Dans le domaine des plantes, la formation de la fleur a été un pas crucial dans la capacité des végétaux à coloniser une grande diversité de niches écologiques sur notre planète. Les deux espèces Petunia x hybrida et Arabidopsis thaliana représentent deux groupes majeurs des plantes à fleur. Nous avons montré que les gènes à homéodomaine d’une famille appelée WOX (Wuschel homeobOX) sont fortement impliqués dans le développement des organes dotés de polarité (dont les feuilles et des organes de la fleur : sépales, pétales, carpelles). Un double mutant (maw mawb), chez le Pétunia, développe des pétales en forme de filament, avec disparition du tube floral. De plus, nous avons découvert que ces mêmes gènes interagissent au niveau génétique avec d’autres gènes (appelés gènes à boite MADS) dans la formation des ovules, structures à partir desquelles les graines se forment. Nous avons aussi montré que des gènes de la même famille sont impliqués dans la formation d’autres structures chez le Pétunia : les trichomes ou poils aériens de surface. Ces derniers sont impliqués dans plusieurs taches, qui vont de la protection contre les pathogènes à celles contre les stress abiotiques. Grâce à des études de génétique fonctionnelle nous avons pu montrer un recrutement différentiel des gènes WOX ici étudiés, dépendant de l’organe et de l’espèce. Ces travaux de thèse montrent l’importance de cette famille génique pour les études d’evo-devo (Biologie Evolutionniste du Développement). Finalement, une analyse de RNA-Seq (séquençage du transcriptome), dévoile les réseaux génétiques contrôlés par ces gènes WOX. / In the Kingdom of Plants, the emergence of flowers was a crucial step in their ability to colonize a large variety of ecological niches on our planet. The two species Petunia x hybrida and Arabidopsis thaliana represent two major groups of flowering plants. In this work, we have shown that HOMEOBOX genes from the WOX family (Wuschel homeoboxes) are heavily involved in polar organ development (such as leaves and sepals, petals, and carpels at the flower level). The maw mawb double mutant in Petunia displays string-like petals, with consequent disappearance of the floral tube. Moreover, we found that these two genes genetically interact with genes from a different family (the MADS family) in ovule identity (ovules are the structures from which seeds develop). We have also shown that other genes from the WOX family are involved in development of a different kind of structures in Petunia: the trichomes. Trichomes are involved in different tasks, protecting the plant from pathogens or abiotic stress. Thanks to functional genetics studies, we have shown functional genetic recruitment of these WOX genes among different plant organs and among different species. This PhD thesis provides evidence for the importance of the WOX family in Evo-Devo studies. Eventually, we unravelled genetic networks controlled by MAW and MAWB trough RNA-Seq analysis.

L’évolution de la dentition des mammifères se caractérise par d’importantes innovations morphologiques comme la mise à occlusion et l’hétérodontie. Parmi rongeurs, dont la formule dentaire est fortement réduite, les arvicolinés possèdent une dentition hautement dérivée, avec des molaires prismatiques et hypsodontes. L’objectif de cette thèse est d’explorer les différentes innovations morphologiques de la dentition au travers des aspects développementaux et adaptatifs. Les méthodes de morphométrie géométrique sont utilisées sur les molaires, les incisives et les mandibules afin d’explorer les dynamiques de développement et d’évolution de la dentition. Un modèle développemental permettant de prédire les proportions de molaires inférieures est examiné et validé à l’échelle de l’ordre des rongeurs ; il peut également être étendu à la prémolaire. De plus, le lien entre la morphologie dentaire, notamment les proportions de molaires, et le régime alimentaire est complexe, un caractère morphologique ne reflétant pas directement une alimentation. Cependant les covariations entre les molaires marquent le mouvement de mastication et ainsi la fonction. Nos résultats confirment une imbrication complexe des contraintes historiques, fonctionnelles et développementales dans l’interprétation des morphologies. Les différentes composantes de la mandibule présentent une organisation hiérarchique complexe. Le développement de la dentition des mammifères est gouverné par des processus similaires mais des mécanismes tels que l’hétérochronie ont pu conduire à une diversification des phénotypes au cours du temps. / The evolution of mammalian dentition is defined by profound morphological modifications as occlusion and heterodonty. Among rodents, characterized by a reduced dental formula, arvicolines have a highly derived dentition, with prismatic and hypsodont molars. The aim of this Ph.D thesis is to explore various morphological innovations through developmental and adaptive aspects. Geometric morphometric methods were used on molars, incisors and mandibles to investigate the dynamics of development and evolution of dentition. A developmental model predicting molar proportions is tested and confirmed for the rodent order; it could be also extended to the premolar. The relationship between dental morphology, in particular molar proportions, and diet is complex, diet being not directly inferred from one morphological trait. Yet, covariations between molars inform on masticatory movement and thus on function. Our results confirmed that morphologies could be understood from a complex combination of historical, functional and developmental constraints. The various structures of the mandible have a complex hierarchical organization. The development of mammalian dentition is controlled by similar processes but through times, mechanisms as heterochrony may lead to a diversification of phenotypes.

Evolution of developmental genes is an important mechanism for plant morphological evolution. The LRL genes are an ancient group of bHLH transcription factors that positively regulate root hair development in angiosperms. Here I show that, in the moss Physcomitrella patens, two LRL genes are present and they positively regulate rhizoid and caulonema (a rhizoid-like cell type) development. GUS-transcriptional reporter plants show that both PpLRL1 and PpLRL2 are expressed in tissues giving rise to caulonemata. Loss-of-function mutants in either PpLRL1 or PpLRL2 led to defective rhizoid and caulonema development, and the Pplrl1 Pplrl2 double loss-of-function mutants completely lack rhizoids and caulonemata. Consistent with this, gain-of-function mutants show enhanced rhizoid and caulonema development. In addition, I show that the stimulatory effects of auxin and low phosphate on the development of rhizoids and/or caulonemata required PpLRL gene function. Together, these results show that LRL genes are conserved, positive regulators in tip-growing rooting cell development in land plants. To elucidate whether LRL genes belong to part of a conserved gene network, I use qRT-PCR to determine the transcriptional interaction between LRL genes and the Class I RSL genes, which is another group of conserved regulators of rhizoids and root hairs. Comparing the LRL-RSL network between P. patens and A. thaliana reveals that LRL and Class I RSL genes are transcriptionally independent of each other in P. patens but one LRL gene is transcriptionally downstream of Class I RSL genes in A. thaliana. This suggests that the gene network controlling tip-growing rooting cell development has changed since mosses and angiosperms last shared a common ancestor.

The homeobox superfamily is one of the most significant gene families in the evolution of developmental processes in animals. Within this superfamily the ANTP class has expanded exclusively in animals and, therefore, the reconstruction of its origin and diversification into the different ‘modern' families have become prominent questions in the ‘evo-devo' field. The current burgeoning availability of animal genome sequences is improving the resolution of these questions, putting them in a genome evolution context, as well as providing the field with a large, detailed and diverse catalogue of animal homeobox complements. Here I have contributed with a new hypothesis on the origin and evolution of the Hox and ParaHox loci and the new term, ghost loci, referring to homologous genome regions that have lost their homeobox genes. This hypothesis proposes that the last common ancestor of all animals had a much more complex genome (i.e. differentiated Hox, ParaHox and NK loci) that underwent a simplification in the early animal lineages of sponges and placozoans. In collaboration with the Adamska group I resolved the orthology of the first ever ParaHox genes reported in calcareous sponges. This finding serves as an independent confirmation of the ghost loci hypothesis and further resolves the events of secondary simplification within the sponge lineage. Finally, I have catalogued the homeobox complement of the newly sequenced arthropod, the myriapod Strigamia maritima, and examined the linkage and clustering of these genes. This has furthered our understanding of the evolution of the ANTP class. The diversity of the homeobox complement and the retention in this myriapod and the retention of some homeobox genes not previously described within arthropods, in combination with the interesting phylogenetic position that this lineage occupies relative to other arthropods, makes this complement an important point of reference for comparison within the arthropods and in a broader perspective in the ecdyzosoans. These findings have provided significant further insights into the origin and evolution of the homeobox superfamily, with important implications for animal evolution and the evolution of development.

L’origine des symétries et des polarités est l’un des thèmes centraux de l’évolution animale. Classiquement considérée comme une innovation propre aux animaux à symétrie bilatérale (Bilateria), la bilatéralité est en fait très largement répandue chez les cnidaires, groupe-frère des Bilateria, principalement au sein de la classe des anthozoaires. La découverte que la voie BMP étai différentiellement exprimé selon l’axe secondaire de N. vectensis a fait que sur la base d’arguments moléculaires certains travaux postulent que la bilatéralité est antérieure à la divergence cnidaires/bilateria (Finnerty et al. 2004, Matus et al. 2006), alors que d’autres chercheurs mettent en avant l’hypothèse d’une convergence sur la base d’arguments anatomiques et phylogénétiques (Manuel 2009). Chez Nematostella les gènes Hox sont différentiellement exprimés dans l’axe directeur et leur expression est contrôlée par la voie BMP. Notre étude avec l’espèce Antipathes caribbeana, un corail noir (Antipatharia) a permet âpre confirmation de ça anatomie a interne a symétrie bilatéral l’étude de l’expression de ces gènes et a discuter l’origine de la bilatéralité. / The origin of body axis is one of the central themes on animal evolution. Usually regarded as an innovation of Bilateria, the bilateral symmetry is broadly distributed in the Anthozoan class of Cnidarians. The molecular basis of this Anthozoan bilaterality have been studied in Nematostella vectensis (Actiniaria), and the discovery that the BMP-pathway was differentially expressed along the secondary axis lead authors to presume that bilaterality was ancestral to the Cnidaria/Bilateria divergence (Finnerty et al. 2004, Matus et al. 2006), while Manuel (2009) preferred a convergence hypothesis based on comparative anatomy and phylogeny. In opposition to Bilateria, HOX genes have recently been shown to be differentially expressed along the secondary axis of N. vectensis. In order to do evolutive inferences from these results it is necessary to study the HOX genes and BMP genes expression patterns in other Anthozoan species. Our study with the antipatharian colonial species Antipathes caribbeana focuses on the detailed anatomy of the polyp, confirming the previously doubtful bilateral organization of its polyps. In order to compare Antipatharian species to N. vectensis, a comparison between the mesenteric formation and symmetries on the different groups of anthozoans is presented, allowing to establish the homology between their secondary axis. The study of the expression of HOX and BMP genes in A. caribbeana shows that they are, as in Nematostella, differentially expressed along the secondary axis. Reinforcing the idea that bilaterality is ancestral to the Cnidaria/Bilateria divergence and that HOX genes have a patterning role on the secondary axis of Anthozoans.

This dissertation investigates the embryonic specification of a specific group of cells: the germ cells. Germ cells, which give rise to sperm and egg, are the only cells in sexually-reproducing animals that directly contribute hereditary information to the next generation. Germ cells are therefore a universal cell type across animals, and represent a profound novelty that likely arose near the base of the animal phylogeny. Yet despite their conserved, essential function in all animals, there is surprising diversity in the mechanisms that specify these cells during embryonic development. In this dissertation, I address the diversity of germ cell specification mechanisms in insects. I focus on two species, the milkweed bug Oncopeltus fasciatus (Hemiptera) and the cricket Gryllus bimaculatus (Orthoptera), which both branch basally to the Holometabola (those insects which undergo metamorphosis, including the well-studied fruit fly Drosophila melanogaster), and thus provide important phylogenetic breadth to our understanding of germ cell specification across insects. Using functional genetic approaches, I show that germ cell specification in both Oncopeltus and Gryllus differs fundamentally from germ cell specification in Drosophila. Specifically, I provide evidence that germ cells arise via inductive cell signaling during mid-embryogenesis, rather than via maternally-supplied cytoplasmic determinants localized in the oocyte, as is the case for Drosophila. These data suggest that Drosophila employs an evolutionarily derived mode of germ cell specification. In further support of this hypothesis, I show that several of the genes required for Drosophila germ cell specification perform other functions in both Oncopeltus and Gryllus. I demonstrate that one of these genes, oskar, which is the only gene both necessary and sufficient for germ cell specification in Drosophila, instead functions in nervous system of the cricket, both during embryonic development and in the adult brain. I suggest that the evolution of the derived mode of germ cell specification seen in Drosophila may have involved co-opting oskar into the germ cell specification pathway from an ancestral role in the nervous system.

Todos los animales, vivos y fósiles, están comprendidos dentro de 35 fila. Éstos abarcan la enorme diversidad de morfologías que se han generado durante la evolución animal, desde una medusa, hasta una mosca o nosotros mismos, el hombre. Cada una de las diferentes morfologías son en último término el resultado de un proceso de desarrollo embrionario muy finamente regulado en el que participan cientos de genes, y que forman parte de decenas de redes génicas que interactúan unas con otras. A lo largo del tiempo, estas morfologías han ido evolucionando de forma que se han ido generando nuevas especies a partir de otras preexistentes o ancestros, compartidos por las especies que derivan de él. Dado este marco, cobra fuerza una disciplina relativamente reciente, la Evo-Devo o Evolución del Desarrollo, que pretende explicar la evolución de la morfología animal buscando los cambios en los genes del desarrollo embrionario, ya que la primera es fruto del segundo. Sin embargo, la mayoría de los genes del desarrollo son los mismos en todos los animales, algo que se conoce como el toolkit genético, y esto lleva a lo que se conoce como la paradoja de la Evo-Devo: ¿cómo se explica entonces la gran diversidad morfológica, si los diferentes animales están construidos con los mismos genes? Hay que buscar por tanto las diferencias que existan en los procesos del desarrollo de los diferentes animales. Una de estas diferencias puede recaer en cómo los genes del desarrollo se regulan. En esta tesis, se han utilizado los genes Hox como modelos de evolución genómica, y se han analizado el patrón de expresión de estos genes en la especie europea de cefalocordado, Branchiostoma lanceolatum. Se ha identificado el patrón de expresión de casi todos los genes del clúster Hox de este animal, constituido por 15 genes Hox. De ellos, los genes Hox1, 2, 3, 4 y 6 ya estaban descritos en la especie americana B. floridae, aunque se ha encontrado un patrón diferente para el gen Hox6. Además, para los genes Hox6 y Hox14, se ha encontrado un patrón de regulación modular, donde parte del patrón de expresión está regulado por ácido retinóico. En otra fase de la tesis, se han identificado putativos elementos reguladores en las regiones intergénicas de estos genes mediante una estrategia de "phylogenetic footprinting". Esto ha sido realizado mediante la comparación de regiones ortólogas de los genes Hox de las dos especies de anfioxo y humando. Algunas de estas, como las que rodean el gen Hox4, están conservadas también con pez cebra, y son capaces de dirigir la expresión de un gen reporter en tejidos donde se expresan los genes endógenos. Además, siguiendo la misma estrategia, hemos identificado una región de regulación global que está presente en vertebrados, situándose su origen al menos en el ancestro de los cordados. / "Hox complex as models for genomic evolution: characterization and regulation of Hox genes expression of European Hox cluster". TEXT:Hox genes are key developmental genes involved in patterning the antero-posterior axis of most metazoans studied so far. They generally are linked in genomic cluster and expressed with spatial and temporal colinearity in amphioxus and vertebrates. The closer to the 3' extreme of the cluster the gene is, the earlier and more anteriorly it is expressed. Nonetheless, this is fully true for all genes only in vertebrate clusters, since the expression of almost all central and all posterior Hox genes of amphioxus, which represents the closest relative to the chordate ancestor, is not known, and the expression in hemichordates and tunicates is not always colinear. In this thesis, we present a complete expression profile of amphioxus Hox genes and interestingly report the breaking of both spatial and temporal colinearity of some central and posterior Hox genes. Posterior Hox genes are expressed in structures like the notochord and posterior parts of the gut. Hox14 had the most divergent expression pattern, being also present in the anterior cerebral vesicle and pharyngeal endoderm. This is the first report of Hox expression in the most anterior part of a central nervous system. We also show that Hox14 expression is partially regulated by retinoic acid (RA) (in notochord and hindgut), like it happens for more anterior Hox genes are. On the other hand, Hox14 expression in the cerebral vesicle and pharynx are not influenced by RA. The lack of constriction in the posterior part of vertebrate and cephalochordate Hox cluster may be the cause of their independent expansion and their co-option for patterning different structures, allowing the breaking of colinearity in deuterostomes.

Submitted by Mendes Eduardo (dasilva@ufba.br) on 2013-07-18T09:49:29Z No. of bitstreams: 1 DISSERTAÇÃO Wellington.pdf: 3714522 bytes, checksum: 840c610f1ad6fef2f736981fb10b926a (MD5) / Approved for entry into archive by Vilma Conceição (vilmagc@ufba.br) on 2014-02-06T14:15:59Z (GMT) No. of bitstreams: 1 DISSERTAÇÃO Wellington.pdf: 3714522 bytes, checksum: 840c610f1ad6fef2f736981fb10b926a (MD5) / Made available in DSpace on 2014-02-06T14:15:59Z (GMT). No. of bitstreams: 1 DISSERTAÇÃO Wellington.pdf: 3714522 bytes, checksum: 840c610f1ad6fef2f736981fb10b926a (MD5) / Fapesb / Este artigo relata os resultados de uma análise de conteúdo comparativa de três livros didáticos de biologia evolutiva e três livros didáticos de zoologia de vertebrados, muitos adotados em ementas de cursos de formação superior de biologia de diversas universidades de países de línguas latinas e anglo-saxônicas. Através de uma análise documental quali-quantitativa dos livros didáticos, realizada através de metodologia de análise de conteúdo, empreendemos uma investigação sobre a abordagem e recontextualização de conteúdos relativos à biologia evolutiva do desenvolvimento (evo-devo) e ao pluralismo de processos presentes nos livros selecionados. Com base nesta investigação, buscamos responder à seguinte pergunta: em que medida e de que maneira os referidos conteúdos, relacionados a avanços importantes que tiveram lugar na biologia evolutiva das últimas duas décadas, estão sendo recontextualizados em livros didáticos de evolução e nas discussões sobre evolução presentes em livros didáticos de zoologia de vertebrados? Os achados deste estudo indicam que os livros de evolução se encontram ainda em uma fase inicial de recontextualização dos conteúdos relativos ao pluralismo de processos e, assim, ao que tem sido denominada a síntese estendida no campo da biologia evolutiva. Contudo, eles se encontram em um estágio mais avançado de recontextualização que os livros de zoologia de vertebrados analisados, nos quais foi observada uma diversidade substancialmente menor de mecanismos evolutivos, com uma grande ênfase apenas sobre a seleção natural. Estes achados não são surpreendentes, uma vez que a idéia de uma síntese estendida ainda não está bem estabelecida na própria biologia evolutiva. No que diz respeito aos conteúdos relativos à evo-devo, foi constatado um nível mais significativo de recontextualização nos livros didáticos de ambos os campos de estudo, o que mostra que ao menos parte do conteúdo da chamada síntese estendida já alcançou o ensino superior de biologia. / Salvador

Multiple rounds of whole genome duplication (WGD) have played a pivotal role in the expansion, elaboration, and evolutionary diversification of vertebrate genomes. In addition to sharing two rounds of whole genome duplication with all other vertebrates, a teleost-specific genome duplication (TGD) occurred in the stem of the teleost lineage ~350 million years ago (MYA) and is thus a genomic synapomorphy shared by all ~26,000 extant species. The TGD has variously been implicated in accelerated speciation, evolution of morphological complexity, increased rates of molecular evolution, and the evolution of novelty, and therefore is therefore of significant interest for its impact on teleost evolution and also as a model for understanding the evolutionary patterns and processes which accompany WGDs more generally. Investigation of the TGD has contributed extensively to the general understanding of WGDs however, until the present work, a relatively narrow taxonomic sampling of species within a single teleost subdivision, Clupeocephala, have been investigated. This taxonomic bias has left potentially relevant evolutionary changes to the teleost genome in the immediate wake of the TGD obscured. Due to their deeply branching ancestry, species belonging to the two other major teleost subdivisions, Osteoglossomorpha and Elopomorpha, are well positioned for deeper comparative genomic analyses of the TGD and the accompanying phenomenon of diploidization. The focus of the present work has been to develop the first genomic resources specifically for osteoglossomorphs and to investigate the evolutionary patterns and processes which accompanied diploidization prior the deep divergence of the three extant teleost subdivisions. To this end, I have generated de novo genome and transcriptome data from four osteoglossomorph taxa (Pantodon buchholzi, Osteoglossum bicirrhosum, Chitala ornata, and Gnathonemus petersii) and conducted comparative genomic and phylogenetic analysis with other teleosts and pre-TGD vertebrates including the gar Lepisosteus oculeatus. With a focus on Hox and other ANTP class homeobox-containing transcription factor families I provide evidence that speciation of the major teleost subdivisions occurred prior to the termination of the diploidization process following TGD and discuss the evolutionary implications of this model. Beginning with an analysis of the Hox clusters in P. buchholzi I show that divergent resolution of TGD-generated Hox duplicates occurred both at the individual gene level as well as at the level of whole cluster losses. Detailed phylogenetic analyses of the P. buchholzi Hox clusters further revealed that the transition from polyploid alleles to full paralogs during the diploidization process can occur independently in different lineages when speciation rapidly follows WGDs, causing duplicated genes to exhibit a special case of four-way gene homology which I have termed 'tetralogy'. A genome-wide survey of ANTP class homeobox genes in a de novo assembly of the P. buchholzi genome revealed that ancient TGD duplicates of at least 14 subfamilies were preserved uniquely in the P. buchholzi genome and lost from clupeocephalan teleosts. Finally, by comparing the Hox complements in gar and P. buchholzi with three additional osteoglossomorphs I show that the diversity in potential duplicate resolution patterns is also highly variable between osteoglossomorph families. Overall, this work highlights the importance of considering not only the relative timing of gene duplication and speciation in comparative genomic analyses but also their timing relative to diploidization. Going forward, the research community will need to carefully evaluate the effects differences in diploidization rate and pattern, both between lineages and across the genome, have had in influencing the fate of individual gene duplicates as well as upon the macroevolutionary phenomena frequently correlated with WGDs more generally.

No description available.