A panel of 48 single nucleotide polymorphism markers (SNPs) was developed for use in a population genetic analysis of the Eastern Oyster Crassostrea virginica sampled from the lower Chesapeake Bay. The SNPs were developed from published and unpublished sequencing data and developed to be used on a Fluidigm Biomark. A selection of 95 SNPs were chosen initially for development and the best 48 were selected for downstream applications. This project was a collaboration with the non-profit Chesapeake Bay Foundation (CBF) to examine their oyster reef restoration project in the Lafayette River, Virginia. The CBF wanted to test a hydrodynamic connectivity model designed to predict where oyster larvae produced in the Lafayette River would settle within the river. To test the model, oysters from Tangier Island, VA and the Haskin NEH hatchery strain were planted in the Lafayette River at locations corresponding to locations within the model with the expectation that the oysters would spawn the following summer. Baseline geographic oyster samples were taken from the nearby rivers; the Lafayette, Elizabeth and James Rivers before deployment of the planted test oysters. Newly recruited oyster spat were sampled from the Lafayette River in the summer following deployment of the planted test oysters. The baseline samples and spat were genotyped and compared to each other with the panel of 48 SNPs. Assignment tests were performed to identify the source population(s) for the spat. There was no population structure defined by FST values among oysters sampled from the lower Chesapeake Bay. The Haskin NEH oysters were genetically different from the other oysters in the study; however, the Tangier Island oysters were not different from the oysters in the lower Chesapeake Bay. The low FST values among the oysters from the lower Chesapeake Bay suggest that the connectivity of the reefs is high. The hydrodynamics of the region mix drifting larvae produced by oysters across the region as seen in the genotypic profile of the spat recovered in the Lafayette River. Heterozygote deficiencies suggestive of a Wahlund effect were observed; however, high rates of migration likely work to counterbalance stable population substructure. Alternatively, the heterozygote deficiencies could represent hidden variation not accessible by the methods used in this thesis. Some population structure exists with increasing geographic distance consistent with a pattern of isolation by distance among the populations sampled for this project. Assignment tests did not identify any spat as a product of the NEH oysters and assignment of spat to Tangier Island origin is inconclusive. The genetic data obtained were not able to provide unequivocal support for the predictions of oyster spat distributions by the connectivity model, although, the data do support the overall circulation patterns in the region predicted by the model.

No description available.

In 1999 a mass mortality of the American lobster (Homarus americanus) occurred in western Long Island Sound (WLIS). Although the etiology remains unknown, warm bottom water temperature, hypoxia, heavy metal poisoning, and pesticides have been suggested as casual factors. Subsequently, lobsters from WLIS have continued to display symptoms of morbidity that include lethargy and cloudy grey eyes, caused by idiopathic lesions. The effects of these lesions on lobster vision are unknown. We therefore used electoretinography (ERG) to document changes in visual function in lobsters obtained from WLIS, while simultaneously using histology to quantify the extent of damage. Of the lobsters collected from WLIS, seventy three percent showed damage to photoreceptors and optic nerve fibers including necrosis of the optic nerve, breakdown of the rhabdom, and hemocyte infiltration through the basement membrane into the ommatidia. Animals with more than 15% of photoreceptors exhibiting histological damage also exhibited markedly reduced responses to 10 ms flashes of a broad-spectrum white light. Specifically, the maximum voltage (Vmax) response was significantly lower and occurred at a lower light intensity as compared to responses from lobsters without idiopathic lesions. Lobsters from outside WLIS did not show such reduced changes to their vision. Lobsters from WLIS still appear to be subjected to an unknown stressor with an idiopathic etiology that is causing significant functional damage to their visual system.

Establishing the relationships between recruitment indices and estimates of adult abundance using fishery-independent data continues to remain one of the principal challenges faced by fisheries scientists due to the lack of concurrent monitoring programs designed to target different life stages of the same species. In Chesapeake Bay, however, multiple, fishery-independent surveys currently monitor the relative abundance of YOY and adult fishes. Using the available data from these surveys, the relationships between estimates of relative abundance for young-of-year and adults of striped bass (Morone saxatilis), weakfish (Cynoscion regalis), and Atlantic croaker (Micropogonias undulatus) were examined. Year-class strength was reflected in subsequent estimates of age-specific adult abundance; however, the strength of the relationships varied greatly with age. For all three species, the initial lack of significant correlations across all age classes indicated the need for improving the recruitment indices to more appropriately reflect YOY abundance. To ensure that the recruitment indices reflect patterns in abundance of YOY fishes, the following information was examined: assignment of the index period and strata and the distributional assumptions of the YOY catch data. For striped bass, a Bay-wide recruitment index appears to more accurately reflect year-class strength than the individual VA and MD recruitment indices. The recruitment indices for weakfish and Atlantic croaker improved when changes were made to the index period; however, further investigation is necessary to determine how depth influences the distribution and, ultimately, abundance of these two species. Identifying the distribution of the YOY catch data from the VIMS juvenile finfish surveys is also critical for obtaining unbiased recruitment indices. Here, the striped bass and weakfish catch data were gamma distributed; whereas, the Atlantic croaker catch data were lognormally distributed. The application of the delta-lognormal distribution did not improve the recruitment indices for any of the species in this study. An ageing study was conducted to determine if historically-defined length threshold values accurately distinguish YOY fish from older individuals in present day samples of striped bass, weakfish, and Atlantic croaker collected from the juvenile finfish surveys. The length threshold value for striped bass was determined to be approximately 30 mm too high. Although the current recruitment index for striped bass is not likely influenced by the small number of 1-year olds measured as YOY fish, reducing the length threshold value would ensure that only YOY fish are included in the calculation of the recruitment index. Further research is needed to determine if the length threshold values are appropriate for weakfish. For Atlantic croaker, length threshold values for the early portion of the index period (May, June) were appropriate; whereas, values used for the latter half of the index period (July, August) were too high, allowing for older individuals to be considered YOY based on their length. Consequently, the use of an earlier index period for Atlantic croaker would ensure that older fish are not being considered as YOY fish based upon their length.

Polar zooplankton and fish safeguard against the seasonality of food availability by using the summer months to build large reserves of lipids, which in turn are utilized to meet the metabolic demands of apex predators such as penguins, seals, and whales. A warming trend in the northern part of the western Antarctic Peninsula (WAP) has led to a decrease in perennial and summer sea ice, an increase in heat content over the shelf, and lower phytoplankton biomass, which could affect prey quality. We compared prey quality, including elemental (C, N) content and ratios, total, neutral, and polar lipid content, and energy densities, of known top-predator prey items (krill Euphaush1 superba, 17Jysanoessa macrura, and Euphausia crystallorophias; and fish Pleuragramma antarcticum, and Electrona antarctica) along the W AP latitudinal gradient in January of 2009-20 II as part of the Palmer Antarctica Long-Term Ecological Research study. E. antarctica had the highest prey quality in terms of total lipid content and energy density, followed by T. macrura and P. antarcticum, then E. c1ystallorophias and E. superba. For all species, variations in carbon and nitrogen content were best correlated with by the animals' neutral lipid content, in that animals with larger neutral lipid stores had significantly higher carbon and lower nitrogen content. Across all sexes and maturity stages, E. superba in the South had ca. 20% higher total lipid content than E. superba in the North. Total lipid content was also significantly higher in the South for E. crystallorophias, though this was largely due to the presence of larger individuals in the south combined with a significant positive relationship between length vs. weight-specific total lipid content for this species. For all prey species except T. macrura, there was a positive relationship between latitude or 0-120 m integrated Chi a vs. lipid content (neutral, polar, or total lipids), and a negative relationship between 0-120 m mean water temperature vs. lipid content. Trends opposite to those above found for T. macrura, suggest an optimal habitat for this species in the northern W AP which is characterized by warmer temperatures and lower Chi a. Patterns in Chi a were more important than upper water column temperature in explaining the observed latitudinal trends. If regional warming persists, the prey quality trends described for E. superba, combined with their regional abundance decline in the northern, coastal W AP could affect the ability of apex predators that rely on E. superba to meet their energetics demands.

An energetics model was constructed as an alternative method to length frequency analysis for the estimation of growth for juvenile silver perch, Bairdiella chrysoura. The model approach was adopted since estimation of juvenile estuarine fish growth by only collecting length or weight frequency data is difficult due to the large bodies of water and variety of microhabitats that must be regularly sampled over short time intervals. Field and laboratory data was included in analysis of model compartments for growth, metabolism, food intake and energy loss in waste products. Food habit studies indicated that silver perch is a planktivore that feeds on calanoid copepods during the day and mysids at night. Estimated energy utilization for silver perch at maintenance and maximum rations were similar to literature values for yellow perch, Perca flavescens, and brown trout, Salmo trutta. Model simulation of growth for silver perch in the York River, Virginia from July through October 1981, contained less variation in the size prediction than growth rates determined by length frequency analysis. The model did not contain periods of negative growth as did the field data. By the end of the season, model predictions of silver perch length matched the average length of silver perch captured in the lower York River. The construction of energy utilization models through complementary laboratory and field research has been demonstrated to be a viable method for estimating growth for juvenile fishes. Length frequency analysis is limited to only expressing growth over time. The advantages of an energetics model are that it also defines trophic and ecological interactions as well as environmental factors that impact growth.

The effects of salinity on cadmium toxicity to the bay mysid, Mysidopsis bahia Molenock were studied in a series of experiments examining salinity tolerance, effect of salinity on intermolt period, osmoregulatory capacity, interaction of salinity with acute cadmium toxicity, role of changes in cadmium speciation, modification due to calcium antagonism and effects of cadmium on osmoregulatory ability. Upper and lower tolerance limits increased with increasing acclimation salinity. Intermolt duration decreased slightly with increasing salinity. Mysidopsis bahia osmoregulates at salinities from 5 to 37&\perthous& and exhibits an isosmotic point of 24&\perthous&. Hemolymph osmolality attained steady-state condition by 95 min post-transfer to high and low salinity water. The 96-h LC&\sb{lcub}50{rcub}& (as total cadmium, Cd&\sb{lcub}\rm T{rcub}&) increased in a general linear fashion with salinity. When toxicity was expressed in terms of free cadmium ion (Cd&\sp{lcub}2+{rcub}&) rather than Cd&\sb{lcub}\rm T{rcub}&, CdCl&\sp+& or CdCl&\sb2& only a slight salinity effect was apparent, suggesting that Cd&\sp{lcub}2+{rcub}& is the primary toxic species. Mysids were more tolerant of Cd&\sp{lcub}2+{rcub}& at an intermediate salinity of 22&\perthous&. Toxicity of Cd&\sp{lcub}2+{rcub}&, when varied by use of the artificial ligand nitrilotriacetic acid (NTA), was independent of Cd&\sb{lcub}\rm T{rcub}& concentration at a given salinity but increased with increasing salinity and/or NTA concentration. Calcium exerted a sparing effect on Cd&\sp{lcub}2+{rcub}& toxicity although the effect was not as pronounced as were effects due to Cd&\sp{lcub}2+{rcub}&-salinity interactions. Molt rate was significantly increased by Cd&\sp{lcub}2+{rcub}&-salinity interaction. It is postulated that the increase in apparent molt rate may at least partially explain the residual salinity effect that is observed even when speciation and calcium effects are considered. No significant effects on hemolymph osmoregulation were observed following exposure for up the 48 h to Cd&\sp{lcub}2+{rcub}& levels approximating the 96-h LC&\sb{lcub}50{rcub}& at 12 to 30&\perthous& salinity.

This research investigated the relationship between juvenile abundance indexes (JAIs) for anadromous blueback herring (Alosa aestivalis) and abiotic factors (river flow and temperature) during the spawning and nursery period in the tidal freshwater areas of James, Pamunkey, Mattaponi, and Rappahannock Rivers in Virginia. Accomplishing this objective required the evaluation of the JAI methodology, specifically the effect of phototactic behavior on diel changes in the surface availability to the pushnet sampling gear, and obtaining population dynamics information (hatch dates, growth, natural mortality) during early life history from otolith microstructure of samples collected in 1991 and 1992. Mean catch-per-unit effort (CPUE) at night was one to two orders-of-magnitude higher than daytime mean CPUE. Availability dramatically increased approximately 30 minutes after sunset when light intensity was 10&\sp{lcub}-2{rcub}& to 10&\sp{lcub}-3{rcub}& &u&E/m&\sp2&/s. After the occurrence of this isolume, consecutive catches were order independent and varied without trend. A corresponding change in availability of prey did not occur, indicating that juveniles migrate to surface water in a specific isolume and not as a response to prey movement. Phototropic research verified the appropriateness of the JAI sampling methodology. Otolith microstructure analysis indicated that later larval emergence, reduced relative abundance, depressed growth, and increased mortality were associated with low water temperature and high river flow from a major episodic event. Results suggest that high river flows during the early larval period increase turbidity and reduce prey visibility, potentially causing depressed growth and starvation of newly hatched larvae. No linear or nonlinear relationship, however, was evident between any of the seasonal and monthly abiotic factors and the annual JAIs for the period 1979-95. All correlation and multiple regression analyses failed to reject (P &>& 0.05) the hypothesis of no effect. While the statistical power to detect a strong effect was high (&>&0.80), the power to detect weak effects was low, perhaps because of limited sample size and the lack of major runoff events during the study period. Power analyses indicated that the detection of a weak effect with the observed variance would require 25 or more years of data.

Striped bass (Morone saxatilis) in Chesapeake Bay, USA, are experiencing an epizootic of mycobacteriosis. This disease, caused by bacteria in the genus Mycobacterium, causes granulomatous lesions of the skin and viscera. Diseased fish are often emaciated, and fish with skin lesions may be significantly disfigured. The overall goal of this work was to examine aspects of the pathobiology of mycobacteria in striped bass via laboratory exposure studies and cellular assays. Striped bass were injected intraperitoneally with a sublethal dose of Mycobacterium marinum, M. shottsii, or M. gordonae and sampled for histology and bacteriology at regular intervals to 45 weeks post-injection (p.i.). Fish injected with M. marinum developed granulomas in the mesenteries, spleen and anterior kidney. Acid-fast bacilli (AFB) were rare in initial stages of disease whereas granulomas at 8 weeks p.i. and later frequently contained large numbers of AFB. Secondary disease was observed in some fish between 26 and 45 weeks p.i., with granuloma disintegration, severe inflammation, and elevated splenic bacterial densities. Relative to fish injected with M. marinum, fish injected with M. shottsii or M. gordonae did not develop severe pathology. Granulomas were observed in the mesenteries, but were not observed in the spleen or, with one exception, anterior kidney. M. shottsii and M. gordonae both established persistent splenic infections. The ultrastructure of developing M. marinum granulomas in experimentally infected bass was examined. Formation of large macrophage aggregations containing intracellular bacilli was observed within the peritoneal cavity shortly after injection. M. marinum were always contained within phagosomes, and apparent phagolysosomal fusion was frequently observed. Epithelioid transformation of macrophages was observed. Ultrastructural observation of bacilli within granulomas agreed with histologic findings. The in vitro interaction between macrophages and intracellular M. marinum was examined ultrastructurally and with a quantitative bactericidal assay. Phagosomes containing M. marinum were fused at high rates by pre-labeled lysosomes. No differences in lysosomal fusion rates were observed between phagosomes containing live or heat-killed M. marinum. Intracellular M. marinum remained largely viable for the duration of the assay (72 hours). Heat-killed M marinum were resistant to lysis within phagolysosomes.

Validation of daily increment deposition in otoliths of juvenile striped bass up to 80 days of age was provided through sequential sacrifice of known age hatchery-reared fish in 1987 and 1989, and through tetracycline marking of otoliths of cage-cultured striped bass in 1989. Ages of fish between 80-110 days old were consistently underestimated by 1-3 growth increments. Known age juvenile striped bass were raised in the laboratory in 1989 under controlled environmental conditions. These experiments provided evidence of an endogenous circadian rhythm controlling daily increment deposition in juvenile striped bass otoliths. Juvenile striped bass were collected in the 4 Virginia river systems in 1986 and 1987. A total of 542 otoliths were aged using daily growth increments. Comparisons of back-calculated birthdate distributions between populations showed consistency between rivers within years, but not between years. Variations in cohort growth rates appeared to be related to the relative cohort size of fish surviving to the juvenile stage. A comparison of mortality for 14-day cohorts showed no trends between early and late hatched fish, and no relationship was found mortality and average growth rates for these cohorts. Population growth rates for the period June-September were linearly modelled, and ranged from 0.301-0.597 mm/day and 0.027-0.124 g/day. Mortality estimates for 60-90 day old striped bass ranged from 1.88-3.98% loss/day. Catch-per-unit-effort, as measured as the number of fish per seine haul, ranged from 4.0-29.6. Growth rates in both length and weight were positively correlated with condition factor and stomach fullness, suggesting food availability may play an important role in regulating juvenile striped bass growth. There was no apparent relationship between growth and CPUE. The relationships between growth and mortality, and mortality and CPUE, are ambiguous, and more estimates are needed to determine whether a density-dependent effect is controlling year-class strength and recruitment into the juvenile stage.