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Tafonomia dos icnofósseis de vertebrados da formação Guará (jurássico superior?) Rio Grande do SulDias, Paula Camboim Dentzien January 2007 (has links)
Os primeiros registros de icnofósseis para o Mesozóico do Rio Grande do Sul surgiram apenas no final do Século XX. Dentre as unidades dessa Era, a Formação Guará (Jurássico Superior), é a unidade mais rica em icnofósseis (pegadas e trilhas de saurópodes, terópodes e ornitópodes e crotovinas de mamíferos(?)). Seus icnofósseis são encontrados apenas nas fácies eólicas (lençóis de areia e dunas). Nos lençóis de areia, as pegadas não estão bem preservadas devido ao intenso pisoteio e só são reconhecidas devido a deformação das laminações. Em alguns casos é possível ver esta deformação em planta e em perfil. Nas paleodunas, até o momento, só foram encontradas duas pegadas de terópode, mostrando estruturas de escorregamento e a deformação da estratificação, que ocorreu enquanto o pé do animal penetrava na areia, durante a subida na duna. Estas e outras pegadas que podem ser vistas em corte mostram uma boa preservação, indicando que uma pequena quantidade de água estava presente no substrato (< 1%), aumentando significantemente a coesão do sedimento e permitindo a preservação da pegada juntamente com as deformações verticais bem desenvolvidas, além do mais, a preservação destas indica que elas escaparam da erosão ou do pisoteio por terem sido enterradas rapidamente. No mesmo afloramento em que foram encontradas pegadas de terópodes na paleoduna foram encontradas crotovinas, identificadas pela presença de elipses de arenito maciço, com cerca de 20 cm de largura, que ocorrem cortando os foresets. Estes icnofósseis representam a única evidência de vertebrados para a Formação Guará, conseqüentemente a preservação dos mesmos é de fundamental importância para o conhecimento dos animais que viveram no Rio Grande do Sul no final do Jurássico. / In the state of Rio Grande do Sul, Brazil, eolian facies of the Guará Formation of probable Late Jurassic age, revealed footprints and trackways of dinosaurs, as well as burrows made by small vertebrates (mammals?). All the footprints and trackways are preserved in the eolian facies, including dunes and sand sheets. Footprints made in the sand sheets are not well preserved due to intense trampling and can be distinguished only by deformation of the sandstone laminations. In some cases it is possible to see this deformation on surface and in section. Tracks of theropods, ornithopods and middle-sized sauropods can be identified. Two footprints preserved in the foreset of a paleodune permitted to recognize slide structures and even identify the trackmaker, a theropod. The burrows were found at this same paleodune, cutting horizontally the foresets. They are represented by ribbons of massive sandstone – interpreted as the partial filling of the base of the burrows - covered by little blocks of stratified sandstone – suggesting the collapse of the roof inward the burrow. On an active dune, the softest, most easily deformed substrate underlies the slip face, footprints usually do not show good preservation. However, this site demonstrates that when tracks are made on the dry slip faces of dunes they can be preserved in considerable detail. Because the slip face lies within the zone of flow separation, tracks made on grainflows are better protected from wind erosion than those made on any other dune surface. The good preservation of some footprints indicates that they escaped erosion or further trampling, by rapid burial. There is no record of bone remains in the Guará Formation, consequently, the preservation of these tracks provides an unique evidence of widespread dinosaur activity in southern Brazil during the end of the Jurassic.
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A caça no Brasil: panorama histórico e atualFerreira, Hugo Fernandes 05 December 2014 (has links)
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Previous issue date: 2014-12-05 / historical and current scenario. In Brazil, hunting is widely practiced throughout the territory since ancient times, causing dramatic environmental consequences, although there has never been a comprehensive analysis that addressed this issue at a national level under a conservation perspective. In summary, it is known that the Brazilian hunting is a problem, but no one knows for sure what it is, what its history and what the actual size of the problem. Thus, this research aims to analyze the hunting in Brazil and the historical, socioeconomic and cultural contexts associated with such activity, with the main focus on wildlife involved in different ways to human use, the techniques used for hunting and conservation implications associated with such uses, in a comparative analysis between different biomes. The manuscript was divided into two volumes. The first one deals with the historical aspect. In the Chapter I, the survey of official documents, paintings, accounts of natural history expeditions, scientific chapters, books and papers involving hunting in Brazil were conducted. It was possible to analyze the evolution of the use of the techniques; indigenous and European influences; data on regional extinction of species; preferences of game species for food consumption, among many other factors. In the Chapter II, we realized an historical survey and listed the changes of legislation and the perceptions of the national mass media involving hunting activities to establish if there is a correlation between these factors and what the possible consequences of these changes for wildlife conservation. We demonstrate that this correlation exists and has evolved interdependently. The second volume deals with the current situation and was accomplished through 529 interviews in 25 localities from 12 states and in all Brazilian biomes. The first chapter aimed to inventory, describe and categorize these techniques in all biomes. Moreover, further analysis on the Index of Cultural Significance of these strategies, which were discussed in regional and national levels have been proposed. Altogether, 39 techniques have been documented, described and categorized according to purpose, autonomy, lethality, selectivity of species and abundance of specimens captured. The Chapter II proposes to conduct an inventory of the wildlife hunting related in food purposes of rural communities in localities of all biomes of the country, through interviews and literature review. We documented 344 species, although our estimates indicate that this number could reach more than 525, where 46% are birds, 42% are mammals, 11% are reptiles and 1% is amphibians. The last chapter aimed to point out what is the region historically most impacted by hunting in Brazil, assuming the Northeast region as hypothesis. Data were quantified to calculate the Use of Frequency Value (UFV) and statistically analyzed with data from the biomass of each species cited in each area. The results indicate a national trend of high UFV’s for large species. This pattern is followed in the Amazon, Pantanal, Cerrado and Pampas. In contrast, the areas of the Atlantic Forest and mainly Caatinga, both in Northeastern Brazil, present the reverse of this pattern, indicating depletion and local extinction of large animals. This can be explained by the history of occupation, economic aspects, ecological support capacity, difficulty in livelihood alternatives and specific cultural patterns. / No Brasil, atividades cinegéticas são amplamente realizadas em todo o território e desde períodos remotos, provocando drásticas consequências ambientais, embora nunca tenha havido uma análise abrangente que abordasse esse tema em nível nacional, sob uma óptica conservacionista. Em resumo, sabe-se que a caça brasileira é um problema, mas não se conhece ao certo o que é, qual sua história e qual o tamanho real desse problema no país. Desse modo, a pesquisa tem como objetivo principal analisar as atividades cinegéticas do Brasil e os contextos históricos, socioeconômicos e culturais associados a tais atividades, com foco principal na fauna envolvida em diferentes formas de uso humano, as técnicas de caça utilizadas e as implicações conservacionistas associadas a tais usos, em uma análise comparada entre os diferentes biomas brasileiros. A Tese foi dividida em dois volumes. O primeiro trata do aspecto histórico. No Capítulo I, foi realizado o levantamento de documentos oficiais, pinturas, relatos de expedições naturalistas, além de livros didáticos, artigos de periódicos, livros e capítulos de livros científicos envolvendo as atividades cinegéticas no Brasil. Foi possível analisar a evolução do uso das técnicas; as influências indígenas e europeias; dados sobre extinção regional de espécies; preferências de espécies para consumo alimentar, dentre diversos outros fatores. No Capítulo II, elencamos as mudanças da legislação e das percepções da mídia nacional envolvendo as atividades cinegéticas para estabelecer se há uma correlação entre tais fatores e quais as possíveis consequências dessas mudanças para a conservação da fauna silvestre. Demonstramos que essa correlação existe e que evoluiu de forma interdependente. O segundo volume trata do panorama atual e foi realizado através de 529 entrevistas em 25 localidades, pertencentes a 12 estados em todos os biomas do Brasil. O primeiro capítulo objetivou inventariar, descrever e categorizar essas técnicas em todos os biomas do país. Além disso, foram adaptadas novas análises sobre o Índice de Significância Cultural (ISC) dessas estratégias. Ao todo, 39 técnicas foram documentadas, descritas e categorizadas quanto à finalidade, autonomia, letalidade, seletividade de espécies e abundância de espécimes capturados. O Capítulo II se propôs a realizar um inventário sobre a fauna cinegética relacionada a fins alimentares de comunidades rurais em localidades situadas em todos os biomas do país, através de entrevistas e revisão bibliográfica. Foram documentadas 344 espécies, embora as estimativas apontem que esse número pode atingir mais que 525, sendo 46% aves, 42% mamíferos, 11% répteis e 1% anfíbios. O último capítulo teve como objetivo analisar qual a região historicamente mais impactada pela caça no Brasil, assumindo como hipótese a Região Nordeste. Os dados foram quantificados pelo cálculo do Valor de Frequência de Uso e analisados estatisticamente com os dados da biomassa de cada espécie citada em cada área. Os resultados apontam uma tendência nacional de maior valoração de uso para espécies de grande porte. Esse panorama é seguido na Amazônia, Pantanal, Cerrado e nos Pampas. Em contraste, as áreas de Mata Atlântica do Nordeste e principalmente a área de Caatinga apontam o inverso desse padrão, indicando extinção local e depleção de grandes animais. Isso pode ser explicado através do histórico de ocupação, aspectos econômicos, capacidade de suporte ecológico, dificuldade em alternativas de subsistência e padrões culturais específicos.
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Tafonomia dos icnofósseis de vertebrados da formação Guará (jurássico superior?) Rio Grande do SulDias, Paula Camboim Dentzien January 2007 (has links)
Os primeiros registros de icnofósseis para o Mesozóico do Rio Grande do Sul surgiram apenas no final do Século XX. Dentre as unidades dessa Era, a Formação Guará (Jurássico Superior), é a unidade mais rica em icnofósseis (pegadas e trilhas de saurópodes, terópodes e ornitópodes e crotovinas de mamíferos(?)). Seus icnofósseis são encontrados apenas nas fácies eólicas (lençóis de areia e dunas). Nos lençóis de areia, as pegadas não estão bem preservadas devido ao intenso pisoteio e só são reconhecidas devido a deformação das laminações. Em alguns casos é possível ver esta deformação em planta e em perfil. Nas paleodunas, até o momento, só foram encontradas duas pegadas de terópode, mostrando estruturas de escorregamento e a deformação da estratificação, que ocorreu enquanto o pé do animal penetrava na areia, durante a subida na duna. Estas e outras pegadas que podem ser vistas em corte mostram uma boa preservação, indicando que uma pequena quantidade de água estava presente no substrato (< 1%), aumentando significantemente a coesão do sedimento e permitindo a preservação da pegada juntamente com as deformações verticais bem desenvolvidas, além do mais, a preservação destas indica que elas escaparam da erosão ou do pisoteio por terem sido enterradas rapidamente. No mesmo afloramento em que foram encontradas pegadas de terópodes na paleoduna foram encontradas crotovinas, identificadas pela presença de elipses de arenito maciço, com cerca de 20 cm de largura, que ocorrem cortando os foresets. Estes icnofósseis representam a única evidência de vertebrados para a Formação Guará, conseqüentemente a preservação dos mesmos é de fundamental importância para o conhecimento dos animais que viveram no Rio Grande do Sul no final do Jurássico. / In the state of Rio Grande do Sul, Brazil, eolian facies of the Guará Formation of probable Late Jurassic age, revealed footprints and trackways of dinosaurs, as well as burrows made by small vertebrates (mammals?). All the footprints and trackways are preserved in the eolian facies, including dunes and sand sheets. Footprints made in the sand sheets are not well preserved due to intense trampling and can be distinguished only by deformation of the sandstone laminations. In some cases it is possible to see this deformation on surface and in section. Tracks of theropods, ornithopods and middle-sized sauropods can be identified. Two footprints preserved in the foreset of a paleodune permitted to recognize slide structures and even identify the trackmaker, a theropod. The burrows were found at this same paleodune, cutting horizontally the foresets. They are represented by ribbons of massive sandstone – interpreted as the partial filling of the base of the burrows - covered by little blocks of stratified sandstone – suggesting the collapse of the roof inward the burrow. On an active dune, the softest, most easily deformed substrate underlies the slip face, footprints usually do not show good preservation. However, this site demonstrates that when tracks are made on the dry slip faces of dunes they can be preserved in considerable detail. Because the slip face lies within the zone of flow separation, tracks made on grainflows are better protected from wind erosion than those made on any other dune surface. The good preservation of some footprints indicates that they escaped erosion or further trampling, by rapid burial. There is no record of bone remains in the Guará Formation, consequently, the preservation of these tracks provides an unique evidence of widespread dinosaur activity in southern Brazil during the end of the Jurassic.
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Tafonomia dos icnofósseis de vertebrados da formação Guará (jurássico superior?) Rio Grande do SulDias, Paula Camboim Dentzien January 2007 (has links)
Os primeiros registros de icnofósseis para o Mesozóico do Rio Grande do Sul surgiram apenas no final do Século XX. Dentre as unidades dessa Era, a Formação Guará (Jurássico Superior), é a unidade mais rica em icnofósseis (pegadas e trilhas de saurópodes, terópodes e ornitópodes e crotovinas de mamíferos(?)). Seus icnofósseis são encontrados apenas nas fácies eólicas (lençóis de areia e dunas). Nos lençóis de areia, as pegadas não estão bem preservadas devido ao intenso pisoteio e só são reconhecidas devido a deformação das laminações. Em alguns casos é possível ver esta deformação em planta e em perfil. Nas paleodunas, até o momento, só foram encontradas duas pegadas de terópode, mostrando estruturas de escorregamento e a deformação da estratificação, que ocorreu enquanto o pé do animal penetrava na areia, durante a subida na duna. Estas e outras pegadas que podem ser vistas em corte mostram uma boa preservação, indicando que uma pequena quantidade de água estava presente no substrato (< 1%), aumentando significantemente a coesão do sedimento e permitindo a preservação da pegada juntamente com as deformações verticais bem desenvolvidas, além do mais, a preservação destas indica que elas escaparam da erosão ou do pisoteio por terem sido enterradas rapidamente. No mesmo afloramento em que foram encontradas pegadas de terópodes na paleoduna foram encontradas crotovinas, identificadas pela presença de elipses de arenito maciço, com cerca de 20 cm de largura, que ocorrem cortando os foresets. Estes icnofósseis representam a única evidência de vertebrados para a Formação Guará, conseqüentemente a preservação dos mesmos é de fundamental importância para o conhecimento dos animais que viveram no Rio Grande do Sul no final do Jurássico. / In the state of Rio Grande do Sul, Brazil, eolian facies of the Guará Formation of probable Late Jurassic age, revealed footprints and trackways of dinosaurs, as well as burrows made by small vertebrates (mammals?). All the footprints and trackways are preserved in the eolian facies, including dunes and sand sheets. Footprints made in the sand sheets are not well preserved due to intense trampling and can be distinguished only by deformation of the sandstone laminations. In some cases it is possible to see this deformation on surface and in section. Tracks of theropods, ornithopods and middle-sized sauropods can be identified. Two footprints preserved in the foreset of a paleodune permitted to recognize slide structures and even identify the trackmaker, a theropod. The burrows were found at this same paleodune, cutting horizontally the foresets. They are represented by ribbons of massive sandstone – interpreted as the partial filling of the base of the burrows - covered by little blocks of stratified sandstone – suggesting the collapse of the roof inward the burrow. On an active dune, the softest, most easily deformed substrate underlies the slip face, footprints usually do not show good preservation. However, this site demonstrates that when tracks are made on the dry slip faces of dunes they can be preserved in considerable detail. Because the slip face lies within the zone of flow separation, tracks made on grainflows are better protected from wind erosion than those made on any other dune surface. The good preservation of some footprints indicates that they escaped erosion or further trampling, by rapid burial. There is no record of bone remains in the Guará Formation, consequently, the preservation of these tracks provides an unique evidence of widespread dinosaur activity in southern Brazil during the end of the Jurassic.
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Molecular evolution of voltage-gated calcium channels of L and N types and their genomic regionsWidmark, Jenny January 2012 (has links)
The expansion of the voltage-gated calcium channel alpha 1 subunit families (CACNA1) of L and N types was investigated by combining phylogenetic analyses (neighbour-joining and maximum likelihood) with chromosomal data. Neighbouring gene families were analysed to see if the chromosomal regions duplicated through whole genome doublings in vertebrates. Results show that both types of CACNA1 expanded in two ancient whole genome duplications as parts of larger genomic regions. Many gene families in these regions obtained copies in an additional teleost-specific genome duplication. This diversification of CACNA1 genes probably contributed to evolutionary innovations in nervous system function.
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Contribution of Lipophilic Secondary Metabolites to the Toxicity of Strains of Freshwater Cyanobacterial Harmful Algal Blooms, Identified Using the Zebrafish (Danio rerio) Embyo as a Model for Vertebrate DevelopmentJaja-Chimedza, Asha D 21 March 2014 (has links)
Cyanobacteria (“blue-green algae”) are known to produce a diverse repertoire of biologically active secondary metabolites. When associated with so-called “harmful algal blooms”, particularly in freshwater systems, a number of these metabolites have been associated - as “toxins”, or commonly “cyanotoxins” - with human and animal health concerns. In addition to the known water-soluble toxins from these genera (i.e. microcystins, cylindrospermopsin, and saxitoxins), our studies have shown that there are metabolites within the lipophilic extracts of these strains that inhibit vertebrate development in zebrafish embryos. Following these studies, the zebrafish embryo model was implemented in the bioassay-guided purification of four isolates of cyanobacterial harmful algal blooms, namely Aphanizomenon, two isolates of Cylindrospermopsis, and Microcystis, in order to identify and chemically characterize the bioactive lipophilic metabolites in these isolates.
We have recently isolated a group of polymethoxy-1-alkenes (PMAs), as potential toxins, based on the bioactivity observed in the zebrafish embryos. Although PMAs have been previously isolated from diverse cyanobacteria, they have not previously been associated with relevant toxicity. These compounds seem to be widespread across the different genera of cyanobacteria, and, according to our studies, suggested to be derived from the polyketide biosynthetic pathway which is a common synthetic route for cyanobacterial and other algal toxins. Thus, it can be argued that these metabolites are perhaps important contributors to the toxicity of cyanobacterial blooms. In addition to the PMAs, a set of bioactive glycosidic carotenoids were also isolated because of their inhibition of zebrafish embryonic development. These pigmented organic molecules are found in many photosynthetic organisms, including cyanobacteria, and they have been largely associated with the prevention of photooxidative damage. This is the first indication of these compounds as toxic metabolites and the hypothesized mode of action is via their biotransformation to retinoids, some of which are known to be teratogenic. Additional fractions within all four isolates have been shown to contain other uncharacterized lipophilic toxic metabolites. This apparent repertoire of lipophilic compounds may contribute to the toxicity of these cyanobacterial harmful algal blooms, which were previously attributed primarily to the presence of the known water-soluble toxins.
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Revisão sistemática do gênero Mourasuchus (Alligatoroidea, Caimaninae), com comentários sobre filogenia, biogeografia e paleoecologia de Caimaninae / Systematic revision of the Mourasuchus genus (Alligatoroidea, Caimaninae), with comments on the phylogeny, biogeography and paleoecology of CaimaninaeGiovanne Mendes Cidade 09 June 2015 (has links)
Mourasuchus (Alligatoroidea, Caimaninae) é um táxon extinto de crocodilianos restrito ao Cenozoico da América do Sul. Representa um dos grupos de crocodilianos mais peculiares de todos os tempos, devido ao formato longo, largo e achatado de seu rostro (lembrando o bico de um pato) entre outras características. Apesar dessas peculiaridades, relativamente poucos trabalhos foram feitos sobre esse grupo. A maioria das descrições morfológicas dos fósseis do gênero são sucintas e breves, incluindo as dos holótipos de duas das quatro espécies a ele assinaladas: M. amazonensis e M. arendsi. Do mesmo modo, as diagnoses das quatro espécies também se mostram sucintas. Poucas também são as análises filogenéticas realizadas com Mourasuchus a maioria das quais, porém, recupera Orthogenysuchus olseni, do Eoceno dos Estados Unidos, como táxon-irmão de Mourasuchus, gerando um impasse biogeográfico. Além disso, a maneira exata pela qual Mourasuchus se alimentava, fazendo uso de seu peculiar rostro bico de pato, bem como seus itens alimentares, ainda não foram plenamente esclarecidos, ainda que algumas teorias tenham sido propostas na literatura. Assim, este trabalho se propôs a: oferecer uma re-descrição dos holótipos de M. amazonensis e M. arendsi; revisar as diagnoses das espécies e do próprio gênero; realizar uma análise filogenética investigando as relações das espécies entre si e do gênero, como um todo, em Caimaninae; investigar a relação de Orthogenysuchus olseni como táxon-irmão de Mourasuchus; elucidar o modo de forrageio e os itens alimentares consumidos pelo grupo. As re-análises das diagnoses das espécies revelaram que duas delas constituem, na verdade, espécies não-válidas, enquanto a análise de um novo material craniano descrito neste trabalho (MCNC-PAL-110-72V) revelou a existência de uma nova espécie de Mourasuchus, fazendo com que este trabalho reconheça três espécies válidas para o gênero. A análise filogenética revelou M. atopus como o táxon mais basal, enquanto M. amazonensis e a nova espécie proposta formam um clado mais derivado. Orthogenysuchus olseni não foi recuperado como táxon-irmão de Mourasuchus em nenhuma das análises, mas seu posicionamento ainda dentro de Caimaninae faz com que impasses biogeográficos permaneçam. Este trabalho defende que Mourasuchus coletava presas em grande quantidade usando a musculatura da parte de baixo de seu rostro uma alimentação coletora enquanto ainda não há evidências de que esses animais fariam uma filtração da massa alimentar coletada. É possível, também, que tal hábito tenha evoluído a partir do hábito alimentar durófago exibido por Caimaninae basais, especialmente o gênero Gnatosuchus. / Mourasuchus (Alligatoroidea, Caimaninae) is an extinct crocodilian taxon restricted to the Cenozoic of South America. It represents one of the most peculiar crocodilian groups of all time, due to the long, wide, flattened shape of its rostrum (resembling the beak of a duck), among other features. Regardless these peculiarities, relatively few works have been done about this group. Most of morphological descriptions of the fossils belonging to this genus are shot and brief, including those of two from the four species assigned to it: M. amazonensis and M. arendsi. Similarly, the diagnoses of all the four species are also very brief. The phylogenetic analyses involving Mourasuchus are also very few most of them, however, recover Orthogenysuchus olseni, from the Eocene of the United States, as Mourasuchus sister-taxon, creating a biogeographically problematic scenario. Furthermore, the exact way by which Mourasuchus feed itself, using its peculiar beak of duck rostrum, as well as its prey items, are yet to be determined, even though some proposals have already been made in the literature. As such, this work had the following objectives: offer a redescription of the holotypes of M. amazonensis and M. arendsi; re-evaluate the diagnoses of Mourasuchus species and the genus itself; perform a phylogenetic analysis to evaluate the relationships between Mourasuchus species and of this group, as a whole, within Caimaninae; evaluate the position of Orthogenysuchus olseni as a sister-taxon of Mourasuchus; elucidate the foraging tactics and the prey items consumed by this group. The re-evaluation of the diagnoses of the species revealed that two are in reality non-valid species, while the analysis of a new cranial material described in this work (MCNC-PAL-110-72V) revealed the existence of a new species of Mourasuchus, taking this work to recognize the existence of three valid species for the genus. The phylogenetic analysis recovered M. atopus as the basalmost taxon, while M. amazonensis and the new species proposed in this work form a more derived clade. Orthogenysuchus olseni was not recovered as a Mourasuchus sister-taxon in any of the analyses made, but its position still within Caimaninae maintains biogeographically problematic scenarios in this clade. This work defends that Mourasuchus collected a high number of prey items using the musculature between the lower jaws a collecting foraging tactic while there is still no evidence that these animals could perform a straining of the entire concentration of food it collected. It is possible, as well, that such habit may have evolved from the durophagous feeding habit of some basal Caimaninae, especially Gnatosuchus.
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Improving genome assemblies of non-model non-vertebrate animals with long reads and Hi-CGuiglielmoni, Nadege 07 September 2021 (has links) (PDF)
The corpus of reference genomes is rapidly expanding as more and more genome assemblies are released for a wide variety of species. The constant progress in sequencing technologies has led to the release in 2021 of a first complete, telomere-to-telomere, gap-less assembly of a human genome, yet a myriad of eukaryote species still lack genomic resources. For animals, genomic projects have focused on species closely related to humans (vertebrates) and those with an impact on health and agriculture. By contrast, there is still a dearth of non-vertebrate genomes that poorly represents their tremendous diversity (about 95% of animal diversity).Haploid chromosome-level genome assemblies using long reads and chromosome conformation capture (such as Hi-C) have become a standard in recent publications. To provide a haploid representation of diploid and polyploid genomes, assemblers collapse haplotypes into a single sequence, yet they are sensitive to high levels of heterozygosity and often yield fragmented assemblies with artefactual duplications. I tackled these shortcomings with two strategies: improving collapsed assemblies with a comprehensive long-read assembly methodology tuned for highly heterozygous genomes; and separating haplotypes to obtain phased assemblies using long reads and Hi-C. The assemblies were finally brought to chromosome-level scaffolds with a new Hi-C scaffolder, which demonstrated its efficiency on genomes of non-model organisms.These methods were applied to generate chromosome-level assemblies of three species for which none or few assemblies of closely related species were available: the bdelloid rotifer Adineta vaga, the coral Astrangia poculata, and the chaetognath Flaccisagitta enflata. These high-quality assemblies contribute to filling the current gaps in non-vertebrate genomics and pave the way for future sequencing initiatives aiming to generate such reference assemblies for all the species on Earth. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished
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Regulation of Oscillatory Gene Expression by Alternative PolyadenylationBraunreiter, Kara M. January 2020 (has links)
No description available.
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GENETIC ANALYSIS OF PUTATIVE WALLEYE AND SAUGEYE IN RIVERS NEAR FORT WAYNE, INDIANAGabriel L Curtis (9182993) 03 August 2020 (has links)
<p>A saugeye is the progeny of a
female walleye (<i>Sander vitreus)</i> and
male sauger (<i>Sander canadensis)</i>. In
the United States, hybrid saugeyes are considered important for recreational
fisheries and as a potential food source. Saugeyes grow exceptionally faster than their non-hybrid parents and are more tolerant of a broader range
of water conditions. They are also of interest to anglers due to their
increased growth rate and ease to catch. Rather unexpectedly, biologists have
recently observed fish that they believe to be saugeye in the Fort Wayne Rivers
even though only walleye have been stocked in the area. The fish in Hurshtown Reservoir are believed to be walleye and the
identification of those in the Three Rivers is unknown. A potential source for
saugeye in the Fort Wayne Rivers is St. Marys State Fish Hatchery in Ohio. This
research aims to determine if the fish found in the Fort Wayne Rivers are
walleye or saugeye using microsatellite analysis. Microsatellites at seven loci
were genotyped for 20 reference walleye, sauger, and saugeye as well as 21
unknown fish caught near Fort Wayne. Of the fish caught near Fort Wayne, three
are from Hurshtown Reservoir and 18 are from the Three Rivers. Assignment tests
of genotypes were completed using model and non-model based cluster analysis.
Genotypic variation clearly resolved the two parent species from their hybrid
offspring. Sixteen of eighteen <i>Sander</i> (unknown species) caught in Fort Wayne Rivers between 2018
and 2019 were determined to be first generation saugeye. The other two were
walleye found in the Maumee River downstream of Hosey Dam. The three <i>Sander</i> caught in Hurshtown Reservoir
were verified to be walleye. Sauger have never been stocked in the Fort Wayne
Rivers and connecting waterways. Therefore, it is not likely that the saugeye
found in the analysis are from natural reproduction. It is speculated that
saugeye are swimming to Fort Wayne from hatcheries within the Maumee watershed.
There are many potential sources for walleye in the Fort Wayne Rivers. </p>
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