Les progrès technologiques récents nous permettent d'accéder à la variation des génomes complets ce qui nous ouvre la porte d'une meilleure compréhension de leur diversification via des approches de génomique des populations et de génomique du paysage. Ce travail de thèse se base sur l'analyse des données de génomes complets (WGS) pour caractériser la diversité génétique des petits ruminants (chèvre et moutons) et rechercher les bases génétiques d'adaptations locales.Dans un premier temps, ce travail appréhende un aspect méthodologique et examine la précision et le biais de différentes approches d'échantillonnage des génomes pour caractériser la variabilité génétique, en les comparant aux données WGS. Nous mettons en évidence un fort biais des approches classiques (i.e. puces à ADN, capture de l'exome) ainsi que des séquençages de génomes à faibles taux de couverture (1X et 2X), et nous suggérons des alternatives basées sur un échantillonnage aléatoire de marqueurs dont la densité est variable selon les objectifs d'étude (évaluation de la diversité neutre, déséquilibre de liaison, signatures de sélection). Le jeu de données produit a permis d'évaluer l'état des ressources génétiques de différentes populations domestiques (races locales marocaines, iraniennes, races industrielles) et sauvages (aegagre, mouflon asiatique). Nous relevons une très forte diversité génétique dans les populations indigènes et sauvages qui constituent des réservoirs d'allèles et peuvent jouer un rôle important pour préserver le potentiel adaptatif des petits ruminants domestiques dans un contexte de changement climatique. L'étude plus approfondie des populations de chèvres du Maroc montre une forte diversité génétique faiblement structurée géographiquement, et met en évidence des portions de génome présentant des signaux de sélection. Leur étude montre l'existence de mécanismes adaptatifs potentiellement différents selon les populations (e.g. transpiration/halètement dans l'adaptation probable à la chaleur).Enfin, nous explorons les bases génétiques de l'adaptation locale à l'environnement chez les moutons et chèvres via une approche de génomique de paysage. En scannant les génomes de 160 moutons et 161 chèvres représentant la diversité éco-climatique du Maroc, nous identifions de nombreux variants et gènes candidats qui permettent d'identifier les voies physiologiques potentiellement sous-jacentes à l'adaptation locale. En particulier, il apparait que les mécanismes respiratoires et les processus cardiaques joueraient un rôle clé dans l'adaptation à l'altitude. Les résultats suggèrent que les chèvres et moutons ont probablement développé différents mécanismes adaptatifs pour répondre aux mêmes variations environnementales. Cependant, nous identifions plusieurs cas probables de voies adaptatives communes à plusieurs espèces. Par ailleurs, nous avons caractérisé les patrons de variations du niveau de différenciation de régions chromosomiques sous sélection en fonction de l'altitude. Cela nous permet de visualiser la diversité des réponses adaptatives selon les gènes (par exemple, sélection de variants à faible et/ou haute altitude). Ainsi, ce travail pose les bases de la compréhension de certains mécanismes d'adaptation locale. / Recent technological developments allow an unprecedented access to the whole genome variation and would increase our knowledge on genome diversification using population and landscape genomics. This work is based on the analysis of Whole Genome Sequence data (WGS) with the purpose of characterising genetic diversity in small ruminants (sheep and goats) and exploring genetic bases of local adaptation.First, we addressed a methodological aspect by investigating the accuracy and possible bias in the widely used genotyping approaches to characterize genetic variation in comparison with WGS data. We highlighted strong bias in conventional approaches (SNP chips and exome capture) and also in low-coverage whole genome re-sequencing (1X and 2X), and we suggested effective solutions based on sampling panels of random markers over the genome depending the purpose of the study (assessing neutral diversity, linkage disequilibrium, selection signatures). The various datasets produced allowed assessing genetic resources in various domestic (Moroccan and Iranian indigenous breeds and industrials) and wild populations (bezoars and Asiatic mouflons). We identified a very high diversity in indigenous and wild populations. They constitute a reservoir of alleles allowing them to play a possible key role in the preservation of these species in the context of global changes. The deep study of Moroccan goats showed a high diversity that is weakly structured in geography and populations, and highlighted numerous genomic regions showing signatures of selection. These regions identified different putative adaptive mechanisms according to the population (e.g. panting/sweating to adapt to warm/desert environment).Then, we explored genetic bases of local adaptation to the environment in sheep and goats using a landscape genomics framework. We scanned genomes of 160 sheep and 161 goats representing the eco-climatic Moroccan-wide diversity. We identified numerous candidate variants and genes, which allowed for identifying physiological pathways possibly underlying local adaptation. Especially, it seems that respiration and cardiac process have key roles in the adaptation to altitude. Our results suggest dissimilar adaptive mechanisms for the same environment in sheep and goats. However, we highlighted several cases of common metabolic pathways in different species. Moreover, we characterized some patterns for the variation of genetic differentiation in some candidate genomic regions over environmental gradients. This allowed us to visualise different adaptive reaction depending genes. This work points the way towards a better understanding of some mechanisms underlying local adaptation.

L'adaptation locale est un phénomène micro-évolutif qui peut survenir lorsque des populations d'une même espèce sont exposées à des conditions environnementales différentes.Si cet environnement exerce une pression sous forme de sélection naturelle, qu'il existe un potentiel adaptatif au sein des populations et que le flux de gènes est suffisamment modéré, les populations vont alors tendre vers un optimum adaptatif local.Dans cette thèse, je m'intéresse aux moyens méthodologiques de l'étude de l'adaptation locale d'une part, et à l'étude de ce phénomène le long d'un gradient d'altitude chez la plante alpine Arabis alpina d'autre part.Dans la première partie méthodologique, je montre que les méthodes de scan génomique pour détecter les marqueurs génétiques sous sélection peuvent souffrir de forts taux de faux positifs lorsqu'exposées à des jeux de données complexes, mais réalistes.Je présente ensuite une méthode statistique de détection de marqueurs génétiques sous sélection qui, contrairement aux méthodes existantes, utilisent à la fois la notion de différentiation génétique (ou Fst) et une information environnementale.Cette méthode a été développée de manière à limiter son taux de faux positifs de manière générale.J'offre enfin une perspective concernant les liens entre une expérience ancienne en biologie évolutive (l'expérience de jardin commun) et les nouveaux développements moléculaires et statistiques modernes.Dans la seconde partie empirique, je présente une analyse de la démographie d'A. alpina dans six populations naturelles. Outre qu'elle révèle des caractéristiques biologiques intéressantes sur cette espèce (faible espérance de vie, reproduction et survie très différentielle...), cette analyse montre que la croissance diminue et la survie augmente chez cette espèce avec la baisse de la température moyenne (donc avec l'altitude).Puisque ces analyses ne permettent pas d'exclure des hypothèses de dérive et de plasticité phénotype, je présente une analyse en jardin commun sur A. alpina qui permet de lisser les problèmes de plasticité phénotypique et qui, combinée à des analyses moléculaires, permettent d'exclure l'hypothèse de dérive.Les résultats montrent qu'il existe un syndrome phénotypique adaptatif lié à la température moyenne qui tend à des plantes plus petites, plus compactes, qui croissent et se reproduisent moins, dans les milieux froids.À l'aide des données moléculaires et de méthodes de scan génomique, je présente une liste de 40 locus qui peuvent être impliqués dans ce processus.Pour finir, je discute l'ensemble de ces résultats empiriques dans un contexte plus général d'écologie alpine. Je résume ensuite les principaux obstacles méthodologiques à l'étude de l'adaptation locale et je fourni quelques perspectives méthodologiques. / Local adaptation is a micro-evolutionary phenomenon, which arises when populations of the same species are exposed to contrasted environmental conditions.If this environment exert some natural selection pressure, if an adaptive potential exists among the populations and if the gene flow is sufficiently mild, populations are expected to tend toward a local adaptive optimum.In this thesis, I study the methodological means of the study of local adaptation on the one hand, and I investigate this phenomenon along an elevation gradient in the alpine plant Arabis alpina on the other hand.In the first, methodological part, I show that the genome scan methods to detect selection using genetic markers might suffer strong false positive rates when confronted to complex but realistic datasets.I then introduce a statistical method to detect markers under selection, which, contrary to existing methods, make use of both the concept of genetic differentiation (or Fst) and environmental information.This method has been developed in order to reduce its global false positive rate.Finally, I present some perspectives regarding the relationships between the relatively old ``common garden'' experiment and the new developments in molecular biology and statistics.In the second, empirical part, I introduce an analysis of the demographic characteristics of A. alpina in six natural populations. Besides providing interesting biological information on this species (low life expectancy, strongly contrasted reproduction and survival...), these analyses show that growth increase and survival decrease with the decrease of average temperature (hence with altitude).Since these analyses do not allow us to rule out hypotheses such as drift and phenotypic plasticity, I show the results of a common garden experiment which enable us to smooth phenotypic plasticity and, when combined with molecular data, enable us to rule out the hypothesis of drift.The results show the existence of an adaptive phenotypic syndrome, in which plants are smaller, are more compact, grow slower and reproduce less in cold temperature environments.Using the molecular data, I draw a list of 40 locus which might be involved in this adaptive process.In the end, I discuss these empirical findings as a whole to place them in a more general context of alpine ecology. I sum up the main methodological challenges when studying local adaptation and offer some methodological perspectives.

Robinia pseudoacacia L. est un arbre nordaméricain qui est largement répandu à travers l’Europe. Afin d’évaluer les mécanismes évolutifs pouvant expliquer son potentiel invasif, il est indispensable d’identifier les populations sources de l’introduction et de comprendre quels traits ont contribué à son succès dans l’aire européenne Une étude de génétique des populations a été réalisée, un large échantillonnage a été conduit au sein des deux aires et 818 individus provenant de 63 populations ont été génotypés grâce à 113 marqueurs SNPS. En premier lieu, nous avons démontré que le robinier européen provenait d’un nombre restreint de populations situées au nord du plateau des Appalaches, ce qui est en accord avec les données historiques. Au sein des ÉtatsUnis la structure reflète des processus évolutifs au long cours tandis qu’en Europe, la structure est plus ténue et pourrait être due à l’activité humaine, notamment aux programmes de sélection entrepris en Europe centrale depuis le 18ème siècle. En deuxième lieu, un goulot d’étranglement génétique associé à une perte de diversité a été mis en évidence dans l’aire d’introduction. Enfin un plus fort taux de clonalité a été observé au sein des populations d’Europe Conjointement à cette étude de génétique des populations. Une expérimentation de génétique quantitative a été réalisée afin d’évaluer la différenciation de traits juvéniles entre populations des deux aires (3000 individus de 20 populations) cultivées dans 3 conditions de température différentes (18°C ; 22°C et 31°C). Les résultats ont révélé une augmentation du taux de germination parmi les populations européennes par rapport aux américaines (88% vs 60%) quelles que soient les conditions environnementales. Un scénario possible est que l’Homme aurait sélectionné et propagé les meilleures graines en Europe favorisant alors l’évolution du taux de germination. De plus, les traits phénotypiques juvéniles sont extrêmement plastiques à la température avec une tendance générale à l’augmentation de la valeur du trait avec la température. Cela suggère qu’un réchauffement climatique favoriserait le développement de l’espèce, au moins en conditions d’alimentation en eau non limitante. Cependant, seules les populations américaines montrent un signal une adaptation locale à la température d’origine Dans tous les cas, ils semblent que l’action de l’Homme sur le potentiel reproductif, sexué ou asexué, a probablement influencé le potentiel invasif du robinier en Europe / Robinia pseudoacacia L. is a North American tree which has now broadly spread in Europe. In order to evaluate the evolutionary mechanisms behind its invasiveness, it is crucial to identify the population sources of the introduction and to understand which traits contributed to its success in the European range. To undertake a population genetics study, we performed a large sampling both in the invasive and native ranges; 818 individuals from 63 populations were genotyped using 113 SNPs. First, we demonstrated that European black locust was introduced from only a limited number of populations located in the Northern plateau of the Appalachians Mountains; this is in agreement with historical records. Within America, population structure reflected long time evolutionary processes whereas in Europe, it was largely impacted by human activities. In the European range, the genetic clustering may be a signal of evolution caused by artificial selection due to human oriented mass selection or tree breeding initiated in Central Europe since the 18th century. Second, we evidenced a genetic bottleneck among ranges with a decrease in allelic richness and in the total number of alleles in Europe. Lastly, we found more clonality within the European populations. Conjointly to the population genetic analysis, we conducted a quantitative genetics experiment to evaluate juvenile traits of both native and invasive black locust populations (3000 individuals from 20 populations) grown under 3 different temperature conditions. Results revealed an enhanced germination rate among European populations compared to that of the native American populations whatever the environmental condition (88% vs 60%). Thus a possible scenario may be that Man would have selected and propagated the best seeds in the new range that would have favored an evolution of germination rate through European populations. Phenotypic traits of juvenile development are extremely plastic in response to temperature (18/22/31°C), with a general tendency to increasing trait values with increasing temperature. This suggests that global warming would favor the development of the species, at least under nonlimiting water supply conditions. However, only American populations demonstrated a signal of local adaptation to the temperature at the sampling location. In any case, the human role on the reproductive potential, both sexual and asexual, within the introduced rangewould likely be a key process in the success of black locust dynamics in Europe.

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.

Abstract A central goal in evolutionary biology is to identify the ecological and genetic mechanisms that give rise to adaptation and speciation. Importantly, a large body of theoretical work has modelled the adaptive evolution under selection, migration and drift. Yet to test these predictions on an empirical level has proven a challenging task. The aim of my thesis is to explore outstanding questions in local adaptation and reproductive isolation using natural populations of Arabidopsis lyrata: How does differential selection lead to adaptive divergence in the face of gene flow and drift? What traits underlie both short- and large-scale adaptive differentiation? And what reproductive barriers are involved in incipient speciation? By combining whole-genome based demography simulations with a multi-year reciprocal transplant experiment, I confirmed that alpine and lowland populations of A. lyrata are adapted to their local environments despite high gene flow and strong drift. Patterns of trait differentiation, supported by analysis of phenotypic selection, further suggested that flowering traits have contributed to the adaptive divergence. Selection patterns at the sequence level confirmed that the genetic architecture underlying the local adaptation conforms to theory: populations under higher levels of gene flow had fewer adaptive loci that were also found in areas of reduced recombination. Although most selection outliers were population specific, indicating conditional neutrality, a small proportion showed potential for genetic trade-offs (antagonistic pleiotropy). The analysis also revealed important traits and biological processes linked to alpine and lowland adaptation. The role of seed germination in large-scale adaptation and reproductive isolation was also studied. Populations representing the European and North American subspecies exhibited germination patterns consistent with adaptive differentiation. Comparisons against first- and second-generation hybrids then indicated that genetic incompatibilities impede germination of the hybrid seeds. Furthermore, genetic mapping helped to clarify the genetic basis of these phenotypic traits. Taken together, the three studies in this thesis highlight the value of combining traditional organismal methods with next-generation genomics, by providing novel insights into processes underlying adaptation and speciation. / Tiivistelmä Evoluutiobiologian keskeinen tehtävä on sopeutumiseen ja lajiutumiseen johtavien prosessien selvittäminen. Vaikka evoluutiovoimien – luonnonvalinnan, geenivirran ja geneettisen satunnaisajautumisen – vaikutusta adaptiivisen muuntelun määrään on mallinnettu laajalti, teoreettisten ennusteiden tarkastelu empiirisellä tasolla on usein osoittautunut haastavaksi. Tässä väitöskirjatyössä pyrin vastaamaan eräisiin paikallissopeutumisen ja lajiutumisen kannalta tärkeisiin kysymyksiin, hyödyntäen kasvilaji idänpitkäpalkoa (Arabidopsis lyrata) malliorganismina: Kuinka luonnonvalinta johtaa paikallissopeutumiseen tilanteessa, jossa geenivirta samankaltaistaa eriytyvien populaatioiden perimää? Mitkä ominaisuudet vaikuttavat adaptiiviseen erilaistumiseen eri etäisyyksillä olevien populaatioiden välillä? Sekä millaiset lisääntymisesteet johtavat alkavaan lajiutumiseen? Yhdistämällä genomisekvensointiin perustuvan demografia-analyysin ja monivuotisen siirtoistutuskokeen, selvitin kuinka idänpitkäpalkopopulaatiot ovat sopeutuneet elinympäristöihinsä runsaasta geenivirrasta ja voimakkaasta satunnaisajautumisesta huolimatta. Fenotyyppisen muuntelun ja kelpoisuuden yhteys vahvisti myös, että kukkimisominaisuudet ovat vaikuttaneet populaatioidenväliseen adaptiiviseen erilaistumiseen. Valinnan merkkien etsiminen sekvenssitasolla osoitti, että havaintoni paikallissopeutumisen geneettisestä arkkitehtuurista tukevat teoreettisia ennusteita: populaatioista, joihin kohdistuu voimakasta geenivirtaa, löytyi vähemmän adaptiivisia lokuksia ja ne olivat keskittyneet matalamman rekombinaation alueille. Suurin osa adaptiivisista lokuksista löytyi ainoastaan yhdestä populaatiosta, ollen näin todennäköisesti valinnan alla ainoastaan tietyssä elinympäristössä. Pieni osuus lokuksista vastasi kuitenkin harvoin havaittua tilannetta, jossa hajottava valinta on johtanut eri alleelien runsastumiseen populaatioissa, joita yhdistää geenivirta. Tutkin myös, miten itämisajan muuntelu vaikuttaa sopeutumiseen pitkällä aikavälillä. Eurooppalaista ja pohjoisamerikkalaista alalajia edustavat populaatiot itivät tavalla, joka viittaa adaptiiviseen erilaistumiseen. Ensimmäisen ja toisen hybridisukupolven siementen vertailu paljasti lisäksi, että geneettiset yhteensopimattomuudet haittaavat hybridien itämistä, toimien näin lisääntymisesteenä. Geenikartoitus auttoi myös selventämään näiden itämisominaisuuksien geneettistä taustaa. Tämän väitöskirjan kolme osatyötä korostavat miten perinteisten yhteiskenttäkokeiden ja uuden sukupolven genomimenetelmien yhdistelmä voi tuottaa arvokasta lisätietoa sopeutumisen ja lajiutumisen mekanismeista.

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.

Connaitre et appréhender les mécanismes de la diversification des espèces est important pour la gestion des écosystèmes, la prévision des impacts des changements climatiques et la compréhension de la biodiversité actuelle et passée. Le but de cette thèse est de comprendre et de déceler les mécanismes génétiques à l’origine de la diversification des espèces en présence de flux de gènes. Cette thèse se focalise sur le modèle biologique Symphonia globulifera, qui compte deux écotypes : le S.globulifera spécialiste de la terra firme et le S.sp1, spécialiste des bas-fonds. Ces deux écotypes montrent une faible différenciation génétique, malgré la présence de deux phénotypes différents.Une première étape a été de mettre en évidence la présence d’une adaptation locale au sein de cette espèce, par le biais d’une expérimentation de jardins de transplantation réciproques, permettant d’expliquer la répartition des écotypes dans leur habitat naturel. Ensuite, dans le but d’identifier les mécanismes sous-jacent à cette adaptation locale, j’ai testé l’hypothèse que la méthylation des gènes pourrait être une marque de l’épigénétique contribuant à la divergence des écotypes, par l’utilisation d’enzyme sensibles à la méthylation dans un protocole de génotypage AFLP. Enfin, un séquençage haut-débit du transcriptome des écotypes en jardins de transplantation réciproques m’a permis de mettre en évidence une expression différentielle des gènes entre les écotypes, qui pourrait expliquer les différences phénotypiques observées entre les écotypes malgré une faible différentiation génétique. Ces travaux de thèse s’appuie, ainsi, sur des données de traits phénotypiques, de génotypage AFLP et de séquençage à haut débit du transcriptome pour montrer la valeur importante de la régulation des gènes dans la divergence des écotypes adaptés localement, et un faible rôle de la méthylation de l’ADN dans l’établissement cette adaptation locale. / Understanding of the mechanisms driving diversification of species is a significant way to improve the management of ecosystems, predict the impacts of climate change and understand the actual and past biodiversity level. The aim of this thesis is to understand and comprehend genetic mechanisms behind the diversification of species in the presence of gene flow. This thesis is focused on the biological model Symphonia globulifera, which presents two ecotypes: the S.globulifera, specialist of seasonally flooded lowlands and S.sp1, specialist of terra firme. These two ecotypes show low genetic differentiation, despite the presence of two apparent phenotypes. A first part of this thesis was to test the presence of local adaptation of this using reciprocal transplant experiment gardens, allowing the understanding of the ecotypes distributions in their natural habitats. Then, this local adaptation in the presence of gene flow, directed me to the regulation of gene methylation in order to see the role this brand of epigenetics can have in the divergence of the ecotypes. In a third part of the thesis, new generation sequencing of the transcriptome ecotypes in reciprocal gardens transplantations allowed me to show the evidence of gene regulation to differentiate the ecotypes. This work thesis is based on phenotype records data, AFLP genotyping and high-throughput sequencing of the transcriptome, in order to show the important value of gene regulation in the divergence of the locally adapted ecotypes, and a weak role of DNA methylation in the establishment of local adaptation.

Abstract Local adaptation is important evolutionary process leading to adaptive population differentiation. Currently, examining its genetic basis is a major goal of evolutionary and ecological genetics. In my thesis I studied local adaptation and its genetic basis in populations of a perennial outcrossing model plant Arabidopsis lyrata by combining common garden experiments at the native field sites and in controlled conditions with quantitative trait locus mapping. Estimates of fitness in the field – both at the level of multiple components as well as hierarchical total fitness – showed that populations of A. lyrata were locally adapted. The studied populations were also phenotypically differentiated in ecologically relevant traits. Different components of fitness were important for the advantage of the locals depending on the environment. Local alleles were associated with high fitness in the field, suggesting that differing directional selection pressures have been involved in phenotypic differentiation. Mostly different genomic regions governed local adaptation in different environments, but the results also suggested that some of these regions could involve rarely documented fitness tradeoffs (antagonistic pleiotropy). Loci governing flowering time differentiation differed between the studied environments, highlighting the need to conduct experiments both in the wild and in controlled conditions. In contrast to most existing studies, F2 hybrids in general had surprisingly high fitness at one study site, largely due to beneficial dominance effects at loci governing survival in that environment. In addition to nuclear genes, cytoplasmic genomes also were found to have a role in local adaptation. / Tiivistelmä Luonnonvalinta saa aikaan paikallista sopeutumista ja adaptiivista erilaistumista. Paikallisen sopeutumisen perinnöllisen taustan selvittäminen on tällä hetkellä yksi tärkeimpiä evolutiivisen ja ekologisen genetiikan tavoitteita. Tässä väitöskirjatyössä tutkin paikallista sopeutumista ja sen geneettistä taustaa monivuotisella, ristipölytteisellä mallikasvilla, idänpitkäpalolla (Arabidopsis lyrata). Käytin työssäni geenikartoitusta kasveilla joita kasvatettiin yhdenmukaisissa oloissa sekä populaatioiden luontaisilla kasvupaikoilla että kontrolloiduissa olosuhteissa. Kenttäolosuhteissa arvioitu kelpoisuus osoitti idänpitkäpalkopopulaatioiden olevan paikallisesti sopeutuneita sekä yksittäisten kelpoisuuteen vaikuttavien ominaisuuksien että hierarkkisen kokonaiskelpoisuuden tasolla. Tutkitut populaatiot olivat myös erilaistuneita ekologisesti tärkeissä ominaisuuksissa. Kelpoisuuteen vaikuttavat ominaisuudet myös poikkesivat ympäristöjen välillä. Paikalliset alleelit olivat yhteydessä korkeaan kelpoisuuteen luonnossa, minkä perusteella voitiin päätellä erisuuntaisen luonnonvalinnan vaikuttaneen populaatioden erilaistumiseen. Kromosomiston eri alueet olivat tärkeitä sopeutumisessa eri ympäristöihin, mutta myös joidenkin samojen genomin alueiden havaittiin mahdollisesti vaikuttavan vastakkaisesti kelpoisuuteen eri ympäristöissä. Myös kukkimisajan erilaistumiseen vaikuttavat genomin alueet poikkesivat eri ympäristöjen välillä erityisesti verrattaessa kenttäkokeita kasvatushuone- ja kasvihuonekokeisiin. Toisin kuin useimmissa tutkimuksissa on havaittu, F2-sukupolven jälkeläistön kelpoisuus oli yllättävän korkea yhdessä kenttäkoeympäristössä. Tähän vaikuttivat kelpoisuuden kannalta suotuisat dominoivat geenivaikutukset, jotka paransivat kasvien selviytymistä kyseisessä ympäristössä. Tumassa sijaitsevien geenien lisäksi myös soluelimien perimällä havaittiin olevan yhteys paikalliseen sopeutumiseen.

Anther smuts (Microbotryum violaceum s.l.) represent a well-known system for studying pathogens of wild plants and coevolution between pathogens and hosts. Infected plants produce sterile flowers with anthers filled with fungal spores which are transmitted to other host plants by pollinators. Data from existing research come mainly from the genus Silene. However, the applicability of these findings to other host plants of anther smuts is largely unknown. Therefore, this thesis focuses on a different host species - Dianthus carthusianorum. First, the pattern of disease was surveyed in natural populations of D. carthusianorum in a small area in Střední Povltaví. Most populations were infected to various degrees and only a few populations remained completely healthy. The prevalence of disease was positively correlated with size and density of host populations. On the other hand, environmental factors and the degree of connectedness had very little effect on disease prevalence. Second, additional data were collected from a subset of populations to determine plant resistance and densities of pollinators. Differences in resistance among populations (as inferred from flower inoculations) were not significant. Populations differed in densities of pollinators, but there was no correlation between densities...

En augmentant la distribution des ressources dans l'espace, la fragmentation du paysage contraint le mouvement des organismes. Deux types de stratégies adaptatives antagonistes ont été mises en évidence en réponse à cette pression : une diminution ou une augmentation de la propension et de la capacité des organismes à se déplacer. La majorité de la littérature traite de la diminution des mouvements en réponse à la fragmentation du paysage. En étudiant un organisme contraint de traverser la matrice pour achever son cycle de vie (i.e. Bufo bufo), je me suis intéressée à la stratégie d'augmentation et d'optimisation des mouvements en réponse à la fragmentation. Peu d'études permettent de conclure sur l'existence de plasticité phénotypique, d'effets maternels ou d'évolution des traits liés au mouvement en réponse à la fragmentation. J'ai ainsi inclus dans ma démarche expérimentale des élevages en conditions standardisées afin d'étudier l'évolution des caractéristiques du mouvement en réponse à la fragmentation. Plus précisément, j'ai étudié l'évolution des capacités de navigation en m'intéressant à la vitesse dévolution, à la base magnétique et à l'influence de l'orientation vectorielle sur la dispersion. Je me suis également intéressée à l'évolution du comportement exploratoire en réponse à la fragmentation / Landscape fragmentation increases resource distribution and constrains animal movements. Two kinds of adaptive strategy have been revealed in response to this selective pressure: an increase or a decrease of animal capacity and propensity to move. I studied the resistance strategy (i.e. increase of movements) which is poorly documented in the literature. To do so I focused on an organism facing the need to cross the matrix to achieve its life cycle (Bufo bufo). Only a few studies enable to disentangle phenotypic plasticity, maternal effect and evolution of movement characteristics. I used common garden rearing and cross-breeding experiments in order to focus on the evolutionary dimension of movement characteristics changes induced by landscape fragmentation. More precisely, I studied the evolution of navigation capacities by focusing on vector orientation, its evolutionary rate, its genetic basis, its magnetic basis and its influence on dispersal. I also studied the evolution of the exploratory behaviour in response to landscape fragmentation and searched for convergent evolution of this behaviour