The Chesapeake Bay is the largest estuary in the United States and is highly productive making it a key habitat for species like striped bass and summer flounder. Striped bass and summer flounder have exhibited changes in abundance over recent years within the Chesapeake Bay. There is a lack of understanding of how environmental factors may be impacting striped bass and summer flounder abundance and how other species may be responding to these environmental drivers. To improve our understanding of striped bass, summer flounder and the aquatic community we set out to identify the environmental drives of their abundance changes from local to global scales. The fish community in the Bay has previously shifted due to environmental perturbations, so we also investigate if the community has changed more recently. We used a hurdle model to standardize interannual abundance of fish species caught in the Chesapeake Bay from two sources of fishery-independent trawl survey data. This standardization process led to relative abundance indices for 58 late juvenile to adult species from 2002-2018, and relative abundance indices for 26 juvenile species from 1995-2019. Species with similar and contrary abundance trends with striped bass and summer flounder were identified through a correlation analysis, and life history traits were assessed between species to determine mechanisms of change. We then used nonmetric multidimensional scaling (nMDS) to see if the community structure had drastically changed, the applied a principal response curve (PRC) to investigate the spatial and functional group change of the community. Among the factors examined, sea surface temperature (SST) in the Bay has increased since 2006 based on change point analysis while the mean Bay SST range and gradient have both decreased. Striped bass have had variable abundance in the Bay but exhibited a positive correlation with increasing SST. Summer flounder have declined in abundance since 2006 in the Bay and exhibited a negative correlation with increasing SST. Striped bass and summer flounder had relationships with global climate oscillations such as the winter North Atlantic Oscillation, Atlantic Multidecadal Oscillation, and the Gulf Stream North Wall oscillation. From a community perspective, our results showed that the late juvenile to adult fish community shifted after 2011, which coincided with the freshwater surge due Hurricane Irene and Tropical Storm Lee. The increase in abundance of striped bass, Bay anchovy, and Atlantic menhaden, and decrease in abundance of summer flounder, weakfish, spot, and Atlantic croaker were the main species that contributed to the difference in community structure after 2011. The change in functional group structure after 2011 was defined by a decline in opportunistic demersal fish, and this change was significantly different in the portion of the Bay north of the Potomac River. We did not identify any significant correlation between functional groups and environmental factors but did discover the important relationship that top predators like striped bass and summer flounder have with their key fish prey species, both in presence and population trends. Long term monitoring and further research in to how the community changed over smaller periods and the distribution changes of species could improve our understanding of what is impacting the Chesapeake Bay community to inform better management strategies. / Master of Science / The Chesapeake Bay is an important habitat for many animals, including fish. Of the fish species that inhabit the Bay, striped bass and summer flounder are two highly sought after commercial and recreational species, and are top predators, which means they are economically and ecologically important. Striped bass and summer flounder have exhibited changes in abundance over recent years within the Chesapeake Bay, and there is a lack of understanding what environmental factors may be driving their abundance trends and if other species are responding similarly. To conserve striped bass and summer flounder, management strategies should consider the relationship these species have with their environment and other species. Through this research, we set out to understand what environmental factors are impacting their population trends, and the trends of the aquatic community which can be used to inform effective management decisions for the future. To accomplish our research goals, we first used a hurdle model to determine the interannual abundance of 58 adult and 26 juvenile fish species from 2002-2018 and 1995-2018 respectively. We then investigated whether any environmental factors exhibited relationships with striped bass and summer flounder. Again, through correlation analysis, we identified species with similar and contrary abundance trends with striped bass and summer flounder and compared the traits of these species to try to identify the mechanisms of their abundance trends. To visualize if and how much the fish community composition had changed over time we used nonmetric multidimensional scaling (nMDS), then applied a principal response curve (PRC) to investigate the spatial change and life history trait change in the fish community. The results showed us that striped bass and summer flounder do exhibit relationships with environmental factors. Sea surface temperature (SST) in the Bay has increased, while the range and gradient has decreased, and an increase in the mean SST occurred in 2006. We found that striped bass had variable abundance in the Bay but correlated positively with increasing SST, however summer flounder abundance has decreased since 2006 in the Bay and has a negative correlation with SST. Striped bass and summer flounder exhibited relationships with global climate-oscillations that impact the Chesapeake Bay, making those factors important to consider for their management. The results of the community assessment showed that the late juvenile to adult fish community shifted after 2011. This change in community structure coincided with a decrease in water quality and a freshwater surge in 2011 that was caused by Hurricane Irene and Tropical Storm Lee. After the community shift, striped bass, Bay anchovy, and Atlantic menhaden increased in abundance, while summer flounder, weakfish, spot and Atlantic croaker decreased in abundance. These species were the top species that contributed to the change in community structure. The change in community structure was greatest, and significant in the northern portion of the Bay. From these results we identified the important relationship between predators and prey both in species presence and abundance trends. Striped bass abundance increased alongside an increase of their key prey species, Bay Anchovy and Atlantic menhaden, while summer flounder abundance decreased along with two of their key prey species spot and Atlantic croaker. This research identified environmental factors that contribute to abundance trends of striped bass and summer flounder and highlighted the importance of multispecies interactions within the aquatic Chesapeake Bay community. Long term monitoring and more research into finer scale spatial and temporal changes of fish in the Bay could further improve management recommendations.

This dissertation contains three papers from two projects. The first two papers (Chapter Two and Chapter Three) are from a project entitled “Managing Flounder Openings for Maximum Revenue.” The objective of this project is to (1) estimate the monthly dockside price of summer flounder and identify seasonality in this price; and (2) set up a mathematical programming model to maximize the landing revenue by allocating the federal government quota on summer flounder across twelve months. In the first paper (Chapter Two), various forms of inverse demand equations are used to estimate the dockside price of summer flounder. These models are evaluated based on their out-of-sample forecasting performance. A structural functional form is selected. In the second paper (Chapter Three), the selected price equation for summer flounder is applied into a revenue maximization model with both the federal government quota constraint and biological constraints from twelve months. The model is solved using CONPOT Solver of GAMS 21.5. The results of the scenarios indicate that the industry should move the landing effort from the period of October – February to the period of March – August. Comparing with historical data, this method can increase $44.73 million for the industry of landing summer flounder from 1991 to 2005. The third paper (Chapter Four) investigates how China's soybean import prices and domestic prices of soybeans and soybean products affect China's soybean imports. Since 2000, soybeans have been the U.S. leading agricultural exports for bulk commodities. China is the largest importer of U.S. soybean exports. For China's soybean crushing industry, imported soybeans are inputs rather than final products and used to produce soybean meal and oil. A differential production model, which is derived from a two-stage profit maximization model in producer theory, is adopted in this research. Estimates are used to calculate conditional and unconditional price elasticities for China's soybean imports from its major source countries – the United States, Argentina, and Brazil. In addition, the Divisia index and unconditional output price elasticities are obtained for China's soybean imports. Estimation results support the hypothesis that China's soybean imports are determined by its domestic demand for soybean meal, rather than soybean oil. This implies that U.S. agribusinesses should pay attention to the dominant role of China's demand for soybean meal and animal feed. U.S. agribusinesses can also use results in this research to evaluate how China's soybean imports from different source countries will change when either international market prices or China's domestic market prices change. / Ph. D.

The American horseshoe crab (HSC), Limulus polyphemus, is one of four species of horseshoe crabs found throughout the world, and the only one found in North America. It is an economically and ecologically important species throughout its native range from Maine to the Yucatan Peninsula. Harvested for fertilizer and livestock feed in the 19th century, the species is now harvested as bait for whelk and eel fisheries, and for their blood by the biomedical industry. The Atlantic States Marine Fisheries Commission (ASMFC) started to formally manage HSC in 1998 with its Interstate Fisheries Management Plan (IFMP). Unique emphasis and harvest limits have been placed on the Delaware Bay stock, as it is commercially exploited and a critical food source for the threatened red knot, Calidris canutus rufa. Previously, estimates of relative and total abundance of HSC in the Delaware Bay area were based on a design-based approach using a stratified random sampling design. In Chapter 1 of this work, I developed hurdle models for each of the six HSC demographic groups to standardize catch-per-unit-effort (CPUE) and estimate relative abundance using a model-based approach. It was determined that while the two approaches resulted in mostly convergent estimates of relative abundance, external factors such as month, time-of-day, and average depth have major effects on the observed CPUE of all demographic groups. Chapter 2 involved the development of hurdle models for the three species of bycatch frequently caught in our trawls, channeled whelk (Busysotypus canaliculatus), knobbed whelk (Busycon carica), and summer flounder (Paralichthys dentatus). It was found that channeled whelk relative abundance has been at a historical low since 2016, while summer flounder has been at a consistent high. Recent estimates of knobbed whelk relative abundance have been less variable than previously seen, with estimates since 2016 being similar to those seen before 2012. These results provide the first estimates for whelk population trends in the mid-Atlantic region and add to the growing knowledge of summer flounder relative abundance in the area. In Chapter 3, I applied the hurdle models developed in Chapter 1 to estimate the total abundance of HSC in the Delaware Bay area. For this work, I developed two spatio-temporal variograms to estimate bottom temperature and bottom salinity at unmeasured cells per month in the time series. The results showed that night estimates of total abundance were consistently higher than daytime estimates, and estimates from September or November resulted in the highest estimated catch for all demographic groups. The results suggest that when comparing September model-based estimates at night to those of the design-based approach, nearly a third of all previous design-based estimates significantly underestimated the total abundance of HSC in the Delaware Bay area. This result suggests that the ASMFC can recommend increased harvest limits for mature individuals if that action aligns with the goals of their adaptive resource management (ARM) framework. / Master of Science / The American horseshoe crab (HSC), Limulus polyphemus, is one of four species of horseshoe crabs found throughout the world, and the only one found in North America. It is an economically and ecologically important species throughout its native range from Maine to the Yucatan Peninsula. Harvested by the millions in the 19th century, the species is still harvested as bait for whelk and eel fisheries, and for their blood by the biomedical industry, on the order of hundreds of thousands. Formal management of HSC by the Atlantic States Marine Fisheries Commission (ASMFC) began in 1998, and allowable catch and landings have decreased since 1999. A strong focus has been placed on the Delaware Bay population, as it is the center of HSC abundance and provides a critical food source for the threatened red knot, Calidris canutus rufa, while also being commercially exploited. To effectively manage the species, it is important to accurately estimate relative and total abundance so that proper harvest limits can be set. Previously, estimates of relative and total abundance of HSC in the Delaware Bay area were based on a design-based approach using a stratified random sampling design. In Chapter 1 of this work, I developed hurdle models (a generalized linear model that models the probability of observations and the observed positive counts using two separate regression models that are then combined) for each of the six HSC demographic groups to remove the effect of external factors (year, latitude, longitude, depth [inshore/offshore], topography, average trawl depth, time-of-day, month, bottom temperature, bottom salinity, and distance from shore) on our observed catch-per-unit-effort (CPUE) and estimate relative abundance using a model-based approach. It was determined that while the two approaches resulted in mostly convergent estimates of relative abundance, factors like month, time-of-day, and average depth had major effects on the observed CPUE of all demographic groups. Chapter 2 involved developing similar hurdle models for three species of bycatch frequently caught in our trawls, i.e., channeled whelk (Busysotypus canaliculatus), knobbed whelk (Busycon carica), and summer flounder (Paralichthys dentatus). It was found that channeled whelk relative abundance has been at a historical low since 2016, while summer flounder has been at a consistent high. Recent estimates of knobbed whelk relative abundance have been less variable than previously seen, with estimates since 2016 being similar to those seen before 2012. These results provide the first estimates for whelk population trends in the mid-Atlantic region and add to the growing knowledge of summer flounder relative abundance in the area. In Chapter 3, I applied the hurdle models developed in Chapter 1 to estimate the total abundance of HSC in the Delaware Bay area. To do this, the bottom temperature and salinity had to be estimated for each geographic cell. This was accomplished by developing two spatio-temporal variograms which allowed me to estimate either variable at an unmeasured point and time based on its spatial and temporal distance from a measured value in a process known as spatio-temporal kriging. The results showed that night estimates of total abundance were consistently higher than daytime estimates and that estimates from September or November resulted in the highest estimated total abundance for all demographic groups. The results suggest that when using September model-based estimates at night to compare against the design-based approach, nearly a third of all previous design-based estimates significantly underestimated the total abundance of HSC in the Delaware Bay area. This outcome could justify ASMFC increasing recommended harvest limits for mature individuals if that action aligns with the goals of their adaptive resource management (ARM) framework.