Thesis (Ph. D.)--Joint Program in Physical Oceanography (Massachusetts Institute of Technology, Dept. of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 297-213). / This thesis explores the role that the circulation in the Gulf of Maine (GOM) plays in determining the distribution of dense aggregations of copepods. These aggregations are an important part of the marine ecosystem, especially for endangered North Atlantic right whales. Certain ocean processes may generate dense copepod aggregations, while others may destroy them; this thesis looks at how different characteristics of the GOM circulation fit into these two categories. The first part of the thesis investigates a hypothetical aggregation mechanism in which frontal circulation interacts with copepod behavior to generate a dense patch of copepods. The first two chapters of this thesis address this mechanism in the context of coastal river plumes and salinity fronts. One chapter describes the characteristics and variability of coastal freshwater and salinity fronts using a historical dataset and a realistic numerical model. The seasonal variability of freshwater is tied in part to seasonality in river discharge, while variability on shorter time scales in the frontal position is related to wind stress. Another chapter applies the hypothetical mechanism to idealized river plumes using a suite of numerical models. The structure of the plume and plume-relative circulation change the resulting copepod aggregation from what is expected from the hypothetical mechanism. The second part of the thesis discusses the GOM circulation and how it may eliminate copepod patches. The summertime mean surface circulation and eddy kinetic energy are computed from a Lagrangian drifter dataset and an adaptive technique that allows for higher spatial resolution while also keeping uncertainty low. Eddy diffusivity is also computed over different regions of the GOM in an attempt to quantify the spreading of a patch of copepods, and is found to be lower near the coast where right whales are often found feeding on copepod patches. In the next chapter, a numerical drifter dataset is used to understand how the results of the previous chapter depend upon the quantity of observations. It is found that the uncertainty in estimating eddy diffusivity is tightly coupled to the number of drifters in the calculation. / by Nicholas W. Woods / Ph.D.

Regions containing gradients of vertical flow are often associated with sharp changes in hydrographic and biochemical water properties in coastal marine ecosystems. Often these are sites of dense plankton aggregations of critical ecological importance. In this study, a recirculating flume apparatus with a laminar, planar free jet (the Bickley jet) was used to create finescale gradients of fluid velocity (shear) in both upwelling and downwelling configurations for zooplankton behavioral assays. Particle image velocimetry (PIV) was used to fully resolve the velocity fields allowing us to fine-tune experimental parameters to match fluid mechanical conditions commonly measured in the field. Zooplankton behavioral assays with two tropical calanoid copepods, Acartia negligens and Clausocalanus furcatus, an estuarine mysid, Neomysis americana, and the larvae of an estuarine mud crab, Panopeus herbstii, were conducted in control (stagnant), upwelling, and downwelling flow configurations. Statistical analyses (ANOVA) of individual zooplankton trajectories revealed the potential for individual behavioral responses to persistent finescale vertical shear layers to produce population scale aggregations, which is proposed here as a mechanism of patchiness in coastal marine ecosystems. Results from behavioral analyses reveal species-specific threshold shear strain rates that trigger individual behavioral responses. Furthermore, results show statistically significant changes in behavior (relative swimming speed, turn frequency, heading) for all species tested in response to a coherent shear structure in the form of finescale upwelling and downwelling jets. The results show that changes in individual behavior can increase Proportional Residence Time (PRT = percent time spent in the jet structure). On a population scale, the increase in PRT can lead to dense aggregations around persistent flow features, which is consistent with numerous field studies. These dense, patchy aggregations of zooplankton have profound trickle-up ecological consequences in coastal marine ecosystems.