Antarctic seabirds including Adelie penguins (Pygoscelis adeliae), south polar skuas (Catharacta maccormicki), southern giant petrels (Macronectes gigantus) are high trophic level predators that accumulate persistent organic pollutants (POPs) present in the food webs in which they forage. Little is known about the levels of POPs in some Antarctic organisms (e.g. southern giant petrels), as well as the long-term trends of POPs in the Antarctic ecosystem. Samples from all three seabird species were collected post mortem, including eggs, from the Western Antarctic Peninsula (WAP) and in the Ross Sea throughout the austral summer breeding seasons of 2004--2006. The samples were analyzed for C and N stable isotopes and POPs including organochlorine pesticides, polychlorinated biphenyls (PCBs), and brominated diphenyl ethers (BDEs). The objectives of this study were to: (1) evaluate the long-term trends of POP residues in Adelie penguins, (2) compare POP levels within livers of the three seabird species based on migratory patterns and trophic level using stable isotope analysis of delta15N and delta13C, and (3) demonstrate POPs can be used as tracers of Antarctic seabird ecology. POPs in Antarctic biota were first evaluated using Adelie penguin tissues and a long-term analysis including data from the current study showed SigmaDDT has not declined in WAP penguins for more than 30 years. Indeed, the presence of p,p'-DDT in these birds indicates that there is a current source of DDT to the WAP marine food web, and both measurements and calculations suggest that this source of DDT is related to climate driven environmental change in the region. A more broad analysis including all three seabird species showed SigmaPCBs, SigmaDDTs, Sigmachlordanes and mirex are 3--100 times higher in migratory seabird livers than the endemic penguins, while hexachlorobenzene (HCB) exhibits no difference in concentration between the three seabird species. Model predictions compared to measured output of delta13C and delta13N indicate a stronger correlation between delta13C and less volatile POP concentrations demonstrating the heavy influence of winter migration on the contaminant loads of seabirds that breed in Antarctica. Finally, discrepancies in POP ratios between migratory and endemic seabird eggs and fat in combination with stable isotope signatures gave insight into seabird evolutionary breeding strategies. For example, the relative abundance of SigmaPCBs was highest in south polar skua eggs and endogenous lipid input into skua eggs was estimated at >79% by examining discrepancies in contaminant ratios. The combined stable isotope and contaminant data indicate that south polar skuas and southern giant petrels employee different combinations of income and capital breeding strategies.

Previous knowledge of the seed ecology of the clonal seagrass Zostera marina L. (eelgrass) suggests that sexual reproduction is not very important to the population dynamics of eelgrass; however, researchers have hypothesized long-distance dispersal for nearly a century. From a bay-wide sampling effort, viable eelgrass seeds in the seed bank were found throughout most of the lower and middle Chesapeake Bay, but abundance of seeds was highly variable. Lower seed-bank densities were found in middle Chesapeake Bay, the region with slow recovery of eelgrass populations. From natural and artificially created eelgrass populations, regional environmental conditions were found to have a greater impact on reproductive shoot (reproductive effort) and seed (reproductive output) production than small-scale influences of location and patch structure. Detached reproductive shoots of eelgrass (containing viable seeds) held in greenhouse tanks remained buoyant for several weeks before they degraded, sank, and lost all their seeds. In offshore shoal areas, suitable for eelgrass growth and survival, seventy percent of tube caps of the polychaete Diopatra cuprea (found throughout the shallow regions of Chesapeake Bay) had fragmented reproductive shoots built into its walls, suggesting a mechanism for seeding these shallow areas. Viable eelgrass seeds were found throughout the shoreline of south Chesapeake Bay, up to 34 km away from the nearest bed. Additionally, a GIS exercise identified new eelgrass patches up to 108 km from the nearest source population. The use of burlap bags for protecting seeds from predation, burial, or lateral transport maximized germination success over unprotected seeds in the field and provides a new mechanism for restoration efforts. An ecological model of eelgrass reproduction highlighted the potentially significant contribution of seeds to the long-term productivity of eelgrass at different water depths. Exploring theoretical scenarios, the model can be used to predict the total number of seeds produced for one to germinate and successfully establish as a seedling, as well as determine the size of patches, newly created from seeds, based on the number of viable seeds in the seed bank and the vigor of the seedlings that develop.

Fisheries sustainability is inherently linked to an understanding of the population-level effects of fishing. With an accurate characterization of historical fish and fishery dynamics, management agencies are more equipped to create regulations that sustain fishery resources over the long term. The overarching goal of this dissertation is to contribute to the advancement of fisheries stock assessment and promote resource sustainability. My research focused on highly migratory species (HMS), particularly fishes that reside in the open ocean. These species constitute some of the highest valued global fisheries; however, numerous factors compromise HMS stock assessment and management. These challenges are fully described in Chapter 1, which also includes corresponding research and management recommendations. A key limitation in HMS assessments underlying my research is the lack of independent scientific monitoring programs. In the absence of research surveys, HMS stock assessments must rely on fishery catch and effort data. Therefore, special care is required to infer population dynamics from entities that were not established to monitor populations. In particular, the habitat in which fishing occurs largely dictates the amount and composition of fishes captured. Unfortunately, habitat effects on fishery-dependent data are not commonly accounted for in HMS assessments. Chapter 2 presents the results of a performance evaluation of methods used for estimating HMS abundance trends, including traditional generalized linear models (GLMs), an existing method that considers habitat (statHBS), and a proposed method that hybridizes traditional and habitat-based approaches (HabGLM). I demonstrate that HabGLM was most accurate of those evaluated, while exhibiting minimal sensitivity to errors in input data. I recommend the use of HabGLM in future HMS stock assessments; however, despite being most accurate, there were scenarios where HabGLM still did not sufficiently capture the true abundance pattern. In Chapter 3, the HabGLM was applied to 35 HMS in the Atlantic Ocean using fisher logbook data from the US pelagic longline fishery. This comprehensive analysis portrays an HMS community in the Atlantic as generally depleted, with current abundances of 76% of the species at less than half of their 25-year observed maxima. However, despite these depletions, 26% of the species exhibited population growth, suggesting recent fishing intensities may be adequate for sustaining or rebuilding certain populations. While interpretations of abundance trends can be informative, fisheries management is more often guided by the output of stock assessments. Thus, in Chapter 4, I present the results of a study that evaluated the effects of abundance index quality on the performance of a stock assessment model (Stock Synthesis), with a focus on Atlantic blue marlin (Makaira nigricans). In general, assessment model performance was superior when based on abundance indices estimated using HabGLM; however, the management quantities derived from this best case scenario were still overly optimistic, and when the fisheries were regulated accordingly, population biomass was projected to be well below the management target level. Overall, my research emphasizes that (1) habitat should be directly incorporated into HMS stock assessments, and (2) independent stock monitoring programs are essential for effective fisheries management.

The amphipods of Lake Baikal, Russia, are a taxonomically and morphologically diverse group, and have been cited as a classic example of adaptive radiation. An unfortunate consequence of this diversity has been an instability of Baikal amphipod classification, with frequent revisions spurred by differing opinions about the phylogenetic utility of different characters. Classifications have never been based on a rigorous phylogenetic analysis of morphological data and only recently has the phylogeny of Lake Baikal's amphipods been examined using molecular tools. Unfortunately, most of these studies have led to a limited expansion of our understanding of Baikal amphipod systematics. Phylogenetic relationships of selected amphipod species from Lake Baikal were constructed using molecular data from portions of two mitochondrial genes, 16S rDNA and COI, and 121 morphological characters. Additionally, patterns of morphological change and the phylogenetic utility of different characters were examined by tracing the 121 morphological characters upon the most parsimonious 16S phylogeny. While the molecular datasets resulted in similar topologies, the morphological data were not congruent with either molecular dataset. A combined molecular/morphological analysis resulted in a topology that was not very different than the combined molecular phylogeny. When plotted on the most parsimonious 16S tree, the morphological data was very homoplastic, although the level of homoplasy differed among types of morphological characters. Contrary to recent popular opinion, body armour and processes characters were the least homoplastic of all types, while characters that have been considered phylogenetically useful, such as mouthpart characters, were the most homoplastic. The molecular phylogenies obtained in this study lead to a better understanding of the phylogenetic history of Baikal's amphipods. The large, morphologically diverse family Acanthogammaridae is strongly supported as a monophyletic group, and likely to have radiated from a single ancestral species within the lake. Conversely, the fossorial, morphologically uniform family Micruropodidae seem to be composed of two relatively unrelated groups, one of which is closely related to the monotypic Macrohectopidae, the lake's morphologically highly modified pelagic planktivore, suggesting a disjunction between morphological and molecular evolution. Finally, this study suggests that the amphipod fauna of Lake Baikal is not monophyletic; the cosmopolitan Gammarus lacustris may share recent common ancestry with some Baikal taxa.

For many shallow water environments, ecosystem function depends on the cycling and flow of materials and energy between benthic and pelagic subsystems. Benthic suspension feeders often are important links between the water column and sediment in coastal ecosystems. Populations of the suspension feeding polychaete Chaetopterus pergamentaceus (previously reported as Chaetopterus variopedatus) are widely distributed along the United States East Coast, ranging from New England to Florida. This species is a structurally and functionally important member of the lower Chesapeake Bay benthic community, where it has maintained stable populations for at least the last 15 years. Little is known regarding the dynamics of this population and its role in benthic-pelagic coupling. For this study, I elucidated demographics, identified the organic matter sources fueling growth and production, determined the in situ behavior, rates and allometry of filtration, and developed an energy budget for this polychaete within the lower Chesapeake Bay estuary. Chaetopterus pergamentaceus exhibited high seasonal and interannual variability in growth, reproduction, and secondary production. High secondary production was mainly due to the rapid growth and maturation of new recruits during summer. Highly variable interannual production was due to inconsistency in recruitment success. Spatial variations in population processes, concordant with major environmental gradients, may influence the population dynamics. Locally produced organic matter, primarily fresh phytoplankton and secondarily recycled material from microbial sources with minimal to no terrestrial input, was utilized for growth and reproduction. Chaetopterus pergamentaceus has a filtration rate comparable to oysters and has the potential to transfer large quantities of matter from the water column to the benthos. This polychaete may filter a large portion of, or an amount equivalent to, the net water column community production on an annual basis. When considered on a daily basis, the potential carbon flux may be greater than net community production. Thus, this organism plays an important role in benthic-pelagic coupling in the lower Chesapeake Bay.

A computational framework is built and demonstrated which is capable of testing plant growth strategies. The framework consists of Vgrass, a carbon based simulation model of a single Zostera marina plant, and the genetic algorithm (GA). Vgrass is based on published seagrass models, published photosynthetic data, and general plant physiology information. The model grows individual leaves whose initiation times are based on degree-day intervals. Leaf size is computed and combined with shoot density to compute population self shading. Leaf length is an emergent property since leaf growth is limited by light attenuation caused by self shading. The model is able to show the relationship between leaf size and shoot density in response to light availability. Degree-days is also shown to be an effective method in modeling the emergence of Zostera marina leaves. The GA and Vgrass are combined to demonstrate the GA as an optimization method and to demonstrate a secondary sensitivity analysis. In an optimization exercise, the RMS error between Vgrass biomass and that of another published model is minimized. Solutions with fitness ranking within 10% of the smallest RMS error are compared in a secondary sensitivity analysis. The analysis can be used to indicate parameter sensitivity in regards to the models ability to attain the optimization goal. Plant growth strategies are tested by searching for configurations of Vgrass parameters best able to: maximize relative growth rate, maximize biomass, and maximize net primary production. Configurations found by the GA lead to plant growth patterns that are not biologically realistic; plant growth strategies based on maximizing "growth" lead to unrealistic plant growth. The plant growth patterns from each of the tests are discussed in relation to ecological and economic principles. Configurations found by the GA search are unique to the optimization goal and the resulting plant growth patterns are shown to support the given goal. Therefore, the computational framework is shown to be successful in testing plant growth strategies. Further, this study shows that care must be taken when defining the fitness function and that the GA is and that the GA is an effective tool at finding "holes" in a model.

The northern diamondback terrapin (Malaclemys terrapin ) is the only estuarine turtle residing along western Atlantic and Gulf of Mexico coasts of North America. Through predation, terrapins may be a key species in coastal marine habitats by exerting top-down control on marsh invertebrates, and thereby help to maintain healthy marshes. Despite the terrapin's ecological importance, there has not been a thorough study of terrapin foraging ecology and movements in lower Chesapeake Bay. In this dissertation, the research focused on the foraging habits of diamondback terrapins and their effects within salt marsh and seagrass habitats of lower Chesapeake Bay. I provided detailed analysis of the diet of diamondback terrapins captured from both salt marsh and seagrass habitats that showed preferred foraging in seagrass beds when present, as well as prey differentiation by terrapin size, i.e., small vs. large terrapins. Three general patterns in dietary overlap based on terrapin size were common for M. terrapin. By habitat, there was substantial overlap in prey choice, though further analyses determined selectivity for barnacles Balanus spp. by small terrapins in seagrass beds. Small terrapins from marsh-mudflat habitats consumed more periwinkles than large terrapins from marshes or all terrapins from marsh-SAV habitats. The size of ingested periwinkles was related to terrapin size with snails ingested by mature females presenting a bimodal distribution. Two mesocosm prey choice experiments showed that terrapins had a preference for juvenile blue crabs (Callinectes sapidus) over periwinkles and mottled dog whelks (Nassarius vibex). A third revealed terrapins were less successful in finding and consuming blue crabs with increasing percent cover of vegetation. An acoustic telemetry study confirmed that small terrapins, which included all males and juvenile females, had better-defined home ranges than adult females and stayed mostly in shallow near-shore water in seagrass beds of lower York River, whereas large females entered these areas on flood and high tides. A logistic regression model predicted that small terrapins were less likely to move out of an area than large females. Males made infrequent, long distances trips within the study area not associated with mating. Both genders and size classes also frequently moved between non-connected Zostera marina beds in the study area. This research provided the first field evidence that terrapins ingested viable eelgrass seeds incidental to consuming Z. marina epifauna. A second logistic regression model revealed that small terrapins were more likely to consume seeds than large terrapins. The diamondback terrapin is considered a "species of concern" in Virginia, but it has minimal protection with little enforcement. This dissertation provides empirical evidence supporting the diamondback terrapin's ecological importance within Chesapeake Bay that can be incorporated into conservation strategies to promote recovery and protection of the species within Virginia.

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