The dominantly held view in evolutionary theory focuses on gradual or punctuated change, primarily via natural selection, as the mechanism by which novel traits arise and evolution occurs. Noticeably absent from this portrayal of evolution is mention of the conservation of general characteristics, such as homologous morphological features or conserved nucleotide sequences, commonly observed across even distantly related groups at both the molecular and organismal levels. This raises at least the following questions: a) How does the evolution of conserved traits fit into an evolutionary theory that emphasizes change? b) What components of an evolving system provide the capacity for adaptation in spite of this apparent conservation of general traits? And c) How do these components affect the evolution of lineages? Here I suggest that heritable traits such as DNA methylation and histone modifications provide one place to look when addressing these questions. Current quantitative and population genetic models reflect the dominant view of evolution described above, and act as the foundation for both formal and informal descriptions and predictions of evolutionary change. Using results from recent work in molecular epigenetics, I consider the evolutionary implications for these traits, and show how current models of evolution fail to accurately capture this influence. In doing so, I also address some of the philosophical implications for how we conceptualize evolution, and what potential changes might be necessary for a more complete theory. / Master of Arts

This thesis analyzes the political, economic and social changes during the presidency of Evo Morales in Bolivia and Hugo Chávez in Venezuela. Its main goal is to find out whether Evo Morales follows Hugo Chávez directions and to compare the recent results of the applied reforms.

La thèse aborde le problème de l’évolution de la forme à travers l’exemple d’une différence de forme de branches ventrales mâles liée à l’isolement reproducteur chez deux espèces soeurs : Drosophila yakuba et Drosophila santomea. L’objectif de ce travail est d’identifier les gènes impliqués dans l’évolution de cette différence de forme ainsi que les causes évolutives de cette différence entre espèces. Dans une première partie, la thèse interroge la notion de “gène” et sa recherche. Puis sont caractérisées, dans un cadre formel, les questions de type "comment" et "pourquoi" et leur lien avec la distinction causes prochaines/causes ultimes ou évolutives. Ces réflexions philosophiques sont ensuite reliées à l’Evo-Devo et au projet expérimental. Dans la deuxième partie, par morphométrie géométrique et une nouvelle méthode de génotypage à haut débit, le MSG, nous identifions un locus de 2.7 méga-bases situé sur le chromosome 3L comme étant impliqué dans l’évolution de la forme des branches ventrales entre D. yakuba et D. santomea. Ces résultats sont mis en perspective avec notre analyse quantitative de la variation de forme dans plusieurs souches naturelles, souches de laboratoire et souches élevées à différentes températures qui apportent des indices sur les causes évolutives de cette différence de forme / The thesis tackles the problem of the evolution of shape through the example of a shape difference in the male ventral branches linked to reproductive isolation in two sister species: Drosophila yakuba and Drosophila santomea. The goal is to identify the genes involved in the evolution of this shape difference and the evolutionary causes of such difference. In a first part, the thesis interrogates the concept of “gene” and its search. Then are scientifically characterized the “how” and “why” questions and their link with the distinction of proximal/ultimate, or evolutionary, causes; these philosophical grounds are then linked to Evo-Devo and the experimental work presented in the thesis. In a second part, through geometric morphometrics and a new high-throughput genotyping method, MSG, we identify a loci of 2.7 mega-bases located on chromosome 3L as involved in the evolution of the shape of ventral branches between D. yakuba and D. santomea. These results are linked to our quantitative analysis of shape variation in multiple natural and laboratory strains and strains reared at different temperatures which bring light into the evolutionary causes of this shape difference

Submitted by Wellington Bittencourt dos Santos (biowell@hotmail.com) on 2017-09-25T20:45:01Z No. of bitstreams: 1 TESE VERSAO CORRIGIDA 11.09.17.pdf: 9731589 bytes, checksum: 9ad3be10d785ad17dd91e309980486e2 (MD5) / Approved for entry into archive by NUBIA OLIVEIRA (nubia.marilia@ufba.br) on 2017-12-06T19:43:04Z (GMT) No. of bitstreams: 1 TESE VERSAO CORRIGIDA 11.09.17.pdf: 9731589 bytes, checksum: 9ad3be10d785ad17dd91e309980486e2 (MD5) / Made available in DSpace on 2017-12-06T19:43:04Z (GMT). No. of bitstreams: 1 TESE VERSAO CORRIGIDA 11.09.17.pdf: 9731589 bytes, checksum: 9ad3be10d785ad17dd91e309980486e2 (MD5) / CAPES (que além de fornecer a minha bolsa regular de doutorado, também me contemplou com uma bolsa PDSE, que permitiu a realização do meu estágio de doutorado sanduíche na Sorbonne, Paris). / O objetivo do estudo aqui relatado se refere a uma análise de conteúdo realizado através do tratamento de redes conceituais. Buscamos analisar a relação entre ideias internalistas e externalistas na evo-devo, tal qual exposto nos livros técnicos do campo. Ferramentas computacionais analíticas foram utilizadas para gerar e investigar as redes conceituais, como uma forma de explorar o arcabouço conceitual subjacente aos discursos dos livros. As redes conceituais foram construídas a partir das conectividades estabelecidas entre os conceitos-chave, previamente selecionados e validados por especialistas em biologia evolutiva, evo-devo e filosofia da biologia. Estes conceitos-chave foram utilizados como indicadores das abordagens internalista e externalista nos livros analisados. Utilizamos diversas métricas da teoria das redes complexas para entender o papel dos conceitos na estrutura da rede. Essas métricas nos permitiram avaliar a centralidade dos conceitos em relação às conectividades estabelecidas na rede. Também realizamos a partição de redes em comunidades conceituais, formadas por conceitos que estão mais fortemente conectados entre si. Posteriormente, buscamos compreender como essas comunidades estão relacionadas com a homofilia (estabelecimento de vínculos com membros de uma mesma comunidade) e heterofilia (estabelecimento de vínculos com membros das outras comunidades) entre os conceitos que compõem as redes. A estruturação de redes dos quadros conceituais na evo-devo nos permitiu: (i) investigar possíveis integrações atuais entre o pensamento externalista, que prevaleceu na síntese evolucionária moderna, e o pensamento internalista, que tem sido importante na história das ideias evolutivas e tem novamente recebido mais atenção desde o surgimento da biologia evolutiva do desenvolvimento; (Ii) fornecer um quadro analítico útil do panorama atual da reestruturação teórica experimentada pela biologia evolutiva. / The objective of the study reported here is a content analysis performed by the treatment of conceptual networks. We seek to analyze a relationship between internal and external ideas in evo-devo, such as approaches in field technical books. Analytical computational tools used to generate and investigate as conceptual networks, as a form of exploration or conceptual framework underlying the discourses of books. The conceptual networks were constructed from selected key concepts that were validated by specialists in evolutionary biology, evo-devo and philosophy of biology. These key concepts were used as indicators of the internal and external approaches in the books analyzed. We use several metrics in complex network theory to understand the topologic structure of the conceptual network. These metrics are oriented towards the evaluation of a centrality of the concepts in relation to the connectivities established in the network. We also perform a network partition in conceptual communities, formed by concepts that are strongly connected to each other. Later, we looked at how these communities are related with the homophilia (heterogeneity of ties with members of the same community) and the heterophilia among the concepts that make up the networks. The structuration of conceptual frameworks in evo-devo makes it possible: (i) to investigate possible current integrations between externalist thinking, which prevailed in the modern evolutionary synthesis, and internalist thinking, which has been important in the history of evolutionary ideas and has gained more attention since the emergence of evolutionary developmental biology; (ii) to provide a useful analytical framework of the current panorama of theoretical restructuring experienced by evolutionary biology.

Le genre de plantes carnivores à Nepenthes comporte au moins 120 espèces, réparties dans le sud est asiatique avec les iles de Bornéo et de Sumatra comme centres d'endémisme et de diversité. Ce sont des lianes, dont les feuilles modifiées en urnes comportent un faisceau d'adaptations physicochimiques et morphologiques qui concourent à l'attraction, la capture et la digestion d'arthropodes. La très grande diversité morphologique du genre est couplé e à une diversité fonctionnelle : les mécanismes de rétention sont variables d'une espèce à l'autre. A côté de cette diversité interspécifique, certaines espèces voient la morphologie et le fonctionnement de leurs urnes se modifier au cours de leur ontogénie. Cette thèse fait le lien entre les mécanismes du piégeage et l'écologie de quelques espèces et l'histoire évolutive et de la diversification du genre. / The carnivorous genus encompasses at least 120 species mainly distributed in SE Asia with Borneo and Sumatra recognized as endemism and diversity centers. They are vines whose leaves modified as pitchers exhibit an array of morphological and physicochemical adaptations that compete to the attraction, the capture and the digestion of arthropods. Besides the great morphological diversity the genus comprises a functional diversity exists: retentive mechanisms vary between species and in some species pitcher morphologies and functioning can also change throughout ontogeny. This thesis attempts to describe the trapping mechanisms and the ecology of some species to the evolutionary history of the diversification of the genus.

Le but de toute étude en biologie évolutive du développement est l’étude des mécanismes développementaux à l’origine des diversifications morphologiques. Dans ce contexte, j’ai décidé de me focaliser sur l’émergence des Vertébrés au cours de l’évolution, par la mise en œuvre d’études comparatives entre différents modèles de Deutérostomiens. Le travail réalisé durant ma thèse est subdivisé en trois projets: (i) j’ai abordé le lien entre l’évolution du cerveau chez les Chordés et les modifications de la signalisation à l’acide rétinoïque (AR) au cours du développement. En particulier, j’ai examiné les rôles de l’AR au cours du développement du cerveau chez la lamproie Lampetra fluviatilis, et j’ai comparé les résultats obtenus chez cette espèce aux mécanismes développementaux agissant chez l’amphioxus, un Chordé invertébré, et chez les modèles gnathostomes classiques. Les données obtenues lors de ces analyses comparatives ont permis une meilleure compréhension de l’évolution de la régionalisation cérébrale chez les Vertébrés. (ii) j’ai étudié l’évolution des séquences régulatrices présentes au sein des clusters de gènes hox, connus pour agir dans la régionalisation du système nerveux des Chordés. L’identification d’éléments non-codants conservés ainsi que d’éléments de réponse à l’AR (RARE) potentiels dans des clusters hox de Chordés, combinée à la caractérisation de RAREs in vivo en cellules murines a permis une vision intégrée de l’évolution du contrôle des gènes hox par l’AR, chez les Chordés. (iii) j’ai analysé l’évolution des microARNs chez les Chordés en comparant les répertoires microARN chez plusieurs espèces de Deutérostomiens. Cette étude a permis d’émettre de nouvelles hypothèses quant à l’émergence des microARNs chez les animaux. Toutes ces analyses ont abordé différents aspects de l’évolution des Chordés avec pour objectif la proposition d’une vision intégrée des mécanismes moléculaires à l’origine de l’émergence des Vertébrés. / The aim of the evolutionary developmental biology is to study the developmental mechanisms at the base of morphological diversification. In this context, I decided to focus my attention on the emergence of vertebrates during evolution by carrying out comparative analyses in several deuterostome models. The work carried out during of my thesis can be subdivided into three major projects: (i) I addressed the link between brain evolution and modifications in retinoic acid (RA) signaling during chordate development. In particular, I investigated the roles of RA signaling in brain development in a jawless vertebrate, the lamprey Lampetra fluviatilis, and compared the results with developmental mechanisms in the invertebrate chordate amphioxus and classical developmental model systems in jawed vertebrates. Data obtained from these comparative studies provided insights into the evolution of brain patterning in vertebrate evolution. (ii) I investigated the evolution of the regulatory landscape of hox gene clusters that are known to be fundamental for the patterning of the chordate central nervous system. The identification of conserved non-coding elements and putative RA response elements (RAREs) in hox clusters of different chordate species combined with the in vivo characterization of functional RAREs in mouse F9 cells provided an integrated view of the evolution of RA-dependent hox cluster regulation in chordates. (iii) I studied the roles of microRNAs (miRNAs) in chordate evolution by comparing the miRNA complements of different deuterostome species. This analysis provided novel insights about the general mechanisms of miRNA emergence in animals and highlighted species-specific miRNA complement amplifications in different deuterostome lineages. In sum, these studies have tackled different aspects of chordate evolution from an evo-devo perspective, aiming at an integrated view of the molecular mechanisms underlying vertebrate diversification.

L’espèce Astyanax mexicanus est composée de deux morphotypes de poissons radicalement différents : le très classique poisson de surface vivant dans des rivières et le poisson cavernicole (CF, cavefish) aveugle et dépigmenté. Ces deux morphotypes diffèrent sur de nombreux aspects, aussi bien en termes de modalités sensorielles, qu’en termes de physiologie ou de comportement. L’approche « Evo-Devo » consiste à tenter de relier des différences développementales précoces à des modifications phénotypiques plus tardives. Dans le cadre de ce travail, nous nous sommes concentrés sur les modifications précoces de l’hypothalamus et de l’œil du CF. Nous montrons que des modifications précoces de signalisation de morphogènes tels que Shh ou Fgf conduisent à une modification de la taille des groupes de neurones peptidergiques au sein de l’hypothalamus, via les facteurs de transcription Lhx, impliqués dans la spécification neuronale. Plus particulièrement, nous montrons l’augmentation de taille des groupes de neurones NPY ainsi qu’hypocretine, qui à son tour provoque une réduction du sommeil chez le CF.Nous nous sommes aussi intéressés à l’oeil du CF, qui commence par se développer avant de dégénérer. Une réduction du quadrant ventral de la rétine avait été précédemment décrit. Nous rafinons cette description grâce à une étude de la régionalisation de la coupe optique du CF qui suggère une réduction de la rétine temporale plus spécifiquement. Nous proposons également une première description de la morphogénèse de l’oeil du CF grace à l’imagerie live de lignées transgéniques fluorescentes. Cette étude révèle un défaut d’invagination de la coupe optique chez le CF. Globalement, ce travail ouvre la voie vers une meilleure compréhension de l’évolution de la tête du CF. / Astyanax mexicanus is a fish species comprising two strikingly different morphotypes : the classical river-dwelling surface fish and the blind depigmented cavefish. These two morphs differ in many aspects in terms of sensorial modalities, physiology and behaviour. In the Evo-Devo approach, we try to link early developmental differences to later phenotypic modifications. Here we focus on the early modification of the hypothalamus and the eye of the cavefish. We show that early signalling modification of morphogens such as Shh or Fgfs lead to the modification of neuropeptidergic clusters in the hypothalamus via the neuronal fate-specifying transcription factors Lhx. More particularly, we show an increase in NPY and hypocretin cluster size. In turn, this increased hypocretin cluster size triggers a reduction of sleep in the cavefish larva.We also examine the embryonic eye of the cavefish which first develops before degenerating. This eye was previously reported to have a reduced ventral retina. We refine this description by studying the regionalisation of the cavefish optic cup and suggest that this reduction concerns more specifically the temporal retina. We also attempt a first description of the cavefish eye morphogenesis by live imaging on fluorescent transgenic lines. This description reveals a defect in the optic cup invagination of the cavefish. Overall, this work started deciphering the developmental evolution of the cavefish head.

Submitted by VANDA MARIA MARTINS SOUTO (vandammsouto@hotmail.com) on 2018-09-28T20:07:33Z No. of bitstreams: 1 Microsoft Word - TESE UNESP -VANDA MARIA MARTINS SOUTO.pdf: 12642348 bytes, checksum: 08b277c85bf6a924b1f33cb0f8a73f9d (MD5) / Approved for entry into archive by Satie Tagara (satie@marilia.unesp.br) on 2018-10-01T13:46:56Z (GMT) No. of bitstreams: 1 souto_vmm_dr_mar.pdf: 12642348 bytes, checksum: 08b277c85bf6a924b1f33cb0f8a73f9d (MD5) / Made available in DSpace on 2018-10-01T13:46:56Z (GMT). No. of bitstreams: 1 souto_vmm_dr_mar.pdf: 12642348 bytes, checksum: 08b277c85bf6a924b1f33cb0f8a73f9d (MD5) Previous issue date: 2018-08-28 / Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A presente tese pretende discutir a política externa brasileira dos governos do ex-presidente Luís Inácio Lula da Silva (2003-2010), com ênfase na relação entre o Brasil e a Bolívia. A partir do dado de que a Bolívia é um país de economia dependente e possui uma massa de trabalhadores desempregados, levanta-se a seguinte questão: haveria na relação entre os dois países uma espécie de subimperialismo manifestado a partir da transnacionalização de empresas brasileiras, tendo como um de seus mecanismos um processo de dependência e superexploração do trabalho na Bolívia? Trata-se de uma pesquisa histórico-concreta que se articula, teórica e metodologicamente, com uma literatura construída a partir do complexo categorial do que o campo das Ciências Sociais reconhece como “materialismo históricodialético”. O estudo resulta da análise dos documentos do Arquivo Histórico do Itamaraty, do Ministério das Relações Exteriores, do Banco Nacional do Desenvolvimento (BNDES) e da Petrobras. Tem como objetivo mensurar os embates da política externa brasileira com base nas obras executadas pelas multinacionais com financiamento do BNDES, além de debater o papel da Petrobras diante da nacionalização dos hidrocarbonetos na Bolívia. Apresenta-se, aqui, o resultado da pesquisa, relacionando-o com as leituras da teoria de Ruy Mauro Marini, e sustenta-se a tese de que o subimperialismo tem sua origem nas leis próprias da economia dependente, cujos fundamentos são a superexploração do trabalho e a transferência de valor. A partir do estudo da política externa brasileira, o trabalho em tela lança luzes sobre a caracterização da política externa brasileira em relação a Bolívia, o que poderá servir de parâmetro para uma crítica atual do capitalismo na América do Sul. Desse modo, foram mensuradas as variantes da relação bilateral e analisados os contextos mais gerais de cada um dos países, percebendo que a história é sempre forjada em lutas, conflitos e disputas de interesse. Ao fim e ao cabo, a relação estudada foi determinada por uma dialética entre as correlações de forças internas das nações em questão. De fato o que se pode mensurar foi à expansão do capital monopolista imperialista no continente latino-americano, incluindo setores da burguesia brasileira. Pode-se dizer, portanto, que a correlação de forças internas de cada país configurou um cenário em que, embora com todos os elementos apontando para tal, não se pode falar de subimperialismo do Brasil com relação à Bolívia entre 2003 e 2010, mas que a política externa brasileira, voltada para a integração regional econômica, foi adequada para a expansão do capital imperialista. / This thesis aims to discuss the Brazilian foreign policy of former president Luís Inácio Lula da Silva (2003-2010), with emphasis on the relationship between Brazil and Bolivia. Given the fact that Bolivia is a dependent economy and has a number of unemployed workers, the following question arises: would there be in the relationship between the two countries a sort of sub-imperialism manifested by the transnationalization of Brazilian companies, based on mechanisms dependency of labor overexploitation in Bolivia? It is a historical-concrete research that articulates, theoretically and methodologically, a literature built from the categorial complex called by the Social Sciences "historical-dialectical materialism". The study results from the analysis of the documents of the Itamaraty Historical Archive, the Ministry of Foreign Affairs, the National Development Bank (BNDES) and State Oil Company (Petrobras). Its objective is to measure the conflicts of Brazilian foreign policy based on the works executed by the multinationals and funded by BNDES, in addition to discussing Petrobras' role in the nationalization of hydrocarbons in Bolivia. The results of the research are presented here, relating it to the readings of Ruy Mauro Marini's theory, and we hold the thesis that sub-imperialism has its origin in the own laws of the dependent economy, whose foundations are the overexploration of labor and the transfer of value. From the study of Brazilian foreign policy, the work on the screen brings light to the characterization of Brazilian foreign policy towards Bolivia, which may serve as a parameter for a current critique of capitalism in South America. In this way, the variants of the bilateral relationship were measured and analyzed the more general contexts of each country, realizing that history is always forged in struggles, conflicts and disputes of interest. The relation studied was determined by a dialectical relation between the internal correlation of forces in the nations in question. In fact, what can be measured was the expansion of imperialist monopoly capital in the Latin American continent, including sectors of the Brazilian bourgeoisie. It can be said, therefore, that the internal correlation of forces of each country has set up a scenario in which, although with all the elements pointing to it, one can not speak of Brazil's sub-imperialism in relation to Bolivia between 2003 and 2010, in this way, Brazilian foreign policy focused on regional economic integration was adequate for the expansion of imperialist capital. / El presente trabajo busca discutir la política externa brasileña de los gobiernos del ex Presidente Luís Inácio Lula da Silva (2003-2010), destacando la relación entre Brasil y Bolivia. A partir del hecho de que Bolivia es un país de economía dependiente y posee una masa de trabajadores desempleados, se coloca la siguiente cuestión: ¿habría en la relación entre los dos países una especie de subimperialismo manifestado a partir de la transnacionalización de empresas brasileñas, teniendo como uno de sus mecanismos un proceso de dependencia superexplotación del trabajo en Bolivia? Se trata de una investigación histórico-concreta articulada, teórica y metodológicamente, con una literatura construirá a partir del complejo categorial que en el campo de las ciencias sociales se reconoce como “materialismo histórico-dialectico”. El estudio resulta del análisis de documentos del Arquivo Histórico del Itamaraty, del Ministério de Relações Exteriores, del Banco Nacional de Desenvolvmento (BNDES) y de la Petrobras. El objetivo es mensurar los embates de la política externa brasileña a partir de las obras ejecutadas por las multinacionales con el financiamiento del BNDES, además de discutir el papel de la Petrobras frente a la nacionalización de los hidrocarburos en Bolivia. Se presenta, aquí, el resultado de la investigación, relacionándolo con las lecturas de la teoría de Ruy Mauro Marini, y sustentando la tesis de que el subimperialismo se origina en las leyes propias de la economía dependiente, cuyos fundamentos son la superexplotación del trabajo y la transferencia de valor. A partir del estudio de la política externa brasileña, el trabajo contribuye para la caracterización de la política externa brasileña con relación a Bolivia, lo que podrá servir de parámetro para una crítica actual del capitalismo en América del Sur. De esta manera, fueron mensuradas las variantes de la relación bilateral y analizados los contextos más generales de cada uno de los países, percibiendo que la historia es siempre forjada en luchas, conflictos y disputas de interese. Al fin y al cabo, la relación estudiada fue determinada por una dialéctica entre las correlaciones de fuerzas internas de las naciones en cuestión. De hecho lo que se puede medir fue a la expansión del capital monopolista imperialista en el continente latinoamericano, incluyendo sectores de la burguesía brasileña. Se puede decir, por lotanto, que la correlación de fuerzas internas de cada país ha configurado un escenario en que no se pueda hablar de subimperialismo de Brasil con relación a Bolivia entre 2003 y 2010, entretanto la política exterior brasileña, orientada hacia la integración regional económica, fue adecuada para la expansión del capital imperialista.

The main theme of the thesis is the influence of the ascending indigenous movement on the international position of the states Bolivia and Peru. Based on the analysis of internal changes and through comparison of both countries from the perspective of the international environment, the work tries to answer whether the international environment reflects these internal changes or not. For comparison are used the attitudes of regional economic and political partners, as well as USA and European Union and four non-governmental organizations. The work contains the history of indigenous peoples in the territory of Bolivia and Peru, the internal changes under the government of Evo Morales in Bolivia and APRA government in Peru.

Thesis (M.A.)--University of California, San Diego, 2009. / Title from first page of PDF file (viewed September 17, 2009). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 80-83).