Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references (leaves 52-56). / Functional screening of environmental genomic libraries permits the identification of clones expressing activities of interest without requiring prior knowledge of the genes responsible. In this study, protocols were optimized for the construction of mid-size DNA insert, inducible expression environmental genomic plasmid libraries for this purpose. A library with a mean insert size of 5.2 kilobases was constructed with environmental DNA isolated from surface ocean water collected at Hawaii Ocean Time-series station ALOHA in plasmid cloning vector pMCL200 under the inducible control of the PLAC promoter. To begin to evaluate the utility of such libraries for gene expression-based screens, this library was screened phenotypically for clones expressing genes that confer fluorescence or distinctive coloration on colonies of host Escherichia coli cells, and results were compared to those for a fosmid library constructed from the same marine microbial DNA sample. Ecologically relevant sequences were identified in both libraries, and each was observed to offer both advantages and disadvantages. Results of this study suggest that mid-size insert plasmid libraries under the control of inducible promoters can provide a useful and complementary approach for both functional screening and shotgun sequencing of environmental genomic libraries. / by Jennifer C. Braff. / S.M.

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. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 59-65). / Estimates of natural climate variability during the past millennium provide a frame of reference in which to assess the significance of recent changes. This thesis investigates new methods of reconstructing low-latitude sea surface temperature (SST) and hydrography, and combines these methods with traditional techniques to improve the present understanding of western North Atlantic climate variability. A new strontium/calcium (Sr/Ca) - SST calibration is derived for Atlantic Montastrea corals. This calibration shows that Montastrea Sr/Ca is a promising SST proxy if the effect of coral growth is considered. Further analyses of coral growth using Computed Axial Tomography (CAT) imaging indicate growth in Siderastrea corals varies inversely with SST on interannual timescales. A 440-year reconstruction of low-latitude western North Atlantic SST based on this relationship suggests the largest cooling of the last few centuries occurred from -1650-1730 A.D., and was -I°C cooler than today. Sporadic multidecadal variability in this record is inconsistent with evidence for a persistent 65-80 year North Atlantic SST oscillation. Volcanic and anthropogenic radiative forcing are identified as important sources of externally-forced SST variability, with the latter accounting for most of the 20th century warming trend. An 1800-year reconstruction of SST and hydrography near the Gulf Stream also suggests SSTs remained within about I°C of modern values. This cooling is small relative to other regional proxy records and may reflect the influence of internal oceanic and atmospheric circulation. / (cont.) Simulations with an atmospheric general circulation model (AGCM) indicate that the magnitude of cooling estimated by proxy records is consistent with tropical hydrologic proxy records. / by Casey Pearce Saenger. / 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), 2007. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Includes bibliographical references (p. 257-267). / The water circulation and evolution of water temperature over the inner continental shelf are investigated using observations of water velocity, temperature, density, and bottom pressure; surface gravity waves; wind stress; and heat flux between the ocean and atmosphere during 2001-2007. When waves are small, cross-shelf wind stress is the dominant mechanism driving cross-shelf circulation. The along-shelf wind stress does not drive a substantial cross-shelf circulation. The response to a given wind stress is stronger in summer than winter. The cross-shelf transport in the surface layer during winter agrees with a two-dimensional, unstratified model. During large waves and onshore winds the crossshelf velocity is nearly vertically uniform, because the wind- and wave-driven shears cancel. During large waves and offshore winds the velocity is strongly vertically sheared because the wind- and wave-driven shears have the same sign. The subtidal, depth-average cross-shelf momentum balance is a combination of geostrophic balance and a coastal set-up and set-down balance driven by the cross-shelf wind stress. The estimated wave radiation stress gradient is also large. The dominant along-shelf momentum balance is between the wind stress and pressure gradient, but the bottom stress, acceleration, Coriolis, Hasselmann wave stress, and nonlinear advection are not negligible. The fluctuating along-shelf pressure gradient is a local sea level response to wind forcing, not a remotely generated pressure gradient. In summer, the water is persistently cooled due to a mean upwelling circulation. The cross-shelf heat flux nearly balances the strong surface heating throughout mid-summer, so the water temperature is almost constant. The along-shelf heat flux divergence is apparently small. In winter, the change in water temperature is closer to that expected due to the surface cooling. Heat transport due to surface gravity waves is substantial. / by Melanie Rinn Fewings. / 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), 2008. / Includes bibliographical references (p. 155-161). / The subtidal circulation of the southeast Greenland shelf is described using a set of high resolution hydrographic and velocity transects occupied in summer 2004. The main feature present is the East Greenland Coastal Current (EGCC), a low-salinity, high velocity jet with a wedge-shaped hydrographic structure characteristic of other surface buoyancy-driven currents. The EGCC was observed along the entire Greenland shelf south of Denmark Strait, while the transect north of the strait showed only a weak shelf flow. This observation, combined with evidence from chemical tracer measurements that imply the EGCC contains a significant Pacific Water signal, suggests that the EGCC is an inner branch of the polar-origin East Greenland Current (EGC). A set of idealized laboratory experiments on the interaction of a buoyant current with a submarine canyon also supported this hypothesis, showing that for the observed range of oceanic parameters, a buoyant current such as the EGC could exhibit both flow across the canyon mouth or into the canyon itself, setting the stage for EGCC formation. Repeat sections occupied at Cape Farewell between 1997 and 2004 show that the along shelf wind stress can also have a strong influence on the structure and strength of the EGCC and EGC on timescales of 2-3 days. Accounting for the wind-induced effects, the volume transport of the combined EGC/EGCC system is found to be roughly constant (-2 Sv) over the study domain, from 68*N to Cape Farewell near 60°N. The corresponding freshwater transport increases by roughly 60% over this distance (59 to 96 mSv, referenced to a salinity of 34.8). This trend is explained by constructing a simple freshwater budget of the EGCC/EGC system that accounts for melt water runoff, melting sea-ice and icebergs, and net precipitation minus evaporation. / (cont.) Variability on inter annual timescales is examined by calculating the Pacific Water content in the EGC/EGCC from 1984-2004 in the vicinity of Denmark Strait. The PW content is found to correlate significantly with the Arctic Oscillation index, lagged by 9 years, suggesting that the Arctic Ocean circulation patterns bring varying amounts of Pacific Water to the North Atlantic via the EGC/EGCC. / by David A. Sutherland. / 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), 2007. / Includes bibliographical references. / The North Atlantic right whale, Eubalaena glacialis, one of the most critically endangered whales in the world, is subject to high anthropogenic mortality. Vessel-whale collisions and entanglement in fishing gear were indicated in 27 (67.5%) of the 40 right whales necropsied between 1970 and December 2006. Of those, at least 9 deaths (22.5%) resulted from blunt contact with a vessel. To reduce the likelihood of fatal collisions, speed restrictions are being considered for vessels traversing critical habitat, although the effects of speed on collision outcomes have not been specifically evaluated from a biomechanics perspective. The ultimate goal of a larger collaborative project is to evaluate the efficacy of speed restrictions for reducing blunt collision mortality using a multi-scale finite element model. Complete, transverse fracture of the right whale mandible, an injury seen only in right whales killed by vessels, is used as a proxy for mortality in the model. Vital for that model are the material properties and biomechanical behavior of the right whale mandible. Here, the internal structure and physical properties of right whale jawbone tissue are reported. The average apparent densities, 0.4258 g/cc ±0.0970 and 1.2370 g/cc ±0.0535 for trabecular and cortical bone respectively, indicate that the bone is of relatively low density. Average ash content for trabecular bone (64.38% ±1.1330) is comparable with values from other species, indicating that low density results from a reduction of bone mass, not mineralization. Mechanical properties of right whale bone (Young's modulus of elasticity and Poisson's ratio) were determined via uniaxial compression testing. / (cont.) These data are incorporated into the finite element model simulating different loading conditions (e.g. vessel speeds) that likely lead to mandibular failure and thereby mortality from blunt vessel collisions. Model results (e.g. risk of fracture) are used to determine the effect of speed restrictions on collision outcomes. / by Regina Campbell-Malone. / Ph.D.

Thesis (S.M. in Electrical Engineering and Computer Science)--Joint Program in Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science; and the Woods Hole Oceanographic Institution), 2011. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 113-114). / Current underwater acoustic channel estimation techniques generally apply linear MMSE estimation. This approach is optimal in a mean square error sense under the assumption that the impulse response fluctuations are well characterized by Gaussian statistics, leading to a Rayleigh distributed envelope. However, the envelope statistics of the underwater acoustic communication channel are often better modeled by the K-distribution. In this thesis, by presenting and analyzing field data to support this claim, I demonstrate the need to investigate channel estimation algorithms that exploit K-distributed fading statistics. The impact that environmental conditions and system parameters have on the resulting distribution are analyzed. In doing so, the shape parameter of the K-distribution is found to be correlated with the source-to-receiver distance, bandwidth, and wave height. Next, simulations of the scattering behavior are carried out in order to gain insight into the physical mechanism that cause these statistics to arise. Finally, MAP and MMSE based algorithms are derived assuming K-distributed fading models. The implementation of these estimation algorithms on simulated data demonstrates an improvement in performance over linear MMSE estimation. / by Alison Beth Laferriere. / S.M.in Electrical Engineering and Computer Science

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), 2007. / Includes bibliographical references (p. 183-191). / This thesis covers a comprehensive analysis of long-range, deep-ocean, low-frequency, sound propagation experimental results obtained from the North Pacific Ocean. The statistics of acoustic fields after propagation through internal-wave-induced sound-speed fluctuations are explored experimentally and theoretically. The thesis starts with the investigation of the North Pacific Acoustic Laboratory 98-99 data by exploring the space-time scales of ocean sound speed variability and the contributions from different frequency bands. The validity of the Garret & Munk internal-wave model is checked in the upper ocean of the eastern North Pacific. All these results impose hard bounds on the strength and characteristic scales of sound speed fluctuations one might expect in this region of the North Pacific for both internal-wave band fluctuations and mesoscale band fluctuations. The thesis then presents a detailed analysis of the low frequency, broadband sound arrivals obtained in the North Pacific Ocean. The observed acoustic variability is compared with acoustic predictions based on the weak fluctuation theory of Rytov, and direct parabolic equation Monte Carlo simulations. The comparisons show that a resonance condition exists between the local acoustic ray and the internal wave field such that only the internal-waves whose crests are parallel to the local ray path will contribute to acoustic scattering: This effect leads to an important filtering of the acoustic spectra relative to the internal-wave spectra. We believe that this is the first observational evidence for the acoustic ray and internal wave resonance. Finally, the thesis examined the evolution with distance, of the acoustic arrival pattern of the off-axis sound source transmissions in the Long-range Ocean Acoustic Propagation EXperiment. / (cont.) The observations of mean intensity time-fronts are compared to the deterministic ray, parabolic equation (with/without internal waves) and (one-way coupled) normal mode calculations. It is found the diffraction effect is dominant in the shorter-range transmission. In the longer range, the (internal wave) scattering effect smears the energy in both the spatial and temporal scales and thus has a dominant role in the finale region. / by Jinshan Xu. / Ph.D.

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.

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.