In many cases in the past fish bones recovered during archaeological excavations at Upper Palaeolithic sites were often assumed to result from human activity without any consideration for alternate accumulation processes. Many of these assemblages had not been analysed in a scientifically rigorous manner, with some receiving no consideration at all. A review of current evidence and results of new analyses indicate that salmonids (salmon and trout) are the most frequently recorded fish at the European Palaeolithic cave sites. Two potential accumulation agents for fish remains were explored: brown bears (Ursus arctos) and eagle owls (Bubo bubo). Controlled feeding experiments integrated with ecological studies indicate that salmonid remains survive the digestive systems of both species and result in distinctive patterning in assemblage characteristics. Post-depositional taphonomic processes, such as trampling, also produce distinct taphonomic signatures and are an agent of differential inter-species preservation. A thorough consideration of depositional and post-depositional processes of archaeological assemblages in central Italy (Grotta di Pozzo, Maritza, La Punta and Ortucchio) and Spain (El Juyo, Altamira, Salitre, Castillo and Rascaño) shows that the fish remains from these sites result from human activity. The overrepresentation of cranial elements at the Italian sites suggest that fish were processed by removing the head to perhaps smoke or dry before transportation to other locations for consumption. This research lead to improved methods of analysis, and thus enhanced understanding of the role of fishing and fish consumption in Upper Palaeolithic hunter-gatherer societies.

<p>Salmonids, such as rainbow trout, form social hierarchies, consisting of dominant and subordinate individuals, when in groups in environments with limiting resources, such as space or food. There were two main objectives for this thesis: to investigate the physiological consequences of being in a social hierarchy as well as to investigate whether grouped social status or individual behaviour most accurately recorded physiological data for a hierarchy and secondly, to investigate the behavioural and physiological changes of groups of rainbow trout exposed to ammonia concentrations which are above chronic protected guidelines.</p> <p>To create social hierarchies, groups of four fish were fed by a new method using a darkened feeding container, twice daily (morning and evening) for eight days. Each morning feeding was videotaped in order to record aggressive behaviour. Each aggressive act was scored, allowing for fish to be assigned a social status. For ammonia exposures, groups of fish were exposed to either 700, 1200 and 1500 µM total ammonia (or 2.97, 5.10, 6.37 µM NH3, respectively) 24 hours before first feeding and these concentrations were maintained throughout the experiment. On day 5 and day 10, physiological parameters were taken in fish fasted for 24-h in control and 700 µM total ammonia exposed hierarchies.</p> <p>Social hierarchies were created in all ammonia-free and 700 µM total ammonia groups, with no hierarchies formed in 1200 and 1500 µM total ammonia groups. In M.Sc. Thesis – Josias (Si) Grobler McMaster University – Department of Biology iv ammonia-free hierarchies, one fish would become dominant, while the three subordinate individuals would each assume a stable social rank and display similar physiology which was different from the dominant fish.</p> <p>Fish from the 700 µM total ammonia group showed reductions in various physiological parameters during period 1, however, these fish displayed similar values as what was reported in ammonia-free hierarchies during period 2. This suggests biochemical or physiological changes occurring in these fish in order to acclimate to the high ammonia environment</p> / Master of Science (MSc)

This study investigated the regulation of Na⁺ Ca²⁺ Cl⁻ during development in embryonic rainbow trout (Oncorhynchus mykiss). Because there is a close relationship between pH regulation and ion uptake mechanisms in adult teleosts, pH, pCO₂, and NH₄⁺ levels in unstirred layers (USLs) adjacent to whole eggs and dechorionated embryos were determined using double-barrel ion-selective microelectrodes (ISMEs). Whole eggs accumulated Na⁺, Ca²⁺ and Cl⁻ during the last 20 days of embryonic development, suggesting an ionoregulatory ability prior to hatching. Na⁺ uptake by whole eggs was linearly related to external [Na⁺], suggesting that Na⁺ crosses the chorion by diffusion. The uptake by dechorionated embryos was saturable, indicating the presence of active transport or facilitated diffusion mechanisms on the surface of embryos prior to hatching. Ca²⁺ uptake by whole eggs and dechorionated embryos was saturable, suggesting that specific pathways or binding sites are present in the chorion, and that active transport or facilitated diffusion mechanisms are present at the surface of embryos. The much higher Jₘₐₓ for whole eggs than dechorionated embryos suggests a role of the perivitelline fluid (pvf) or chorion in ion uptake. Jₘₐₓ was lower in dechorionated embryos than in hatchlings suggesting that Ca²⁺ uptake mechanisms may not be fully developed in dechorionated embryos. Low pH and high [NH₄⁺] were measured in the USLs adjacent to whole eggs and dechorionated embryos, relative to the bulk water. A high Pcₒ₂ measured adjacent to the gills suggests that CO₂ excretion was the primary source of USL acidification. pH was lower in the USL adjacent to the gills and trunk than in the USL adjacent to the yolk sac. [NH₄⁺] was highest adjacent to the gills and trunk than adjacent to the yolk sac. There was no change in the extent of USL acidification or in [NH₄⁺] over the last half of embryonic development. After hatching, however, there was a significant increase in [NH₄⁺] adjacent to the gills, which was not accompanied by a change in USL pH. It is possible that a change in permeability of the transporting surfaces (i.e. gills, trunk, yolk sac) occurs after hatching. / Thesis / Master of Science (MS)

The expression of the estradiol-responsive genes in the liver of rainbow trout, Salmo gairdnerii, has been studied as a system which may permit quantitative measure of adverse sublethal effects of various xenobiotics. Upon administration of 17 β-estradiol to male or immature female rainbow trout, the expression of two genes are markedly enhanced. One of these genes codes for the egg yolk precursor protein, vitellogenin, whereas the other codes for another, as yet unidentified, protein. Complementary DNA (cDNA) genes of these two proteins have been employed as probes to characterize the dose-response relationship as well as the time course induction of these two classes of transcripts in liver both in vivo and in vitro. The maximal net transcription of pRTC 2 occurs at 20 ug β -estradiol per 100 gram fish body weight whereas those encoded for by pRTC 5 display maximal transcription at 5 μg β-estradiol per 100 gram fish body weight. With doses exceeding the dose required for maximal induction of transcripts, both classes of transcripts reach their maximal levels between 4 and 8 hours after primary and secondary induction. Transcripts homologous to pRTC 5 return to control levels by 16 hours and 2 days after primary and secondary induction respectively. Those homologous to pRTC 2 however, were not observed to recover to normal levels in the primary induction even 16 days after stimulation with estradiol. However, upon secondary induction pRTC 2 transcripts returned to control levels 8 days post-inoculation with estradiol. The effect of various xenobiotics on the induction of these two estradiol-responsive genes was investigated. Pretreatment with β-naphthoflavone resulted in neither the induction or repression of both classes of transcripts. Administration of Kepone prior to a subsequent stimulation with estradiol, resulted in a decrease in the accumulation of pRTC 2 transcripts only. In contrast, an isomer of DDT, p,p'-DDT, was found to enhance the expression of pRTC 5 transcripts in fish subsequently administered β-estradiol. Oncogenes have been found to be activated in transformed cells or cells treated with various xenobiotics. In this study, I have shown that the cellular oncogene, pRTC-myc 1-81, is expressed in the liver at an elevated level in response to estradiol treatment. The two classes of polyadenylated transcripts were detected (2.5 kb and 5.6 kb). The three estradiol-responsive genes mentioned above (pRTC 2, pRTC 5, and pRTC-myc 1-81) were also shown to be transcribed in an established rainbow trout hepatoma cell line. Transcriptional activities of all three genes, as well as the translational activity of vitellogenin, were diminished upon growth in serum stripped of endogenous hormones. Further characterization of this rainbow trout hepatoma cell line is warranted so that it may be employed in a sensitive and quantitative bioassay for assessing the pathobiochemical effects of environmental xenobiotics on fish reproduction. Such an index may be beneficial for establishing adequate guidelines for water contaminants that potentially could affect aquatic and human reproductive success. / Thesis / Master of Science (MS)

No description available.

Aquatic animals, such as fish and shellfish, provide important economic and nutritional benefits for human society. Due to overexploitation of natural fish sources through traditional wild-caught fisheries, aquaculture (generally described as fish farming or culturing) has grown into an economically important industry. A major focus area for the aquaculture field is related to sustainability by ensuring the health and welfare of the aquatic animals. Communities of microorganisms inhabiting the various niches of a given host comprise its microbiome and provide several key health benefits. The microbiome impacts nutrient acquisition, gut homeostasis, protection against pathogens, and immune system modulation. Therefore, much attention has been placed on studying how various culturing conditions and host factors impact the microbiomes of aquatic animals. Here, multiple studies were conducted to elucidate the impacts of various parameters on the microbiomes of rainbow trout, steelhead trout, and Nile tilapia, including dietary supplementation, administration of probiotics and animal age. Though there is a significant correlation between the diet fed to fish and their microbiome communities, small dietary changes such as the inclusion of a dried and lysed yeast product, acting as a protein source alternative to unsustainable fishmeal did not significantly alter the intestinal adherent microbiome of rainbow trout. Moreover, an optimal percentage of yeast replacement that did not negatively impact weight gain for the aquaculture-raised fish was identified, suggesting its efficacy for the industry. Similarly, the intestinal adherent microbiomes of steelhead trout were not significantly altered by diet supplementation with a Bacillus subtilis probiotic. The total microbiome of steelhead trout (mucosa combined with digesta) was instead significantly changed when they were only fed the probiotic additive at an early stage of intestinal development. This change in the microbiome of steelhead trout correlated with a significant increase in weight gain compared to fish only fed the probiotic during later stages of intestinal development. These findings also corroborate previous observations wherein the intestinal microbiome of fish varies during their developmental stages but then stabilizes over time. Determining the core set of bacteria present in fish microbiomes, independent of treatment variables, is another important factor when considering attempts to manipulate the microbiome. To that end, a literature review was conducted in which the phyla Firmicutes, Proteobacteria and, to a lesser extent, Actinobacteria, Bacteroides, and Tenericutes were identified as likely members of the rainbow trout core microbiome. Bacterial families identified as part of the core phyla included Lactobacilliaceae that are commonly used as probiotics and Mycoplasmataceae that lack cell walls. Preventing dysbiosis of the rainbow trout microbiomes will be crucial to ensuring the health of the fish hosts and increasing longevity and profitability of the aquaculture industry. Another important aquaculture-raised species is the Eastern oyster. This animal is critical for the ecological health of the Chesapeake Bay, and it is also an important source of revenue. A significant portion of the revenue flow is the harvest and sale of live oysters for consumption. Unfortunately, consumption of raw or undercooked oysters is the most common route of infection by the human pathogen Vibrio parahaemolyticus (VP) as oysters are a natural reservoir for VP. This bacterium is responsible for a debilitating acute gastroenteritis with potential to cause fatal septicemia. Despite efforts to mitigate infection by this CDC-reportable pathogen, cases continue to increase. The understudied host-microbe relationship between the Eastern oyster and VP has been implicated as a path to research for potential future therapeutics. A novel culturing system for oysters was created using fermentation jars within a BSL-2 ready biosafety cabinet. Using this system, the effect of harvest season was tested against the inoculation efficiency of VP. It was found that higher native Vibrio levels within the oysters were present during the summer compared to the winter. Moreover, addition of the bacteriostatic antibiotic chloramphenicol (Cm) enabled a higher inoculation efficiency by VP during both the summer and winter compared to oysters not exposed to the antibiotic. During the winter, exposure to Cm led to the highest inoculation efficiency (~100%). These findings confirm the importance of the existing microbial communities against exogenous inoculation. Therefore, a year-long study was conducted to investigate the microbiome of oysters during each season. This pan-microbiome study identified a significant impact of harvest season on the microbiome structure. An increased diversity, including higher levels of Cyanobacteriaceae, was observed during the summer. Whereas an increase in Arcobacteriaceae was observed during the winter. Bacteria that persisted throughout the year included Mycoplamataceae and Spirochaeteacae; these families may represent potential members of the Eastern oyster core microbiome. Further work is needed to study the localization patterns of VP within oysters. Such work includes further optimization of immunohistochemistry (IHC) and intracellular colonization assay methods under development here. Collectively, studies of the oyster-microbe interactions will help improve aquaculture methods and identify mitigation targets to reduce VP-related clinical infections. / Doctor of Philosophy / Fish and shellfish provide important economic and nutritional benefits for human society across the globe. Unfortunately, over-fishing of traditional sources of fish and shellfish has led to a reduced supply for world markets, even as the human population increases. Aquaculture, or fish farming, has been around for centuries, but its role in society has significantly increased in the past 50 years. It currently provides about half of fish and other aquatic products on the market today. To better maintain and increase the sustainability and profitability of this industry, more focus is being placed on the health of the fish. The microbiome is the collection of communities of microorganisms, including bacteria, fungi, and archaea, that inhabit various environments including animal hosts. The majority of this dissertation focuses on the impact of factors like diet and age on the microbiomes of aquaculture-raised animals, especially fish. Dietary changes such as the addition of dried yeast-products had a significant impact on fish health but not on the microbiome communities. However, a common probiotic, Bacillus subtilis, did significantly increase not only the growth rate of trout but it also significantly altered the total intestinal microbiome found in the feces and the intestinal mucosal layer. Moreover, it was found that early exposure of the animals to the probiotic had enhanced benefits even though the microbiome appeared to stabilize over time as the fish developed. Maintaining or improving the microbiomes of fish, paying close attention to the microbes that exist as part of a core group of bacteria always present, is vital to ensuring fish health and understanding vertebrate host-microbe relationships. Thus, an analysis of the core microbiome of trout was performed. The final set of projects within this dissertation focused on the relationship between the Eastern oyster, a mollusk native to the Chesapeake Bay, and the bacterial human pathogen Vibrio parahaemolyticus (VP). VP is the leading cause of seafood-borne acute gastroenteritis worldwide, and efforts are needed to mitigate the increasing rate of human infections. Therefore, a simple system using fermentation jars within the laboratory biosafety cabinet was designed to enable safe culture of oysters that were exposed to VP under experimentally controlled conditions. Oysters harvested during the summer naturally harbored higher amounts of native Vibrio organisms in contrast to the winter oysters that harbored much lower levels. A separate microbiome analysis revealed large shifts in the oyster microbiome between summer and winter, although some microbes were continually present. The lower levels of existing Vibrio species detected in winter oysters may have allowed for the higher efficiency of inoculation of winter animals by VP. In fact, these winter animals had Vibrio microbiomes that were completely dominated by the inoculated strain which will enable future work to observe the pattern by which VP localizes, or colonizes, the oysters. Ultimately, these efforts may lead to the development of future disease mitigation strategies against VP.

With World Health Organization estimation of population increase to over 9 billion by 2050, malnutrition and food insecurity are predicated to be two of the main challenges facing the world in the future. Fish is a source of protein that can have a significant contribution for solving the global food crisis. Fish for human consumption is provided by both the aquaculture industry and the capture fisheries, however, the flat-lined production of seafood from capture fisheries means aquaculture production should double in number to provide enough protein by 2050. Culturing fish at higher densities is being used as a way to increase the global aquaculture production. Modern aquaculture intensified practices expose the fish to various stressors that can negatively impact their welfare. Good nutrition can improve the health status of aquacultured fish while accumulation of specific nutrient can add value to the fillet. In line with that, the studies described in this dissertation aimed to examine the vital role of fish in human health and evaluate strategies to improve the sustainable aquaculture production of fish using novel aquafeeds. This was completed by conducting a survey of the essential minerals and heavy metals of commercially available catfish, salmon, and tilapia fillets in the United States marketplace and three fish nutritional trials to evaluate the impacts of novel aquafeeds on production and health of fish and the food quality of their respective fillets. Selenium with the established health benefit for human and fish was the trace mineral of interest in this dissertation. This element is the main component of a group of selenium containing proteins called selenoproteins that are antioxidant and maintain oxidative homeostasis of fish and human. Additionally, selenium is an antagonist for many heavy metals such as mercury. The market study revealed that catfish, salmon and tilapia samples available in United States marketplace are good source of selenium, zinc and phosphorous. The concentration of heavy metals in all the samples were lower than safety standards. Nile tilapia (Oreochromis niloticus) and rainbow trout (Oncorhynchus mykiss), which are two economically important aquacultured fish, were used as animal models in the fish nutritional trials. Different forms of selenium supplemented to Nile tilapia diet. The form of Dietary Se form did not have any significant (p>0.05) effect on growth, and plasma and hepatic GPX activity of Nile tilapia. However, organic selenium supplement showed significantly (p<0.05) higher bioavailability and accumulated in the fillets at the significantly higher concentration. In the second fish trial selenoneine, a novel selenium containing compound, was supplemented at various concentrations to rainbow trout diet. Other than growth parameters multiple other health biomarkers (lysozyme, glutathione peroxidase, superoxide dismutase activities) were examined to determine whether selenoneine supplementation had a positive impact on fish health. Selenoneine enriched diet significantly(p<0.05) increased the weight gain, lysozyme and oxidative enzymes activities of rainbow trout. Lastly rainbow trout feed was supplemented with commercially available probiotic (Actisaf®), prebiotic (Safmmann®), and their mixture (synbiotic). These dietary supplements did not have any significant effect on fish production but led to a significant increase in activity of oxidative enzymes in plasma when compared to control diet. These results suggest that feed supplements used in this dissertation can be used to promote the fish health raised in recirculating aquaculture systems and support an economically and environmentally sustainable aquaculture. / PHD / Fish contributes significantly to human’s diet in terms of high quality, easily digestible animal protein that helps fight malnutrition and food insecurity. More than half of the fish for human consumption is produced by the aquaculture industry and the growth of the industry is very critical for meeting the future needs for protein. Other than production of high-quality protein the aquaculture industry has made a great contribution to people’s livelihood, poverty alleviation, income generation, employment and, trade globally. To continue contributing effectively to global food security aquaculture industry should overcome various obstacles such as disease and sustainable production of high-quality feed. In this dissertation, important roles of fish in human diet was examined by measuring the mineral composition of commercially available catfish, salmon and tilapia in the United States market place. Also diets of Nile tilapia and rainbow trout were supplemented with various forms of selenium, prebiotics, and/or probiotics which have positive effect on health of both human and fish. These supplementations led to production of valued-added fish fillets enriched in selenium and improved the fish growth and health.

The brook trout <i>Salvelinus fontinalis</i> is the only salmonid native to the southern Appalachian Mountains, and is distributed across eastern North America from Canada to Georgia. This species was once abundant in coldwater lakes and streams throughout its range, but environmental disturbances and the introduction of non-native species have drastically reduced the number and sizes of wild populations. Genetic evidence suggests a division at the subspecies level between southern- and northern-derived brook trout populations, with the break between the two forms occurring roughly at the New River watershed. Before the subspecies structure was recognized, brook trout of northern origin were widely stocked throughout the Southeast. The primary objective of this study was to determine the phylogenetic origin of all wild brook trout populations in southwestern Virginia using allozyme markers. Seventy-eight streams believed to contain brook trout in the New, James, Holston, and Yadkin river drainages were sampled by backpack electrofishing. Muscle tissue samples were collected from 916 individuals from 56 populations using a non-lethal biopsy technique. The samples were analyzed by cellulose acetate gel electrophoresis and histochemical staining techniques. Variation at four polymorphic loci, including the diagnostic creatine kinase (<i>CK-A2*</i>) locus, was quantified in terms of genetic diversity and population genetic differentiation. Allele frequencies indicated that 19 populations were of putative southern origin, 5 of northern origin, and 32 of mixed genetic origin. The secondary objective was to determine the geographic distribution of southern- and northern-form brook trout populations throughout the native range using data compiled from all known genetic studies. A map of these data showed that the break between the southern and northern form is sharp, occurring at the New/Roanoke-James watershed divide. Populations from the New River drainage expressed the southern allele at a frequency of 85%, suggesting that their historic native character is southern, and that the presence of northern alleles is due to stocking or stream-capture events. The persistence of the southern form, despite the heavy stocking of northern-derived individuals, may be evidence of an adaptive advantage for the southern form of the species. Existence of adaptive genetic differentiation supports the case for conservation of the southern form of the species in future management of brook trout. / Master of Science

Barriers to fish movement can cause aquatic habitat fragmentation by reducing the amount of available habitat. The primary goal of my research was to investigate applications of population genetic analysis tools as indicators of barrier effects on brook trout populations in fragmented subwatersheds. In chapter1, I tested the hypothesis that brook trout population genetic differentiation (FST) above and below barriers will differ in relation to barrier height and gradient. I also tested the hypothesis that average gene diversity per locus (H) and the numbers of alleles (A) differed between samples below and above each barrier. There was no significant difference in average number of alleles (A) or average gene diversity per locus (H) between the above- and below-barrier samples, but linear regression identified a statistically significant relationship between barrier height and FST values. Unrooted neighbor-joining consensus trees of Cavalli-Sforza and Edwards (1967) chord distances provided evidence of genetic differentiation between samples of resident brook trout above and below natural barriers. Additionally, average total allelic diversity (A), average gene diversity per locus (H), average number of private alleles per locus per sample, and total alleles per sample differed between Level III Ecoregions. In chapter 2 I tested the hypothesis that the presence of a barrier, total habitat potentially isolated above a barrier (km), road density, and percent forest cover within a subwatershed (USGS 6th-level Hydrologic Units) were significant habitat fragmentation factors affecting the effective population size (Ne) of brook trout in the Blue Ridge Level III Ecoregion. Multivariable linear regression indicated that total habitat above the barrier (km) and road density were significant variables retained in the model to predict Ne. In chapter 3, the objective of the study was to infer relationships between barriers and family structure in brook trout populations. Maximum likelihood analysis of pairwise kinship relationships between above- and below-barrier individuals indicated the presence of parent-offspring relationships between above- and below-barrier individuals at six sites in the Blue Ridge Level III Ecoregion and five sites in the Northern Lakes and Forests Level III Ecoregion, which indicated movement of individuals between the above- and below-barrier locations. / Ph. D.

Although strategies to meet most management objectives are relatively clearcut in single-species catchable trout programs, strategies become much more complex when two or more species are involved. A difficult problem that must be faced in evaluating catchable trout fisheries management strategies is defining management objectives. One approach to testing alternative management strategies in complex resource systems, such as catchable trout fisheries, is systems simulation. A computer-implemented catchable trout fishery simulator (CATS) was developed to evaluate fishery response under various management strategies in a multi-species stocking program. The user of CATS can select alternative management strategies and functions which generate predictions of fishing pressure on a particular fishery. To evaluate the effect of each system component, CATS was exercised over a wide range of potential system component alterations. Predominant stocking of brook trout appreciably increased average catch per angler hour and percentage return to creel. Altering the stocking ratio to favor brown trout substantially increased the number of angler hours. Stocking predominantly rainbow trout reduced the effects caused by stocking predominantly brook or brown trout. Estimates of expected angling pressure ru1d catchability coefficients of each species stocked are of primary importance because of their considerable effect on other system components. A user must have a sound objective before deciding where, when, which species, and how many fish to plant. The primary utility of CATS is to enable the user to evaluate management strategies prior to implementation. / Master of Science