Living organisms exhibit daily rhythms as a way to anticipate predictable fluctuations in their environment. Such daily rhythmicity is the phenotypic outcome of oscillating genes and proteins, driven by an endogenous biological clock. Clock-controlled behavioral rhythms are inherently "flexible" since their phase, amplitude, and period can change throughout an animal's life hallmarked by changes in so-called chronotype. How this inherent plasticity of clock-controlled rhythms is linked to plasticity of behavior is still an open question in biology. Characterizing the various mechanistic links between plasticity of the animal clock and behavioral state will not only shed light on the molecular underpinnings of animal behavior, but also lead to novel chronotherapeutic interventions to treat human disorders that affect the behavioral state such as bipolar disorder and Alzheimer's. While clock-controlled behavioral plasticity is crucial to a species' survival and fitness, it has also been hypothesized to be a target for manipulative parasites that need to induce timely changes in host behavior to facilitate growth and transmission. Using the Florida carpenter ant Camponotus floridanus as a model, this dissertation attempts to bridge some of the existing knowledge gaps in sociobiology, chronobiology, and parasitology. In the first chapter, we have identified a mechanistic link between plasticity of the C. floridanus clock and its behavioral state. Subsequently, in chapter two, we have provided evidence showing that Ophiocordyceps camponoti-floridani, a fungal parasite that induces timely changes in C. floridanus behavior targets the pre-existing links between host behavior and chronobiological plasticity we have found in chapter one. In the final chapter, we characterize how the clock of O. camponoti-floridani functionally differs from the clock of a non-manipulating fungal parasite, Beauveria bassiana, and put forward a regulatory mechanism via which the manipulating parasite's clock might be inducing timely changes in host behavior.

The Chesapeake Bay region values oysters for the ecosystem services, lucrative fishery, and historical significance that the species embodies; however, over the last half century, oyster abundances have been reduced to historical lows. Two protozoan parasites, Perkinsus marinus and Haplosporidium nelsoni, have been major influences on oyster populations, especially in high-salinity regions. Today, the population is recovering; catches have increased and oysters have expanded spatially. to investigate the cause of the recovery, three measurements were made on slides of oysters from a histological archive collected during summer at Wreck Shoal in the James River from 1988–2017: oocyte diameter, oocyte density, and gonad area fraction. Gametogenic investment served as a proxy for the fitness of oysters; it was hypothesized that an outbreak of P. marinus in the 2000s led to a tolerance response that can be detected as an increase in reproduction. Oocyte diameter has remained variable yet steady overall, except for a decrease in 2001 and 2002. Oocyte density and gonad area fraction increased sharply around 2003. Mean oocyte densities increased by a factor of 2.05 and gonad area fraction by a factor of 2.04. Oocyte density has been maintained at these higher counts in recent years. The increase in gonadal area ratio is presently decreasing slowly yet significantly (p=0.00429). The cause of the increase is still not well understood, as a variety of environmental variables were significant predictors of reproduction as well as the hypothesized cause, P. marinus weighted prevalence. Regardless of the cause, changes in reproductive patterns signify a positive change on the part of the oyster. The ability of the wild oyster population to adapt supports management strategies that protect old oysters, like sanctuaries and slot fisheries. These strategies allow fit oysters to grow to old age and pass on their beneficial traits to future generations. in the face of doubts about the efficacy of restoration, conservation emerges as a path forward.

For years bluefin tuna has been the poster child for overfishing and poor management. However, recent improvements in data collection, catch monitoring and international cooperation are providing an opportunity to reverse the perception of a fishery that is doomed to collapse. Stock assessments are conducted routinely to monitor the abundance and productivity of exploited fish stocks so managers can determine how many fish can be sustainably harvested each year. Should a stock be declared overfished or under-going overfishing, the science behind stock assessments also equip managers with the knowledge necessary to make decisions about what short-term and long-term management measures should be taken to help reverse these trends. in that light, the goal of my research has been to use newly available age data to improve the quality and reliability of assessments for Atlantic bluefin tuna by reducing uncertainty about the data and methods used to infer growth and age composition. A secondary goal has been to provide managers with the knowledge necessary to implement effective stock rebuilding programs for Pacific bluefin tuna. Chapter 2 is focused on cohort slicing, a method routinely used in the Atlantic bluefin tuna assessment to estimate catch-at-age from catch-at-size information. This chapter explores how errors in cohort sliced catch-at-age data can bias estimates of total mortality rate derived from catch curve analysis. Recommendations are provided concerning the appropriate mortality estimator and plus group to use depending on the parameters characterizing the stock. Chapter 3 provides updated growth estimates for western Atlantic bluefin tuna, which were adopted in 2017 as the basis for defining growth in the assessment. Chapter 4 provides an overview of the theory behind age-length keys with particular emphasis on the assumptions that govern each method and provides notes of caution concerning their applications to real data. Chapter 5 evaluates through simulation the relative performance of different methods for estimating age composition of western Atlantic bluefin tuna catches and applies the best performing technique, the combined forward-inverse age-length key, to actual western Atlantic bluefin tuna data. Chapter 6 moves over to the Pacific and focuses on evaluating the potential impacts of different minimum size regulations on the stock of Pacific bluefin tuna and explores ways in which to minimize short-term pain to the industry while still achieving long-term yield and conservation goals. Overall, this work has contributed major improvements to the stock assessment process of Atlantic bluefin tuna and implications of this work resonate beyond the bluefin tuna world to other highly migratory species faced with similar problems.

The barotropic and baroclinic responses of the Chesapeake Bay to forcings from two hurricanes were investigated by using unstructured-grid three-dimensional hydrodynamic models. The model domain includes Chesapeake Bay proper, the tributaries, and its extended continental shelf in the mid-Atlantic Bight. Two hurricanes were studied: Hurricane Floyd of September, 1999 and Hurricane Isabel of September, 2003, both of which made landfall within 100 km of the Chesapeake Bay mouth. Hurricane Floyd in 1999 passed through the entrance of the Bay from southwest to northeast along the coastlines of Virginia as a Category 1 storm, whereas Hurricane Isabel in 2003 made landfall on the east coast of North Carolina and moved inland toward the northwest as a Category 2 storm. For the barotropic simulation of the Bay responding to the hurricanes, the model results were compared with Bay-wide water level observations and the model showed reasonable prediction skill. It was found that the storm surge has two phases: a primary surge induced by the remote winds and a secondary surge induced by the local winds. For both hurricanes, the primary surge induced by remote winds propagated into the Bay initially, but the subsequent phase, influenced by the local wind, was notably different. Hurricane Floyd was followed by northerly (down-Bay) winds, that reduced the primary surge effect and caused a localized set-down; Hurricane Isabel was followed by southerly (up-Bay) winds, which superimposed on the primary surge effect and caused a localized set-up. The volume and salt fluxes were estimated at selected cross-sectional transects throughout the Bay, and it was found consistently for each transect that the net influx dominated during Hurricane Isabel while the net outflux dominated during Hurricane Floyd. For the Bay's tributaries, the large inland river discharge at the headwater can couple with the storm surge event to increase sea surface elevation on the second phase of sea surface elevation rise, which has a significant impact on inundation in the local low-lying areas. For the baroclinic response of the Bay to the hurricanes, the model results agreed reasonably well with additional observed data: sea surface elevation, velocity, and salinity profiles. From the perspective of salt flux, oceanic saltwater influx was evidently pushed into the Bay from the continental shelf at the initial phase of Hurricanes Floyd and Isabel associated with storm surge and salt intrusion. In the second phase, follow up with, down-bay local winds of eastern-type storms tend to enhance the stratification whereas up-Bay local winds of western-type storms tend to reduce the stratification. The hurricane surface wind stress is the primary agent for destratifying water column by transferring generated turbulent kinetic energy to the lower layer. The wind-induced straining during Hurricane Floyd was verified using non-dimensional parameters that incorporated the wind direction and the horizontal salinity gradient. Direct precipitation of hurricane rainfall acted more like a point source onto the Bay surface water, which created a layer of low surface salinity on the sea surface. It has an implication dynamically on generating a sea surface horizontal pressure gradient and re-distributing salinity field after the storm. Extra efforts have been made to conduct idealized experiments for comparing long-term recovery of the Bay to the disturbance created by the two hurricanes. Realistic hurricane wind forcing was applied in a 4-day window with the same initial condition applied in the beginning, and the quasi-steady state condition achieved in the end. Through this exercise, it was found that it took Bay 5-7 days to return to normal condition from the sea surface elevation disturbances for both Hurricanes Floyd and Isabel. For the salinity fields, it took within a range of 20-30 days to recover to the pre-storm condition for the middle and southern portions of the Bay. For the northern portion of the Bay, however, due to the landward barotropic pressure gradient generated a strong salinity rebound and the associated oscillation subsequently after Hurricane Floyd passed, it required twice as long to recover. Sensitivity testing of the effect of river discharge (immediately after the storm) on the recovery time has also been performed. Lastly, the influences of continental shelf dynamics on the Bay's response to the hurricane were examined. It was found that the along shelf wind contributed to the inflow and ouflow at the Bay mouth in the form of Ekman transport, which complemented the contribution generated by the Bay's local wind. The onshore and offshore shelf wind also played a significant role. Because the cyclonic pattern of the hurricane wind field, when the hurricane made the landfall in the US East coast, an along-the-shelf pressure gradient from the north to the south was generated. This pressure gradient, coupled with the Coriolis and friction forces, can generate a quasi-geostrophic balance flow serving to prevent or enhance the inflow across the Bay mouth. The effect is particularly noticeable in the relaxation period during the hurricane passage.

Particulate levels within marine, estuarine and freshwater vegetated shallows are often lower than in nearby open water, although most of the studies quantifying this trend are from non-tidal, freshwater systems. The potential positive feedbacks between vegetation, water clarity, and zooplankton clearance and the potential negative feedback from microbially-mediated sulfide production were investigated in several eelgrass (Zostera marina) beds in the lower York River and Mobjack Bay, Chesapeake Bay, Virginia and through the construction of a computer simulation model. Paired automated chlorophyll a and turbidity sensors were deployed for eight one-week periods to compare particulate levels inside and outside of eelgrass beds. The vegetated estuarine shallows monitored appeared to behave differently than those in freshwater vegetated systems, in that they were not able to consistently maintain improved water clarity relative to adjacent, unvegetated areas. Predictive equations for particulate levels inside the eelgrass beds were developed by regressing chl a and turbidity against wind and tidal influences for use in a Zostera simulation model. Zooplankton were sampled during two summer seasons to quantify their impact on water clarity. In 2006, zooplankton densities were significantly higher in vegetated than non-vegetated areas, but not in 2007. Zooplankton densities were significantly higher at night, both inside and outside of the vegetated beds. Overall, the zooplankton densities encountered within the SAV beds had the potential to filter approximately 2-6% of the water column per day, much less than typically encountered in freshwater. Eelgrass density, sediment organic content and porewater sulfide levels were quantified in situ in several SAV beds throughout spring and summer. There was no significant difference in [S] between vegetated and unvegetated areas, [S] was not correlated with eelgrass cover or sediment organic levels, but field results demonstrated that porewater [S] above 900-1000 muM inhibited eelgrass growth within the study area. An iron enrichment experiment demonstrated some potential for iron to positively affect Z. marina growth and survival, but responses were site specific and highly variable. Finally, a computer simulation model was constructed that incorporated positive and negative effects within Z. marina beds, including tidal- and wind-induced particulate loading, resulting attenuation of light, particulate removal due to biological and physical filtration, temperature stress and sulfide toxicity. Modeled Z. marina responded to reduced light with approximately proportional reductions in year-end shoot and root/rhizome biomass. The model was less sensitive to increased sulfides; increases of 1.5, 2.0 and 2.5 times background sulfide levels resulted in incremental reductions of year-end shoot biomass by 20-25% and root/rhizome biomass by 15-20%. The model was most sensitive to temperature; a 1??C increase reduced year-end shoot and root/rhizome biomass by 41%; sulfide and temperature stress combined reduced shoot and root/rhizome biomass by 64%. With eelgrass in the Chesapeake Bay growing near its southern limits, model results indicate that either sulfide or temperature stress may limit restoration efforts and induce continued losses of eelgrass. Internal feedbacks reduce some of the stress caused by light limitation, but do not compensate for a 1??C increase in temperature or increases in sulfide levels.

In estuarine crabs, there is a gradient of larval dispersal from retention within hatching habitats to export to the continental shelf. This dissertation examined the influence of physical transport and nutritional stress on recruitment success in species with different larval dispersal. In the first chapter, I examined larval vertical migration. Larvae from different families exhibited different tidally and light driven behaviors. The role of transport in selecting behaviors is associated with constraints on larval survival within the estuary. The transport of larvae was examined using a hydrodynamic model. This study compared the dispersal of vertically migrating larvae to that of non-migrating particles. Tidal migration and light limited behaviors influenced advective dispersal. Tidal shear fronts influenced larval distribution and likely effect the strength of biotic interactions. In chapter 3, I examined the impact of starvation and food quality on survival and biochemical composition of larvae with different dispersal strategies. Larvae that develop on the continental shelf generally had greater resistance to starvation than those that develop in the estuary, and they showed more efficient utilization of essential biochemical constituents during nutritional stress. Phospholipid metabolism was important in the starvation response. The biochemical composition of larvae in the field was examined to assess variability in nutritional condition over tidal time scales. Larvae in the plankton were larger and had higher contents of energetic lipids than those in laboratory studies. In the natural habitat, nutritional stress is rare and feeding conditions promote the accumulation of energetic reserves. There was a large degree of short term variability in phospholipid composition of larvae associated with small scale physical factors driving contact between zoeae and their prey. The results from this dissertation highlight the importance of small scale processes in the recruitment success of crab zoeae. While large scale gradients play an important role in selecting for dispersal, larval vertical migration behaviors reflect the influence of both small and large scale selective pressures. Tidal fronts with short durations play an important role in driving the distribution of larvae and likely influence larval feeding. Small-scale physical processes strongly influence variability in recruitment success of crab zoeae.

Habitat fragmentation leads to small, isolated habitat patches in which ecological processes may differ substantially from those in larger, continuous habitats. Seagrass is a structurally complex but fragmented subtidal habitat that serves as a refuge from predation for juveniles of the blue crab, Callinectes sapidus Rathbun. I compared the effects of eelgrass ( Zostera marina L.) patch size and shoot density on juvenile blue crab survival both before (June) and after (September) shoot defoliation and cownose ray disturbance changed eelgrass habitat, and used artificial seagrass to determine the influence of eelgrass patch size on juvenile blue crab survival in the absence of covarying shoot density. Under natural conditions, eelgrass patch size, eelgrass shoot density and density-dependent cannibalism all influenced juvenile blue crab survival, but crab survival varied temporally. Crab survival was inversely correlated with eelgrass patch size in the absence of covarying shoot density, in contrast to patterns typically observed in fragmented terrestrial landscapes; this was likely due to low predator abundance in small patches. I tested the hypothesis that crab survival is maximized at an intermediate level of seagrass fragmentation due to the inverse relationship between crab survival and patch size by modeling the joint effects of patch size and proportional cover on juvenile blue crab survival. When I assumed predation on crabs to be independent of crab density, maximal crab survival (ca. 34%) occurred at intermediate values of seagrass fragmentation. Approximately 18% of crabs survived irrespective of the proportion of the landscape covered by seagrass when crab survival was assumed to be density-dependent. My findings indicate that (i) effects of habitat fragmentation on survival may differ between seagrass and terrestrial landscapes, (ii) seagrass habitat fragmentation has a significant but not overriding influence on faunal survival, and (iii) seagrass patch size, seagrass complexity, and blue crab density all influence juvenile blue crab survival, but their effects vary temporally. Habitat fragmentation studies should incorporate multiple scales of space and time, as well as potentially confounding environmental variables.

The shallow water region is an important portion of the estuarine and coastal waters, since it encompasses the entire land-water margin as the buffer zone and supports one of the most productive ecosystems. When light can penetrate to the sediment, it triggers the benthic microalgae community to perform photosynthesis, resulting in a benthic-pelagic exchange flux different from that of the deeper water. This study utilized the laboratory-measured benthic flux, and a suite of well-calibrated numerical models to examine the eutrophication process in the Lynnhaven River Inlet system with special emphasis on: the role played by benthic microalgae, and nutrient budgets (sources, sinks, and pathways) of the system. An unstructured grid hydrodynamic model UnTRIM developed for the shallow water environment was applied to the Lynnhaven to quantify the transport time scale and as the input for the water quality model. Based on the skill assessment result, it was clear that the presence of benthic microalgae is indispensable for an accurate and realistic calibration of the water quality model. Analysis of field samples in the laboratory experiments demonstrated that benthic microalgae performed photosynthesis under light conditions in surficial sediments, resulting in the net uptake of nutrients and the release of oxygen both to the overlying water column and down to the sediment. Based on the results of annual nutrient budgets, it was shown that the major external source for nitrogen and phosphorus was from nonpoint source loadings. There were three comparable sinks: export to the Bay, burial in the deep sediment, and ditrification in the case of nitrogen. One of the major pathways for nitrogen and phosphorus was the internal recycling. The regenerated dissolved nutrients that were recycled in the water column were more than two times larger than the current total nutrient external loadings. Sensitivity tests showed that, due to their retention capacity, benthic microalgae's presence could decrease the overall export to the Bay, enhance the internal recycling, and increase the denitrification rate in the sediment.

There currently exists a major dichotomy in the nesting population trends of leatherback turtles (Dermochelys coriacea) worldwide. Eastern Pacific populations have been declining precipitously while populations in the Atlantic and western Indian Oceans have been either stable or increasing. The populations in the western Pacific have also declined with some near extirpation. Factors attributed to the Pacific population decline are incidental fishery mortality and egg harvesting. Fishery mortality occurs throughout all basins, and with the exception of the western Pacific population, egg harvesting has not been a major factor at the major nesting complexes for almost two decades. Populations in the Atlantic and western Indian Oceans currently tolerate mortality from top-down factors, while the eastern Pacific populations continue to decline. Therefore, trophic forcing from bottom-up factors may be the major cause of this dichotomy. This study addressed the effects of bottom-up and climatic forcing on leatherback populations worldwide, with an emphasis on leatherbacks in the eastern Pacific. Nesting leatherbacks in the eastern Pacific were highly influenced by ENSO. Cool, highly productive La Nina events caused a high nesting probability whereas warm, less productive El Nino events caused a low probability. Areas of the equatorial Pacific that produced the most accurate nesting estimates, as indicated by sea surface temperature anomalies, were located around the northeast. Foraging conditions in the eastern equatorial Pacific were a function of ENSO governed primary production transitions that determined leatherback nesting numbers in Costa Rica. It appeared that resource availability in the temperate, southeastern Pacific was not sufficient on its own to support vitellogenesis and the nesting process. While coastal foragers were common among most leatherback populations worldwide, they were rare within the eastern Pacific population, possibly from high mortality associated with coastal gillnet fisheries along Central and South America. Among populations worldwide, eastern Pacific leatherbacks had the lowest reproductive output derived from climate driven, inconsistent resource availability. This study demonstrated that the highly sensitive nature of eastern Pacific leatherbacks to anthropogenic mortality derived from interannual and multidecadal climate variation in their foraging areas, thus accounting for their decline rates despite continued beach protection.

Community models predict the effects of stress on community structure and processes. I tested the Menge and Sutherland 1987 model in an estuarine epifaunal community experiencing low oxygen stress, termed hypoxia. Epifauna, animals living on the surfaces of substrates, are ecologically important in many estuaries where hypoxia occurs, yet little is known about the effects of hypoxia on these communities. Epifauna formed dense communities in the York River, a tributary of the Chesapeake Bay, USA, despite frequent hypoxia. Abundance and species composition was similar in two areas of the river, even though the downstream study area often experienced lower oxygen concentrations during hypoxic episodes than the upstream study area. Many dominant species exposed to high and low oxygen in the laboratory had a median lethal time (LT50) in hypoxia greater than the duration of typical hypoxic episodes in the York River, suggesting that hypoxia may cause little mortality for many species in this system. Predation by a variety of taxa decreased during hypoxia in the laboratory, because many mobile predators had higher mortality than sessile prey, and because predation rates decreased. Peak recruitment of dominant taxa, and of total epifauna, in the York River occurred during neap tides in the downstream study area, coinciding with the lowest oxygen concentrations. In the laboratory, low oxygen decreased recruitment of dominant taxa, but some recruitment continued in hypoxia for most taxa, indicating that larvae of dominant epifauna are tolerant of hypoxia. Larval tolerance of hypoxia may allow communities to persist even though the recruitment season of many epifaunal species coincides with the peak season of hypoxia. These findings supported some predictions of the consumer stress model, but not all. as predicted, when stress increased, the importance of disturbance for determining community structure increased, while the importance of predation decreased. Unlike predictions, stress changed recruitment rates in the laboratory. There were few effects of stress on abundance and diversity, possibly because in this system hypoxia is mild, brief, and because the species in this community can tolerate stress, colonize disturbed areas quickly, and grow quickly enough to complete life-cycles between hypoxic episodes.