No ano de 2011, a Bolívia enfrentou um de seus conflitos sociais mais graves desde que Evo Morales assumiu a presidência do país em 2006. Os indígenas residentes no Parque Nacional e Território Indígena Isiboro Sécure (TIPNIS) organizaram uma marcha para protestar contra a construção do trecho de uma rodovia que atravessaria seu território. Tal mobilização se transformou em um conflito de amplitude nacional e internacional, pois evidenciou contradições na política interna de Evo Morales que se refletiram na política externa boliviana. As contradições entre a retórica ecologista e indigenista do presidente e sua política nacional neoextrativista ficam evidentes. Assim, o estudo de caso do conflito no TIPNIS ilustra o embate entre duas concepções opostas de organização socioeconômica do país: uma baseada na manutenção do capitalismo extrativista-exportador e outra que propõe a ruptura com essa prática secular e a valorização da convivência harmoniosa entre o ser humano e a natureza, denominada buen vivir. / In 2011, Bolivia faced one of its most serious social conflicts since Evo Morales became president of the country in 2006. The indigenous people resident in the National Park and Indigenous Territory Isiboro Sécure (TIPNIS) organized a march to protest against the construction of the stretch of a highway that would cross their territory. Such mobilization became a conflict of national and international scale, revealing contradictions in the internal politics of Evo Morales and reflecting in the Bolivian foreign policy. The contradictions among indigenous and environmentalist president’s rhetoric and his neoextractive national political became evident. Thus, the case study of the conflict in TIPNIS illustrates the clash between two opposite conceptions of socioeconomic organization of the country: one based on the maintenance of extractive capitalism and other proposing to break with this secular practice and to valorize harmonious coexistence between human being and nature, called buen vivir. / En 2011, Bolivia se enfrentó a uno de sus conflictos sociales más graves desde que Evo Morales asumió la presidencia del país en 2006. Los habitantes indígenas en el Parque Nacional y Territorio Indígena Isiboro Sécure (TIPNIS) organizaran una marcha para protestar contra la construcción del tramo de una carretera que atravesaría su territorio. Esta movilización se convirtió en un conflicto de escala nacional e internacional, revelando contradicciones en la política interna de Evo Morales y en la política exterior boliviana. Las contradicciones entre la retórica indígena y ambientalista del presidente y su política nacional neoextrativista se quedaron evidentes. Por lo tanto, el estudio de caso del conflicto en el TIPNIS ilustra el enfrentamiento entre dos concepciones opuestas de organización socioeconómica del país: uno basado en el mantenimiento del capitalismo extractivista-exportador y otro que propone romper con la referida práctica secular y valorar de la convivencia entre el ser humano y la naturaleza, llamado buen vivir.

MADS-box genes are important regulators of reproductive development in seed plants, including both flowering plants and conifers. In this thesis the evolution of the AGAMOUS subfamily of MADS-box genes, and what the ancestral function of this group of genes might have been in the early seed plants about 300 million years ago, was addressed by the discovery of two novel conifer genes, both basal to all previously known AGAMOUS subfamily genes. DAL20, the most basal of these genes, was exclusively expressed in roots, unlike all previously known AGAMOUS subfamily genes. I also studied the evolutionary mechanisms leading to functional diversification of duplicated genes in two different subfamilies of MADS-box genes; the AGAMOUS and AGL6 subfamilies. Focus was on studying changes in gene expression pattern, representing changes in the transcriptional regulation between the genes, and on comparing the functional properties of the gene products, representing changes in the protein-coding sequence between the genes. Duplicated genes in the AGL6 subfamily were found to have evolved by both mechanisms. In the AGAMOUS subfamily I found duplicated spruce genes; DAL2 and DAL20, that appear to have functionally diversified mainly by changes in the transcriptional regulation. Conifer AGAMOUS subfamily genes were also used in a comparative developmental-genetics approach to evaluate hypotheses, based on the morphology of fossil and extant conifer seed cones, on the identity of the female reproductive organ, the ovuliferous scale, and the evolution of seed cone morphology in the conifer families Pinaceae, Taxodiaceae and Cupressaceae. Seed cones in these families have been hypothesized to have homologous ovule-bearing organs, but I found substantial differences in the expression patterns of orthologous AGAMOUS subfamily genes in seed cones of these families that are not compatible with this hypothesis, indicating that the evolutionary history of conifer seed cones is more diverse than previously thought.

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No ano de 2011, a Bolívia enfrentou um de seus conflitos sociais mais graves desde que Evo Morales assumiu a presidência do país em 2006. Os indígenas residentes no Parque Nacional e Território Indígena Isiboro Sécure (TIPNIS) organizaram uma marcha para protestar contra a construção do trecho de uma rodovia que atravessaria seu território. Tal mobilização se transformou em um conflito de amplitude nacional e internacional, pois evidenciou contradições na política interna de Evo Morales que se refletiram na política externa boliviana. As contradições entre a retórica ecologista e indigenista do presidente e sua política nacional neoextrativista ficam evidentes. Assim, o estudo de caso do conflito no TIPNIS ilustra o embate entre duas concepções opostas de organização socioeconômica do país: uma baseada na manutenção do capitalismo extrativista-exportador e outra que propõe a ruptura com essa prática secular e a valorização da convivência harmoniosa entre o ser humano e a natureza, denominada buen vivir. / In 2011, Bolivia faced one of its most serious social conflicts since Evo Morales became president of the country in 2006. The indigenous people resident in the National Park and Indigenous Territory Isiboro Sécure (TIPNIS) organized a march to protest against the construction of the stretch of a highway that would cross their territory. Such mobilization became a conflict of national and international scale, revealing contradictions in the internal politics of Evo Morales and reflecting in the Bolivian foreign policy. The contradictions among indigenous and environmentalist president’s rhetoric and his neoextractive national political became evident. Thus, the case study of the conflict in TIPNIS illustrates the clash between two opposite conceptions of socioeconomic organization of the country: one based on the maintenance of extractive capitalism and other proposing to break with this secular practice and to valorize harmonious coexistence between human being and nature, called buen vivir. / En 2011, Bolivia se enfrentó a uno de sus conflictos sociales más graves desde que Evo Morales asumió la presidencia del país en 2006. Los habitantes indígenas en el Parque Nacional y Territorio Indígena Isiboro Sécure (TIPNIS) organizaran una marcha para protestar contra la construcción del tramo de una carretera que atravesaría su territorio. Esta movilización se convirtió en un conflicto de escala nacional e internacional, revelando contradicciones en la política interna de Evo Morales y en la política exterior boliviana. Las contradicciones entre la retórica indígena y ambientalista del presidente y su política nacional neoextrativista se quedaron evidentes. Por lo tanto, el estudio de caso del conflicto en el TIPNIS ilustra el enfrentamiento entre dos concepciones opuestas de organización socioeconómica del país: uno basado en el mantenimiento del capitalismo extractivista-exportador y otro que propone romper con la referida práctica secular y valorar de la convivencia entre el ser humano y la naturaleza, llamado buen vivir.

No ano de 2011, a Bolívia enfrentou um de seus conflitos sociais mais graves desde que Evo Morales assumiu a presidência do país em 2006. Os indígenas residentes no Parque Nacional e Território Indígena Isiboro Sécure (TIPNIS) organizaram uma marcha para protestar contra a construção do trecho de uma rodovia que atravessaria seu território. Tal mobilização se transformou em um conflito de amplitude nacional e internacional, pois evidenciou contradições na política interna de Evo Morales que se refletiram na política externa boliviana. As contradições entre a retórica ecologista e indigenista do presidente e sua política nacional neoextrativista ficam evidentes. Assim, o estudo de caso do conflito no TIPNIS ilustra o embate entre duas concepções opostas de organização socioeconômica do país: uma baseada na manutenção do capitalismo extrativista-exportador e outra que propõe a ruptura com essa prática secular e a valorização da convivência harmoniosa entre o ser humano e a natureza, denominada buen vivir. / In 2011, Bolivia faced one of its most serious social conflicts since Evo Morales became president of the country in 2006. The indigenous people resident in the National Park and Indigenous Territory Isiboro Sécure (TIPNIS) organized a march to protest against the construction of the stretch of a highway that would cross their territory. Such mobilization became a conflict of national and international scale, revealing contradictions in the internal politics of Evo Morales and reflecting in the Bolivian foreign policy. The contradictions among indigenous and environmentalist president’s rhetoric and his neoextractive national political became evident. Thus, the case study of the conflict in TIPNIS illustrates the clash between two opposite conceptions of socioeconomic organization of the country: one based on the maintenance of extractive capitalism and other proposing to break with this secular practice and to valorize harmonious coexistence between human being and nature, called buen vivir. / En 2011, Bolivia se enfrentó a uno de sus conflictos sociales más graves desde que Evo Morales asumió la presidencia del país en 2006. Los habitantes indígenas en el Parque Nacional y Territorio Indígena Isiboro Sécure (TIPNIS) organizaran una marcha para protestar contra la construcción del tramo de una carretera que atravesaría su territorio. Esta movilización se convirtió en un conflicto de escala nacional e internacional, revelando contradicciones en la política interna de Evo Morales y en la política exterior boliviana. Las contradicciones entre la retórica indígena y ambientalista del presidente y su política nacional neoextrativista se quedaron evidentes. Por lo tanto, el estudio de caso del conflicto en el TIPNIS ilustra el enfrentamiento entre dos concepciones opuestas de organización socioeconómica del país: uno basado en el mantenimiento del capitalismo extractivista-exportador y otro que propone romper con la referida práctica secular y valorar de la convivencia entre el ser humano y la naturaleza, llamado buen vivir.

L’acide rétinoïque (AR) est le dérivé actif majeur de la vitamine A et a de multiples rôles au niveau cellulaire ainsi que pendant le développement. L’AR agit via deux familles de récepteurs nucléaires : les Récepteurs de l’Acide Rétinoïque (RAR) et les Récepteurs X des Rétinoïdes (RXR). Ces récepteurs sont des facteurs de transcription dépendants du ligand et leur activité est régulée par des phosphorylations via des kinases activées par l’AR. Durant ma thèse, je me suis intéressé à l’étude fonctionnelle et évolutive de la voie de l’AR et de la phosphorylation des RAR chez le poisson-zèbre Danio rerio. En étudiant l’activité des différents sous-types de RAR chez le poisson-zèbre, nous avons mis en avant qu’il existe une activité transcriptionnelle propre à chaque sous-type dans un embryon précoce de poisson-zèbre. De plus, mes travaux ont montré qu’au cours de l’évolution, l’acquisition d’un site de phosphorylation chez RARα permet une régulation fine de son activité chez les mammifères. Enfin, en étudiant les mécanismes moléculaires à l’origine de la diversification de la denture chez les poissons, mes travaux mettent en avant un rôle de la voie de l’AR dans la genèse de nouveaux traits phénotypiques. / Retinoic acid (RA) is the main active metabolite of vitamin A and plays multiple roles in cellular processes but also during embryonic development. RA acts through two families of nuclear receptors: Retinoic Acid Receptors (RAR) and Retinoid X Receptors (RXR). Those receptors act as ligand-dependent transcription factors and their transcriptional activity is also regulated by phosphorylation processes through kinases activated by RA. During my PhD, I focused on the functional and evolutionary study of RA pathway and of the phosphorylation of RARs using zebrafish (Danio rerio). By studying the activity of the different RAR subtypes in zebrafish, we provide evidences that they can regulate gene expression in a subtype-specific fashion in the early zebrafish embryo. Furthermore, my work showed that during evolution, the acquisition of a phosphorylated residue in RARα promotes the fine-tuned regulation of its activity in mammals. Finally, aiming at deciphering the molecular mechanisms behind dentition diversification in fish, we propose a role for RA signaling in generating morphological novel traits during evolution.

Esta tesis de máster trata del discurso de la política comercial del presidente de Bolivia Evo Morales, con respecto a la negociaciones del pilar comercial del Acuerdo de Asociación entre la Comunidad Andina y la Unión Europea. Mediante un análisis del discurso de Morales, se responde a las preguntas de cómo puede caracterizarse el discurso de Morales, en qué se fundamenta y qué fines estratégicos tiene. El hilo conductor del trabajo es que Bolivia tiene un presidente que representaría la imagen social de los pueblos originarios y cuando Europa propone un nuevo proyecto como el Acuerdo de Asociación, este proyecto sería percibido como neocolonialista, donde es Europa quien decide en los asuntos internos de su socio latinoamericano. Se analizan 23 declaraciones de Morales, concluyendo que las alusiones a la Colonización es la característica más central de su discurso y que este tema ha afectado la posición de Bolivia en las negociaciones.

Convergent evolution is a central theme in biology. Birds are an ideal system to examine the mechanisms underlying convergent evolution. Although bird patterning is diverse, within-feather patterns have repeatedly converged on the same four types: mottled patterns, scales, bars and spots. Other avian patterns occur, e.g. stripes, but are rare. In my thesis I examine the four main mechanisms underlying convergent evolution in plumage patterns: evolutionary genetics, evolutionary development, natural selection for signaling and camouflage. Japanese quail (Coturnix japonica) is a model system in developmental biology. Examining the developmental basis of pattern formation using molecular techniques, the dorsal patterning of embryonic quail is likely due to activation of the melanocortin-1 receptor, which is a highly conserved pathway in vertebrates. I examined whether a reaction-diffusion based theoretical model of pattern formation may predict developmental constraint in two groups that have different lifestyles and spectacular patterns: waterfowl (Anseriformes) and gamebirds (Galliformes). Tracing the evolutionary trajectory of pattern evolution with Bayesian comparative modeling there was evidence for developmental constraint in pattern evolution. Adaptive explanations may also result in convergence. Cuckoo-hawk mimicry has been demonstrated in the common cuckoo (Cuculus canorus) and the Eurasian sparrowhawk (Accipiter nisus), but may be prevalent in Old World cuckoos. Randomly selecting a parasitic cuckoo from each genera of Old World cuckoos and <8 sympatric raptors, I quantified their barred patterns using digital image analysis and found that parasitism can explain convergent evolution in the patterns of parasitic cuckoos and raptors. Patterns may have evolved due to ecological selection. Examining the patterns of 80% of all avian species worldwide, I found that habitat does not predict patterning, and that all four patterns are found in all habitats. These results demonstrate that the mechanisms of convergent evolution are diverse, and that development and natural selection have contributed to pattern evolution.

Nos ultimos anos o uso de tecnicas de aprendizado computacional tornou se uma das tarefas comumente realizadas, pois tem inumeras aplicacoes de reconhecimento de padroes, tais como: reco- nhecimento de voz, classificacao de texto, reconhecimento facial, diagnostico por imagens medicas, entre outras. Dessa forma, um grande numero de tecnicas que lidam com este tipo de problema tem sido desenvolvido ate o momento. Neste trabalho apresentamos uma alternativa para melhorar a taxa acerto de classificacao do classificador binario SLS, que apresentou resultados comparaveis com as SVMs. Nesse metodo, o Gradiente Descendente e utilizado para otimizar a posicao final dos conjuntos de segmentos de reta que representarao cada classe. Embora convirja rapidamente a um valor otimo, muitas vezes e possivel o algoritmo parar em uma regiao de otimos locais, que nao representa o minimo global. Dado esse problema, foram utilizados diferentes algoritmos evolutivos em combinacao com o Gradiente Descendente a fim de melhorar a acuracia do classificador SLS. Adicionalmente a aplicacao de algoritmos evolutivos na fase de treinamento do classificador SLS, foram exploradas duas propostas: (i) explorar o uso de diferente numero de segmentos de reta para representar a distribuicao de dados de cada classe. Dado que no algoritmo original do metodo SLS o numero de segmentos de reta e igual para cada classe, o qual pode significar alguma perda de acuracia ou sobreposicao dos segmentos de reta; (ii) estimar a melhor combinacao de segmentos de reta a serem usados para cada classe. O uso de diferentes quantidades de segmentos de reta por classe pode ser de ajuda na obtencao de melhores porcentagens de acerto, mas determinar uma quantidade otima que permita representar cada classe, e um trabalho dificil. Assim, usamos o algoritmo X-Means, que e um algoritmo de agrupamento, para estimar o numero de segmentos de reta. As propostas exibiram bons resultados que possibilitam a aplicacao do classificador SLS, com um algoritmo de treinamento hibrido, em problemas reais. / During the past years, the use of machine learning techniques have become into one of the most frequently performed tasks, due to the large amount of pattern recognition applications such as: voice recognition, text classification, face recognition, medical image diagnosis, among others. Thus, a great number of techniques dealing with this kind of problem have been developed until now. In this work, we propose an alternative training algorithm to improve the accuracy of the SLS binary Classifier, which produces good results that can be compared to Support Vector Machines. In that classifier, the Gradient Descent method has been used to optimize the final positions of two sets of straight line segments that represent each class. Although, this method quickly converges to an optimum, it is possible that the algorithm stops at a local optimum region, which does not guarantee a global minimum. Given that problem, we combine evolutive optimization algorithms with the gradient descent method to improve the accuracy of the SLS Classifier. In addition to our proposal of using evolutive algorithms, we also developed two proposals: (i) we explore the use of different number of straight line segments to represent the data distribution. Since the original SLS classifier algorithm uses the same number of segments for each class, which could lead to a loss of accuracy or straight line segments overlapping. So, using different number of segments could be the way to improve the accuracy; (ii) estimate the best combination of straight line segments to represent each class. Finding an optimal combination, can be a very difficult problem, so we propose the X-Means algorithm to determine the number of segments. The proposed methodology showed good results which can be used to solve some other real problems with the SLS classifier using the proposed hybrid training algorithm.

Les ascidies présentent des propriétés remarquables au sein des métazoaires qui en font un modèle particulièrement intéressant pour étudier le fonctionnement et l’évolution des éléments cis-régulateurs dans un contexte développemental. Ciona intestinalis et Phallusia mammillata, deux espèces d’ascidies qui ont divergé il y a environ 300 millions d’années, combinent une grande conservation de leurs processus développementaux avec une grande divergence de leur séquence génomique. Pour comprendre comment « fabriquer » des embryons similaires avec des génomes divergents, nous avons identifié les éléments cis-régulateurs actifs au cours du développement de Ciona intestinalis et Phallusia mammillata en développant et en appliquant la méthode de ChIP-Seq sur des modifications d’histones sur des jeunes gastrulae. La définition puis la validation fonctionnelle de différentes catégories d'éléments cis-régulateurs nous a permis de révéler quelques propriétés de la cis-régulation au sein de génomes compacts et intensément remaniés. En sus, les données que nous avons produites constituent une resource fonctionnelle unique pour la caractérisation des éléments cis-régulateurs chez les ascidies et l'étude de leur évolution au sein des Chordés. / Ascidians display remarkable features within metazoans making them particularly suited for the study of function and evolution of cis-regulatory elements in the context of embryonic development. Ciona intestinalis and Phallusia mammillata, two ascidian species that diverged about 300M years ago, combine high conservation of their developmental processes with high divergence of their genome sequence. To understand how to “make” similar embryos with divergent genomes, we identified active cis-regulatory elements during Ciona intestinalis and Phallusia mammillata development by developing and applying the ChIP-Seq method on histone modifications in early-gastrula embryos. Definition then functional validation of different categories of cis-regulatory elements led us to reveal some features of cis-regulation within compact and highly dynamic genomes. Together, our data constitute a unique functional resource for characterizing cis-regulatory elements in ascidians and questioning their evolution within the Chordates.