Tanya L. Darden

Assessing Red Drum Juvenile Stocking in a South Carolina Estuary Using Genetic Identification

Abstract The South Carolina Department of Natural Resources has been stocking red drum Sciaenops ocellatus since 1988 to evaluate parameters critical to their successful survival and recruitment in South Carolina estuaries. From 1999 to 2002, between 600,000 and 1,000,000 juvenile red drum were stocked each year in two tributaries of Charleston Harbor. The harbor and each tributary were partitioned into three independent strata and randomly sampled monthly for two decades, allowing population trends before, during, and after stocking to be evaluated. Using microsatellite-based parentage analysis, we examined the contribution of stocked age-0 juvenile red drum (15–60 mm total length) to the local population 1 year after release by using fishery-independent sampling. Analysis of these data showed that the highest contributions (88.9%) were close to the stocking site in years with low natural recruitment, whereas in years with high natural recruitment, contributions were lower and stocking was less effective...

Genetic Population Structure of US Atlantic Coastal Striped Bass (Morone saxatilis)

Genetic population structure of anadromous striped bass along the US Atlantic coast was analyzed using 14 neutral nuclear DNA microsatellites. Young-of-the-year and adult striped bass (n = 1114) were sampled from Hudson River, Delaware River, Chesapeake Bay, North Carolina, and South Carolina. Analyses indicated clear population structure with significant genetic differentiation between all regions. Global multilocus F ST was estimated at 0.028 (P < 0.001). Population structure followed an isolation-by-distance model and temporal sampling indicated a stable population structure more than 2 years at all locations. Significant structure was absent within Hudson River, whereas weak but significant genetic differences were observed between northern and southern samples in Chesapeake Bay. The largest and smallest effective striped bass population sizes were found in Chesapeake Bay and South Carolina, respectively. Coalescence analysis indicated that the highest historical gene flow has been between Chesapeake Bay and Hudson River populations, and that exchange has not been unidirectional. Bayesian analysis of contemporary migration indicated that Chesapeake Bay serves as a major source of migrants for Atlantic coastal regions from Albemarle Sound northward. In addition to examining population genetic structure, the data acquired during this project were capable of serving as a baseline for assigning fish with unknown origin to source region.

Genetic Parentage Analysis of Red Drum in South Carolina and the Use of Genotypic Data from Archived Otoliths

Abstract The red drum Sciaenops ocellatus is an estuarine-dependent fish that is the focus of a large recreational fishery along the U.S. Atlantic coast and in the Gulf of Mexico. In response to dramatic declines in juvenile abundance, the South Carolina Department of Natural Resources has been experimentally stocking local estuaries since the late 1980s. Here we report on the genetic parentage approach that has been employed to identify fish of hatchery origin through DNA isolated from fin clips collected from wild-caught fish. In some cases tissue samples were not available, making it necessary to find an alternative source of DNA. Thus, we also examined the use of archived otoliths as a source of genetic material for parentage analysis. Amplification resulted from 96% of the extractions obtained from the extracellular tissue remaining on otoliths. In comparison with extractions obtained from fin clips, otoliths appear to be a reliable DNA source. These results not only present a method for nonlethally ...

Population genetics of Cobia (Rachycentron canadum): implications for fishery management along the coast of the southeastern United States

Cobia (Rachycentron canadum) is a pelagic, migratory species with a transoceanic distribution in tropical and subtropical waters. Recreational fishing pressure on Cobia in the United States has increased substantially during the last decade, especially in areas of its annual inshore aggregations, making this species potentially susceptible to overfishing. Although Cobia along the Atlantic and Gulf coasts of the southeastern United States are currently managed as a single fishery, the genetic composition of Cobias in these areas is unclear. On the basis of a robust microsatellite data set from collections along the U.S. Atlantic coast (2008–09), offshore groups were genetically homogenous. However, the 2 sampled inshore aggregations (South Carolina and Virginia) were genetically distinct from each other, as well as from the offshore group. The recapture of stocked fish within their release estuary 2 years after release indicates that some degree of estuarine fidelity occurs within these inshore aggregations and supports the detection of their unique genetic structure at the population level. These results complement the observed high site fidelity of Cobias in South Carolina and support a recent study that confirms that Cobia spawn in the inshore aggregations. Our increased understanding of Cobia life history will be beneficial for determining the appropriate scale of fishery management for Cobia.

Genetic Characterization of American Shad in the Edisto River, South Carolina, and Initial Evaluation of an Experimental Stocking Program

Abstract The American shad Alosa sapidissima is an anadromous clupeid with once-prolific stocks that have experienced major coastwide declines in abundance over the past century. The American shad spawning run in the Edisto River (South Carolina) has been exhibiting the same decreases as spawning runs in other coastal rivers, and stocking is now being considered as a restoration option for this river system. We utilized a suite of 13 microsatellite loci to provide a baseline genetic characterization of the Edisto River spawning run prior to supplementation and to evaluate the initial success of an experimental stocking program enacted from 2008 to 2010. No significant temporal genetic differentiation was found between sampling years, indicating that the genetic composition of the Edisto River spawning run is temporally stable over short time frames. Estimates of genetic diversity for Edisto River American shad were high (observed heterozygosity = 0.82–0.85) and similar to those observed in other river sys...

Genetic Structure of Striped Bass in the Southeastern United States and Effects from Stock Enhancement

AbstractUnderstanding the genetic relationships of Striped Bass Morone saxatilis populations within and between watersheds is necessary to identify appropriate management units. Determining temporal changes in genetic relationships as well as the genetic diversity of the populations is important in understanding how stock enhancement influences population units. A suite of 12 microsatellites was used to evaluate patterns of Striped Bass gene flow both spatially and temporally across watersheds in the southeastern United States. Populations from the study watersheds were genetically diverse with the exception of the Savannah River, South Carolina–Georgia, which is recovering from a major population decline. Striped Bass in the Roanoke and Cape Fear rivers, North Carolina, represented a single population, most likely due to historical transfer stocking across the state from Roanoke River stock. Watersheds in South Carolina contained genetically distinct Striped Bass populations, although the difference betw...

Three Multiplexed Microsatellite Panels For Striped Bass

Abstract Microsatellite multiplexing is a useful technique that minimizes the time, reagents, and cost associated with genetic studies in fisheries biology. Striped Bass is an important sport and aquaculture species commonly stocked throughout the United States. We have developed three multiplexed panels that collectively incorporate twelve different established microsatellite loci. All loci were tested for Hardy-Weinberg equilibrium, linkage disequilibrium, Mendelian inheritance, and null alleles in two populations. Loci were comparably polymorphic in two river systems with similar allele size ranges observed; therefore, these multiplexed panels should be useful for genetic population studies of Striped Bass both within and between disparate geographic distributions.

Genetic differentiation of spring-spawning and fall-spawning male Atlantic sturgeon in the James River, Virginia

Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus, Acipenseridae) populations are currently at severely depleted levels due to historic overfishing, habitat loss, and pollution. The importance of biologically correct stock structure for effective conservation and management efforts is well known. Recent improvements in our understanding of Atlantic sturgeon migrations, movement, and the occurrence of putative dual spawning groups leads to questions regarding the true stock structure of this endangered species. In the James River, VA specifically, captures of spawning Atlantic sturgeon and accompanying telemetry data suggest there are two discrete spawning groups of Atlantic sturgeon. The two putative spawning groups were genetically evaluated using a powerful microsatellite marker suite to determine if they are genetically distinct. Specifically, this study evaluates the genetic structure, characterizes the genetic diversity, estimates effective population size, and measures inbreeding of Atlantic sturgeon in the James River. The results indicate that fall and spring spawning James River Atlantic sturgeon groups are genetically distinct (overall FST = 0.048, F’ST = 0.181) with little admixture between the groups. The observed levels of genetic diversity and effective population sizes along with the lack of detected inbreeding all indicated that the James River has two genetically healthy populations of Atlantic sturgeon. The study also demonstrates that samples from adult Atlantic sturgeon, with proper sample selection criteria, can be informative when creating reference population databases. The presence of two genetically-distinct spawning groups of Atlantic sturgeon within the James River raises concerns about the current genetic assignment used by managers. Other nearby rivers may also have dual spawning groups that either are not accounted for or are pooled in reference databases. Our results represent the second documentation of genetically distinct dual spawning groups of Atlantic sturgeon in river systems along the U.S. Atlantic coast, suggesting that current reference population database should be updated to incorporate both new samples and our increased understanding of Atlantic sturgeon life history.

Genetic Characterization of Atlantic Blue Crab (Callinectes sapidus) in Charleston Harbor, South Carolina

ABSTRACT The Atlantic blue crab [Callinectes sapidus (Rathbun, 1896)] is a commercially and recreationally important decapod crustacean found in estuarine and nearshore waters of the western Atlantic. Recent declines in abundance, compounded with a scarcity of biological and genetic information, have made blue crab a high-priority species for research and conservation in South Carolina (SC). A suite of microsatellite loci was used to estimate the genetic diversity and effective population size of blue crab collected from Charleston Harbor, SC, in 2012 to 2013. Genetic diversity of the Charleston Harbor blue crab population was relatively high, whereas inbreeding was fairly low. Effective size estimates were on the order of several hundred to several thousand individuals. The results of our study exhibit good indications for the overall genetic “health” of the Charleston Harbor blue crab population and provide valuable information that can be incorporated into management plans to aid in the conservation of blue crab in SC.

Effects of Cold Winters on the Genetic Diversity of an Estuarine Fish, the Spotted Seatrout

Abstract Spotted Seatrout Cynoscion nebulosus are recreationally important fish that have been harvested in South Carolina for centuries. The Spotted Seatrout in South Carolina suffered substantial declines in estuarine abundance during the cold winters of 2000, 2009, and 2010, when water temperatures dropped below their tolerance threshold. As these population declines may result in genetic bottlenecks and their repetitive occurrence over a short timescale could reduce the populations adaptive potential, we estimated the genetic diversity and effective population size (Ne) of the Charleston Harbor Spotted Seatrout population at six time points related to recent cold winters using a suite of 13 microsatellite markers. Grouping individuals by year-class (fish spawned in the same year) was the most appropriate and effective method for measuring interannual fluctuations in observed and expected heterozygosity and allelic richness, superior to partitioning fish by collection year. The genetic diversity of Spotted Seatrout was significantly influenced by catch per unit effort, although only minor changes were observed and Ne remained high. Short overlapping generations appear to allow Spotted Seatrout to genetically recover during population growth and maintain moderate levels of genetic diversity.