VTechWorks Repository :: Browsing by Author "Hallerman, Eric M."

Browsing by Author "Hallerman, Eric M."

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Ammonia-oxidizing bacteria and archaea within biofilters of a commercial recirculating marine aquaculture system
Huang, Zhitao; Jiang, Yuli; Song, Xiefa; Hallerman, Eric M.; Peng, Lei; Dong, Dengpan; Ma, Teng; Zhai, Jieming; Li, Wensheng (2018-02-10)
While biofilters are widely used to metabolize ammonia and other wastes in marine recirculating aquaculture systems, the ammonia-oxidizing bacterial and archaeal communities have not been characterized across a diversity of production systems. Using a metagenomics approach, we characterized the ammonia-oxidizing microbiological community of biofilters in a commercial recirculating marine aquaculture system producing hybrid grouper (Epinephelus lanceolatus × E. fuscoguttatus). Cloning and sequencing of the amoA gene showed that nitrifying bacteria included Nitrosomonas europea, N. stercoris, N. cryotolerans, N. eutropha, N. estuarii, eight strains of N. marina, and 15 strains not associated with described species. Nitrifying archaea included eight strains of Nitrosopumilus maritimus, N. koreensis, N. piranensis, N. adriaticus, undescribed congeners, and other undescribed archaea. The species composition of the bacterial and especially the archaeal communities was beyond that yet reported for aquaculture biofilters. While ammonia flux through the respective communities has yet to be estimated, the diverse environmental adaptations of the bacterial and archaeal communities suggest resilience of function under a range of environmental conditions.
Analysis of Inbreeding in a Closed Population of Crossbred Sheep
MacKinnon, Kathryn Michelle (Virginia Tech, 2003-08-20)
Genetic diversity and the effect of lamb and dam inbreeding on multiple traits were analyzed in an 11-yr closed population of sheep established in 1983 and remained closed after 1987, with 50% Dorset, 25% Rambouillet, and 25% Finnsheep breeding to determine selection response for spring fertility. The population had been randomly divided in 1987 into a fall-lambing selection line (S) of 125 ewes and 10 rams, fall-lambing environmental control line (E) of 55 ewes and 5 rams, and a spring-lambing genetic control line (G) of 45 ewes and 5 rams. Inbreeding effects were estimated from 2678 lambs and 556 dams present after the creation of the respective lines. The traits assessed were ewe spring-fertility, lambing date, lamb birth, 60 d, and 120 d weight, and lamb survival to 1, 3, and 14 d. Genetic diversity was assessed by estimating change in inbreeding per generation (ΔF) and effective number of breeding animals (N_e), and parameters derived from gene drop simulations and an iterative procedure developed by Boichard et al. (1997); effective number of founders (f_e), effective number of ancestors (f_a), founder genome equivalents (f_g), and two additional measures of genetic diversity (GD₁, GD2). In order to estimate the diversity available in S and G, three sets of animals from the end of the study and one set of animals at line formation were considered in each line: all lambs born (including dead lambs), all matings (including potential offspring, even if a lamb was not born), and all rams and ewes available at the end of the study and at line formation. At the time of line formation, most of the loss in diversity was due to unequal founder representation. The smaller population of G, as compared to S, caused a greater decrease in diversity due to bottlenecks at line formation. Very little diversity was lost due to additional drift by the time of line formation because selection had not occurred and a random mixing of founders was the goal. Allelic diversity decreased moderately; of the 322 founder alleles, there were 71% in S and 58% in G of rams and ewes (RE) that appeared in at least 50 runs of gene drop. By the end of the study in 1998, the amount of allelic diversity had decreased substantially. Of the alleles possible in RE at the end of the study in S and G, only 6 and 8 %, respectively, appeared in greater than 50 simulations of gene drop. The measures of f_e, f_a, and f_g revealed there was not much additional loss in diversity from the line founders to the end of the study due to unequal founder representation, but there was a larger amount of loss due to bottlenecks and additional drift. The diversity loss was similar, which was the goal of the selection study, when values for RE were compared in S and G. The effects of lamb and dam inbreeding were estimated from REML analysis. Effects of lamb or dam inbreeding were negative but not significant for lambing date or survival to 1, 3, or 14 d. Spring fertility was estimated to decrease by 0.70 ± 0.30 %/% inbreeding of the ewe (P < 0.01), which seems even greater since the average spring fertility was only 47.5 %. Effects of lamb inbreeding on birth, 60-d, and 120-d weights were -0.012 ± 0.006 (P < 0.05), -0.045 ± 0.020 (P < 0.05), and -0.130 ± 0.034 kg/% (P < 0.01), respectively. Dam inbreeding had smaller effects on birth, 60-d, and 120-d weights of -0.008 ± 0.010 (ns), -.033 ± 0.034 (ns), and -0.087 ± 0.056 (P < 0.1) kg/%, respectively.
The application of microsatellite DNA markers for forensic analysis of koi carp (Cyprinus carpio)
Grobler, J. P.; Kotze, A.; Swart, H.; Hallerman, Eric M. (Academy of Science of South Africa, 2005)
We describe the use of microsatellite DNA markers, previously developed for common carp, to investigate a forensic case involving ornamental koi carp. Two South African breeders offered koi strains for sale, which a third breeder claimed were taken illegally from his ponds. Screening of four microsatellite markers provided polymorphic results for koi, demonstrating their applicability for forensic studies. Amplification product sizes were comparable to those published for common carp at three of the four loci. We observed higher allelic diversity among koi carp than had been reported for a panel of inbred common carp. Coefficients of population differentiation showed no significant differences between the populations involved. Consequently, our analyses could not convincingly prove or disprove foul play. The latter ambiguity was most likely the result of sampling constraints rather than the suitability of the markers. Our results provide a foundation for future application of microsatellite markers for forensic investigation, marker-assisted breeding, and population diversity analysis in koi.
Aquaculture-Mediated Invasion of the Genetically Improved Farmed Tilapia (Gift) into the Lower Volta Basin of Ghana
Anane-Taabeah, Gifty; Frimpong, Emmanuel A.; Hallerman, Eric M. (MDPI, 2019-10-02)
The need for improved aquaculture productivity has led to widespread pressure to introduce the Genetically Improved Farmed Tilapia (GIFT) strains of Nile tilapia (Oreochromis niloticus) into Africa. However, the physical and regulatory infrastructures for preventing the escape of farmed stocks into wild populations and ecosystems are generally lacking. This study characterized the genetic background of O. niloticus being farmed in Ghana and assessed the genetic effects of aquaculture on wild populations. We characterized O. niloticus collected in 2017 using mitochondrial and microsatellite DNA markers from 140 farmed individuals sampled from five major aquaculture facilities on the Volta Lake, and from 72 individuals sampled from the wild in the Lower Volta River downstream of the lake and the Black Volta tributary upstream of the lake. Our results revealed that two farms were culturing non-native O. niloticus stocks, which were distinct from the native Akosombo strain. The non-native tilapia stocks were identical to several GIFT strains, some of which showed introgression of mitochondrial DNA from non-native Oreochromis mossambicus. We also found that the non-native cultured tilapias have escaped into the wild and interbred with local populations, and also observed potentially admixed individuals on some farms. Our results highlight aquaculture as a vector in the spread of invasive non-native species and strains, and underscore the importance of genetic baseline studies to guide conservation planning for wild populations.
Are Road Crossings Fragmenting Populations of Clinch Dace?
Bourquin, Rebecca M.; Orth, Donald J.; Hallerman, Eric M.; Stauffer, Dean F. (Humboldt Field Research Institute, 2020-11-16)
Chrosomus sp. cf. saylori (Clinch Dace) is a newly recognized species of minnow with a restricted distribution in southwestern Virginia. We analyzed genetic variation and abundance at paired sites above and below road crossings. Road crossings did not have a strong effect on presence, abundance, or genetic differentiation of Clinch Dace. Of all sites where Clinch Dace were found, only 1 perched culvert presented a barrier to upstream migration; however, no genetic differentiation was found between collections above and below that or any other culvert. Distribution and abundance of Clinch Dace populations were not influenced by habitat variables measured at the site level. Low abundance in small headwaters, nest association, and high mobility appear to be characteristics of this species of Chrosomus.
Aspects of Reproduction and Cub Survival in a Hunted Population of Virginia Black Bears
Echols, Kim Needham (Virginia Tech, 2000-06-09)
We measured black bear (Ursus americanus) reproduction and cub survival during 1994 - 1998, and 1995 - 1999, respectively, in the George Washington and Jefferson National Forests in Virginia to determine age-specific and overall cub production and cub survival. We observed females in estrus between 6 June and 22 August; the mean date of estrus was 17 July. Ages of primiparity ranged between 3 and 5 years with an average of 3.36 years (n=11, SE=0.15). Average litter size for 1995 - 1998 was 2.32 cubs/litter (SE=0.11, n=53) and 85.7% of available females ≥ age 4 (those not accompanied by cubs) reproduced in a given den season. We monitored 98 (48M:50F) black bear cubs equipped with expandable radio-collars (Higgins 1997) or radio transmitters implanted subcutaneously between 1995 and 1999 to estimate cub survival. Kaplan-Meier staggered entry analysis provided 306-day survival rates for 82 cubs. The survival estimates for males and females were 73% (0.49, 0.96) and 91% (0.80, 1.00), respectively. The overall 306-day survival rate for all cubs was 81% (0.67,0.94) using Kaplan-Meier and 76% (0.63, 0.92) using Heisey-Fuller (Mayfield) methods. We also evaluated the utility of radio transmitters implanted subcutaneously in 42 (21M:21F) wild black bear (Ursus americanus) cubs from 2 study areas in Virginia between 1996 and 1999 to monitor first year cub survival. More than 64% (27 of 42) of the implants fell out prematurely (2-198 days), and 16.6% (7 of 42) failed for unknown reasons. Less than 5% (2 of 42) of these cubs denned wearing failed implants, and 9.5% (4 of 42) experienced mortality less than 1 month after implant surgery. About 9.5% (4 of 42) of implanted black bear cubs wore working transmitters through to the following den season.
Assessment of morphological and molecular genetic variation of freshwater mussel species belonging to the genera Fusconaia, Pleurobema, and Pleuronaia in the upper Tennessee River basin
Schilling, Daniel Edward (Virginia Tech, 2015-07-07)
Select freshwater mussels in the genera Fusconaia, Pleurobema, and Pleuronaia were collected primarily in the upper Tennessee River basin from 2012 to 2014 for phylogenetic and morphological assessments. Freshwater mussels in these genera are similar in appearance, hence the need for phylogenetic verification and morphological assessment. Phylogenetic analyses of the mitochondrial gene ND1 and the nuclear gene ITS1 revealed three unrecognized, phylogenetically distinct species. These species were separated from their closest congener by 2.85%, 3.17%, and 6.32% based on pairwise genetic distances of ND1. Gaps created from aligning ITS1 sequences were coded as fifth characters, which phylogenetically separated most closely related species. Analyses of ND1 agreed with previous literature on the phylogenetic distinctiveness of Pleuronaia species, with the exception of the DNA sequences of P. gibberum, which grouped outside this genus based on the analyses conducted in this study. Morphological variation was recorded for eight of the species to include quantitative and qualitative characters as well as geometric morphometric analyses. Three decision trees were created from quantitative and qualitative characters using classification and regression tree analyses. The best-performing tree used quantitative and qualitative characters describing shell-only scenarios and obtained 80.6% correct classification on terminal nodes. Canonical variates analysis on geometric morphometric shell data revealed large morphological overlap between species. Goodall's F-tests between pairs of species revealed significant differences (a=0.05) between all but one species pairs; however, examination of landmarks on shells concluded large overlap of landmarks between species pairs. Lack of morphologically distinct characters to readily identify these phylogenetically distinct species indicates large morphological overlap among these species. Biologists need to be cognizant that morphologically cryptic species may exist in systems often explored. Three dichotomous keys were created from classification trees to identify select individuals in the genera Fusconaia, Pleurobema, and Pleuronaia; two of these keys, one for shells and one for live mussels were tested by participants with varying mussel identification skills to represent novices and experts. Both keys used continuous (quantitative) and categorical variables to guide participants to identifications. Novices, who had no prior mussel identification experience, correctly identified mussels with a 50% accuracy using the shell key and with a 51% accuracy using the live key. Experts, who had at least three years of experience identifying mussels, correctly identified mussels with a 58% accuracy using the shell key and with a 68% accuracy using the live key; however one expert noted that they did not use the live key to correctly identify one mussel. Morphological overlap of variables between mussels likely resulted in failure to consistently identify mussels correctly. Important management decisions and project implementations require accurate assessment of species' localities and populations. Incorrect species identification could hinder species' recovery efforts or prevent projects that otherwise could have continued if species are misidentified. If a mussel collection is thought to be a new record or could affect a project, I recommend that molecular genetic identifications be used to verify the species identity.
Assessment of the performance of stocked northern and Florida largemouth bass and their progeny in Briery Creek Lake, Virginia
Hoover, Randall S. (Virginia Tech, 1992-02-05)
This study examined the suitability of Florida largemouth bass (Micropterus salmoides floridanus) for introduction into Virginia and other mid-latitude waters by comparing the performance of northern (M. s. salmoides), Florida, and hybrid largemouth bass in a 342 ha south-central Virginia reservoir, Briery Creek Lake (BcL). Fingerling northern and Florida largemouth bass were stocked into Briery Creek Lake in 1986, following impoundment, and in 1987. Largemouth bass were collected for genotypic and performance analyses in the autumn and spring beginning in 1989 and ending spring 1991. Electrophoretic analyses demonstrated that hybrid largemouth bass (F1 and Fx) dominated the 1987-1990 cohorts and indicated that one or both founding stocks were genetically impure. Comparisons of electroshock catch composition showed no survival advantage for Florida largemouth bass (FLMB) age-1 and older and no differential vulnerability to angling among the four presumptive genotypes of largemouth bass in Briery Creek Lake. Age-O FLMB proportions declined over both winters (1989-1990 and 1990-1991) indicating relatively high first-mortality in the thermal regime of Briery Creek Lake (3,875 annual mean of heating degree days). Statistical comparisons of growth revealed no consistent differences among the respective bass genotypes, although survival and growth tended to be slightly higher for PI hybrid bass. The average total length of largemouth bass in BCL was below the state's average by age three. Total lengths of age-O FI and northern largemouth bass (NLMB) were higher than FLMB and Fx bass in October, perhaps as a result of earlier spawning among NLMB and between the subspecies. Relative weights of largemouth bass in BCL were generally below 95; and few significant differences in (Wr) were observed among the presumptive largemouth bass genotypes. The suboptimal condition (Wr) of largemouth bass in BCL coupled with the decline in growth and condition of bass with increasing age suggested inadequate prey abundance in Briery Creek Lake. Overall, Florida subspecific alleles did not increase in BCL over time, but the population genetic composition shifted toward an Fx mixture in the 1990 year class; future generations of largemouth bass should be dominated by Fx individuals. Results of this study did not demonstrate substantial performance differences among northern and Florida largemouth bass, and their hybrids, except for poorer first-year survival of the Florida subspecies. Therefore, this study provides no support for the continued introduction of Florida largemouth bass in Virginia or other mid-latitude regions.
An Assessment of the Relationship among Oxidative Stress, Adaptive Immunity and Genetic Variations in the Chicken, Gallus gallus
Deng, Hui (Virginia Tech, 2010-09-01)
Oxidative stress (OS) has been associated with aging and age-related diseases in humans, as well as with the decline in economic trait performance in poultry and other domesticated animals. However, the potential effects of OS on the poultry immune system are not well understood. In addition, the impact of bird genetic variation on redox balance remains to be elucidated. Thus, the central hypothesis of this dissertation is: The bird's adaptive immunocompetence is impacted by their OS level, which is not only influenced by environmental factors, but also related to genetic phenotype of either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA). In the first phase of this study, White Leghorn chickens were provided ethanol at different concentrations in drinking water to induce OS. Biomarkers including malondialdehyde (MDA), glutathione (GSH), and plasma uric acid (PUA) were measured to assess OS before and after ethanol treatment. The adaptive immune response during an OS event was measured by plasma IgG and IgM levels, major lymphoid organ weights, CD4+/CD8+ cell ratio, and histopathological analysis of the immune organs. Results showed that when OS was induced by 10% ethanol, chicken adaptive immune responses decreased; however, when birds were exposed to 2% ethanol, there was an enhancement in antioxidant defense and immune response; These results would suggest a negative correlation between OS level and chicken adaptive immune response. In the second phase of the study, subsets of chickens were selected based on their high (H)- or low (L)-OS to assess for variations in their genetic phenotypes. Using MDA levels, 36 chickens were chosen to scan a 2734-bp region of mtDNA, but no definitive SNP was detected. In another experiment, 40 chickens were conversely selected according to three biomarkers for OS. Although no variation was found at eight SNP loci tested across the mitochondrial genome, mtDNA damage measured by 8-hydroxy-2′-deoxy-guanosine was shown to increase with time, and at higher levels in the high OS birds (p < 0.05). Thses results suggest that long-term high OS levels in chickens may increase the somatic mutation of their mtDNA. In the final phase of this dissertation, the effect of nDNA on OS, measured via a genome-wide association study was performed with 18 H and 18 L chickens using the latest chicken 60k SNP microarray for genotyping. Among 56,483 SNPs successfully genotyped, 13 SNPs across five independent loci were associated with OS at significance level of p ≤ 0.001, and another 144 SNPs were also associated with OS (p ≤ 0.01). These results indicate new loci and related genes for their genetic influence upon redox balance. In general, experiments carried out on White Leghorn chickens here have shown that adaptive immune response is tightly related to changes of OS. Further, genetic variance in nDNA is associated with the risk of high OS or the ability to better resist it.
Bayesian hierarchical approaches to analyze spatiotemporal dynamics of fish populations
Bi, Rujia (Virginia Tech, 2020-09-03)
The study of spatiotemporal dynamics of fish populations is important for both stock assessment and fishery management. I explored the impacts of environmental and anthropogenic factors on spatiotemporal patterns of fish populations, and contributed to stock assessment and management by incorporating the inherent spatial structure. Hierarchical models were developed to specify spatial and temporal variations, and Bayesian methods were adopted to fit the models. Yellow perch (Perca flavescens) is one of the most important commercial and recreational fisheries in Lake Erie, which is currently managed using four management units (MUs), with each assessed by a spatially-independent stock-specific assessment model. The current spatially-independent stock-specific assessment assumes that movement of yellow perch among MUs in Lake Erie is statistically negligible and biologically insignificant. I investigated whether the assumption is violated and the effect this assumption has on assessment. I first explored the spatiotemporal patterns of yellow perch abundance in Lake Erie based on data from a 27-year gillnet survey, and analyzed the impacts of environmental factors on spatiotemporal dynamics of the population. I found that yellow perch relative biomass index displayed clear temporal variation and spatial heterogeneity, however the two middle MUs displayed spatial similarities. I then developed a state-space model based on a 7-year tag-recovery data to explore movements of yellow perch among MUs, and performed a simulation analysis to evaluate the impacts of sample size on movement estimates. The results suggested substantial movement between the two stocks in the central basin, and the accuracy and precision of movement estimates increased with increasing sample size. These results demonstrate that the assumption on movements among MUs is violated, and it is necessary to incorporate regional connectivity into stock assessment. I thus developed a tag-integrated multi-region model to incorporate movements into a spatial stock assessment by integrating the tag-recovery data with 45-years of fisheries data. I then compared population projections such as recruitment and abundance derived from the tag-integrated multi-region model and the current spatial-independent stock-specific assessment model to detect the influence of hypotheses on with/without movements among MUs. Differences between the population projections from the two models suggested that the integration of regional stock dynamics has significant influence on stock estimates. American Shad (Alosa sapidissima), Hickory Shad (A. mediocris) and river herrings, including Alewife (A. pseudoharengus) and Blueback Herring (A. aestivalis), are anadromous pelagic fishes that spend most of the annual cycle at sea and enter coastal rivers in spring to spawn. Alosa fisheries were once one of the most valuable along the Atlantic coast, but have declined in recent decades due to pollution, overfishing and dam construction. Management actions have been implemented to restore the populations, and stocks in different river systems have displayed different recovery trends. I developed a Bayesian hierarchical spatiotemporal model to identify the population trends of these species among rivers in the Chesapeake Bay basin and to identify environmental and anthropogenic factors influencing their distribution and abundance. The results demonstrated river-specific heterogeneity of the spatiotemporal dynamics of these species and indicated the river-specific impacts of multiple factors including water temperature, river flow, chlorophyll a concentration and total phosphorus concentration on their population dynamics. Given the importance of these two case studies, analyses to diagnose the factors influencing population dynamics and to develop models to consider spatial complexity are highly valuable to practical fisheries management. Models incorporating spatiotemporal variation describe population dynamics more accurately, improve the accuracy of stock assessments, and would provide better recommendations for management purposes.
Biology, Captive Propagation, and Feasibility of Pearl Culture in the Pink Heelsplitter (Potamilus Alatus) (Say, 1817) (Bivalvia: Unionidae)
Hua, Dan (Virginia Tech, 2005-08-15)
Pink heelsplitter (Potamilus alatus) mussels collected from Kentucky Lake, TN were held at two bottom locations (0.6 m, 2.5 m) and suspended in pocket nets (at depth about 1.0 - 1.5 m) in a pond at the Freshwater Mollusk Conservation Center (FMCC), Virginia Tech, for 1 yr. Survival of mussels after 1 yr was significantly different, with poorest survival (30 %) in the bottom of the deep end; and no difference between the shallow end (83.3 %) and the suspended pocket nets (63.3 %). Survival of mussels was inversely related to water temperature (r = - 0.72); lowest monthly survival occurred in summer, resulting in a significant difference among the three locations with a similar trend after 1 yr. The glycogen reserves of mussels in captivity for 1 yr differed by pond location, higher in mussels at the shallow end than those in suspended pocket nets and at the deep end. Therefore, the shallow end of pond was more suitable for holding mussels long-term, while the suspended pocket nets are an alternative site for holding captive mussels. Additionally, dissolved oxygen was very low at the deep end (1.9 mg/L) in summer, while it was adequate (range from 5.7 - 6.4 mg/L) at the location of suspended pocket nets, and 5.0 mg/L at the shallow end (24.7 °C). Data for 40 specimens indicated that sexual dimorphism in valve shape occurred in P. alatus. Female mussels had a significantly (p < 0.0001) greater ratio of height (H) to length (L) (52.3 %) and width (W) to length (31.8 %) than males (H/L: 48.4 %; W/L: 28.8 %), respectively. The posterior ends were somewhat round to oval in males and bluntly squared or truncated in females. Female mussels were more inflated than males. These morphological differences can be used to distinguish females from males during field collections. The red drum (Sciaenops ocellatus) was identified as a new fish host for P. alatus, as 48 active juveniles were transformed by this species, which is not a natural host. Four glochidia were observed on the fins versus 2,307 on the gills of five red drum. Freshwater drum also was verified as a suitable host fish, but black crappie (Pomoxis nigromaculatus), banded sculpin (Cottus carolinae), yellow perch (Perca flavescens) and nile tilapia (Oreochromis nilotica) did not support transformation of glochidia to juveniles. Survival and growth of propagated juveniles of P. alatus were assessed regarding the effects of algal diets (Nannochloropsis oculata and Neochloris oleoabundans) and substrate type (fine sediment and sand). Overall, survival of juveniles after 17 d ranged from 23.8 to 66.8 %, with mean of 48.5 %; however, survival dramatically declined during the next 2 wk period to only 5.8 % (range of 1.8 to 7.8 %). Survival rate of juveniles was significantly different (p = 0.027) between substrates, but not in diets (p = 0.520), with the lowest survival rate of 23.8 % in sand substrate and fed N. oculata. Juveniles grew faster in fine sediment (23.0 % increase in shell length) than in sand substrates (10.5 % increase) (p = 0.002). Moreover, mean growth rate of juveniles was 4.9 μm/d during the first 2 wk, but decreased to 0.2 μm/d in the remaining 2 wk. Therefore, fine sediments seemed more appropriate for juvenile culture compared to sands. Both species of algae, N. oculata and N. oleoabundans, can be used to feed juveniles in the laboratory. Adult pink heelsplitters were used to study feasibility of pearl production by using two surgical implants (non-nucleated implant = NNI, and image pearl implant = IPI) in two ponds of different nutrient levels (FMCC pond and Duck pond). NNI and IPI pearls with purple or purplish luster were successfully produced in P. alatus. Pearl weight was not significantly different (p = 0.562) between two ponds. No differences in monthly survival rates of mussels were observed in either pond (p = 0.051), or among mussels with surgical implants and the no-surgery control mussels (p = 0.881). Consequently, P. alatus can be considered a potential species for producing purple pearls in pearl culture. Additionally, mussels in the Duck pond had higher (p < 0.0001) glycogen levels, similar to those in wild collected mussels, than those in the FMCC pond, indicating that this pond environment may be more suited for holding implanted mussels in captivity.
Biosecurity in the Recirculation Sector of Finfish Aquaculture in the United States and Canada
Delabbio, Juliette Lee (Virginia Tech, 2003-04-21)
In aquaculture, biosecurity consists of policies, procedures and measures used to prevent or control the spread of fish disease. The focus of this research was the practice of biosecurity in the recirculation sector of finfish aquaculture in the United States and Canada. Specifically, this research: 1) identified and characterized finfish recirculation facilities in the United States and Canada; 2) assessed biosecurity utilization in these facilities; 3) examined the relationship between biosecurity utilization and fish culture variables; 4) examined the relationship between biosecurity utilization and socio-demographics of personnel operating these facilities; 5) described the attitudes, perceptions and beliefs about fish disease and biosecurity utilization of personnel, and 6) described the lived-experience of biosecurity practice of workers at these facilities. This research was comprised of two separate components using different methodologies. The first component was a self-administered, mail-back questionnaire sent to the managers of 152 finfish recirculation facilities in the United States and Canada in fall of 2001. The second component was a series of in-depth interviews conducted with 31 workers at 12 salmonid recirculation facilities in spring of 2002. Grounded theory methodology was used for the interview process and subsequent data analysis for the second component. An 86% response rate was achieved in the mail survey. Aquaculture activities using recirculation technologies were quite varied in purpose of operation, size of production, and life stages held. Four groups of fishes dominated the recirculation sector and constituted the primary production of over 45% of this sector of aquaculture. This sector was heavily reliant on ground water resources. Forty-one percent of finfish recirculation facilities did not have a secondary source of water supply. Biosecurity utilization is not homogenous within the recirculation sector. Frequency of biosecurity utilization was related to primary water source, type of fish grown, purpose of the operation and country of operation. Biosecurity was an important concern of facility operators, although among facility operators there were differences in perception of disease risk and benefits of biosecurity utilization. Analysis of results of this study resulted in formulation of the Practice of Biosecurity Theory (PBT). The theory describes a three-phase process in the practice of biosecurity: (1) orientation, when workers begin their initiation into the practice of biosecurity; (2) routine, when practice of biosecurity becomes a habitual behavior; and (3) thoughtful approach, where knowledge of fish health needs and biosecurity practices are integrated into a repertoire of biosecurity strategies that are situation- and site-specific. The practice of biosecurity was affected by three environmental conditions; personal biography, management's role, and peer pressure. This research gives educators, extension agents, researchers and government policy-makers a quantitative description of finfish recirculation aquaculture in the United States and Canada. It also provides baseline information on biosecurity utilization in recirculation aquaculture. This research provides insight into the human dimensions aspect of the practice of biosecurity and, therefore, may have application to other areas of agri-business.
Book Review: Aquaculture and Fisheries Biotechnology: Genetic Approaches
Hallerman, Eric M. (Commercial Fish and Shellfish Technologies Program, Virginia Tech, 2005-06-01)
Brook Trout Population Genetic Tools for Natural Barriers in Fragmented Subwatersheds
Timm, Anne Louise (Virginia Tech, 2010-09-08)
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.
Characteristics of the Recirculation Sector of Finfish Aquaculture in the United States and Canada
Delabbio, Juliette L.; Murphy, Brian R.; Johnson, G. R.; Hallerman, Eric M. (Commercial Fish and Shellfish Technologies Program, Virginia Tech, 2003-06-01)
In the autumn of 2001, a survey was conducted to examine basic farm production and human resource characteristics of recirculation facilities in the United States and Canada currently growing finfish. An 86% response rate was achieved. The survey data indicate that this sector of aquaculture is quite heterogeneous. The number and pounds of fish produced is quite variable, with presence of small-, medium- and large sized farms in this sector. Recirculation technologies are employed to culture a wide variety of both warmwater and coldwater fishes in both saltwater and freshwater situations. The four fishes most commonly grown in recirculation units in the United States and Canada are Atlantic salmon smolts, tilapia, hybrid striped bass and ornamental fishes. A high proportion of facilities using recirculation technologies use pumped groundwater as a primary water source. Over 40% of facilities represented in the survey rely on a single water source to sustain their operation and have no secondary water source as backup. Management personnel of recirculation facilities are highly educated; more than 74% of respondents reported holding at least an undergraduate degree. The majority of personnel managing recirculation facilities are middle-aged individuals who have over 10 years of related work experience. The findings of this study represent the first empirical description of the recirculation sector of finfish aquaculture in the United States and Canada.
Characterization of the molecular genetic variation in wild and farmed Nile tilapia Oreochromis niloticus in Ghana for conservation and aquaculture development
Anane-Taabeah, Gifty (Virginia Tech, 2019-02-01)
The Nile tilapia Oreochromis niloticus is native to Africa and middle East, and is an important source of nutrition for many in sub-Saharan Africa. Understanding the genetic diversity within and differentiation among wild populations can help identify O. niloticus populations that are imperiled and require directed management, especially because of increasing threats to the species' long-term persistence in the wild, including habitat destruction, overfishing, climate change, and hybridization with farmed populations. Knowledge of the genetic variation among wild populations also can contribute to foundation and selection of genetically diverse populations for aquaculture. I assessed the genetic variation among tilapia populations using fin-clips collected between December 2014 and July 2017 from 14 farmed sources, mostly originating from cage farms on the Volta Lake, and 13 wild sources from nine river basins in Ghana. I also conducted a laboratory growth experiment in Ghana with two wild populations to evaluate the tolerance of different genotypes to high temperatures, to inform their development for aquaculture in West Africa. I found that pure O. niloticus populations persist in the wild but some have been extensively introgressed with the closely related species, O. aureus, which has not previously been documented in Ghana. Additionally, some wild populations appear to have recently declined significantly in numbers, likely due to overfishing and habitat modification, the latter primarily as a result of illegal alluvial mining ongoing in Ghana. Analysis of the farmed populations revealed that at least two farms were growing the unapproved genetically improved farmed tilapia (GIFT) and related strains, and that escaped individuals are admixed into some wild populations. The results of my laboratory experiment showed that O. niloticus populations occurring in northern Ghana already may be adapted to warmer temperatures and could be developed and used purposefully in aquaculture, taking advantage of their adaptation. To protect remnant pure O. niloticus populations in the wild, timely conservation decisions should be made and implemented. Protecting wild O. niloticus populations also would ensure that pure germplasms are available to develop aquaculture stocks from native populations.
A Comparative Analysis of Three Biofilter Types Treating Wastewater Produced in Recirculating Aquaculture Systems
Hall, Antar Gamble (Virginia Tech, 1999-12-01)
Nine recirculating systems at the Virginia Tech Aquaculture Center were placed on line and stocked with yellow perch, Perca flavescens, fingerlings. Fish were stocked at a density of approximately 455 fish m³. Biofilter types were the only factor differing among system designs and were an upflow pulsed bed bead filter, packed tower trickling filter and a rotating biological contactor (RBC). After stocking, systems were allowed to acclimate using ammonia excreted by the yellow perch. Following acclimation, a comparative analysis on biofilter performance began. To evaluate filter performance, water quality parameters tested were temperature (°C), pH, dissolved oxygen (DO), total ammonia-nitrogen (TAN), nitrite-nitrogen (NO₂⁻-N), nitrate-nitrogen (NO₃⁻-N), alkalinity (as CaCO₃), water hardness (as CaCO₃), carbonaceous biochemical oxygen demand (cBOD₃), dissolved organic carbon (DOC), and total suspended solids (TSS). Basic water quality analysis encompassed samples drawn at 8 AM. TAN mass removal analysis encompassed water quality samples drawn at 8 AM and over 24 hours. Higher TAN mass removal rates were achieved in trickling and RBC filters than in bead filters for 8 AM (0.037, 0.14, and 0.004 g/m²/d, respectively) and diurnal sample periods. Analysis of areas under mass removal curves depicted RBC filters as surface area limited. Trickling filters proved most effective at carbon dioxide stripping and pH maintenance and also effectively removed TSS from the culture water. The study did not show filter type as having a significant effect on median organic water quality parameter values.
Comparative Ecology of Juvenile Striped Bass and Juvenile Hybrid Striped Bass in Claytor Lake, Virginia
Rash, Jacob Michael (Virginia Tech, 2003-12-08)
Since the introduction of hybrid striped bass M. chrysops x M. saxatilis to Claytor Lake, Virginia in 1993, relative abundance of striped bass Morone saxatilis has dropped disproportionately to stocking density. Potentially deleterious interactions between the two fishes that may limit recruitment to age 1 were considered in terms of trophic relationships, physiological indices of health, overwinter survival, and post-stocking predation. Both fishes preferred habitat types characterized by structure-free sand or gravel substrates, but striped bass and hybrid striped bass did not exhibit significant diet overlap during the growing season. At a total length of approximately 120 mm, the juvenile moronids shifted from a mixed diet of zooplankton and invertebrates to a diet comprised primarily of age-0 fishes. However, after becoming piscivorous striped bass preyed primarily upon age-0 alewife Alosa pseudoharengus, while hybrid striped bass consumed age-0 sunfishes. Striped bass achieved mean total lengths of 229 and 173 mm by the end of the growing season in 2001 and 2002, respectively. Stocked into the reservoir three months later than striped bass, mean hybrid striped bass total lengths reached 133 mm at the end of the 2002 growing season. Condition factor, relative weight, and lipid index values were low, but nearly equivalent for both striped bass and hybrid striped bass throughout this study. Overwinter starvation of smaller (< 150 mm total length) striped bass was observed for the 2001-2002 sampling season. Predation upon stocked fingerlings was not considered significant in limiting juvenile survival; only three fingerling moronids were found in the examination of stomach contents of 200 potential predators captured near stocking sites. It does not appear that resource competition with hybrid striped bass during the growing season resulted in increased overwinter mortality of juvenile striped bass. Delayed stocking of hybrid striped bass lessens the potential for trophic competition between striped bass and hybrid striped bass at this early life-stage.
Comparative Growth of All-Female Versus Mixed Sex Yellow Perch (Perca flavescens) in Recirculating Aquaculture Systems
Schmitz, Mark Harvey (Virginia Tech, 1999-05-20)
Nine, production-scale, recirculating aquaculture systems were utilized to compare the growth parameters between all-female and mixed sex yellow perch stocks. Each system was stocked with 455 fish m⁻³ and contained one of three different biofilter types: a rotating biological contactor, a trickling filter or a bead filter. The all-female fingerlings (S1) used were originally derived from Lake Mendota, Wisconsin. The mixed-sex fingerlings (S2) used were originally derived from Lake Erie. Temperature and photoperiod (23°C, 16H-L) were maintained at levels for optimal growth. Absolute growth rates ranged from 0.27-0.48 g/day. Mean final density within treatments was 42.8 kg/m³ and ranged from 37.2-50.2 kg/m³. The main effect of stock did not have a significant effect on growth (p > .1). All-female treatments exhibited more uniform growth. The main effect of filter type did have a significant effect on fish growth (p < .01), with fish in tanks containing trickling filters exhibiting significantly higher growth. Total feed conversion averaged 1.61 across all treatments and ranged from 1.38-1.78. S1 treatments consumed a significantly higher percent body weight per day than S2 treatments (p < .05). Analysis of PIT tagged individuals revealed that the mean relative growth rate was significantly higher in S2 individuals (513.9%) compared to S1 individuals (315.3%: p < .01). S2 females (597.8%) grew 1.9 times faster than S1 females (315.3%: p < .01). Within S2 individuals, females (597.8%) grew 1.5 times faster than males (395.2%: p < .05). For all individuals, 33.6% of the variation in final weight was explained by the variation in initial weight. Differences in the geographic strain or culture history of these stocks may have had a larger overall effect on growth than sexual classification (all- female or mixed sex). Dress percentage of skin-on butterfly fillets was examined in 20 individuals per stock and in six groups of 20 individuals per stock. Within S2 individuals, 73.7% were female. Mean fillet yield was significantly greater in S1 individuals (47.6%) compared to S2 individuals (43.0%: p < .01). Mean GSI in S1 individuals (1.01%) was significantly higher than S2 individuals (0.54%: p < .05). Within S2 individuals, mean GSI was significantly higher in females (0.70%) when compared to males (0.08%: p < .05). Fillet yield was significantly greater in S1 groups (47.2%) compared to S2 groups (44.9%: p < .01). Within each stock fillet yield increased with size. The difference in fillet yield demonstrated between these stocks may be a result of differences in strain of origin. The identification of superior yellow perch strains or strain crosses with regard to growth rate and fillet percentage is of considerable importance to the industry.
A Comparison of Systematic Quadrat and Capture-Mark-Recapture Sampling Designs for Assessing Freshwater Mussel Populations
Carey, Caitlin; Jones, Jess W.; Butler, Robert S.; Kelly, Marcella J.; Hallerman, Eric M. (MDPI, 2019-08-07)
Our study objective was to compare the relative effectiveness and efficiency of quadrat and capture-mark-recapture (CMR) sampling designs for monitoring mussels. We collected data on a recently reintroduced population of federally endangered Epioblasma capsaeformis and two nonlisted, naturally occurring species—Actinonaias pectorosa and Medionidus conradicus—in the Upper Clinch River, Virginia, over two years using systematic quadrat and CMR sampling. Both sampling approaches produced similar estimates of abundance; however, precision of estimates varied between approaches, years, and among species, and further, quadrat sampling efficiency of mussels detectable on the substrate surface varied among species. CMR modeling revealed that capture probabilities for all three study species varied by time and were positively associated with shell length, that E. capsaeformis detection was influenced by sex, and that year-to-year apparent survival was high (>96%) for reintroduced E. capsaeformis. We recommend that monitoring projects use systematic quadrat sampling when the objective is to estimate and detect trends in abundance for species of moderate to high densities (>0.2/m²), whereas a CMR component should be incorporated when objectives include assessing reintroduced populations, obtaining reliable estimates of survival and recruitment, or producing unbiased population estimates for species of low to moderate densities (≤0.2/m²).

Browsing by Author "Hallerman, Eric M."

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