Surface wave and storm surge prediction during Hurricane Sandy

Hurricane Sandy was the largest storm on historical record in the Atlantic Ocean basin with extensive coastal damage caused by large waves and high storm surge. The primary objectives of this thesis are to compare and evaluate three different spatially-varying surface wind fields of Hurricane Sandy to investigate the impact of the differences between the complex wind fields on predictions of the sea surface evolution, and to evaluate the impact of the storm on the hydrodynamics in Great South Bay (GSB) and the discharge of ocean water into the back-barrier bay from overwash over Fire Island. Three different spatially-varying surface wind fields were evaluated and compared to wind observations, including the parametric Holland (1980) model (H80), the parametric Generalized Asymmetric Holland Model (GAHM), and results from the WeatherFlow Regional Atmospheric Modelling System (WRAMS). The winds were used to drive the coupled Delft3D-SWAN hydrodynamic and ocean wave models on a regional grid. The results indicate that the WRAMS wind field produces wave model predictions in the best agreement with significant wave height observations, followed by the GAHM and H80 wind fields and that a regional atmospheric wind model is best for hindcasting hurricane waves and water levels when detailed observations are available, while a parametric vortex model is best for forecasting hurricane sea surface conditions. Using a series of four connected Delft3D-SWAN grids to achieve finer resolution over Fire Island and GSB, a higher resolution WRAMS was used to predict waves and storm surge. The results indicate that strong local winds have the largest influence on water level fluctuations in GSB. Three numerical solutions were conducted with varying extents of barrier island overwash. The simulations allowing for minor and major overwash indicated good agreement with observations in the east end of GSB and suggest that island overwash provided a significant contribution of ocean water to GSB during the storm. Limiting the overwash in the numerical model directly impacts the total discharge into GSB from the ocean through existing inlets. The results of this study indicate that barrier island overwash had a significant impact on the water levels in eastern GSB.

Strontium isotopes and sedimentology of a marine Triassic succession (upper Ladinian) of the westernmost Tethys, Spain

Chemical Stratigraphy, or the study of the variation of chemical elements within sedimentary sequences, has gradually become an experienced tool in the research and correlation of global geologic events. In this paper 87Sr/ 86Sr ratios of the Triassic marine carbonates (Muschelkalk facies) of southeast Iberian Ranges, Iberian Peninsula, are presented and the representative Sr-isotopic curve constructed for the upper Ladinian interval. The studied stratigraphic succession is 102 meters thick, continuous, and well preserved. Previous paleontological data from macro and micro, ammonites, bivalves, foraminifera, conodonts and palynological assemblages, suggest a Fassanian-Longobardian age (Late Ladinian). Although diagenetic minerals are present in small amounts, the elemental data content of bulk carbonate samples, especially Sr contents, show a major variation that probably reflects palaeoenvironmental changes. The 87Sr/86Sr ratios curve shows a rise from 0.707649 near the base of the section to 0.707741 and then declines rapidly to 0.707624, with a final values rise up to 0.70787 in the upper part. The data up to meter 80 in the studied succession is broadly concurrent with 87Sr/86Sr ratios of sequences of similar age and complements these data. Moreover, the sequence stratigraphic framework and its key surfaces, which are difficult to be recognised just based in the facies analysis, are characterised by combining variations of the Ca, Mg, Mn, Sr and CaCO3 contents

Hans Blumenberg and Feminism

The German philosopher Hans Blumenberg [1920-1996] was interested in feminist issues during the last two decades of his life as shown their dedication and effort in compiling selected cuts in the media related to the topic of women and their development of multiple short essays inspired by the latter and countless curious anecdotes. Hans Blumenberg and feminism seeks to inform the reader about the existence of a blumenberguian thought line of research totally unexplored so far. It can only be revealed through the study of the philosopher ‘Nachlaβ’ found in the Deutsches literaturarchiv Marbach (Stuttgart) which I personally had a chance to dig through the award of a research grant from the DAAD (Deutscher Akademischer Dienst Austage).

Sedimentology of sites 14-141, 41-366, 47-397 and 79-544B

Along the N-S-transect of DSDP-Sites 5446, 397, 141, and 366, oxygen and carbon isotopes, flux rates of calcium carbonate, terrigenous matter, and biogenic opal, clay minerals and the size distribution of terrigenous partictes were determined in order to assess the ties between atmospheric and oceanic surface and deep-water circulation off northwest Africa during the late Neogene. During the last 9 m.y., both the paleoceanography in the eastern Atlantic and west African paleodimates were intimately correlated with the evolution of the polar ice sheets as reflected in the benthos d18O curves of the 4 DSDP-Sites. These records make it possible to distinguish six major time intervals which were charaterized by long-term persistent regimes of climatic stability or climatic change. Short-term, "Milankovitch"-type cycles superimpose the long-term climatic evolution and may reflect the chronostratigraphic control fluctuations of the solar insolation persisting back to pre-Pleistocene times. Relatively stable, warm climates prevailed during the late Tortonian/early Messinean, 9 to 6 m.y., and the early Pliocene, 4.5 to 3.5 m.y. ago. Based on d18O curves, the amplitudes of short-term climatic variation were generally low, and the ice sheets were smaller than during peak Holocene time. Oceanic circulation and resulting paleoproductivity in upwelling zones were insignificant. The strength of dust supplying meridional trade winds was low (3 to 5 m/s), interglacial-style zonal winds near the ITCZ were dominant, as indicated by the high abundance of kaolinite. Phases of fluvial sediment supply were common. Humidity was characteristic of the climate in northwest Africa for the major part of this time. Major episodes of climatic deterioration in the subtropics occurred in the latest Miocene/early Pliocene, between some 5.6 and 5.2 and between 4.9 and 4.6 m.y. ago, in the late Pliocene, between 3.2 and 2.4 m.y. ago, and again in the Quaternary, near 1 m.y. ago. The episodes were correlated with marked increases of the global ice volume, as revealed by drastic increases of d18O values. They suggest sea-level falls of up to 70 m below the present sea level in the latest Miocene and earliest Pliocene and of 145 m in the latest Pliocene and Quaternary. The climatic changes resulted in strongly enhanced meridional trade winds as suggested by coarser terrigenous grain-sizes, increased mass accumulation rates of eolian dust, and changes in clay-mineral composition from dominantly kaolinite to illite and chlorite. The meridional trade winds reached speeds of 8 to 10 m/s with a maximum near 15 m/s. The enhanced winds probably led t o intensified coastal upwelling as shown by the contemporaneous local increase i n the deposition of biogenic silica and the local depletion of 13C at Site 397. The most drastic environmental changes near 2.4 and 1 m.y. ago coincide with hiatuses which may indicate phases of general erosion due to strongly enhanced deep-water circulation in the northeast At1antic along the northwest African continental margin. The occasional occurrence of quartz grains coarser than 250 µm may suggest ice-rafted debris in sediments off Morocco. During these time intervals the climate in NW-Africa was dominantly arid. Nevertheless, fluvial runoff (and humidity) continued to be important during intermittent warm phases of the short-term climatic cycles. During the end and the beginning of (inter-) glacial times, fluvial supply of nutrients seems to be the dominant factor, controling phases of enhanced paleoproductivity observed off northwest Africa, whereas during phases of glacial maximum strenger fertility of (increased) coastal upwelling becomes more important. A long-term evolution of paleoenvironments during the last 40 m.y. is depicted in the sediments of Site 366 and is clearly controlled by the plate tectonic route of this Site. During Oligocene times, Site 366 lay in the center of the equatorial upwelling, as shown by the high content of biogenic silica contributing up to 100 % of the carbonate-free sediment fraction >6 µm. The influence of equatorial upwelling abruptly terminated near 15 m.y. ago, a change in the record exaggerated by a hiatus of about 2 m.y. Prior to 25 m.y., the terrigenous input at the paleolatitude of Site 366 was restricted t o eolian sediment supply from South Africa by southeasterly trade winds, as shown by dominantly illite and chlorite in the clay fraction and extremely fine-grained terrigenous matter. Near the Oligocene/Miocene boundary, Site 366 drifted across the equator into the belt of the northeasterly trade winds, which is inferred from the increased content of kaolinite and coarser grain sizes of the terrigenous sediment fraction. The clay-mineral and grain-size compositions of Site 366 do not reflect a noteworthy northward shift of the ITCZ during late Miocene and early Pliocene times, i.e. no marked global circulation asymmetry due to the possible absence of a major Northern Hemisphere glaciation (Flohn 1981). This lack of a more northerly position of the ITCZ may result from a bipolar glaciation already existing during late Miocene times, such as also suggested by the evidence of tillites on Iceland and in southern Alaska during those intervals (e.g., Denton & Amstrong 1969, Mudie & Helgason 1983).

Phylum-wide transcriptome analysis of oogenesis and early embryogenesis in selected nematode species

Oogenesis is a prerequisite for embryogenesis in Metazoa. During both biological processes important decisions must be made to form the embryo and hence ensure the next generation: (1) Maternal gene products (mRNAs, proteins and nutrients) must be supplied to the embryo. (2) Polarity must be established and axes must be specified. While incorporation of maternal gene products occurs during oogenesis, the time point of polarity establishment and axis specification varies among species, as it is accomplished either prior, during, or after fertilisation. But not only the time point when these events take place varies among species but also the underlying mechanisms by which they are triggered. For the nematode model Caenorhabditis elegans the underlying pathways and gene regulatory networks (GRNs) are well understood. It is known that there the sperm entry point initiates a primary polarity in the 1-celled egg and with it the establishment of the anteroposterior axis. However, studies of other nematodes demonstrated that polarity establishment can be independent of sperm entry (Goldstein et al., 1998; Lahl et al., 2006) and that cleavage patterns, symmetry formation and cell specification also differ from C. elegans. In contrast to the studied Chromadorea (more derived nematodes including C. elegans), embryos of some marine Enoplea (more basal representatives) even show no discernible early polarity and blastomeres can adopt variable cell fates (Voronov and Panchin 1998). The underlying pathways controlling the obviously variant embryonic processes in non-Caenorhabditis nematodes are essentially unknown. In this thesis I addressed this issue by performing a detailed unbiased comparative transcriptome analysis based on microarrays and RNA sequencing of selected developmental stages in a variety of nematodes from different phylogenetic branches with C. elegans as a reference system and a nematomorph as an outgroup representative. In addition, I made use of available genomic data to determine the presence or absence of genes for which no expression had been detected. In particular, I focussed on components of selected pathways or GRNs which are known to play essential roles during C. elegans development and/or other invertebrate or vertebrate model systems. Oogenesis must be regulated differently in non-Caenorhabditis nematodes, as crucial controlling components of Wnt and sex determination signaling are absent in these species. In this respect, I identified female-specific expression of potential polarity associated genes during gonad development and oogenesis in the Enoplean nematode Romanomermis culicivorax. I could show that known downstream components of the polarity complexes PAR-3/-6/PKC-3 and PAR-1/-2 are absent in non-Caenorhabditis species. Even PAR-2 as part of the polarity complex does not exist in these nematodes. Instead, transcriptomes of nematodes (including C. elegans), show expression of other polarity-associated complexes such as the Lgl (Lethal giant larvae) complex. This result could pose an alternative route for nematodes and nematomorphs to initiate polarity during early embryogenesis. I could show that crucial pathways of axis specification, such as Wnt and BMP are very different in C. elegans compared to other nematodes. In the former, Wnt signaling, for instance, is mediated by four paralogous beta-catenins, while other Chromadorea have fewer and Enoplea only one beta-catenin. The transcriptomes of R. culicivorax and the nematomorph show that regulators of BMP (e.g. Chordin), are specifically expressed during early embryogenesis only in Enoplea and the close outgroup of nematomorphs. In conclusion, my results demonstrate that the molecular machinery controlling oogenesis and embryogenesis in nematodes is unexpectedly variable and C. elegans cannot be taken as a general model for nematode development. Under this perspective, Enoplean nematodes show more similarities with outgroups than with C. elegans. It appears that certain pathway components were lost or gained during evolution and others adopted new functions. Based on my findings I can conjecture, which pathway components may be ancestral and which were newly acquired in the course of nematode evolution.

HPC management and engineering in the hybrid cloud

The evolution and maturation of Cloud Computing created an opportunity for the emergence of new Cloud applications. High-performance Computing, a complex problem solving class, arises as a new business consumer by taking advantage of the Cloud premises and leaving the expensive datacenter management and difficult grid development. Standing on an advanced maturing phase, today’s Cloud discarded many of its drawbacks, becoming more and more efficient and widespread. Performance enhancements, prices drops due to massification and customizable services on demand triggered an emphasized attention from other markets. HPC, regardless of being a very well established field, traditionally has a narrow frontier concerning its deployment and runs on dedicated datacenters or large grid computing. The problem with common placement is mainly the initial cost and the inability to fully use resources which not all research labs can afford. The main objective of this work was to investigate new technical solutions to allow the deployment of HPC applications on the Cloud, with particular emphasis on the private on-premise resources – the lower end of the chain which reduces costs. The work includes many experiments and analysis to identify obstacles and technology limitations. The feasibility of the objective was tested with new modeling, architecture and several applications migration. The final application integrates a simplified incorporation of both public and private Cloud resources, as well as HPC applications scheduling, deployment and management. It uses a well-defined user role strategy, based on federated authentication and a seamless procedure to daily usage with balanced low cost and performance.

Ecological and evolutionary effects of dispersal on freshwater zooplankton

A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate the fields of ecology and evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species identity, trait distributions, and genetic composition may be maintained among ecologically divergent habitats. New theories and hypotheses (e.g., metacommunity theory and the Monopolization hypothesis) have been developed to understand better the processes occurring in spatially structured environments and how the movement of individuals among habitats contributes to ecology and evolution at broader scales. As few empirical studies of these theories exist, this work seeks to further test these concepts. Spatial and temporal dispersal are the mechanisms that connect habitats to one another. Both processes allow organisms to leave conditions that are suboptimal or unfavorable, and enable colonization and invasion, species range expansion, and gene flow among populations. Freshwater zooplankton are aquatic crustaceans that typically develop resting stages as part of their life cycle. Their dormant propagules allow organisms to disperse both temporally and among habitats. Additionally, because a number of species are cyclically parthenogenetic, they make excellent model organisms for studying evolutionary questions in a controlled environment. Here, I use freshwater zooplankton communities as model systems to explore the mechanisms and consequences of dispersal and to test these nascent theories on the influence of spatial structure in natural systems. In Chapter one, I use field experiments and mathematical models to determine the range of adult zooplankton dispersal over land and what vectors are moving zooplankton. Chapter two focuses on prolonged dormancy of one aquatic zooplankter, Daphnia pulex. Using statistical models with field and mesocosm experiments, I show that variation in Daphnia dormant egg hatching is substantial among populations in nature, and some of that variation can be attributed to genetic differences among the populations. Chapters three and four explore the consequences of dispersal at multiple levels of biological organization. Chapter three seeks to understand the population level consequences of dispersal over evolutionary time on current patterns of population genetic differentiation. Nearby populations of D. pulex often exhibit high population genetic differentiation characteristic of very low dispersal. I explore two alternative hypotheses that seek to explain this pattern. Finally, chapter four is a case study of how dispersal has influenced patterns of variation at the community, trait and genetic levels of biodiversity in a lake metacommunity.

SOCIAL AND ECOLOGICAL FACTORS INFLUENCING COLLECTIVE BEHAVIOR IN GIANT DANIO

A fundamental problem in biology is understanding how and why things group together. Collective behavior is observed on all organismic levels - from cells and slime molds, to swarms of insects, flocks of birds, and schooling fish, and in mammals, including humans. The long-term goal of this research is to understand the functions and mechanisms underlying collective behavior in groups. This dissertation focuses on shoaling (aggregating) fish. Shoaling behaviors in fish confer foraging and anti-predator benefits through social cues from other individuals in the group. However, it is not fully understood what information individuals receive from one another or how this information is propagated throughout a group. It is also not fully understood how the environmental conditions and perturbations affect group behaviors. The specific research objective of this dissertation is to gain a better understanding of how certain social and environmental factors affect group behaviors in fish. I focus on two ecologically relevant decision-making behaviors: (i) rheotaxis, or orientation with respect to a flow, and (ii) startle response, a rapid response to a perceived threat. By integrating behavioral and engineering paradigms, I detail specifics of behavior in giant danio Devario aequipinnatus (McClelland 1893), and numerically analyze mathematical models that may be extended to group behavior for fish in general, and potentially other groups of animals as well. These models that predict behavior data, as well as generate additional, testable hypotheses. One of the primary goals of neuroethology is to study an organism's behavior in the context of evolution and ecology. Here, I focus on studying ecologically relevant behaviors in giant danio in order to better understand collective behavior in fish. The experiments in this dissertation provide contributions to fish ecology, collective behavior, and biologically-inspired robotics.

Humankindness: Illness, Animality, and the Limits of the Human in the Victorian Novel

This project posits a link between representations of animals or animality and representations of illness in the Victorian novel, and examines the narrative uses and ideological consequences of such representations. Figurations of animality and illness in Victorian fiction have been examined extensively as distinct phenomena, but examining their connection allows for a more complex view of the role of sympathy in the Victorian novel. The commonplace in novel criticism is that Victorian authors, whether effectively or not, constructed their novels with a view to the expansion of sympathy. This dissertation intervenes in the discussion of the Victorian novel as a vehicle for sympathy by positing that texts and scenes in which representations of illness and animality are conjoined reveal where the novel draws the boundaries of the human, and the often surprising limits it sets on sympathetic feeling. In such moments, textual cues train or direct readerly sympathies in ways that suggest a particular definition of the human, but that direction of sympathy is not always towards an enlarged sympathy, or an enlarged definition of the human. There is an equally (and increasingly) powerful antipathetic impulse in many of these texts, which estranges readerly sympathy from putatively deviant, degenerate, or dangerous groups. These two opposing impulses—the sympathetic and the antipathetic—often coexist in the same novel or even the same scene, creating an ideological and affective friction, and both draw on the same tropes of illness and animality. Examining the intersection of these different discourses—sympathy, illness, and animality-- in these novels reveals the way that major Victorian debates about human nature, evolution and degeneration, and moral responsibility shaped the novels of the era as vehicles for both antipathy and sympathy. Focusing on the novels of the Brontës and Thomas Hardy, this dissertation examines in depth the interconnected ways that representations of animals and animality and representations of illness function in the Victorian novel, as they allow authors to explore or redefine the boundary between the human and the non-human, the boundary between sympathy and antipathy, and the limits of sympathy itself.

Strategic divide management in pharmaceutical alliances: A partner’s strategic evolution as a reason for strategic divide

Strategic alliances are widely used in the pharmaceutical industry and, ideally, they are long-lasting structures that bring many benefits and value to the alliance partners. However, organizations continuously encounter pressures to enhance performance, while the environment in which they operate evolves. Therefore, an alliance partner might be forced to change its strategy, which can lead to the partners’ misaligned priorities and strategic divide. The academic literature acknowledges the impact a partner’s strategic change can have on the value of the alliance, but the phenomenon is not studied further, which is why the purpose of this study is to understand the role that a partner’s strategic evolution plays in strategic alliances within the pharmaceutical industry. The main purpose is further divided into three sub-objectives: 1) Describe reasons behind the strategic direction change of a partner firm, 2) Understand the consequences of partners’ misaligned priorities, and 3) Describe proactive and reactive ways to manage strategic divide between alliance partners. Since the phenomenon is not studied much, the empirical part of the study was conducted as a qualitative analysis using expert interviews to better understand, how the partner’s strategic evolution affects the alliance. The empirical data was organized into themes, according to the researcher’s interpretations on the interviews. The research findings demonstrated, how the partners change their strategies if the external or organizational environments change. The strategic changes, again, cause strategic divides between the alliance partners that are likely to have an impact on the alliance value. The findings revealed that the interviewees consider anticipation of the partner’s strategic change to be really difficult, but, at the same time, it was noted that a proactive strategic divide management could help to prevent and detect some divides. Additionally, the results showed that, after the detection, a reactive approach in a controlled manner was seen to be the most beneficial for the alliance’s future performance. This study proved that a partner’s strategic evolution affects the partners’ priority alignment and alliance value, which is why the strategic divide management is important in organizations that are involved with strategic alliances. In order to understand the role of a partner’s strategic evolution and provide managers with a tool to manage alliances and strategic divides, the study combined the alliance lifecycle as well as the proactive and reactive approaches to strategic divide, and presented a framework for strategic divide management.

New Perspective On The Haplosporidian Parasites Of Molluscs

The protist phylum Haplosporidia comprises over 40 described species with representatives infecting a range of mollusc hosts, including several ecologically and economically significant pathogens. Continuing exploration of haplosporidian diversity has added ten new species in recent years and brought the phylogenetics of the group into somewhat clearer focus, with monophyletic Bonamia and Minchinia lineages continuing to be supported. However, the addition of new sequences to phylogenetic analyses has left the paraphyletic genus Haplosporidium’s picture less resolved. It is not clear that even two genera will be enough to accommodate the species presently drawn to the Haplosporidium regions of the haplosporidian tree. In this review, we summarize recent findings in haplosporidian diversity and phylogenetics, and provide a synthesis of our understanding of the life cycles and environmental influences on haplosporidians, with particular emphasis on the important pathogens Haplosporidium nelsoni and Bonamia ostreae. Additionally, we consider the evolution of the “microcell haplosporidian” lifestyle of Bonamia parasites, and suggest that colonization of high-density oyster host populations in relatively stable euhaline marine environments may have been an important development favoring the evolution of the microcell haplosporidian life strategy.

Reuse and integration of specification logics: the hybridisation perspective

Hybridisation is a systematic process along which the characteristic features of hybrid logic, both at the syntactic and the semantic levels, are developed on top of an arbitrary logic framed as an institution. It also captures the construction of first-order encodings of such hybridised institutions into theories in first-order logic. The method was originally developed to build suitable logics for the specification of reconfigurable software systems on top of whatever logic is used to describe local requirements of each system’s configuration. Hybridisation has, however, a broader scope, providing a fresh example of yet another development in combining and reusing logics driven by a problem from Computer Science. This paper offers an overview of this method, proposes some new extensions, namely the introduction of full quantification leading to the specification of dynamic modalities, and exemplifies its potential through a didactical application. It is discussed how hybridisation can be successfully used in a formal specification course in which students progress from equational to hybrid specifications in a uniform setting, integrating paradigms, combining data and behaviour, and dealing appropriately with systems evolution and reconfiguration.

Close-in planets around giant stars: lack of hot-Jupiters and prevalence of multiplanetary systems

Extrasolar planets abound in almost any possible configuration. However, until five years ago, there was a lack of planets orbiting closer than 0.5 au to giant or subgiant stars. Since then, recent detections have started to populated this regime by confirming 13 planetary systems. We discuss the properties of these systems in terms of their formation and evolution off the main sequence. Interestingly, we find that 70.0 ± 6.6% of the planets in this regime are inner components of multiplanetary systems. This value is 4.2σ higher than for main-sequence hosts, which we find to be 42.4 ± 0.1%. The properties of the known planets seem to indicate that the closest-in planets (a< 0.06 au) to main-sequence stars are massive (i.e., hot Jupiters) and isolated and that they are subsequently engulfed by their host as it evolves to the red giant branch, leaving only the predominant population of multiplanetary systems in orbits 0.06 and evolution of hot Jupiters.

TAXONOMY, MORPHOLOGY, AND RNA-SEQ TRANSCRIPTOMICS OF THE CUBOZOAN ALATINA ALATA, AN EMERGING MODEL CNIDARIAN

Cnidarians are often considered simple animals, but the more than 13,000 estimated species (e.g., corals, hydroids and jellyfish) of the early diverging phylum exhibit a broad diversity of forms, functions and behaviors, some of which are demonstrably complex. In particular, cubozoans (box jellyfish) are cnidarians that have evolved a number of distinguishing features. Some cubozoan species possess complex mating behaviors or particularly potent stings, and all possess well-developed light sensation involving image-forming eyes. Like all cnidarians, cubozoans have specialized subcellular structures called nematocysts that are used in prey capture and defense. The objective of this study is to contribute to the development of the box jellyfish Alatina alata as a model cnidarian. This cubozoan species offers numerous advantages for investigating morphological and molecular traits underlying complex processes and coordinated behavior in free-living medusozoans (i.e., jellyfish), and more broadly throughout Metazoa. First, I provide an overview of Cnidaria with an emphasis on the current understanding of genes and proteins implicated in complex biological processes in a few select cnidarians. Second, to further develop resources for A. alata, I provide a formal redescription of this cubozoan and establish a neotype specimen voucher, which serve to stabilize the taxonomy of the species. Third, I generate the first functionally annotated transcriptome of adult and larval A. alata tissue and apply preliminary differential expression analyses to identify candidate genes implicated broadly in biological processes related to prey capture and defense, vision and the phototransduction pathway and sexual reproduction and gametogenesis. Fourth, to better understand venom diversity and mechanisms controlling venom synthesis in A. alata, I use bioinformatics to investigate gene candidates with dual roles in venom and digestion, and review the biology of prey capture and digestion in cubozoans. The morphological and molecular resources presented herein contribute to understanding the evolution of cubozoan characteristics and serve to facilitate further research on this emerging cubozoan model.

Dinoflagellate Genomic Organization and Phylogenetic Marker Discovery Utilizing Deep Sequencing Data

Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets.