207 research outputs found
Towards production of genome‐edited aquaculture species
No full textForeign Agricultural Service of the U.S. Department of Agriculture; U.S. Department of AgriculturePublished versionThe work of author Eric M. Hallerman in this area is supported by a grant from the Foreign Agricultural Service of the U.S. Department of Agriculture. The work of author Diane Wray-Cahe is supported by the U.S. Department of Agriculture.Public domain – authored by a U.S. government employe
Fig. 2. Unrooted haplotype network for mitochondrial D in Genetic structuring of Salminus hilarii Valenciennes, 1850 (Teleostei: Characiformes) in the rio Paraná basin as revealed by microsatellite and mitochondrial DNA markers
No full textFig. 2. Unrooted haplotype network for mitochondrial D-loop sequences of Salminus hilarii generated by NETWORK 4.1.1.2 based on the median joining algorithm. Sizes of the circled areas are proportional to the frequencies of the haplotypes at issue. Blue circles: rio Grande -Igarapava (GRI); Green circles: rio Grande -Lavras (GRL); Yellow circles: upper rio Tietê (UTR), and Red circles: rio Parapanema (PAR).Published as part of Silva, Juliana Viana da, Hallerman, Eric M., Orfão, Laura Helena & Hilsdorf, Alexandre Wagner Silva, 2015, Genetic structuring of Salminus hilarii Valenciennes, 1850 (Teleostei: Characiformes) in the rio Paraná basin as revealed by microsatellite and mitochondrial DNA markers, pp. 547-556 in Neotropical Ichthyology 13 (3) on page 551, DOI: 10.1590/1982-0224-20150015, http://zenodo.org/record/463937
Recommended from our members
Population Genetics: Principles and Applications for Fisheries Scientists
No full textAult reviews Population Genetics: Principles and Applications for Fisheries Scientists edited by Eric M. Hallerman
Use of Molecular Tools for Research and Improvement of Aquaculture Stocks
No full textAbstract Development of molecular genetic markers provides aquaculture with tools for a number of research and practical applications. Genetic marking of experimental groups allows their evaluation in the same rearing units, increasing statistical power within limited research infrastructure. Parentage can be inferred for individuals in mixed-progeny groups, quantifying the contributions of individual parents and supporting the estimation of sire and dam effects. Building upon parentage assignment, walk-back selection entails retention of the best members of each family as broodstock for the next generation. Molecular markers can be used to detect the segregation of quantitative trait loci (QTL) and knowledge of such linkages can be used for marker-assisted selection. Gene expression profiling can identify genes affecting traits of interest, providing candidates for QTL or functional analysis. Purposeful genetic marking can be used to identify proprietary stocks, marketed products, and fish out-planted or escaping into natural ecosystems. Although each application has been demonstrated, genetic markers are not routinely used in commercial aquaculture. The limited practical application can be explained by the limited development of broodstocks for most aquaculture species, the small size and limited scope of most aquaculture operations, and the costs of genetic screening. Introduction Although quantitative and molecular genetics developed independently, over the past 20 years their interface has become an area of rapid advancement. Molecular genetic markers have a wide range of applications in aquaculture research and for improvement of aquaculture stocks (Hallerman and Beckmann
Genetics and Biotechnology—The Section Editor-in-Chief’s View
No full textGenetics and biotechnology make increasingly important contributions to fishery science, fishery management, aquaculture, and related fields [...
Comparisons of tilapia seed production under various broodstock densities and fry stocking densities
No full textFour methods of seed (eggs, sac-fry, and fry) production for Rocky Mt. White hybrid® tilapia, (0. niloticus x O. aureus), were compared under green water conditions over a six month period in an environmentally controlled greenhouse at the Virginia Polytechnic Institute and State University's Aquaculture Research Laboratory. Twelve 3 m2 rectangular tanks were stocked with brood stock (mean wt. 680 g), at a sex ratio of 3 females to 1 male. Nine tanks were stocked at one of three densities (1, 2, and 4 females m-2), and seed was collected from females' mouths weekly. Three additional tanks were stocked at a density of 2 females m-2, and fry were collected from the edges of the tanks when seen.
Seed production was among the highest seen for related studies. Average number of viable fry produced at I females m-2, 1660 fry female- I month-I, was significantly higher than the combined average production of densities 2 females m-2 (629 fry female- I month-I) and 4 females m-2 (695 fry female-1 month- 1) (p0.05), the highest density consistently produced more fry meter-2. No significant difference was observed in viable fry production between the two seed collection methods (Clutch removal- 629 fry female-1 month-I; Natural mouth-brooding- 520 fry female-1 month-I) (p>0.05).
The effects of stocking density on growth and survival were evaluated by stocking 14-16 day old artificially incubated fry (25.5 ± .32 mg, 12.1 ± .04 mm), into 150 liter troughs at three densities (3, 6, and 12 fry liter-I) under green water conditions for 30 days. The mean monthly hatchery seed survival was 65.7 ± 2.3%, which varied largely depending on initial seed developmental stage. Significant differences were observed between mean weight, length, survival, and feed conversion ratios among the various fry stocking densities (p<O.05). The greatest growth was at a density of 3 fry liter 1 , while survival was not affected until a density of 12 fry liter-I.
These results that to maximize fry production and reduce labor, a density of 4 females m-2 or higher be used under the natural mouth brooding seed collection method. They also suggest a fry density between 6 to 12 fry liter-1 should be used with periodic grading or sex reversal to reduce cannibalism and increase growth.Master of Scienc
Population Fragmentation and Genetic Diversity of Chrosomus sp. cf. saylori (Clinch Dace)
No full textClinch Dace (Chrosomus sp. cf. saylori) is a newly recognized species of minnow with a restricted distribution in southwestern Virginia. Field sampling and genetic analysis support the hypothesis that Clinch Dace populations are small and fragmented. Analysis of neutral genetic markers shows that most Clinch Dace populations have undergone past bottleneck events and are being operated upon by random genetic drift. Bayesian cluster analysis showed that three out of the seven populations found in 2017 are distinct, while the other four show signs of more recent admixture. However, Fst values among streams were high and analysis of molecular variance indicated differentiation among populations in all streams. These findings support the view that these populations are genetically isolated. Effective populations sizes were low at most sites, enhancing the likelihood of loss of alleles to genetic drift. Low M-ratios, non-zero Fis values, and high degrees of relatedness among individuals indicate that some inbreeding is taking place. Habitat analysis did not identify variables affecting distribution or abundance of Clinch Dace populations. As the collection sites were targeted near known Clinch Dace occupied sites, it is likely that habitat variables known to impact Clinch Dace, such as conductivity, were within the species' range of tolerance. Results showed that Clinch Dace seem particularly resilient to sedimentation, corroborating earlier work showing a negative relationship between Clinch Dace abundance to sediment size. That is, small sediment size does not seem to have a negative impact on Clinch Dace abundance. Of all sites where Clinch Dace were found, only one culvert at one site was clearly perched and may present a barrier to upstream migration, a possibility which is supported by the genetic differentiation found among collections above and below that culvert. While this study demonstrates that selectively neutral genetic differentiation has taken place among Clinch Dace populations, it does address any local adaptation that may be taking place which would render translocations a risk for outbreeding depression. The findings of this study can inform conservation management in identifying possible sources of individuals for translocations among populations or for augmentation following captive breeding.Master of ScienceThe Clinch Dace is a small, threatened minnow in the Clinch River basin that was unknown until 1999. Since then, research has addressed the biology, life history, and distribution of this fish. This study used data from selectively neutral genetic markers to analyze the population structure and degree of differentiation of Clinch Dace populations. My study sites were targeted at road crossings near known Clinch Dace populations to assess the effect of habitat fragmentation on Clinch Dace populations and to maximize the likelihood that I would collect enough genetic material for analysis. Genetic analyses showed that while there is some admixture among certain populations of Clinch Dace, there is differentiation at neutral genetic markers. This differentiation does not necessarily indicate adaptive variation among populations which could result in outbreeding depression should populations be mixed through translocations, but it is reason to proceed with caution. Road crossings were generally not found to be a cause of further population fragmentation in Clinch Dace, as demonstrated by genetic analysis and statistical analysis. Almost all of the occupied road crossing sites in this study were either embedded, free-flowing culverts that were not perched or small bridges, and these were not deemed to be obvious barriers to fish movement. The only exception was Hart Creek 2, where the culvert is slightly perched and Fst is high between populations in the upstream and downstream reaches. The results of this study will help to inform managers as to what conservation actions can be taken to improve population viability. One potential management action from this study could be the retrofitting of culverts that have become perched and are acting as barriers to Clinch Dace movement. Another potential conservation strategy is to translocate individuals from large population to small populations. The study determined: 1) which translocations might be acceptable based on the degree of genetic differentiation among populations, and 2) identified potential donor and receiving streams for translocations
Northeastern Naturalist
No full textHigh-throughput DNA sequencing can generate large genetic datasets in a cost-effective manner. Although the diet of Eptesicus fuscus (Big Brown Bat) has been studied widely in natural and rural systems using visual identification of prey items in feces, our aim was to more completely assess diet using a metabarcoding approach across a wide urban-natural landscape gradient in the mid-Atlantic region. Concordant with our expectations and previous Big Brown Bat diet studies from visual identification, we observed a high abundance of Coleoptera (beetles) relative to other insect orders. Although a possible improvement over visual techniques for studying food habits, we suggest caution in interpreting metabarcoding results in diet studies. We noted observations of environmental or contaminant taxa within these data, and designed a stringent filtering method that we used to eliminate these taxa, but that also removed previously documented prey taxa from our dataset.National Park Service NRPP and WNS Support programs through Southern Appalachian and Chesapeake Bay Cooperative Ecosystem Study Unit grants [P16AC00821, P17AC01616]; Virginia Agricultural Experiment Station through the National Institute for Food and AgriculturePublished versionThis work was supported by the National Park Service NRPP and WNS Support programs through Southern Appalachian and Chesapeake Bay Cooperative Ecosystem Study Unit grants P16AC00821 and P17AC01616 to the Virginia Tech Department of Fish and Wildlife Conservation. Additional in-kind support was provided by the US Geological Survey Cooperative Research Unit program, Marine Corps Base-Quantico Natural Resources Department, Maryland Department of Natural Resources, Virginia Department of Game and Inland Fisheries, and the District of Columbia Department of Energy and Environment. Special thanks to E. Barr, S. Freeze, and L. Rohrbaugh for collecting samples. Fieldwork was performed by T. Calhoun, S. Dermody, R. Lesagonicz, G. Mosley, A. Morrison, M. Sellers, A. Silvis, and H. Taylor. The participation of E. Hallerman was supported in part by the Virginia Agricultural Experiment Station through the National Institute for Food and Agriculture. The findings and conclusions in this article are those of the author(s) and do not necessarily represent the views of the US Fish and Wildlife Service. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the US Government.Public domain – authored by a U.S. government employe
Comparative Growth of All-Female Versus Mixed Sex Yellow Perch (Perca flavescens) in Recirculating Aquaculture Systems
No full textNine, 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.Master of Scienc
Ecology of Mid-Atlantic bats after white-nose syndrome: communities, reproduction, and diet within an urban-to-rural gradient
No full textWhite-nose syndrome (WNS) has reduced the abundance of many bat species within the United States' mid-Atlantic region, including the endangered Indiana (Myotis sodalis), threatened Myotis septentrionalis (northern long-eared bat) and other bats of conservation concern, such as Perimyotis subflavus (tri-colored bat), Myotis leibii (eastern small-footed bat) and Myotis lucifugus (little brown bat). Impacts to Eptesicus fuscus (big brown bat) populations have been negative, positive or neutral. Migratory bat species such as Lasiurus borealis (eastern red bat) are not impacted by WNS. To determine changes within the National Park Service National Capital Region bat communities, I surveyed the area with mist netting and active acoustic sampling (2016–2018) and compared findings to pre-WNS (2003–2004) data. I documented a significant reduction in the numbers and distributions of M. lucifugus and P. subflavus, a decrease in the distribution of M. septentrionalis, and an increase in Eptesicus fuscus. Documented M. septentrionalis reproduction suggests that portions of the National Capital Region may be important bat conservation areas.
To explore the relationship between bat life history and passive acoustic sampling echolocation call data, as well as to review the sampling effort required to detect the presence of extant species, I used mist-netting captures and acoustic call data collected 2015 – 2018 within the District of Columbia, Maryland, Pennsylvania, Virginia, and West Virginia. Based on locally estimated scatterplot smoothing line calculations, I determined that the highest levels of maternity season acoustic activity for Eptesicus fuscus and Lasiurus borealis corresponded primarily to lactation periods. To determine sampling effort, I developed simulations based on species accumulation curves for individual species within different physiographic regions and land-cover types. I determined that the smallest sampling efforts typically corresponded to sampling additional sites versus sampling the same sites with more nights. Detection effort varied greatly by species, physiographic region and land-cover type.
Eptesicus fuscus diet has been well-studied throughout North America with visual identification methods from fecal and stomach content samples. Next-generation sequencing provides large genetic data sets analyses in a cost-effective manner and has been used to identify bat prey items. I collected Eptesicus fuscus fecal samples from mid-Atlantic regions and used next-generation sequencing to identify their prey. I documented high variation between survey areas, but did not note a clear pattern of urbanization or fragmentation impacts upon Insecta diversity. All order-level taxa that I documented had been previously documented in morphological studies; however, I did document new families, genera and species. However, I would suggest caution in using next-generation sequencing technologies as authoritative sources for documenting new diet taxa, as I noted frequent occurrences of confounding environmental DNA within the samples.Doctor of PhilosophyWhite-nose syndrome (WNS) has reduced the abundance of many bat species within the United States' mid-Atlantic region, including the endangered Indiana (Myotis sodalis), threatened Myotis septentrionalis (northern long-eared bat) and other bats of conservation concern, such as the Perimyotis subflavus (tri-colored bat), Myotis leibii (eastern small-footed bat) and Myotis lucifugus (little brown bat). WNS-impacts to Eptesicus fuscus (big brown bat) populations have been negative, positive or neutral. Migratory bat species such as Lasiurus borealis (eastern red bat) are not impacted by WNS. To determine changes within the National Park Service National Capital Region bat communities, I captured bats with mist-netting techniques and recorded bat echolocation calls with active acoustics (20-minute periods; 2016–2018) and compared findings to pre-WNS (2003–2004) data. I documented a significant reduction in the numbers and distributions of M. lucifugus and P. subflavus, a decrease in the distribution of M. septentrionalis, and an increase in Eptesicus fuscus. Documented M. septentrionalis reproduction suggests that portions of the National Capital Region may be important bat conservation areas.
To explore the relationship between bat echolocation calls recorded with passive (over-night) acoustic data and bat reproduction trends, as well as the amount of effort required to document bat species, I sampled 849 sites with passive acoustics and 482 sites with mist-netting during 2016 – 2018 within the District of Columbia, Maryland, Pennsylvania, Virginia, and West Virginia. I determined that the highest levels of acoustic activity for Eptesicus fuscus and Lasiurus borealis (eastern red bat) within the maternity season are associated with the period of highest levels of lactation. To determine sampling effort, I used simulations to detect species in different landscape conditions. I determined that sampling additional sites requires less sampling effort than sampling more nights. The amount of effort required to detect each bat species varied, as did the impact of different landscape conditions.
Eptesicus fuscus diet has been well-studied throughout North America by identifying insect parts in feces and stomach contents. Next-generation sequencing is a process which produced large amounts of genetic data sets in a cost-effective manner, and it can be used to identify prey within bat feces. I collected Eptesicus fuscus fecal samples from mid-Atlantic regions and used next-generation sequencing to identify potential prey. I determined that bat diet varied greatly based on survey area and number of feces analyzed. At the order-level, I did not document new taxa: however, I did document new families, genera and species. However, I would suggest caution in using next-generation sequencing technologies as authoritative sources for documenting new diet taxa, as many taxa apparent within my samples were subsequently excluded, as the bats may have been incidentally ingested them
- …
