Submitted by Mario BC (mario@bc.ufrpe.br) on 2016-09-23T12:47:02Z No. of bitstreams: 1 Rafaela Lima de Araujo.pdf: 5175233 bytes, checksum: a9acd861166189ddbd0b21c9b3ec9f11 (MD5) / Made available in DSpace on 2016-09-23T12:47:02Z (GMT). No. of bitstreams: 1 Rafaela Lima de Araujo.pdf: 5175233 bytes, checksum: a9acd861166189ddbd0b21c9b3ec9f11 (MD5) Previous issue date: 2014-01-20 / The Psidium guineense species, popularly known as strawberry guava, belongs to the Myrtaceae family, which is native to South America having a broad geographical distribution. In the Brazilian Northeast, is found on the coast, in the Forest Zone region. The fruit of the strawberry guava flavor is slightly reminiscent of the guava, although it is slightly more acidic and sharper scent. The culture of strawberry guava (P. guinenese) has no economic significance in the context of the national fruit production, not even existing commercial orchards. It is necessary, studies of genetic population level character, since there is little information on ecological and genetic aspects of the species. In order to provide information on the genetic resources of strawberry guava (P. guineense) in the State of Pernambuco, the objectives of this study were to evaluate the genetic diversity of four natural populations of P. guineense distributed in the Forest Zone of Pernambuco and characterize the genetic structure of these four populations from isozyme markers. Eighteen loci were used to estimate allele frequencies relating to 114 individuals in four populations: Itamaracá Arariba, Marieta and Palmares. Populations had generally high level of polymorphism and average of 1.5 alleles per locus. The heterozygosity observed was higher than heterozygosity expected, which ranged between 0.22 and 0.23 and the heterozygosity expected ranged between 0.34 and 0.40. The fixation index ranged from = -0.794 to = -0.549, presenting all negative, indicating the absence of inbreeding and heterozygosity excess. The estimated population in pairs all showed gene flow are generally high, ranging from Nm = 3.23 to Nm = 20.77 showing a high proportion of migrants among populations. / A espécie P. guineense, conhecida popularmente como araçá, pertence à família Mirtácea, que é originária da América do Sul apresentando uma ampla área de distribuição geográfica. Nos Estados do Nordeste Brasileiro, é encontrada no litoral, na região da Zona da Mata. O fruto do araçazeiro tem sabor que lembra um pouco o da goiaba, embora seja ligeiramente mais ácido e de perfume mais acentuado. A cultura do araçá (P. guinenese) não possui expressão econômica no contexto da fruticultura nacional, não existindo, inclusive, pomares comerciais. Faz-se necessário, estudos de caráter genético a nível populacional, uma vez que existem poucas informações sobre aspectos ecológicos e genéticos da espécie. Com o intuito de disponibilizar informações sobre os recursos genéticos do araçá (P. guineense) no Estado de Pernambuco, os objetivos do presente trabalho foram avaliar a diversidade genética de quatro populações naturais de P. guineense distribuídas na Zona da Mata do Estado de Pernambuco e caracterizar a estrutura genética dessas quatro popurações a partir de marcadores isoenzimáticos. Dezoito locos foram utilizados para estimar as frequências alélicas referentes aos 114 indivíduos, nas quatro populações: Itamaracá, Arariba, Marieta e Palmares. As populações apresentaram em geral, alto nível de polimorfismo com média de 1,5 alelos por loco. A heterozigosidade observada apresentou-se maior do que a esperada, onde variou entre 0,22 e 0,23 e variou entre 0,34 e 0,40 . O índice de fixação variou de = -0,549 a = -0,794, apresentando-se negativo para todos, indicando ausência de endogamia e excesso de heterozigosidade. O fluxo gênico estimado para as populações aos pares apresentou-se em geral elevado variando de Nm= 3,23 a Nm= 20,77 evidenciando alta proporção de migrantes entre populações.

Orientador: Vera Nisaka Solferini / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-17T13:24:18Z (GMT). No. of bitstreams: 1 Rocha_ReneAlvarez_M.pdf: 1173301 bytes, checksum: 5aba68a3572ed5b79a802c158affd58a (MD5) Previous issue date: 2011 / Resumo: A estrutura genética de uma espécie é determinada pelo balanço entre deriva genética, fluxo gênico e seleção natural, que são processos fortemente influenciados pela demografia e distribuição espacial das populações. Utetheisa ornatrix é uma mariposa da família Arctiidae muito conhecida por seus mecanismos de defesa e sistema de acasalamento, mas a estrutura genética de suas populações é pouco estudada. Este trabalho investigou a estrutura genética de Utetheisa ornatrix de populações coletadas no Estado de São Paulo com base em três locos de DNA de microssatélite. Foram analisados os genótipos de 203 indivíduos de 10 populações. Os resultados encontrados mostram populações com grande deficiência de heterozigotos, baixa estruturação genética e ausência de correlação entre distância geográfica e diferenças genéticas. Tais resultados indicam que mesmo sendo uma espécie cuja fêmea apresenta comportamento promíscuo, essa promiscuidade não reflete em diminuição da endogamia. Possivelmente a deficiência de heterozigotos se deve ao fato da fêmea não evitar acasalamento com machos aparentados, ser fecundada pelo esperma de poucos machos e haver forte seleção sexual na espécie, o que pode formar subgrupos dentro de uma população. A deficiência de heterozigotos também pode ser devido à dinâmica populacional da espécie: populações estão sujeitas à constantes diminuições de populações e fluxo gênico, o que pode resultar em populações formadas por subgrupos de indivíduos oriundos de diferentes manchas de plantas-hospedeiras, logo a freqüência de heterozigotos não corresponde as freqüências alélicas encontradas. A baixa estruturação genética e ausência de correlação entre distância geográfica e diferenças genéticas indicam que U. ornatrix é uma espécie com alta capacidade de dispersão, o que é conflitante com a elevada endogamia encontrada. Os resultados revelam questões que podem ser respondidas em 2 trabalhos posteriores que estudem a dinâmica populacional e a variabilidade genética de cada população ao longo do tempo. Outra questão levantada é se a espécie hospedeira de Crotalaria em que o indivíduo nasce influencia na escolha de parceiros para acasalamento, visto que duas das três populações que mais contribuíram para o nível de estrutura genética encontrado estavam em locais onde haviam espécies diferentes de planta hospedeira. / Abstract: The genetic structure of a species is determined by the balance between genetic drift, gene flow and natural selection processes that are strongly influenced by demography and spatial distribution of population. Utetheisa ornatrix is a moth of the Arctiidae family well known for their defense mechanisms and mating system, but the genetic structure of their populations is little studied. This study investigated the genetic structure of Utetheisa ornatrix populations collected in the State of São Paulo, Brazil, based on three microsatellite loci. We analyzed the genotypes of 203 individuals from 10 populations. The results show populations with high inbreeding, low genetic structure and no correlation between geographic distance and genetic differences. These results indicate that even as a species whose female has promiscuous behavior, promiscuity does not reduce inbreeding. Possibly the heterozygote deficiency is due to the fact that females did not avoid mating with related males, are fertilized by sperm from few males, and sexual selection is very strong in this species, which can form subgroups within a population. The heterozygote deficiency may also be due to its population dynamics: populations are subject to constant reductions and gene flow, which can result in populations composed of subgroups of individuals from different patches of host plants, so the frequency of heterozygotes does not match the allele frequencies found. The low genetic structure and lack of correlation between geographic distance and genetic differences indicate that U. ornatrix is a species with high dispersal ability, which is conflicting with the high inbreeding found. The results show questions that can be answered in further studies to examine the population dynamics and genetic variability of each population over time. Another question is if the host species of Crotalaria in which the individual was born influences the choice of mating partners, because two of the three 4 populations that most contributed to the level of genetic structure were found in locals with presence of different species of host plant. / Mestrado / Ecologia / Mestre em Ecologia

Submitted by Erika Demachki (erikademachki@gmail.com) on 2014-10-29T14:42:08Z No. of bitstreams: 2 Tese - Marina Zanin Gregorini - 2014.pdf: 10952620 bytes, checksum: bc9f9431ac9ea502525179cb6f912f05 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2014-10-30T10:07:47Z (GMT) No. of bitstreams: 2 Tese - Marina Zanin Gregorini - 2014.pdf: 10952620 bytes, checksum: bc9f9431ac9ea502525179cb6f912f05 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2014-10-30T10:07:48Z (GMT). No. of bitstreams: 2 Tese - Marina Zanin Gregorini - 2014.pdf: 10952620 bytes, checksum: bc9f9431ac9ea502525179cb6f912f05 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2014-03-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Nosso trabalho teve como objetivo investigar o efeito da perda e fragmentação de habitat sobre os felinos (Carnivora: Felidae), testando hipóteses relacionadas ao tema, bem como fazendo inferências para a conservação. Apresentamos aqui três capítulos no formato de artigo científico e uma breve discussão geral, que consiste na compreensão geral proveniente dos resultados dos três primeiros. Iniciamos essa tese com uma revisão sistemática e quantitativa da literatura sobre o efeito da perda e fragmentação do habitat sobre felinos. Esse trabalho consistiu no passo inicial dessa tese, pois permitiu identificar as lacunas de conhecimento, tendências gerais e metodologias eficientes a serem aplicadas nas outras etapas do trabalho. No entanto, nossa revisão se estende além da avaliação do “estado da arte”, pois testamos também hipóteses relativas a alocação do esforço de pesquisa. / Nosso trabalho teve como objetivo investigar o efeito da perda e fragmentação de habitat sobre os felinos (Carnivora: Felidae), testando hipóteses relacionadas ao tema, bem como fazendo inferências para a conservação. Apresentamos aqui três capítulos no formato de artigo científico e uma breve discussão geral, que consiste na compreensão geral proveniente dos resultados dos três primeiros. Iniciamos essa tese com uma revisão sistemática e quantitativa da literatura sobre o efeito da perda e fragmentação do habitat sobre felinos. Esse trabalho consistiu no passo inicial dessa tese, pois permitiu identificar as lacunas de conhecimento, tendências gerais e metodologias eficientes a serem aplicadas nas outras etapas do trabalho. No entanto, nossa revisão se estende além da avaliação do “estado da arte”, pois testamos também hipóteses relativas a alocação do esforço de pesquisa.

Este estudo trata da estrutura e diversidade genética de uma espécie típica do Cerrado brasileiro, Qualea grandiflora Mart (Vochysiaceae), presente nas diversas fisionomias do bioma. Foram desenvolvidos oito locos microssatélites para analisar 420 amostras de indivíduos adultos pertencentes a quatro populações distribuídas no estado de São Paulo, sendo três delas em unidades administradas pelo Instituto Florestal de São Paulo (Assis, Itirapina e Pedregulho) e uma em propriedade particular (Brotas) além de 300 progênies coletadas de 25 matrizes na área de estudo em Assis. Os resultados mostraram a ocorrência média de 12,9 alelos por loco, sendo que o número médio de alelos efetivos foi seis, além de terem sido encontrados 26 alelos exclusivos nas populações. A média dos valores de Heterozigosidade esperada foi de 0,803 enquanto de Heterozigosidade observada foi de 0,512. O Conteúdo de Informação Polimórfica (PIC) variou de 0,708 a 0,801 nos locos estudados. A média dos valores de fixação foi de 0,349 indicando a presença de endogamia nas populações. Não há presença de clones em nenhuma população. O teste de adesão ao Equilíbrio de Hardy Weinberg confirma o desvio de equilíbrio em todas as populações. Há formação de estrutura populacional nas primeiras classes de distância em todas as populações estudadas, variando de 30 a 40 metros e há uma formação de 3 possíveis grupos de genótipos. A influência do efeito Wahlund foi variável nas populações (de 8,5% até 53,3%). As estimativas de tamanho efetivo populacional foram baixas (menos de 10 indivíduos) e a área mínima viável foi estimada de 4 a 184 hectares, considerando estimativas de curto, médio e longo prazos. Com relação ao sistema reprodutivo, os resultados indicam que Q. grandiflora Mart se reproduz por cruzamentos entre indivíduos parentes e não parentes (0,913). A taxa uniloco foi de 0,632, indicando que há mais cruzamentos entre não aparentados do que aparentados. A taxa de autofecundação foi baixa (0,087) indicando que a espécie é alógama, com pouca pré disposição para autofecundação. Aproximadamente 35% das plantas dentro de progênies eram parentes no grau de irmãos-completos e aproximadamente 57% eram meios-irmãos. Além disso, aproximadamente 8% das progênies eram irmãos de autofecundação. O coeficiente de coancestria estimado nas progênies foi de 0,139 enquanto o índice de fixação foi de aproximadamente 27%. A estimativa do tamanho efetivo indicou que a representatividade genética da descendência é inferior à esperada em progênies de cruzamentos aleatórios: as amostras analisadas correspondem a apenas 13,2 indivíduos de uma população panmítica ideal. Os resultados demonstram que a espécie possui potencial para conservação genética in situ embora a coleta de sementes para manter o tamanho efetivo deva utilizar de um número elevado de árvores. Sugere-se que as áreas estudadas sejam tratadas como Unidades Significativas Evolutivas (USE) e como Unidades Independentes para o Manejo (UIM). / This study deals with the structure and genetic diversity of a species typical of the Brazilian Cerrado, Qualea grandiflora Mart (Vochysiaceae), present in different physiognomies of this biome. We developed eight microsatellite loci to analyze 420 samples of adult individuals from four populations distributed in the state of São Paulo, three of them in units managed by the Forestry Institute of Sao Paulo (Assis, Itirapina and Pedregulho) and one in a private property (Brotas). We also analyzed 300 progeny collected from 25 matrix in Assis. The results showed an average occurrence of 12.9 alleles per locus. The average number of effective alleles was six, and 26 exclusive alleles were found in the populations. The average expected heterozygosity was 0.803 while the observed heterozygosity was 0.512. The polymorphic information content ranged from 0.708 to 0.801 at the loci studied. The mean fixation was 0.349, therefore indicating the presence of inbreeding within populations. There is no presence of clones in the populations. The test of adherence to the Hardy Weinberg Equilibrium confirms the deviation from equilibrium in all populations. There is formation of population structure in the first distance classes in all populations studied, ranging from 30 to 40 meters, and there is a formation of three possible genotype groups. The influence of the Wahlund effect varied among populations (from 8.5% to 53.3%). The effective population size estimates were low (less than 10 individuals) and the minimum viable area was estimated between 4 to 184 hectares, taking into account estimates of short, medium and long terms. Regarding the reproductive system, results indicate that Q. grandiflora Mart reproduces by crosses between relatives and unrelated individuals (0.913). The single locus rate was 0.632, indicating that there are more crosses between unrelated than related individuals. The self-fertilization rate was low (0.087), therefore indicating that the species is allogamous, with little predisposition for self-fertilization. Approximately 35% of the plants within progenies were full-sibs and approximately 57% were half-sibs. In addition, approximately 8% of progenies were self-fertilized brothers. The estimated coefficient of coancestry in progenies was 0.139, while the rate of fixation was about 27%. The estimated effective size indicated that the genetic representativeness of the offspring is lower than the expected in random cross progenies: the samples analyzed account for only 13.2 individuals in a ideal panmitic population. The results show that this species has potential for in situ genetic conservation, although the collection of seeds to maintain the effective size should use a large number of trees. It is suggested that the studied areas be treated as evolutionary significant units and as independent units for management.

Orientador:: Vera Nisaka Solferini / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-22T17:59:16Z (GMT). No. of bitstreams: 1 Bartoleti_LuizFilipedeMacedo_M.pdf: 981663 bytes, checksum: 9efdfd02f5146e866175388d02da7638 (MD5) Previous issue date: 2013 / Resumo: Processos históricos e contemporâneos moldaram os padrões de variabilidade genética das espécies da Mata Atlântica, um dos biomas mais diversos do mundo. Além disso, a fragmentação recente das florestas brasileiras pode causar sérios efeitos na estruturação genética das populações naturais, intensificando processos como deriva genética e endogamia. Os efeitos da fragmentação dependem principalmente da matriz entre os fragmentos e das características de dispersão da espécie. As aranhas são organismos que possuem modos de vida bastante diversos e as características de dispersão podem também variar bastante. Nephila clavipes é uma aranha que possui ampla distribuição na Mata Atlântica e considera-se que a espécie é capaz de dispersão por balonismo (dispersão aérea). Os objetivos desse trabalho foram estudar os padrões de variabilidade e estruturação genética em populações de fragmentos de Mata Atlântica, usando N. clavipes. Os estudos foram realizados em micro e macro escala, para inferir padrões de fluxo gênico e relacionar os resultados a aspectos ecológicos e comportamentais da espécie. Além disso, buscou-se explorar aspectos da história evolutiva da espécie e sua corrente distribuição em populações. Para isso, foi sequenciado o gene mitocondrial Citocromo Oxidase I de 323 indivíduos coletados em 15 populações de cinco Estados. Foram calculados índices de diversidade genética, além de parâmetros filogeográficos, por meio de análises bayesianas e de máxima verossimilhança. Todas as populações apresentaram polimorfismo sendo que, em geral, as populações de Minas Gerais apresentaram índices de diversidade mais altos. Os valores médios de diversidade ficaram próximos aos encontrados para outras espécies do gênero. Foi encontrada grande estruturação genética, principalmente em distâncias médias e grandes, com FST geral de 0,30178. O FST no Estado de São Paulo (a microescala geográfica) foi de apenas 0,02996, indicando baixa estruturação em baixas distâncias. A distância genética não apresentou claras relações com a distância geográfica (Teste de Mantel, p > 0,05), o que pode ser devido à dispersão por agentes, inclusive antrópicos. A análise dos valores de FST obtidos apenas com as fêmeas indica que os machos podem ter efeito de manutenção do fluxo gênico em baixas distâncias. A rede de haplótipos e as árvores de máxima verossimilhança e bayesiana indicaram a presença de três clados genéticos, não inteiramente concordantes com a distribuição dos grupos geográficos. As estimativas apontam para divergências entre esses clados genéticos datadas do Pleistoceno, assim como reportado em vários outros organismos que habitam a Mata Atlântica. Nossos resultados mostram uma espécie de invertebrado apresentando padrões filogeográficos semelhantes aos encontrados para organismos de outros grupos, o que pode indicar processos em comum na diversificação das espécies da Mata Atlântica / Abstract: Historic and contemporary processes have shaped the patterns of genetic variability of the species from Brazilian Atlantic Rainforest, one of the world's most diverse biomes. Furthermore, the recent fragmentation of Brazilian Rainforests may cause serious effects in genetic structure of natural populations, intensifying processes like genetic drift and endogamy. Fragmentation effects depend mainly on the matrix between the fragments and the species' dispersion characteristics. Spiders are organisms that show different lifestyles, and dispersion characteristics may also vary within the group. Nephila clavipes is a spider that is widely distributed in the Atlantic Rainforest and it is widely accepted that it is capable of ballooning (aerial dispersal). In the present work, we sought to study the patterns of genetic variability and structure in populations from fragments of Atlantic Rainforest, using N. clavipes. The studies have been made in micro and macro scale, looking forward to infer gene flow patterns and relate the results to ecologic and behavioral aspects of the species. Furthermore, we sought to explore aspects of the species' evolutionary history and its current distribution in populations. With those objectives in mind, we sequenced the mitochondrial gene Cytochrome Oxidase I from 323 individuals sampled in 15 populations from five States. We calculated genetic diversity indexes, phylogeographic parameters, and performed bayesian and maximum likelihood analysis. All populations presented polymorphism and, in general, Minas Gerais populations showed higher diversity indexes. Diversity mean values were close to that found in others species from the genera. We found high genetic structure, mainly at medium and great distances, with a FST value of 0,30178. The FST in São Paulo State (the geographic micro scale) was as low as 0,02996, showing low genetic structure at short distances. The genetic distance didn't show clear relationships with the geographic distance (Mantel test, p > 0,05), which may be due to the agent-guide dispersal, including anthropic agents. The analysis of the FST values obtained exclusively from the females indicates that the males may have a gene flow maintenance effect at short distances. The haplotype network and the bayesian and maximum likelihood phylogenetic trees reported the presence of three genetic clades, not entirely in agreement with the geographic groups' distribution. The estimates point to divergences between the genetic clades dated from the Pleistocene, like reported for various other organisms that live in the Atlantic Rainforest. Our results present an invertebrate species showing phylogeographic patterns similar to that found to other groups, which may indicate common processes in the diversification of Atlantic Rainforest species / Mestrado / Genetica Animal e Evolução / Mestre em Genética e Biologia Molecular

Among dinitrogen (N2)-fixing some cyanobacteria can establish symbiosis with a broad range of host plants from all plant lineages including bryophytes, ferns, gymnosperms, and angiosperms. In the boreal forests, the symbiosis between epiphytic cyanobacteria and feathermosses Hylocomium splendens and Pleurozium schreberi is ecologically important. The main input of biological N to the boreal forests is through these cyanobacteria, and thus, they greatly contribute to the productivity of this ecosystem. Despite the ecological relevance of the feathermoss symbiosis, our knowledge about the establishment and maintenance of cyanobacterial-plant partnerships in general is limited, and particularly our understanding of the feathermoss symbiosis is rudimentary. The first aim of this thesis was to gain insight on the genomic rearrangements that enabled cyanobacteria to form a symbiosis with feathermosses, and their genomic diversity and similarities with other plant-symbiotic cyanobacteria partnerships. Genomic comparison of the feathermoss isolates with the genomes of free-living cyanobacteria highlighted that functions such as chemotaxis and motility, the transport and metabolism of organic sulfur, and the uptake of phosphate and amino acids were enriched in the genome of plant-symbiotic cyanobacteria. The second aim of this PhD study was to identify cyanobacterial molecular pathways involved in forming the feathermoss symbiosis and the regulatory rewiring needed to maintain it. Global transcriptional and post-transcriptional regulation in cyanobacteria during the early phase of establishment of the feathermoss symbiosis, and after colonization of the moss were investigated. The results revealed that the putative symbiotic gene repertoire includes pathways never before associated with cyanobacteria-plant symbioses, such as nitric-oxide sensing and regulation, and the transport and metabolism of aliphatic sulfonate. The third aim was to explore the role of the cyanobacterial community in contributing to the temporal variability of N2-fixation activity. Results from a field-study showed that temporal variation in N2-fixation rates could be explained to a high degree by changes in cyanobacterial community composition and activity. In particular, the cyanobacteria belonging to the genus Stigonema - although not dominating the community- appeared to be the main contributors to the N2-fixation activities. Based on this result, it is suggested that this genus is responsible for the main input of N in the boreal forest ecosystems. The last aim was to understand how the relationship between cyanobacterial community composition and N2-fixation activity will be affected by climatic changes such as, increased temperature (11oC compared to 19oC) and CO2 level (500 ppm compared to 1000 ppm). Laboratory experiments highlighted that 30 weeks of combined elevation of temperature and CO2 resulted in increased N2-fixation activity and moss growth rates. The observed increases were suggested to be allocated to reduced cyanobacterial diversity and changes in community composition, resulting in the dominance of cyanobacteria adapted to the future abiotic condition. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Manuscript.</p>

Les génomes sont affectés par des régimes de sélection conflictuels. Ceci est particulièrement bien illustré par le concept de barrière semi-perméable au flux génique, issu de la littérature des zones hybrides. Certains gènes contribuent à empêcher le mélange entre lignées génétiques différenciées, soit parce qu'ils participent à l'adaptation aux conditions environnementales locales, soit parce qu'ils sont incompatibles avec les gènes d'autres lignées. D'autres parties du génome sont soit neutres, soit soumises à une sélection qui tend à homogénéiser les différentes lignées entre elles. Dans la première partie de cette thèse, des modèles d'évolution de l'isolement reproductif sont présentés pour expliquer les patrons d'isolements observés dans les expériences d'hybridation au laboratoire. Par modélisation classique d'incompatibilités génétiques de type Dobzhansky-Muller, il est montré que l'asymétrie et la complexité des incompatibilités sont imparfaitement expliquées par un filtre évolutif, c.a.d. une vitesse d'accumulation différente entre types d'incompatibilité. Une approche complémentaire de modélisation quantitative à l'aide d'une extension du modèle géométrique de Fisher a permis de préciser quelles conditions de divergence entre lignées isolées conduisaient à un effet fortement délétère des mutations dans les génotypes hybrides. L'importance relative du niveau d'épistasie moyen, de la distribution des effets des mutations et des modalités de l'adaptation de chaque lignée est discutée. La seconde partie de cette thèse profite des avancées techniques de la génomique pour étudier l'histoire de la spéciation et de l'adaptation dans un complexe d'espèces non-modèles, les moules du genre Mytilus. Une méthode statistique d'inférence de scénarios de spéciation est présentée. Les résultats montrent que les moules Européennes ont connu une histoire complexe de divergence stricte suivie d'une période de connectivité périodique. En accord avec le concept de barrière semi-perméable au flux génique, il est montré que les taux d'introgression sont hétérogènes le long du génome. Ensuite, des scans génomiques de la différenciation ont été menés entre paires de populations du complexe d'espèces. L'analyse de la variation génétique et des généalogies d'allèles sur une échelle chromosomique localisée a permis de reconstituer l'histoire évolutive de plus de 1000 régions du génome des moules. Cette analyse a révélé qu'une cause majeure, mais insoupçonnée, de la différenciation génétique intraspécifique est l'introgression différentielle d'allèles étrangers. Globalement, cette thèse montre non seulement le rôle majeur de la biogéographie de la spéciation, c.a.d. des patrons temporels et spatiaux du flux de gènes, dans notre compréhension de la biodiversité actuelle, mais aussi sa surprenante complexité et l'étendue de ses conséquences sur l'évolution des génomes. / Genomes are affected by conflicting selective regimes. This is particularly well illustrated by the concept of semi-permeable barriers to gene flow, as found in the hybrid zones literature. Some genes contribute to the prevention of mixing between differentiated genetic lineages, either because they are involved in adaptation to local environmental conditions, or because they are incompatible with alleles from other genetic lineages. Other parts of the genome are either neutral, or subjected to selection which tends to homogenize the genetic lineages. In the first part of this thesis, models of the evolution of reproductive isolation are presented to explain the isolation patterns observed in experimental hybridizing crosses between incipient species. Using standard models of Dobzhansky-Muller genetic incompatibilities, it is shown that the asymmetry and complexity of incompatibilities are not well explained by there being an “evolutionary sieve”, i.e. a different rate of accumulation between incompatibilities. A complementary approach to quantitative modeling (an extension of Fisher's Geometric Model) then clarifies which conditions of divergence between allopatric lines led to highly deleterious effects in hybrid genotypes. The relative importance of mean levels of fitness epistasis, the distribution of mutation sizes, and the way lineages adapt to new environmental conditions is discussed. The second part of this thesis takes advantage of technical advances in genomics to study the history of speciation and adaptation in a non-model species complex, Mytilus mussels. A statistical method of inferring speciation scenarios is presented. Results show that European mussels experienced a complex history of strict divergence followed by a period of periodic connectivity. In agreement with the concept of semi-permeable barriers to gene flow, it is shown that introgression rates are heterogeneous along the genome. Next, genome scans of differentiation were conducted between pairs of populations of the species complex. The analysis of genetic variation and allele genealogies on a small chromosomal scale allowed to reconstruct the evolutionary history of more than 1000 genomic regions. This analysis reveals that a major cause of intraspecific differentiation is the differential introgression of foreign alleles. Overall, this thesis shows not only that biogeography of speciation, i.e. the temporal and spatial patterns of gene flow, play a major role in our understanding of existing biodiversity, but also its amazing complexity and extent of its impact on genome evolution.

Les activités d'origines anthropiques entraînent des modifications profondes du paysage : dans ce contexte, le succès de dispersion revêt une grande importance pour la persistance à long terme des populations animales et végétales. La génétique du paysage est une discipline récente qui permet de détecter et de modéliser les flux de dispersion de manière indirecte par le biais de l'identification des flux de gènes dans l'espace. Bien qu'il ait été suggéré delongue date qu'un échantillonnage individu-centré pouvait permettre de s'affranchir de certains biais liés à unedélimitation a priorides populations, les études portant sur des organismes présentant une distribution spatiale discontinue restent malgré tout le plus souvent basées sur un échantillonnage réalisé à l'échelle populationnelle. C'est sur cette thématique qu'ont porté mes travaux de thèse. Des résultats obtenus par simulations montrent qu'augmenter le nombre de points échantillonnés dans l'espace au détriment du nombre d'individus par agrégat peut permettre une meilleure détection de l'influence de la matrice sur les flux de gènes, quelque soit le régime de dispersion et le contexte paysager considérés. Appliqué à l'étude de la dispersion du triton alpestre Ichthyosaura alpestris, d'une part en paysage fragmenté par des infrastructure linéaires de transport (isolation par barrières aux flux de gènes IBB) et d'autres part en paysage agricole (isolation par résistance de la matrice paysagère IBR), l'échantillonnage individu-centré apparaît comme une alternative flexible et efficace à l'échantillonnnage populationnel classique. / Anthropogenic activitites lead to profound landscape alterations : dispersal success thus holds a paramount importance for long-term persistence of populations. Landscape genetics is a recent discipline aiming to detect and describe dispersal patterns through indirect estimations of gene flow. Although the use of an individual-based sampling scheme has been proposed for a ;ong time to get round the issue of an a priori delimitation of population boundaries, most landscape gentic studies are still based on a population-based sampling scheme. results from simulations showed that decreasing the sampling coverage on individuals within populations in favour of a better sampling coverage of aggregates through space allowed a better detection of the impacts of landscape on gene flow, whatever the individual dispersal behaviour or the landscape configuration. when considering the dispersal patterns in the alpine newt Ichthyosaura alpestris, both in the vicinity of large transport infrastructures (Isolation-by-barrier IBB) and in agricultural landscape (Isolation-by-landscape-resistance IBR), the individual-based sampling scheme proved to be a flexible and efficient methodological alternative to the more conventional population-based sampling scheme.

Cette thèse étudie le processus de spéciation entre la lamproie fluviatile (Lampetra fluviatilis) et la lamproie de Planer (L. planeri). Les deux espèces présentent des stratégies d'histoire de vie extrêmement différentes : L. fluviatilis est parasite et anadrome alors que L. planeri n'est pas parasite et reste strictement dulcicole. Toutefois, leur degré d'isolement reproducteur et leur histoire de divergence demeurent méconnus. Ces questions ont été abordées par des approches expérimentales, de génomique de populations et de simulations démographiques. Des croisements expérimentaux ont révélé un faible isolement reproducteur, confirmé par des degrés variables de flux géniques dans les populations naturelles. Les analyses génétiques ont montré que les deux taxons représentaient probablement des écotypes avec un isolement reproducteur partiel suggérant que les barrières reproductives endogènes ne réduisaient que partiellement la migration efficace entre écotypes. L'importance du contexte géographique actuel et passé dans l'étude de la spéciation a aussi été mise en évidence par des analyses à l'échelle du génome. Ainsi, les populations isolées de L. planeri évoluent principalement sous l'effet de la dérive génétique et ont une diversité réduite. Les inférences démographiques ont suggéré que la divergence a été initiée en allopatrie puis suivie de contacts secondaires résultant en un parallélisme génomique partiel entre réplicas de paires de populations. Une hétérogénéité de la divergence génomique a démontré que les ilots génomiques de différenciation ne résultaient pas de l'action récente de la divergence écologique. En outre, nos résultats suggèrent un impact faible de la fragmentation anthropique des cours d'eau sur la diversité génétique des populations de L. planeri. Les populations résidentes possèdent une diversité génétique plus grande lorsque le flux de gènes avec L. fluviatilis dans les parties aval des cours d'eau. Globalement cette thèse a démontré que les paires d'écotypes parasites et non-parasites de lamproies représentent un excellent modèle d'étude de la spéciation et notamment de l'architecture génomique de la divergence. / This thesis investigates the process of speciation between the European lampreys Lampetra fluviatilis and L. planeri. The two species have drastically different life history strategies: L. fluviatilis is parasitic and anadromous while L. planeri is non-parasitic and strictly freshwater resident. Yet their level of reproductive isolation and history of divergence remain poorly understood. A multidisciplinary approach including experiments, population genomics analyses and historical reconstruction was undertaken to address these issues. Experimental crosses revealed a very low level of reproductive isolation, partially mirrored by variable levels of gene flow in wild populations. Genetic analyses revealed that the two taxa were best described as partially reproductively isolated ecotypes suggesting that endogenous genetic barriers partially reduced effective migration between ecotypes. Genome wide analyses showed the importance of the current and ancient geographical context of speciation. In particular, parapatric L. planeri populations diverged mostly through drift and displayed a reduced genetic diversity . Demographic inferences suggested that divergence have likely emerged in allopatry and then secondary contacts resulted in partial parallelism between replicate population pairs. A strong heterogeneity of divergence across the genome was revealed by sympatric populations suggesting that genomic islands of differentiation were not linked to ongoing ecological divergence. Further investigations showed that the genetic diversity of L. planeri populations was weakly affected by human-induced river fragmentation. Resident populations displayed a higher diversity when gene flow was possible with L. fluviatilis populations in downstream sections of rivers. Overall this thesis showed that parasitic and non-parasitic lamprey ecotypes represent a promising model for studying speciation and notably the genomic architecture of divergence.

Dans une première partie de mon projet de thèse, je me suis intéressée aux hybridations interspécifiques et à l’histoire évolutive des espèces de pommiers en Europe. L’analyse de génomes complets m’a permis de confirmer que l’ancêtre du pommier cultivé est bien le pommier sauvage asiatique M. sieversii, mais aussi que de nombreuses variétés cultivées originaires de l’Europe forment un groupe génétique distinct de cette espèce sauvage. Ces variétés montrent des traces d’introgressions par le pommier sauvage européen M. sylvestris et une structuration de populaton selon un axe est-ouest. Les introgressions depuis le pommier cultivé sont également abondantes dans les populations de pommier sauvage européen M. sylvestris, et menacent leur intégrité génétique. Les niveaux des introgressions étaient corrélés aux activités anthropiques d’exploitation des pommiers et les hybrides n’avaient pas de réduction détectable de valeur sélective sur les caractères mesurés. Notre étude de la phylogéographie du pommier sauvage européen dans l’ensemble de son aire de distribution nous a permis de détecter des groupes génétiques différenciés résultant de l’histoire climatique passée de la planète. Ces groupes représentent autant d’unités de conservation différentes.Dans une seconde partie, j'ai étudié la coévolution entre espèces de plantes et espèces de champignons pathogènes dans deux systèmes différents. Je me suis tout d'abord intéréssée à l’histoire évolutive combinée des pommiers cultivés et sauvages d’Asie centrale et du champignon causant la tavelure, Venturia inaequalis. Dans les montagnes du Kazakhstan, le pommier cultivé a été réintroduit au cours des deux derniers siècles, créant une zone de contact secondaire, non seulement entre M. domestica et M. sieversii, mais aussi entre les populations de V. inaequalis de types agricole et sauvage. Alors que l’invasion des populations sauvages par le pommier cultivé semble encore limité géographiquement, le pathogène de type agricole est largement répandu dans les forêts et sur l’hôte sauvage. Cependant, le nombre d’hybrides détectés chez le pathogène reste limité, probablement en raison de barrières intrinsèques à la reproduction, puisque les deux types de pathogènes infectent les mêmes arbres hôtes. Dans un second temps, j’ai comparé les structures génétiques et spatiales à l’échelle européenne de la plante Silene latifolia et de son pathogène Microbotryum lychnidis-dioicae. Notre jeu de données constitué du génotype d’un pathogène et de la plante qu’il infectait nous a permis de comparer la structure à très fine échelle et celle-ci apparait remarquablement congruente. Trois groupes phylogéographiques ont été identifiés chez les deux organismes, correspondant à l’histoire de contraction-expansion des aires de distribution des espèces tempérées lors de la dernière glaciation. Une structure génétique plus fine a également été détectée chez le pathogène, suggérant la possibilité d’une histoire plus complexe. / In the first part of my thesis project, I studied the evolutive history of apple tree species in Europe, including interspecific hybridizations. Analyses of whole genome data confirmed that the progenitor species of the cultivated apple tree was M. sieversii, a Central Asia wild apple tree, but also that a high proportion of European cultivated varieties form a genetic group distinct from the wild species. These varieties show traces of introgressions from M. sylvestris and of population subdivision along an East-West axis. Microsatellite markers also showed that introgressions from the cultivated apple were also quite frequent in wild apple tree populations and thus threaten their genetic integrity. We found that introgression levels were correlated to anthropic activities of apple tree cultivation and gave rise to hybrids with no detectable reduced fitness on the traits measured. Our study of the European wild apple tree phylogeography allowed us to detect differentiated genetic groups resulting from the past climatic history of the planet and which should be considered as different evolutionary significant units in conservation.In the second part of my thesis project, I studied coevolution between plant species and their pathogenic fungi in two different systems. I first compared the evolutive history of cultivated and wild apple trees in Central Asia and that of their scab pathogen, Venturia inaequalis. In the Kazakhstan Mountains, the cultivated apple tree has been reintroduced back from Europe during the last two centuries. This created a secondary contact zone, not only between the two apple tree species, but also between the agricultural and the wild types of V. inaequalis. While the invasion of natural populations by the cultivated apple trees still seems geographically limited, the agricultural pathogen is widespread in the forests and on the wild host trees. However, the number of hybrids in the pathogen was limited, probably because of intrinsic reproductive barriers since no ecological barriers were found. I also compared spatial genetic structures at the European scale in the plant Silene latifolia and its anther-smut pathogen Microbotryum lychnidis-dioicae. Our dataset included genotypes from the pathogens and the plants on which they were collected, and the population structures appeared remarquably congruent. Three phylogenetic groups were identified in these both species, corresponding with the temperate species range contraction-expansion cycles during the past glaciations. A substructure was identified in the pathogen suggesting the possibility of a more complex history.