The primary purpose of this research is to further morphological studies on larval ascidians and to encourage greater reliance on larval structures in ascidian taxonomy. This may necessitate some revisions in current classifications, but it is hoped that such revisions will lead to a better understanding of the group. Some general considerations of ascidians are here included for the benefit of those who may not be familiar with them. All specimens used in this study were collected at the Pacific Marine Station area at Dillon Beach, California, during June, July, and August of 1957.

Background: The colonial ascidian Didemnum vexillum, sea carpet squirt, is not only a key marine organism to study morphological ancestral patterns of chordates evolution but it is also of great ecological importance due to its status as a major invasive species. Non-coding RNAs, in particular microRNAs (miRNAs), are important regulatory genes that impact development and environmental adaptation. Beyond miRNAs, not much in known about tunicate ncRNAs. Results: We provide here a comprehensive homology-based annotation of non-coding RNAs in the recently sequenced genome of D. vexillum. To this end we employed a combination of several computational approaches, including blast searches with a wide range of parameters, and secondary structured centered survey with infernal. The resulting candidate set was curated extensively to produce a high-quality ncRNA annotation of the first draft of the D. vexillum genome. It comprises 57 miRNA families, 4 families of ribosomal RNAs, 22 isoacceptor classes of tRNAs (of which more than 72% of loci are pseudogenes), 13 snRNAs, 12 snoRNAs, and 1 other RNA family. Additionally, 21 families of mitochondrial tRNAs and 2 of mitochondrial ribosomal RNAs and 1 long non-coding RNA. Conclusions: The comprehensive annotation of the D. vexillum non-coding RNAs provides a starting point towards a better understanding of the restructuring of the small RNA system in ascidians. Furthermore it provides a valuable research for efforts to establish detailed non-coding RNA annotations for other recently published and recently sequences in tunicate genomes.

Tunicata umfasst 3000 marine Arten, mit sehr unterschiedlichen Lebensstrategien. Als eines der drei großen Taxa innerhalb der Chordata, stellt die Evolution der Tunikaten eine Schlüsselkomponente bei der Aufklärung der Evolution der Chordaten und Cranioten dar. Dafür ist ein Verständnis der Merkmalstransformationen innerhalb der Tunikaten notwendig. Leider sind die internen Verwandtschaftsverhältnisse der fünf großen Tunikatentaxa in verschiedenen molekularphylogenetischen Studien widersprüchlich. Bisher gibt es nur wenige morphologische phylogenetische Analysen. Ein Schwerpunkt dieser Arbeit liegt auf der Untersuchung neuroanatomischer Merkmale, da das Nervensystem wahrscheinlich phylogenetische Informationen enthält. Durch das Anwenden moderner morphologischer Methoden, wie hochauflösende konfokale Laserscan- und Elektronenmikroskopie (REM und TEM), und 3d Rekonstruktionen basierend auf lichtmikroskopischen Schnitten, wurde die Verfügbarkeit neuroanatomischer Daten wesentlich verbessert. Die Ergebnisse zeigen, dass die Variation neuroanatomischer Merkmale größer ist als bisher angenommen und dass sich die Gehirnanatomie und die Verteilung von Neurotransmittern in den zwei Stadien der Thaliaceen unterscheidet. Neue unabhängige Merkmale des Nervensystems wurden in einer Matrix kodiert. Ergänzt mit traditionellen in der Tunikatentaxonomie verwendeten Merkmalen, entstand die bisher umfangreichste morphologische Datenmatrix, die 116 Merkmale für insgesamt 54 Arten umfasst. Die kladistische Analyse ergab monophyletische Tunicata, in denen die Appendicularia die Schwestergruppe der übrigen Tunikaten bildet. Ascidiacea ist monophyletisch, während „Thaliacea“ paraphyletisch ist. Zusätzlich wurde eine kombinierte phylogenetische Analyse basierend auf den morphologischen Daten und 18S rDNA-Sequenzen durchgeführt. Eine stufenweise stärkere Gewichtung phänotypischer Merkmale zeigt, dass die morphologischen Daten das Ergebnis der kladistischen Analyse stark beeinflussen. / Tunicata comprises 3000 marine species with diverse life-history strategies. As one of the three major chordate taxa, the evolution of tunicates plays a key role to elucidate chordate and craniate evolution. Therefore, a broader understanding of character transformations within tunicates is essential, but the interrelationships of the five main tunicate subtaxa in previous molecular phylogenetic analyses were contradictory. Morphological phylogenetic analyses are rare. In this comparative study emphasis was given to neuroanatomical characters, as the nervous system probably contains phylogenetic information. Applying modern morphological techniques like high-resolution confocal laser scanning microscopy and electron microscopy (SEM and TEM), serial sectioning for light microscopy, and digital 3d reconstruction, the number of available tunicate neuroanatomical data was considerably increased. It was revealed that the variation of neuroanatomical characters is higher than previously assumed, a specific pattern of serotonin-like immunoreactive cells in ascidians is present, and that brain anatomy and distribution of neurotransmitters in the two thaliacean life-cycle stages differs. Novel independent characters of the central nervous system were coded in a matrix for a cladistic analysis. Including traditional morphological from tunicate literature this effort resulted in the largest morphological data matrix to date, containing 116 phenotypic characters and 54 species. The cladistic analysis resulted in monophyletic Tunicata, with Appendicularia the sister taxon to the remaining tunicates. Furthermore, the monophyly of Ascidiacea is supported, whereas “Thaliacea” are paraphyletic. An additional phylogenetic analysis combining morphological and 18S rDNA-sequence data was performed. A reevaluation of this dataset with a successively increased weighting of the phenotypic data showed that morphological data strongly influence the outcome of the cladistic analysis.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 91-99). / Trade-offs between filtration rate and swimming performance among several salp species with distinct morphologies and swimming styles were compared. Small-scale particle encounter at the salp filtering apparatus was also explored. Observations and experiments were conducted at the Liquid Jungle Lab, off the pacific coast of Panama in January 2006 through 2009. First, time-varying body volume was calculated by digitizing salp outlines from in situ video sequences. The resulting volume flow rates were higher than previous measurements, setting an upper limit on filtration capacity. Though each species possessed a unique combination of body kinematics, normalized filtration rates were comparable across species, with the exception of significantly higher rates in Weelia cylindrica aggregates, suggesting a tendency towards a flow optimum. Secondly, a combination of in situ dye visualization and particle image velocimetry (PIV) measurements were used to describe properties of the jet wake and swimming performance variables including thrust, drag and propulsive efficiency. All species investigated swam via vortex ring propulsion. Though Weelia cylindrica was the fastest swimmer, Pegea confoederata was the most efficient, producing the highest weight-specific thrust and wholecycle propulsive efficiency. Weak swimming performance parameters in Cyclosalpa afinis, including low weight-specific thrust and low propulsive efficiency, may be compensated by comparatively low energetic requirements. / (cont.) Finally, a low Reynolds number mathematical model using accurately measured parameters and realistic oceanic particle size concentrations showed that submicron particles are encountered at higher rates than larger particles. Results from feeding experiments with 0.5, 1 and 3 [mu]m po- lystyrene microspheres corroborated model predictions. Though 1 to 10 pm-sized particles (e.g. flagellates, small diatoms) are predicted to provide four times as much carbon as 0.1 to 1 pm- sized particles (e.g. bacteria, Prochlorococcus), particles smaller than the mesh size (1.4 [mu]m) can still fully satisfy salp energetic needs. / by Kelly Rakow Sutherland. / Ph.D.

Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro / As comunidades marinhas são afetadas por diversos fatores, que dentro do contexto de estrutura trófica, podem ser divididos em forças bottom-up (forças ascendentes), como por exemplo, a disponibilidade de nutrientes, e forças top-down (forças descendentes), como por exemplo, a predação. Além de modificações na estrutura das comunidades e populações de organismos, essas forças podem influenciar a produção de metabólitos secundários pelos organismos. O presente trabalho teve como objetivo avaliar o efeito das perturbações ambientais geradas pelas manipulações separadas e interativas de exclusão de macropredadores e enriquecimento com nutrientes sobre a estrutura e sobre as respostas metabólicas de comunidades marinhas incrustantes de substratos artificiais no costão rochoso de Biscaia, Baía da Ilha Grande, RJ. O desenho experimental utilizou blocos de concreto como substrato artificial, os quais foram espalhados aleatoriamente na região de infralitoral do costão rochoso. O experimento compreendeu o uso de blocos Controle (ausência de manipulação) e quatro tratamentos, todos com cinco réplicas cada. Os tratamentos foram: tratamento Exclusão de predação (gaiola contra a ação de macropredadores), tratamento Nutriente (sacos de fertilizante de liberação lenta), tratamento Nutriente + exclusão de predação (gaiola contra ação de macropredadores e sacos de fertilizante de liberação lenta) e o tratamento Controle de artefatos (gaiola semifechada para avaliar geração de artefatos). Uma área de 15 x 15 cm do bloco foi monitorada a cada 20 dias, totalizando dez medições. Foram utilizados métodos de monitoramento visual e digital de porcentagem de cobertura por espécie. O enriquecimento com nutrientes foi avaliado através de medições da concentração dos nutrientes Ortofosfato, Nitrato, Nitrito e Amônio na água do entorno do bloco. Para analisar os possíveis artefatos foi realizado experimento de fluxo de água (método Clod card) e a luminosidade dentro das gaiolas foi medida. Os dados demonstraram modificações na estrutura das comunidades bentônicas incrustantes dos substratos artificiais devido às manipulações realizadas, ou seja, pelo enriquecimento com nutrientes, pela exclusão de predação e pela interação entre os dois fatores (Nutriente + exclusão de predação). Além disso, diferenças metabólicas foram detectadas nas substâncias extraídas dos organismos dos diferentes tratamentos do experimento. Esses resultados indicam a existência de controle top-down e bottom-up sobre a comunidade bentônica do local. / Marine communities can be affected by many factors. Within the context of trophic structure, these factors can be divided into bottom-up forces, such as nutrient availability, and top-down forces, for example, predation. In addition to changes in the structure of communities and populations of organisms, these forces can influence the production of secondary metabolites. This study aimed to evaluate the effect of environmental perturbations generated by separate and interactive manipulations of macropredators exclusion and nutrient enrichment on the communitys structure and the metabolic responses of marine fouling communities of artificial substrates in Biscaia rocky shores, Ilha Grande Bay, RJ. The experimental design used concrete blocks as artificial substrate. The blocks were randomly scattered in the sub tidal region of the rocky shore. The experiment involved the use of Control blocks (no manipulation) and four treatments with five replicates each. The treatments were: Predator Exclusion treatment (cages excluding macropredators), Nutrient treatment (packs with slow-releasing fertilizer), Nutrient + predator exclusion treatment (cage excluding macropredators and packs with slow-releasing fertilizer), and Artifacts control treatment (semi-closed cage to assess artifacts effects). An area of 15 x 15 cm of each block was monitored every 20 days, totaling ten measurements. Visual and digital species percentage coverage methods were used. To assess nutrient water enrichment, we measured concentration of nutrients (orthophosphate, nitrate, nitrite and ammonium) in the water. To evaluate possible cages experimental artifacts, a water flow test (Clod card method) was performed, and luminosity inside the cages was measured. Data demonstrated changes in the structure of fouling communities on artificial substrates due to the manipulations performed, i.e., the nutrient enrichment, predation exclusion and the interaction between these two factors (Nutrient + predator exclusion). Moreover, differences were observed in substances extracted from organisms in different treatments of the experiment. These results indicate the existence of top-down and bottom-up controls on the benthic community of this site.

Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro / As comunidades marinhas são afetadas por diversos fatores, que dentro do contexto de estrutura trófica, podem ser divididos em forças bottom-up (forças ascendentes), como por exemplo, a disponibilidade de nutrientes, e forças top-down (forças descendentes), como por exemplo, a predação. Além de modificações na estrutura das comunidades e populações de organismos, essas forças podem influenciar a produção de metabólitos secundários pelos organismos. O presente trabalho teve como objetivo avaliar o efeito das perturbações ambientais geradas pelas manipulações separadas e interativas de exclusão de macropredadores e enriquecimento com nutrientes sobre a estrutura e sobre as respostas metabólicas de comunidades marinhas incrustantes de substratos artificiais no costão rochoso de Biscaia, Baía da Ilha Grande, RJ. O desenho experimental utilizou blocos de concreto como substrato artificial, os quais foram espalhados aleatoriamente na região de infralitoral do costão rochoso. O experimento compreendeu o uso de blocos Controle (ausência de manipulação) e quatro tratamentos, todos com cinco réplicas cada. Os tratamentos foram: tratamento Exclusão de predação (gaiola contra a ação de macropredadores), tratamento Nutriente (sacos de fertilizante de liberação lenta), tratamento Nutriente + exclusão de predação (gaiola contra ação de macropredadores e sacos de fertilizante de liberação lenta) e o tratamento Controle de artefatos (gaiola semifechada para avaliar geração de artefatos). Uma área de 15 x 15 cm do bloco foi monitorada a cada 20 dias, totalizando dez medições. Foram utilizados métodos de monitoramento visual e digital de porcentagem de cobertura por espécie. O enriquecimento com nutrientes foi avaliado através de medições da concentração dos nutrientes Ortofosfato, Nitrato, Nitrito e Amônio na água do entorno do bloco. Para analisar os possíveis artefatos foi realizado experimento de fluxo de água (método Clod card) e a luminosidade dentro das gaiolas foi medida. Os dados demonstraram modificações na estrutura das comunidades bentônicas incrustantes dos substratos artificiais devido às manipulações realizadas, ou seja, pelo enriquecimento com nutrientes, pela exclusão de predação e pela interação entre os dois fatores (Nutriente + exclusão de predação). Além disso, diferenças metabólicas foram detectadas nas substâncias extraídas dos organismos dos diferentes tratamentos do experimento. Esses resultados indicam a existência de controle top-down e bottom-up sobre a comunidade bentônica do local. / Marine communities can be affected by many factors. Within the context of trophic structure, these factors can be divided into bottom-up forces, such as nutrient availability, and top-down forces, for example, predation. In addition to changes in the structure of communities and populations of organisms, these forces can influence the production of secondary metabolites. This study aimed to evaluate the effect of environmental perturbations generated by separate and interactive manipulations of macropredators exclusion and nutrient enrichment on the communitys structure and the metabolic responses of marine fouling communities of artificial substrates in Biscaia rocky shores, Ilha Grande Bay, RJ. The experimental design used concrete blocks as artificial substrate. The blocks were randomly scattered in the sub tidal region of the rocky shore. The experiment involved the use of Control blocks (no manipulation) and four treatments with five replicates each. The treatments were: Predator Exclusion treatment (cages excluding macropredators), Nutrient treatment (packs with slow-releasing fertilizer), Nutrient + predator exclusion treatment (cage excluding macropredators and packs with slow-releasing fertilizer), and Artifacts control treatment (semi-closed cage to assess artifacts effects). An area of 15 x 15 cm of each block was monitored every 20 days, totaling ten measurements. Visual and digital species percentage coverage methods were used. To assess nutrient water enrichment, we measured concentration of nutrients (orthophosphate, nitrate, nitrite and ammonium) in the water. To evaluate possible cages experimental artifacts, a water flow test (Clod card method) was performed, and luminosity inside the cages was measured. Data demonstrated changes in the structure of fouling communities on artificial substrates due to the manipulations performed, i.e., the nutrient enrichment, predation exclusion and the interaction between these two factors (Nutrient + predator exclusion). Moreover, differences were observed in substances extracted from organisms in different treatments of the experiment. These results indicate the existence of top-down and bottom-up controls on the benthic community of this site.