Biology Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2749
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Item DEVELOPMENT AND EVALUATION OF SPATIALLY-EXPLICIT POPULATION MODELS FOR ESTIMATING THE ABUNDANCE OF CHESAPEAKE BAY FISHES(2024) Nehemiah, Samara; Wilberg, Michael J.; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Although fish populations typically experience spatially varying abundance and fishing mortality, stock assessments that inform management decisions commonly model a population that is assumed to be well-mixed with homogenous mortality rates. When assumptions about population mixing are not met, these models can result in biased estimates. Spatial population estimates are particularly beneficial to the Chesapeake Bay because this region faces unique challenges as a result of climate change and fishing pressure. However, use of spatial population models for fisheries management relies on models that can provide more accurate estimates of biological parameters than non-spatial models. Objectives for this research were to 1) develop and implement a multi-stock, spatially-explicit population model for Striped Bass (Morone saxatilis) to estimate abundance and fishing mortality in the Chesapeake Bay and along the Atlantic coast; 2) assess the performance of spatially-explicit models compared to spatially-implicit models (i.e., fleets-as-areas) to estimate abundance, determine how improved data quality (e.g., stock composition) affects model performance, and determine the effect of aging error on model accuracy; and 3) determine how spatial model performance is affected by potential changes in population dynamics resulting from climate change (e.g., time-varying natural mortality). The population model was a two-stock model with two sub-annual time-steps and two regions with stock and age-specific occupancy probabilities representing movement into and out of the Chesapeake Bay. Fishing mortality was estimated to be higher in the Ocean than the Chesapeake Bay, and abundance increased during 1982-2004 for both stocks before declining slightly until 2017. Simulations were conducted to test the ability of models to estimate abundance and fishing mortality under alternative scenarios of data availability and quality. Spatially-explicit estimates were approximately unbiased when they closely matched the assumptions of the data generating model. Models that ignored potential aging bias in datasets resulted in highly biased estimates of abundance and fishing mortality. Although the performance of all models degraded under most climate change scenarios, spatially-explicit models produced the most accurate model estimates compared to fleets-as-areas models. This research highlights the potential benefits of implementing spatially-explicit population models for Striped Bass and ecologically valuable fish species in the Chesapeake Bay.Item EFFECTS OF ENVIRONMENTAL VARIABLES AND CHANGES IN SEASONAL PATTERNS ON SPATIAL DISTRIBUTIONS OF JONAH CRABS (CANCER BOREALIS) AND ATLANTIC ROCK CRABS (CANCER IRRORATUS) IN GEORGES BANK AND THE MID-ATLANTIC BIGHT, USA(2023) Wade, Kaitlynn Jean; Wilberg, Michael J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The economic and commercial importance of Jonah crabs (Cancer borealis) and Atlantic rock crabs (Cancer irroratus) has increased greatly in the USA. The objectives of my research were to determine spatial distributions, habitat preferences, and potential seasonal movements of both species. Data were obtained from the offshore Northeast Fishery Science Center bottom trawl surveys. Analyses included kernel density estimates, generalized additive models, empirical cumulative distribution functions, and ANOVAs. The spatial distributions of Jonah and Atlantic rock crabs changed over time during the 1970s – 2000s. Compared to Atlantic rock crabs, Jonah crabs preferred slightly warmer temperatures, deeper depths, and muddier sediments. Seasonally, Jonah crabs were found farther offshore in the winter and closer to shore in the fall and spring. Atlantic rock crabs were found closer inshore in the winter and spring and more offshore in the fall. Both species were found to have different seasonal patterns in the Mid-Atlantic BightItem Investigating the Utility of Environmental DNA Analysis for the Monitoring and Management of Mid-Atlantic Alosine Fishes(2023) Fowler, Chelsea; Plough, Louis V; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Environmental DNA (eDNA) tools can address gaps in fish assessment data while reducing the cost and the impact of sampling on threatened anadromous alosine fishes in Chesapeake Bay. Here, I tested the ability of high-frequency eDNA sampling of river herring to predict fish abundances from sonar-based fish counts on the Choptank River and developed and validated novel species-specific eDNA assays for American and hickory shads. River herring eDNA concentrations from daily eDNA sampling were highly correlated to sonar-based fish counts (Spearman’s Rho = 0.84). This relationship informed a model that could accurately predict fish count from eDNA and relevant covariates (R2 = 0.88). The two new shad assays are highly specific and quantitative, and field testing validated detections in Delaware, Maryland, and North Carolina. This work provides a set of eDNA monitoring tools for the Mid-Atlantic alosines and highlights the capacity for eDNA data to generate quantitative metrics of fish abundance.Item Expanding the Fisheries Management Tackle Box: A Multiple-Model Approach to Support Better Decisions(2023) Hayes, Christopher Glenn; Wainger, Lisa; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Marine fisheries provide critical ecosystem services but face an array of stressors like climate change and overfishing. Managing fisheries is challenging due to limited information and the need to make complex tradeoffs among ecological and social objectives. Decision processes that include integrated social-ecological models and equitable stakeholder engagement are increasingly recognized as approaches to improve the likelihood of achieving management goals compared to those that rely solely on stock assessment models with limited stakeholder input. Additionally, advanced technologies offer new opportunities to understand marine ecosystem dynamics, including human behavior. This research adds two examples of underutilized tools: multi-criteria decision analysis (MCDA) and agent-based models (ABMs). In the first case, I compared management recommendations for the Chesapeake Bay oyster fishery arising from A) stakeholder engagement using group negotiations and B) preferences elicited from individuals using an MCDA approach. The recommendations were consistent across methods, suggesting that group effects did not bias group negotiation outcomes. The second case investigated New England groundfish reporting behavior based on stock dynamics, quota markets, and fishery observer coverage. First, having an observer onboard was found to significantly reduce the probability and magnitude of reporting error (ie., an observer effect) using a linear mixed effects model of data from vessel trip reports and remote vessel monitoring systems. Next, an ABM was used to explore emergent responses to policy changes - varying levels of observer coverage and the strength of the observer effects - on fish catch, reporting error, and profit outcomes, given fisher interactions and responses to fish population dynamics. Scenarios with strong observer effects resulted in increasing marginal improvements in reporting accuracy at high levels of observer coverage. MCDA and ABM can contribute to a multiple-model approach by allowing fisheries managers to integrate diverse stakeholder perspectives and use additional data sources that could lead to better fishery outcomes.Item TOOL DEVELOPMENT TO CONSTRAIN AND OPTIMIZE SHELLFISH AQUACULTURE GEAR PERFORMANCE(2022) Campbell, Brendan; Gray, Matthew W; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)To produce virginica cultured Crassostrea more efficiently, current grow out techniques require better understanding to allow for more consistent growth and quality. While the basic physical conditions that influence shellfish growth have been well researched, there are limited studies that consider how physical conditions (i.e. water flow and wave motion) influence shellfish growth within the context of an off-bottom aquaculture farm. Since oysters are suspension feeders, they require food to be delivered to their siphons through ambient processes. Changes in water flow can influence the overall survival, growth rate, and quality of oysters. Additionally, the motion, or jostling, of cages are thought to cause chipping on the outer portion of oyster shells, influencing the overall shape and growth of oysters. There are many techniques and equipment that have the potential to influence the water delivery and movement of oysters in containerized culture; however, little research has addressed how culture practices influence physical forcing surrounding cultured oysters and what impact those changes have on oyster performance. The biophysical relationship occurring in shellfish aquaculture is not being properly characterized partially due to a lack of affordable tools capable of monitoring physical forces in constrained spaces. This dissertation summarizes the current understanding of how culture practices influence oyster aquaculture production and demonstrates the novel use of affordable and commonly available tools that can be utilized in shellfish aquaculture research across multiple operational scales. The development of a novel clod card method and predictive model was attempted for use in characterizing mass transfer rate of water. The clod card, along with accelerometer loggers were utilized to understand the effects of physical forcing on the production of off-bottom cultured oysters when exposed to a range of biofouling mitigation treatments, grown using different culture methods, and spatially across an active shellfish aquaculture lease. These experiments validated the value in characterizing physical forcing in shellfish aquaculture and identified trade-offs between oyster shell growth and market quality that are linked to changes in the physical environment, which were produced by changing culture practices. Additionally, these validation experiments determined that variability in oyster growth and performance can change over small spatial scales, smaller than the typical grow-out shellfish aquaculture lease, which can influence water movement inside cages, water quality, and the efficiency of a commercial shellfish operation. By considering the local physical environment, growers can strategically employ culture practices that optimize the water flow through and movement of oysters to enhance farm profitability.Item STAKEHOLDER CHALLENGES AND OPPORTUNITIES: APPLYING A SOCIO- ECOLOGICAL FRAMEWORK TO INTEGRATE HUMAN DIMENSIONS WITH U.S. WILDLIFE MANAGEMENT(2021) Gedeon, Taylor Marie; Shaffer, L. Jen; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Wildlife practitioners face growing pressures to work at the interface of ecological and social issues yet the model they use in the United States, the North American Model of Wildlife Conservation (NAMWC), relies heavily on natural sciences. Inclusion of social science perspectives is needed to provide a consistent methodology to assess the current and desired conditions of both wildlife and humans. Current state wildlife practitioners offer a unique perspective into the challenges that exist barring this integration. Through semi-structured interviews with wildlife managers in Maryland and Florida, this research explores current definitions of the term stakeholder, stakeholder role, agency role, and the applicability of a socio- ecological approach for native versus nonnative species. Interviews revealed inherent issues with the NAMWC, and challenges and opportunities for the integration of human dimensions. By understanding existing challenges and opportunities, agencies can begin to develop holistic solutions for the increasing demands of human-wildlife conflict.Item Evaluating white perch (Morone americana) fecundity in select Chesapeake Bay tributaries in repsonse to pathology and fitness(2020) Shaner, Jacob; Harrell, Reginal M; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Fecundity studies have emerged as a complement to generalized stock assessment methods in an effort to more accurately determine reproductive potential, as well as explain a lack of stock recovery in some cases. The Chesapeake Bay presents an interesting case study, in that widespread anthropogenic influence has created the potential to reduce reproductive fitness among resident species, including white perch (Morone americana). This study seeks to investigate white perch population fecundity in response to habitat quality, as well as disease and nutrition, through the use of stereological and automated counting methods to assess agreement between stock assessments and reproductive potential. Results indicate lack of impact on fecundity from degraded habitat, limited impact of individual nutrition, and no conclusive effect from disease. These findings, coupled with stable recruitment, indicate that white perch reproduction in the Chesapeake Bay is unaffected by increased population stress.Item Co-producing Environmental Knowledge with Community Stakeholders(2020) Todd-Rodriguez, Alana; Paolisso, Michael J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)To generate robust and integrated solutions to complex sustainability problems requires the co-production of environmental knowledge. Co-production focuses on the socio-ecological contexts and knowledge forms of diverse actors in iterative dialogue to collectively generate new knowledge and practices relevant to societal challenges and decision-making. Despite its growing popularity, there remain a range of challenges and structural barriers obstructing the inclusion of local communities and place-based knowledge in co-producing environmental research and management. This thesis presents results from a comprehensive review of the co-production literature in general and focuses in particular on case studies where local environmental knowledge and stakeholders are included within the co-production process. Key findings suggest that additional attention to institutional capacity constraints, such as socio-political processes, space, funding, timing, and facilitation, as well as power and inclusion constraints, such as representation and knowledge, provide opportunities for increased integration of local environmental knowledge in the co-production process.Item MORTALITY AND REOVIRUS INFECTION IN SOFT-SHELL BLUE CRAB (CALLINECTES SAPIDUS) AQUACULTURE(2019) Spitznagel, Matthew Isaac; Schott, Eric J; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Soft-shell blue crab production the United States is an undervalued aquaculture practice experiencing high crab mortality rates from a series of stressors, including disease. The impact of one disease, the reovirus CsRV1, remains unquantified in major soft-shell crab production regions, despite the virus’ known ubiquity and lethality. My research examined the mortality and CsRV1 infection rates of pre- and post-production crabs in Maryland, Virginia, and Louisiana soft-shell crab production facilities in 2016-2017, attempting to link these rates to water quality and aquaculture practice variables. I found that recirculating aquaculture systems lost half the proportion of crabs (16%) that flow-through systems did (33%). CsRV1 infection was the primary predictor of crab death in Chesapeake aquaculture, presenting in 75% of dead crabs compared to 22% of dead crabs in Louisiana aquaculture. Multi-state data suggests crab losses worth over $2 million are attributable to CsRV1, indicating a need for aquaculture effluent and discard control.Item Influence of partial migration and environmental change on the population dynamics of white perch (Morone americana) within the Hudson River Estuary(2016) Gallagher, Brian; Secor, David H; Marine-Estuarine-Environmental Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)White perch are a common estuarine fish that exhibit a complex life cycle, characterized by partial migration and sensitivity to ecosystem characteristics. Field collections, otolith microchemistry, otolith microstructure and environmental and biological monitoring data were used to investigate the prevalence of partial migration and environmental influence across life history stages of white perch within the Hudson River. Otolith strontium:calcium profiles identified a freshwater resident contingent and a migratory contingent which utilized brackish habitats. Demographic analyses indicated that migratory fish hatched earlier and experienced cooler temperatures as larvae compared to residents, and subsequently grew faster as juveniles and adults. Comparisons of early-life characteristics before (1974-1991) and after (1992-2013) the invasion of zebra mussels indicated that juvenile abundance became more sensitive to density-dependence and freshwater flow after the invasion, while growth and spatial distribution changed little. Partial migration and environmental sensitivity will shape Hudson River white perch responses to future climate change.