Use of molecular tools for research and improvement of aquaculture stocks

Development of molecular genetic markers provides aquaculture with tools for a number of research and practical applications. Genetic marking of experimental groups allows their evalu- ation 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 parent- age 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 can- didates for QTL or functional analysis. Purposeful genetic marking can be used to identify pro- prietary 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 devel- opment of broodstocks for most aquaculture species, the small size and limited scope of most aquaculture operations, and the costs of genetic screening

Genetic Characteristics of Southern and Northern Brook Trout (Salvelinus fontinalis) Populations at the Zone of Contact

Population genetic evidence suggests differentiation among evolutionarily significant units of southern and northern Appalachian brook trout, with the zone of contact in southwestern Virginia. Before this differentiation was recognized, brook trout of northern origin were stocked throughout the southeastern United States. In order to determine this differentiation, established allozyme markers were used to classify 56 southwest Virginia populations as southern, northern, or introgressed. Variation at 4 polymorphic loci, including the diagnostic creatine kinase (CK-A2*) locus, indicated that 19 populations were of southern origin, 5 of northern origin, and 32 of mixed genetic origin. Data compiled among genetic studies of brook trout in the southern Appalachians showed that the southern/northern break is sharp, occurring at the New/Roanoke-James watershed divide. New River drainage populations exhibited the southern allele at high frequency, suggesting their historic native character as southern, with presence of northern alleles due to stocking or stream capture events. In conclusion, the present study suggests that management of southern Appalachian brook trout should include: (1) genetically cognizant planning of stocking events, (2) management of populations on a stream-by-stream basis, (3) prioritized conservation of pure southern brook trout populations, and (4) use of southern Appalachian hatchery stocks in restoration efforts

Multi-metric Conservation Assessment for the Imperiled Clinch Dace

Planning frameworks allow managers to spatially prioritize actions to promote species conservation. Traditional aquatic conservation planning frameworks are often organized at the ecological community or ecosystem level, which often neglect imperiled taxa occupying species-poor assemblages. In this study, we develop a multi-metric conservation assessment for the 15 geographically distinct candidate conservation areas (CCAs) occupied by the imperiled Clinch Dace (Chrosomus sp. cf. saylori). Clinch Dace habitat is threatened by anthropogenic landscape alterations, especially for coal mining and timber harvest. Our framework used four metrics to assess the conservation value of each subpopulation of Clinch Dace namely: “habitat condition”, “viability”, conservation “opportunity” and conservation “feasibility”. Occupancy models were used to determine the most influential habitat variables to Clinch Dace presence and habitat data collected for each occupied stream were used to score habitat condition in each CCA. Clinch Dace survey data were used to assess demographic population viability to highlight areas where Clinch Dace are most likely to persist. Next, we used the metrics of opportunity and feasibility to identify opportunities for reclamation as well as landownership patterns that may be bridges or barriers to conservation action. Habitat condition and viability varied among our 15 CCAs and highlighted opportunities for specific management actions including habitat conservation in some watersheds and needs for restoration in others. The feasibility metric showed that variation exists in the average lot-parcel size along occupied stream reaches, which may affect the success of some conservation actions. We recommend that managers utilize the data summarized in this study, along with stakeholder input, in a structured-decision making approach to develop specific outreach and management plans targeted to stakeholders in individual watersheds and provide an example of such a framework

Testing a global standard for quantifying species recovery and assessing conservation impact.

Recognizing the imperative to evaluate species recovery and conservation impact, in 2012 the International Union for Conservation of Nature (IUCN) called for development of a "Green List of Species" (now the IUCN Green Status of Species). A draft Green Status framework for assessing species' progress toward recovery, published in 2018, proposed 2 separate but interlinked components: a standardized method (i.e., measurement against benchmarks of species' viability, functionality, and preimpact distribution) to determine current species recovery status (herein species recovery score) and application of that method to estimate past and potential future impacts of conservation based on 4 metrics (conservation legacy, conservation dependence, conservation gain, and recovery potential). We tested the framework with 181 species representing diverse taxa, life histories, biomes, and IUCN Red List categories (extinction risk). Based on the observed distribution of species' recovery scores, we propose the following species recovery categories: fully recovered, slightly depleted, moderately depleted, largely depleted, critically depleted, extinct in the wild, and indeterminate. Fifty-nine percent of tested species were considered largely or critically depleted. Although there was a negative relationship between extinction risk and species recovery score, variation was considerable. Some species in lower risk categories were assessed as farther from recovery than those at higher risk. This emphasizes that species recovery is conceptually different from extinction risk and reinforces the utility of the IUCN Green Status of Species to more fully understand species conservation status. Although extinction risk did not predict conservation legacy, conservation dependence, or conservation gain, it was positively correlated with recovery potential. Only 1.7% of tested species were categorized as zero across all 4 of these conservation impact metrics, indicating that conservation has, or will, play a role in improving or maintaining species status for the vast majority of these species. Based on our results, we devised an updated assessment framework that introduces the option of using a dynamic baseline to assess future impacts of conservation over the short term to avoid misleading results which were generated in a small number of cases, and redefines short term as 10 years to better align with conservation planning. These changes are reflected in the IUCN Green Status of Species Standard

Use of Molecular Tools for Research and Improvement of Aquaculture Stocks

Abstract 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

Genetics and biotechnology make increasingly important contributions to fishery science, fishery management, aquaculture, and related fields [...

Extensive Dispersal of Endangered Roanoke Logperch Inferred Using Genetic Marker Data

The dispersal ecology of most stream fishes is poorly characterised, complicating conservation efforts for these species. We used microsatellite DNA marker data to characterise dispersal patterns and effective population size (Ne) for a population of Roanoke logperchPercina rex, an endangered darter (Percidae). Juveniles and candidate parents were sampled for 2 years at sites throughout the Roanoke River watershed. Dispersal was inferred via genetic assignment tests (ATs), pedigree reconstruction (PR) and estimation of lifetime dispersal distance under a genetic isolation-by-distance model. Estimates of Ne varied from 105 to 1218 individuals, depending on the estimation method. Based on PR, polygamy was frequent in parents of both sexes, with individuals spawning with an average of 2.4 mates. The sample contained 61 half-sibling pairs, but only one parent–offspring pair and no full-sib pairs, which limited our ability to discriminate natal dispersal of juveniles from breeding dispersal of their parents between spawning events. Nonetheless, all methods indicated extensive dispersal. The AT indicated unrestricted dispersal among sites ≤15 km apart, while siblings inferred by the PR were captured an average of 14 km and up to 55 km apart. Model-based estimates of median lifetime dispersal distance (6–24 km, depending on assumptions) bracketed AT and PR estimates, indicating that widely dispersed individuals do, on average, contribute to gene flow. Extensive dispersal of P. rex suggests that darters and other small benthic stream fishes may be unexpectedly mobile. Monitoring and management activities for such populations should encompass entire watersheds to fully capture population dynamics

Direct and Molecular Observation of Movement and Reproduction by Candy Darter, <i>Etheostoma osburni</i>, an Endangered Benthic Stream Fish in Virginia, USA

Direct and indirect measures of individual movement provide valuable knowledge regarding a species’ resiliency to environmental change. Information on patterns of movement can inform species management and conservation but is lacking for many imperiled fishes. The Candy Darter, Etheostoma osburni, is an endangered stream fish with a dramatically reduced distribution in Virginia in the eastern United States, now known from only four isolated populations. We used visual implant elastomer tags and microsatellite DNA markers to directly describe movement patterns in two populations. Parentage analysis based on parent-offspring pairs was used to infer movement patterns of young-of-year and age-1 individuals, as well as the reproductive contribution of certain adults. Direct measurements of movement distances were generally similar between methods, but microsatellite markers revealed greater distances moved, commensurate with greater spatial frames sampled. Parent-offspring pairs were found throughout the species’ 18.8-km distribution in Stony Creek, while most parent-offspring pairs were in 2 km of the 4.25-km distribution in Laurel Creek. Sibship reconstruction allowed us to characterize the mating system and number of spawning years for adults. Our results provide the first measures of movement patterns of Candy Darter as well as the spatial distribution of parent-offspring pairs, which may be useful for selecting collection sites in source populations to be used for translocation or reintroductions. Our results highlight the importance of documenting species movement patterns and spatial distributions of related individuals as steps toward understanding population dynamics and informing translocation strategies. We also demonstrate that the reproductive longevity of this species is greater than previously described, which may be the case for other small stream fishes

Defining Management Units for Wild Nile Tilapia Oreochromis niloticus from Nine River Basins in Ghana

Despite the global importance of the Nile tilapia Oreochromis niloticus, especially to aquaculture, knowledge of genetic variability within native populations is still limited. While several studies have assessed genetic differentiation across the major drainage basins of Africa, relatively little effort has focused on characterizing genetic differentiation at finer scales. We assessed genetic variation in O. niloticus within and among nine drainage basins in Ghana using nuclear microsatellite DNA markers as the basis for identifying potential units of conservation among wild populations. We screened 312 wild individuals using eight nuclear microsatellite DNA markers. We found moderate genetic diversity within and differentiation among all wild populations studied, with strong signals of recent demographic bottlenecks in several populations. Genetic structure among 11 populations suggested the presence of up to ten management units (MUs). In particular, the Black Volta and the Tano&ndash;Asuhyea populations, which were the most genetically distinct and geographically isolated and may be most at risk of loss of genetic diversity over time, may well represent evolutionary significant units. Therefore, at the minimum, the Black Volta and Tano&ndash;Asuhyea populations should be prioritized for conservation actions to sustain them over the long-term