Les perturbations anthropiques en Amazonie liées au déboisement de la forêt tropicale conduisent à une mosaïque de paysages constituée de végétations secondaires (forêts secondaires, palmeraies, jachères) et de pâturages. Ces modifications favorisent la prolifération de grands palmiers héliophiles invasifs de la famille Attalea spp., palmiers qui constituent l'écotope principal des espèces de Rhodnius, punaises hématophages vectrices de Trypanosoma cruzi, agent étiologique de la Maladie de Chagas en Amérique Latine. Cette étude a porté sur différentes unités de paysage de trois communautés rurales du bas Tapajós (Amazonie brésilienne) ayant une époque d'installation différente sur le territoire (25-75 ans). Six unités de paysage ont été définies sur le terrain et appliquée via une classification supervisée à une image SPOT 5, afin d'obtenir une cartographie du risque environnemental associé à la présence de palmiers dans la région. Sur les cent trente trois palmiers disséqués appartenant aux trois espèces Attalea maripa, A. phalerata et A.speciosa, 73 (54.88%) étaient infestés par R. robustus (742 insectes récoltés). Des diminutions significatives de densité de triatomes ont été observées chez A. maripa, dans la communauté la plus récemment établie (Araipá) et dans les unités de paysage les plus anthropisées. L'infection des insectes par T. cruzi et T. rangeli a été examinée à l'aide de méthodes moléculaires (mini exon SL_IR and sno-RNA-C11). Respectivement 123 (16.57%) et 69 (9.3%) insectes dans 31 (23.3%) et 17 (13.82%) palmiers ont été identifiés positifs à T cruzi et à T.rangeli. Aucune infection n'a été trouvée dans les insectes collectés à Araipá et aucune différence significative n'a été mise en évidence entre les différentes unités de paysage. Les souches de Trypanosoma cruzi identifiées à l'aide de 4 marqueurs moléculaires (mini exon SL-IR, GPI, HSP60 et D7-24α-rRNA) appartiennent à la lignée TcId et 10 (8.13%) individus présentent une infection mixte TcI-TcII. Vingt espèces d'hôtes réparties en trois classes (mammifères, oiseaux, sauropsidés) ont été identifiées comme sources alimentaires à partir du repas sanguin contenu dans le tube digestif des insectes, à l'aide d'amorces cytochrome b, spécifiques de vertébrés. Quatre-vingts et un pourcent des repas détectés ont été effectués sur des mammifères, hôtes potentiels de T.cruzi dont Tamandua tetradactyla, source alimentaire principale. Cet hôte a été clairement identifié comme réservoir de T.rangeli ainsi que suggéré pour T.cruzi. L'analyse phylogénique réalisée à l'aide de séquences de cytochrome b démontre que les individus de Rhodnius identifiés dans la région du Tapajos appartiennent au clade II, ce qui correspond à une extension de l'aire précédemment décrite pour ce clade. L'utilisation du marqueur mitochondrial cytochrome b a permis de mettre en évidence une structuration phylogénétique (haplogroupes) non retrouvée à l'aide des marqueurs microsatellites. Ce résultat montre que l'histoire des gènes (génome mitochondrial) ne retrace pas l'histoire des individus (microsatellites, 10 locus). L'analyse de génétique des populations conduite à l'aide des deux types de marqueurs n'a pas révélé de structuration génétique au sein de la zone d'étude entre les communautés ou les unités de paysage. Cette étude met en évidence des flux géniques importants peu sensibles à la fragmentation du milieu, la dynamique d'invasion des palmiers assurant aux insectes une connectivité fonctionnelle entre les différentes unités de paysages et les communautés. La prédiction du risque environnemental lié à la situation du Tapajós va vers une augmentation du risque de transmission de la Maladie de Chagas dans cette région, du fait de l'abondance des palmiers, de leur forte connectivité, et de la présence de vecteurs et d'hôtes infectés circulant entre les différentes communautés et unités du paysage / Anthropic disturbances from deforestation of Amazon tropical forest leads to a mosaic of landscapes composed of secondary vegetation (secondary forest, palm groves, fallows) and pasture. These changes result in the proliferation of invasive heliophilous palm trees of the family Attalea spp., the principal ecotope of Rhodnius species, bloodsucking bug vectors of Trypanosoma cruzi, the etiologic agent of Chagas disease in Latin America. The present study focuses on different land cover classes of three rural communities of the lower Tapajós (Brazilian Amazon) with different settlement times (25-75 years). Six different land-cover classes were identified on the field and applied through supervised classification on a SPOT 5 image of the study area in order to cartography environmental risk associated to palm tree presence in the area. Three hundred and thirty palms trees of three species Attalea maripa, A. phalerata and A.speciosa were dissected of which 73 (54.88%) were infested with R. robustus (742 insects collected). The distribution of palm species varied in each community, A.maripa was the only species found in the most recently settled community (Araipá). Significant decreases in bug density were observed in A.maripa, in the community most recently established (Araipá) and in the two most anthropogenic landcover classes.Infection of insects by T. cruzi and T. rangeli was examined using molecular methods (mini exon SL_IR and sno-RNA-C11). Respectively, 123 (16.57%) and 69 (9.3%) insects in 31 (23.3%) and 17 (13.32%) palms were identified as positive for T. cruzi and T. rangeli. A lack of infection was detected in Araipá but no differences were observed between the different land cover classes. The strains of Trypanosoma cruzi were identified using four distinct molecular markers (mini-exon SL-IR, GPI, HSP60 and D7-24α-rRNA) as belonging to the lineage TCI specifically TcId and 10 (8.13%) individuals showed a mixed infection TCI-TCII. Twenty host species divided into three classes were identified (mammals, birds, reptiles) were identified as food source from blood meal from the bug gut with cytochrome b primers, specific for vertebrates (25.74% of meals). Eighty-one percent of meals were conducted on mammals, potential hosts of T. cruzi, specially on Tamandua tetradactyla,identified as the main food source. This host was clearly identified as a reservoir for T.rangeli and also suggested for T. cruzi.Phylogenetic analysis performed using cytochrome b sequences, identified Rhodnius individuals in the Tapajos region within clade II, which represent an extension of the range previously described for this clade. The use of the cytochrome b marker also revealed a phylogenetic structure (haplogroups) not found using microsatellite markers. This result showed that the history of the genes (mitochondrial genome) does not match the history of individuals (microsatellites, 10 loci). Population genetics analysis conducted using both markers did not reveal genetic structure within the study area between the communities or the landcover classes. The study revealed significant gene flow, which was not restricted by the fragmentation of the environment. The invasive dynamics of Attalea palm trees provide a functional connectivity for insects to move between the different landcover classes and communities. Due to the abundance of palm trees and their high connectivity, the presence of vectors and infected hosts moving between the different communities and landcover classes, the environmental risk constituted by Attalea palm tree presence of Chagas disease in Tapajós region will presumably continue to increase

To assess the status of a rare plant species, we must first understand the factors that affect the size of populations and their numbers. In this thesis, I study processes affecting plant species prosperity on local scale (paper 1), factors influencing species distribution in landscape and ability of species to colonize new habitats (paper 2) and species traits responsible for gene flow between established populations (paper 3). Since I work with rare plants, I also aim to turn theoretical knowledge into practical recommendations for nature conservation (paper 4) to help effectively preserve rare and endangered species. In the first 3 papers, I work with two rare fern species restricted to serpentine rocks, Asplenium adulterinum and A. cuneifolium, in a study system covering 10 × 10 km. I found that both species are long living (several decades) and in the study region, populations are in a good state and slowly growing. Even very small populations (10 individuals) have quite high chance to survive. In both fern species, I found dispersal limitation, which might be surprising regarding huge production of small spores in ferns (paper 2). The species differ in ploidy and thus, also mating system. A. adulterinum is tetraploid and its main breeding system is intragametophytic selfing. A. cuneifolium is...

A UGRHI-17 da bacia hidrográfica do Médio Paranapanema (São Paulo, Brasil) é reconhecidamente uma área de alta biodiversidade de espécies de Biomphalaria e possui grande vulnerabilidade a acometimentos ambientais e em saúde, no caso da esquistossomose. O objetivo do estudo foi identificar áreas de maior risco para a ocorrência da esquistossomose utilizando dados de transmissão da esquistossomose e de diversidade genética molecular, associando-os às ferramentas geoespaciais, e com isso estabelecer áreas potenciais para a vigilância malacológica e da infecção em coleções de água doce na região do Médio Paranapanema. Os moluscos do gênero de Biomphalaria foram identificados por meio de características morfológicas e moleculares; enquanto os outros grupos taxonômicos (Drepanotrema, Lymnaea, Melanoides, Physa e Pomacea) foram identificados por características conchiológicas ou morfológicas. A análise filogenética das espécies de Biomphalaria foi realizada por meio da análise de sequências dos genes mitocondriais COI, 16S rRNA e COI+16S. As sequências do gene COI referentes ao trecho DNA Barcode foram testadas quanto à similaridade com sequências depositadas no GenBank e analisadas em ABDG, bPTP e GMYC para delimitação de espécies putativas. Na análise espacial foram utilizadas as estatísticas de varredura, Gi e de fluxo. Foram utilizadas as fichas notificação e investigação dos casos de esquistossomose na região de estudo entre 1978-2016. Foi calculado as taxas de incidência e foi avaliado a dependência espacial entre os casos autóctones e importados com a função K12 de Ripley. Foram gerados mapas da distribuição espacial dos caramujos do gênero Biomphalaria; dos casos de esquistossomose ocorridos na região de estudo; e da diversidade genética em haplótipos do gene 16S. Além disso, foi realizada modelagem de nicho para estimar cenários futuros de alteração na distribuição dos caramujos, utilizado o algoritmo de máxima entropia. Foram utilizados os dados de variáveis climáticas e topográficas obtidas no WorldClim, HydroSHEDS e TOPODATA e o modelo climático regional HadGEM2-ES do período de 2041-2060, considerando dois cenários de mudança climática possíveis: RCP2.6 e RCP8.5. Foram identificados aglomerados de alto risco para ocorrência de esquistossomose em Ourinhos, Assis e Ipaussu. Entretanto, ao longo dos anos, os casos passaram a ocorrer em baixa densidade em Ourinhos e deixaram de ocorrer nos demais municípios da região. Dos caramujos coletados, 75.5% eram Biomphalaria, 11.2% Drepanotrema e 13.3% de outros gêneros não planorbídeos. O modelo de máxima entropia mostrou que há probabilidade futura da espécie B. glabrata permanecer nos municípios de Ourinhos e Assis, e uma probabilidade em torno de 50% de a espécie expandir sua colonização a corpos de água doce de outros municípios da região de estudo, isto em função das mudanças climáticas. Os resultados para B. straminea mostram que esta espécie tem maior probabilidade de expansão de colonização no futuro, especialmente nos municípios próximos a Ourinhos. A análise filogenética mostrou árvores com cinco ramos monofiléticos com alto suporte estatístico. A diversidade de haplótipos está distribuída de forma diferente em cada um dos cinco taxa analisados. Conclui-se, em um dos resultados deste trabalho, que atualmente a esquistossomose, como problema de saúde pública no Médio Paranapanema, está restrita a Ourinhos. Tal fato pode estar relacionado à presença de B. glabrata em pontos específicos e à cobertura deficiente do saneamento básico. Desta forma, o estudo contribuiu para eleger áreas prioritárias para o combate aos caramujos e à doença para evitar ou reduzir transmissões futuras nesta região. / The UGRHI-17 of the Middle Paranapanema watershed (São Paulo, Brazil) is recognized as an area of high biodiversity of Biomphalaria species and great vulnerability to environmental and health impacts for schistosomiasis. The objective of the study is to identify areas of greatest risk for the occurrence of schistosomiasis using transmission data from schistosomiasis and molecular genetic diversity, associating them with the geospatial tools, and thereby establishing potential areas for malacological surveillance and infection in collections of freshwaters in the region of Middle Paranapanema. Molluscs of the genus Biomphalaria were identified by morphological and molecular characteristics; while the other taxonomical groups (Drepanotrema, Lymnaea, Melanoides, Physa and Pomacea) were identified through conchiological or morphological characteristics. Molecular genetic analysis of the species was done through sequence analysis of the mitochondrial genes COI, rRNA16S and COI+16S. The COI gene sequences related to DNA Barcode portions were tested for similarity to sequences deposited in GenBank and analyzed ABDG, BPTP and GMYC for delimiting putative species. In the spatial analysis we used the scan statistics, Gi and flow maps. Reporting and investigation records of cases schistosomiasis in the study regions between 1978 and 2016 were used. Incidence were calculated and the existence of spatial dependence between autochthonous and imported cases was evaluated using Ripley\'s K12-function. Maps of the spatial distribution of snails of the genus Biomphalaria; cases of schistosomiasis occurred in the study region; and the genetic diversity in haplotypes of the 16S gene were generated. In addition, the ecological niche modeling to estimate future scenarios of alteration in the distribution of snails, used the maximum entropy algorithm in MaxEnt software. Climate and altitude data obtained from WorldClim, HydroSHEDS and TOPODATA and the regional climate model HadGEM2-ES from the period of 2041-2060 were used, considering two possible scenarios of climate change: Representative Concentration Pathways - RCP2.6 and RCP8.5. High-risk clusters were identified for the occurrence of schistosomiasis in Ourinhos, Assis and Ipaussu. However, over the years, cases occurred in low density in Ourinhos and ceased to occur in other municipalities in the region. Of the snails collected, 75.5% were Biomphalaria, 11.2% Drepanotrema and 13.3% of other non-planorbid genera. The maximum entropy model showed that B. glabrata is a future likely to remain in the municipality of Ourinhos and Assis and a probability around 50% of species to expand their colonization to freshwater bodies of other municipality of the study region, due to the climatic changes. The results for B. straminea showed that this is the species most likely to expand colonization in the future, especially in the municipalities near Ourinhos. The phylogenetic analysis showed trees with five monophyletic branches with high statistical support. The diversity of haplotypes is distributed differently at each of the five taxa analyzed. As one of the results of this work it was concluded that, currently, schistosomiasis as a public health problem in the Middle Paranapanema is restricted to Ourinhos. This may be related to the presence of B. glabrata at specific point and poor coverage of basic sanitation. In this way, the study contributed to the selection of priority areas for combating snails and disease in order to avoid or reduce future transmissions in this region.

Estudos de genética de populações de pragas agrícolas têm destacado a importância de se conhecer a estruturação genética e os padrões de fluxo gênico entre populações para o refinamento de estratégias de Manejo Integrado de Pragas (MIP). A lagarta-da-maçã do algodoeiro, Heliothis virescens (F.), é um inseto praga amplamente distribuído e importante economicamente por causar danos consideráveis à cultura do algodão no Brasil. O controle dessa praga tem sido feito principalmente pelo uso de inseticidas e de plantas geneticamente modificadas (GM) que expressam proteína(s) de Bacillus thuringiensis Berliner e o potencial de evolução da resistência é alto. O conhecimento de quanto as populações de H. virescens são capazes de trocar informação genética entre si é de fundamental importância para a implantação de estratégias de manejo dessa praga. No entanto, pouco se sabe sobre a estrutura genética e os padrões de fluxo gênico em H. virescens em escalas locais e regionais no Brasil. Assim, o objetivo desse trabalho foi avaliar a variabilidade genética em populações de H. virescens utilizando marcadores microssatélites. Foram amostrados indivíduos de H. virescens oriundos de populações coletadas nas safras de 2007/08, 2008/09 e 2009/10 nas principais regiões produtoras de algodão e soja no Brasil. Foram estudados nove locos polimórficos em 12 populações, em um total de 205 indivíduos. O número médio de alelos por loco foi de 14,11. Os valores de heterozigosidade média esperada (HE) e observada (HO) foram de 0,303 e 0,438, respectivamente. O coeficinete de endocruzamento da espécie f foi de 0,294 (IC 95% de 0,178 a 0,406). As estimativas de estruturação genética foram = 0,132 (IC 95% de 0,072 a 0,218) e RST = 0,252. Esses valores indicam uma estruturação genética moderada entre as populações. Estimativas do número de migrantes indicaram um pequeno fluxo gênico, principalmente no sentido Centro- Oeste Nordeste, embora a maioria dos indivíduos dentro das populações seja residente; adicionalmente, foi verificado que o estabelecimento das populações do algodão ocorre a partir de indivíduos migrantes da soja ou descendentes desses indivíduos. Análises de Componentes Principais e de atribuição usando inferência Bayesiana revelaram a formação de dois grupos, porém não foi possível identificar um padrão de agrupamento (por região, safra ou hospedeiro). Desta forma os resultados do presente trabalho sugerem uma estruturação genética incipiente para as populações de H. virescens no Brasil. Desse modo, é importante levar esses resultados em consideração para que o MIP em geral, e especificamente para que as abordagens para retardar a evolução da resistência sejam implementadas de forma efetiva para o manejo de H. virescens no Brasil. / Agricultural pests population genetics studies have emphasized the importance of genetic structure and patterns of gene flow knowledge for Integrated Pest Management (IPM) strategies. The tobacco budworm, Heliothis virescens (F.), is a widespread and economically important insect pest renowned for causing considerable damage in cotton fields in Brazil. This pest has been controlled by the use of insecticides and genetic modified plants (GM) expressing proteins from Bacillus thuringiensis Berliner, and it has already been shown to present a high potential to develop resistance to these control technologies. To a successful application of these strategies it is needed to know the capacity of the pest populations to exchange genetic information among them. However, for H. virescens a scarce amount of information about genetic structure and patterns of gene flow is available at local and regional scales in Brazil. In this way, the main objective of this study was to evaluate the genetic variability of H. virescens based on microsatellite markers. Specimens were sampled during 2007/08, 2008/09 and 2009/10 from the main cotton and soybean producers regions in Brazil. From this, nine polymorphic loci from 12 populations were studied in 205 specimens. The average number of alleles was 14.11. Expected (HE) and observed (HO) heterozygosity were 0.303 and 0.438, respectively. Inbreeding coefficient f was 0.294 (IC 95% 0.178 - 0.406). Genetic structure indices were: = 0.132 (IC 95% 0.072 0.218) and RST = 0.252. These values point to a moderate genetic structure among H. virescens populations. Migrants estimative indicate a low gene flow, mainly in the Center-Western Northern direction, although most individuals are residents within populations; additionally it was suggested that immigrants to cotton populations come from soybean fields. Genetic relationships inferred by Principal Component Analysis and Bayesian assignment tests identified two groups, although no group pattern was recognized, even by geographic region, year of sampling or host plant. These results suggest an incipient genetic structuring for H. virescens populations within Brazil. Thus, such results should be considered for IPM strategies aiming in an efficient control of H. virescens in Brazil.

A estrutura populacional e o desequilíbrio de ligação são dois processos fundamentais para estudos evolutivos e de mapeamento associativo. Tradicionalmente, ambos têm sido investigados por meio de métodos clássicos comumente utilizados. Tais métodos certamente forneceram grandes avanços no entendimento dos processos evolutivos das espécies. No entanto, em geral, nenhum deles utiliza uma visão genealógica de forma a considerar eventos genéticos ocorridos no passado, dificultando a compreensão dos padrões de variação observados no presente. Uma abordagem que possibilita a investigação retrospectiva com base no atual polimorfismo observado é a teoria da coalescência. Assim, o objetivo deste trabalho foi analisar, com base na teoria da coalescência, a estrutura populacional e o desequilíbrio de ligação de um painel mundial de acessos de sorgo (Sorghum bicolor). Para tanto, análises de mutação, migração com fluxo gênico e recombinação foram realizadas para cinco regiões genômicas relacionadas à altura de plantas e maturidade (Dw1, Dw2, Dw4, Ma1 e Ma3) e sete populações previamente selecionadas. Em geral, elevado fluxo gênico médio (Μ = m/μ = 41,78 − 52,07) foi observado entre as populações considerando cada região genômica e todas elas simultaneamente. Os padrões sugeriram intenso intercâmbio de acessos e história evolutiva específica para cada região genômica, mostrando a importância da análise individual dos locos. A quantidade média de migrantes por geração (Μ) não foi simétrica entre pares recíprocos de populações, de acordo com a análise individual e simultânea das regiões. Isso sugere que a forma pela qual as populações se relacionaram e continuam interagindo evolutivamente não é igual, mostrando que os métodos clássicos utilizados para investigar estrutura populacional podem ser insatisfatórios. Baixas taxas médias de recombinação (ρL = 2Ner = 0,030 − 0,246) foram observadas utilizando o modelo de recombinação constante ao longo da região. Baixas e altas taxas médias de recombinação (ρr = 2Ner = 0,060 − 3,395) foram estimadas utilizando o modelo de recombinação variável ao longo da região. Os métodos tradicional (r2) e via coalescência (E[r2 rhomap]) utilizados para a estimação do desequilíbrio de ligação mostraram resultados próximos para algumas regiões genômicas e populações. No entanto, o r2 sugeriu padrões descontínuos de desequilíbrio em várias ocasiões, dificultando o entendimento e a caracterização de possíveis blocos de associação. O método via coalescência (E[r2 rhomap]) forneceu resultados que pareceram ter sido mais consistentes, podendo ser uma estratégia eventualmente importante para um refinamento dos padrões não-aleatórios de associação. Os resultados aqui encontrados sugerem que o mapeamento genético a partir de um único pool gênico pode ser insuficiente para detectar associações causais importantes para características quantitativas em sorgo. / Population structure and linkage disequilibrium are two fundamental processes for evolution and association mapping studies. Traditionally, both have been investigated using classical methods that are commonly used. These methods certainly provided important advances for the understanding of the evolution processes of the species. However, in general, none of them uses a genealogical view to consider genetic events occurred in the past, making difficult the understanding of the variation patterns observed in the present. An approach that enables the retrospective investigation based on the actual observed polymorphism is the coalescent theory. Here, we used the coalescent theory to analyze the population structure and linkage disequilibrium of a worldwide sorghum (Sorghum bicolor) accession panel. To reach this purpose, analyses of mutation, migration with gene flow and recombination were performed to five genomic regions related to plant height and maturity (Dw1, Dw2, Dw4, Ma1 e Ma3) and seven previously selected populations. In general, high average gene flow (Μ = m/μ = 41,78 − 52,07) was observed between populations considering each genomic region and all the regions simultaneously. The patterns suggested a high exchance of accessions between populations and a specific evolutionary history for each genomic region, showing that the individual analysis of each locus was important. The average number of migrants per generation (Μ) was not symmetric between reciprocal pairs of populations, according to the specific and simultaneous analyses of the regions. This result suggests that the historical and recent evolutionary relations between populations are not equal, showing that the classical methods to investigate population structure may be unsatisfactory. Low average recombination rates (ρL = 2Ner = 0,030 − 0,246) were observed using a constant recombination model along the region. Low and high average recombination rates (ρr = 2Ner = 0,060 − 3,395) were estimated using a variable recombination model along the region. Both traditional (r2) and coalescent (E[r2 rhomap]) methods for the estimation of linkage disequilibrium showed similar results for some genomic regions and populations. However, r2 suggested discontinuous patterns of linkage disequilibrium in several cases, making difficult the understanding and definition of the association blocks. The coalescent method (E[r2 rhomap]) provided results that seemed to be more consistent and could be an eventually important strategy to refine the non-random association patterns. The results detected here suggest that the genetic mapping from a unique gene pool may be insufficient to detect important causal associations for quantitative traits in sorghum.

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.

Le lion de mer Australien a un cycle de reproduction non-annuel et asynchrone entre les colonies.Contrairement aux autres pinnipèdes, ce système unique offre l’opportunité aux mâles de se reproduiredans plusieurs sites lors d’une saison de reproduction. L’accès des mâles à plusieurs sites dereproduction pourrait contrecarrer le fort degré de structure génétique de population chez les femellesdûe à une fidélité extrême au site de reproduction. J'ai utilisé deux méthodes indépendantes maiscomplémentaires, moléculaire et acoustique, afin d’étudier la structure de la population et le systèmede reproduction. Pour l'analyse moléculaire, j'ai développé une banque de microsatellites spécifiques àl'espèce. Ces marqueurs ont été utilisés pour examiner le flux génétique des mâles dans les différentescolonies de reproduction, le succès reproducteur, et les taux de paternité inter- et intra-colonies. Deplus, j'ai mesuré la variation géographique dans les cris des mâles, ce qui représente une approchealternative pour mesurer les convergences/divergences entre colonies. J'ai montré que si les mâlesprésentent une certaine dispersion entre colonies, elle est limitée à une courte échelle en dépit del’opportunité des mâles de se reproduire dans différents sites. Les analyses acoustiques des cris demâles ont révélé des variations géographiques significatives entre colonies, qui ne reflètent pas lastructure génétique. Les analyses de paternité indiquent un faible taux de polygynie, la majorité desmâles ne produisant qu’un ou deux jeunes par saison. Des stratégies alternatives de reproduction(nomade ou sédentaire) sont présentes dans cette espèce, certains mâles se déplaçant activement entredifférentes colonies proches. Le système de reproduction unique du lion de mer Australien semblefortement influer à la fois les modalités de dispersion, mais aussi la structure de population et lesystème de reproduction. / The Australian sea lion has a non-annual and asynchronous breeding cycle across geographically closecolonies. In contrast to other pinnipeds, this unique reproductive system provides the opportunity formales to breed in different colonies during one breeding cycle. Male mating success across differentcolonies could counteract the high degree of structure driven by extreme site fidelity in females. I usedtwo, independent but complementary methods, molecular and acoustic to investigate their populationstructure and mating system. For molecular analysis I developed a species-specific microsatellitelibrary. These markers were used to examine the extent and rate of male mediated gene-flow acrossbreeding colonies but also to determine the breeding success and paternity both within and acrossspatially close colonies. Also, I investigated the geographical variation in male barking call. Thisrepresents an alternative approach to measure boundaries and relationships between colonies. Malesexhibit dispersal; however, this is limited to remarkably small scale in regards to the high potential fordispersal and opportunity to breed in different colonies. Acoustic analyses of the male barking callsrevealed significant geographical variation across sites; however this observed acoustic variation didnot reflect the genetic structure. Paternity analyses revealed that males display relatively modest ratesof polygyny with the majority of successful males siring only one or two pups per breeding cycle. Thepresence of alternative mating strategies (roaming vs staying) is apparent in this species with somemales actively moving and breeding between close colonies. It appears that the unique breedingbiology of Australian sea lion influences dispersal patterns, population structure and mating system.

La mise en place de réseaux écologiques est considérée comme l'un des moyens de pallier aux effets néfastes de la fragmentation sur la biodiversité. Dans les paysages agricoles, les éléments linéaires non cultivés peuvent constituer de larges réseaux, et jouer un rôle d'habitat-refuge et/ou de corridor de dispersion pour les espèces végétales. L'objectif de cette thèse est de comprendre quel rôle un réseau dense de fossés de drainage peut jouer dans le maintien et la dispersion d'espèces végétales dans un paysage agricole intensif du nord de la France. Nous avons également cherché à savoir dans quelle mesure les caractéristiques du paysage, la connectivité du réseau et les traits d'histoire de vie des espèces végétales impactent la dispersion des propagules au sein du réseau de fossés. Nos résultats montrent que les fossés jouent bien un rôle de corridor écologique pour les espèces végétales. En ciblant plus précisément les espèces hydrochores, nous avons démontré qu'elles dépendaient essentiellement de la composition et de la connectivité du réseau de fossés et des éléments immédiatement adjacents aux berges. Le réseau détermine également la structuration des flux de gènes chez deux espèces végétales de berges de fossés. Enfin, nos résultats montrent que la réponse des espèces à un gradient de connectivité du réseau dépend d'une combinaison de traits de dispersion, et qu'une diminution de cette connectivité entraîne une convergence fonctionnelle de ces traits à l'échelle de la métacommunauté. L'ensemble de ces résultats permet de mieux comprendre le rôle de corridor des fossés pour les espèces végétales, afin de permettre leur intégration au sein des projets de continuités écologiques dans les paysages agricoles. / The establishment of ecological networks is considered as one of the solutions to mitigate the negative effects of fragmentation on biodiversity. In agricultural landscapes, non-crop linear elements may form large networks, and constitute refuge habitats and/or dispersal corridors for plant species. The objective of this study is to understand which role may a dense drainage ditch network play for the maintenance and dispersal of plant species in an intensive agricultural landscape located in northern France. In addition, we also investigated the impact of landscape characteristics, network connectivity and plant species life-history traits on propagule dispersal within the ditch network. Our results indicate that ditches are indeed ecological corridors for plant species. By focusing more specifically on hydrochorous species, we demonstrated that they essentially depend on ditch network composition and connectivity and on elements immediately adjacent to the banks. The network also drives patterns of gene flow for two ditch bank plant species. Finally, our results also indicate that species’ response to ditch network connectivity depends on a combination of dispersal traits, and that connectivity reduction leads to functional convergence of those traits at the metacommunity scale. Together, these results provide a better understanding of the corridor role of ditches for plant species, in order to include these features into ecological network planning in agricultural landscapes.

The presence of triploid individuals, whether hybrids arising from crosses of diploid and tetraploid plants, or spontaneously generated triploid hybrids diploid populations, is increasingly important in plant populations. However, the possible evolutionary role of the triploid hybrids is closely connected to the frequency of their occurrence, to their relative fitness (compared to parental cytotype) and fertility. As a model plant I choosed Tripleurospermum inodorum, in which a relatively frequent occurrence of triploid hybrids was documented in mixed populations of tetraploids and diploids. This annual plant achieves realy quick its reproductive maturity and is easily cultivated, making it an ideal model for cultivation and pollinating experiments. Compared to parental cytotypes, the triploid hybrids of T. inodorum take approximately the same (mostly mediated) fitness values. In vitro conditions were cultivated to measure of germination rates. Germination rate of triploid seeds was comparable to diploid parental cytotype. In the subsequent comparative cultivation, nearly 150 plant individuals (2x, 3x, 4x, and aneuploid cytotype) in the greenhouse showed that the triploids had intermedial values of their parental cytotypes or close to one of the parents. Thus, the vitality of the triploid plants is...

The dog was the first animal to be domesticated and the process started at least 15 000 years ago. Today it is the most morphologically diverse mammal, with a huge variation in size and shape. Dogs have always been useful to humans in several ways, from being a food source, hunting companion, guard, social companion and lately also a model for scientific research. This thesis describes some of the changes that have occurred in the dog’s genome, both during the domestication process and later through breed creation. To give a more comprehensive view, three genetic systems were studied: maternally inherited mitochondrial DNA, paternally inherited Y chromosome and biparental autosomal chromosomes. I also sequenced complete mitochondrial genomes to view the effect new living conditions might have had on dogs’ genes after domestication. Finally, knowledge of the genetic structure in purebred dogs was used to test analytic methods usable in other species or in natural populations where little information is available. The domestication process appears to have caused a relaxation of the selective constraint in the mitochondrial genome, leading to a faster rate of accumulation of nonsynonymous changes in the mitochondrial genes. Later, the process of breed creation resulted in genetically separated breed groups. Breeds are a result from an unequal contribution of males and females with only a few popular sires contributing and a larger amount of dams. However, modern breeder preferences might lead to disruptive selective forces within breeds, which can result in additional fragmentation of breeds. The increase in linkage disequilibrium that this represents increases the value of purebred dogs as model organisms for the identification and mapping of diseases and traits. Purebred dogs’ potential for these kinds of studies will probably increase the more we know about the dog’s genome.