Styelid ascidians are diverse in developmental modes, varying from strictly sexual solitary species to highly integrated colonies. Circulatory stem cells (CSCs) accomplish fundamental roles in developmental processes of styelid ascidians. In the colonial styelids, CSCs enable budding and are capable of giving origin to the germline in certain species. The function of these cells have been tested experimentally in models within Styelidae. However, the understanding of coloniality as an evolutionary novelty requires reconstructing the possible ancestral CSCs characteristics in Styelidae. To address this issue, this work analyzes the possible developmental origin and the identity of putative CSCs among blood cell populations. The first chapter of this dissertation aimed to characterize and compare the hemocyte populations in two solitary styelids: Styela plicata and Styela canopus. In addition, the early development, the metamorphosis and the early maturation were compared in both species. After metamorphosis, S. canopus briefly develops a network of extracorporeal vessels with numerous terminal ampullae. These characters are usually associated to colonial ascidians, and were not found in S. plicata. With respect to the hemocyte populations, similar morphotypes were present in both species. However, S. canopus shows a lower frequency of vacuolated cells, which may be due to a reduced level of cytotoxicity in the tunic relative to S. plicata. These differences observed between S. canopus and S. plicata may be related to differences in the degrees of gregariousness or body size among the two species. In order to investigate possible approaches to distinguish and isolate CSC populations in a solitary styelid model, I used imaging flow cytometry. Putative CSCs were identified through measurement of morphological parameters and aldehyde dehydrogenase (ALDH) activity. The correlation between these parameters allowed to determine 2 gates enriched with particular cell types. A significant difference was found on the ALDH+ population within a gate of cells with low granularity, suggesting the presence of cells among circulatory hemocytes. To scrutinize the biogenesis of CSCs in S. plicata, I present a description of a candidate hematopoietic niche in this species. An exhaustive histological survey for hemoblast-like cells was performed, and complemented with immunohistochemistry with stem cell (piwi) and proliferation (pHH3) markers. The morphological and expression profiles of the intestine support the intestinal submucosa (IS) as a hematopoietic niche. At this region there are aggregations of cells with and undifferentiated morphological profile, corroborated by ultrastructural analysis. Furthermore, the IS holds high cellular proliferation and frequency of piwi+ cells. Ascidians are considered interesting models to investigate asexual reproduction and modular development. This study represents an advancement towards understanding the processes, cell populations and structures that may be related to facilitating the appearance of this evolutionary novelty / As ascídias da família Styelidae são diversas em modos de desenvolvimento, variando de espécies estritamente sexuais solitárias até colônias altamente integradas. As células-tronco circulatórias (CTCs) desempenham papéis fundamentais nos processos do desenvolvimento de ascídias styelídeas. Nas especies coloniais deste grupo, as CTCs permitem a brotação e são capazes de originar a linha germinativa em certas espécies. A função dessas células tem sido testada experimentalmente em modelos dentro de Styelidae. No entanto, a compreensão da colonialidade como uma novidade evolutiva requer reconstruir as características das possíveis CTCs ancestrais para Styelidae. Com o fim de abordar essa questão, este trabalho analisa a possível origem do desenvolvimento e a identidade de CSCs putativas entre populações de células sanguíneas de styelídeas solitárias. O primeiro capítulo desta dissertação teve como objetivo caracterizar e comparar as populações de hemócitos em dois espécies solitárias: Styela plicata e Styela canopos. Além disso, o desenvolvimento inicial, a metamorfose e a maturação do juvenil foram comparados em ambas as espécies. Após a metamorfose, S. canopus desenvolve brevemente uma rede de vasos extracorpóreos com numerosas ampolas terminais. Esses caracteres são geralmente associados a ascídias coloniais e não foram encontrados em S. plicata. Com relação às populações de hemócitos, morfotipos semelhantes estavam presentes em ambas as espécies. No entanto, o S. canopos apresenta menor frequência de células vacuoladas, o que pode ser devido a um nível reduzido de citotoxicidade na túnica em relação a S. plicata. Essas diferenças observadas entre S. canopos e S. plicata podem estar relacionadas a diferenças nos graus de gregariedade ou tamanho corporal entre as duas espécies. A fim de investigar possíveis abordagens para distinguir e isolar populações de CTCs em um modelo de styelídeo solitário, usei citometria de fluxo com adquisição de imagem. As CTCs putativas foram identificadas através da medição de parâmetros morfológicos e da atividade da aldeído desidrogenase (ALDH). A correlação entre estes parâmetros permitiu determinar 2 gates enriquecidos com tipos celuláres particulares. Uma diferença significativa foi encontrada na população ALDH+ dentro de um gate de células com baixa granularidade, sugerindo a presença de células-tronco circulatórias. Para examinar a biogênese das CTCs em S. plicata, foi realizada uma descrição de um nicho hematopoiético candidato nesta espécie. Um exame histológico exaustivo para células semelhantes a hemoblastos foi realizado e complementado com imunohistoquímica com marcadores de células-tronco (piwi) e proliferação (pHH3). Os perfis morfológicos e de expressão do intestino sustentam a submucosa intestinal (SI) como nicho hematopoiético. Nesta região há agregações de células com morfolia indiferenciada, corroborada pela análise ultraestrutural. Além disso, a SI mantém alta proliferação celular e freqüência de células piwi+. As ascídias são consideradas modelos interessantes para investigar a reprodução assexuada e o desenvolvimento modular. Este estudo representa um avanço na compreensão dos processos, populações celulares e estruturas que podem estar relacionadas a facilitar o surgimento desta novidade evolutiva

Styelid ascidians are diverse in developmental modes, varying from strictly sexual solitary species to highly integrated colonies. Circulatory stem cells (CSCs) accomplish fundamental roles in developmental processes of styelid ascidians. In the colonial styelids, CSCs enable budding and are capable of giving origin to the germline in certain species. The function of these cells have been tested experimentally in models within Styelidae. However, the understanding of coloniality as an evolutionary novelty requires reconstructing the possible ancestral CSCs characteristics in Styelidae. To address this issue, this work analyzes the possible developmental origin and the identity of putative CSCs among blood cell populations. The first chapter of this dissertation aimed to characterize and compare the hemocyte populations in two solitary styelids: Styela plicata and Styela canopus. In addition, the early development, the metamorphosis and the early maturation were compared in both species. After metamorphosis, S. canopus briefly develops a network of extracorporeal vessels with numerous terminal ampullae. These characters are usually associated to colonial ascidians, and were not found in S. plicata. With respect to the hemocyte populations, similar morphotypes were present in both species. However, S. canopus shows a lower frequency of vacuolated cells, which may be due to a reduced level of cytotoxicity in the tunic relative to S. plicata. These differences observed between S. canopus and S. plicata may be related to differences in the degrees of gregariousness or body size among the two species. In order to investigate possible approaches to distinguish and isolate CSC populations in a solitary styelid model, I used imaging flow cytometry. Putative CSCs were identified through measurement of morphological parameters and aldehyde dehydrogenase (ALDH) activity. The correlation between these parameters allowed to determine 2 gates enriched with particular cell types. A significant difference was found on the ALDH+ population within a gate of cells with low granularity, suggesting the presence of cells among circulatory hemocytes. To scrutinize the biogenesis of CSCs in S. plicata, I present a description of a candidate hematopoietic niche in this species. An exhaustive histological survey for hemoblast-like cells was performed, and complemented with immunohistochemistry with stem cell (piwi) and proliferation (pHH3) markers. The morphological and expression profiles of the intestine support the intestinal submucosa (IS) as a hematopoietic niche. At this region there are aggregations of cells with and undifferentiated morphological profile, corroborated by ultrastructural analysis. Furthermore, the IS holds high cellular proliferation and frequency of piwi+ cells. Ascidians are considered interesting models to investigate asexual reproduction and modular development. This study represents an advancement towards understanding the processes, cell populations and structures that may be related to facilitating the appearance of this evolutionary novelty / As ascídias da família Styelidae são diversas em modos de desenvolvimento, variando de espécies estritamente sexuais solitárias até colônias altamente integradas. As células-tronco circulatórias (CTCs) desempenham papéis fundamentais nos processos do desenvolvimento de ascídias styelídeas. Nas especies coloniais deste grupo, as CTCs permitem a brotação e são capazes de originar a linha germinativa em certas espécies. A função dessas células tem sido testada experimentalmente em modelos dentro de Styelidae. No entanto, a compreensão da colonialidade como uma novidade evolutiva requer reconstruir as características das possíveis CTCs ancestrais para Styelidae. Com o fim de abordar essa questão, este trabalho analisa a possível origem do desenvolvimento e a identidade de CSCs putativas entre populações de células sanguíneas de styelídeas solitárias. O primeiro capítulo desta dissertação teve como objetivo caracterizar e comparar as populações de hemócitos em dois espécies solitárias: Styela plicata e Styela canopos. Além disso, o desenvolvimento inicial, a metamorfose e a maturação do juvenil foram comparados em ambas as espécies. Após a metamorfose, S. canopus desenvolve brevemente uma rede de vasos extracorpóreos com numerosas ampolas terminais. Esses caracteres são geralmente associados a ascídias coloniais e não foram encontrados em S. plicata. Com relação às populações de hemócitos, morfotipos semelhantes estavam presentes em ambas as espécies. No entanto, o S. canopos apresenta menor frequência de células vacuoladas, o que pode ser devido a um nível reduzido de citotoxicidade na túnica em relação a S. plicata. Essas diferenças observadas entre S. canopos e S. plicata podem estar relacionadas a diferenças nos graus de gregariedade ou tamanho corporal entre as duas espécies. A fim de investigar possíveis abordagens para distinguir e isolar populações de CTCs em um modelo de styelídeo solitário, usei citometria de fluxo com adquisição de imagem. As CTCs putativas foram identificadas através da medição de parâmetros morfológicos e da atividade da aldeído desidrogenase (ALDH). A correlação entre estes parâmetros permitiu determinar 2 gates enriquecidos com tipos celuláres particulares. Uma diferença significativa foi encontrada na população ALDH+ dentro de um gate de células com baixa granularidade, sugerindo a presença de células-tronco circulatórias. Para examinar a biogênese das CTCs em S. plicata, foi realizada uma descrição de um nicho hematopoiético candidato nesta espécie. Um exame histológico exaustivo para células semelhantes a hemoblastos foi realizado e complementado com imunohistoquímica com marcadores de células-tronco (piwi) e proliferação (pHH3). Os perfis morfológicos e de expressão do intestino sustentam a submucosa intestinal (SI) como nicho hematopoiético. Nesta região há agregações de células com morfolia indiferenciada, corroborada pela análise ultraestrutural. Além disso, a SI mantém alta proliferação celular e freqüência de células piwi+. As ascídias são consideradas modelos interessantes para investigar a reprodução assexuada e o desenvolvimento modular. Este estudo representa um avanço na compreensão dos processos, populações celulares e estruturas que podem estar relacionadas a facilitar o surgimento desta novidade evolutiva

4 Neural crest-derived cellular cartilage is one of the defining characteristics of vertebrates. Elaboration of this tissue and its patterning allowed the evolution of jaws in the gnathostome lineage. Together these hallmarks helped jawed vertebrates become one of the dominant taxons in the animal kingdom. Lampreys, as basal jawless vertebrates, lie at a unique phylogenetic position that makes them ideal organisms for the study of evolution of vertebrate/gnathostome novelties. Larval lampreys possess a special oral skeleton composed of a tissue related to cartilage, termed mucocartilage. Despite considerable attention that has been paid to the evolutionary significance of mucocartilage, it is not yet clear, how this unique feature arises in development and to what extent it is homologous to gnathostome jaws. In this study, the development of oro-pharyngeal region was analyzed in the sea lamprey Petromyzon marinus. SEM imaging revealed shaping and topographic relationships of embryonic tissues, detailed plastic histology coupled with expression analyses of several molecular markers were used to describe origin, histogenesis and morphogenesis of mucocartilage. Furthermore, genetic regulation of the tissue was investigated in order to identify its unique or shared features. Mucocartilage is seen to...

A major challenge to evolutionary developmental biology is to understand the how modifications to gene regulatory networks can lead to biological diversity. Heliconius butterfly wing patterns provide an excellent example of this diversity. In particular, the species H. melpomene and H. erato display wide variation in wing pattern across their ranges in Central and South America, but wherever they co-occur, they have converged on remarkably similar wing patterns due to Müllerian mimicry. Linkage analysis of wing pattern genes has shown that in both species, there are three genomic loci that are responsible for most of the pattern variation, and that these loci are homologous. One locus, containing the transcription factor optix, is responsible for red pattern elements. A set of non-coding sequences linked to some of the red pattern elements have been identified. Another locus, containing the gene WntA, has been linked to the shape of the forewing band elements and is responsible for variation in wing pattern development in several species of lepidoptera. A third locus, responsible for yellow pattern elements, contains multiple candidate genes that may affect wing pattern development, including the gene cortex, which is also linked to the industrial melanism phenotype in the moth Biston betularia, as well as the genes domeless and washout, linked to the Bigeye mutant in Bicyclus anynana. I first investigated modifications to regulatory sequence near the transcription factor optix, detecting a module associated with the band pattern element. I also found that for some pattern regulatory modules at optix, the same sequence has independently evolved the same function in H. melpomene and H. erato, in association with non-coding sequences conserved throughout the Lepidoptera. I then investigated gene expression differences in two morphs from either side of a hybrid zone that vary only in the presence or absence of a yellow pattern element, in order to determine a role for candidate genes at the yellow pattern locus. In H. melpomene the gene cortex was upregulated in the larval wing discs of the black morph, whereas in H. erato it was upregulated in the larval wing discs of the yellow morph. In pupal wings, washout was differentially expressed, again in the opposite pattern in the two species, suggesting the same locus is responsible for convergent pattern modification, but by a different mechanism. Finally, I investigated the spatial transcriptomic landscape across the wings of three different heliconiine butterflies. I identified candidate factors for regulating the expression of wing patterning genes, including genes with a conserved expression profile in all three species, and others, including genes in the Wnt pathway, with markedly different profiles in each of the three species. Each of these studies contributes to our understanding of how gene regulatory networks can be modified to create diversity: first, at the level of cis-regulation, second at the level of gene interaction and expression, and lastly at the level of developmental bias and constraint.

No description available.

Panarthropoda is a monophyletic group comprised of arthropods and lobopods, molting animals with a segmented body, paired appendages, dorsal brain, and ventral nerve cords. Evolutionary Developmental Biology (EvoDevo) is an interdisciplinary field that seeks to understand how changes in development form the basis for variations in morphology and phenotypic evolution, including the genetic network underlying these processes. To study the evolution of panarthropods from such an EvoDevo perspective, one typically uses standard molecular techniques. A first step here is to investigate the expression of a gene of interest in order to find out where and when it is transcribed during development. A hallmark of EvoDevo studies is its comparative character, often with respect to model organisms such as the fruit fly Drosophila melanogaster. Recently developed single-cell RNA sequencing technologies allow the profiling of a plethora of gene expression on the level of individual cells, and thus provide a much more detailed insight into gene expression. In Paper I, I applied standard molecular techniques used in EvoDevo research such as PCR, gene cloning, probe synthesis and whole mount in situ hybridization, to investigate the embryonic expression patterns of the tiptop/teashirt (tio/tsh) and spalt (sal) genes in a range of arthropods representing all main groups of this phylum, and an onychophoran. In the arthropod model Drosophila, these genes act as trunk-specifiers, and the objective of my work was to find out if this is conserved in Arthropoda or even Panarthropoda as a whole. I provide comprehensive data on arthropod tio/tsh and sal expression, including the first data from an onychophoran. The results support the idea that tio/tsh genes are involved in the development of ‘trunk’ segments by regulating limb development. In addition, my data suggest that the function of Sal is unlikely to be conserved in trunk vs head development. Early expression of sal, however, is in line with a potential homeotic function of this gene, at least in Arthropoda. In Paper II, I provide an embryonic tissue dissociation protocol for embryos of the common house spider Parasteatoda tepidariorum that I developed and that I successfully applied for single-cell RNA sequencing. In addition, I report on the progress of this experiment, and provide and discuss preliminary results.

Variationen in der Genexpression spielen eine zentrale Rolle bei der evolutionären Divergenz, die zur Speziation führt. Dies wird durch Veränderungen sowohl in nicht-kodierenden cis-wirkenden regulatorischen Elementen (CREs) wie Promotoren und Enhancern als auch in trans-wirkenden regulatorischen Elementen bestimmt. Veränderungen in den regulatorischen Sequenzen können Entwicklungsmuster verändern und wirken als eine der treibenden Kräfte der Evolution der Genexpression. Hier untersuche ich die Anwendung der Einzelzell-Multiomik in der evolutionären vergleichenden Genomik, wobei der Schwerpunkt auf den funktionellen Auswirkungen der Divergenz bei cis-regulatorischen Elementen liegt. Unter Verwendung von Hybrid-Embryonen von Drosophila melanogaster und sechellia generiere ich ein diploides Referenzgenom und führe allelspezifische Einzelzellanalysen von scRNA-seq und scATAC-seq durch. Zusammen können diese beiden komplimentären Ansätze einen integrativen Überblick über die Transkription und die Zugänglichkeit des Chromatins liefern, wodurch CREs identifiziert und mit allelspezifischen Veränderungen in den Genen, die sie regulieren, in Verbindung gebracht werden können. Die computergestützte Rekonstruktion verschiedener Zellidentitäten durch Clustering einzelner Zellen ermöglicht es uns auch zu untersuchen, wie sich das Allel-Ungleichgewicht während der Zelltyp-Spezifikation räumlich verändern kann. Im Gegensatz zu früheren Forschungsarbeiten stelle ich fest, dass Gene, die an der Entwicklung und Musterbildung beteiligt sind, ein unterschiedliches allelisches Ungleichgewicht in der Expression und Zugänglichkeit über die Zelltypen hinweg aufweisen. Diese Arbeit zeigt das Potenzial der Kombination von Einzelzell-Multiomik und artübergreifenden Vergleichen in der vergleichenden Genomik und wirft ein neues Licht auf die Rolle von cis-regulatorischen Elementen in der adaptiven Evolution. / Variation in gene expression plays a pivotal role in the evolutionary divergence that leads to speciation. This is determined by changes in both non-coding cis-acting regulatory elements (CREs) like promoters and enhancers, as well as trans-acting regulatory elements. Changes in regulatory sequences can alter developmental patterns, acting as one of the driving forces behind gene expression evolution. However, poor sequence conservation of CREs makes it challenging to identify them and link changes in regulatory sequences to new phenotypes. Here, I explore the application of single cell multiomics in evolutionary comparative genomics, with a focus on functional effects of divergence in cis-regulatory elements. Using hybrid embryos of Drosophila melanogaster and Drosophila sechellia, I generate a diploid reference genome and conduct single cell allele-specific analysis of scRNA-seq and scATAC-seq data. Together, these two assays can provide an integrative read-out of transcription and chromatin accessibility, allowing CREs to be identified and linked to allele-specific changes (allelic imbalance) in the genes they regulate. The computational reconstruction of different cell identities via single cell clustering also allows us to investigate how allelic imbalance may vary spatially during cell-type specification. In contrast to previous research, I find that genes involved in development and patterning display differential allelic imbalance in expression and accessibility across cell types. In addition, I investigate the role of neurodevelopmental allelic imbalance in the sechellia lineage and identify candidate genes for sechellia-specific adaptations. While highlighting current computational limitations, this thesis demonstrates the potential of combining single cell multiomics and cross-species comparisons in comparative genomics and shedding new light on the role of cis-regulatory elements and mechanisms of adaptive evolution.