2016-12-27T12:54:04Z (GMT). No. of bitstreams: 2 Dissertação - Ramilla dos Santos Braga - 2015.pdf: 3958526 bytes, checksum: 5fd3bdc31a219fa6ad48dc842f1f6cb3 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2015-09-29 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Hymenaea stigonocarpa é uma espécie amplamente distribuída nas regiões do Cerrado brasileiro. Em função de diferenças morfológicas nas folhas, a literatura reconhece três variedades botânicas para esta espécie. Essas variedades são: H. stigonocarpa var. stigonocarpa, com folhas lisas; H. stigonocarpa var. pubescens, com folhas pilosas e H. stigonocarpa var. brevipetiolata, apresentando pecíolo curto, com folhas lisas ou pilosas. O conhecimento da divergência genética intervarietal e análise da estrutura genética espacial é interessante para entender o comportamento dessa espécie em subpopulações naturais e como os processos microevolutivos atuam na organização da sua variabilidade genética. Sendo assim, o objetivo deste trabalho foi verificar o nível de diferenciação genética existente entre as variedades botânicas, a magnitude da variabilidade genética entre e dentro as subpopulações de H. stigonocarpa, bem como o padrão espacial da variabilidade genética encontrada. Para tanto, foram realizadas expedições de coleta em regiões do Cerrado, onde amostrou tecido foliar de 32 subpopulações de H. stigonocarpa, num total de 1.034 indivíduos. A variabilidade genética foi acessada por meio de nove locos microssatélites, em que todas as subpopulações foram caracterizadas geneticamente por meio das estatísticas descritivas. A divergência genética entre variedades foi avaliada com a AMOVA, técnicas de agrupamento multivariadas e inferência Bayesiana. A estrutura genética foi estimada dentro e entre as 32 subpopulações de H. stigonocarpa. Estatísticas espaciais foram realizadas para avaliar a existência de padrões espaciais na variabilidade genética. Além disso, análises de complementariedade genética foram utilizadas para selecionar subpopulações potenciais para conservação. Os nove locos microssatélites foram polimórficos, apresentando níveis moderados de diversidade genética. A AMOVA revelou divergência genética considerável entre as variedades botânicas e aliada às análises de agrupamento indica que a variedade brevipetiolata é a mais diferente geneticamente quando comparado às variedades stigonocarpa e pubescens, que formaram um único grupo. As 32 subpopulações apresentaram baixa endogamia (f= 0,082; p<0,01), mas considerável diferenciação genética entre populações (FST= 0,161; p<0,01) e alta endogamia total (FIT= 0,230; p<0,01). Junto à estatística RST, que foi igual a 0,221 e significativa ao nível de 1% percebe-se que a mutação e deriva genética são importantes para a estruturação genética nesta espécie. As estatísticas espaciais foram obtidas para 30 subpopulações, pois a variedade brevipetiolata foi fortemente diferenciada sobre as demais e assim foi retirada destas análises. O teste de Mantel mostrou uma correlação matricial baixa, porém significativa (rm= 0,239; p=0,0014) entre distância geográfica e o FST par a par. O correlograma de Mantel identificou um padrão clinal na diferenciação genética, sugerindo que as subpopulações se comportam num modelo de isolamento por distância. A autocorrelação espacial, quantificada pelo índice I de Moran, foi baixa nas frequências alélicas entre os pares de subpopulações em cada classe de distância, gerando um correlograma médio sem padrão espacial nítido (rm=0,053; p=0,0005). O algoritmo de Monmonier identificou possíveis barreiras genéticas entre as subpopulações do extremo Norte do Cerrado, mas que precisam ser avaliadas com cautela. A complementariedade genética identificou 16 subpopulações que representam toda a variabilidade genética encontrada para a espécie nos locos avaliados e que foram selecionadas como prioritárias para conservação. As informações obtidas com este trabalho mostram que as estratégias reprodutivas da espécie são importantes para a conectividade genética entre subpopulações a longas distâncias, causando uma fraca estruturação genética espacial. Assim, é sugerido que não apenas o espaço esteja atuando na diferenciação genética, mas outros processos estocásticos. Além disso, a divergência genética entre variedades botânicas torna-se um componente importante para entender a sua estrutura genética, em que este trabalho traz um conhecimento relevante para estudos taxonômicos de H. stigonocarpa, podendo ser mais uma evidência para delimitação de espécies. / Hymenaea stigonocarpa é uma espécie amplamente distribuída nas regiões do Cerrado brasileiro. Em função de diferenças morfológicas nas folhas, a literatura reconhece três variedades botânicas para esta espécie. Essas variedades são: H. stigonocarpa var. stigonocarpa, com folhas lisas; H. stigonocarpa var. pubescens, com folhas pilosas e H. stigonocarpa var. brevipetiolata, apresentando pecíolo curto, com folhas lisas ou pilosas. O conhecimento da divergência genética intervarietal e análise da estrutura genética espacial é interessante para entender o comportamento dessa espécie em subpopulações naturais e como os processos microevolutivos atuam na organização da sua variabilidade genética. Sendo assim, o objetivo deste trabalho foi verificar o nível de diferenciação genética existente entre as variedades botânicas, a magnitude da variabilidade genética entre e dentro as subpopulações de H. stigonocarpa, bem como o padrão espacial da variabilidade genética encontrada. Para tanto, foram realizadas expedições de coleta em regiões do Cerrado, onde amostrou tecido foliar de 32 subpopulações de H. stigonocarpa, num total de 1.034 indivíduos. A variabilidade genética foi acessada por meio de nove locos microssatélites, em que todas as subpopulações foram caracterizadas geneticamente por meio das estatísticas descritivas. A divergência genética entre variedades foi avaliada com a AMOVA, técnicas de agrupamento multivariadas e inferência Bayesiana. A estrutura genética foi estimada dentro e entre as 32 subpopulações de H. stigonocarpa. Estatísticas espaciais foram realizadas para avaliar a existência de padrões espaciais na variabilidade genética. Além disso, análises de complementariedade genética foram utilizadas para selecionar subpopulações potenciais para conservação. Os nove locos microssatélites foram polimórficos, apresentando níveis moderados de diversidade genética. A AMOVA revelou divergência genética considerável entre as variedades botânicas e aliada às análises de agrupamento indica que a variedade brevipetiolata é a mais diferente geneticamente quando comparado às variedades stigonocarpa e pubescens, que formaram um único grupo. As 32 subpopulações apresentaram baixa endogamia (f= 0,082; p<0,01), mas considerável diferenciação genética entre populações (FST= 0,161; p<0,01) e alta endogamia total (FIT= 0,230; p<0,01). Junto à estatística RST, que foi igual a 0,221 e significativa ao nível de 1% percebe-se que a mutação e deriva genética são importantes para a estruturação genética nesta espécie. As estatísticas espaciais foram obtidas para 30 subpopulações, pois a variedade brevipetiolata foi fortemente diferenciada sobre as demais e assim foi retirada destas análises. O teste de Mantel mostrou uma correlação matricial baixa, porém significativa (rm= 0,239; p=0,0014) entre distância geográfica e o FST par a par. O correlograma de Mantel identificou um padrão clinal na diferenciação genética, sugerindo que as subpopulações se comportam num modelo de isolamento por distância. A autocorrelação espacial, quantificada pelo índice I de Moran, foi baixa nas frequências alélicas entre os pares de subpopulações em cada classe de distância, gerando um correlograma médio sem padrão espacial nítido (rm=0,053; p=0,0005). O algoritmo de Monmonier identificou possíveis barreiras genéticas entre as subpopulações do extremo Norte do Cerrado, mas que precisam ser avaliadas com cautela. A complementariedade genética identificou 16 subpopulações que representam toda a variabilidade genética encontrada para a espécie nos locos avaliados e que foram selecionadas como prioritárias para conservação. As informações obtidas com este trabalho mostram que as estratégias reprodutivas da espécie são importantes para a conectividade genética entre subpopulações a longas distâncias, causando uma fraca estruturação genética espacial. Assim, é sugerido que não apenas o espaço esteja atuando na diferenciação genética, mas outros processos estocásticos. Além disso, a divergência genética entre variedades botânicas torna-se um componente importante para entender a sua estrutura genética, em que este trabalho traz um conhecimento relevante para estudos taxonômicos de H. stigonocarpa, podendo ser mais uma evidência para delimitação de espécies.

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.

Le chêne rouge d’Amérique (Quercus rubra L.) est un arbre originaire d’Amérique du Nord et introduit en Europe à partir de la fin du XVIIème siècle pour l’ornementation et le commerce du bois. Le but de cette thèse est de comprendre les mécanismes écologiques et évolutifs qui contribuent à la dynamique et au succès de l’introduction de Q. rubra en Europe. Nous avons montré que cette espèce naturalisée et plantée dans certains pays européens parvient aisément à se développer de façon naturelle dans les forêts de feuillus et de conifères. La dispersion de ses glands est notamment rendue possible par des animaux fouisseurs-disperseurs, tels que les écureuils et les mulots, qui cependant préfèrent les glands du chêne natif Q. robur. Lors de l’introduction d’une espèce dans un nouvel environnement, des processus évolutifs sont susceptibles de se produire et d’engendrer des modifications phénotypiques et génétiques au sein des populations introduites. Une analyse comparative de la structure et de la diversité génétique des populations natives et introduites de Q. rubra a démontré que seulement deux des trois groupes génétiques de l’aire américaine sont actuellement présents en Europe. Aucun goulot d’étranglement fort n’a été détecté lors de l’introduction des populations en Europe laissant supposer que des introductions multiples ont pu maintenir la diversité génétique dans les populations introduites. Une analyse comparative des traits phénotypiques a permis de montrer que les populations introduites de Q. rubra présentent une croissance supérieure par rapport aux populations natives. Une différenciation génétique au sein des populations introduites est en cours pour le trait de débourrement foliaire suggérant une possible évolution adaptative rapide depuis l’introduction. / Northern Red Oak (Quercus rubra L.) is a tree native to North America and introduced in Europe at the end of the 17th century as an ornamental and forestry species. The aim of this dissertation is to understand the ecological and evolutionary mechanisms contributing to its dynamics and success in Europe. We demonstrated that this species naturalized and planted insome European countries can easily naturally grow in deciduous and conifer forests. Acorn dispersal away from mother-trees was made possible by scatter-hoarding animals such as squirrels and mice that take away acorns, although the animals still preferred acorns of the native oak Q. robur. During species introduction in a new environment, evolutionary processes can occurand lead to phenotypic and genetic changes. A comparative analysis of the genetic structure and diversity of Q. rubra populations from the native and introduced ranges demonstrated that onlytwo of the three genetic clusters encountered in North America are currently present in Europe.No strong bottleneck event was detected during the introduction of Q. rubra populations in Europe suggesting that multiple introductions could have maintained genetic diversity in introduced populations. A comparative analysis of phenotypic traits showed that introduced populations of Q.rubra present a higher growth compared to that of native populations. A genetic differentiation within European populations is on going regarding phenology of leaf budburst suggesting apossible rapid adaptive evolution since introduction.

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.

Understanding the ability of species to respond to climate change is essential for prediction of their future distribution. When migration is not adequate, reaction via phenotypic plasticity and/or genetic/epigenetic adaptation is necessary. The main aim of this study is to determine mechanisms of response to climate change in dominant grass species Festuca rubra. The study used reciprocal transplant experiment with growth chambers simulating different climatic conditions. Original localities in western Norway represent factorially crossed gradients of temperatures and precipitations, thus it was possible to study the effect of temperature and moisture separately as well as combined. In first part of the experiment, plastic responses were separated from genetic differentiation. To do this, plants with different genotypes from original localities were transplanted to growth chambers set to simulating temperature and moisture course in the four extreme localities (wettest and driest combined with warmest and coldest). After five months, ecophysiological photosynthetic-related traits were measured. These traits are important for species ability to adapt and maintain high fitness and thus they are essential for plants function. Specifically, it was net photosynthetic rate (PN), fluorescence of...