Detectability, the probability that a species is encountered if it inhabits a site, is often overlooked in fisheries research despite its potential to obscure habitat use inferences. Detectability can be estimated using models that also provide an estimate of occupancy (Ψ), the probability that a species inhabits a site. I used these models to estimate both probabilities, and to examine factors affecting detectability and occupancy for three fishes in Chesapeake Bay tributaries: young-of-the-year striped bass (Morone saxatilis), yearling Atlantic croaker (Micropogonias undulatus), and spottail shiner (Notropis hudsonius). Occupancy models were fitted to data from a seine survey conducted during summer, 2008 and 2009, in two Chesapeake Bay tributaries. Key assumptions of occupancy models relate to the extent and timing of fish movement: sites are independent, and no site-specific emigration or immigration occurs. A mark-recapture study of striped bass, and previously published studies of Atlantic croaker and spottail shiner, suggested that these assumptions were reasonable. Detectability differed among species and variation was explained by both gear-related and environmental factors. Effective net length (i.e., the distance from shore the seine was deployed) explained variation in detectability for all species; generally, when the effective seine length exceeded 12 m, detectability was higher and less variable. Detectability varied from early to late summer for Atlantic croaker and spottail shiner but not for striped bass. This variation may be attributed to increased net avoidance by Atlantic croaker during late summer and increased relative abundance of spottail shiner due to recruitment of individuals to the gear. Occupancy of striped bass and Atlantic croaker, both of which are transient species, was high (Ψ>0.80), whereas the resident spottail shiner occupied fewer sites (Ψ=0.59±0.21; mean±SE) and occupancy varied by river (ΨMattaponi=0.36±0.11; ΨPamunkey=0.82±0.10). Occupancy models are useful to identify factors affecting detectability of fishes captured by seines in Chesapeake Bay tributaries, but other fisheries studies would benefit from sampling design modifications that maximize detectability and improve habitat-use inferences.

Aquaculture of the hard clam Mercenaria mercenaria is a valuable industry on the east coast. At high planting densities, cultured bivalves can become limited by food availability, resulting in reduced growth. Centric diatoms are considered the dominant food source to cultured bivalves. Alternative sources may also be important, including resuspended benthic microalgae (pennate diatoms) and detritus from macroalgae growing on predator exclusion nets. This study measured (1) the availability of different food sources in clam beds at Cherrystone Inlet in Chesapeake Bay, including the effects of macroalgae on food availability, and (2) the clearance rates and absorption efficiencies by cultured clams on individual and mixed food treatments in laboratory feeding experiments. Abundances of benthic microalgae (pennate diatoms) were similar to or greater than centric diatoms. Detritus availability under nets was related significantly to macroalgal abundance. Mass-specific clearance rates and absorption efficiencies were similar among food sources, but differences in the percentage of clams feeding on each treatment suggest macroalgal detritus was less utilized by clams than either phytoplankton or benthic microalgae. Both phytoplankton and benthic microalgae appeared to be valuable food sources to clams, both in terms of in situ abundance and relative food value indices calculated from feeding studies. Though food value was lower for macroalgal detritus, the high availability of this source to clams during blooms suggests it may be important seasonally. Lower diatom concentrations under nets compared to above during a macroalgal bloom suggest dense blooms may limit diatom availability to clams. Future modeling of cultured bivalve carrying capacity should consider the importance of multiple food sources in aquaculture environments.

No description available.

This study investigated vegetation changes in a former tidal freshwater marsh (TFM) to determine the role that salinity intrusion plays in vegetation dynamics. Field observations along a narrow salinity gradient in the Pamunkey River revealed that vegetation is shifting to fewer dominants with increasing salinity. Two remaining dominants, Peltandra virginica and Zizania aquatica (hereafter Peltandra and Zizania, respectively), had variable net CO2 assimilation throughout the growing season. Peltandra net CO2 assimilation declined both over the growing season and in marshes with higher salinity; whereas, Zizania generally increased over the growing season peaking in late summer. The same species' tissue nutrients tracked similarly when compared across marshes of different salinity throughout the season, suggesting that the plants have adapted to their environment. Soils, however, contained higher carbon (C) and nitrogen (N) in a TFM relative to higher salinity marshes across years and within a single season. The soil N: phosphorus (P) ratio is relatively stable and well above 16:1 in the TFM, suggesting P-limitation. The other marshes appeared to be in transition with high fluctuations throughout the season and variability within the marsh. Soils responded to changes in salinity faster than vegetation by adsorbing or releasing nutrients. A mesocosm testing plant traits subjected to four low salinity levels found Spartina alterniflora (hereafter Spartina) unresponsive to salinity ranging from 0 to 6, although CO2 assimilation decreased between treatments fresh and 6. Two TFM species, Peltandra and Leersia oryzoides (hereafter Leersia ), responded to salinity over 2 with decreases in aboveground and belowground biomass. The same two species exhibited an improvement in biomass quality (measured by C:N and C:P) over the salinity gradient, and both held greater N and P in the vegetation pool relative to Spartina. The pool of nutrients held in vegetation may shift with salinity intrusion, and the enhanced biomass quality may lead to greater herbivory due to improved palatability. A second mesocosm study paired Spartina, a facultative halophyte, with each of three TFM species: Peltandra, Leersia, and Phragmites australis (hereafter Phragmites). Spartina outperformed Peltandra in all aspects measured -- both aboveground and belowground. In the presence of Leersia, Spartina offered mixed responses, but Phragmites changed Spartina responses considerably. The results of this experiment suggest that Spartina can succeed in less benign environments in the presence of at least some species. A field manipulation excluding insect herbivory within treatments in three marshes along a salinity gradient found that overall biomass did not respond to the removal of insect herbivory, except for Peltandra in Cumberland Marsh (TFM). Peltandra biomass in TFM exclosures was approximately double that of controls, but this result was not significant in other marshes. Zizania N-content was higher in exclosures, suggesting a loss of this nutrient with herbivory, perhaps from rebuilding scarred tissue and/or loss through guttation. Given Peltandra's salt intolerance and Spartina's ability to outperform common species, it is possible that Sweet Hall Marsh, a previous TFM transitioning to an oligohaline marsh, will become a Spartina-Phragmites marsh in the future driven by bottom-up controls.

Young-of-year (YOY) population dynamics of American shad and blueback herring in Virginia's rivers were examined with an emphasis on variability in growth and mortality rates. In addition, an analysis was conducted to relate juvenile abundance indices of American shad to adult indices to establish a stock-recruitment relationship. to accomplish the stock recruitment relationship, an additional study that examined maturation schedules and inter-annual variability in maturation schedules among stocks was performed. Results of population dynamics studies found that growth and mortality rates of American shad and blueback herring varied by river and year and that conspecific abundance was an important factor in predicting size at the end of summer indicating density-dependent regulation of growth. For both species, instantaneous growth was highest at 40 d and decreased by 100 d as water temperatures decreased each year. American shad Mortality rates increased from 2005 to 2007 with highest rates observed in the James River, while mortality rates for blueback herring had no clear pattern. Large year-classes of Alosa spp. that are smaller in size prior to emigration into the coastal ocean may experience higher mortality rates resulting in recruitment stabilization. Despite the close proximity of four river systems studied, there were persistent differences in growth and mortality rates that support observed trends in year-class strength. High mortality rates observed in the James River support the observation of almost complete recruitment failure of wild American shad in this system. Furthermore, low mortality rates observed in the Rappahannock River are consistent with an increasing trend in recruitment of maturing females, while lower mortality rates and similar growth rates observed in the Mattaponi River compared with the Pamunkey River support long term observations of greater juvenile production of American shad in the Mattaponi River. Young-of-year blueback herring recruitment in Virginia rivers was an episodic process with multiple peaks observed throughout summer indicating that cohorts were not fully vulnerable to sampling and that there may be movement out of adjacent habitats. Maturation of American shad showed consistent patterns with most American shad mature by age 5. However, year-class specific estimates ranged from 50% to 85% mature in the James River, from 59% to 79% in the Rappahannock River, and from 60% to 87% in the York River. Based on current monitoring, the age of full recruitment to the staked gillnet fishery is age 5, corresponding to the age when the largest proportion of the population reaches maturity. Harvest of age 5 females in the historical fishery was probably a contributing factor to its collapse during the 1980s. Persistent differences in maturity schedules of American shad between the James and York rivers, and to a lesser extent with those from the Rappahannock River, show that neighboring stocks that experience similar climate regimes can have stock-specific maturity patterns that persist through time. Using juvenile abundance indices (or hatchery release in the case of the James River), the estimated maturity schedule, and estimated adult mortality rates, resulted in a predicted index that matched observed trends from 1998 to 2006 for three stocks of American shad. This study demonstrates that population dynamics of juvenile Alosa spp. is highly variable in a temporal and spatial context involving density-dependent processes that act to regulate year class production.

No description available.

A nationwide survey of shellfish mariculturists was used in conjunction with a literature review and review of state and federal laws and regulations, to identify impediments to commercial shellfish mariculture development. The results of the survey and reviews were utilized to identify likely impediments to commercial shellfish mariculture in Virginia and to develop recommendations to address the identified impediments, should Virginia wish to pursue efforts to enhance development of this industry. This study suggests there are state laws, regulations, and policies which act as impediments to commercial shellfish mariculture development in Virginia. Mar,y of the identified regulatory impediments result from the applicability of laws and regulations designed to manage and protect the natural resources and more traditional uses of the coastal zone. Because this study relies heavily on subjective input from individuals representing the mariculture industry and did not involve individuals who may have attempted to enter the industry and failed, it may not accurately identify all of the actual impediments to the industry's development. However, the study should provide valuable input into any comprehensive state effort to enhance shellfish mariculture development in the Commonwealth of Virginia.

No description available.

One system used for bivalve mollusc culture is flowthrough larval culture, which provides a continuous flow of food and seawater to the tank. Flowthrough culture enables larvae to be reared at stocking densities up to 100 larvae/mL, a characteristic that should recommend it as the culture system of choice for the East coast; however, Eastern oyster larvae have never been tested in flowthrough culture, discouraging implementation of the system. The thesis objectives are designed to address questions regarding the survival, growth, competent period, cell consumption, growth efficiency, and cell selection of oyster larvae reared in flowthrough culture. The objectives are: to describe larval tolerance to metabolic waste products, to determine how stocking densities influence clogging of the banjo screen and how those stocking densities coupled with exchange rate influence survival, growth, duration of the competent period, cell consumption, and cell selectivity, and to examine replication of flowthrough culture and establish data for the variables measured. To obtain a basic understanding of larval tolerance to their metabolic waste, twelve static tanks were set up at the Aquaculture Genetics and Breeding Technology Center’s hatchery at the Virginia Institute of Marine Science. Larvae were exposed to a range of concentrations of ammonia, nitrite, and nitrate and their survival and growth were monitored. Ammonia was the only metabolic waste that caused detrimental effects to larvae at a concentration of 10 mg/L. To address the remaining objectives, six 400 L conical flowthrough tanks were set up at Oyster Seed Holdings, a commercial hatchery. To determine if banjo screen clogging (the cause of tank overflow) was affected by the day and density at which larvae were introduced to flowthrough culture, larvae were introduced at two days old at three different stocking densities. The banjo screen, a circular plastic band with mesh screen on both sides, retains larvae in flowthrough culture while allowing water to exit. The banjo screen was monitored for clogging every 12 hours for 60 hours. Larvae can be introduced to flowthrough culture at two days old at densities as high as 50 larvae/mL without risking banjo clogging. To examine the effects of different flowthrough culture parameters on larval development, larvae were stocked in flowthrough cultures at 10, 20, and 50 larvae/mL and reared at five and ten exchanges of water/day. Five exchanges of water/day and a stocking density between 10 – 20 larvae/mL resulted in the highest survival, fastest growth, and greatest amount of competent larvae harvested. Variation among flowthrough cultures stocked with 10 larvae/mL and reared at five and ten exchanges of water/day was examined. Five exchanges of water/day generally had lower variation, with the smallest being survival and length. The results for survival, length, cell consumption, duration of the competent period, and growth efficiency were characterized as the established values for the thesis’s flowthrough system and were compared with data obtained from the controls in Chapter Three to distinguish anomalous data.

No description available.