Advances in molecular technologies have provided conservation biologist with the opportunity to quantify the genetic structure of a population and, in turn develop management guidelines and policies aimed at preserving the genetic diversity of fish stocks challenged by human activities. This thesis examines the status of genetics as applied to the management of freshwater fisheries by state natural resource agencies with a purpose of understanding the keys to a successful genetics program. An online survey was used to investigate the breadth of molecular marker application to freshwater fisheries management by state natural resource departments. Seven questions were posed to 50 state agencies addressing species of concern, type of genetic resources used, type of molecular marker used, and management concerns. Genetics was listed as a concern in the management of 18 freshwater fish families representing 70 distinct species, with Salmonid species the most frequently reported (20%#37;). A majority of agencies rely on outside resources to perform genetics testing (65%#37;). The most common analysis technique used by state agencies was microsatellite DNA analysis (35%#37;) and the most frequently reported management concerns were genetic stock identification and management boundaries (23%#37;). The application of a specific molecular technology to a conservation question was addressed by investigating the mechanisms of unnatural selection in the form of a study of trait heritability. Microsatellite parentage analysis was used to reconstruct familial relationships of juvenile Florida bass (Micropterus floridanus) displaying variable traits of growth and aggressiveness in a culture setting. Differences in the parentage of high growth and aggression (HGA) and baseline growth and aggression (BGA) offspring showed that certain parent-pairings contribute disproportionally to certain size classes and levels of aggression. These results suggest that the selective pressures of recreational harvest may negatively impact the fitness of wild fish stocks. Overall, this work provides natural resource managers with the basic information required to successfully develop and employ strategies aimed at preserving the genetic integrity of freshwater fisheries.

Common snook, Centropomus undecimalis, is a popular game fish species that occurs throughout central and southern Florida, yet many questions remain unanswered regarding their reproductive strategies, including estimates of fecundity with relation to size, age, and condition of the female. These relationships are critical to improving stock assessments and fundamental to estimating spawning potential ratio, the measure by which snook are managed. Spawning snook were collected from a known spawning site, Rattlesnake Key, Tampa Bay, Florida, during three consecutive spawning seasons (2009-2011) and batch fecundity for snook was reported for the first time. Of the 43 females suitable for fecundity analysis, batch fecundity was highly variably and ranged from 258,913 to 2,663,737 eggs. The mean batch fecundity was (984,689 eggs/batch, median = 781,330 eggs/batch) and the mean relative fecundity was 465 eggs/gram body weight (median = 402 eggs/gram body weight). Average batch fecundity did not vary by collection year, despite a severe cold event in the winter of 2010, which killed about 25% of the spawning population. However, analysis of proximate composition indicated that liver lipid percent was significantly reduced in 2010, likely due to reduced prey availability, increased energetic expenditures, or both, while enduring and recovering from cold exposure. A significant positive relationship in 2009 between batch fecundity and condition was reported that entirely disappeared in 2010. Additionally, in a preliminary investigation, we detected sub-population differences between known-spawning `bay fish' and `river fish' using barium as an indicator of freshwater habitat usage via otolith microchemistry. Our results are directly relevant to enhancing stock assessments and indicated that reproductive strategies of snook are both complicated and robust. Future research should further investigate reproductive strategies (e.g. skipped spawning) and possible sub-population life history, as both can have significant impacts on stock assessment models.

This thesis presents an assessment concerning the potential of horizontally integrated aquaculture, with outcomes assessed from a systems-based perspective. A literature review concerning the negative impacts and the limitations of current wastewater management approaches demonstrated that improved strategies are required. Horizontally integrated aquaculture was proposed, where the productive reuse of aquaculture wastewater ameliorates associated negative impacts. A definition for horizontally integrated aquaculture is presented and management strategies that conform to this definition reviewed. The development and application of the ADEPT bioeconornic model to assess the potential of a constructed wetland and trout fishery to treat wastewater from a commercial smolt unit in Scotland is described. The model outputs were tested against observations from commercial facilities operating under comparable conditions to those envisaged for horizontally integrated systems. Findings demonstrated that the modelling approach adopted was generally effective in predicting the composition of wastewater outputs from the farm and the effect of the selected treatment strategies. The model was applied to two further case studies. One assessed the potential of treating wastewater from shrimp farms in Thailand using a constructed mangrove wetland; the second evaluated the possible advantages of a rational design approach to lagoon-based wastewater treatment and reuse, as opposed to a conventional design and traditional practices developed in peri-urban Calcutta.

Thesis (Ph. D.)--University of Hawaii at Manoa, 2003. / Includes bibliographical references (leaves 109-118).

The specimens studied during this investigation were taken incidentally during a general faunal survey of certain peculiar streams flowing from underground channels. On casual examination it was evident that they belonged to the cave fish group but were not the well known almost colorless blind variety. After checking the descriptions in various vertebrate manuals it appeared that they were probably a new species. There are three groups of cave fishes, the non-blind, the semi-blind and the blind. Chologaster, or the Rice Field Minnows of South Carolina, are members of the non-blind group. Forbesichthys of southern Illinois and Kentucky is an example of the semi-blind group, and Typhlichthys, the true blind cave fish, found in the caves of Kentucky and Tennessee, is an example of the blind group. It appeared probably that they belonged in the intermediate group, and a check of the literature disclosed the fact that no intensive studies had been made on the group to which these forms appeared to belong, and very little is known concerning their food and general habits. It was therefore thought worthwhile to make a comprehensive study of these fishes. One hundred or more specimens were collected, some being immediately preserved while others were placed in an aquarium and kept alive for the study of behavior and general environmental relations. This investigation was then attempted for the purpose of determining more definitely some important facts concerning this species, such as the type of food that makes up the diet of the fish, to establish a few facts concerning the general habits, including behavior and general environmental relations, and to further clarify the matter of the description.

Diet of cougars (Felis concolor) was studied from December 1978 to August 1981, on a 4500 km2 study area near Escalante, Utah. Prey eaten was determined from analysis of 112 animals consumed as prey, and from 239 cougar scats. Mule deer (Odocoileus hemionus) were the major prey item, comprising 81% of biomass consumed. Lagomorphs, large rodents, and smaller predators were also important components. Cattle comprised Motion-sensitive radio-transmitters were placed on 15 cougars, from 3 months to 7-9 years of age. Three parameters of the radio signal were used to determine activity levels during 6843 1-minute sampling periods: number of changes in pulse rate, predominant pulse mode, and signal integrity, based on 308 minutes of "known" acti vity. Cougars showed distinct crepuscular (sunrise, sunset ± 2 hrs) activity peaks (P Estimates of energetic costs of basal metabolism, and of activity, growth, and reproduction were used in a predictive model of energy cost of free-existence. Information on dietary composition, live weight and energy content of prey animals, and assimilation efficiencies were used to provide estimates of the frequency at which deer were killed (deer/day) and consumed (kg/day). Single adults were estimated to kill 1 deer per 8-16 days. Females with 3 large cubs would kill 1 deer as often as every 2-3 days. A known population of 8 adult cougars was predicted to consume 417 deer per year.

Management agencies documented a decline in the mountain whitefish (Prosopium williamsoni) population on the Big Lost River, and unscreened diversions were recognized as a potential factor for this decline. Research suggests the Big Lost River mountain whitefish population is genetically unique, and it has been petitioned for protection under the Endangered Species Act. In 2007, a basin-wide synopsis of diversions was conducted to describe relative entrainment and identify diversions that entrained the most mountain whitefish. This larger scaled synopsis facilitated a more precise assessment of entrainment by a subset of diversions in 2008. In 2008, the volume that was diverted and the available stream-flows were assessed to identify correlations between discharge and increased entrainment. Lastly, a stage-structured population matrix model was used to describe the potential effect that entrainment is having on the mountain whitefish population. Entrainment was evaluated in canals using multiple-pass electrofishing depletions in conjunction with block-nets. Entrainment was estimated using simple or stratified random population estimates. Entrainment varied widely among diversions and between water years. Variations in entrainment were attributed to seasonal patterns, population densities, and the physical characteristics of the diversion. A positive correlation was identified (R2 = 0.81) between the number of mountain whitefish entrained and the volume of water diverted annually. I observed substantial numbers of fish entrained by two diversions on the upper Big Lost River. I illustrate how reducing entrainment at these diversions will increase recruitment to adulthood and increase the viability of the population overall.

Zooplankton of the littoral and limnetic zones of Bear Lake, Idaho- Utah, were collected over a 17 -month period. Twenty-three species of zooplankton were recorded, as well as nine other species represented by both flora and fauna. At the time of sampling 17 physical and chemical parameters were a lso measured. Methods of analysis for the plankton and the environment are described and discussed. The objectives of this project were fourfold: To establish a record of the current zooplankton population before changes due to the increase o f organic nutrients occur. To compile a qualitative and quantitative standard against which future populations can be compared. To assess the source and the amount of present nutrients which are being contributed to the lake. To investigate the effect the present addition of nutrients is having on zooplankton productivity. The physical and chemical analysis of the Bear Lake waters showed a number of interesting trends. The measurement of total dissolved solids, when compared with previous investigations, showed a decline: i.e., it appears that a great dilution had taken place in the lake waters since 1912. The measurement of salinity revealed two chemical patterns in Bear Lake waters. First: chloride, sulfate, sodium, and potassium showed a decrease in concentration on a long-term basis. Second, calcium showed a slight rise with a leveling off, and magnesium showed a decline with a leveling off over the same period. Calcium is being precipitated as calcium carbonate, and the removal of sodium, potassium , sulfate, magnesium, and chloride is achieved through the pumping of lake waters outside the basin. Nitrogen was measured with respect to three of its forms--ammonia, nitrite, and nitrate. Ammonia was comparatively evenly distributed throughout the water column at all depths. The cycling of ammonia appeared to follow that of known oligotrophic lakes. Generally, the nitrite was low in the limnetic and allochthonous waters and higher in the littoral zone. The littoral and limnetic water exhibited lower nitrate levels than the allochthonous sources. This is believed to be due to the prevailing land use patterns. The production of cattle and sheep and the cultivation of extensively fertilized crops appear to give the most plausible answer. The littoral waters appeared to be higher with respect to ammonia, nitrite, and nitrate, in the microhabitats that are natural, and in others that are man-made: i.e., harbors, breakwaters, and shore based homes. The distribution of phosphate-phosphorous in the waters varied little during the study. The mean values were quite similar for the littoral and limnetic waters. The allochthonous waters had approximately four times the phosphate concentration of the lake waters. The chemical analysis of the bottom muds revealed that phosphorous as phosphate and as P2O5 were significantly higher in concentration between the 50- and 200-foot contours than at lesser depths. The low levels of soluble phosphate and the slight variation encountered in the water column seem to be related to the orthograde nature of the oxygen curve found in the lake. Relationships between chemical analysis and the zooplankton associated within a particular station in the lake were completed by correlation and regression analysis. Associations between independent and dependent variables apparently defined various environmental preferences or requirements necessary for the maintenance of particular individual species. In light of the basic taxonomic considerations these proposals appear to be within reason. Individual correlation and regression analysis were completed for three lake zones investigated: littoral, limnetic, and the haptobenthos. Individual analysis of variances were completed within the three Bear Lake zones in order to assess the affect of habitat on the plankton population. The statistical analyses were compared to the means for these several stations within one zone, and biological and statistical explanations were made. Supplementary water quality analyses were conducted in order to explain some abnormal chem1cal and biological results. Bacteriological testing of the Bear Lake waters revealed that a large percentage of the littoral and allied limnetic zone presented definite problems with respect to water quality and public use.

Strawberry Reservoir, Utah is an 8.000 acre lake at the elevation of 7,550 feet; it has a maximum depth of 52 feet and an average depth of 18 feet. The supply of cutthroat trout eggs used to replenish and distribute this trout throughout the state are taken from two spawning traps located on reservoir tributaries. Because it has not proven economical to raise cutthroat to a larger size than newly hatched fry, it is at this site they are planted. Because of competition, predation, and lack of space the planting back of fry to maintain the fishery and spawning run presents a serious problem. Tributaries are at carrying capacity from being closed to fishing and the reservoir supports a tremendous population of trash fish; mainly the Utah chub, Gila atraria (Girard); yellow perch, Perca flavescens (Mitchell); redside shiner, Richardsonius balteatus (Cope); mountain sucker, Pantosteus delphinus Cope; and dace. Rhinichthys osculus Cope. The rainbow trout, Salmo gairdneri Richardson. and the cutthroat trout dominate the game fish population. It has been the policy of the Utah State Department of Fish and Game to trap and artificially spawn spawn every possible fish, leaving most of the spawning ground unused. This cost, plus the unknown advantage, if any, of artificial over natural reproduction led to the study of the possibilities of natural reproduction for replenishment of the cutthroat trout in the reservoir.

The purposes of this study were to gain a better understanding of anglers and angler preferences and to examine differences between subgroups of anglers based on level of specialization. Understanding these similarities and differences between user groups will provide valuable input for more effective fisheries management. A randomized mail survey was sent to resident, adult fishing-license holders in Utah. A 68% response rate yielded 1216 usable returns for data analysis. An analysis of three recreation specialization dimensions (participation, equipment and investment, and lifestyle) and further analysis of participation and investment variables were used to develop a typology of Utah anglers. Three specialization subgroups and four typology subgroups were then compared to determine differences in motivations for fishing, preferences toward various fishing and management attributes and the desirability of available fish species. Anglers with different levels of specialization differed significantly in their motivations for fishing, preferences for fishery resource attributes and desirability ratings of available fish species. Typology subgroups were found to not differ significantly in motivations, preferences or species desirability ratings. However, level of participation (number of fishing trips taken in past year) and investment (money invested in fishing equipment) were each valuable in identifying differences in motivations and preferences, but not in species desirability ratings. By identifying sportsmen constituencies based on specialization characteristics, managers can better provide fishing opportunities consistent with angler needs. Fisheries managers will have a tool to match sportsmen with the type of setting and management strategy desired or to match the management to the sportsmen, thus maximizing satisfaction.