The present study explored the spatial and temporal demographic trends in oyster population dynamics and their relationships to freshwater inflows and the pathogen Dermo (Perkinsus marinus) on three reefs (Shell, Mad Island, and Sammy?s) in West Matagorda Bay, Texas. The objectives were to design and link three population models that simulate oyster population dynamics and integrate the environmental factors that influence growth, reproduction and settlement of larvae among these three reefs. The following variables were evaluated: relative abundance of oyster spat, submarket- and market-size oysters, average weighted incidence of Dermo and percent Dermo infection (prevalence) in submarket- and market-size oysters and their relationships to environmental variables of salinity, temperature, flow and distance from freshwater sources. Using a 30-month continuous dataset, environmental variables accounted for 36% of the variation in Dermo-related variables among the three reefs, and were also positively correlated with distance from freshwater sources. The relative abundance of spat and dead oysters was related to peaks in freshwater inflows occurring 30 days prior to larval settlement. Using these spatial and temporal relationships among biological and environmental variables, and data from five years of monitoring three reefs in Matagorda Bay, an integrated Stella model was developed that simulated oyster population responses to stochastic environmental changes over a 50-year period. Although the geological and structural complexity of each reef appeared to be similar, the model showed the relationship of growth, spawning and spat set were related to hydrologic variation between different reefs and time periods. The model revealed that up-estuary reefs relied on the distribution of larvae from down-estuary reefs following mortality related to freshwater inflow. The model also indicated that loss of freshwater inflows to down-estuary reefs resulted in higher sustained Dermo infections, thus loss of spawning potential and subsequent distribution of larvae to up-estuary reefs. The three oyster populations in West Matagorda Bay provide spawning connectivity and function as an integrated resource for sustaining all oyster reef populations in this bay system. The model presented in this research provides a basis for understanding the population dynamics of WMB as well as a better understanding of the interaction among the reefs that sustain these populations. The model developed in this investigation provides a basis for developing oyster population models for other bay systems and for future research regarding hydrologic influences on oyster population dynamics.

The present study explored the spatial and temporal demographic trends in oyster population dynamics and their relationships to freshwater inflows and the pathogen Dermo (Perkinsus marinus) on three reefs (Shell, Mad Island, and Sammy?s) in West Matagorda Bay, Texas. The objectives were to design and link three population models that simulate oyster population dynamics and integrate the environmental factors that influence growth, reproduction and settlement of larvae among these three reefs. The following variables were evaluated: relative abundance of oyster spat, submarket- and market-size oysters, average weighted incidence of Dermo and percent Dermo infection (prevalence) in submarket- and market-size oysters and their relationships to environmental variables of salinity, temperature, flow and distance from freshwater sources. Using a 30-month continuous dataset, environmental variables accounted for 36% of the variation in Dermo-related variables among the three reefs, and were also positively correlated with distance from freshwater sources. The relative abundance of spat and dead oysters was related to peaks in freshwater inflows occurring 30 days prior to larval settlement. Using these spatial and temporal relationships among biological and environmental variables, and data from five years of monitoring three reefs in Matagorda Bay, an integrated Stella model was developed that simulated oyster population responses to stochastic environmental changes over a 50-year period. Although the geological and structural complexity of each reef appeared to be similar, the model showed the relationship of growth, spawning and spat set were related to hydrologic variation between different reefs and time periods. The model revealed that up-estuary reefs relied on the distribution of larvae from down-estuary reefs following mortality related to freshwater inflow. The model also indicated that loss of freshwater inflows to down-estuary reefs resulted in higher sustained Dermo infections, thus loss of spawning potential and subsequent distribution of larvae to up-estuary reefs. The three oyster populations in West Matagorda Bay provide spawning connectivity and function as an integrated resource for sustaining all oyster reef populations in this bay system. The model presented in this research provides a basis for understanding the population dynamics of WMB as well as a better understanding of the interaction among the reefs that sustain these populations. The model developed in this investigation provides a basis for developing oyster population models for other bay systems and for future research regarding hydrologic influences on oyster population dynamics.

Thesis (M.S.)--Virginia Polytechnic Institute and State University, 2004. / Title from PDF t.p. (viewed on Dec. 7, 2005). Vita. In abstract the "E" in HE is subscript. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2001. / Vita. Includes bibliographical references (leaves 164-192).

Oyster reef habitats have declined from historic levels due to a variety of reasons, including overharvest, disease, and degraded water quality. The harvesting of oysters has led to a loss of reef habitat for both oysters and reef-associated fauna. When oysters spawn, the larval oysters, or spat, depend on hard substrate for settlement and growth. Oyster shell is the preferred substrate for use in restoration because it most closely matches natural reef habitat, but it is often expensive and in limited supply. This study incorporated field and laboratory experiments to assess the relative habitat value of alternative substrates (crushed concrete, porcelain, crushed limestone, and river rock, as well as oyster shell) for larval oyster recruitment as well as reef resident fishes and macro-invertebrates. Replicate trays of each substrate type were deployed in St. Charles Bay, TX for four months during spring and summer 2012 and assessed for oyster recruitment and faunal diversity and density. Concrete, river rock, limestone and porcelain had similar spat recruitment densities compared to oyster shell (1300-2300 spat). Spat shell heights were also larger on these substrates (13-16 mm), while spat on porcelain substrates were slightly smaller (10-13 mm). All substrates except bare sediment had similar fauna species densities (200-500 individuals m-2). Limestone had lower fauna diversity (H’; 0-1) than concrete and shell (1-2). Laboratory experiments compared the effectiveness of these substrates in providing prey refuge from pinfish and blue crab predators. All substrates performed similarly resulting in very low (<20 %) prey mortality rates for either predator. Results may enable future restoration plans to be implemented at a lower cost while providing similar habitat functions.

Thesis (M.Mar.Archaeol.) -- Flinders University, Department of Archaeology, 2006. / "A thesis submitted in partial fulfilment of the requirements for the degree of Master of Maritime Archaeology, Department of Archaeology, Flinders University". "May 2006". Includes bibliographical references (leaves 101-105). System requirements for remote version: Adobe Acrobat Reader to view PDF file.

Public and private concern over the decline of Virginia's oyster industry prompted the General Assembly (GA) in 1977 and 1983 to commission its Joint Legislative Audit and Review Commission (JLARC) to examine the State's oyster grounds management policies. In response to JLARC's findings the GA directed Virginia Marine Resources Commission (VMRC) to construct and implement an oyster fisheries management plan. The GA set as the plan's objective to achieve the greatest production level possible subject to limits of physical resource availability and technical feasibility. That the plan should be attentive to cost-effectiveness was also expressed by the GA. In developing its management plan VMRC must consider a variety of environmental, economic and political factors affecting the production and harvest of market oysters. A linear programming model developed for VMRC's use in evaluating alternative oyster grounds management strategies is described. The objective of the programming model is to minimize the public plus private cost of producing a prespecified level of market oyster harvest over a ten year planning horizon. The model includes as its activities the different aquacultural techniques used by private planters and VMRC in its repletion program. The many environmental, economic and political factors are incorporated into the model's constraints and technical coefficients. Several management alternatives are evaluated with the model. The results of these analyses indicate that without a fundamental in the oyster repletion program, even if new oyster grounds management policies are considered, there would be little change in public grounds market oyster harvest over current levels. Under revised repletion program practices, however, marked increases in public grounds harvest could be effected for relatively small increases in repletion program budget allocations over current levels. / Master of Science

A demographic population simulation model was developed to examine alternative fishery management strategies and their likely effects on the probability of extirpation of local eastern oyster (Crassostrea virginica) populations in the Chesapeake Bay. Management strategies include varying the minimum shell length-at-harvest, harvest rate, and rate and frequency of stocking of oyster seed with respect to varying salinities and oyster population densities. We also examined the rate of disease-mediated mortality that can be tolerated by a viable population. High density populations at low salinity sites remained viable under a 100% harvest rate and 76.6 minimum shell length-at-harvest due to increased fertilization efficiency in high densities, which increased reproduction. Low density populations at low salinity sites remained viable when harvest rate was set at 0.5 and minimum shell length-at-harvest was set at 85 mm. Neither reducing harvest rate nor minimum shell length-at-harvest produced a viable population at high salinity sites. The effects of disease-mediated mortality were too great for these management options to decrease the probability of extirpation to zero. Supplemental stocking conducted regularly reduced extirpation probabilities to zero and pulse stocking (every five to ten years) did as well, although it required a much larger number of oysters to be stocked. Decreasing disease-mediated mortality rates by 20% in high density populations and by 80% in low density populations reduced the probability of extirpation to zero, suggesting the degree of genetic improvement needed to rebuild eastern oyster populations in the Chesapeake Bay. Culture of a non-native species, such as the Suminoe oyster (Crassostrea ariakensis), could supplement harvest of the declining eastern oyster fishery in Chesapeake Bay. Because of possible ecological impacts from introducing a fertile non-native species, introduction of sterile triploid oysters has been proposed. However, recent data show that a small percentage of triploid individuals progressively revert toward diploidy, introducing the possibility Suminoe oyster might establish self-sustaining populations. To assess the risk of Suminoe oyster populations becoming established in Chesapeake Bay, a demographic population model was developed. Inputs modeled included: salinity, stocking density, reversion rate, reproductive potential, natural and harvest mortality, growth rates, and effects of various management strategies, including harvest criteria. Results showed decreased probability of a Suminoe oyster population becoming self-sustaining when oysters are grown at low salinity sites, certainty of harvest is high, minimum shell length-at-harvest is small, and stocking density is low. Results of the model suggest management strategies that will decrease the probability of a Suminoe oyster population becoming self-sustaining. Policy makers and fishery managers can use the model to predict potential outcomes of policy decisions, supporting the ability to make science-based policy decisions about the proposed introduction of triploid Suminoe oysters into the Chesapeake Bay. / Master of Science

Live holding systems are used as temporary storage facilities for shellfish. The potential for mishandling of shellfish stored in these systems is high. The objective of the project was to examine the effects of storing oysters in a spray and an immersion systems on the survival of Escherichia coli and Vibrio vulnificus within the oysters. The effects of physiological stress imposed on oysters, as a result of interstate shipping, were examined by monitoring the level of E. coli in these oysters during storage in a spray tank. The survival rates of naturally-present E. coli and V. vulnificus in oysters were also observed. The research examined the distribution of artificially- and naturally-present V. vulnificus in oyster tissues during storage in an immersion system. There was no significant difference (p = 0.12) in the artificially-inoculated bacterial population of oysters after 120 hr of storage in a spray live holding tank. The level of E. coli in oysters which were subject to physiological stress did not change significantly (p = 0.30) after 96 hr in the spray tank. Naturally-present E. coli and V. vulnificus in oysters at harvest persisted during the 72 hr storage in the spray tank. V. vulnificus was loosely associated with mucus on the surfaces of the adductor and the mantle tissues in artificially-inoculated oysters. As a result, the bacterial level was reduced on these surfaces during the 72 hr of depuration. V. vulnificus on the gills and the digestive system of artificially-inoculated oysters may become entrapped in cilia and mucus. There was no significant reduction in the bacterial population on the gills (p = 0.11) and on the digestive system (p =0.21). There was no significant difference in the population of V. vulnificus in the adductor muscle (p = 0.37), the mantle (p = 0.16), the gills (p = 0.5), and the digestive system (p = 0.5) of summer oysters naturally-infected with the bacterium. It seems unlikely that depuration of V. vulnificus from oysters naturally harboring the bacterium may be effective. / Ph. D.

The United States Pacific Northwest is well known for its shellfish farming. Historically, commercial harvests were dominated by the native Olympia oyster, Ostrea lurida, but over-exploitation, habitat degradation, and competition and predation by non-native species has drastically depleted their densities and extirpated many local populations. As a result, shellfish aquaculture production has shifted to the introduced Pacific oyster, Crassostrea gigas. An underlying objective of this dissertation is the use of molecular genetics to improve our ability to accurately identifying optimal oyster broodstock for either restoration of Olympia oysters or farming of Pacific oysters. The ecological benefits provided by oysters as well as the Olympia oyster's historical significance, has motivated numerous restoration/supplementation efforts but these efforts are proceeding without a clear understanding of the genetic structure among extant populations, which could be substantial as a consequence of limited dispersal, local adaptation and/or anthropogenic impacts. To facilitate this understanding, we isolated and characterized 19 polymorphic microsatellites and used 8 of these to study the genetic structure of 2,712 individuals collected from 25 remnant Olympia oyster populations between the northern tip of Vancouver Island BC and Elkhorn Slough CA. Gene flow among geographically separated extant Olympia oyster populations is surprisingly limited for a marine invertebrate species whose free-swimming larvae are capable of planktonic dispersal as long as favorable water conditions exist. We found a significant correlation between geographic and genetic distances supporting the premise that coastal populations are isolated by distance. Genetic structure among remnant populations was not limited to broad geographic regions but was also present at sub-regional scales in both Puget Sound WA and San Francisco Bay CA. Until it can be determined whether genetically differentiated O. lurida populations are locally adapted, restoration projects and resource managers should be cautious of random mixing or transplantation of stocks where gene flow is restricted. As we transition from our Olympia oyster population analysis to our Pacific oyster quantitative analysis, we recognize that traditional quantitative trait locus (QTL) mapping strategies use crosses among inbred lines to create segregating populations. Unfortunately, even low levels of inbreeding in the Pacific oyster (Crassostrea gigas) can substantially depress economically important quantitative traits such as yield and survival, potentially complicating subsequent QTL analyses. To circumvent this problem, we constructed an integrated linkage map for Pacific oysters, consisting of 65 microsatellite (18 of which were previously unmapped) and 212 AFLP markers using a full-sib cross between phenotypically differentiated outbred families. We identified 10 linkage groups (LG1-LG10) spanning 710.48 cM, with an average genomic coverage of 91.39% and an average distance between markers of 2.62 cM. Average marker saturation was 27.7 per linkage group, ranging between 19 (LG9) and 36 markers (LG3). Using this map we identified 12 quantitative trait loci (QTLs) and 5 potential QTLs in the F1 outcross population of 236 full-sib Pacific oysters for four growth-related morphometric measures, including individual wet live weight, shell length, shell width and shell depth measured at four post-fertilization time points: plant-out (average age of 140 days), first year interim (average age of 358 days), second year interim (average age of 644 days) and harvest (average age of 950 days). Mapped QTLs and potential QTLs accounted for an average of 11.2% of the total phenotypic variation and ranged between 2.1 and 33.1%. Although QTL or potential QTL were mapped to all Pacific oyster linkage groups with the exception of LG2, LG8 and LG9, three groups (LG4, LG10 and LG5) were associated with three or more QTL or potential QTL. We conclude that alleles accounting for a significant proportion of the total phenotypic variation for morphometric measures that influence harvest yield remain segregating within the broodstock of West Coast Pacific oyster selective breeding programs. / Graduation date: 2012