Estudos filogeográficos para distintas espécies de Medusozoa (Cnidaria) foram conduzidos enfatizando a área nerítica central do Atlântico Sul-ocidental (ASO), entre os litorais sudeste do Brasil e o litoral da província de Buenos Aires na Argentina. Estes foram baseados em sequências de DNA dos genes mitocondriais COI e 16S e do íntron nuclear ITS1, levando em consideração tanto a heterogeneidade atual e a historia geológica das condições oceanográficas do ASO, como também as capacidades dispersivas de Liriope tetraphylla, Olindias sambaquiensis e Acharadria crocea, inferidas pelos seus ciclos de vida. Adicionalmente, a estrutura filogeográfica de Pelagia noctiluca foi avaliada em outras regiões oceânicas, considerando o Atlântico (Atl.) e o Mediterrâneo (Med.) e utilizando os marcadores COI, 16S e ITS1. Este estudo foi conduzido através de calibrações de taxas de substituição baseadas em uma divergência significativa embora filogeneticamente rasa, entre populações do Atl. e do Pacífico. Os resultados específicos indicam: 1) padrões comuns, de expansões populacionais e estruturação genética acompanhada de padrões filogenéticos sem uma correlação geográfica evidente, para as três espécies estudadas do ASO, os quais remetem a alterações de área habitável em períodos glaciais e interglaciais a partir do Pleistoceno médio ou tardio; 2) uma estrutura filogeográfica entre populações de P. noctiluca do Atl. e do Med. que remete a possíveis efeitos de isolamento entre ambas bacias durante o Gelasiano. Além disso, aspectos dos resultados que sugerem a importância de se considerar que a demografia não seria apenas afetada pela história biogeográfica são discutidos. A demografia também modularia o grau de resposta das populações aos eventos biogeográficos, podendo ser uma característica comum para populações de espécies que mostram padrões filogeográficos similares, a despeito de possuírem biologias marcadamente distaintas. É importante salientar que a prevalência na interpretação da influência da história natural nos estudos biogeográficos não se restringe a estudos microevolutivos. A origem dos metazoários é geralmente associada ao impacto biológico de mudanças ambientais que teriam desencadeando a chamada explosão cambriana. Entretanto, a atividade tectônica que propiciou estas mudanças é pouco discutida dentro de uma abordagem biogeográfica, a qual é considerada controversa. Resultados indicadores de que as principais linhagens de Cnidaria teriam surgido ao longo do Criogeniano e o Ediacarano foram obtidos, Períodos em que novos mares e áreas de plataforma rasa estavam surgindo como resultado da fragmentação da placa continental de Rodínia. A relação entre estes eventos geológicos e um possível surgimento de biotas marinhas diversificadas, as quais poderiam ser consideradas as primeiras cladogêneses em Eumetazoa relacionadas a eventos vicariantes, é uma nova hipótese a ser considerada / Phylogeographic studies for different species of Medusozoa (Cnidaria) were performed, emphasizing the central neritic area of the South-Western Atlantic (SWA), localized between the southeastern Brazilian coast and the coast of the Buenos Aires province in Argentina. These were based on DNA sequences of the mitochondrial genes COI and 16S, and the nuclear intron ITS1. They considered both the heterogeneity of the geological history and the present oceanographic conditions of the SWA, as well as the dispersal capabilities of Liriope tetraphylla, Olindias sambaquiensis and Acharadria crocea, inferred by their life cycles. Additionally, the phylogeographic structure of Pelagia noctiluca was evaluated in other oceanic regions, considering the Atlantic (Atl.) and Mediterranean (Med.) and using COI, ITS1 and 16S as molecular markers. This study was conducted through calibrations of substitution rates based on a significant but phylogenetically shallow divergence, between populations from the Atl. and the Pacific. Specific results indicate: 1) common patterns of population expansion and genetic structure associated to phylogenetic patterns without a clear geographical correlation, for the three species of the ASO, which refer to changes of the habitable area during glacial and interglacial periods since the middle or late Pleistocene; 2) genetic structure between populations of P. noctiluca from the Atl. and Med., referring to possible isolation effects between the two basins during the Gelasian. Moreover, the results also suggest the importance of considering that the demographic aspects would not be affected only by the biogeographical history. The demography would also modulate the degree of response of populations to biogeographic events, and could be a common feature for populations of species that exhibit similar phylogeographic patterns, in spite of having markedly different biological features. It is important to notice that the prevalence in the interpretation of the influence of natural history in biogeographical studies is not restricted to microevolutionary studies. The origin of metazoans is generally associated with the biological impact of environmental changes that would have triggered the Cambrian explosion. However, the tectonic activity that resulted in such changes is not discussed within a biogeographic approach, which is considered controversial. Results indicating that the main lineages of Cnidaria emerged during the Cryogenian and Ediacaran were obtained, at that Period new seas and areas of shallow platform were emerging as a result of the fragmentation of the Rodinia continental plate. The relationship between those geological events and the possible emergence of a diverse marine biota, whose could be considered as the firsts cladogenesis in Eumetazoa related to vicariant events, is a new hypothesis to be considered

The Capsalidae is a diverse family of ectoparasites of marine fish (Platyhelminthes: Monogenea). It is a large family with approximately 180 described species and many more yet to be discovered. Capsalids have a global distribution and parasitise a diversity of hosts from the Chondrichthyes to bony fishes. A morphological classification exists for the family based on a few key characters such as testes number, their arrangement and morphology of the posterior attachment organ (haptor). Phylogenetic relationships within the family and its position within the Monogenea are largely unexplored. I have used various molecular phylogenetic techniques to resolve relationships and explore the evolution and radiation of this family. Specimens from the Capsalidae and other monogenean families (outgroups) were obtained through fresh collections and generous donations by other parasitologists. Specimens were stored in 95% undenatured ethanol. Three unlinked nuclear genes (28S ribosomal RNA, Histone 3 and Elongation Factor 1 α) and two mitochondrial genes (Cytochrome Oxidase 3 and Cytochrome B) were amplified for 78 capsalid taxa in 28 genera representing all nine subfamilies and 30 outgroup taxa (eight Polyopisthocotylea and 22 Monopisthocotylea). Analyses showed the Capsalidae is monophyletic, with the sister group remaining unresolved. Some analyses supported Gyrodactylidae and Udonellidae as the sister group but in other analyses, it was unresolved with the Monocotylidae and Microbothriidae also possible sister groups. The Capsalinae, Encotyllabinae and Nitzschiinae are monophyletic, but analyses did not support monophyly for the Benedeniinae, Entobdellinae and Trochopodinae. Monophyly was supported for Capsala, Capsaloides, Encotyllabe, Entobdella, Listrocephalos, Neobenedenia, Nitzschia and Tristoma, but Metabenedeniella is paraphyletic and Benedenia and Neoentobdella are polyphyletic. Comparisons of the distribution of character states for the small number of morphological characters on a molecular phylogeny show a high frequency of apparent homoplasy. Consequently the current morphological classification for the Capsalidae shows little correspondence with the phylogenetic hypotheses I present. I also sequenced the first complete mitochondrial (mt) genome for a capsalid species, Benedenia seriolae. The mt genome of B. seriolae shows some tRNA rearrangements in comparison to three Gyrodactylus spp. (Gyrodactylidae), the only other complete monopisthocotylean mt genomes sequenced. It also lacks the duplicated, conserved non-coding regions present in Gyrodactylus spp. making the genome smaller in size. I combined this genome with other available platyhelminth mt genomes to investigate the monophyly of Monogenea and the evolution of diet across the Neodermata. Results confirm paraphyly for the Monogenea and also suggest paraphyly for the epidermal feeding Monopisthocotylea. I hypothesise that the Monopisthocotylea represent the first shift to parasitism in the Neodermata from a free living ancestor and following this, there was a dietary shift to blood feeding (Polyopisthocotylea). The Digenea and Cestoda independently evolved dietary specialisations to suit their diverse microhabitats and broad range of vertebrate final hosts. Using Elongation Factor 1 α I have estimated molecular divergence dates for the Neodermata, Monogenea and Capsalidae. Molecular clock analyses estimate the Neodermata diverged from the free living platyhelminths 513 million years ago (mya) (95% HPD [highest posterior density]: 473–605) before the appearance of vertebrates in the fossil record. The Monogenea diverged from the other neodermatan classes 441 mya (95% HPD: 420–547) coinciding with the appearance of fish in the fossil record. The most recent common ancestor of the Capsalidae arose approximately 235 million years ago (95% HPD: 200–274) following the Permian/Triassic extinction event and coinciding with the diversification of bony fishes in the marine environment. I compared the capsalid phylogeny to a phylogeny of fishes that I generated using eight nuclear and three mt genes to explore the evolution and the radiation of the Capsalidae across fishes. There is no significant global signal of coevolution with only five parasite-host associations that may be a result of coevolution. Estimated molecular divergence dates are also compared and do not reveal temporal congruence. Radiation of the family may have been driven by host switching constrained by shared host ecology, biology, behaviour and plasticity in morphological adaptations by the parasites. This study advances our understanding of the evolution of this monogenean family and provides insights into the evolution of the Neodermata and the complicated realities of reconstructing the evolutionary history of parasitic groups. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1522353 / Thesis (Ph.D.) -- University of Adelaide, School of Earth and Environmental Sciences, 2010

Estudos filogeográficos para distintas espécies de Medusozoa (Cnidaria) foram conduzidos enfatizando a área nerítica central do Atlântico Sul-ocidental (ASO), entre os litorais sudeste do Brasil e o litoral da província de Buenos Aires na Argentina. Estes foram baseados em sequências de DNA dos genes mitocondriais COI e 16S e do íntron nuclear ITS1, levando em consideração tanto a heterogeneidade atual e a historia geológica das condições oceanográficas do ASO, como também as capacidades dispersivas de Liriope tetraphylla, Olindias sambaquiensis e Acharadria crocea, inferidas pelos seus ciclos de vida. Adicionalmente, a estrutura filogeográfica de Pelagia noctiluca foi avaliada em outras regiões oceânicas, considerando o Atlântico (Atl.) e o Mediterrâneo (Med.) e utilizando os marcadores COI, 16S e ITS1. Este estudo foi conduzido através de calibrações de taxas de substituição baseadas em uma divergência significativa embora filogeneticamente rasa, entre populações do Atl. e do Pacífico. Os resultados específicos indicam: 1) padrões comuns, de expansões populacionais e estruturação genética acompanhada de padrões filogenéticos sem uma correlação geográfica evidente, para as três espécies estudadas do ASO, os quais remetem a alterações de área habitável em períodos glaciais e interglaciais a partir do Pleistoceno médio ou tardio; 2) uma estrutura filogeográfica entre populações de P. noctiluca do Atl. e do Med. que remete a possíveis efeitos de isolamento entre ambas bacias durante o Gelasiano. Além disso, aspectos dos resultados que sugerem a importância de se considerar que a demografia não seria apenas afetada pela história biogeográfica são discutidos. A demografia também modularia o grau de resposta das populações aos eventos biogeográficos, podendo ser uma característica comum para populações de espécies que mostram padrões filogeográficos similares, a despeito de possuírem biologias marcadamente distaintas. É importante salientar que a prevalência na interpretação da influência da história natural nos estudos biogeográficos não se restringe a estudos microevolutivos. A origem dos metazoários é geralmente associada ao impacto biológico de mudanças ambientais que teriam desencadeando a chamada explosão cambriana. Entretanto, a atividade tectônica que propiciou estas mudanças é pouco discutida dentro de uma abordagem biogeográfica, a qual é considerada controversa. Resultados indicadores de que as principais linhagens de Cnidaria teriam surgido ao longo do Criogeniano e o Ediacarano foram obtidos, Períodos em que novos mares e áreas de plataforma rasa estavam surgindo como resultado da fragmentação da placa continental de Rodínia. A relação entre estes eventos geológicos e um possível surgimento de biotas marinhas diversificadas, as quais poderiam ser consideradas as primeiras cladogêneses em Eumetazoa relacionadas a eventos vicariantes, é uma nova hipótese a ser considerada / Phylogeographic studies for different species of Medusozoa (Cnidaria) were performed, emphasizing the central neritic area of the South-Western Atlantic (SWA), localized between the southeastern Brazilian coast and the coast of the Buenos Aires province in Argentina. These were based on DNA sequences of the mitochondrial genes COI and 16S, and the nuclear intron ITS1. They considered both the heterogeneity of the geological history and the present oceanographic conditions of the SWA, as well as the dispersal capabilities of Liriope tetraphylla, Olindias sambaquiensis and Acharadria crocea, inferred by their life cycles. Additionally, the phylogeographic structure of Pelagia noctiluca was evaluated in other oceanic regions, considering the Atlantic (Atl.) and Mediterranean (Med.) and using COI, ITS1 and 16S as molecular markers. This study was conducted through calibrations of substitution rates based on a significant but phylogenetically shallow divergence, between populations from the Atl. and the Pacific. Specific results indicate: 1) common patterns of population expansion and genetic structure associated to phylogenetic patterns without a clear geographical correlation, for the three species of the ASO, which refer to changes of the habitable area during glacial and interglacial periods since the middle or late Pleistocene; 2) genetic structure between populations of P. noctiluca from the Atl. and Med., referring to possible isolation effects between the two basins during the Gelasian. Moreover, the results also suggest the importance of considering that the demographic aspects would not be affected only by the biogeographical history. The demography would also modulate the degree of response of populations to biogeographic events, and could be a common feature for populations of species that exhibit similar phylogeographic patterns, in spite of having markedly different biological features. It is important to notice that the prevalence in the interpretation of the influence of natural history in biogeographical studies is not restricted to microevolutionary studies. The origin of metazoans is generally associated with the biological impact of environmental changes that would have triggered the Cambrian explosion. However, the tectonic activity that resulted in such changes is not discussed within a biogeographic approach, which is considered controversial. Results indicating that the main lineages of Cnidaria emerged during the Cryogenian and Ediacaran were obtained, at that Period new seas and areas of shallow platform were emerging as a result of the fragmentation of the Rodinia continental plate. The relationship between those geological events and the possible emergence of a diverse marine biota, whose could be considered as the firsts cladogenesis in Eumetazoa related to vicariant events, is a new hypothesis to be considered

The Tremarctinae are a subfamily of bears endemic to the New World, including two of the largest terrestrial mammalian carnivores that have ever lived: the giant, short-faced bears Arctodus simus from North America and Arctotherium angustidens from South America (greater than or equal to 1000 kg). Arctotherium angustidens became extinct during the Early Pleistocene, whereas Arctodus simus went extinct at the very end of the Pleistocene. The only living tremarctine is the spectacled bear (Tremarctos ornatus), a largely herbivorous bear that is today only found in South America. The relationships among the spectacled bears (Tremarctos), South American short-faced bears (Arctotherium) and North American shortfaced bears (Arctodus) remain uncertain. In this study, we sequenced a mitochondrial genome from an Arctotherium femur preserved in a Chilean cave. Our molecular phylogenetic analyses revealed that the South American short-faced bears were more closely related to the extant South American spectacled bear than to the North American short-faced bears. This result suggests striking convergent evolution of giant forms in the two groups of short-faced bears (Arctodus and Arctotherium), potentially as an adaptation to dominate competition for megafaunal carcasses.

Molecular dating (or molecular clock) is a powerful technique that uses the mutation rate of biomolecules to estimate divergence times among organisms. In the last two decades, the theory behind the molecular clock has been intensively developed, and it is now possible to employ sophisticated evolutionary models on genome-scaled datasets in a Bayesian framework. The molecular clock has been successfully applied to virtually all types of organisms and molecules to estimate timing of speciation, timing of gene duplications, and generation times: this knowledge allows contextualizing past and present events in the light of (paleo)ecological scenarios. Molecular clock studies are routinely used in evolutionary and ecological studies, but their use in applied fields such as agricultural and medical entomology is still scarce in particular because of a paucity of genome data. Genome-scaled clocks have been successfully applied, for example, to various model organisms such as Anopheles and Drosophila, as well as to invasive mosquitoes Aedes aegypti and Aedes albopictus. Many other invasive pests are emerging worldwide aided by global trade, increased connectivity among countries, lack of prevention, and flawed invasive species management. Among them, there is Aedes koreicus and Aedes japonicus, two invasive mosquito species which are monitored for public health concerns because of their harboured human pathogenic viruses. For these, as well as for other insects of societal relevance, such as the parasitoid Trissolcus japonicus, there is a paucity of gene markers and no genome data for large scale molecular clock studies. Invasive pests are typically studied using microevolutionary approaches that tackle events at an intraspecific level: these approaches provide important information for the pest management, for example, by revealing invasion routes and insecticide resistances. Approaches that tackle the deep-time evolution of the pest, such as the molecular clock, are instead less used in pest science. Many important traits associated with invasiveness have evolved by speciation over a long time frame: the molecular clock can reveal the paleo-ecological conditions that favoured these traits helping a better understanding of pest biology. Molecular clock, when coupled with phylogenomics, can further identify genes and patterns that characterize the pest: this knowledge can be used to enhance management practices. Although this is a data-driven thesis, its major aim is to provide new results to demonstrate the utility of the molecular clock in pest science. This has been done by systematically apply the molecular clock to various neglected organisms of medical and agricultural relevance. To this aim, I generated new genome data and/or assembled the largest genome-scaled data to date. I studied the molecular clock in mosquitoes, focusing on the Aedini radiation (Chapter 2) and identified a strong incongruence between the mitochondrial and nuclear phylogeny for what concerns their molecular clock. This result highlighted the importance of employing genome scaled data for these species to exclude stochastic effects due to poor/inaccurate sampling in clock studies. To tackle the absence of data, I further assembled the whole mitogenome of emerging invasive species Aedes koreicus and Aedes japonicus with the aim of producing useful data for molecular typing and of inferring divergence estimates using whole mitogenomes (Chapter 3). Dated phylogenies point toward more recent diversification of Aedini and Culicini compared to estimates from previous works, addressing the issue of taxon sampling sensitivity in dated phylogeny. Although it is possible to perform molecular clock studies on single/few gene markers, the current trend is to couple this methodology with genome-scaled datasets to reduce the stochastic effect of using few genes. For this reason, I sequenced the draft genome of A. koreicus and A. japonicus (Chapter 4). The assemblies were extremely fragmented, highlighting the problem of sequencing large genomes using short reads. The assemblies provided, however enough information for genome skimming allowing extraction of BUSCO genes for downstream analyses, whole mitogenome assemblies (used in Chapter 3), and characterisation of the associated metagenome. These data need to be integrated by long reads; it provides, however a first framework to investigate the genome evolution of these species. I further sequenced and assembled the genome of Trissolcus japonicus, the parasitoid wasp of the invasive pest Halyomorpha halys. To elucidate its divergence, estimate and define an intraspecific typing system to differentiate strains for biocontrol strategies, I reconstructed the mitochondrial genomes of two populations: the mitogenomes were surprisingly identical, suggesting that they belong to the same de facto population. I further provide a detailed clock investigation of Zika, a virus harboured and transmitted by some Aedes species (Chapter 5). Using the largest set of genomes to date, I could set the origin of ZIKV in the middle age and its first diversification in the mid-19th century. From a methodological point of view, the clocking of this virus highlighted the importance of checking for recombination and for cell-passages to obtain correct divergence estimates. I finally show my contributions to molecular clock studies of three other invasive species (Chapter 6): I helped disentangle the divergence times of Bactrocera, a genus of invasive fruit files pest of agriculture; I contributed in performing a phylogenomics study of opsin genes in Diptera; I used chloroplast and nuclear genome data to reconstruct the divergences of the invasive reed Arundo. In the various Chapters of my thesis, I highlighted the limits and the problems of current molecular clock methodologies and identified the best practices for different types of organisms in order to develop a cross-discipline understanding of the molecular clock techniques. The various results presented in this thesis further demonstrate the utility of the molecular clock approach in pest studies.

O grupo Bothrops neuwiedi é composto por serpentes neotropicais que desempenham grande impacto na saúde pública, em decorrência de acidentes ofídicos. O grupo apresenta ampla distribuição ao longo da diagonal seca de formações abertas, desde o nordeste do Brasil até o noroeste da Argentina. A taxonomia atual, baseada principalmente em dados morfológicos qualitativos, não recupera as linhagens evolutivas apontadas pelas abordagens moleculares. O objetivo deste trabalho foi investigar o grupo B. neuwiedi utilizando análises filogenéticas, filogeográficas, biogeográficas, estimativa de datação e delimitação de espécies em um total de 276 indivíduos amostrados ao longo de toda a sua distribuição, incluindo representantes do Brasil, Bolívia, Argentina, Paraguai e Uruguai. As análises contemplaram três genes mitocondriais, dois nucleares, dois introns e 33 locos de microssatélites obtidos por sequenciamento de nova geração. Estimou−se, por meio do método de delimitação de espécies e análises filogeográficas, que o grupo B. neuwiedi possui ao menos 14 espécies, das quais oito já são reconhecidas (B. erythromelas, B. lutzi, B. mattogrossensis, B. marmoratus, B. neuwiedi, B. pauloensis, B. pubescens e B. diporus) e seis possíveis espécies (Bothrops sp. 1 a Bothrops sp. 6). O grupo teria se originado durante o Mioceno e diversificado durante o Plio-Pleistoceno. As flutuações climáticas do Pleistoceno, decorrentes dos ciclos glaciais e interglaciais, desempenharam um importante papel na diversificação das espécies e suas populações. Adicionalmente, eventos tectônicos que ocorreram durante este período também teriam influenciado na estruturação espacial da diversidade genética. Foi revelada uma intrincada relação do domínio biogeográfico Chaquenho (áreas abertas) com os domínios do Sudoeste da Amazônia e do Paraná (áreas de floresta). Nuances na temperatura e aridez, ora permitiram a expansão do Cerrado sobre as florestas, ora possibilitaram a expansão do Chaco sobre o Cerrado, levando à interrupção da conexão entre as populações de manchas de Cerrado nestes domínios florestais. Os resultados evidenciaram a complexidade da diversificação das serpentes na diagonal seca de formações abertas e, dependendo da linhagem, diferentes padrões puderam ser observados. A Linhagem Leste−Oeste (B. marmoratus, B. neuwiedi, Bothrops sp. 1) apresentou elevado grau de diversidade genética e elevada estruturação espacial, concordante com unidades geomorfológicas do relevo. Nas linhagens do sul do Brasil (B. pubescens e B. diporus) verificou−se um padrão de diversificação consistente com espécies incipientes em estágios iniciais do processo de especiação. Na região central do Cerrado, propõe−se que as espécies B. marmoratus, B. pauloensis e B. mattogrossensis apresentam forte estruturação no DNAmt e baixa estruturação nos marcadores nucleares em decorrência de fluxo gênico desigual mediado por machos. Baseado nas informações obtidas neste trabalho, sugerimos fortemente que o grupo Bothrops neuwiedi seja revisado sob uma perspectiva multidisciplinar. / The Bothrops neuwiedi group is composed of Neotropical snakes that have a serious impact on Brazilian public health, as they are responsible for a large number of snakebite accidents. The group is widespread along the dry diagonal of open formations in South America (Chacoan dominion), since northeast Brazil to northwest Argentina. Current taxonomic arrangement is based on blotches and color pattern, which does not represent the evolutionary lineages uncovered in molecular analyses. This study aims to investigate the B. neuwiedi group using phylogenetic analyses, biogeography, phylogeography, estimates of divergence, and species delimitation. A total of 276 representatives of the B. neuwiedi group were obtained throughout the geographic distribution of the group, including samples from Brazil, Bolivia, Argentina, Paraguay, and Uruguay; in addition, three mitochondrial and two nuclear genes, two introns, and 33 microsatellite loci were used. According species delimitation and phylogeographic approach, 14 species in the B. neuwiedi group could be delimited as follows: eigth species already recognized (B. erythromelas, B. lutzi, B. mattogrossensis, B. marmoratus, B. neuwiedi, B. pubescens, B. diporus, and B. pauloensis) and six other putative species (Bothrops sp. 1 to Bothrops sp. 6). Estimates of divergence placed the origin of the B. neuwiedi group in the Miocene and diversification in the Plio−Pleistocene. Climatic fluctuations and tectonic events during the Pleistocene probably played an important role in the species and populations diversification. An intricate network was revealed with Chacoan dominion (open area) and South-west and Paraná dominion (forested areas). Nuances in temperature and aridity, sometimes allowed the expansion of the Cerrado on forests, sometimes allowed the expansion of the Chaco on the Cerrado, leading to the interruption of the connection between the populations of Cerrado patches of forest in these areas. The results showed the complexity of the diversification of snakes in the dry diagonal of open formations and depending on the lineage studied, different patterns were observed. East−West Lineage (B. marmoratus, B. neuwiedi, Bothrops sp. 1) presented high genetic diversity and high genetic and spatial structure associated with Brazilian geomorphology. B. pubescens and B. diporus revealed a pattern consistent with incipient species in the early stages of speciation. B. marmoratus, B. pauloensis and B. mattogrossensis presented strong structure in mtDNA and and weak structure in nuclear markers due to male−biased gene flow.

Les relations de parentés profondes au sein des Angiospermes ont été longtemps incertaines. A la fin des années 90, les études phylogénétiques à grande échelle ont contribué à l’obtention de l’arbre actuel des Plantes à fleurs, dans lequel Eudicotylédones, Monocotylédones et Magnoliidae forment les trois plus grands clades. Contrairement aux Monocotylédones et aux Eudicotylédones, la monophylie des Magnoliidae (Canellales, Laurales, Magnoliales et Piperales) n’a été soutenue que plus récemment. Les Magnoliidae contiennent actuellement 20 familles et environ 10 000 espèces majoritairement présentes sous les tropiques. Avant cette thèse, de nombreuses parties de ce groupe avaient été étudiées en détail mais l’histoire évolutive du groupe dans son ensemble était encore mal connue. Le premier chapitre est une étude phylogénétique des relations entre les familles et les ordres de Magnoliidae. Pour réaliser cette étude, j’ai échantillonné 199 espèces du groupe et 12 marqueurs moléculaires issus des trois génomes. J’ai ensuite mené des analyses phylogénétiques avec les méthodes de parcimonie, d’inférence bayésienne et de maximum de vraisemblance. Les résultats confirment avec un plus fort soutien la présence de deux clades dans ce groupe : Canellales + Piperales et Laurales + Magnoliales. De plus, les relations entre les 20 familles sont généralement bien soutenues, les Lactoridaceae et les Hydnoraceae étant incluses dans les Aristolochiaceae (Piperales). Dans le second chapitre, j’ai révisé l’âge et la position de 10 fossiles identifiés comme appartenant aux Magnoliidae. Le but de cette étude était de fournir de nouveaux points de calibration fiables afin de conduire de nouvelles analyses de datation moléculaire. Parmi les nombreux fossiles du groupe, nous avons choisi ces espèces car elles avaient été placées phylogénétiquement par des études antérieures. Le schéma de calibration résultant de ce travail inclut six contraintes fiables d’âges minimum. Le troisième chapitre est une étude de datation moléculaire utilisant ce schéma de calibration et le même jeu de données moléculaires que le chapitre 1. Les résultats tendent à repousser l’âge des Magnoliidae (127.1-198.9 Ma), et des quatre ordres Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma) et Magnoliales (115.0-164.2 Ma). Dans ce même chapitre, j’ai également étudié le mode de diversification du groupe. Les variations importantes du nombre d’espèces entre les différentes parties de l’arbre s’expliquent le mieux par des modèles de diversification incluant 6 à 14 transition du taux net de diversification. Enfin, dans le dernier chapitre de la thèse, j’ai retracé l’histoire évolutive de 26 caractères floraux pour reconstruire les fleurs ancestrales de nœuds-clés des Magnoliidae. Pour ce faire, j’ai tiré parti de la phylogénie du premier chapitre et utilisé les mêmes espèces dans ma matrice morphologique. Les résultats montrent que l’ancêtre commun le plus récent des Magnoliidae présentait des fleurs bisexuées et actinomorphes avec un périanthe différencié de deux cycles trimères à tépales libres et probablement trois étamines libres. Ce travail de thèse apporte des résultats importants sur l’évolution des Magnoliidae et soulève de nombreuses questions telles que l’impact des crises géologiques sur la diversification du groupe ou l’influence des pollinisateurs et de l’environnement sur l’évolution de la morphologie florale. / Deep phylogenetic relationships in the angiosperms had long been uncertain. However, by the end of the 1990s, large-scale studies contributed to the current well resolved picture of the tree of flowering plants, in which eudicots, monocots, and magnoliids are the three largest clades. Whereas monocots and eudicots have been recognized since the very first phylogenetic analyses, the monophyly of magnoliids (Canellales, Laurales, Magnoliales, and Piperales) is a more recent result. Magnoliidae, as now circumscribed, consist of 20 families and ca. 10,000 species mostly distributed in the tropics. Before the present thesis, several parts of the magnoliid tree had been well studied, but little was known about the evolutionary history of Magnoliidae as a whole. The first chapter of this thesis is a phylogenetic study conducted to clarify the relationships among families and orders of Magnoliidae. To do so, I sampled 199 species of Magnoliidae and 12 molecular markers from the three genomes and conducted phylogenetic analyses using parsimony, maximum likelihood, and Bayesian methods. The results confirm, with a greater level of support, two clades in Magnoliidae: Canellale + Piperales, and Laurales + Magnoliales. In addition, the relationships among the 20 families are generally well supported, and Lactoridaceae and Hydnoraceae are nested within Aristolochiaceae (Piperales). In the second chapter, the ages and phylogenetic positions of 10 fossils attributed to Magnoliidae were reviewed in detail. The goal of this study was to provide new reliable calibration points in order to conduct molecular dating analyses. These fossils were selected from the rich fossil record of the group because of their previous inclusion in phylogenetic analyses with extant taxa. The resulting calibration scheme provides six solid, internal minimum age constraints. The third chapter includes molecular dating analyses using the present calibration scheme and the same molecular dataset of Chapter 1. This study tends to push back in time the ages of the crown nodes of Magnoliidae (127.1-198.9 Ma), and of the four orders, Canellales (126.3-141.0 Ma), Piperales (88.2-157.7 Ma), Laurales (111.8-165.6 Ma), and Magnoliales (115.0-164.2 Ma). In the same chapter, I investigated the mode of diversification in the group. The strongly imbalanced distribution of species appears to be best explained by models of diversification with 6 to 14 diversification rate shifts. Finally, in the last chapter, I traced the evolution of 26 floral characters to reconstruct the ancestral flowers in key nodes of Magnoliidae. I used the phylogeny of Chapter 1 and an exemplar approach. Our results show that the most recent common ancestor of all Magnoliidae was a tree bearing actinomorphic, bisexual flowers with a differentiated perianth of two alternate, trimerous whorls of free perianth parts (outer and inner tepals) and probably three free stamens. This work provides key results on the evolution of Magnoliidae and raises several new questions such as the impact of geological crises on diversification of the group or the influence of pollinators and the environment on the evolution of floral morphology.

Orientador: Ana Maria Goulart de Azevedo Tozzi / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-11-22T11:41:59Z (GMT). No. of bitstreams: 1 Perez_AnaPaulaFortuna.pdf: 113775491 bytes, checksum: dc9fcc546ebf65c955179362f9b0675f (MD5) Previous issue date: 2009 / Resumo: Zornia J.F. Gmel. possui distribuição pantropical e contém 75 espécies, das quais 36 ocorrem no Brasil. Para o gênero, têm sido reconhecidos dois subgêneros: Zornia subg. Myriadena (Desv.) Mohlenbr. e Zornia subg. Zornia; o último está dividido em três seções: Zornia sect. Zornia, Zornia sect. Isophylla Mohlenbr. e Zornia sect. Anisophylla Mohlenbr. Há problemas nesta classificação infragenérica, pois muito dos caracteres diagnósticos utilizados são subjetivos e nem sempre se mostram descontínuos. Zornia, que está incluído no clado Adesmia, junto com mais cinco gêneros ocorrentes na América do Sul, Adesmia DC., Poiretia Vent., Amicia Kunth, Chaetocalyx DC. e Nissolia Jacq., é caracterizado principalmente pelas flores dispostas em inflorescências espiciformes com bractéolas peltadas, aos pares, protegendo cada flor. Considerando a expressiva diversidade de táxons de Zornia existente no Brasil, a pouca descontinuidade entre os caracteres diagnósticos infragenéricos e a escassez de revisões taxonômicas recentes deste gênero, este estudo teve por objetivos: a) realizar a revisão taxonômica das espécies de Zornia ocorrentes no Brasil; b) estudar a filogenia de Zornia no intuito de verificar as relações infragenéricas e determinar padrões de evolução morfológica; c) determinar tempo de diversificação e padrões biogeográficos do gênero. A revisão taxonômica foi realizada através de análise morfológica de exsicatas e observações de populações em campo. As matrizes dos estudos moleculares foram analisadas sobs os critério de parcimônia e de bayesiana. Foram reconhecidas e descritas até o momento 36 espécies de Zornia para o Brasil, incluindo duas novas. Descrições com comentários sobre relações taxonômicas e morfológicas e distribuição geográfica para as espécies são fornecidas. Os estudos filogenéticos morfológicos e moleculares feitos neste estudo sugerem que Zornia seja monofilético, ao mesmo tempo em que revela que os subgêneros e seções atualmente reconhecidos para o gênero mostraram-se para ou polifiléticos. A datação molecular mostrou que ocorreu um único evento migratório de Zornia da América para África ou Austrália há 4,61 milhões de anos, e esta disjunção se deve provavelmente à dispersão a longa distância. / Abstract: Zornia J.F. Gmel. has a pantropical distribution and consists of 75 species. Thirty six of theses species occur in Brazil. For this genus, two subgenera have been recognized: Zornia subg. Myriadena (Desv.) Mohlenbr. and Zornia subg. Zornia; the latter is divided into three sections: Zornia sect. Zornia, Zornia sect. Isophylla Mohlenbr. and Zornia sect. Anisophylla Mohlenbr. This infrageneric classification is problematic, because most of the diagnostic characters used are subjective and they are not always discontinuous. Zornia is included in the Adesmia clade together with five more genera that occur in South America (Adesmia DC., Poiretia Vent., Amicia Kunth, Chaetocalyx DC. and Nissolia Jacq.). The genus Zornia is characterized mainly by flowers arranged in spiciform inflorescences, with paired peltade bracteoles protecting each flowers. Considering the expressive diversity of Zornia taxons in Brazil, the little morphological discontinuity between the infrageneric diagnostic characters, and the lack of recent taxonomic revisions of this genus, this study aimed at: a) carrying out a taxonomic revision of Zornia species that occur in Brazil; b) studying Zornia phylogeny in order to verify the infrageneric relationships; c) determining divergence time and biogeography patterns for the genus. The taxonomic revision was done by morphological analysis of herbarium materials and by observing field populations. The matrices of molecular studies were analyzed by Parsimony and Bayesian analyses. So far thirty six species of Zornia have been described for Brazil, including two new species. Descriptions with comments on taxonomic and morphological relationships, and on geographic distribution of the species have been provided. The phylogenetic studies in this work suggest that Zornia is monophyletic. At the same time this study shows that the subgenera and the sections currently acknowledged for the genus are paraphyletic or polyphyletic. The molecular dating shows that only one migratory event of Zornia occurred 4.61 Ma ago from America to Africa or Australia, and this disjunction is probably due to long distance dispersal. / Universidade Estadual de Campi / Biologia Vegetal / Doutor em Biologia Vegetal

O grupo Bothrops neuwiedi é composto por serpentes neotropicais que desempenham grande impacto na saúde pública, em decorrência de acidentes ofídicos. O grupo apresenta ampla distribuição ao longo da diagonal seca de formações abertas, desde o nordeste do Brasil até o noroeste da Argentina. A taxonomia atual, baseada principalmente em dados morfológicos qualitativos, não recupera as linhagens evolutivas apontadas pelas abordagens moleculares. O objetivo deste trabalho foi investigar o grupo B. neuwiedi utilizando análises filogenéticas, filogeográficas, biogeográficas, estimativa de datação e delimitação de espécies em um total de 276 indivíduos amostrados ao longo de toda a sua distribuição, incluindo representantes do Brasil, Bolívia, Argentina, Paraguai e Uruguai. As análises contemplaram três genes mitocondriais, dois nucleares, dois introns e 33 locos de microssatélites obtidos por sequenciamento de nova geração. Estimou−se, por meio do método de delimitação de espécies e análises filogeográficas, que o grupo B. neuwiedi possui ao menos 14 espécies, das quais oito já são reconhecidas (B. erythromelas, B. lutzi, B. mattogrossensis, B. marmoratus, B. neuwiedi, B. pauloensis, B. pubescens e B. diporus) e seis possíveis espécies (Bothrops sp. 1 a Bothrops sp. 6). O grupo teria se originado durante o Mioceno e diversificado durante o Plio-Pleistoceno. As flutuações climáticas do Pleistoceno, decorrentes dos ciclos glaciais e interglaciais, desempenharam um importante papel na diversificação das espécies e suas populações. Adicionalmente, eventos tectônicos que ocorreram durante este período também teriam influenciado na estruturação espacial da diversidade genética. Foi revelada uma intrincada relação do domínio biogeográfico Chaquenho (áreas abertas) com os domínios do Sudoeste da Amazônia e do Paraná (áreas de floresta). Nuances na temperatura e aridez, ora permitiram a expansão do Cerrado sobre as florestas, ora possibilitaram a expansão do Chaco sobre o Cerrado, levando à interrupção da conexão entre as populações de manchas de Cerrado nestes domínios florestais. Os resultados evidenciaram a complexidade da diversificação das serpentes na diagonal seca de formações abertas e, dependendo da linhagem, diferentes padrões puderam ser observados. A Linhagem Leste−Oeste (B. marmoratus, B. neuwiedi, Bothrops sp. 1) apresentou elevado grau de diversidade genética e elevada estruturação espacial, concordante com unidades geomorfológicas do relevo. Nas linhagens do sul do Brasil (B. pubescens e B. diporus) verificou−se um padrão de diversificação consistente com espécies incipientes em estágios iniciais do processo de especiação. Na região central do Cerrado, propõe−se que as espécies B. marmoratus, B. pauloensis e B. mattogrossensis apresentam forte estruturação no DNAmt e baixa estruturação nos marcadores nucleares em decorrência de fluxo gênico desigual mediado por machos. Baseado nas informações obtidas neste trabalho, sugerimos fortemente que o grupo Bothrops neuwiedi seja revisado sob uma perspectiva multidisciplinar. / The Bothrops neuwiedi group is composed of Neotropical snakes that have a serious impact on Brazilian public health, as they are responsible for a large number of snakebite accidents. The group is widespread along the dry diagonal of open formations in South America (Chacoan dominion), since northeast Brazil to northwest Argentina. Current taxonomic arrangement is based on blotches and color pattern, which does not represent the evolutionary lineages uncovered in molecular analyses. This study aims to investigate the B. neuwiedi group using phylogenetic analyses, biogeography, phylogeography, estimates of divergence, and species delimitation. A total of 276 representatives of the B. neuwiedi group were obtained throughout the geographic distribution of the group, including samples from Brazil, Bolivia, Argentina, Paraguay, and Uruguay; in addition, three mitochondrial and two nuclear genes, two introns, and 33 microsatellite loci were used. According species delimitation and phylogeographic approach, 14 species in the B. neuwiedi group could be delimited as follows: eigth species already recognized (B. erythromelas, B. lutzi, B. mattogrossensis, B. marmoratus, B. neuwiedi, B. pubescens, B. diporus, and B. pauloensis) and six other putative species (Bothrops sp. 1 to Bothrops sp. 6). Estimates of divergence placed the origin of the B. neuwiedi group in the Miocene and diversification in the Plio−Pleistocene. Climatic fluctuations and tectonic events during the Pleistocene probably played an important role in the species and populations diversification. An intricate network was revealed with Chacoan dominion (open area) and South-west and Paraná dominion (forested areas). Nuances in temperature and aridity, sometimes allowed the expansion of the Cerrado on forests, sometimes allowed the expansion of the Chaco on the Cerrado, leading to the interruption of the connection between the populations of Cerrado patches of forest in these areas. The results showed the complexity of the diversification of snakes in the dry diagonal of open formations and depending on the lineage studied, different patterns were observed. East−West Lineage (B. marmoratus, B. neuwiedi, Bothrops sp. 1) presented high genetic diversity and high genetic and spatial structure associated with Brazilian geomorphology. B. pubescens and B. diporus revealed a pattern consistent with incipient species in the early stages of speciation. B. marmoratus, B. pauloensis and B. mattogrossensis presented strong structure in mtDNA and and weak structure in nuclear markers due to male−biased gene flow.

No description available.