The effect of the Asian grass carp (Ctenopharyngodon idella Val.) and aquatic vegetation upon the zooplankton in four adjacent experimental ponds (0.139 ha each) was studied for one year. Zooplankton were collected with a newly designed shallow-water sampler. Pond 1 contained no aquatic vegetation. Ponds 2, 3, and 4 contained nine species of rooted aquatic plants. Grass carp were stocked into Pond 2 (65 per ha) and Pond 3 (611 per ha). Physicochemical parameters were similar among the ponds. Eighty-eight zooplankton species were enumerated. The abundance of zooplankton groups (Rotifera, Cladocera, and Copepoda) was not significantly different among the ponds containing grass carp. No significant differences existed between Pond 3 (high grass carp stocking rate) and Pond 4 (no carp) for species diversity (d) and species dominance. The number of species and species diversity (d) was found to be significantly different in Pond 2 (low grass carp stocking rate) when compared to Ponds 3 and 4; those differences probably were not due to the grass carp. Grass carp did not appear to affect the water quality of the ponds. In general, it was concluded that grass carp had little, if any, direct or indirect affect upon the zooplankton. Species commonness was greatest among ponds containing vegetation. Rotifers were the dominant zooplankton group in those ponds. Zooplankton ware moat abundant in the pond without vegetation and were dominated by copepods (notably Tropocyclops prasinus). That pond contained the lowest number of species and had the largest species diversity (d) of the ponds. The annual mean for the Simpson Index (species dominance) was highest in Pond 1. The lack of vegetation may have influenced the abundance and diversity of the zooplankton in Pond 1 compared to the other ponds. Those differences also may have been due to selective predation by mosquitofish (Gambusia affinis); that fish was significantly less abundant in Pond 1.

Grass carp Ctenopharyngodon idella have been stocked throughout the world due to their utility as a biological control. In the United States, the species has been used to successfully control invasive, aquatic weeds such as hydrilla Hydrilla verticillata. Despite the large body of research surrounding the use of grass carp, few studies have demonstrated widely applicable methods for evaluating the success of weed control based on grass carp behavior and population dynamics. Classic methods of biological control using grass carp often rely on a single, large stocking of fish. Few of these studies have demonstrated success in achieving intermediate levels of weed control. Managers would be better equipped to make decisions regarding stocking and maintenance grass carp populations with better information about behavior, survival, and population structure. Improved decision making could result in reduced cost and increased effectiveness of stocking. In order to examine current knowledge gaps for management, I investigated the movements and habitat use of grass carp, post-stocking survival, age-specific survival rates, and population dynamics of grass carp in Lake Gaston, North Carolina and Virginia. I characterized relationships between grass carp behavior and environmental factors using radio-telemetry. The average rate of movement for grass carp in Lake Gaston was about 137 m/d. Rapid dispersal after stocking was followed by long periods of no movement. However, when time after stocking was held constant in models of behavior, fish moved about 200 m/d more in the second year after stocking than in the first year, and were found closer to shore. On average, grass carp were found about 40 m from shore in about 2.5-3.5 m of water, although mean depth of water at grass carp locations varied seasonally, being shallowest in summer and deepest in winter. Although depth of water at grass carp locations did not vary by stocking location, Grass carp were found closer to shorelines in the upper reservoir than in the lower reservoir. I found significant relationships between grass carp behavior and hydrological processes such as lake elevation and dam releases in the reservoir, as well as with other environmental factors such as water temperature, photoperiod, and weather conditions. The results of this study should be useful in better understanding how behavior can affect management decisions. Specifically, grass carp behavior appears to change with age and environmental conditions within large reservoir systems. Future research should focus more closely on the effects of large-scale flow dynamics on grass carp behavior. I estimated age-1 survival of grass carp from mark-recapture models designed for radio-tagged animals, and characterized relationships between age-1 survival and factors under the control of management, such as stocking locations and size at stocking. . According to the most-plausible model developed in this study, survival of age-1 grass carp in Lake Gaston varied throughout the year, and the probability of an individual grass carp surviving to the end of its first year (±SE) was 0.57(±0.10). According to the second-most-plausible model developed in this study, grass carp survival varied between stocking locations, and was twice as high in the upper reservoir (0.87±0.09) than in the lower reservoir (0.43±0.11). The differences in survival between stocking locations suggest that the cost-effectiveness of grass carp stocking could be improved by focusing stocking efforts in specific regions of Lake Gaston. Furthermore, none of the models developed in this study that incorporated the effects of size (length and weight) or condition factor accounted for a meaningful amount of the total model weights. These results suggest that costs of grass carp stocking could be reduced in Lake Gaston by using a smaller minimum size (352 mm, TL) than is commonly referred to in the literature (450 mm, TL). I used grass carp collected by bowfishers in Lake Gaston to characterize the age, growth, and survival of grass carp in the system. From these data, I characterized relationships between fish population dynamics and annual hydrilla coverage. Grass carp collected from Lake Gaston ranged in age 1-16 years. Growth of grass carp in Gaston was described by the von Bertalanffy growth function as Lt = 1297(1-e -0.1352 (t+1.52)). I estimated mortality from the von Bertalanffy growth parameters using methods based on growth, temperature, and age; and with each mortality estimate I estimated population size and standing biomass of grass carp. Use of age-specific mortality rates produced lower estimates of grass carp numbers and standing biomass in Lake Gaston than did the use of a single, instantaneous mortality rate for all ages. I determined that growth of grass carp slowed considerably after the fourth year and that slowed growth, in combination with changes in mortality, resulted in a decrease in the amount of hydrilla controlled by a given cohort after four years in Lake Gaston. This phenomenon resulted in an approximately linear relationship between the biomass of grass carp at year i and hectares of hydrilla at year i+3. Based on this relationship, I predicted that the biomass of grass carp necessary to reduce hydrilla coverage to the target level of 120 ha in Lake Gaston is about 91,184 kg (±38,146 kg) and that the current biomass of grass carp in Lake Gaston is about 108,073 kg (±3,609 kg). I conclude that grass carp biomass is at or near levels that should reduce hydrilla coverage to 120 ha between 2013 and 2018. This research provides an effective means for synthesis of information that is critical to understanding sterile, triploid grass carp populations when assumptions of other methods cannot be met. The results of this study should be of immediate utility to hydrilla management efforts in Lake Gaston and other systems. Furthermore, the age-specific mortality rates developed in this study should be useful as starting values for grass carp management in similar systems. / Master of Science

Knowledge of natal environments and dispersal of Silver Carp (Hypophthalmichthys molitrix) inhabiting the Ohio River, and Kentucky and Barkley lakes would inform development of strategies to control established and emerging populations. However, the principal natal environments supporting the emerging bigheaded carp population in the Ohio River basin are unknown. There is also a need to assess the role of tributaries as nursery sites to increase understanding of dispersal patterns and better target young fish. The goal of this study was to identify recruitment sources and determine dispersal patterns of Silver Carp in the Ohio River basin using evidence from otolith core trace element compositions relative to ambient water elemental measurements. Fish were collected from the Ohio River, and Kentucky and Barkley lakes from 2014-2017 and water samples were taken during summer 2012-2017. Water samples maintained temporal stability and spatial differentiation for the Ohio River and tributaries during the sampling period. Results suggest that most Silver Carp in the Ohio River are utilizing tributaries during early life. Results also suggest there is passage of carp through the locks into the lakes from the Ohio River and natural reproduction is occurring in or above Kentucky and Barkley lakes. Results will inform development of efforts to target and remove spawning and young bigheaded carps as well as direct management efforts in the Tennessee and Cumberland River systems.

Ph.D. (Zoology) / Please refer to full text to view abstract

When a species is introduced outside their native range, the genetic diversity of the introduced population is generally decreased due to the founder effect, and the fitness of individuals in the introduced population may decrease due to inbreeding depression. Invasive species are a paradox to this paradigm because while the initial population size of an invasive species may be small in their non-native range, the individuals are able to survive, eat, and reproduce so successfully, that they have deleterious effects on native species. One mechanism that invasive species use to overcome a lack of genetic diversity and adapt to their new environment is CpG methylation, a heritable and environmentally influenced epigenetic modification that regulates the expression of certain genes to alter phenotypes without altering an organism’s DNA sequence.Bighead and silver carps, two species of bigheaded carp native to eastern Asia, are believed to have been introduced to the United States in the 1970s. Since that time, populations of both bighead and silver carp have surged, particularly in the Mississippi River drainage, where they compete with native planktivores for food, injure boaters, and threaten the multi-million dollar fisheries industry in the Great Lakes. In this study, methylation-sensitive amplified fragment length polymorphisms (MS-AFLPs) were used to analyze the genetic and epigenetic diversity of bighead and silver carp from the Gan, Pearl, and Yangtze rivers in their native China and from the Illinois River in the United States. While the heterozygosity of silver carp in Illinois was not found to be significantly lower than that of silver carp in China, the silver carp in Illinois did show a significantly higher level of methylation compared to Chinese silver carp. There is evidence that CpG methylation may play a significant role in allowing silver carp to adapt and thrive in an introduced environment.

The aim of the study was to compare the yield of scaly carp and mirror carp, two major representatives of the common carp (Cyprinus carpio), predominantly bred in the Czech Republic. The yield comparisons were performed in a newly created company store, where it was important to assess the suitability of fish for different products. A partial objective was, through a questionnaire survey, to determine the popularity and frequency of the consumption of carp. Finally, the intensity of individual forms of carp was monitored. The experiment was conducted in the years 2012-2013 during the four seasons spring, summer, autumn and after relaying. The evaluation took place for two types of carp, the mirror carp and the scaly carp. Another reference subject was two ponds, the naturally fed Vrbský Pond and the feeding pond Musik. Both carp are characterized by distinct developmental and life cycles. The mirror carp, the body structure of which is smaller than the scaly carp, demonstrated a higher yield in all monitored aspects at the end of the evaluation. At the same time, the fillet yield of both representatives achieved similar values and ranged from about 43-48%. The carp from the feeding pond Musik gave a surprising result, where a lower yield was expected due to the lower amount of plankton and zoobenthos, a natural food for fish. During the monitored period, the highest yield was recorded in the period after relaying, while the lowest yield in the spring, due to the selected increased fish stock for the given year.

published_or_final_version / Biological Sciences / Master / Master of Philosophy

The nutritional value of novel yeast products were evaluated for warmwater fish species. A yeast co-product (yeast protein concentrate unrefined (YPCU)) obtained from a bio-ethanol process using wheat was tested using iso-nitrogenous (38% crude protein) and iso-lipidic (8%) diets for juvenile mirror carp (Cyprinus carpio). The fishmeal (FM) protein component of a basal diet was replaced by (YPCU) at 7.5, 15, 20, and 50% of total dietary protein. After an 8 week feeding trial, all fish fed YPCU yielded better growth performance than the control fed fish, with diets containing 15% and 20% YPCU being optimal. Whole body composition was unaffected by dietary treatment, however, ash levels were elevated in fish fed >15% YPCU. Hepatic alanine amino transferase (ALAT) and aspartate amino transferase (ASAT) were measured as bio-indicators of liver function in carp. Only ASAT activity was significantly lower for carp fed 20% and 50% YPCU. Additionally, histological assessment of liver and intestinal tissues gave no indication of impairment, but high YPCU inclusion (>15%) elevated the number of goblet cells present in the posterior intestine. Molecular microbiological analysis using DGGE revealed no definitive changes in intestinal microbial communities. In a second study, bio-ethanol yeast (refined YPCR and unrefined YPCU) and dried distillers grain with solubles (DDGS) a co-product of the bio-fuel process and distillery yeast from potable alcohol (whisky) production (YPCPA) were evaluated as before for carp. FM was replaced with 30% of YPCU, YPCR and YPCPA and 15, or 30 % DDGS with a combination of 10% YPCR. Weight gain, and Apparent Net Protein Utilization (ANPU%) were higher in fish fed YPCU 30%, equivalent for fish fed FM, YPCR 30%,DDGS 15% and DDGS 30%, and lower in fish fed YPCPA 30% diets. Feed conversion ratio was significantly increased in carp fed YPCU 30% and decreased for carp fed DDGS 30% and YPC PA 30% compared with the control group. A significant improvement of net mineral retention was seen for carp feed the yeast supplementation diets compared to the fishmeal control group. The YPCU 30% diet produced the highest mineral retention in fish fed yeasts and the YPCPA 30% gave lowest retention. The microvilli density of the intestinal tract decreased for carp fed YPCR 30%, but microvilli length significantly increased in fish fed YPCU 30% compared with other groups, thus indicating changes in gut integrity. In the third study, four diets were formulated to replace 0, 10, 20 and 30% of the fishmeal with refined yeast protein concentrate (YPCR) for Nile tilapia (O. niloticus) of mean weight 12.39g. Growth performance and feed efficiency were not affected with up to 20% replacement with YPCR. There were no obvious changes in the liver structure, but high yeast inclusion showed higher numbers of intestinal goblet cells with increasing YPCR dietary inclusion suggesting enhanced intestinal integrity. Microvilli density and length was significantly (P = 0.025) improved with up to 10% and 30% YPCR inclusion in comparison to other dietary treatments. It was generally concluded that YPC co-products were effectively viable for both juvenile carp and tilapia offering an option for partial fish meal replacement.

Sensitive and accurate detection methods are critical for monitoring and managing the spread of aquatic invasive species, such as invasive Silver Carp (SC; Hypophthalmichthys molitrix) and Bighead Carp (BH; Hypophthalmichthys nobilis) near the Great Lakes. A new detection tool called environmental DNA (eDNA) sampling, the collection and screening of water samples for the presence of the target species’ DNA, promises improved detection sensitivity compared to conventional surveillance methods. However, the application of eDNA sampling for invasive species management has been challenging due to the potential of false positives, from detecting species’ eDNA in the absence of live organisms. In this dissertation, I study the sources of error and uncertainty in eDNA sampling and develop statistical tools to show how eDNA sampling should be utilized for monitoring and managing invasive SC and BH in the United States. In chapter 2, I investigate the environmental and hydrologic variables, e.g. reverse flow, that may be contributing to positive eDNA sampling results upstream of the electric fish dispersal barrier in the Chicago Area Waterway System (CAWS), where live SC are not expected to be present. I used a beta-binomial regression model, which showed that reverse flow volume across the barrier has a statistically significant positive relationship with the probability of SC eDNA detection upstream of the barrier from 2009 to 2012 while other covariates, such as water temperature, season, chlorophyll concentration, do not. This is a potential alternative explanation for why SC eDNA has been detected upstream of the barrier but intact SC have not. In chapter 3, I develop and parameterize a statistical model to evaluate how changes made to the US Fish and Wildlife Service (USFWS)’s eDNA sampling protocols for invasive BH and SC monitoring from 2013 to 2015 have influenced their sensitivity. The model shows that changes to the protocol have caused the sensitivity to fluctuate. Overall, when assuming that eDNA is randomly distributed, the sensitivity of the current protocol is higher for BH eDNA detection and similar for SC eDNA detection compared to the original protocol used from 2009-2012. When assuming that eDNA is clumped, the sensitivity of the current protocol is slightly higher for BH eDNA detection but worse for SC eDNA detection. In chapter 4, I apply the model developed in chapter 3 to estimate the BH and SC eDNA concentration distributions in two pools of the Illinois River where BH and SC are considered to be present, one pool where they are absent, and upstream of the electric barrier in the CAWS given eDNA sampling data and knowledge of the eDNA sampling protocol used in 2014. The results show that the estimated mean eDNA concentrations in the Illinois River are highest in the invaded pools (La Grange; Marseilles) and are lower in the uninvaded pool (Brandon Road). The estimated eDNA concentrations in the CAWS are much lower compared to the concentrations in the Marseilles pool, which indicates that the few eDNA detections in the CAWS (3% of samples positive for SC and 0.4% samples positive for BH) do not signal the presence of live BH or SC. The model shows that >50% samples positive for BH or SC eDNA are needed to infer AC presence in the CAWS, i.e., that the estimated concentrations are similar to what is found in the Marseilles pool. Finally, in chapter 5, I develop a decision tree model to evaluate the value of information that monitoring provides for making decisions about BH and SC prevention strategies near the Great Lakes. The optimal prevention strategy is dependent on prior beliefs about the expected damage of AC invasion, the probability of invasion, and whether or not BH and SC have already invaded the Great Lakes (which is informed by monitoring). Given no monitoring, the optimal strategy is to stay with the status quo of operating electric barriers in the CAWS for low probabilities of invasion and low expected invasion costs. However, if the probability of invasion is greater than 30% and the cost of invasion is greater than $100 million a year, the optimal strategy changes to installing an additional barrier in the Brandon Road pool. Greater risk-aversion (i.e., aversion to monetary losses) causes less prevention (e.g., status quo instead of additional barriers) to be preferred. Given monitoring, the model shows that monitoring provides value for making this decision, only if the monitoring tool has perfect specificity (false positive rate = 0%).

Lateral habitats provide a multitude of benefits to riverine fishes, including invasive Silver Carp (Hypophthalmicthys molitrix) and Bighead Carp (H. nobilis), hereafter bigheaded carp. Harvesters have focused removal efforts in lateral habitats (e.g., backwaters and side channels); however, little research has examined the lateral habitat use of bighead carps. The Starved Rock Pool (SRP) is the downstream most pool in the upper Illinois River where contracted commercial fishermen target bigheaded carp to reduce dispersal pressure towards the Laurentian Great Lakes. To examine bigheaded carps’ movement between the main channel and lateral habitats in SRP, fish were implanted with transmitters and tracked using acoustic telemetry. The ranges and detection probabilities of acoustic telemetry receivers have typically been modelled and examined in with linear distance tools. To derive more realistic receiver ranges and detection probabilities, this study used minimum bounding geometry on detected transmissions obtained from boat-mounted transmitters. Receiver detection ranges estimated using minimum bounding geometry were smaller than those estimated using the linear distance method, but estimated detection probabilities within receiver ranges were higher using the minimum bounding method compared to the linear distance method. Detection histories of bigheaded carp implanted with transmitters were examined to assess fish habitat use from June 2016 to April 2018. During 2017, multiple environmental variables (temperature, river discharge, chlorophyll a, dissolved oxygen, total dissolved solids, and turbidity) were measured weekly and zooplankton samples were collected during June and August to assess potential associations between environmental variables and bigheaded carp habitat use that might be useful for informing locations and times for focusing contracted harvest of bigheaded carps. Habitat selection was also examined using a resource selection index (W) and a mark-recapture multistate model in program MARK. Across all seasons, bigheaded carp used lateral habitats more frequently than main channel habitats. Habitat use was strongly influenced by temperature and marginally by main channel discharge. No strong associations between zooplankton and bigheaded carp habitat use were observed during this study; however, there were some differences in zooplankton community structure and abundance among lateral habitats related to rotifers that may have potentially been related to use of specific lateral habitats by bigheaded carp. While having high return percentages to all lateral habitats, bigheaded carp disproportionately selected for a few individual habitats, possibly due to those habitats being locations where tagging was conducted. Harvest efforts in lateral habitats, especially prior to spawning (spring staging), during lower temperature periods (overwintering), and during higher discharges should be most effective because of bigheaded carps’ particularly high use of lateral habitats during these times. Recurring removal efforts in lateral habitats within SRP may facilitate targeting of individuals that frequently return to these lateral habitats and may also reduce bigheaded carp abundance in nearby locations.