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), 2002. / Includes bibliographical references (p. 130-138). / Mark-recapture analysis of populations is becoming an important tool in population biology. Mark-recapture methods can be used to estimate transition probabilities among life-stages from capture histories of marked individuals for which stages can be determined at each sampling occasion. This method is called a multi-stage mark-recapture (MSMR) method. In this thesis, I describe advances I made in the MSMR method and present analyses that apply this method to actual data. The advances I made in the MSMR method are motivated by a need to provide a link between mark-recapture data and demographic models such as matrix population models and integrodifference models. I resolve some issues that are commonly encountered during sampling, such as the fact that the sex or life-stage of some individuals is unknown during some sampling occasions and that individuals become unobservable during some life-stages. I introduce a stage-structure that permits simple conversion of estimated transition probabilities into a matrix population model. I describe an algorithm to simplify programming for parameter estimation. I also introduce a method to estimate the distribution of dispersal displacements (a dispersal kernel) from mark-recapture data. I apply some of the methods described above to data of the North Atlantic right whale (Eubalaena glacialis). The right whales are considered one of the most endangered mammals. The current population size is about 300 in the northwestern Atlantic, and the number is declining. I applied the multi-stage mark-recapture statistics to the 17-year in- dividual sighting history data. / (cont.) Using the estimated transition probabilities, I constructed a population projection matrix, which was used for further demographic analyses. I found that the population was slowly increasing in 1980, but it started to decline slowly around 1992. I show that (1) this change was caused by increased mortality of females that have just given birth, (2) protecting two females a year from the deaths is enough to prevent the declining trend, and (3) demographic stochasticity is a more important factor influencing their long-term viability than environmental stochasticity. / by Masami Fujiwara. / 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. / Cataloged from PDF version of thesis. / Includes bibliographical references. / At the land-ocean interface, terrestrial groundwater interacts with seawater to form a subterranean estuary, which can play host to dynamic biogeochemical cycling of nutrients, trace metals and radionuclides. This chemically altered groundwater enters the ocean through submarine groundwater discharge (SGD), a process that is driven by a number of physical processes acting on aquifers and the coastal ocean. In this thesis, seasonal variability in chemical cycling and associated loading to the coastal ocean was observed in a monthly time series within the Waquoit Bay (MA, USA) subterranean estuary. The position of the aquifer mixing zone moved seaward with an increase in hydraulic gradient, resulting in low salinity conditions and reduced mixing, while a decrease in gradient led to landward movement, high salinity groundwater and enhanced mixing. At this location, seasonal variability in sea level, not groundwater level, was the dominant variable driving the hydraulic gradient and therefore SGD. Fluxes of sediment bound cations to the ocean increased coincidently with sea level rise due to desorption. There was enhanced nitrogen attenuation during winter, potentially due to longer groundwater residence times, with greater nutrient delivery to coastal waters during the spring and summer bloom. Interannual climate fluctuations that control sea level and precipitation may ultimately control the timing and magnitude of chemical and water flux via SGD. In addition to temporal variability, aquifer lithology influences chemical export. This thesis also demonstrates that SGD from karst subterranean estuaries may play a role in local and global element budgets. The potential for the chemical signature of SGD to be recorded in the coral record was tested through a combination of coral culture experiments and field and modeling studies in the Yucatan Peninsula. Coral barium was well correlated with precipitation for a twelve-year record, with coral geochemistry reflecting the passage of a hurricane in 2002. While additional complexities in deciphering coral records remain, this proxy offers the potential to extend SGD records into the past. / by Meagan Joan Eagle Gonneea. / Ph. D.

Thesis (Ph.D.)--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), 2012. / 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 (p. 91-98). / This thesis presents a system for automatically building 3-D optical and bathymetric maps of underwater terrain using autonomous robots. The maps that are built improve the state of the art in resolution by an order of magnitude, while fusing bathymetric information from acoustic ranging sensors with visual texture captured by cameras. As part of the mapping process, several internal relationships between sensors are automatically calibrated, including the roll and pitch offsets of the velocity sensor, the attitude offset of the multibeam acoustic ranging sensor, and the full six-degree of freedom offset of the camera. The system uses pose graph optimization to simultaneously solve for the robot's trajectory, the map, and the camera location in the robot's frame, and takes into account the case where the terrain being mapped is drifting and rotating by estimating the orientation of the terrain at each time step in the robot's trajectory. Relative pose constraints are introduced into the pose graph based on multibeam submap matching using depth image correlation, while landmark-based constraints are used in the graph where visual features are available. The two types of constraints work in concert in a single optimization, fusing information from both types of mapping sensors and yielding a texture-mapped 3-D mesh for visualization. The optimization framework also allows for the straightforward introduction of constraints provided by the particular suite of sensors available, so that the navigation and mapping system presented works under a variety of deployment scenarios, including the potential incorporation of external localization systems such as long-baseline acoustic networks. Results of using the system to map the draft of rotating Antarctic ice floes are presented, as are results fusing optical and range data of a coral reef. / by Clayton Gregory Kunz. / Ph.D.

Thesis (S.M.)--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. 99-100). / Signal detection and synchronization in the time varying ocean environment is a difficult endeavor. The current common methods include using a linear frequency modulated chirped pulse or maximal length sequence as a detection pulse, then match filtering to that signal. In higher signal to noise ratio (SNR) environments (- 0 dB and higher) this has been a suitable solution. As the SNR drops lower however, this solution no longer provides an acceptable probability of detection for a given tolerable probability of false alarm. The issue derives from the inherent coherence issues in the ocean environment which limit the useful matched filter length. This thesis proposes an alternative method of detection based on a recursive least squares linearly adaptive equalizer which we term the Adaptive Linear Equalizer Detector (ALED). This detectors performance has demonstrated reliable probability of detection with minimal interfering false alarms with SNR as low as -20 dB. Additionally this thesis puts forth a computationally feasible method for implementing the detector. / by Ryan Thomas Gieleghem. / 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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / As the only low-latitude connection between ocean basins, the Indonesian Throughflow allows the direct transmission of heat and salinity between the Pacific and Indian Oceans. Despite its potential importance, the role of the Indonesian Throughflow in global ocean circulation and regional climate is still not clear due to sparse measurements and the relative difficulty of modeling the region. The Mg/Ca and [delta]¹⁸0 of calcite of the calcitic planktic foraminifera Globigerinoides ruber (G. ruber) were used to estimate the sea surface temperature and [delta]¹⁸0 of water, an indicator of hydrologic conditions, over the past 20,000 years. I also attempted to estimate thermocline structure using the foraminifera, Pulleniatina obliquiloculata, but the Mg/Ca and [delta]¹⁸0 of calcite data yield conflicting interpretations, indicating further work on this proxy is required. The G. ruber Mg/Ca results suggest that the sea surface temperature of the outflow passages was influenced by high latitude Southern Hemisphere temperature. This connection is likely via intermediate waters that upwell in the Banda Sea. At approximately 10,000 years before present, there was a warming in the Makassar Strait. This local warming was coincident with the flooding of the Sunda Shelf, which opened a connection between the South China Sea and the Indonesian Throughflow. Regional [delta]¹⁸0 of seawater reconstructions show that during the last glacial maximum the [delta]¹⁸0 of seawater pattern was very similar to modern, but there were relatively enriched values over the equatorial IndoPacific during high latitude Northern Hemisphere cold events (Heinrich Stadial 1 and the Younger Dryas). From these results we postulate that the mean position of the Intertropical Convergence Zone was approximately the same as modern at the last glacial maximum and was likely displaced to the south during the Younger Dryas and Heinrich Stadial 1, suggesting the Intertropical Convergence Zone primarily responds to changes in the interhemispheric temperature gradient. These results shed light on the primary controls of the temperature and hydrology of Indonesian Throughflow region. / by Fern Tolley Gibbons. / 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. / 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. / Seafloor digital imagery and bathymetric data are used to evaluate the volcanic characteristics of the 85°E segment of the ultraslow spreading Gakkel Ridge (9 mm yr-¹). Imagery reveals that ridges and volcanic cones in the axial valley are covered by numerous, small-volume lava flows, including a few flows fresh enough to have potentially erupted during the 1999 seismic swarm at the site. The morphology and distribution of volcaniclastic deposits observed on the seafloor at depths of ~3800 m, greater than the critical point for steam generation, are consistent with having formed by explosive discharge of magma and CO² from source vents. Microearthquakes recorded on a 200 m aperture seismometer network deployed on the Trans-Atlantic Geotraverse active mound, a seafloor massive sulfide on the Mid-Atlantic Ridge at 26°N, are used to image subsurface processes at the hydrothermal system. Over nine-months, 32,078 local microearthquakes (ML = -1) with single-phase arrivals cluster on the southwest flank of the deposit at depths <125 m. Microearthquakes characteristics are consistent with reaction-driven cracking driven by anhydrite deposition in the shallow secondary circulation system. Exit fluid temperatures recorded at diffuse vents on the mound during the microearthquake study are used to explore linkages between seismicity and venting. / by Claire Willis Pontbriand. / 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), 2012. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Despite widespread concerns about the effects of anthropogenic noise on baleen whales (suborder Mysticeti), we lack basic information about their auditory physiology for comprehensive risk assessments. Hearing ranges and sensitivities could be measured if customized equipment and methods were developed based on how baleen whales receive sound. However, sound reception pathways in baleen whales are currently unknown. This thesis presents an integrative approach to understanding hearing in baleen whales through dissections, biomedical imaging, biochemical analyses, and modeling sound propagation through a whale head using the Finite Element Method (FEM). We focused on the minke whale (Balaenoptera acutorostrata) because it is one of the smallest and most abundant mysticete species, reducing logistical difficulties for dissections and experiments. We discovered a large, well-formed fat body extending from the blubber region to the ears and contacting the ossicles. Although odontocetes, or toothed whales, are thought to use specialized "acoustic fats" for sound reception, no such tissues had been described for mysticetes to date. Our study indicates that the basic morphology and biochemical composition of the minke whale "ear fats" are very different from those of odontocete acoustic fats. However, the odontocete and mysticete fatty tissues share some characteristics, such as being conserved even during starvation, containing fewer dietary signals compared to blubber, and having well-defined attachments to the tympano-periotic complex, which houses the middle and inner ears. FE models of the whale head indicated that the ear fats caused a slight increase in the total pressure magnitude by the ears, and this focusing effect could be attributed to the low density and low sound speed of the ear fats in the models. Fatty tissues are known to have lower densities and sound speeds than other types of soft tissues, which may explain why they are an important component of the auditory system of odontocetes, and perhaps mysticete cetaceans as well. In an aquatic habitat where the pinna and air-filled ear canal are no longer effective at collecting and focusing so'und towards the ears, we propose that both odontocete and mysticete cetaceans have incorporated fatty tissues into their auditory systems for underwater sound reception. / by Maya Yamato. / Ph.D.

京都大学 / 新制・課程博士 / 博士(地球環境学) / 甲第24768号 / 地環博第240号 / 新制||地環||47(附属図書館) / 京都大学大学院地球環境学舎環境マネジメント専攻 / (主査)准教授 浅利 美鈴, 講師 BAARS ROGER CLOUD, 教授 宇佐美 誠 / 学位規則第4条第1項該当 / Doctor of Global Environmental Studies / Kyoto University / DFAM

Thesis: S.M., Joint Program in Applied Ocean Physics and Engineering (Massachusetts Institute of Technology, Department of Aeronautics and Astronautics; and the Woods Hole Oceanographic Institution), 2019 / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 99-103). / The recent success of object detection systems motivates object-based representations for robot navigation; i.e. semantic simultaneous localization and mapping (SLAM), in which we aim to jointly estimate the pose of the robot over time as well as the location and semantic class observed objects. A solution to the semantic SLAM problem necessarily addresses the continuous inference problems where am I? and where are the objects?, but also the discrete inference problem what are the objects?. We consider the problem of semantic SLAM under non-Gaussian uncertainty. The most prominent case in which this arises is from data association uncertainty, where we do not know with certainty what objects in the environment caused the measurement made by our sensor. The semantic class of an object can help to inform data association; a detection classified as a door is unlikely to be associated to a chair object. / However, detectors are imperfect, and incorrect classification of objects can be detrimental to data association. While previous approaches seek to eliminate such measurements, we instead model the robot and landmark state uncertainty induced by data association in the hopes that new measurements may disambiguate state estimates, and that we may provide representations useful for developing decisionmaking strategies where a robot can take actions to mitigate multimodal uncertainty. The key insight we leverage is that the semantic SLAM problem with unknown data association can be refrained as a non-Gaussian inference problem. We present two solutions to the resulting problem: we first assume Gaussian measurement models, and non-Gaussianity only due to data association uncertainty. We then relax this assumption and provide a method that can cope with arbitrary non-Gaussian measurement models. / We show quantitatively on both simulated and real data that both proposed methods have robustness advantages as compared to traditional solutions when data associations are uncertain. / "Supported by the Office of Naval Research under grants N00014-18-1-2832 and N00014-16-2628, as well as the National Science Foundation (NSF) Graduate Research Fellowship"--Page 5 / by Kevin J. Doherty. / S.M. / S.M. Joint Program in Applied Ocean Physics and Engineering (Massachusetts Institute of Technology, Department of Aeronautics and Astronautics; and the Woods Hole Oceanographic Institution)

Thesis: S.M., 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), 2020 / Cataloged from student-submitted PDF of thesis. / Includes bibliographical references. / Arctic marine and lacustrine systems are experiencing rapid warming due to climate change. These changes are especially important at the interface between sediments and surface waters because they are hotspots for biogeochemical transformations such as redox reactions, nutrient consumption and regeneration, organic matter leaching and degradation, and mineral weathering. Radium isotopes (²²³Ra, ²²⁴Ra, ²²⁶Ra, ²²⁸Ra) and radon-222, naturally occurring radioactive isotopes produced in sediments, are well-suited as tracers of nutrients, trace metals, and organic matter cycling processes at the sediment-water interface. In this thesis, I have applied radon-222 and the quartet of radium isotopes to study fundamental processes in subarctic lakes and on the Arctic continental shelf. First, radon-222 is used to quantify groundwater discharge into a shallow, tundra lake on the Yukon-Kuskokwim Delta in Alaska in summer of 2017. / Radon-derived groundwater fluxes were then paired with methane (CH₄) measurements to determine delivery rates of methane into the lake via groundwater. Groundwater CH₄ fluxes significantly exceeded diffusive air-water fluxes from the lake to the atmosphere, suggesting that groundwater is an important source of CH₄ to Arctic lakes and may drive observed CH₄ emissions. Higher CH₄ emissions were observed compared to those reported previously in high latitude lakes, like due to higher CH₄ concentrations in groundwater. These findings indicate that deltaic lakes across warmer permafrost regions may act as important hotspots for methane release across Arctic landscapes. Then, the quartet of radium isotopes is used to study the impacts of storms and sea ice formation as drivers of sediment-water interaction on the Alaskan Beaufort shelf. / The timeseries presented in this study is among the first to document the combined physical and chemical signals of winter water formation in the Beaufort Sea, made possible by repeat occupations of the central Beaufort shelf. Radium measurements are combined with inorganic nitrogen and hydrographic measurements to elucidate the episodic behavior of winter water formation and its ability to drive exchange with bottom sediments during freeze-up. / by Jessica Stephanie Dabrowski. / S.M. / S.M. 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)