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), 2008. / Includes bibliographical references. / In this thesis, I provide quantitative descriptions of toothed whale echolocation and foraging behavior, including assessment of the effects of noise on foraging behavior and the potential influence of ocean acoustic propagation conditions on biosonar detection ranges and whale noise exposure. In addition to presenting some novel basic science findings, the case studies presented in this thesis have implications for future work and for management. In Chapter 2, I describe the application of a modified version of the Dtag to studies of harbor porpoise echolocation behavior. The study results indicate how porpoises vary the rate and level of their echolocation clicks during prey capture events; detail the differences in echolocation behavior between different animals and in response to differences in prey fish; and show that, unlike bats, porpoises continue their echolocation buzz after the moment of prey capture. Chapters 3-4 provide case studies that emphasize the importance of applying realistic models of ocean acoustic propagation in marine mammal studies. These chapters illustrate that, although using geometric spreading approximations to predict communication/target detection ranges or noise exposure levels is appropriate in some cases, it can result in large errors in other cases, particularly in situations where refraction in the water column or multi-path acoustic propagation are significant. Finally, in Chapter 5, I describe two methods for statistical analysis of whale behavior data, the rotation test and a semi-Markov chain model. I apply those methods to test for changes in sperm whale foraging behavior in response to airgun noise exposure. Test results indicate that, despite the low-level exposures experienced by the whales in the study, some (but not all) of them reduced their buzz production rates and altered other foraging behavior parameters in response to the airgun exposure. / by Stacy Lynn DeRuiter. / Ph.D.

Thesis: S.M., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 54-56). / The spatial and temporal evolution of stratified shear instabilities is quantified in a highly stratified and energetic estuary. The measurements are made using high-resolution acoustic backscatter from an array composed of six calibrated broadband transducers connected to a six-channel high-frequency (120-600 kHz) broadband acoustic backscatter system. The array was mounted on the bottom of the estuary and looking upward. The spatial and temporal evolution of the waves is described in terms of their wavelength, amplitude and turbulent dissipation as a function of space and time. The observed waves reach an arrested growth stage nearly 10 times faster than laboratory and numerical experiments performed at much lower Reynolds number. High turbulent dissipation rates are observed within the braid regions of the waves, consistent with the rapid transition to arrested growth. Further, it appears that the waves do not undergo periodic doubling and do not collapse once their maximum amplitude is reached. Under some conditions long internal waves may provide the perturbation that decreases the gradient Richardson number so as to initiate shear instability. The initial Richardson number for the observed instabilities is likely between 0.1 and 0.2 based on the slope and growth rate of the shear instabilities. / by Jonathan Randall Fincke. / S.M.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 148-152). / Wind waves in the ocean are a product of complex interaction of turbulent air flow with gravity driven water surface. The coupling is strong and the waves are non-stationary, irregular and highly nonlinear, which restricts the ability of traditional phase averaged models to simulate their complex dynamics. We develop a novel phase resolving model for direct simulation of nonlinear broadband wind waves based on the High Order Spectral (HOS) method (Dommermuth and Yue 1987). The original HOS method, which is a nonlinear pseudo-spectral numerical technique for phase resolving simulation of free regular waves, is extended to simulation of wind forced irregular broadband wave fields. Wind forcing is modeled phenomenologically in a linearized framework of weakly interacting spectral components of the wave field. The mechanism of wind forcing is assumed to be primarily form drag acting on the surface through wave-induced distribution of normal stress. The mechanism is parameterized in terms of wave age and its magnitude is adjusted by the observed growth rates. Linear formulation of the forcing is adopted and applied directly to the nonlinear evolution equations. Development of realistic nonlinear wind wave simulation with HOS method required its extension to broadband irregular wave fields. Another challenge was application of the conservative HOS technique to the intermittent non-conservative dynamics of wind waves. These challenges encountered the fundamental limitations of the original method. Apparent deterioration of wind forced simulations and their inevitable crash raised concerns regarding the validity of the proposed modeling approach. The major question involved application of the original HOS low-pass filtering technique to account for the effect of wave breaking. It was found that growing wind waves break more frequently and violently than free waves. / (cont.) Stronger filtering was required for stabilization of wind wave simulations for duration on the time scale of observed ocean evolution. Successful simulations were produced only after significant sacrifice of resolution bandwidth. Despite the difficulties our modeling approach appears to suffice for reproduction of the essential physics of nonlinear wind waves. Phase resolving simulations are shown to capture both - the characteristic irregularity and the observed similarity that emerges from the chaotic motions. Energy growth and frequency downshift satisfy duration limited evolution parameterizations and asymptote Toba similarity law. Our simulations resolve the detailed kinematics and the nonlinear energetics of swell, windsea and their fast transition under wind forcing. We explain the difference between measurements of initial growth driven by a linear instability mechanism and the balanced nonlinear growth. The simulations validate Toba hypothesis of wind-wave nonlinear quasi-equilibrium and confirm its function as a universal bound on combined windsea and swell evolution under steady wind. / by Alexander G. Kalmikov. / S.M.

Thesis (Ph. D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2009. / Includes bibliographical references (p. 271-277). / The Basin Acoustic Seamount Scattering Experiment (BASSEX) of 2004 was conducted to measure forward-scattering around the Kermit-Roosevelt Seamount Complex in the Northeast Pacific. The BASSEX experiment was focused on the bathymetric effects on acoustic propagation, in particular, on direct blockage, horizontal refraction, diffraction, and scattering by the seamounts. A towed hydrophone array, with 64 sensors cut for 250Hz (3m spacing), was used to measure the signals transmitted from the aforementioned broadband sources at many locations around the Kermit-Roosevelt and Elvis seamounts. Utilizing the measured broadband signals from the towed array, the size of the shadow zone was obtained. The measured data in the BASSEX experiment strongly support the understanding of the complicated phenomena of sound propagation around the seamounts. In addition, the experimental data could be used to validate current 2D and 3D theoretical models and develop new models to properly realize the sound propagation with such complicated phenomena. In this thesis, the reconciliation between the measured pulse arrivals from the BASSEX experiment and various two-dimensional (2D) and three-dimensional (3D) theoretical models is carried out to investigate the physical characteristics of the sound propagation around seamounts: First, the 2D Parabolic Equation (PE) model and the 2D ray tracing model are used to reconcile each ray arrival with the BASSEX experiment in terms of arrival time and grazing angle. / (cont.) We construct a sound speed field database based on the sound speed profiles from the BASSEX experiment, World Ocean Atlas (WOA) 2005, and CTD casts using the objective analysis. Second, 3D broadband sound propagation around a conical seamount is investigated numerically using the 3D spectral coupled-mode model (W. Luo, PhD Thesis, MIT, 2007). Since the calculation of 3D broadband pulses with the spectral coupled-mode model requires extensive computation time, a parallel program is developed with a clustered computing system to obtain results in reasonable time. The validation of the 3D spectral coupled-mode model is performed by a series of comparisons between the various 2D and 3D models for a shallow-water waveguide. The Kermit-Roosevelt seamount is modeled by a simple conical seamount for the 3D model. The computed 3D broadband pulses for the modeled conical seamount are compared with those from the BASSEX experiment and the 2D PE simulation. Through this analysis, we examine the limit of the application of the sound propagation models and improve the efficiency of the 3D sound propagation model using parallel computing to obtain a broadband pulse in a reasonable amount of time. / by Hyun Joe Kim. / 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), 2010. / "February 2010." Cataloged from PDF version of thesis. / Includes bibliographical references. / Primary producers play a critical role in the oceanic food chain and the global cycling of carbon. The marine diazotroph Trichodesmium is a major contributor to both primary production and nitrogen fixation in the tropical and subtropical oceans. These regions are often characterized by low phosphorus (P) concentrations, and P deficiency of Trichodesmium could limit growth, and constrain nitrogen fixation by this genus. Three key components of P metabolism in cyanobacteria include: inorganic phosphate (Pi) uptake, dissolved organic phosphorus (DOP) hydrolysis, and polyphosphate (polyP) biosynthesis and catabolism. These three pathways lay the foundation for the four chapters that make up the body of this thesis. Chapter two examines the relative importance of Pi and DOP in Trichodesmium in the Sargasso Sea by measuring uptake rates and uptake kinetics of ³³pi and DOP (using alpha labeled adenosine-5'-triphosphate ³³P-ATP as a model P ester compound). The in situ uptake rates suggest that the contribution of P ester to total P uptake can be greater than 25% for Trichodesmium, and therefore P esters are important for supplementing Trichodesmium's P demand. Chapter three confirms the presence of polyP in the Sargasso Sea populations. This is the first detection of polyP in an oligotrophic system and may indicate micro-scale variability in DIP or DOP supply. Chapter four examines the regulation of several genes involved in P scavenging in cultures of Trichodesmium erythraeum IMS101: two copies of a high affinity phosphate binding protein (pstS and sphX) and two putative alkaline phosphatases (phoA and phoX). / (cont.) Chapter five calibrates the expression of phoX to decreases in nitrogen fixation rate in Trichodesmium cultures allowing the use of phoX expression as a molecular indicator of P limitation of nitrogen fixation. Detection of phoX expression in the North Atlantic and South Pacific identified the extent and magnitude of P limitation in these regions. Taken together this thesis provides new insights into how Trichodesmium survives in low P environments, utilizes DOP, stores polyP, and the extent to which P can limit nitrogen fixation by this genus. / by Elizabeth Duncan Orchard. / 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. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Every genome tells a story. This dissertation contains four such stories, focused on shared themes of marine population dynamics and rapid change, with an emphasis on invasive marine species. Biological invasions are often characterized by a range expansion, during which strong genetic drift is hypothesized to result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. In this dissertation, population genetic and genomic tools are used to approach complex and previously intractable fundamental questions pertaining to the non-equilibrium dynamics of species invasions and rapid range expansions in two invasive marine species: the lionfish, Pterois volitans; and the shrimp, Palaemon macrodactylus. Using thousands of loci sequenced with restriction enzyme associated DNA sequencing in these two systems, this research tests theoretical predictions of the genomic signatures of range expansions. Additionally, the first chapter elucidates patterns of population genetic connectivity for deep-sea invertebrates in the New Zealand region demonstrating intimate relationships between genetics, oceanographic currents, and life history traits. Invasive shrimp results extend our understanding of marine population connectivity to suggest that human-mediated dispersal may be as important - if not more important - than oceanographic and life history considerations in determining genetic connectivity during specific phases of marine invasions. In invasive populations of lionfish, measures of genomic diversity, including a difference between observed and expected heterozygosity, were found to correlate with distance from the point of introduction, even in the absence of spatial metapopulation genetic structure. These results indicate a signal of rapid range expansion. The final study in this dissertation uses an innovative temporal approach to explore observed genomic patterns in the lionfish. In all, this dissertation provides a broad perspective through the study of multiple species undergoing superficially parallel processes that, under more intense scrutiny, are found to be mechanistically unique. It is only through comparative approaches that predictable patterns of population dynamics will emerge. / by Eleanor Kathleen Bors. / Ph. D.

Thesis (Ph.D.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2010. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Biological activity has shaped the surface of the earth in numerous ways, but life's most pervasive and persistent global impact has been the secular oxidation of the surface environment. Through primary production - the biochemical reduction of carbon dioxide to synthesize biomass - large amounts of oxidants such as molecular oxygen, sulfate and ferric iron have accumulated in the ocean, atmosphere and crust, fundamentally altering the chemical environment of the earth's surface. This thesis addresses aspects of the role of marine microorganisms in driving this process. In the first section of the thesis, biomarkers (hydrocarbon molecular fossils) are used to investigate the early history of microbial diversity and biogeochemistry. Molecular fossils from the Transvaal Supergroup, South Africa, document the presence in the oceans of a diverse microbiota, including eukaryotes, as well as oxygenic photosynthesis and aerobic biochemistry, by ca. 2.7Ga. Experimental study of the oxygen requirements of steroid biosynthesis suggests that sterane biomarkers in late Archean rocks are consistent with the persistence of microaerobic surface ocean environments long before the initial oxygenation of the atmosphere. In the second part, using Prochlorococcus (a marine cyanobacterium that is the most abundant primary producer on earth today) as a model system, we explored how microbes use the limited nutrient resources available in the marine environment to make the protein catalysts that enable primary production. Quantification of the Prochlorococcus proteome over the diel cell-division cycle reveals that protein abundances are distinct from transcript-level dynamics, and that small temporal shifts in enzyme levels can redirect metabolic fluxes. This thesis illustrates how molecular techniques can contribute to a systems-level understanding of biogeochemical processes, which will aid in reconstructing the past of, and predicting future change in, earth surface environment / by Jacob Richard Waldbauer. / 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. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Cataloged from PDF student-submitted version of thesis. "September 2014." / Includes bibliographical references (pages 191-201). / Synechococcus is a ubiquitous marine primary producer. Our understanding of the factors that determine its abundance has been limited by available observational tools, which have not been able to resolve population dynamics at timescales that match response times of cells (hours-days). Development of an automated flow cytometer (FlowCytobot) has enabled hourly observation of Synechococcus at the Martha's Vineyard Coastal Observatory (MVCO) since 2003. In order to ascribe changes in cell abundances to either growth or loss processes, information on division rate is needed. I refined a matrix population model that relates diel changes in the distribution of cell volume to division rate and demonstrated that it provides accurate estimates of daily division rate for both cultured and natural populations. Application of the model to the 11-year MVCO time series reveals that division rate is temperature limited during winter and spring, but light limited during fall. Inferred loss rates closely follow division rate in magnitude over the entire seasonal cycle, suggesting that losses are mainly generated by biological processes. While Synechococcus cell abundance, division rate, and loss rate demonstrate striking seasonal patterns, there are also significant shorter timescale variations and important multi-year trends that may be linked to climate. Interpretation of population dynamic patterns is complicated by the diversity found within marine Synechococcus, which is partitioned into 20 genetically distinct clades. Each clade may represent an ecotype, with a distinct ecological niche. To understand how diversity may affect population dynamics, I assessed the diversity at MVCO over annual cycles with culture-independent and dependent approaches. The population at MVCO is diverse, but dominated by clade I representatives throughout the year. Other clades were only found during summer and fall. High through-put sequencing of a diversity marker allowed a more quantitative investigation into these patterns. Five main Synechococcus oligotypes that comprise the population showed seasonal abundance patterns: peaking either during the spring bloom or during late summer and fall. This pattern strongly suggests that features of seasonal abundance are affected by the underlying diversity structure. Synechococcus abundance patterns result from a complex interplay among seasonal environmental changes, diversity, and biological losses. / by Kristen Rachell Hunter-Cevera. / 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), 2008. / Page 362 blank. / Includes bibliographical references. / Understanding how organisms deal with potentially toxic or fitness-reducing allelochemicals is important for understanding patterns of predation and herbivory in the marine environment. The ability of marine consumers to tolerate dietary toxins may involve biochemical resistance mechanisms, which increase the hydrophilicity of compounds and facilitate their active efflux out of sensitive cells and tissues. While several allelochemical-responsive detoxification enzymes have been sequenced and functionally characterized in terrestrial invertebrates feeding on chemically defended host plants, there is virtually no information concerning the role of these biotransformation enzymes that may mediate feeding tolerance in marine invertebrates. The objective of this research was to assess the diversity and dietary regulation of cytochrome P450s (CYP), glutathione S-transferases (GST) and ABC transporters in the generalist marine gastropod Cyphoma gibbosum feeding on a variety of chemically defended gorgonian corals, and to identify those dietary natural products that act as substrates for these proteins. Molecular and proteomic techniques identified both allelochemically-responsive CYPs, and constitutively expressed GSTs and transporters in Cyphoma digestive glands. Inhibition of Cyphoma GST activity by gorgonian extracts and selected allelochemicals (i.e., prostaglandins) indicated that gorgonian diets are likely to contain substrates for molluscan detoxification enzymes. In vitro metabolism studies with recombinant CYPs suggested those Cyphoma enzymes most closely related to vertebrate fatty acid hydroxylating enzymes may contribute to the detoxification ofichthyodeterrent cyclopentenone prostaglandins found in abundance in selected gorgonian species. / (cont.) Finally, the presence and activity of multixenobiotic resistance transporters in Cyphoma and the co-occurring specialist nudibranch, Tritonia hamnerorum, suggests these efflux transporters could function as a first line of defense against dietary intoxication. Together, these results suggest marine consumers that regularly exploit allelochemical-rich prey have evolved both general (GST and ABC transporters) and allelochemical-specific (CYP) detoxification mechanisms to tolerate prey chemical defenses. / by Kristen Elizabeth Whalen. / Ph.D.

Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 87-92). / Observations, theoretical models, and a numerical model (ADCIRC) are used to investigate the effects of tides, waves, bay bathymetry, and changing inlet geometry on the hydrodynamics of the multiple-inlet Katama system, Martha's Vineyard, MA. Momentum fluxes from breaking waves drive water into the inlet, nearly stopping the 2 m/s ebb currents during a hurricane. The evolving morphology of Katama Inlet has a dominant effect on tidal distortion and bay circulation. As Katama inlet lengthened, narrowed, and shoaled between 2011 and 2014, the relative effects of friction (observed and simulated) increased greatly, resulting in reduced circulation energy, an increase in the M6 tidal constituent, and changes in velocity asymmetries that are consistent with an evolution from flood to ebb dominance. The effects of changing inlet parameters (e.g., inlet geometry, bay bathymetry, friction, tidal forcing) are quantified via a lumped element model that accounts for the presence of a shallow flood shoal that limits flow from the ocean into the bay. As the difference in depth between inlet and flood shoal increases, the amplitude and phase of the incoming tide are increasingly modified from predictions without a flood shoal, and flows into the bay are further hindered. / by Mara S. M. Orescanin. / Ph. D.