L'observation des nombreuses espèces au sein des métazoaires permet de rendre compte de leur formidable diversité de morphologies. Ces organismes complexes acquièrent leur plan d'organisation et leurs caractéristiques propres pendant le développement embryonnaire. Au cours de celui-ci, la morphogénèse des différentes structures anatomiques est contrôlée par des réseaux complexes de gènes intervenant dans des territoires et des moments précis. Comprendre quelles modifications des voies développementales au cours de l'évolution sont responsables de cette diversité constitue un champ important de la biologie moderne : l'évo-dévo. Pour comprendre ces modifications, il est important de pouvoir étudier ces changements sur des modèles facilement accessibles et qui possèdent une grande variabilité de formes. Les phanères des vertébrés répondent à ces critères : leur nombre, leur forme et leur taille ont été des caractères très variables au cours de la diversification des mammifères et les données déjà obtenues sur la souris permettent une expérimentation aisée. De nombreuses voies de signalisation sont impliquées dans le développement des phanères, mais une en particulier, impliquée spécifiquement dans le développement des appendices ectodermiques : la voie EDA, composée d'un ligand EDA, de son récepteur EDAR et d'un adaptateur spécifique EDARADD. Dans le but de mieux comprendre le rôle de la voie EDA au cours de l’évolution des mammifères, nous avons orienté ma thèse en 2 axes : le premier vise à étudier le rôle d’Edar dans le patterning de la dent chez la souris, et le second l’impact de la perte d’une des deux isoformes d’EDARADD au cours de l’évolution des mammifères. / The observation of the numerous metazoan species highlights their wonderful morphological diversity. These complex organisms got their body plan and their specific traits during embryonic development. During development, complex gene networks that are tightly regulated through space and time, control morphogenesis. Understanding which modifications of developmental pathways are responsible for the establishment of this diversity is one of the key questions of the biological field: Evo-Devo. To understand these modifications, it is crucial to study accessible models that are representative of this diversity. To do that, ectodermal appendages are a very good model: their number, size, and shape are highly variable during mammals diversification and data had already shown that they exhibit natural variation. Numerous signaling pathways are implicated in their development but one is very specific to them: the Eda pathway and present an big interest for the study of their evolution. To better understand the role of the Eda pathway during mammals evolution, I orientated my thesis in two part: the first one study the impact of Edar in the establishment of the mouse dental tooth row and the second the impact of gain/loss of protein isoforms of the adaptor Edaradd on the evolution of this pathway.

Submitted by Ricardo Cedraz Duque Moliterno (ricardo.moliterno@uefs.br) on 2017-10-16T21:15:42Z No. of bitstreams: 1 ANA NERY DISSERTAC?O 19.11.16_Disserta??o_Ana Nery_Arquivo completo (1)-2.pdf: 3023409 bytes, checksum: 9ffa76f7e2e79ced18b4ef96755be054 (MD5) / Made available in DSpace on 2017-10-16T21:15:42Z (GMT). No. of bitstreams: 1 ANA NERY DISSERTAC?O 19.11.16_Disserta??o_Ana Nery_Arquivo completo (1)-2.pdf: 3023409 bytes, checksum: 9ffa76f7e2e79ced18b4ef96755be054 (MD5) Previous issue date: 2016-08-29 / This dissertation analyzes the Festa de Reis (Feast of Kings) in the city of Concei??o do Coit?, Bahia, between the years 1965 to 2005, focusing on the performance of the Reisado de Cabaceiras Group in a rural community located in this municipality. The proposed research sought to identify the changes and permanence during the festivities, as well as to understand the reasons and instruments used by the ?sambadores? (samba dancers) for these changes to occur, how they are being perceived and experienced by the population that participated in the feast, and how the residents of the Cabaceiras community understood and participated in the reinvention process. In addition, it seeks to understand new meanings and appropriations of other forms of religiosity, such as the interreligious dialogue between the religion of African matrices and the Catholic tradition, which makes it plural in relation to other celebrations in praise of the Holy Kings in the interior of Bahia state. We analyze aspects between the sacred and the profane, besides observing conflicts and divergences between the revelers and the municipal authorities. For that, the narratives of these residents and participants, audiovisual records and written sources were primordial methodological resources, in order to understand the peculiarities of this Christmas party. The work intends to contribute to an analysis of the practices of the feast as an expression of popular religiosity, focusing on the dynamics of the Reisado de Cabaceiras Group, its trajectory and its insertion in the urban spaces of the city of Concei??o do Coit? and Sisaleira Region. / Esta disserta??o analisa a Festa de Reis em Concei??o do Coit? (BA), entre os anos de 1965 a 2005, focando-se na atua??o do Grupo Reisado de Cabaceiras em uma comunidade rural localizada neste munic?pio. A pesquisa proposta buscou identificar as mudan?as e as perman?ncias ocorridas na festa, bem como entender quais os motivos e os instrumentos utilizados pelos sambadores para que essas mudan?as acontecessem, como elas est?o sendo percebidas e vivenciadas pela popula??o que participava da festa e como os moradores da comunidade de Cabaceiras entenderam e participaram do processo de reinven??o. Al?m disso, compreender novos significados e apropria??es de outras formas de religiosidades, a exemplo do di?logo inter-religioso entre as Religi?es de Matrizes Africanas e a tradi??o cat?lica nas festas em louvor aos Santos Reis no interior baiano. Analisamos aspectos da rela??o entre o sagrado e o profano, al?m de observar conflitos e diverg?ncias entre os festeiros e as autoridades municipais. Para tanto, as narrativas desses moradores e participantes, registros audiovisuais e fontes escritas foram recursos metodol?gicos primordiais, a fim de compreender as peculiaridades dessa festa natalina. O trabalho pretende contribuir para uma an?lise das pr?ticas da festa como express?o da religiosidade popular, enfocando a din?mica do Grupo Reisado de Cabaceiras, sua trajet?ria e sua inser??o nos espa?os urbanos da cidade de Concei??o do Coit? e da Regi?o Sisaleira.

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.

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.

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.

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.

No description available.

No description available.

This dissertation clarifies the concept of evolvability, the increased capacity of some organisms or systems to support evolution, especially the evolution of life-like complexity. I survey the literature, which is spread over the fields of population genetics, developmental biology, artificial life, and microbial and molecular evolution. Finding that researchers have often used the term vaguely and incompatibly I identify five distinct kinds or senses of evolvability. I also identify five key constituent ideas, which I discuss in the context of organismic evolvability, a sense of evolvability with deep roots in the traditional fields of animal development and macroevolution. In these fields research into evolvability has historically been hampered by an insufficiently detailed knowledge of development. Research in molecular evolution has produced a thorough knowledge of the folding of RNA into secondary structure, which can be regarded as a model of development. This has motivated new approaches to evolvability based on representing development via a single genotype-phenotype mapping function. I build on these approaches to invent new mathematical methods to formalise the traditional ideas. I create an exact model illustrating a classic example of evolvability, the capacity for repeated segmentation and simple modularity. I analyse this with two new formal approaches. First is the genospace algebra, a propositional calculus based on graph theory. It is a formal language for describing genotype-phenotype maps. It provides a system for making calculations, proofs, and diagrams about mutational structures in genotype space, and it is flexible enough to allow description at arbitrary degrees of resolution. Second is a pair of concepts, the genetic leverage and the genetic fulcrum. The leverage provides a crude numerical measure of evolvability, and the fulcrum provides a heuristic for identifying the genomic and developmental causes of evolvability. Besides its specific relevance to diversification and development, evolvability is also crucial to the fundamental question of how evolution produces ordinary biological life. Simulation systems that implement only a conventional textbook model of evolution -– systems possessing only variation, inheritance, and selection –- fail to evolve anything resembling the complexity of the biological world. Research into evolvability is our best bet to illuminate the "missing ingredient" for life-like evolution.

A major goal of evolutionary developmental biology is to explore mechanisms and events underlying evolution of the myriad body plan morphologies expressed both genetically and phenotypically within the animal kingdom. Arthropods exhibit an astounding array of morphological diversity both within and between representative sub-phyla, thus providing an ideal phylum through which to address questions of body plan innovation and diversification. Major arthropod groups are recognised and defined by the distinct form and number of articulated appendages present along the antero-posterior axis of their segmented bodies. A great deal is known about the developmental genetics of limb development in the model insect Drosophila melanogaster, added to which, much comparative gene expression data and a growing body of functional genetic data is emerging for other arthropod species. Arthropod limb primordia are consistently marked by expression of the homeobox gene Distal-less (Dll), and the focus of this thesis is to compare signalling mediated by early Dll regulatory genes activity along antero-posterior and dorso-ventral embryonic axes during limb specification in Drosophila, with the activity of their orthologs in the widely disparate chelicerate, the spider mite Tetranychus urticae - interpreting new data with that available for other arthropods. Having made a detailed study of spider mite embryonic (and post-embryonic) development, to provide a basis for understanding mRNA transcription and protein activity patterns, I confirmed typical expression of Tetranychus Dll in prosomal limb primordia. I obtained limited results for the candidate antero-posterior positioning genes wingless and engrailed, although one of the two engrailed paralogs I identified is reportedly expressed in posterior segmental compartments, consistent with possible conservation of Engrailed-Wingless interactions in metameric patterning and positive regulation of Dll in arthropod limb specification. In Drosophila, wingless-dependent Dll transcription is restricted along the dorso-ventral axis by dorsal Dpp-mediated and ventral EGFR-mediated signalling gradients. Based on data from Tetranychus and other arthropods, neither dorsal nor ventral signalling regimes appear conserved outside the Drosophila system. Dll suppression in fly abdominal segments occurs due to powerful Hox (Ubx/AbdA) repression of the early Dll cis-regulatory element; this is discussed in relation to the independently evolved limbless chelicerate opisthosoma, informed by hypothetical scenarios of cis (regulatory DNA) and trans (coding sequence) evolution. Given practical difficulties and limitations encountered while working with spider mites, I offer a final assessment of the place of Tetranychus urticae as a non-model, and yet still valuable chelicerate species to consider carrying into the exciting future of evolutionary developmental biology.