Thesis: Ph. D., Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2018. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 138-154). / Highly migratory marine fishes support valuable commercial fisheries worldwide. Yet, many target species have proven difficult to study due to long-distance migrations and regular deep diving. Despite the dominance of oceanographic features, such as fronts and eddies, in the open ocean, the biophysical interactions occurring at the oceanic (sub)mesoscale (< 100 km) remain poorly understood. This leads to a paucity of knowledge on oceanographic associations of pelagic fishes and hinders management efforts. With ever-improving oceanographic datasets and modeling outputs, we can leverage these tools both to derive better estimates of animal movements and to quantify fish-environment interactions. In this thesis, I developed analytical tools to characterize the biophysical interactions influencing animal behavior and species' ecology in the open ocean. A novel, observation-based likelihood framework was combined with a Bayesian state-space model to improve geolocation estimates for archival-tagged fishes using oceanographic profile data. Using this approach, I constructed track estimates for a large basking shark tag dataset using a high-resolution oceanographic model and discovered a wide range of movement strategies. I also applied this modeling approach to track archival-tagged swordfish, which revealed affinity for thermal front and eddy habitats throughout the North Atlantic that was further corroborated by synthesizing these results with a fisheries-dependent conventional tag dataset. An additive modeling approach applied to longline catch-per-unit effort data further highlighted the biophysical interactions that characterize variability in swordfish catch. In the final chapter, I designed a synergistic analysis of high-resolution, 3D shark movements and satellite observations to quantify the influence of mesoscale oceanography on blue shark movements and behavior. This work demonstrated the importance of eddies in structuring the pelagic ocean by influencing the movements of an apex predator and governing the connectivity between deep scattering layer communities and deep-diving, epipelagic predators. Together, these studies demonstrate the breadth and depth of information that can be garnered through the integration of traditional animal tagging and oceanographic research with cutting-edge analytical approaches and high-resolution oceanographic model and remote sensing datasets, the product of which provides a transformative view of the biophysical interactions occurring in and governing the structure of the pelagic ocean. / by Camrin Donald Braun. / Ph. D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), February 2009. / Includes bibliographical references (p. 133-140). / Self-localization of an underwater vehicle is particularly challenging due to the absence of Global Positioning System (GPS) reception or features at known positions that could otherwise have been used for position computation. Thus Autonomous Underwater Vehicle (AUV) applications typically require the pre-deployment of a set of beacons.This thesis examines the scenario in which the members of a, group of AUVs exchange navigation information with one another so as to improve their individual position estimates. We describe how the underwater environment poses unique challenges to vehicle navigation not encountered in other environments in which robots operate and how cooperation can improve the performance of self-localization. As intra-vehicle communication is crucial to cooperation, we also address the constraints of the communication channel and the effect that these constraints have on the design of cooperation strategies. The classical approaches to underwater self-localization of a single vehicle, as well as more recently developed techniques are presented. We then examine how methods used for cooperating land-vehicles can be transferred to the underwater domain. An algorithm for distributed self-localization, which is designed to take the specific characteristics of the environment into account, is proposed. We also address how correlated position estimates of cooperating vehicles can lead to overconfidence in individual position estimates. Finally, key to any successful cooperative navigation strategy is the incorporation of the relative positioning between vehicles. The performance of localization algorithms with different geometries is analyzed and a distributed algorithm for the dynamic positioning of vehicles, which serve as dedicated navigation beacons for a fleet of AUVs, is proposed. / by Alexander Bahr. / Ph.D.

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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), September 2003. / Includes bibliographical references. / The cosmogenic radionuclide ¹⁰Be is a unique tracer of shallow sediment subduction in volcanic arcs. The range in ¹⁰Be enrichment in the Central American Volcanic Arc between Guatemala and Costa Rica is not controlled by variations in ¹⁰Be concentrations in subducting sediment seaward of the Middle America Trench. Sedimentary ¹⁰Be is correlated negatively with ¹⁴³ND/¹⁴⁴Nd, illustrating that ¹⁰Be concentrations varied both between and within cores due to mixing between terrigenous clay and volcanic ash endmember components. This mixing behavior was determined to be a function of grain size controls on ¹⁰Be concentrations. A negative correlation of bulk sedimentary ¹⁰Be concentrations with median grain size and a positive correlation with the proportion of the sediment grains that were <32 [mu]m in diameter demonstrated that high concentrations of ¹⁰Be in fine-grained, terrigenous sediments were diluted by larger grained volcanogenic material. The sharp decrease in ¹⁰Be enrichment in the Central American Volcanic Arc between southeastern Nicaragua and northwestern Costa Rica correlates with changes in fault structure in the subducting Cocos plate. Offshore of Nicaragua, extensional faults associated with plate bending have throw equal to or greater than the overlying subducting sediment thickness. These faults enable efficient subduction of the entire sediment package by preventing relocation of the d6collement within the downgoing sediments. / (cont.) Offshore of Costa Rica, the reduction of fault relief results in basement faults that do not penetrate the overlying sediment. A conceptual model is proposed in which the absence of significant basement roughness allows the d6collement to descend into the subducting sediment column, leading to subsequent underplating and therefore removal of the bulk of the sediment layer that contains ¹⁰Be. Basement fault relief was linearly related to plate curvature and trench depth. The systematic shoaling of the plate from southeastern Nicaragua to northwestern Costa Rica is not explained by changes in plate age for this region. Instead, it is hypothesized that the flexural shape of the plate offshore of southeastern Nicaragua and northwestern Costa Rica represents a lateral response to a buoyant load caused by the thick crust and elevated thermal regime in the Cocos plate offshore of southeastern Costa Rica. / by Robyn K. Kelly. / 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), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references. / The sinking flux of particles is an important removal mechanism of carbon from the surface ocean as part of the biological pump and can play a role in cycling of other chemical species. This work dealt with improving methods of measuring particle export and measuring export on different scales to assess its spatial variability. First, the assumption of ²³⁸U linearity with salinity, used in the ²³⁸U-²³⁴Th method, was reevaluated using a large sample set over a wide salinity range. Next, neutrally buoyant and surface-tethered sediment traps were compared during a three-year time series in the subtropical Atlantic. This study suggested that previously observed imbalances between carbon stocks and fluxes in this region are not due to undersampling by traps. To assess regional variability of particle export, surface and water-column measurements of ²³⁴Th were combined for the first time to measure fluxes on ~20 km scales. Attempts to relate surface properties to particle export were complicated by the temporal decoupling of production and export. Finally, particle export from ²³⁴Th was measured on transects of the Atlantic Ocean to evaluate basin-scale export variability. High-resolution sampling through the water-column allowed for the identification of unique ²³⁴Th features in the intermediate water column. / by Stephanie Anne Owens. / 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), February 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 136-146). / The environmental cues for synchronous reproduction were investigated for two highly abundant, ecologically important crustacean species: the temperate acorn barnacle, Semibalanus balanoides, and the tropical terrestrial crab, Gecarcinus quadratus. Larval ecology of these two species was also studied to determine potential sources of larval mortality and recruitment success. High-frequency observations revealed that early-stage larval abundance of S. balanoides was related to storms, and possibly turbidity. Field observations and experiments studied the effect of turbidity and phytoplankton on larval release response. Release coincided with increased turbidity at three sites along the northeast coast of the United States. A three-year time series of phytoplankton and zooplankton data showed that larval release was not consistently related to phytoplankton abundance (total or single species). When gravid barnacles were exposed to phytoplankton or synthetic beads, they released in response to both, suggesting that presence of particles is more important than identity of particles. Feeding experiments showed that adult cannibalism on newly released larvae is lower in highly turbid conditions. It is suggested here that S. balanoides synchronizes its reproduction with the onset of phytoplankton blooms, but turbidity may fine-tune the timing if it provides predation refuge for larvae. Adult G. quadratus females undertake synchronized breeding migrations to the ocean after the first rains of the rainy season, presumably when the risk of desiccation is lowest. They wait for darkness and an ebbing tide before releasing their eggs into the water. First-stage zoeas have dark pigmentation, long dorsal and rostral spines, and a pair of lateral spines. Hatching in darkness may help zoeas avoid predation from planktivorous diurnal fish, and the zoeal spines may deter predation from planktivorous nocturnal fish. In the laboratory, a G. quadratus zoea reached the megalopa stage in 21 days. A mass migration of megalopae and juveniles out of the water was observed 30 days after adult females released their eggs. Plankton pump samples taken near the island suggest that zoea abundance and distribution may be related to the phase of the internal tide. Synchronous reproduction in these two species appears to be the result of predator avoidance behaviors. / by Joanna Gyory. / Ph.D.

Thesis (S.M.)--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), 2006. / Includes bibliographical references (p. 64-68). / Salt pond is a meromictic system with an outlet to the sea allowing denser seawater to occupy the monimolimnion while the mixolimnion has relatively low salinity and is the site of greater mixing and microbial activity. The density contrast between the two layers allows for a unique geochemical environment characterized by steep redox gradients at the interface. This chemocline is a habitat for magnetotactic bacteria (MB), and the spatial and temporal distribution of MB in the system along with geochemical (Fe2+, H2S, pH, 02 (aq), etc.) profiles have been analyzed from 2002 - 2005. It has been previously observed that magnetite-producing cocci occupy the top of the chemocline and greigite-producing MB occur at the base of the chemocline and in the sulfidic hypolimnion. This distribution may be attributed to analyte profiles within the pond; depth profiles show a sudden drop of dissolved oxygen (DO) at the chemocline associated with an increase in dissolved Fe (II) concentrations that peak where both 02 and H2S are low. In the sulfidic hypolimnion, Fe (II) concentrations decrease, suggesting buffering of Fe(II) by sulfide phases. / (cont.) Maximum concentrations of iron (II) and sulfide are 3 1 gM and 3 mM, respectively. Stability diagrams of magnetite and greigite within EH/pH space and measured voltammetric data verify fields of incomplete oxidation resulting in the production of elemental sulfur, thiosulfate and polysulfides. Calculations of the Gibbs free energy in the Salt Pond chemocline for potential microbial redox reaction involving iron and sulfur species indicate abundent potential energy available for metabolic growth. Oxidation of ferrous iron to ferrihydrite in the upper region of the chemocline consistantly has a yield of over -250 kJ/mol 02 (aq), - 12.5 times the proposed 20 kJ/mol minimum proposed by Schink (1997) necessary to sustain metabolic growth. This translates into biomass yields of ~ 0.056 mg dry mass per liter of upper chemocline water. If these numbers are applied to the dominant bacteria of the chemocline (MB that are 3% dry weight iron) then there could be up to ~ 1.68 mg of iron per liter of upper chemocline water just in the MB. / (cont.) This iron can be permanently sequestered by MB into the sediments after death because the organelles containing the iron phases are resistant to degredation. Geochemical and microbial processes relating to the cycling of iron heavily impact this system and perhaps others containing a chemocline that divides the water column into oxic and anoxic zones. / by Peter A. Canovas, III. / S.M.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Mechanical Engineering; and the Woods Hole Oceanographic Institution), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 79-84). / Estuarine density stratification may be controlled primarily by cross-shore processes (analogous to longitudinal control in narrow estuaries), or by both cross- and alongshore processes (typical of coastal plumes). Here field observations and numerical modeling are used to investigate stratification on the low-sloped, periodically inundated Skagit Bay tidal flats. Advection of stratification by the depth-averaged velocity, straining of the horizontal density gradient by velocity shear, and turbulent mixing are shown to be the dominant processes. On the south-central flats (near the south fork river mouth) velocities are roughly rectilinear, and the largest terms are in the major velocity direction (roughly cross-shore). However, on the north flats (near the north fork river mouth), velocity ellipses are nearly circular owing to strong alongshore tidal flows and alongshore stratification processes are important. Stratification was largest in areas where velocities and density gradients were aligned. The maximum stratification occurred during the prolonged high water of nearly diurnal tides when advection and straining with relatively weak flows increased stratification with little mixing. Simulations suggest that the dominance of straining (increasing stratification) or mixing (decreasing stratification) on ebb tides depends on the instantaneous Simpson number being above or below unity. / by Vera L. Pavel. / Ph.D.

Thesis (Ph. D.)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Ocean Engineering; and the Woods Hole Oceanographic Institution), 2000. / Includes bibliographical references (leaves 134-141). / by Nicole Marie Suoja. / Ph.D.