Molecular genetic markers can be used to assess genetic diversity, assign parentage, quantify inbreeding, and demonstrate structuring of populations across a system. Striped Bass Morone saxatilis, and Walleye Sander vitreus, are widely sought gamefishes in the Commonwealth of Virginia. Striped Bass along the Atlantic Coast and within the Roanoke River drainage exhibit low genetic variation. Screening 12 microsatellite DNA markers across the range to define population genetic structure, I found that anadromous populations in the Southeast and the Chesapeake Bay were differentiated from landlocked populations in the Roanoke River basin, with an average FST of 0.066. Range-wide, Striped Bass are differentiated between the landlocked and anadromous populations, which need to be managed separately. Within stocked populations in the Roanoke River basin, there have been impacts stemming from small numbers of broodstock propagated, and inter-individual relatedness is ~20% within stocked reservoirs. Walleye across the eastern native range were screened to better understand evolutionary history and to identify native marker alleles for the upper New River population. Population genetic variation at eight microsatellite loci showed differentiated stocks in Alabama, Mississippi River, Eastern Highlands (Tennessee, New, and Ohio Rivers), and the Great Lakes drainages. All estimates of effective numbers of breeding individuals were under 25, and all populations within all watersheds had ~15-20% inter-individual relatedness, likely effects of both natural demographic processes and stocking. The extent of Eastern Highlands Walleye includes both the Ohio and Tennessee basins. Although I did not identify new marker alleles for native New River Walleye, I determined that marker-assisted selection has increased the frequencies of existing marker alleles for the native stock. Application of the results of this project will contribute to better fisheries management for both of these important species. / Master of Science / Population genetics have proven useful for defining the most appropriate units for conservational management across a variety of species. Molecular genetic markers can be used to assess genetic diversity, assign parentage, quantify inbreeding, and demonstrate structuring of populations across a system. Striped Bass Morone saxatilis and Walleye Sander vitreus are both widely sought gamefishes in the Commonwealth of Virginia. I applied population genetic approaches to recognize genetically distinct groups of populations and to recommend genetically cognizant management practices. Striped Bass across the Atlantic Coast and in the Roanoke River drainage exhibit low genetic variation. After screening variation at 12 DNA markers, I found that Striped Bass are differentiated between landlocked and migratory populations, which need to be managed separately. Within stocked populations in the Roanoke River basin, there have been impacts stemming from propagation of small numbers of broodstock, and propagation and stocking practices will need to be changed to reduce apparent inbreeding depression. Walleye populations across the eastern native range were screened to better understand evolutionary history and to seek new marker alleles for the native upper New River population. After screening genetic variation at eight DNA marker loci, I identified four evolutionarily distinct stocks of Walleye across eastern North America. Although I did not identify new marker alleles for native upper New River native Walleye, I showed that marker-assisted selection has increased the frequencies of existing marker alleles over the past twenty years. The results of this project can contribute to better fishery management strategies for both of these important gamefish species.

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.

As aquaculture continues to contribute high quality protein to a greater proportion of the worlds growing population, fish producers have been pressured to increase overall production. However, associated with elevated production is greater stress due to crowding, reduced water quality, and other factors. These stressors impact the health and welfare of the farmed animal which has become of increasing concern to a more environmentally aware and health conscious consumer. New strategies must therefore be developed and adopted by the aquaculture industry to counteract negative consumer perceptions of industrial fish production while also stabilizing the industry. Better nutrition may enhance disease resistance of farmed fish, while fillet accumulations of specific health-related nutrients may simultaneously add value to the final product. This thesis summarizes research undertaken in an effort to enhance the nutritional value of fish by increasing fillet levels of selenium (Se). In addition, various biomarkers of fish health (lysozyme, ceruloplasmin and glutathione peroxidase (GSH-Px) activities), were examined to determine whether dietary Se supplementation had a positive impact upon fish immunocompetence. Moreover, the effect of vaccination was also examined using lysozyme and growth as indicators of fish performance. Hybrid striped bass (HSB), the fourth most valuable farmed fish and fifth in tonnage produced in the United States, were employed as a model animal. Se, an essential component of the antioxidant enzyme, glutathione peroxidase with many established health benefits was supplemented to HSB diets at various concentrations but was found to be without effect upon serum immune proteins or GSH-Px activity. This finding likely reflected the use of fishmeal within the dietary formulation, which possessed relatively high Se levels, together with sufficient storage of tissue Se within the experimental animals. Nevertheless, these studies determined that organic sources of Se were more efficiently accumulated in HSB muscle than traditional inorganic sources. A linear response occurred up to the highest dose used (3.2 mg kg⁻¹) over a 6 week study. Fillet Se accumulation (r²=0.95) proved to be a better indicator than the liver (r²=0.87).Se enhanced fish therefor appear to offer a route of entry for fish producers into the lucrative designer food market - especially since many hundreds of millions of people worldwide are believed to be Se-deficient. Studies undertaken with Se-deficient HSB confirmed findings from the aforementioned research and also indicate that Se-enhanced fillets might be produced using a finishing feed containing 1.5 mg Se kg⁻¹ 6-8 weeks prior to harvest. Accumulation of Se using this strategy resulted in a 100g portion of HSB fillets containing between 33-109 µg Se, amounting to a dietary intake of between 25-80 µg Se; a level that would satisfy present daily intake recommendations. Vaccination of HSB with a Streptococcus iniae oil-in-water vaccine was examined for its potential negative impacts upon HSB production performance. Vaccinated fish did not exhibit any significant reductions in growth but microarray studies revealed that together with many hundreds of genes, four immune-related genes were impacted by this procedure. This thesis discusses the results obtained with regard to their practical implications to the industry and welfare of cultured fish. / Master of Science

Hybrid striped bass (Morone chrysops x M. saxatilis) aquaculture is a major commercial enterprise in the United States and internationally. Efforts to decrease diet costs and limit dependence on fishmeal, have led to the development of plant-based diets as an alternative aquafeed. Due to limiting concentrations of amino acids such as methionine, cystine, and taurine in plant meals such as soybean meal, supplementation of these plant-based diets with methionine or other sulfur amino acid compounds is typically required. Therefore, the current study was conducted to evaluate different amino acid supplements in soybean-meal-based diets for hybrid striped bass for possible refinement of diets and reduction of production costs. One feeding trial evaluated methionine hydroxy analog (MHA) and Mintrex® which is MHA containing chelated zinc relative to L-methionine. The second trial evaluated the effects of supplemental taurine or arginine on fish performance and potential health benefits. In the first feeding trial, a basal soybean-meal-based diet (56% soybean meal and 15% fishmeal) marginally deficient in total sulfur amino acids (TSSA) (1.10% methionine and cystine) was supplemented with either L-methionine, Mintrex® or MHA calcium salt and fed to triplicate groups of juvenile hybrid striped bass for 10 weeks. The different methionine supplements provided similar weight gain, feed efficiency ratio (FER) and protein efficiency ratio (PER) values that tended to be greater than observed in fish fed the basal diet. Mintrex® supplementation provided much higher plasma zinc concentrations compared to fish fed the other methionine supplements. In the second feeding trial, soybean-meal based diets which satisfied the requirement for TSAA were supplemented with either taurine or arginine at 1.5% of dry weight. Supplemental taurine or arginine did not provide any improvements in weight gain, FER, PER or survival compared to the basal diet. Thus, taurine or arginine supplementation of soybean-meal-based diets does not appear warranted. However, sulfur amino acid supplementation of plant-based diets is critical, and Mintrex® appears to be an effective supplement to meet the methionine and zinc needs of hybrid striped bass.

In the Maritimes, only two striped bass spawning populations remain: the Miramichi River in New Brunswick and the Shubenacadie – Stewiacke system in Nova Scotia. The Shubenacadie – Stewiacke system is subjected to a well pronounced twice daily tidal bore which induces dramatic changes in water parameters and challenges pelagic life. This system will be subject to potential change through brine discharge, a by-product of the Alton Natural Gas Storage Project. . Examining the temporal distribution of mysids, striped bass eggs and larvae at a fixed location around the Alton Project site will provide baseline information on population structure and insights into how egg and larvae distributions change with respect to tidal cycles, temperature and salinity. Surface plankton net tows from the top 0.75m of the water column were used to collect mysids, striped bass eggs and larvae over 14 months over two years. Daily mean egg abundance surpassed 1000 eggs/m3 once in 2008. A decrease of 1.9 °C in water temperature at the Alton Project site coincided with a cessation of eggs, and presumably, spawning. Spawning resumed when temperatures surpassed 15 °C. In contrast, the largest spawning event of the 2009 season occurred as water temperatures decreased (14 to 12.7 °C). The 2009 spawning season was longer (49 days) than 2008 (31 days) by 18 days, and in both years spawning peaked within the last week of May and first week of June. Two large spawning events, over 4000 daily mean eggs/m3 apiece, were detected May 24 and June 2, 2009. Mysids were present in high numbers throughout May to November, with some tows greater than 14,000 individuals/m3 in June 2008 and August 2009. Over the length of the ebb tide, as salinity decreases, mysid abundance also decreased. Whereas, striped bass egg abundance was consistently lowest at high tide and increased progressively over about 300 minutes through the ebb tide. Both striped bass larvae and mysids displayed patchiness in their temporal distribution suggesting passive transport in the this system. In both 2008 and 2009, larvae were detected at the Alton Project site for 38 days. The colder temperatures and larger tidal range of 2009, coupled with large increase in rainfall during the larval season contributed to the over 30-fold lower abundance over that found in 2008. When abundance was related in concert with temperature and salinity, mysids were ever present at high abundances except on three occasions. Mysid abundance decreased when salinity dropped beneath 5 ‰ during both years, and in 2008 when temperatures were lower than 15 °C. Salinity was impacted according to a seven-day lag after rainfall in both years, although the minimum volume of rainfall and associated impact on salinity have yet to be described.

As aquaculture continues to expand, protein sources have become more costly and less available. Simultaneously, lipid-extracted algal meals (LEA) (co-products of bio-diesel production) are becoming increasingly available as alternative sources of energy are investigated. By integrating LEA into aquaculture diets, feed prices could be lowered and bio-diesel production would have an additional revenue stream. Three feeding trials each of 7 weeks duration were conducted to evaluate five different algal meals as partial replacements for fishmeal and soy protein concentrate in diets for juvenile red drum (Sciaenops ocellatus). Apparent digestibility coefficients (ADCs) for CP and energy in various LEAs also were determined with red drum and hybrid striped bass (HSB). In the first trial, whole algae meal and LEA derived from Navicula sp. replaced 5 or 10% of the crude protein (CP) in the reference diet. Weight gain, feed efficiency (FE), hepatosomatic index (HSI), as well as protein and energy retention were not significantly (P>0.05) affected by the dietary treatments. Algal inclusion significantly affected the ADCs of the various dietary treatments for dry matter, CP, and energy. The inclusion of ash in the form of diatomaceous earth improved digestibility of protein as well as weight gain, survival and FE. A second feeding trial evaluated LEA derived from Chlorella sp. processed at high temperatures, replacing 5, 10, 20, and 25% of the CP in the reference diet. Weight gain, FE, survival, and protein efficiency ratio (PER) were significantly reduced at substitution levels of 20 and 25%. The third feeding trial evaluated LEA derived from Nanochloropsis salina, replacing 5, 7.5, 10, and 15% of the CP in the reference diet. Weight gain, FE, survival, and PER were significantly affected by some dietary treatments, with the 15% substitution levels causing significant reductions in performance. Intraperitoneal fat ratio and whole-body lipids were significantly lower in the fish fed the 15% substitution diet. Based on the results of these experiments, replacement of up to 10% of CP from fishmeal and soy protein concentrate with LEA was possible without causing substantial reductions in fish performance, and the whole algae product provided a more nutritious product. Red drum and HSB showed similar responses in their ability to digest CP and energy from the various algal products, although ADCs varied greatly among the different products and processing methods.

White bass Morone chrysops are native to the Mississippi River and its tributaries. This range includes the Barren River in south central Kentucky. Over the last thirty years, the population of white bass in Barren River Lake, a reservoir of the Barren River, has been in decline. During that same time, two congeners of white bass have been introduced to the lake. Hybrid striped bass Morone chrysops × Morone saxatilis were introduced in 1979 and yellow bass Morone mississippiensis were first discovered in 2000. Due to the similar life histories and spawning strategies of all three Morone species, I hypothesized that the two introduced species are interfering with reproduction of the native white bass. In the springs of 2012 and 2013 I sampled fish from within a five kilometer stretch of Barren River upstream of the lake. I collected 144 white bass, 111 yellow bass and 29 hybrid striped bass. Detection of species at spawning sites was staggered with yellow bass and hybrid striped bass arriving after white bass but leading to a period of co-occurrence. White bass on the spawning sites appeared healthy: fecundity (75,200 to 741,150 eggs per female), mean gonadosomatic indices (peaked at 10.7% and 23.7% in sequential years), mean relative weight (93.8), and length at age (above the 50th percentile). Of the yellow bass stomachs examined, 21.6% contained fish eggs or larval fish. Based on arrival times and evidence of egg and larval fish predation, it is likely that yellow bass are directly impacting white bass spawning success through reproductive interference and the consumption of white bass offspring. Schoener’s index values revealed a significant degree of dietary overlap between white bass and yellow bass in larval fish, post larval fish, and arthropods (Cxy = 0.992,0.994, and 0.804, respectively), and between white bass and hybrid striped bass in arthropods (Cxy = 0.851). Information from this study may elucidate causes of the declining white bass population and aid in its management in Barren River Lake.

Thesis (M.S.)--Montana State University--Bozeman, 2004. / Typescript. Chairperson, Graduate Committee: Christopher S. Guy. Includes bibliographical references (leaves 41-48).

Digenetic trematodes are a common pest problem in aquaculture where their unappetizing appearance often reduces the marketability of food fish. Aquatic snails are intermediate hosts in the trematode lifecycle and are commonly targeted with control measures to prevent the crop fish from becoming infected. I evaluated several chemical and biological snail control strategies as alternatives to the potentially invasive black carp. Copper sulfate, hydrated lime slurry, and several fish and decapod species were tested for effectiveness against physid (Physa spp.) and planorbid (Helisoma spp.) snails in laboratory aquaria trials. Hydrated lime demonstrated effectiveness with the least potential to be toxic to cultured fish in regional application. Hybrid sunfish (redear × green sunfish) consumed large quantities of both snails in ad libitum feedings. The most effective biological (redear × green sunfish) and chemical (hydrated lime) control methods identified in the laboratory were evaluated further in research ponds. Hydrated lime applications of 9.07 kg over 9.14 m2 were found to be effective against Helisoma spp. confined to enclosures along the pond shoreline; average survival was 2%. When stocked in aquaculture ponds, hybrid redear sunfish did not significantly influence snail capture rates; however ponds stocked with redear sunfish experienced a gradual decrease in snail populations throughout the 2008 growing season. Hydrated lime and a combination of redear sunfish and hybrid redear sunfish were evaluated separately and in tandem as a combined chemical/biological treatment in the 2009 growing season. Evaluation occurred under mock production conditions in which hybrid striped bass were raised in the research ponds to determine snail treatment effects on trematode abundance. Ponds stocked with sunfish at 494 fish/ha had snail densities significantly (P ≤ 0.05) lower than control ponds after two months. Ponds treated with hydrated lime at 31.7 kg/31.5 m of shoreline in a 1 m swath experienced 99% estimated reductions in snail densities following application, but snail populations rebounded to previous levels within two months. The mean snail density in ponds treated with both hydrated lime and sunfish was significantly lower than control one month post treatment; this mean rebounded slightly by the conclusion of the trial, but not as much as in the chemical treatment group. Hybrid striped bass examined thoroughly for trematodes revealed a positive relationship between trematode abundance in fish and increasing Helisoma densities. This relationship was most apparent when estimates of snail density from only the beginning of the trial were used. Based on these results, it appears that a nearly complete reduction of Helisoma, particularly at the time of stocking fingerlings, is necessary to avoid a high abundance of trematodes in cultured fish. To this end, an early-season application of molluscicides followed closely by stocking of predator sunfish has potential to achieve a uniformly low density of snails throughout the growing season.

Many sources of protein have been investigated to reduce the use of fish meal (FM) in aquaculture feeds, including soybean meal (SBM). However, FM replacement in feeds for carnivorous species is limited by problems with feed intake, growth rate, and overall health associated with reduced digestibility and anti-nutritional factors found in SBM. However, soy processing strategies can reduce the effects of anti-nutritional factors and improve utilization. Therefore, we examined the possibility of further FM replacement in SBM maximized feeds for hybrid striped bass using refined soy products, soy protein concentrate (SPC) and soy protein isolate (SPI). Results indicate that further FM sparing is possible, beyond what can be achieved with SBM. For example, it is possible to reduce dietary FM content as low as 5% using SPC, and though this negatively affects growth rate, this effect may be reversed by the addition of a betaine-based attractant. Replacement with SPI resulted in such a degree of feeding reluctance that starvation and cannibalization became issues during the trial. Reducing FM content below 5-10% resulted in more variable production performance and, when using SPI, increased incidence of cannibalism. No differences in stress tolerance were observed during the trials; however, there was a trend of increasing handling mortality in fish fed the SPC diets. Refined soy proteins can be used in conjunction with SBM to spare FM, but the cost of these products, along with their acceptability to aquatic livestock, will determine the extent of their utilization in aquafeeds.