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), 2009. / Includes bibliographical references. / Tropical cyclone activity over the last 5000 years is investigated using overwash sediments from coastal lagoons on the islands of Vieques, Puerto Rico and Koshikijima, Japan. A simple sediment transport model can reproduce the landward fining deposits observed at Vieques, and reveals that although the record exhibits centennial-tomillennial changes in hurricane overwash frequency, the magnitude of these flooding events has remained relatively constant. Stochastic simulations of hurricane overwash show that breaks in activity at Vieques are extremely long and unlikely to occur under the current hurricane climatology and the present barrier morphology. Periods of less frequent hurricane deposition at Vieques are contemporaneous with intervals of increased El Nifio occurrences and reduced precipitation in West Africa, suggesting a dominant influence by these two climatic phenomena. Hiatuses in overwash activity between 3600-to-2500 and 1000-500 years ago are longer than what is generated by overwash simulations under a constant El Niflo-like state, indicating that mechanisms in addition to variability in the El Nifio/Southern Oscillation are required to completely produce the overwash variability at Vieques. Periods of low overwash activity at Vieques are concurrent with increased overwash activity at Kamikoshiki and may indicate a correspondence between tropical cyclone activity in the western Northern Atlantic and the western North Pacific. / by Jonathan D. Woodruff. / 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), 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Hydrothermal vents and coral ecosystems are conspicuous biological hot spots in the deep-sea. These ecosystems face increasing threats from human activities. Having thorough taxonomic inventories as well as understanding species' relatedness, genetic diversity, connectivity patterns, and adaptive potential is fundamental for the implementation of conservation strategies that help mitigate these threats. This thesis provides fundamental high-priority knowledge in taxonomic, evolutionary, and ecological aspects of deep-sea coral and vent species, by harnessing the power of genomic tools and overcoming long-standing methodological barriers. First, I develop bioinformatic tools that help guide the design of studies aiming to characterize eukaryotic genome diversity using restriction-site associated DNA sequencing. Using these tools I find that the predictability of restriction site frequencies in eukaryotic genomes is chiefly determined by the phylogenetic position of the target species and the recognition sequence of the selected restriction enzyme. These tools are then applied to test global-scale historical biogeographic hypotheses of vent fauna using barnacles as model. Phylogeographic inferences suggest that the western Pacific was the place of origin of the major vent barnacle lineage, followed by circumglobal colonization eastward along the southern hemisphere during the Neogene. I suggest that the geological processes and dispersal mechanisms discussed here can explain distribution patterns of many other marine taxa in addition to barnacles. Regional-scale analyses indicate that vent barnacle populations are well connected within basins and ridge systems, and that their diversity patterns do not conform to the predictions from the hypothesis that seamounts are centers of endemism. I then move on to resolve long-standing questions regarding species definitions in recalcitrant deep-sea coral taxa, by unambiguously resolving evolutionary relationships and objectively inferring species boundaries. Finally, I explore the adaptive potential of deep-sea coral species to environmental changes by examining a case of adaptation to shallow water from the deep sea. Candidate positive-selection markers shared between pairs of shallow and deep populations are identified as likely makers for genomic regions involved in adaptation. Overall, the results from this thesis constitute critical baseline data with which to assess potential effects of anthropogenic disturbances on deep-sea ecosystems. / by Santiago Herrera Monroy. / 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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Marine populations are increasingly subjected to changing conditions whether through harvest or through broad-scale habitat change. Historically, few models have accounted for such trends over time, and even fewer have been used to study how trends affect optimal harvests. I developed and analyzed several models that explore, first, endogenous change caused by harvest and, second, exogenous change from factors (such as rising ocean temperatures) outside harvesters' control. In these models, I characterized the profit-or yield-maximizing strategy when harvesting damages habitat in a multispecies fishery, when harvest creates a selective pressure on dispersal, and when rising temperatures cause changes in vital rates. I explore this last case in both deterministic and stochastic environments, and also allow the harvester to learn about unknown parameters of the stock recruitment model while harvesting. I also develop an unambiguous definition of and describe a statistical test for a shift in a species' spatial distribution. My results demonstrate that optimal harvesting strategies in a changing environment differ in important ways from optimal strategies in a constant environment. / by Emily Alison Moberg. / Ph. D.

Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution); and, (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2005. / Includes bibliographical references (p. 149-151). / Despite the great achievements obtained with fast-field and parabolic equation models, normal mode programs still remain a very efficient, simple and practical tool for describing ocean acoustics in range-independent environments. Numerical implementations of wave-theory solutions for range-dependent acoustic problems can be classified as: normal-mode techniques (adiabatic or coupled modes); parabolic-approximation techniques (narrow- or wide-angle parabolic equations solved by split-step or finite-difference techniques); and finite-element/finite- difference solutions of the full wave equation. The mode techniques provide approximate field solutions if implemented in the adiabatic approximation, while complete wave theory solutions can be obtained by including full mode coupling. Parabolic approximations to the elliptic wave equation have been extensively studied over the past 10 years([15], [23]). The advantage of using a parabolic wave equation is that it can be efficiently solved by noniterative forward marching techniques. However, any form of the parabolic equation is an approximate wave equation derived under the assumptions of: (1) forward propagation only, and (2) that energy is propagating within a limited angular spectrum around the main propagation direction. The last category of models based on finite-difference and finite-element solutions of the full wave equation([22]) is well suited for providing solutions for propagation in general range-dependent environments. / (cont.) The existing codes, however, are extremely computer intensive. My thesis focuses on a two-dimensional two-way coupled modes model, and then expend it to a three-dimensional coupled modes model for two-dimensional, range- dependent waveguides. Numerical examples of two-dimensional and three-dimensional problems are presented, and comparisons with the results from analytical solution, as well as from COUPLE are also considered. / by Wenyu Luo. / S.M.

Thesis: Ph. D. in Mechanical and Oceanographic Engineering, Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 117-135). / A fundamental problem in autonomous underwater robotics is the high latency between the capture of image data and the time at which operators are able to gain a visual understanding of the survey environment. Typical missions can generate imagery at rates hundreds of times greater than highly compressed images can be transmitted acoustically, delaying that understanding until after the vehicle has been recovered and the data analyzed. While automated classification algorithms can lessen the burden on human annotators after a mission, most are too computationally expensive or lack the robustness to run in situ on a vehicle. Fast algorithms designed for mission-time performance could lessen the latency of understanding by producing low-bandwidth semantic maps of the survey area that can then be telemetered back to operators during a mission. This thesis presents a lightweight framework for processing imagery in real time aboard a robotic vehicle. We begin with a review of pre-processing techniques for correcting illumination and attenuation artifacts in underwater images, presenting our own approach based on multi-sensor fusion and a strong physical model. Next, we construct a novel image pyramid structure that can reduce the complexity necessary to compute features across multiple scales by an order of magnitude and recommend features which are fast to compute and invariant to underwater artifacts. Finally, we implement our framework on real underwater datasets and demonstrate how it can be used to select summary images for the purpose of creating low-bandwidth semantic maps capable of being transmitted acoustically. / by Jeffrey W. Kaeli. / Ph. D. in Mechanical and Oceanographic Engineering

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), 2016. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 145-161). / Chemoautotrophic ecosystems at deep-sea hydrothermal vents were discovered in 1977, but not until 1995 were free-living autotrophic Epsilonproteobacteria identified as important microbial community members. Because the deep-sea is food-starved, the autotrophic metabolism of hydrothermal vent Epsilonproteobacteria may be very important for deep-sea consumers. However, quantifying their metabolic activities in situ has remained difficult, and biochemical mechanisms underlying their autotrophic physiology are poorly described. To gain insight into environmental processes, an approach was developed for incubations of microbes at in situ pressure and temperature (25 MPa, 24°C) with various combinations of electron donors/acceptors (H₂ , O₂ and NO₃- and ¹³HCO₃-) as a tracer to track carbon fixation. During short (18-24 h) incubations of low-temperature vent fluids from Crab Spa (9°N East Pacific Rise), the concentration of electron donors/acceptors and cell numbers were monitored to quantify microbial processes. Measured rates were generally higher than previous studies, and the stoichiometry of microbially-catalyzed redox reactions revealed new insights into sulfur and nitrogen cycling. Single-cell, taxonomically-resolved tracer incorporation showed Epsilonproteobacteria dominated carbon fixation, and their growth efficiency was calculated based on electron acceptor consumption. Using these data, in situ primary productivity, microbial standing stock, and average biomass residence time of the deep-sea vent subseafloor biosphere were estimated. Finally, the population structures of the most abundant genera Sulfurimonas and Thioreductor were shown to be strongly influenced by pO₂ and temperature respectively, providing a mechanism for niche differentiation in situ. To gain insights into the core biochemical reactions underlying autotrophy in Epsilonprotebacteria, a theoretical metabolic model of Sulfurimonas denitrificans was developed. Validated iteratively by comparing in silico yields with data from chemostat experiments, the model generated hypotheses explaining critical, yet so far unresolved reactions supporting chemoautotrophy in Epsilonproteo bacteria. For example, it provides insight into how energy is conserved during sulfur oxidation coupled to denitrification, how reverse electron transport produces ferredoxin for carbon fixation, and why aerobic growth yields are only slightly higher compared to denitrification. As a whole, this thesis provides important contributions towards understanding core mechanisms of chemoautrophy, as well as the in situ productivity, physiology and ecology of autotrophic Epsilonproteobacteria. / by Jesse Christopher McNichol. / Ph. D.

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), February 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 163-170). / Much of the recent research in ocean acoustics has focused on developing methods to exploit the effects that the sea surface and seafloor have on acoustic propagation. Many of those methods require detailed knowledge of the acoustic properties of the seafloor and the sound speed profile (SSP), which limits their applicability. The range-frequency waveguide invariant describes striations that often appear in plots of acoustic intensity versus range and frequency. These range-frequency striations have properties that depend strongly on the frequency of the acoustic source and on distance between the acoustic source and receiver, but that depend mildly on the SSP and seafloor properties. Because of this dependence, the waveguide invariant can be utilized for applications such as passive and active sonar, time-reversal mirrors, and array processing, even when the SSP or the seafloor properties are not well known. This thesis develops a framework for understanding and calculating the waveguide invariant, and uses that framework to develop signal processing techniques for the waveguide invariant. A method for passively estimating the range from an acoustic source to a receiver is developed, and tested on experimental data. Heuristics are developed to estimate the minimum source bandwidth and minimum horizontal aperture required for range estimation. A semi-analytic formula for the waveguide invariant is derived using WKB approximation along with a normal mode description of the acoustic field in a rangeindependent waveguide. This formula is applicable to waveguides with arbitrary SSPs, and reveals precisely how the SSP and the seafloor reflection coefficient affect the value of the waveguide invariant. Previous research has shown that the waveguide invariant range-frequency striations can be observed using a single hydrophone or a horizontal line array (HLA) of hydrophones. This thesis shows that traditional array processing techniques are sometimes inadequate for the purpose of observing range-frequency striations using a HLA. Array processing techniques designed specifically for observing range-frequency striations are developed and demonstrated. Finally, a relationship between the waveguide invariant and wavenumber integrations is derived, which may be useful for studying range-frequency striations in elastic environments such as ice-covered waveguides. / by Kevin L. Cockrell. / 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. / 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.