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), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Coastal and estuarine environments experience large variability and rapid shifts in pCO₂ levels. Elevated pCO², or ocean acidification, often negatively affects early life stages of calcifying marine invertebrates, including bivalves, but it is unclear which developmental stage is most sensitive. I hypothesized that initial calcification is a critical stage during which high pCO₂ exposure has severe effects on larval growth and development of bay scallop (Argopecten irradians). Using five experiments varying the timing of exposure of embryonic and larval bay scallops to high CO₂, this thesis identifies two distinct stages of development during which exposure to high CO₂/low pH causes different effects on bay scallop larvae. I show that any exposure to high CO₂ consistently reduces survival of bay scallop larvae. I also show that high CO₂ exposure during initial calcification (12-24 h post-fertilization) results in significantly smaller shells, relative to ambient conditions, and this size decrease persists through the first week of development. High CO₂ exposure at 2-12 h post-fertilization (pre-calcification), does not impact shell size, suggesting that the CO₂ impact on size is a consequence of water chemistry during calcification. However, high CO₂ exposure prior to shell formation (2-12 h post-fertilization) causes a high incidence of larval shell deformity, regardless of CO₂ conditions during initial calcification. This impact does not occur in response to high CO₂ exposure after the 2-12 h period. The observations of two critical stages in early development has implications for both field and hatchery populations. If field populations were able to time their spawning to occur during the night, larvae would undergo initial calcification during the daytime, when CO₂ conditions are more favorable, resulting in larger veliger larvae. Hatcheries could invest minimal resources to monitor and modify water chemistry only during the first day of development to ensure larva are exposed to favorable conditions during that critical period. / by Meredith Megan White. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from student-submitted PDF version of thesis. / Includes bibliographical references (pages 169-182). / Protists play important roles in grazing and nutrient recycling, but quantifying these roles has been hindered by difficulties in collecting, culturing, and observing these often-delicate cells. During long-term deployments at the Martha's Vineyard Coastal Observatory (MVCO) (Massachusetts, USA), Imaging FlowCytobot (IFCB) made it possible to study live cells in situ without the need to culture or preserve. IFCB records images of cells with chlorophyll fluorescence above a trigger threshold, so taxonomically resolved analysis of protists is limited to mixotrophs and herbivores, which have eaten recently. To overcome this limitation, I coupled a broad-application 'live cell' fluorescent stain with a modified IFCB so that protists which do not contain chlorophyll (such as consumers of unpigmented bacteria and other heterotrophs) can also be recorded. Staining IFCB (IFCB-S) revealed higher abundances of grazers than the original IFCB, as well as some cell types not previously detected. To analyze a 10-year time series of herbivorous ciliates at MVCO and address broad patterns of seasonality of major ciliate classes and their components, I employed a statistical model that estimates a seasonal density pattern and simultaneously accounts for and separates any annual-scale effects. I describe the seasonality of three functional groups: a phototrophic ciliate, a mixotroph, and a group of strict heterotrophs, and comment on potential drivers of these patterns. DNA sequencing has also contributed to the study of protist communities, providing new insight into diversity, predator-prey interactions, and discrepancies between morphologically defined species and genotype. To explore how well IFCB images can be used to detect seasonal community change of the class Spirotrichea, an important and numerous group, I used high-throughput sequencing (HTS), which does not discriminate between chlorophyll-containing cells and the rest of the community. I report on species and genera of ciliates for which morphotype and genotype displayed high congruency. In comparing how well temporal aspects of genotypes and morphotypes correspond, I found that HTS was critical to detect and identify certain ciliates occupying a niche associated with warmer temperatures. I further showed that when these types of analyses are combined with IFCB results, they can provide hypotheses about food preferences. / by Emily Fay Brownlee. / Ph. D.

Nesta dissertação estão apresentados os principais conceitos teóricos envolvidos na ação dos jatos formados em dissipadores tipo salto esqui sobre fossa de erosão pré-escavada, desde o trajeto do jato em sua fase aérea e em sua fase submersa, dando especial ênfase às pressões hidrodinâmicas e sua caraterização junto ao fundo da bacia. Para estudar experimentalmente a ação dos jatos nas bacias de dissipação, utilizou-se de um modelo físico de escala 1:100 construído no Laboratório de Obras Hidráulicas do IPH/UFRGS com ensaios de diferentes vazões e diferentes profundidades de fossas pré-escavadas. Os dados foram extraídos dos ensaios no modelo físico através de vasta instrumentação, utilizando-se comportas, pontas linimétricas, piezômetros, sensores de pressão, imagens e outros equipamentos. Foi realizada uma análise criteriosa dos dados gerados no modelo físico a partir das imagens do jato na sua trajetória aérea e no escoamento do jato em sua fase submersa, comparando os dados do modelo aos resultados obtidos por métodos tradicionais de cálculo. Também foram analisados os dados de pressão gerados durante os ensaios, sendo apresentados os resultados relativos às pressões médias e às pressões dinâmicas. As pressões dinâmicas observadas no modelo físico foram comparadas com as calculadas por meio de metodologia teórica abordada na bibliografia com a finalidade de avaliar a qualidade dessa metodologia para aplicação em projetos de engenharia, onde se observou grandes diferenças de magnitude da pressão quando em colchões rasos, e diferenças de distribuição de pressão ao longo do fundo da bacia de dissipação, principalmente quando em colchões profundos. No sentido de ajustar a metodologia aplicada, foi proposta a variação de parâmetros que regulam a forma do bulbo de pressões e a aplicação de um coeficiente de amortecimento de pressões, sendo que assim foi possível melhorar significativamente a distribuição e a magnitude das pressões calculadas devido à ação dos jatos no fundo da bacia de dissipação. Os resultados se mostram satisfatórios até determinada distância após o pico de pressão provocado pelo jato, sendo que após este ponto os efeitos de ressalto hidráulico prevalecem e devem ser pesquisados em estudos futuros. / In this dissertation are presented the main theorical concepts involved in the action of the jets formed in ski jump spillways on stilling basins type pre-excavated scour hole, from the path of the jet in its air stage and in his submerged phase, with particular emphasis on hydrodynamic pressures and its characterization by the bottom of the basin. To experimentally study the action of the jets in stilling basins, was used a physical model in scale 1:100 built in Hydraulic Works Laboratory of IPH/UFRGS with experiments of different flow rates and different depths of pre-excavated scour hole. The data were extracted from experiments on the physical model through extensive instrumentation, using gates, piezometers, pressure sensors, images and other equipment. A careful analysis of the data generated in the physical model from the jet images in your path through the air was performed and the flow of the jet in its submerged phase, comparing the model data to the results obtained by traditional methods of calculation. The pressure data generated during the tests and presented the results for the mean pressures and dynamic pressures were also analyzed. Dynamic pressures observed in the physical model were compared with those calculated by means of theoretical methods for the purpose of evaluating the quality of this methodology for use in engineering projects, where we observed large differences in magnitude of pressure when in shallow water beds, and diferences in pressure distribution over the stilling basin bottom, especially when in deep water beds. In order to adjust the applied methodology, it was proposed to change parameters governing the shape of the pressure bulb and the application of a pressure damping coefficient, and thus was possible to significantly improved the distribution and magnitude of the calculated pressures due to action of the jets in the stilling basin bottom. The results have been satisfactory up to a certain distance after the peak pressure caused by the jet, and after this point the hydraulic jump effects prevail and should be investigated in future studies.

Esta dissertação investiga soluções para o problema genérico de geração de vistas sintéticas a partir de um conjunto de imagens utilizando a abordagem Depth-Image-Based Rendering. Essa abordagem utiliza um formato compacto para a representação de imagens 3D, composto basicamente por duas imagens, uma colorida para a vista de referência e outra em tons de cinza com a correspondência de disparidade para cada pixel. Soluções para esse problema beneficiam aplicações como Free Viewpoint Television. O maior desafio é o preenchimento de regiões sem informação de projeção considerando o novo ponto de vista, genericamente denominados holes, além de outros artefatos como cracks e ghosts que ocorrem por oclusões e erros no mapa de disparidade. Nesta dissertação apresentamos técnicas para remoção e tratamento de cada uma das classes de potenciais artefatos. O conjunto de métodos propostos apresenta melhores resultados quando comparado com o atual estado da arte em geração de vistas sintéticas com o modelo DIBR para o conjunto de dados Middlebury, considerando-se as métricas SSIM e PSNR. / This dissertation investigates solutions to the general problem of generating synthetic views from a set of images using the Depth-Image-Based Rendering approach. This approach uses a compact format for the 3D image representation, composed basically of two images, one color image for the reference view and other grayscale image with the disparity information available for each pixel. Solutions to this problem benefit applications such as Free Viewpoint Television. The biggest challenge is filling in regions without projection information considering the new viewpoint, usually called holes, and other artifacts such as cracks and ghosts that occur due to occlusions and errors in the disparity map. In this dissertation we present techniques for removal and treatment of each of these classes of potential artifacts. The set of proposed methods shows improved results when compared to the current state of the art generation of synthetic views using the DIBR model applied to the Middlebury dataset, considering the SSIM and PSNR metrics.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 131-143). / Coral reefs are biodiverse ecosystems that are at risk of degradation as a result of environmental changes. Reefs are constantly in a state of flux: the resident species assemblages vary considerably in space and time. However, the drivers of this variability are poorly understood. Tracking these changes and studying how coral reefs respond to natural and anthropogenic disturbance can be challenging and costly, particularly for reefs that are located in remote areas. Because many reef animals produce and use sound, recording the ambient soundscape of a reef might be one way to efficiently study these habitats from afar. In this thesis, I develop and apply a suite of acoustics-based tools to characterize the biological and anthropogenic acoustic activity that largely comprises marine soundscapes. First, I investigate links between reef fauna and reef-specific acoustic signatures on coral reefs located in the U.S. Virgin Islands. Second, I compare those findings to a more expansive study that I conducted in Maui, Hawaii, in which the drivers of bioacoustic differences among reefs are explored. Third, I investigate the distances over which sounds of biological origin may travel away from the reef and consider the range within which these acoustic cues might be usable by pelagic larvae in search of a suitable adult habitat. Fourth, I assess the extent to which the presence of vessel noise in shallow-water habitats changes the ambient soundscape. Finally, I present the results of a modeling exercise that questions how ocean noise levels might change over the next two decades as a result of major projected increases in the number and size of and distance traveled by commercial ships. The acoustics-based tools presented here help provide insight into ecosystem function and the extent of human activity in a given habitat. Additionally, these tools can be used to inform an effective regulatory regime to improve coral reef ecosystem management. / by Maxwell Bernard Kaplan. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 113-127). / White sharks (Carcharodon carcharias) are highly migratory, ecologically important, vulnerable, and understudied marine predators. Ecogeochemistry, which takes advantage of natural variations in chemical signatures recorded in body tissues, can help determine lifetime movement, age, and ontogenetic diet history in difficult to study species. Shark vertebrae are constructed of distinct layers of tissue laid down sequentially over an individual's lifetime and may preserve a chemical record of environmental exposure. In this thesis, I investigate the ecology of the understudied northwest Atlantic (NWA) white shark population by applying several ecogeochemistry techniques to their vertebrae. I generate the first radiocarbon ([delta]¹⁴C) age estimates for adult white sharks, dramatically extending the maximum age and longevity compared to earlier age studies. [delta]¹⁴C results also verify a lack of reworking of vertebral material and hint at possible sexual dimorphism in growth rates. Using amino acid and bulk stable isotope analyses, I show that individual sharks have marked variation in feeding and movement, and that pinnipeds do not constitute a large portion of their diet. Finally, I explore the utility of elemental chemistry to retrospectively infer movement. This work provides an important informational baseline for future NWA white shark ecological studies and conservation and management efforts. / by Li Ling Hamady. / Ph. D.

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), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 147-166). / The ecological integrity of tropical habitats, including mangroves, seagrass beds and coral reefs, is coming under increasing pressure from human activities. Many coral reef fish species are thought to use mangroves and seagrass beds as juvenile nurseries before migrating to coral reefs as adults. Identifying essential habitats and preserving functional linkages among these habitats is likely necessary to promote ecosystem health and sustainable fisheries on coral reefs. This necessitates quantitative assessment of functional connectivity among essential habitats at the seascape level. This thesis presents the development and first application of a method for tracking fish migration using amino acid (AA) 13C analysis in otoliths. In a controlled feeding experiment with fish reared on isotopically distinct diets, we showed that essential AAs exhibited minimal trophic fractionation between consumer and diet, providing a 513C record of the baseline isoscape. We explored the potential for geochemical signatures in otoliths of snapper to act as natural tags of residency in seagrass beds, mangroves and coral reefs in the Red Sea, Caribbean Sea and Eastern Pacific Ocean. The 13C values of otolith essential AAs varied as a function of habitat type and provided a better tracer of residence in juvenile nursery habitats than conventional bulk stable isotope analyses (SIA). Using our otolith AA SIA approach, we quantified the relative contribution of coastal wetlands and reef habitats to Lutjanus ehrenbergii populations on coastal, shelf and oceanic coral reefs in the Red Sea. L. ehrenbergii made significant ontogenetic migrations, traveling more than 30 km from juvenile nurseries to coral reefs and across deep open water. Coastal wetlands were important nurseries for L. ehrenbergii; however, there was significant plasticity in L. ehrenbergii juvenile habitat requirements. Seascape configuration played an important role in determining the functional connectivity of L. ehrenbergii populations in the Red Sea. The compound-specific SIA approach presented in this thesis will be particularly valuable for tracking the movement of species and life-stages not amenable to conventional tagging techniques. This thesis provides quantitative scientific support for establishing realistic population connectivity models that can be used to design effective marine reserve networks. / by Kelton Wells McMahon. / Ph.D.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Biology; and the Woods Hole Oceanographic Institution), 2017. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 159-168). / Thecosome pteropods are planktonic mollusks that form aragonite shells and that may experience increased dissolution and other adverse effects due to ocean acidification. This thesis focuses on assessing the possible biological effects of ocean acidification on the shells and locomotion of pteropods and examining the response of a local pteropod population to environmental change over time. I analyzed shell condition after exposing pteropods to elevated CO₂ as well as in natural populations to investigate the sensitivity of the shells of different species to aragonite saturation state ([omega][subscript A]). The pteropods (Limacina retroversa) from laboratory experiments showed the clearest pattern of shell dissolution in response to decreased [omega][subscript A], while wild populations either had non-significant regional trends in shell condition (Clio pyramidata) or variability in shell condition that did not match expectations due to regional variability in [omega][subscript A] (Limacina helicina). At locations with intermediate [omega][subscript A] (1.5-2.5) the variability seen in L. helicina shell condition might be affected by food availability more than tA. I examined sinking and swimming behaviors in the laboratory in order to investigate a possible fitness effect of ocean acidification on pteropods. The sinking rates of L. retroversa from elevated CO₂ treatments were slower in conjunction with worsened shell condition. These changes could increase their vulnerability to predators in the wild. Swimming ability was mostly unchanged by elevated CO₂ after experiments that were up to three weeks in duration. I used a long-term dataset of pteropods in the Gulf of Maine to directly test whether there has been a population effect of environmental change over the past several decades. I did not observe a population decline between 1977 and 2015, and L. retroversa abundance in the fall actually increased over the time series. Analysis of the habitat use of L. retroversa revealed seasonal associations with temperature, salinity, and bottom depths. The combination of laboratory experiments and field surveys helped to address gaps in knowledge about pteropod ecology and improve our understanding of the effects of ocean acidification on pteropods. / by Alexander Bergan. / Ph. D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2014. / Page 242 blank. Cataloged from PDF version of thesis. / Includes bibliographical references. / Recent work has documented dramatic changes in the West Antarctic Ice Sheet (WAIS) over the past 30 years (e.g., mass loss, glacier acceleration, surface warming) due largely to the influence of the marine environment. WAIS is particularly vulnerable to large-scale atmospheric dynamics that remotely influence the transport of marine aerosols to the ice sheet. Understanding seasonal- to decadal-scale changes in the marine influence on WAIS (particularly sea-ice concentration) is vital to our ability to predict future change. In this thesis, I develop tools that enable us to reconstruct the source and transport variability of marine aerosols to West Antarctica in the past. I validate new firn-core sea-ice proxies over the satellite era; results indicate that firn-core glaciochemical records from this dynamic region may provide a proxy for reconstructing Amundsen Sea and Pine Island Bay polynya variability prior to the satellite era. I next investigate the remote influence of tropical Pacific variability on marine aerosol transport to West Antarctica. Results illustrate that both source and transport of marine aerosols to West Antarctica are controlled by remote atmospheric forcing, linking local dynamics (e.g., katabatic winds) with large-scale teleconnections to the tropics (e.g., Rossby waves). Oxygen isotope records allow me to further investigate the relationship between West Antarctic firn-core records and temperature, precipitation origin, sea-ice variability, and large-scale atmospheric circulation. I show that the tropical Pacific remotely influences the source and transport of the isotopic signal to the coastal ice sheet. The regional firm-core array reveals a spatially varying response to remote tropical Pacific forcing. Finally, I investigate longer-term (-200 year) ocean and ice-sheet changes using the methods and results gleaned from the previous work. I utilize sea-ice proxies to reconstruct long-term changes in sea-ice and polynya variability in the Amundsen Sea, and show that the tropics remotely influence West Antarctica over decadal timescales. This thesis utilizes some of the highest-resolution, most coastal records in the region to date, and provides some of the first analyses of the seasonal- to decadal-scale controls on source and transport of marine aerosols to West Antarctica. / by Alison Sara Criscitiello. / Ph. D.

Thesis (S.M.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / "February 2008." / Includes bibliographical references (p. 133). / I build on the deterministic phytoplankton growth model of Sosik et al. by introducing process error, which simulates real variation in population growth and inaccuracies in the structure of the matrix model. Adding a stochastic component allows me to use maximum likelihood methods of parameter estimation. I lay out the method used to calculate parameter estimates, confidence intervals, and estimated population growth rates, then use a simplified three-stage model to test the efficacy of this method with simulated observations. I repeat similar tests with the full model based on Sosik et al., then test this model with a set of data from a laboratory culture whose population growth rate was independently determined. In general, the parameter estimates I obtain for simulated data are better the lower the levels of stochasticity. Despite large confidence intervals around some model parameter estimates, the estimated population growth rates have relatively small confidence intervals. The parameter estimates I obtained for the laboratory data fell in a region of the parameter space that in general contains parameter sets that are difficult to estimate, although the estimated population growth rate was close to the independently determined value. / by Lorraine Thomas. / S.M.