Using GIS-based tools and a review of the relevant geological and climatic literature, I attempt to identify the key implications of Quaternary glacial cycles for drainage evolution in eastern Patagonia. In doing so, the stage is set for the proper integration of existing biogeographic and phylogeographic ideas to develop a suite of inferences aimed at elucidating how these processes influenced aquatic biodiversity of Patagonian Argentina. A primary finding of this research is that the southern mainland and/or Tierra del Fuego served as an important cryptic refuge for cold-adapted species, including aquatic taxa. At least one additional aquatic refuge is likely to have existed in either central or northern Patagonia. The low position of the Atlantic shoreline during glacial periods also revealed a much larger and inter-connected drainage network in southern Patagonia. During sea-levels stands below 100m, two new drainage coalescence points on the exposed continental shelf can be recognized among the Chico/Santa Cruz, Coyle and Gallegos river basins and between the Grande and Fuego rivers. Enhanced hydrological discharge during the deglaciation period of Late-Quaternary cycles is expected to have facilitated extensive inter-drainage connections within each of the northern and southern regions of eastern Patagonia via proglacial lake and/or stream coalescence. A large proglacial lake in the Nahuel Huapi Lake region is also recognized as the most likely temporary gateway for aquatic organisms to disperse between the Neuquen and Northern Patagonian Tablelands. I also recognize climate-induced drainage reversals as a bidirectional mechanism of trans-Andean dispersal and an important factor in determining the biogeography of widespread aquatic organisms in Patagonia.

The genetic structuring of populations can be influenced by present processes and past events. One of the largest historical events to affect the distribution and genetic characteristics of present-day North American biota is the Pleistocene glaciation. Thus, the study of post-glacial colonization patterns of species in northern landscapes can relay important ecological information, as species had to expand their range extensively following the retreat of the glaciers and are often at the terminal end of their expansion. These species consequently exhibit the genetic fingerprints of sequential founder events, in turn decreasing the genetic variation available for adaptation. Using amphibians to investigate post-glacial range expansion is advantageous, as they have limited dispersal abilities revealing fine-scale patterns and they are thought to be one of the first vertebrates to colonize post-glacial habitat. Therefore, to model the phylogeography of a primary colonizer and the population structure of anurans in northern landscapes, population genetics analyses of wood frogs (Lithobates sylvaticus) were performed in the James Bay area. Wood frogs were sampled from 17 localities around James Bay and genetic analyses were conducted with seven microsatellite loci and mitochondrial DNA sequences of the ND2/tRNATRP genes. Results show that the post-glacial recolonization of the James Bay area by wood frogs originated from the putative refugium in western Wisconsin, an area known as the Driftless Area. Two routes were taken by founders to colonize the James Bay area: one north-west of Lake Superior, colonizing western Ontario, and one through the Upper Peninsula of Michigan, colonizing southern and eastern Ontario and western Québec. Interestingly, the meeting of the two lineages south-west of James Bay led to the establishment of a zone of higher genetic variation than expected under the founder effect hypothesis. Additionally, population structure analyses revealed the segregation of three genetic populations east, north-west, and south-west of the bay, the latter showing the highest genetic variation and likely representing a zone of secondary contact. This study shows that past events such as post-glacial range expansions can explain present patterns of genetic variation and population structure, and that studies in northern landscapes may be very useful in understanding genetic patterns throughout the range of a species.

Studying species at the molecular level can provide insights into how ecological and biological processes interrelate resulting in the diversity we see today. This information can be applied to conserve species at risk of extinction, or to better manage genetic diversity in species of economic importance. Species that inhabit freshwater riverine systems commonly exhibit population structures that are related to their relative dispersal capability, contemporary stream structure and/or historical stream structure. This thesis examined the populations genetic structure of wild and cultured stocks of the commercially farmed freshwater crayfish, C. quadricarinatus (von Martens), using genetic markers characterized by different modes of inheritance. C. quadricarinatus is distributed naturally in riverine systems in northern Australia, and southern Paupa New Guinea (PNG) and inhabits a variety of freshwater ecosystems ranging from ephemeral to permanent. Life history characteristics of C. quadricarinatus suggest a high level of genetic structuring among wild stocks might exist. However, seasonal flooding coupled with low topography across its distribution in northern Australia may promote sufficient gene flow among rivers to produce genetic homogeneity. Historical gene flow may also influence modern genetic structure as many distinct riverine catchments that C. quadricarinatus inhabits, were once connected at times of lower sea level. Insight into genetic relationships among C. quadricarinatus populations will allow for better management practices of wild populations in the future. The study investigated phylogenetic relationships among C. quadricarinatus representing 17 discrete natural drainages across the natural range in Australia and PNG, using 16s and COI gene sequences. Sequence analysis of both genes resolved two distinct genealogical lineages in Australia and three in PNG. The two divergent Australian lineages concur with original taxonomic descriptions of Reik (1969) based on external morphological differences. The three C. quadricarinatus populations sampled in PNG were all genetically distinct from each other, with one exhibiting a close association with an Australia lineage. The immense physical barriers (rugged mountain ranges) to gene flow in PNG will almost certainly have reduced dispersal capabilities for C. quadricarinatus. During times of lowered sea levels in the past, Australia and southern PNG were a single landmass with terrestrial and freshwater organisms theoretically able to disperse over associated land and via freshwater connections. The close genetic relationship between PNG and Australian C. quadricarinatus support a recent freshwater connection and hence gene flow between northern Australia and PNG C. quadricarinatus populations. Genetic differentiation among some C. quadricarinatus lineages exhibit as much genetic divergence at 16s RNA sequences as taxonomically recognised sub-species in the Cherax genus. Since C. quadricarinatus was originally described as different species based on external morphological differences (Reik, 1969), it is recommended that the taxonomy of C. quadricarinatus in Australia and PNG be re-evaluated. C. quadricarinatus specific microsatellite markers were developed for this study. Five variable loci were employed to investigate the extent of contemporary gene flow among fourteen C. quadricarinatus wild river populations in northern Australia. High FST and genetic distance estimates observed among pair wise comparisons of C. quadricarinatus populations are consistent with limited or no gene flow occurring among drainages. Speculation that C. quadricarinatus may disperse between adjacent or nearby drainages at times of flood, either across floodplains, or via flood plumes therefore seems highly unlikely among the populations examined in the current study. No significant correlation was observed between geographic distance and genetic distance among C. quadricarinatus populations here. C. quadricarinatus populations most closely resemble an island-like model, where gene flow is independent of geographic distance among populations and where genetic divergence occurs to a greater or lesser extent as a result of genetic drift within otherwise isolated populations. A significant number of C. quadricarinatus populations showed deviations from expected Hardy-Weinberg equilibrium (HWE). Samples sizes may not have been sufficiently large to reflect a true representation of genotypic proportions present in the sampled populations due to the highly variable nature of microsatellite loci. Deviations from HWE equilibrium, however, can also result from null alleles. Null allele estimates suggested a large proportion of null alleles were present in the C. quadricarinatus populations analysed. This may be a result of C. quadricarinatus populations confined to discrete drainages experiencing independent evolution, resulting in mutations in primer binding sites. The growing economic potential of C. quadricarinatus culture, both domestically and internationally, prompted expanding the current study to examine genetic diversity levels in commercial C. quadricarinatus stocks. The study employed five microsatellite markers to quantify genetic diversity in four Australian and three C. quadricarinatus culture stocks from overseas. Many C. quadricarinatus culture stocks also showed deviations from HWE expectations. This was not a surprising result given that the wild populations also deviated and domestication can also influence HWE. Relatively high levels of genetic diversity were observed. This probably results from intentional mixing of discrete river strains for production of the first commercial stock. Genetic differentiation estimates among culture stocks and assignment tests indicated that overseas culture stocks are most likely derived from the first commercial culture stock developed in Australia and then disseminated widely (the Hutchings stock). Robin Hutchings was a known supplier of live C. quadricarinatus to many international culture initiatives. Assignment of culture stocks back to their wild origins indicated that all C. quadricarinatus culture stocks sampled possess alleles that originate from the Flinders River (proportions ranged from 33-94%). Domestication of C. quadricarinatus to date has not resulted in significant reductions in levels of genetic diversity (heterozygosity or alleles richness) when compared to wild populations sampled in this study. Comparing culture stocks to wild populations to gauge their 'genetic health' may not be a suitable scale for evaluating genetic diversity in culture stocks. Wild populations are essentially evolving independently, are subjected to harsh seasonal environmental fluctuations resulting in periodic population crashes (genetic bottlenecks), with little or no recruitment from neighbouring drainages (gene flow). This study does however indicate that there is a large amount of genetic diversity distributed among wild populations that has yet to be exploited in culture. Genetic diversity in wild populations provides a resource for future stock improvement programs for C. quadricarinatus culture and thus requires careful conservation and appropriate management.

Thesis (Ph. D.)--Washington State University, May 2009. / Title from PDF title page (viewed on Apr. 20, 2010). "School of Biological Sciences." Includes bibliographical references.

Submitted by Felipe Aoki Goncalves (felipe.aoki.goncalves@gmail.com) on 2018-07-21T23:15:39Z No. of bitstreams: 1 Dissertacao_FelipeAokiGoncalves.pdf: 4019040 bytes, checksum: f74776a8e1e4eb45c987837446b58d50 (MD5) / Rejected by Adriana Aparecida Puerta null (dripuerta@rc.unesp.br), reason: Prezado Felipe, O documento enviado para a coleção Campus Unesp Rio Claro foi recusado pelo(s) seguinte(s) motivo(s): - As datas da capa e da página de rosto estão diferentes (uma está fevereiro e outra abril/2018) - Na capa, excluir o texto "Dissertação apresentada..." - Na página de rosto falta o cabeçalho da universidade - No Resumo e no Abstract faltam as palavras-chave e Keywords. Em caso de dúvidas entre em contato pelo email repositoriounesp@reitoria.unesp.br. Agradecemos a compreensão e aguardamos o envio do novo arquivo. Atenciosamente, Biblioteca Campus Rio Claro Repositório Institucional UNESP https://repositorio.unesp.br on 2018-07-23T13:48:49Z (GMT) / Submitted by Felipe Aoki Goncalves (felipe.aoki.goncalves@gmail.com) on 2018-07-27T00:34:47Z No. of bitstreams: 1 Dissertacao_final.pdf: 4850341 bytes, checksum: d57d8babaceaadcbca57c2bb4fd7152e (MD5) / Rejected by Adriana Aparecida Puerta null (dripuerta@rc.unesp.br), reason: Prezado Felipe, O documento enviado para a coleção Campus Unesp Rio Claro foi recusado pelo(s) seguinte(s) motivo(s): - Erro de grafia/digitação no título da capa e na página de rosto. O termo "Tillandsia aeranthos (Lois.)" está sem a letra D. Observe que o arquivo digital deve estar idêntico ao trabalho impresso. Agradecemos a compreensão e aguardamos o envio do novo arquivo. Atenciosamente, Biblioteca Campus Rio Claro Repositório Institucional UNESP https://repositorio.unesp.br on 2018-07-27T16:27:13Z (GMT) / Submitted by Felipe Aoki Goncalves (felipe.aoki.goncalves@gmail.com) on 2018-07-28T08:53:03Z No. of bitstreams: 1 Dissertacao_final.pdf: 4851233 bytes, checksum: 00282da22e9621485fa889dc2eeab49a (MD5) / Approved for entry into archive by Ana Paula Santulo Custódio de Medeiros null (asantulo@rc.unesp.br) on 2018-07-30T12:01:24Z (GMT) No. of bitstreams: 1 gonçalves_fa_me_rcla.pdf: 4841253 bytes, checksum: 6c28e380988306df3a38620b31ae18da (MD5) / Made available in DSpace on 2018-07-30T12:01:24Z (GMT). No. of bitstreams: 1 gonçalves_fa_me_rcla.pdf: 4841253 bytes, checksum: 6c28e380988306df3a38620b31ae18da (MD5) Previous issue date: 2018-05-17 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O continente sul-americano é o mais biodiverso da Terra, sendo palco da interação de complexos processos climáticos e geológicos que moldaram sua biota de forma muito heterogênea. Um crescente numero de estudos estudos de filogeografia de especies Sul Americanos tem auxiliado no entendimento das respostas evolutivas envolvidas em tal diversificação. A família Bromeliaceae é caracterizada por extensa radiação adaptativa, apresenta heterogeneidade de estratégias reprodutivas e padrões distintos de fluxo gênico e estrutura genética. Tillandsia aeranthos (Lois.) L.B. Smith é uma bromeliácea epífita que habita matas ciliares por toda região dos Pampas. Sua ocorrência em densas populações ao longo de ambientes geograficamente distintos a torna um bom modelo para a estudos sobre a influência de fatores geoclimáticos e ecológicos no padrão de distribuição da variabilidade genética e decorrentes processos de especiação ou manutenção da integridade da espécie. Esta dissertação foi dividida em dois manuscritos a fim de fornecer dados e análises úteis para a compreensão da evolução desta espécie neotropical. No Capítulo 1 foi realizada a amplificação heteróloga em Tillandsia aeranthos e Tillandsia recurvata de marcadores microssatélites nucleares previamente desenvolvidos para outras espécies de Bromeliaceae. Conjuntos de sete e seis marcadores apresentaram índices satisfatórios de polimorfismos em T. aeranthos e T. recurvata, respectivamente. A análise dos dados em duas populações de 20 indivíduos de cada espécie apresentou resultados compatíveis com sistemas reprodutivos distintos de cada espécie: fecundação cruzada predominante em T. aeranthos e auto-fecundação predominante em T. recurvata. No Capítulo 2 investigamos os padrões de variabilidade e estrutura genética e sistema reprodutivo de Tillandsia aeranthos ao longo da distribuição geográfica da espécie. Um total de 203 indivíduos de 13 localidades foi analisado a partir de sete marcadores microssatélites nucleares; 12 indivíduos tiveram 13 regiões universais plastidiais sequenciadas; e 74 indivíduos com 543 flores foram submetidos a experimentos de polinização manual. Os dados de microssatélites nucleares apontam altos níveis de diversidade genética em T. aeranthos (HE=0,806; HO=0,745) apesar de todas as regiões plastidiais sequenciadas terem sido monomórficas, sem diferenciação haplotípica. Foi observada também baixa diferenciação populacional (FST=0,031) sem correlação significativa entre as distâncias genéticas e geográficas das populações (isolamento-por-distância). Sinais moderados de eventos recentes de gargalo genético foram detectados em somente quatro das 13 populações, indicando que a maior parte das populações apresentou estabilidade demográfica durante o último máximo glacial. Os experimentos de manipulação polínica evidenciaram auto-incompatibilidade total em T. aeranthos. Em conclusão, os resultados demonstram altos níveis de diversidade genética e estabilidade demográfica na espécie, com fluxo gênico ocorrendo sem barreiras geográficas evidentes dentro da área de ocorrência de Tillandsia aeranthos. / South America is the most biodiverse subcontinent of the planet, bearing interactions between complex geoclimatic processes that heterogeneously molded its biota. An increasing number of Phylographic studies in South American species have helped us to understand the evolutionary responses that gradually formed such great biodiversity. Bromeliaceae is a family of herbaceous plants characterized by extreme adaptive radiation, its species present a wide range of reproductive strategies and distinct patterns of gene flow and genetic structure. Tillandsia aeranhos (Lois.) L.B. Smith is an epiphyte that inhabits mainly riparian forests of the Pampas biome. It occurs in dense populations across distinct habitats and topographic profiles, which makes it a good model species in studies about the influence of geo-climatic and ecologic factors over patterns of genetic variability and structure, as well as subsequent evolutionary processes of speciation or species cohesion maintenance. This dissertation presents two manuscripts aiming to provide data and analysis that will allow a better comprehension of T. aeranthos evolutionary history. In Chapter 1, we performed cross-amplifications of several nuclear microsatellite loci developed for other bromeliad species in Tillandsia aeranthos and T. recurvata. Sets of seven and six markers amplified satisfactorily and were polymorphic in T. aeanthos an T. recurvata respectively. The following analysis were carried in two populations of 20 individuals for each species and results were in accordance to opposite breeding sytems of each species: predominant cross-pollination in T. aeranthos and predominant self-pollination in T. recurvata. In Chapter 2, we investigated patterns of genetic diversity, phylogeographic structure and breeding system in T. aeranthos across most of its geographic distribution. Altogether, 203 individuals were analyzed from seven microsatellite markers; 12 individuals were analyzed from 13 chloroplast regions; and controlled pollinatin experiments were carried in 74 individuals bearing 543 flowers. Nuclear microsatellite data suggests very high levels of genetic diversity (HE=0,806; HO=0,74). Contrastingly, all chloroplast regions were monomorphic, with no haplotype differentiation. Genetic structure was very low (FST=0,031)) and isolation-by-distance hypothesis was refuted. Moderated signs of recent bottleneck events were detected in four out of 13 populations, suggesting that most populations were demographically stable since the last glacial maximum. Controlled pollination experiments showed complete self-incompatibility in T. aeranthos. In conclusion, our results sow high levels of genetic diversity and demographic stability in the species, with gene flow occurring freely without evidence of geographic barriers across the species geographic distribution. / FAPESP: 2016/03777-4 / FAPESP: 2014/15586-6

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2012-07-23T21:39:24Z No. of bitstreams: 1 Luciane Amorim Santos Uso de ferramentas de bioinformática....pdf: 5329323 bytes, checksum: b477ef604e538000e5f8d84e1188ae91 (MD5) / Made available in DSpace on 2012-07-23T21:39:24Z (GMT). No. of bitstreams: 1 Luciane Amorim Santos Uso de ferramentas de bioinformática....pdf: 5329323 bytes, checksum: b477ef604e538000e5f8d84e1188ae91 (MD5) Previous issue date: 2010 / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, Bahia, Brasil / As ferramentas de bioinformática tem sido amplamente utilizada para o melhor entendimento de diversos microorganismos. Neste trabalho foram realizados três estudos utilizando estas ferramentas para avaliar diferentes questões biológicas. No primeiro estudo realizou-se uma caracterização molecular de 57 sequências do gene pol, provenientes de pacientes infectados pelo HIV-1 de Salvador, Bahia, Brasil. Para identificar os subtipos e formas recombinantes do HIV-1 circulante na cidade de Salvador foi realizado análises filogenéticas, e através do algoritmo do banco de dados Stanford HIV resistance as mutações associadas à resistência aos ARVs foram detectadas. Entre as 57 sequências analisadas foram identificados neste estudo 45 (77,2%) pertencem ao subtipo B, 11 (21,0%) recombinantes BF e uma (1,8%) do subtipo F1. Além disto, uma alta frequência de eventos de recombinação entre os subtipos B e F foram detectados com 5 padrões de recombinação, duas intergênicas e três intragênicas, mostrando uma alta diversidade. As mutações encontradas com uma maior prevalência foram: I54V (PI) em 7,0%; M184V (NRTI) em 14,0% e K103N (NNRTI) em 10,5% das sequências analisadas. Estes resultados contribuem para traçar o perfil da epidemiologia molecular e diversidade do HIV-1 em Salvador. O segundo estudo avaliou a filodinâmica do HIV-1 em pares de mãe e filho infectados, e em diferentes fases da infecção, três pares na fase aguda e um na fase crônica, e que apresentavam sequências de diferentes tempos. Para este fim foi realizado inferências filogenéticas bayesianas, onde a hipótese do relógio molecular e de diferentes crescimentos populacional foram testadas. Não foi possível observar uma diferença entre a dinâmica da população viral da mãe e a encontrada no filho. Porém, quando observamos o crescimento populacional e o tamanho da população efetiva, ao longo do tempo, sequências provenientes de pares em fase crônica da infecção tem um crescimento mais constante, enquanto as sequências dos pares na fase aguda da infecção se observa uma dinâmica das populações virais, provavelmente devido à pressão do sistema imune e a não adaptação destes vírus. No terceiro estudo, 104 sequências do genoma completo do WNV, disponíveis no Genebank, foram estudadas para identificar a região genômica que apresenta máximo poder interpretativo para inferir relações temporais e geográficas entre as cepas do vírus. Alinhamentos de cada gene foram submetidos à avaliação do sinal filogenético através do programa TREEPUZZEL. As regiões NS3 e NS4 apresentaram um sinal filogenético acima de 70%, sendo as regiões mais indicadas para construção filogenética. Além disto, árvores bayesianas foram inferidas utilizando as regiões NS3, NS5 e E, onde os clados das árvores NS3 e NS5 apresentaram um maior suporte e estrutural temporal geográfica, diferente da região E. Estes achados mostram que os genes NS3 e NS5 são os mais indicados para análises filogenéticas. Neste trabalho foi demonstrando o uso de ferramentas de bioinformática para a melhor caracterização da diversidade, epidemiologia molecular, dinâmica populacional e determinação das relações temporal e geográfica dos vírus. / The bioinformatics tools have been widely used for better understanding of several microorganisms. Here three studies were performed using these tools to answer different biological questions. In the first study, it was conducted the molecular characterization of 57 HIV-1 pol gene sequences from infected patients from Salvador, Bahia, Brazil. To identify the HIV-1 subtypes and recombinants forms, phylogenetics analyses were performed and the Stanford HIV resistance Database were used to analyze the antiretroviral susceptibility. Among all analyzed sequences, 45 of them were (77.2%) subtype B, 11 (21.0%) were BF recombinant and one sequence was (1.8%) subtype F1. Furthermore, a high frequency of recombination events between subtypes B and F was detected with five different patterns: two intergenic and three intragenic. The mutations found with higher prevalence were: I54V (PI) in 7.0%; M184V (NRTI) in 14.0% and K103N (NNRTI) in 10.5% of the analyzed sequences. These results contribute for the knowledge of the molecular epidemiology and diversity of HIV-1 in Salvador. The second study have evaluated the HIV-1 phylodynamics in mother and child infected pairs in different stages of infections: three pairs acutely infected and one chronically infected. Phylogenetic inference was performed using the Bayesian framework were the molecular clock and different population growth models hypothesis were tested. We did not find any difference of the population dynamics between mother and child. However, when observing the population growth and the effective population size through time, the chronically infected pair sequences showed a constant growth, while the acutely infected pair sequences showed a more dynamic population growth, probably due to the immune system selective pressure. In the third study, 104 WNV full genome sequences were selected from Genbank, to identify the best genomic region, which could provide the maximal interpretative power to infer temporal and geographic relationships among the virus strains. The phylogenetic signal was evaluated using the TREEPUZZEL program. The results showed that the NS3 and NS5 regions are the best ones to infer phylogeny since their phylogenetic signal was higher than 70%. Furthermore, Bayesian trees were constructed using the NS3, NS5 and E regions, and the NS3 and NS5 tree clades showed a higher support and a temporal geographic structure, different from the E region. These findings show that the NS3 and NS5 genes are the most informative genes for phylogenetic analyses. These studies demonstrated the use of bioinformatics tools for the better characterization of the virus diversity, molecular epidemiology, and population dynamics.

The genus Clematis L. (Ranunculaceae) was used as a new model group to assess the role of the Himalayan orogeny on generation of biodiversity through investigations of its phylogeny, phylogeography and taxonomy. Although existing checklists include 28 species of Clematis from Nepal, a comprehensive taxonomic revision of available material in herbaria and additional sampling from fieldwork during this study has led to the recognition of 21 species of Clematis in Nepal, including one species (C. kilungensis) not previously recorded from Nepal. Exisiting phylogenetic and taxonomic concepts were tested with the addition of new samples from Nepal. The results highlight the shortcomings of the previous studies which were poorly resolved and indicate the need for a thorough revision of the sectional classification. Despite the increased sampling the results are still equivocal due to poor statistical support along the backbone of the phylogeny. Groups of species in well supported terminal clades are broadly comparable with results from previous studies although there are fewer clearly recognisable and well supported clades. The published dates for the evolution of Clematis were tested and the methodology of the previous study critically reappraised. The results indicate that the genus Clematis is approximately twice as old as previously reported and evolved in the middle Miocene. The phylogeny also demonstrates that, even allowing for poor support for the relationships between groups of species within Clematis, the extant Nepalese species must have multiple independent origins from at least 6 different colonisations. With their occurrence in the Pliocene and Pleistocene, these events are relatively recent in relation to the Himalayan orogeny, and may be linked more to the dispersal ability of Clematis than to the direct effects of the orogeny. Additional Nepalese samples of Koenigia and Meconopsis were added to exisiting datasets and these were reanalysed. The result from Clematis, Koenigia and Meconopsis were appraised in light of the the geocientific literature and previously published phylogeographic studies to create an overview of the drivers behind speciation in the Himalaya.

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No. of bitstreams: 1 TeseCGM.pdf: 10297481 bytes, checksum: 5ac9b43d80112267888f4b1428db2dd1 (MD5) Previous issue date: 2015-08-21 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Penaeidae family occurs in all oceans, particularly in tropical regions and represents an important global fishing resource. In Brazil, penaeid species have been shown decline, of their populations, which are considered overexploited. Therefore, a greater knowledge about these species is required for the developing of appropriate conservation actions. However, genetic studies of penaeids, including phylogeography, geographic distribution and phylogeny, are still scarce. In the present work, genetic structure and genetic relationships were characterized for different marine shrimp species belonging to the Penaeidae family, with special emphasis on those of occurrence in the Brazilian coast (Xiphopenaeus kroyeri, Farfantepenaeus paulensis, Farfantepenaeus subtilis and Farfantepenaeus brasiliensis). Mitochondrial and nuclear markers were used in order to clarify aspects related to the geographic distribution and genetic relationships among the studied penaeid species and the implications for conservationist approaches. Specific oligonucleotides were designed to amplify four mtDNA regions (COI, 16S, Cytb and DLoop). The results showed efficient patterns for 16 native species of Brazilian and Mozambican coasts. Numts presence and its implication for penaeid genetics were investigated using specific and universal primers for COI gene. Pseudogenes were detected for some penaeid species. Cytb pseudogene for the Penaeidae family was reported by the first time. DNA barcoding approach was tested in several species from Brazilian coast. The barcoding analysis evidenced a high range of intraspecific distance, suggesting the necessity of taxonomic review into Penaeidae. The existence of species complex was investigated for both X. kroyeri and F. subtilis. Phylogeographical signs and population structure were no observed for F. subtilis along the Brazilian coast. F. paulensis populations, collected in Lagoa dos Patos (RS) and Cananéia (SP), showed genetic structuring by analyzing of COI gene. That data can be reflecting the existence of differentiated-genetically adult stocks or ancient structure. Two recent population expansions, one of them before and the other one after the last period of the maximum glacial, were observed for F. paulensis. mtDNA and RAD-seq data were using to study the species X. kroyeri populations. The mtDNA analysis suggested that the upwelling from Cabo Frio (RJ) consists in a semipermeable barrier to X. kroyeri species, limiting the genetic flow between populations from North and South of Cabo Frio for. The analysis of approximately three thousand SNPs revealed three different genetic stocks, possibly related to the hydrodynamic characteristics of the sampled geographic regions, which may be holding different larvae pools. The study herein brings important information about genetic relationships and population structure for Penaeidae species, mainly those species occurring in Brazil. Such data can be help to foment future actions aiming the conservation of penaeid species, which present ecological and socioeconomic relevance. / A família Penaeidae ocorre em todos os oceanos, principalmente nas regiões tropicais e presenta grande importância econômica mundial. No Brasil, os peneídeos têm mostrado declínio nas populações, as quais são consideradas sobreexplotadas. Dessa forma, melhor conhecimento dessas espécies se faz necessário para que medidas conservacionistas mais adequadas sejam tomadas. Estudos genéticos em peneídeos, fincluindo filogeografia, distribuição geográfica e filogenia ainda são escassos. No presente estudo, a estrutura genética e as relações genéticas foram caracterizarizadas para distintas espécies de camarões marinhos pertencentes à família Penaeidae, com ênfase especial nas de ocorrência no litoral brasileiro (Xiphopenaeus kroyeri, Farfantepenaeus paulensis, Farfantepenaeus subtilis and Farfantepenaeus brasiliensis). Marcadores mitocondriais e nucleares, foram usados com o intuito de esclarecer aspectos relacionados à distribuição geográfica e relações genéticas entre as espécies estudadas e suas implicações conservacionistas. Oligonucleotideos específicos foram desenvolvidos para amplificação de quatro regiões mtDNA (COI, 16S, Cytb e DLoop), os quais foram eficientes para 16 espécies nativas da costa brasileira e moçambicana. A presença de numts e suas implicações para a genética de peneideos foi investigada utilizando primers específicos e universais para o gene COI, sendo observada a presença pseudogene em algumas espécies. Foi evidenciada pela primeira vez em Penaeidae a presença de pseudogene Cytb. A eficiência do DNA Barcode foi testada em diversas espécies coletadas no litoral brasileiro. Foi observada uma alta variação da distancia intraespecífica, indicando a necessidade de uma revisão nesta família. A existência de um complexo de espécies foi verificada nas espécies X. kroyeri e F. subtilis. Sinais filogeográficos ou estruturação populacional não foram observadas ao longo da costa brasileira para F. subtilis. Uma leve estruturação populacional foi encontrada para Farfantepenaeus paulensis entre populações da Lagoa dos Patos-RS e Cananéia-SP, utilizando-se o gene COI. Este dado pode estar refletindo a existência de estoques de adultos geneticamente diferentes ou uma estruturação antiga. Duas expansões populacionais recentes foram observadas para esta espécie, sendo uma antes e outra após o período da última glaciação máxima. Dados de mtDNA e RAD-seq foram tilizados para estudar as populações de X. kroyeri. A análise mitocondrial sugeriu que ressurgência em Cabo Frio-RJ apresenta-se como uma barreira semipermeável para esta espécie, limitando o fluxo gênico entre populações situadas ao norte e ao sul de Cabo Frio. A análise de aproximadamente 3mil SNPs revelou três possíveis estoques genéticos, possivelmente relacionado a características hidrodinâmicas das regiões amostradas, as quais podem estar retendo larvas. O presente estudo trás importantes informações sobre as relações genéticas, estrutura de populações e filogeografia de espécies da família Penaeidae, principalmente as de ocorrência no litoral brasileiro. Essas informações podem ajudar futuras tomadas de decisão que visem a conservação dessas espécies, as quais apresentam relevância ecológica e/ou socioeconomica, representando um importante recurso pesqueiro.

Made available in DSpace on 2016-06-07T17:12:09Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-02-26. Added 1 bitstream(s) on 2016-06-07T17:16:42Z : No. of bitstreams: 1 000864243_20170305.pdf: 7143919 bytes, checksum: caed29775e1aef81d31c7ee53b951b52 (MD5) Bitstreams deleted on 2017-03-10T13:07:29Z: 000864243_20170305.pdf,. Added 1 bitstream(s) on 2017-03-10T13:08:14Z : No. of bitstreams: 1 000864243.pdf: 17228237 bytes, checksum: e60fc4adb3f71274c66a6fc0677f3dea (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Introduction: Prematurity is the leading cause of neonatal mortality and serious neonatal morbidity worldwide and the risk is inversely proportional to gestational age at birth. Several studies demonstrate the role of innate immune response and Toll-like receptors (TLRs) in normal and complicated pregnancies, however most studies have focused on the tissues of the maternal-fetal interface. Research of the expression of TLRs in gestational tissues is of great importance for understanding the involvement of innate immunity in normal pregnancies and adverse pregnancy outcomes, but the analysis of these tissues allows for results only after the complete resolution of gestation. In this scenario, a potential biological sample of interest for analysis of TLRs in the ongoing gestation are maternal peripheral blood cells, since they play a crucial role in the immune system and express high levels of many of the TLRs. Main: Evaluate the profile of gene expression of TLR-1, -2, -4 and -6 in peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells (PMNs) and compare these expressions between preterm and term pregnancies. Materials and methods: 119 normal pregnant women were included in the study, subdivided into three groups according to the gestational trimester. In addition, 20 pregnant women in preterm labor and 18 pregnant women at term were evaluated. Gene expression analysis was performed by real-time PCR and protein expression evaluation by flow cytometry. Statistical analyses were performed using the nonparametric Kruskal-Wallis and Mann-Whitney tests by SigmaStat 3.1 software. Results: Regarding PBMCs, there were no significant differences in gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 among the trimesters. The same was observed when comparing PBMCs of preterm and term pregnancies. In relation to neutrophils, gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 remained unchanged throughout normal... / Introduction: Prematurity is the leading cause of neonatal mortality and serious neonatal morbidity worldwide and the risk is inversely proportional to gestational age at birth. Several studies demonstrate the role of innate immune response and Toll-like receptors (TLRs) in normal and complicated pregnancies, however most studies have focused on the tissues of the maternal-fetal interface. Research of the expression of TLRs in gestational tissues is of great importance for understanding the involvement of innate immunity in normal pregnancies and adverse pregnancy outcomes, but the analysis of these tissues allows for results only after the complete resolution of gestation. In this scenario, a potential biological sample of interest for analysis of TLRs in the ongoing gestation are maternal peripheral blood cells, since they play a crucial role in the immune system and express high levels of many of the TLRs. Main: Evaluate the profile of gene expression of TLR-1, -2, -4 and -6 in peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells (PMNs) and compare these expressions between preterm and term pregnancies. Materials and methods: 119 normal pregnant women were included in the study, subdivided into three groups according to the gestational trimester. In addition, 20 pregnant women in preterm labor and 18 pregnant women at term were evaluated. Gene expression analysis was performed by real-time PCR and protein expression evaluation by flow cytometry. Statistical analyses were performed using the nonparametric Kruskal-Wallis and Mann-Whitney tests by SigmaStat 3.1 software. Results: Regarding PBMCs, there were no significant differences in gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 among the trimesters. The same was observed when comparing PBMCs of preterm and term pregnancies. In relation to neutrophils, gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 remained unchanged throughout normal ... / FAPESP: 11/00269-4

Orientador: Claudio de Oliveira / Coorientador: Jonathan Stuart Ready / Banca: Anderson Luis Alves / Banca: Luiz Henrique Garcia Pereira / Banca: Guilherme José da Costa / Banca: Ricardo Cardoso Benine / Resumo: Introduction: Prematurity is the leading cause of neonatal mortality and serious neonatal morbidity worldwide and the risk is inversely proportional to gestational age at birth. Several studies demonstrate the role of innate immune response and Toll-like receptors (TLRs) in normal and complicated pregnancies, however most studies have focused on the tissues of the maternal-fetal interface. Research of the expression of TLRs in gestational tissues is of great importance for understanding the involvement of innate immunity in normal pregnancies and adverse pregnancy outcomes, but the analysis of these tissues allows for results only after the complete resolution of gestation. In this scenario, a potential biological sample of interest for analysis of TLRs in the ongoing gestation are maternal peripheral blood cells, since they play a crucial role in the immune system and express high levels of many of the TLRs. Main: Evaluate the profile of gene expression of TLR-1, -2, -4 and -6 in peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells (PMNs) and compare these expressions between preterm and term pregnancies. Materials and methods: 119 normal pregnant women were included in the study, subdivided into three groups according to the gestational trimester. In addition, 20 pregnant women in preterm labor and 18 pregnant women at term were evaluated. Gene expression analysis was performed by real-time PCR and protein expression evaluation by flow cytometry. Statistical analyses were performed using the nonparametric Kruskal-Wallis and Mann-Whitney tests by SigmaStat 3.1 software. Results: Regarding PBMCs, there were no significant differences in gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 among the trimesters. The same was observed when comparing PBMCs of preterm and term pregnancies. In relation to neutrophils, gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 remained unchanged throughout normal... / Abstract: Introduction: Prematurity is the leading cause of neonatal mortality and serious neonatal morbidity worldwide and the risk is inversely proportional to gestational age at birth. Several studies demonstrate the role of innate immune response and Toll-like receptors (TLRs) in normal and complicated pregnancies, however most studies have focused on the tissues of the maternal-fetal interface. Research of the expression of TLRs in gestational tissues is of great importance for understanding the involvement of innate immunity in normal pregnancies and adverse pregnancy outcomes, but the analysis of these tissues allows for results only after the complete resolution of gestation. In this scenario, a potential biological sample of interest for analysis of TLRs in the ongoing gestation are maternal peripheral blood cells, since they play a crucial role in the immune system and express high levels of many of the TLRs. Main: Evaluate the profile of gene expression of TLR-1, -2, -4 and -6 in peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells (PMNs) and compare these expressions between preterm and term pregnancies. Materials and methods: 119 normal pregnant women were included in the study, subdivided into three groups according to the gestational trimester. In addition, 20 pregnant women in preterm labor and 18 pregnant women at term were evaluated. Gene expression analysis was performed by real-time PCR and protein expression evaluation by flow cytometry. Statistical analyses were performed using the nonparametric Kruskal-Wallis and Mann-Whitney tests by SigmaStat 3.1 software. Results: Regarding PBMCs, there were no significant differences in gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 among the trimesters. The same was observed when comparing PBMCs of preterm and term pregnancies. In relation to neutrophils, gene and protein expressions of TLR-1, TLR-2, TLR-4 and TLR-6 remained unchanged throughout normal ... / Doutor