Drosophila meridionalis é uma espécie endêmica da América do Sul, sendo amplamente distribuída na Costa Atlântica do Brasil. Com o objetivo de elaborar uma hipótese filogeográfica para esta espécie foram obtidas sequências do gene nuclear period e do gene mitocondrial COI. Foram calculados os índices de diversidade nucleotídica e realizados os testes: AMOVA, testes de neutralidade, a Mismatch Distribution, Bayesian Skyline Plot, NCPA. Foram obtidas três redes pelo gene COI, denominadas A (populações do interior), B (populações do litoral sul) e C (populações do litoral sudeste e oriental) e uma única rede obtida para o gene period, esta rede divide as populações em dois grupos sendo o primeiro congruente com a rede A e o segundo compreendendo as redes B e C, do gene COI. A AMOVA mostrou uma estruturação alta e significativa entre as populações do interior e o litoral para os dois genes (ct=0,72 gene COI; ct=0,70 gene period), que pode ser explicada pela presença de barreiras geográficas, como a Serra do Mar. Eventos de expansão populacional e de fluxo gênico restrito com isolamento por distância foram detectados nas populações do litoral e o interior respectivamente. A expansão da área de ocorrência de D. meridionalis provavelmente teve inicio com as populações do litoral do Rio Grande de Sul, em direção ao litoral de Santa Catarina com posterior colonização a longa distância dos estados de São Paulo, Rio de Janeiro e Bahia. Migrações assincrônicas de indivíduos de populações litorâneas de São Paulo e Santa Catarina provavelmente colonizaram o interior de São Paulo, e a partir destas populações, se iniciara uma expansão populacional em direção ao sul pelo interior, colonizando o Paraná e Rio Grande do Sul. A análise bayesiana (MCCT) indicou que o tempo do ancestral comum mais recente (TMRCA) para todos os haplótipos de D. meridionalis é de 81.700 anos atrás, data que marca a separação das populações do interior e do litoral aproximadamente no final do Pleistoceno. Eventos similares têm sido sugeridos para explicar a distribuição geográfica de espécies do cluster D. buzzatii, que ocorrem em simpatria em grande parte com populações de D. meridionalis. Esta espécie, como as espécies do cluster D. buzzatii, apresentou indicativos de flutuações demográficas, podendo estar associadas à expansão e contração da distribuição da vegetação xerofítica, durante as oscilações paleoclimáticas do Pleistoceno. / Drosophila meridionalis is an endemic species of South America, being widely distributed in the Atlantic Coast of Brazil. Aiming to develop a phylogeographic hypothesis for this species, sequences of mitochondrial COI and nuclear period genes were obtained. The diversity indexes, AMOVA, neutrality tests, Mismatch Distribution, Bayesan Skyline Plot and NCPA were calculated. We obtained three networks for the COI gene, denominated A (inland populations), B (south coast populations) and C (eastern and southeastern coast populations) and a single network obtained for the period gene, this network divides the population into two groups, being the first congruent with the network A of the COI gene and the second comprising the networks B and C of the COI gene. The AMOVA results, showed a high and significant structuring among inland and coastal populations, for both genes (ct=0,72 COI gene; ct=0,70 period gene), that can be explained by the presence of geographical barriers, such as Serra do Mar. Population expansion events and restricted gene flow with isolation by distance events were detected in coastal and inland populations respectively. The expansion of the area of occurrence of D. meridionalis probably was initiated with the populations of the coast of Rio Grande do Sul, towards the coast of Santa Catarina with subsequent long-distance colonization of the states of São Paulo, Rio de Janeiro and Bahia. Asynchronic migrations of individuals from coastal populations of São Paulo and Santa Catarina probably colonized the inland of São Paulo, and from these populations, a population expansion towards the south through the inland was initiated, colonizing the states of Paraná and Rio Grande do Sul. The bayesian analysis (MCCT) indicated that the time of the most recent common ancestor (TMRCA) for all haplotypes of D. meridionalis is from 81,700 years ago, a date that marks the separation of inland and coastal populations approximately at the end of the Pleistocene. Similar events have been suggested to explain the geographic distribution of species of the cluster D. buzzatii, occurring in sympatry largely with populations of D. meridionalis. This species, as the cluster D. buzzatii species, presented indicatives of demographic fluctuations, which can be associated with the expansion and contraction of the distribution of xerophytic vegetation, during the paleoclimatic fluctuations of the Pleistocene.

Por que os trópicos sustentam tanta diversidade? Essa é a pergunta principal que motivou este trabalho. Uma das frentes para contribuir ao entendimento deste fenômeno é estudar a origem da diversidade. Diversas hipóteses de diversificação existem, e existe também uma acalorada discussão no campo de estudo que busca testar essas diferentes hipóteses. Uma das hipóteses mais conhecida, se também não a mais polêmica, é a Hipótese de Refúgios. O objetivo deste trabalho foi, portanto, testar a Hipótese de Refúgios na Floresta Atlântica através de um estudo de caso. Para tanto, inicialmente os padrões de distribuição morfológica e genética do marsupial Didelphis aurita Wied, 1826 foram investigados através do método de quadrantes. As medidas cranianas revelaram uma correlação longitudinal para fêmeas, mas ausência de associação geográfica na variação do crânio dos machos. Entretanto, complementarmente, outro critério foi utilizado. Através de uma Análise de Componentes Principais sobre a variação da latitude e longitude resumiu-se a variação geográfica em apenas uma variável. Esta acaba se refletindo em uma diagonal da latitude e longitude, que acompanha a própria distribuição da Floresta Atlântica na costa brasileira. Agora, os grupos são formados se apresentam diferenças significativas ao longo desta diagonal, permitindo que populações biológicas distintas, mas próximas geograficamente, sejam separadas. Assim, verificou-se que a associação longitudinal das fêmeas provém basicamente da diferenciação das populações da Bahia, e mais, isso também afeta os machos. Contudo, o sinal não aparece através do outro critério devido ao fato de machos também apresentarem diferenciações em menor escala dentro da distribuição ao sul da Bahia, possivelmente devido à presença do ecótone entre a Floresta Atlântica e o cerrado latu sensu. Por usa vez, os dados genéticos como explorados através da variação geográfica do marcador mitocondrial citocromo B, revelaram que também existe uma associação com a longitude, e novamente, ela provém principalmente da diferenciação dos extremos da distribuição. Aqui, não só a mesma quebra na Bahia aparece, mas também uma outra quebra mais ao norte, de indivíduos provenientes de Alagoas. Tanto para os dados morfológicos quanto para os moleculares, demonstrou-se que há isolamento por distância no gambá, entretanto, toda a distribuição ao sul da Bahia se comporta como uma grande população panmítica. Essa ausência de estruturação geográfica, também aparente em análises de diferenciação (Fst), unidas aos testes de neutralidade (D de Tajima e F de Fu) negativos e significativos, que dão sinal de expansão demográfica recente mostram, juntos, as assinaturas esperadas pela Hipótese de Refúgios. Contudo, a divergência entre as populações deste sul datam de aproximadamente 140.000≅60.000 anos, o que não pode ser atribuída como sendo reflexo do último interglacial, esperado em cerca de 20.000 anos. Explorando mais a fundo as análises de Fst e os testes de neutralidade, revelou-se que suas estimativas são altamente influenciadas por desbalanço no tamanho de amostras, assim como baixa representatividade e agrupamentos inadequados que unem populações biológicas distintas. Os aparentes sinais de refúgios obtidos foram, portanto, artefato de três população bem amostradas no Rio de Janeiro. Sendo assim, não se pode atribuir esta hipótese como tendo criado diversidade dentro da espécie D. aurita. / How can the tropics present such diversity? This question lies at the very core of this work. While for the origins of diversity, numerous hypotheses have been put forward over time, the pursuit of empirical proofs for them is almost as old as the hypotheses themselves. One of the better known such hypothesis, and at the same time one of the most controversial, is the Refugee Hypothesis. In this context, the main goal of this thesis has been to test the Refugee Hypothesis in the Atlantic Forest by means of a study case. Initially, the morphologic and genetic distribution patterns of Didelphis aurita Wied, 1826 marsupial have been investigated using the grids method. Cranial measurements revealed a longitudinal correlation for the females and, at the same time, the absence of any geographic correlation in the variation of male skulls. By means of a Principal Component Analysis, the latitudinal and longitudinal variations have been reduced to a geographical variation dependent on one variable only _ a diagonal that follows the extension of the Atlantic Forest along the Brazilian coast. Groups have been formed if they presented significant differences along this diagonal, thus allowing distinct, but geographically close populations, to be differentiated. It could hereby be proven that the longitudinal correlation for females reflects mainly the differentiation between populations from Bahia state, and even more, that this differentiation affects the males as well. The signature does not appear in the grid criterium for the males since they also present lower levels of differentiation in the south of Bahia, possibly due to the presence of the ecotone of the Atlantic Forest with the cerrado latu sensu biome. There is, nevertheless, a break in Bahia for both males and females. As for the geographic variation of the molecular mitochondrial marker cytochrome B, it also presented a longitudinal variation, and a clear differentiation between the two extremes of the analyzed distribution. Here, not only a similar break could be seen in Bahia, but another one further north in the specimens from Alagoas state. For both the morphological and the molecular data, while there is isolation by distance effect for the opossum, all the distribution south of Bahia behaves as a large panmitic population. This lack of geographical structuring, also apparent in differentiation analyzes (Fst), together with neutrality tests (Tajima\'s D and Fu\'s F) which point towards recent geographic expansion, show the signatures expected by the Refugee Hypothesis. Since, however, the data indicates that the divergence of southern populations occurred approximately 140,000≅60,000 years ago, the diversification cannot be due to the last inter-glacial period from 20,000 years ago. To understand this seeming contradiction, further in-depth investigations of the Fst analyzes and the neutrality tests revealed that the estimations had been highly influenced by the heterogeneity in the number of samples, as well as by the low representability of some localities and also inadequate grouping of specimens, which mixed distinct biological populations. The apparent refugee signatures have thus been the misleading consequence of three well-sampled populations from Rio de Janeiro state. Therefore, the Refugee Hypothesis cannot be regarded as an explanation for the existing diversity of the species D. aurita.

Espécies de medusozoários com ciclos de vida muito diferentes habitam distintos mares e oceanos ao redor do mundo. Em uma escala regional, algumas espécies de hidrozoários estão amplamente distribuídas no Atlântico Sul-ocidental, (litorais do Brasil e Argentina), com populações habitando ambientes heterogêneos e estruturados. A relação entre a distribuição das espécies e a maior parte dos fatores ambientais é pouco conhecida. Deste modo, o objetivo de nosso estudo é pesquisar os padrões de distribuição e a estrutura genética populacional de duas espécies de hidrozoários do Atlântico Sul-ocidental em relação a: (1) as diferentes histórias naturais e (2) as distintas estruturas de massas d\'água do ambiente marinho. As espécies estudadas foram Olindias sambaquiensis (meroplanctônica, ciclo de vida: ovo ⊲ plânula ⊲ pólipo ⊲ medusa ⊲ ovo) e Liriope tetraphylla (holoplanctônica, ciclo de vida: ovo ⊲ plânula ⊲ medusa ⊲ ovo). Dados sobre a ecologia e história natural de tais espécies foram coletados e análises filogeográficas foram conduzidas utilizando os marcadores mitocondriais 16S e CO1. Nossos resultados revelaram um padrão filogeográfico similar para ambas as espécies. As populações brasileiras são basais e têm uma maior diversidade nucleotídica que as populações argentinas, as quais ocupam uma posição apical. O Rio da Prata não é uma barreira efetiva e introgressão possivelmente ocorre em ambas as espécies, podendo estar relacionada à circulação das massas d\'água. A estrutura genética encontrada para Olindias sambaquiensis pode estar relacionada com seu hábito demersal e afinidade com massas d\'água costeiras, e para Liriope tetraphylla com seu ciclo reprodutivo e auto-recrutamento. / Medusozoan species, with quite different life-cycles, inhabit different seas and oceans around the world. In a regional scale, some hydrozoan species are widespread along the Southwestern Atlantic Ocean (Brazilian and Argentinean shores), with populations distributed along a heterogeneous and structured environment. The relation between the distribution of the species and most of the biological and environmental factors is still largely unknown. Therefore, the aim of this study is to investigate the distributional patterns and genetic structure of populations of two hydrozoan species of SW Atlantic Ocean in relation to: (1) the different life histories and (2) the water masses structures of the marine environment. The species studied were the meroplanktonic Olindias sambaquiensis (life cycle: egg ⊲ planula ⊲ polyp ⊲ medusa ⊲ egg) and the holoplanktonic Liriope tetraphylla (life cycle: egg ⊲ planula ⊲ medusa ⊲ egg). We gathered data on the ecology and natural history of the species, and carried out phylogeographic analyses using CO1 and 16S DNA markers. Our results have shown similar phylogeographical patterns and genetic structures for both species. The Brazilian populations are basal and have a higher nucleotidic diversity than the apical Argentinean populations. The Rio de La Plata river is not an effective barrier, and introgression possibly occurs for both species and might be related to the circulation of the water masses. Biologically, the genetic structure found for Olindias sambaquiensis must be related to its demersal habit and close affinity to coastal water masses, and that found for Liriope tetraphylla must be related to its reproductive cycle and auto-recruitment.

Orientador: Shirlei Maria Recco Pimentel / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-26T03:30:46Z (GMT). No. of bitstreams: 1 Bruschi_DanielPacheco_D.pdf: 18653513 bytes, checksum: 6cab8e91377d38b25d3a8a77e634c16a (MD5) Previous issue date: 2014 / Resumo: Dificuldades na identificação de populações e delimitação taxonômica de espécies, evidências de espécies crípticas e padrões biogeográficos diversos fazem dos anuros gênero Phyllomedusa (Hylidae, Phyllomedusinae) um interessante candidato a estudos taxonômicos e evolutivos. Na presente tese, foram realizados estudos visando acessar diferentes níveis de diferenciação entre os táxons e possibilitar inferência de eventos e processos envolvidos na diversificação das espécies, contribuindo no melhor entendimento das questões taxonômicas e evolutivas do gênero. Utilizando citogenética, filogenia molecular e filogeografia, investigamos aspectos da evolução cromossômica e molecular em representantes do gênero Phyllomedusa. No primeiro capítulo avaliamos o status taxonômico de populações atribuídas à P. hypochondrialis e P. azurea, utilizando dados morfológicos, cromossômicos e filogenia molecular. Reforçamos a dificuldade de distinção entre estas duas espécies baseado somente em seus caracteres de diagnose, já que estes se sobrepõem quando a amostragem é ampliada. Destacamos variações inter- e intrapopulacionais na posição da NOR em P. hypochondrialis. No segundo capítulo, para entender essa variação em P. hypochondrialis, delimitar as populações brasileiras de P. azurea e estimar a diversidade genética entre populações de P. nordestina, foi realizada uma análise filogeográfica dessas três espécies. As inferências filogenéticas indicaram forte estruturação regional entre as populações de P. hypochondrialis amostradas, recuperando quatro clados bem suportados. Processos demográficos históricos foram importantes na distribuição das variações de NOR, sendo que os clados demograficamente estáveis exibiram conservada posição de NOR no par 8, enquanto as populações que experenciaram eventos de rápida expansão demográfica exibiram variação neste marcador. A história evolutiva dessa espécie foi influenciada pela interação entre eventos geomorfológicos na transição Mioceno-Plioceno, que persistiram por episódios de flutuações climáticas ocorridas durante o Pleistoceno. As populações distribuídas dentro de domínios de cerrado demostraram uma recente colonização durante o Pleistoceno, sendo que hipotetizamos que sucessivos ciclos de expansão/retração de matas de galeria permitiram a colonização desta linhagem neste bioma. Recuperamos P. azurea parafilética em relação à P. nordestina. Interessantemente, os dois clados divergentes de P. nordestina estão separados pelo rio São Francisco (SF), definindo um clado localizado na margem esquerda e outro na margem direita desse rio. A estimativa do tempo de divergência entre estes dois grupos são condizentes com o reposicionamento histórico do curso deste rio no nordeste brasileiro, que deve ter contribuído no isolamento destes grupos por um processo de vicariância. Esta barreira geográfica teve papel fundamental na divergência entre as duas linhagens, suportada pelo alto nível de diferenciação entre os grupos de margens opostas do rio e ausência de fluxo gênico entre os grupos. Sugerimos futura reavaliação da taxonomia de populações distribuídas na margem esquerda do rio SF. A história evolutiva de P. azurea, foi marcada por um profundo evento de perda de diversidade genética, que deve ter contribuído para a rápida fixação dos alelos exclusivos encontrados nesta população. No terceiro capítulo, uma abordagem integrativa foi utilizada para descrição de uma nova espécie, filogeneticamente relacionada às espécies do grupo de P. hypochondrialis que habitam ambientes de altitude, condizente com a área na qual o táxon foi encontrado, revelando um interessante padrão biogeográfico. No quarto e quinto capítulo, descrevemos citogeneticamente cinco espécies (P. vaillantii, P. tarsius, P. bahiana, P. distincta e P. ayeaye). Observamos cariótipos conservados, possibilitando o reconhecimento de homeologias cromossômicas. Apesar de ainda existirem lacunas na citogenética do gênero, variações interessantes na posição da NOR reportam uma alta razão de transposição de sítios de rDNA no genoma destes representantes e alertam para seu papel na evolução cromossômica no gênero / Abstract: We conducted cytogenetic, phylogenetic and phylogeographical studies to investigate aspects of chromosomal and molecular evolution in the Neotropical tree frogs of the genus Phyllomedusa genus (Hylidae, Phyllomedusinae), which have been the subject of extensive taxonomical debate. In the first chapter, the study focuses on the morphological variation found in populations attributed to P. hypochondrialis, and examines whether this variation is interspecific or inter-population. The results of this analysis support the need for a thorough revision of the phenotypic features used to discriminate P. azurea and P. hypochondrialis, given the considerable overlap found in these characters when more populations are samples. We also report inter- and intra-population variability in the NOR of P. hypochondrialis. In the second chapter, we use phylogeographic approaches to evaluate the source of the karyotype variation found within P. hypochondrialis, provide a better delimitation of the Brazilian populations of P. azurea, and estimate the genetic diversity within P. nordestina. These three species are closely related, but are associated with distinct South American morphoclimatic domains. Our results reveal a deep genetic structuring in the P. hypochondrialis populations, based four well-supported clades with a low migration signal among haplogroups. The evolutionary history of this species has been influenced by the interaction between the geomorphological changes occurring in the Miocene-Pliocene that have persisted through the episodes of climatic fluctuation that occurred during the Pleistocene. The populations of the Cerrado domain appear to have colonized this region during the Pleistocene period, when successive cycles of forest expansion and retraction may have facilitated expansion into this biome via gallery forests. We were able to recognize two cryptic lineages within the P. nordestina populations, differentiated by the São Francisco River in northeastern of Brazil. Estimates of coalescence time indicated a process of divergence between two geographic clades of P. nordestina during the Pliocene-Pleistocene transition, which is temporally congruent with historical modifications to the course of the São Francisco River. This geographic barrier has had a primary role in the divergence of lineages, supported by the high differentiation between populations from opposite margins of the river and the absence of gene flow between haploclades. A strong signature of genetic decline marks the evolutionary history of the Brazilians populations of P. azurea. While more extensive surveys are needed, Brazilian populations of this species appear to be restricted to the Pantanal biome. In the third chapter, we describe a new species of the P. hypochondrialis group, diagnosed using molecular, morphological and chromosomal approaches. The new species is closely related phylogenetically with all the highland species of the clade, revealing an interesting biogeographical pattern. Finally, in chapters four and five, we present cytogenetic data on four species of the genus Phyllomedusa (P. vaillantii, P. tarsius, P. distincta, P. bahiana and P. ayeaye). We found conservative karyotypes, permitting the recognition of chromosomal homologies. Despite the gaps in the chromosomal studies of this genus, the inter- and intraspecific variation found in the number and location of rDNA sites reflects the rapid rate of evolution of this character in Phyllomedusa, and highlights the important role of this sequence in the chromosomal evolution of this genus / Doutorado / Biologia Celular / Doutor em Biologia Celular e Estrutural

Abstract The amount and distribution of genetic diversity are likely to affect the evolutionary potential of a species. When feasible and cost-effective policies for management and monitoring of endangered populations or species are planned, knowledge of the spatial genetic structure and the type of population dynamics is of great concern. In this thesis the genetic diversity and population structures of two endangered arctic plant species was examined on different geographical scales in Northern Europe. The species were Siberian primrose (Primula nutans) and pendant grass (Arctophila fulva), which both grow in a seashore habitat and have similar distribution patterns on the shores of the Arctic Ocean and the Bothnian Bay. The goal of the present study was to provide basic population genetic information for the study species using microsatellite and AFLP markers. Both markers were used for the first time in these species, and species-specific microsatellite markers were developed during the study. A further aim was to interlink the population genetic processes of the species into distribution patterns at the regional and population levels and to compile a synthesis of the impact of hierarchical spatiotemporal processes and autocorrelation in genetic variation at different levels. The studies of this thesis provided new information on the diversity and population structure of the endangered study species and new markers that are useful in future genetic studies of primrose species. The diversity of Siberian primrose was low, and there was no dispersal between the study regions. In pendant grass, a relatively high amount of variation was found considering the evident clonal reproduction and gene flow that was detected between populations connected by waterways. The results suggested that both clonal and sexual reproduction are important in this species. On a local scale, pendant grass populations had characteristics of “stepping stone” and classical metapopulation models. The results indicated that on a long time scale, both species will continue to decline without efficient management efforts. Most critical for the persistence of the species is the conservation of suitable habitats. Translocations could be considered in order to enhance the diversity of existing populations and establish new populations. By examining the present day structure of Siberian primrose, it was possible to make inferences regarding the colonisation history of the species in the North European area. The current distribution of Siberian primrose seemed to result from a vicariant process that took place after the last ice-age, when the species colonised the area. It spread first to the White Sea area, probably from the east, and subsequently colonised the Bothnian Bay and the Barents Sea in the west. The isostatic land uplift after the retreat of the Eurasian ice sheet uncovered large areas of land from the Baltic Sea basin that previously were under water. These geological changes resulted in the current disjunct distribution of Siberian primrose.

Palmer amaranth (Amaranthus palmeri) is a major weed in United States cotton and soybean production systems. Originally native to the Southwest, the species has spread throughout the country. In 2004 a population of A. palmeri was identified with resistance to glyphosate, a herbicide heavily relied on in modern no-tillage and transgenic glyphosate-resistant (GR) crop systems. This project aims to determine the degree of genetic relatedness among eight different populations of GR and glyphosate-susceptible (GS) A. palmeri from various geographic regions in the United States by analyzing patterns of phylogeography and diversity to ascertain whether resistance evolved independently or spread from outside to an Arizona locality (AZ-R). Shikimic acid accumulation and EPSPS genomic copy assays confirmed resistance or susceptibility. With a set of 1,351 single nucleotide polymorphisms (SNPs), discovered by genotyping-by-sequencing (GBS), UPGMA phylogenetic analysis, principal component analysis, Bayesian model-based clustering, and pairwise comparisons of genetic distances were conducted. A GR population from Tennessee and two GS populations from Georgia and Arizona were identified as genetically distinct while the remaining GS populations from Kansas, Arizona, and Nebraska clustered together with two GR populations from Arizona and Georgia. Within the latter group, AZ-R was most closely related to the GS populations from Kansas and Arizona followed by the GR population from Georgia. GR populations from Georgia and Tennessee were genetically distinct from each other. No isolation by distance was detected and A. palmeri was revealed to be a species with high genetic diversity. The data suggest the following two possible scenarios: either glyphosate resistance was introduced to the Arizona locality from the east, or resistance evolved independently in Arizona. Glyphosate resistance in the Georgia and Tennessee localities most likely evolved separately. Thus, modern farmers need to continue to diversify weed management practices and prevent seed dispersal to mitigate herbicide resistance evolution in A. palmeri.

Fundação de Amparo a Pesquisa no Estado do Rio Grande do Sul / The epoch of Pleistocene was marked by grate climate and flora alterations. On the southern hemisphere, where the glaciations had less intensity, there was the formation of refuges, providing a favorable condition to speciation. The genus Zygothrica (Diptera: Drosophilidae) is characterized by their interaction with fungi. Zygothrica vittimaculosa is considered a generalist species, because it explores even fungi, flowers (genus Cestrum, Solanaceae) and rotting fruits. In this work we identified a new species that is cryptic with Z. vittimaculosa and they are simpatric in almost all distribution area. However, this new species is rarely collected in resources but Cestrum inflorescences, differently of Z. vittimaculosa. Only after molecular analyses we realize it was a new species (posteriorly confirmed by male internal genitalia analyses), due to the external morphology of both species is identical. Also in this work we did the taxonomic description of this new species. A comparative analysis was performed by photographs, with the documentation of the external patterns (morphology and color) and the internal genitalia morphology (considered diagnostic) for both females and males, in addition to a measures table. Finally, was also performed a phylogeographic study based on two mitochondrial markers: COI (Citochrome c Subunit I) and COII (Citochrome c Subunit II). In this case, through collections and climate variables data, we estimate the present distribution of both species as well as an estimated of the Last Glacial Maximum distribution (about 20,000 years), suggesting that the potential distribution of both species seems to be restricted to the already sampled area, besides pointed a high suitability in northern Peru and western Chile for the new species, data not inferred to Z. vittimaculosa. About phylogeographic patterns, we suggest that, through Neutrality tests and Diversity indexes, the newest species had a really recent expansion, and potentially is also in diversification and expansion, while Z. vittimaculosa, despite also presents population expansion signals, these are less intense than their sister-species. To explain this inference, we can assume that because Z. vittimaculosa be more generalist than the other species, it had suffered more selection pressure, diversifying and increasing the number of haplotypes. / A época do Pleistoceno foi marcada por grandes alterações na vegetação e principalmente no clima. No Hemisfério Sul, as glaciações foram menos intensas, onde houve também a formação de refúgios, proporcionando uma condição favorável à especiações. O gênero Zygothrica, pertencente à família Drosophilidae, é característico por sua interação com fungos. Zygothrica vittimaculosa é uma espécie considerado um tanto generalista, por explorar recursos diversos: inflorescências do gênero Cestrum, corpos de frutificação de fungos e frutas em decomposição. Neste trabalho, identificamos uma nova espécie, críptica com Z. vittimaculosa e simpátrica em boa parte de sua distribuição. Porém essa espécie nova é raramente amostrada em outros recursos além de inflorescências de Cestrm, diferentemente de Z. vittimaculosa. De morfologia externa idêntica à de Z. vittimaculosa, apenas após análises moleculares percebeu-se indícios de se tratar de uma espécie nova, confirmada, posteriormente, pela morfologia interna da genitália dos machos. Também nesse trabalho fez-se a descrição taxonômica da nova espécie. Uma análise comparativa com Z. vittimaculosa foi feita e documentada através de fotos de hábitos da morfologia externa e das genitálias, consideradas diagnósticas tanto para machos quanto para femeas, além de uma tabela com as medias taxonômicas. Por fim, foi também performado um estudo filogeográfico com base em dois marcadores moleculares: COI (Citocromo c subunidade I) e COII (Citocromo c subunidade II). Nesse estudo, com base em dados de coletas e dados de variáveis climáticas estimou-se a distribuição atual de ambas as espécies e também a estimativa da distribuição no último máximo glacial (há cerca de 20.000 anos), sugerindo que a distribuição potencial de ambas restringe-se à área de estudo já amostrada, além de apontar uma alta adequabilidade para a espécie nova norte do Peru e no oeste do Chile, que não foram recuperadas para Z. vittimaculosa. Quanto aos padrões filogeográficos, sugere-se que, através de testes de neutralidade e índices de diversidade, a espécie nova teve uma expansão muito recente e potencialmente ainda está se expandindo e diversificando, enquanto Z. vittimaculosa, apesar de apresentar indicativos de expansão populacional também, esse são menos intensos que a de sua espécie irmã. Para esse explicar esse fato, pode-se supor que por Z. vittimaculosa ser mais generalista que a outra espécie, sofreu mais pressões de seleção, diversificando-se e aumentando o número de haplótipos.

Alors que l’épidémiologie de la dengue dans le sud du Vietnam est caractérisée par un régime d’hyper-endémicité, la maladie est en train d’émerger dans le nord du pays depuis une quinzaine d’années. Les incidences annuelles augmentent de façon constante d’année en année et la maladie diffuse à partir de Hanoi vers les zones rurales environnantes. Le travail de recherche effectué durant cette thèse s’intéresse aux déterminants spatiaux et temporels de la transmission de la dengue dans un contexte d’émergence. Les résultats sont organisés en 3 parties. La première se concentre sur l’étude d’une épidémie qui frappa à l’automne 2013 l’île de Cat Ba, au large du Vietnam dans la baie d’Halong. Cette île est caractérisée par une population de petite taille vivant essentiellement de l’exploitation des produits de la mer ainsi que du tourisme. Une grande proportion de cette population vit sur des villages flottant au large de l’île. Nous avons comparé l’épidémiologie de la dengue sur les villages flottants et sur l’île. Pour cela nous avons testé l’agrégation spatio-temporelle des cas de dengue. Nos résultats montrent une incidence de dengue sur les villages flottant plus forte que sur l’île, malgré des densités de moustiques plus faibles. Les cas de dengue étaient également extrêmement agrégés dans le temps et l’espace, suggérant une importation de moustiques infectés plutôt qu’un cycle de transmission local complet.La seconde partie de cette thèse s’est intéressée aux déterminants environnementaux de la transmission de la dengue dans la province de Hanoi. Cette étude est basée sur l’analyse de 31906 cas de dengue géospatialisés de 2008 à 2013 et utilise des méthodes de SIG couplées avec des techniques modernes d’apprentissage automatique dans le but de quantifier en détail les influences de chaque covariable environnementale sur le risque de dengue. Nos résultats montrent une forte influence de la densité de population sur l’incidence de la dengue, comme précédemment documenté dans d’autres régions du monde. L’incidence de la dengue augmente avec la couverture végétale pour de faibles niveaux de couverture végétale et atteint de très faibles niveaux lorsque la couverture végétale est au-dessus d’un certain seuil. Une telle relation est cohérente avec ce qui est actuellement connu sur l’écologie des vecteurs de dengue. Finalement, nos résultats ont montré une forte association entre les incidences de dengue et les zones résidentielles universitaires. Ces zones sont peuplées d’étudiants venant des régions autour de Hanoi où l’incidence est faible. La susceptibilité à la dengue de cette population estudiantine est donc plus forte que dans le reste de la population de Hanoi.La dernière partie de cette thèse s’est intéressée aux relations entre les épidémies successives de dengue à Hanoi de 2011 à 2014. L’épidémiologie de la dengue à Hanoi est très saisonnière avec de très faibles incidences en hiver. Une question majeure dans une telle situation est de savoir si les virus de dengue persistent localement entre chaque épidémie. Si non, alors les cas de dengue observés en hiver correspondraient à des cas d’importation qui pourraient démarrer une nouvelle épidémie chaque été lorsque les conditions climatiques locales deviennent à nouveau favorables pour la transmission de la dengue. Nous avons utilisé une approche de phylogénie moléculaire de virus échantillonnés à Hanoi ainsi que dans d’autres localités en Asie du sud-est d’où les virus de dengue pourraient migrer. L’idée d’une telle approche consiste à comparer les distances phylogénétiques entre des virus circulants dans une localité une année donnée et des virus circulants soit la même année dans d’autres localités, soit durant les années précédentes dans la même localité. Nos résultats suggèrent que, chaque année, les épidémies de dengue à Hanoi démarrent à partir des virus de dengue importés depuis Ho Chi Minh ville. Ce schéma semble être le cas pour les 4 sérotypes de dengue. / While high dengue transmission has been documented in the southern part of Vietnam since the late seventies, the disease started to emerge in the northern part of the country 15 years ago only. In northern Vietnam, annual incidences are consistently increasing from year to year and progressively spreading from Hanoi to the surrounding rural areas. Very little is known on the causes of this recent emergence.The research carried out in this PhD revolves around the spatial and temporal determinants of dengue epidemiological transmission in a context of emergence and the results are organized in 3 parts. The first one focuses on a single epidemic of dengue that occurred during the autumn of 2013 on the small island of Cat Ba, off the coast of Vietnam in Ha Long bay. Cat Ba island is characterized by a population of a small size mostly living from sea farming and tourism. Dengue transmission on this island has been historically rare until the major epidemics that stroke the island in 2013. The population of Cat Ba has this specificity that a large proportion of it lives of floating villages off the island coast. We were interested in investigating whether the epidemics had different behavior on the island and the floating villages. To achieve this aim, we focused on the identification of spatio-temporal clusters of cases. Our results show a higher dengue incidence on the floating villages than on the island despite lower mosquito densities. Dengue cases were also highly clustered in space and time suggesting importation of infected mosquitoes rather than a local complete transmission cycle.The second part focuses on the environmental determinants of dengue transmission in the province of Hanoi. This study is based on the use of 31,906 geospatialized cases of dengue from 2008 to 2013 and applies GIS techniques coupled with modern machine learning techniques in order to quantify in detail the influences of each environmental covariate on dengue risk. Our results showed a strong influence of population density on dengue incidence as previously reported in other parts of the world. Dengue incidence increased with tree coverage for low levels of tree coverage and then reached very low levels for tree coverage above a given threshold. This pattern is consistent with the current knowledge of the dengue vector ecology. Finally we showed a strong association of dengue incidence with academic residential areas. Such areas are populated with students coming from locations around Hanoi with low dengue incidence. The susceptibility of this student population to dengue infection is thus higher than the rest of the Hanoian population.The final part looked at the relationships between the successive epidemics in Hanoi from 2011 to 2014. Dengue epidemiology in Hanoi is very seasonal with very few cases documented in winter. A major question in such situations is whether viruses actually persist locally between epidemics. If not, then observed cases during the winter would correspond to imported cases igniting new epidemics every summer when the local climatic conditions are favorable again for local dengue transmission. To do so, we used phylogenetic analyses of virus sampled in Hanoi combined with virus sampled in other locations in Southeast Asia from where dengue viruses could migrate. The rationale behind this method is to compare the phylogenetic distances between sequences circulating in a given location in a given year and sequences circulating either the same year in other locations or previous years in the same location. Our results suggest that every year dengue epidemics in Hanoi are started from viruses imported from Ho Chi Minh city. This seems to be the case for the 4 dengue serotypes.

Ma thèse s'inscrit dans le cadre de l'étude de l'impact des changements environnementaux sur la biodiversité marine, à une échelle intra-spécifique et inter-spécifique. Les modèles choisis sont des Octocoralliaires méditerranéens (corail rouge; Corallium rubrum, et gorgones Paramuricea clavata et Eunicella cavolini). Mieux comprendre les conséquences génétiques des fluctuations passées sur les organismes permet d'appréhender les conséquences génétiques à venir des changements environnementaux en cours. Durant ma thèse, nous avons donc étudié par une approche de phylogéographie comparée l'évolution de ces espèces : plusieurs marqueurs de séquences ont été utilisés afin de tenter de détecter des changements démographiques passés et de reconstituer l'histoire évolutive de ces espèces. L'étude du complexe d'espèces du genre Eunicella a mis en évidence que des limites d'espèces floues entre E. cavolini et E. singularis liés à de possibles flux de gènes entre elles. Par ailleurs, l'impact du changement climatique en cours a été étudié en conditions expérimentales. En aquarium, les résultats obtenus sur E. cavolini ont permis de détecter des phénomènes d'adaptation en présence de flux de gènes. En complément, l'étude de la phénologie de deux espèces, P. clavata et E. cavolini, a été initiée et suggère la possibilité de maintien de niveaux comparables d'effort reproducteur entre différents régimes thermiques. A travers diverses collaborations, cette thèse a permis à la fois de développer de nouveaux modèles mais aussi de réaliser une approche intégrative de l'étude de l'adaptation des Octocoralliaires de Méditerranée face au changement climatique passé et en cours. / My PhD thesis is in the context of the study of the impact of environmental changes on marine biodiversity, with an intra-specific and inter-specific level. Selected models are Mediterranean octocorals (red coral Corallium rubrum and gorgonians Paramuricea clavata and Eunicella cavolini). Better understanding the genetic consequences of these past fluctuations on organisms will help us understanding the potential future consequences of current climate change. During my PhD, we studied the evolution of these species through comparative phylogeography: several nuclear loci were used to try to detect past demographic changes and to reconstruct the evolutionary history of these species. The study of the Eunicella spp. species complex showed that genetic boundaries between E. cavolini and E. singularis were not clear with potential gene flow between them. Moreover, the impact of ongoing climate change has been studied in experimental conditions. In aquariums, the results obtained on E. cavolini have revealed adaptive processes in the presence of gene flow. Through various collaborations, this thesis has allowed both to develop new models but also to achieve an integrative approach of the study of the adaptation of Mediterranean octocorals facing past and ongoing climate change.

Paracalanus quasimodo and Temora turbinata are two calanoid copepods prominent in the planktonic communities of the southeastern United States. Despite their prominence, the species and population level structure of these copepods is yet unexplored. The phylogeographic, temporal and phylogenetic structure of P. quasimodo and T. turbinata are examined in my study. Samples were collected from ten sites along the Gulf of Mexico and Florida peninsular coasts. Three sites were sampled quarterly for two years. Individuals were screened for unique ITS-1 sequences with denaturing gradient gel electrophoresis. Unique variants were sequenced at the nuclear ITS-1 and mitochondrial COI loci. Sampling sites were analyzed for pairwise community differences and for variances between geographic and temporal groupings. Genetic variants were analyzed for phylogenetic and coalescent topology. Paracalanus quasimodo is highly structured geographically with populations divided between the Gulf of Mexico, temperate Atlantic and subtropical Atlantic, in addition to isolation by distance. No significant differences were detected between the T. turbinata samples. Both P. quasimodo and T. turbinata are stable within sites over time and between sites within a sampling period, with two exceptions. The first was a pilot sample from Miami taken two years prior to the general sampling whose community showed significant differences from most of the other Miami samples. Paracalanus quasimodo had a positive correlation of Fst with time. The second was high temporal variability detected in the samples from Fort Pierce. Phylogenetically, both P. quasimodo and T. turbinata were in well supported, congeneric clades. Paracalanus quasimodo was not monophyletic, divided into two well-supported clades. Temora turbinata variants were in one clade with insignificant support for topology within the clade and very little intraspecific variation. Paracalanus quasimodo and T. turbinata populations show opposite trends. Paracalanus quasimodo occurs near shore and shows population structure mediated by hydrological features and distance, both geographic and temporal. The phylogeny shows two deeply divergent clades suggestive of cryptic speciation. In contrast, T. turbinata populations range further offshore and show little geographic or temporal structure. However, the low genetic variation detected in this region suggests a recent bottleneck event.