Brook Trout (King)

Arctic cisco. Photo credit: Andrew Ramey, USGS

The Alaska Science Center is collaborating with Minerals Management Service (MMS) to conduct a genetic and otolith study on Arctic cisco (Coregonus autumnalis), an important subsistence resource for the native village of Nuiqsut, Alaska.  Subsistence users have expressed concerns over declines in harvests and size of Arctic cisco from the Colville River. This study developed new genetic markers, and tested previously developed molecular and otolith tools to address questions regarding genetic structure and population-of-origin for Arctic cisco captured in the Colville River subsistence fishery.

For more information contact Jennifer L. Nielsen and Christian E. Zimmerman, Alaska Science Center.

Atlantic salmon. Photo credit: Duane Raver, courtesy of USFWS Digital Library System

An Atlantic salmon mixed-stock subsistence fishery exists off the western coast of Greenland composed both of North American (NA) and European origin one-sea-winter age fish.  It is essential to the proper management of this valuable resource on both continents that the relative contributions of these diverse stocks to the west Greenland fishery are determined.  Leetown Science Center researchers have determined the levels of genetic variation at 11 microsatellite DNA loci for over 12,000 Atlantic salmon sampled from over 35 anadromous river populations from south-central Maine, USA to northern Spain.  This suite of moderate to highly polymorphic loci revealed over 300 alleles (5-37 / locus) in this range-wide baseline dataset.  Using genotypic assignment tests based on maximum-likelihood, this genetic variation provided 100% correct classification of Atlantic salmon in the baseline dataset to continent-of-origin and averaged nearly 83% correct classification to region-of-origin across continents.  LSC researchers have provided results for assignment to continent-of-origin of over 7,500 Atlantic salmon landed from 1995-2007 at seven west Greenland locations ranging from Sisimiut to Qaqortoq.  In general, the mixed-fishery appears to be evenly distributed between eastern and western Atlantic origins in salmon landed in the southern-most portion of the study area.   However, western Atlantic fish constitute the majority of the fishery as collections move north and west along the coast.

For more information contact Timothy L. King at the Leetown Science Center.

Atlantic salmon smolts. Photo credit: Peter Steenstra, courtesy of USFWS Digital Library System

At the request of Region 5, U.S. Fish and Wildlife Service, researchers at the Leetown Science Center have addressed questions related to the genetic population structure of Atlantic salmon throughout the range using mitochondrial and nuclear (microsatellite) DNA markers.  Specifically, the D-loop and NADH-1 dehydrogenase (ND-1) regions of mtDNA have been amplified by the PCR and digested with restriction endonucleases.  In addition to the mtDNA variation identified, the researcher’s laboratory has screened nuclear microsatellite DNA loci in over 12,000 individuals to identify population genetic structure in Atlantic salmon collected throughout the range.  The findings have had broad regional and international impacts and have addressed basic, applied, and theoretical questions.  In addition to being highly polymorphic, microsatellite DNA is assumed to be selectively neutral because it constitutes non-coding DNA.  These two characteristics together are allowing unique approaches to broodstock management in sea-run Atlantic salmon in Maine and the Connecticut River program.  LSC researchers are involved in a broodstock management program designed to increase levels of genetic variation in this highly managed broodstock.  Moreover, the survey is used to identify and remove fish possessing genotypes or alleles identified as being of European-origin that have escaped from Maine aquaculture facilities.  In addition to broodstock management, the unique multilocus genotypes have allowed the development of a fry marking system.  This system, based on the mating of individuals of known (unique) multilocus genotypes, allows the creation of families with large numbers of naturally marked fry that are being stocked into selected tributaries of the Narraguagus and Connecticut Rivers.  The ultimate goals of this study are to identify tributary of stocking and other associated ecological and evolutionary attributes.

For more information contact Timothy L. King at the Leetown Science Center.

Atlantic sturgeon. Photo credit: Duane Raver, courtesy of USFWS Digital Library System

Sturgeons present significant challenges to conservation biologists investigating the evolutionary processes shaping the nuclear genomes of extant species due to polyploid ancestry.  Leetown Science Center geneticists have isolated and characterized 24 codominant polymorphic microsatellite DNA markers in the Atlantic sturgeon (Acipenser oxyrinchus oxyrinchus).  A subset of the markers was then tested for cross-species amplification in ten sturgeon species comprising three genera.  The evolutionary conservation of the regions flanking the microsatellites (i.e., sequence homology) in these loci has provided a high rate of successful cross-species amplification using the same primers and amplification conditions in sturgeon comprising three ploidy levels.  Twelve of these markers have been screened in an Atlantic sturgeon family and nine geographic populations representing the species’ range to assess inheritance, levels of genetic diversity, and patterns of phylogeographic structure.  In addition to identifying several discrete populations, this research has provided compelling evidence of reproducing populations within the Chesapeake Bay (e.g., James River).  These research findings were applied to the delineation of Distinct Population Segments in the Status Review conducted by NOAA Fisheries.

For more information contact Timothy L. King at the Leetown Science Center.

Brook trout. Photo credit: VA Trout Unlimited

Little is known of the ecological and evolutionary relationships among brook trout inhabiting National Park Service (NPS) lands and streams throughout the species’ range.  To address this research need, Leetown Science Center geneticists and the National Park Service have collaborated to develop a suite (N=13) of microsatellite DNA markers and conduct an extensive survey of genetic variation in over 8,500 brook trout from 225 collections from the major drainages within five national parks and several other populations comprising the native range of the species in the eastern U.S. and Canada.  This survey identified a high degree of genetic diversity and differentiation at all hierarchical levels studied (i.e., individual to watershed).  In addition to identifying previously undetected evolutionary relationships among populations, this study has proven useful in identifying collections that have experienced small effective population sizes (e.g., bottlenecks) and has highlighted collections that have been impacted by supplemental or restorative stocking.  Sufficient genetic diversity exists to allow delineation of the finest levels of population substructuring. The amount of genetic diversity observed also allows individual-level captive breeding management.  Contemporary genetic tools (e.g., functional genomics) are now being applied to determine and better understand the adaptive significance of the various levels of differentiation.  These results will afford resource managers the ability to manage brook trout at any level of resolution deemed necessary to restore or enhance native populations.

For more information contact Timothy L. King at the Leetown Science Center.

Wild brook trout. Photo credit: Conte Anadromous Fish Research Center

The Leetown Science Center is working with The Nature Conservancy and the U.S. Forest Service (USFS) Northern Research Station to evaluate effects of habitat fragmentation on population persistence on wild brook trout (Salvelinus fontinalis). Our goal is to understand how natural and human-induced habitat fragmentation influence population structure and demographic rates across scales ranging from 1st-2nd order streams to catchments. To address this goal, we have combined detailed tagging studies with genetic analyses of spatial population structure and parentage assignment.

For more information view http://www.lsc.usgs.gov/cafl/ecology/ecology.html and contact Benjamin H. Letcher, Leetown Science Center.

Brook trout. Photo credit: Henry Quinlan, U.S. Fish and Wildlife Service

The Great Lakes Science Center is partnering with the Ontario Ministry of Natural Resources, the U.S. Fish and Wildlife Service, University of Minnesota, University of Wisconsin-Steven’s Point, and State and Tribal agencies to investigate management concerns and recent rehabilitation opportunities for brook trout in Lake Superior.  Questions that have been addressed include resolving the genetic population structure of brook trout from Lake Superior tributaries, the evolutionary status of coaster brook trout, their relationship to riverine tributary brook trout populations, and the effectiveness of stocking in maintaining and restoring coasters.  A comparative analysis of shared samples among four laboratories enabled standardization of genotype scoring and interpretation, which gave researchers a shared toolkit for assessing genetic structure and diversity.  Congruent genetic results indicate that coasters are an ecotype (life history variant) rather than an evolutionary significant unit or genetically distinct strain.  Regional structure exists among brook trout stocks, with coasters being produced from local populations.  Introgression of hatchery genes into wild populations varies regionally, and may relate to local population sizes, habitat integrity and anthropogenic pressures.  Incorporation of genetic data into rehabilitation projects will facilitate monitoring efforts and subsequent adaptive management.

For more information contact Wendylee Stott, Great Lakes Science Center.

Etheostoma osburni; Male; Laurel Creek, West Virginia. Photo credit: John F. Switzer

Etheostoma variatum; Male; Middle Fork Red River, Kentucky. Photo credit: John F. Switzer

The candy darter (Etheostoma osburni) is endemic to the New River drainage of West Virginia and Virginia.  Etheostoma osburni is a species of special concern in West Virginia.  Recently, a closely related species, the variegate darter (E. variatum), has invaded portions of the range of E. osburni, possibly introduced via bait-buckets.  Preliminary genetic evidence indicates that these two species may be hybridizing.  This is an important conservation issue as hybridization may imperil the genetic integrity of E. osburni, potentially leading to extinction.  In order to determine the extent of hybridization between E. osburni and E. variatum a suite of primers were developed for 15 microsatellite DNA loci and used to genotype 286 individuals; in addition, a 1064 bp portion of the mitochondrial cytochrome b gene (cyt b) was sequenced for 115 individuals from the potential hybrid zone.  Analysis of the microsatellite and cyt b data provided evidence for 25 individuals of hybrid ancestry.  The greatest numbers of hybrids were collected at Anthony Cr., the upstream most collection site of E. variatum in the Greenbrier R. drainage, and the only site were E. osburni and E. variatum are known to be syntopic.  Collections of E. variatum from downstream of Anthony Cr. have evidence of E. osburni introgression.  Collections of E. osburni from above Anthony Cr. in the Greenbrier R. drainage do not show evidence of hybridization with E. variatum and appear to be a distinct population, separate from the downstream population of E. variatum and the Gauley R. population of E. osburni.  Future research efforts will use genetic data to determine if the hybrid zone is moving upstream in the Greenbrier R. drainage, further threatening E. osburni.

For more information view the publication "Microsatellite DNA primers for the candy darter, Etheostoma osburni and variegate darter, Etheostoma variatum, and cross-species amplification in other darters (Percidae)," available via Wiley InterScience: http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2007.01946.x, and contact John F. Switzer, Leetown Science Center.

Crystal darter. Photo credit: Konrad P. Schmidt

The crystal darter, Crystallaria asprella, historically occurred throughout the Eastern U.S., but now exists only in geographically isolated populations. The taxonomic status of a newly discovered population in the Ohio River basin, the Elk River, WV, is of particular concern as few animals have been found and landuse practices threaten habitat. An initial genetics study utilizing DNA sequences identified four distinct populations occurring in the upper and lower Mississippi River, the Gulf Coast drainages, and the Ohio River basin represented by the Elk River in West Virginia. Through the analysis of additional gene regions, plus measurements of body and fin dimensions, the four distinct population segments were upheld. The Elk River population appeared the most distinctive, and has recently been described as a new species, Crystallaria cincotta. It has been suggested that C. cincotta be given federal protection under the Endangered Species Act.

For more information view the following publications or contact Cheryl Morrison, Leetown Science Center.

Northern snakehead (Channa argus). Photo credit: USGS Florida Integrated Science Center Photo Library

Introduction and establishment of northern snakehead (Channa argus) populations in the tidal Potomac River is expected to have significant ecological impacts. To develop management strategies in northern snakeheads that will ensure long-term success (i.e., eradication), a thorough understanding of the level of dispersal and gene exchange (effective movement) among tributaries is essential.  Leetown Science Center geneticists have developed microsatellite DNA markers for the northern snakehead and are determining movement patterns of the invasive fish within the Little Hunting Creek, Dogue Creek, Accotink-Pohick Creek, Piscataway Creek, and Pomonkey Creek complex in the Potomac River.  Movements will be confirmed by use of contemporary genetic analyses.  Specific sub-objectives are to: 1) compare the genetic population structure observed in the Potomac River; 2) delineate management units within the Potomac River and attempt to define genetically independent populations that may respond differently to particular control techniques; 3) estimate the effective population size, identify social structure within each geographic population, and determine if dispersal shows a sex bias;  and upon funding approval, 4) use contemporary molecular genetic techniques to test the utility of novel DNA constructs for preventing embryogenesis (e.g., daughterless technology) or direct lethal effects (e.g., engineered underdominance)  in northern snakehead.  Determining the presence, direction, and intensity of gene flow among geographic populations will provide the necessary background to understand the ecological effects of snakehead invasion.

For more information contact Timothy L. King at the Leetown Science Center.

Hybrid sturgeon. Photo credit: Provided courtesy of Jan Dean, U.S. Fish and Wildlife Service

Boats on the Atchafalya River. Photo credit: Provided courtesy of Jan Dean, U.S. Fish and Wildlife Service

National Wetlands Research Center (NWRC) has partnered with U.S. Fish and Wildlife Service (USFWS) Natchitoches National Fish Hatchery in a project to attempt to differentiate the endangered pallid (Scaphirhynchus albus) from shovelnose sturgeon (S. platorynchus).  The project is based on the use of high resolution DNA analysis by flow cytometry, whereby possible genome content differences between the species and intermediate levels in the hybrids in the Lower Mississippi River Basin can allow for the discrimination among the species.  If these DNA content differences exist and are detectable by this method, this technology can be used to assist with recovery and restoration efforts.  Many state and federal partners - from the Upper, Middle, and Lower Basins - are involved with this research, whereby samples will be retained for future molecular biology analyses, and animal morphology data is being simultaneously collected and will be compared with flow cytometric data.

For more information contact Jill A. Jenkins, National Wetlands Research Center.

Pallid sturgeon. Photo credit: Ken Bouc, Nebraska Game and Parks Commission

Leetown Science Center researchers are providing Technical Assistance to the Pallid Sturgeon/Fish and Wildlife Technical Working Group (including both Upper and Lower Basin Working Groups) and the Pallid Sturgeon Recovery Team in the form of increased discrimination between pallid and shovelnose sturgeon and enhanced evaluation of pallid sturgeon reproductive success in the Missouri River.  The developed assays will permit rapid and affordable discrimination of the Scaphirhynchus larvae (including hybrids) and can be used to monitor reproduction in relation to habitat, location, and flow regime as directed by the 2003 USFWS Biological Opinion.  Using three contemporary molecular techniques, Leetown Science Center geneticists are developing Single Nucleotide Polymorphisms (SNPs, pronounced “snips”) markers for discriminating pallid sturgeon from the shovelnose sturgeon that will complement existing microsatellite markers, but will be both less expensive to score and more easily standardized.  Furthermore these markers will be based on genes of known function and thus will potentially be sensitive to adaptive differences between species and thus will focus on traits relevant to evolution and conservation of the pallid sturgeon.  LSC researchers believe pyrosequencing will allow large-scale de novo transcriptome assembly and comparison among the two species.  In essence, the pallid and shovelnose sturgeons will become the model species for all future sturgeon transcriptome work.  In addition, this work will provide a fast, cost-effective, and reliable method for development of nuclear genes for molecular systematic (e.g., are these two entities distinct species), functional genomic analysis (e.g., do metabolic differences exist between these species or between pallids in the upper and lower portions of the Mississippi drainage), and large scale SNP development.  A combination of approaches could lead to an enormous number of SNPs as well as important evolutionary and ecological breakthroughs for sturgeons.

For more information contact Timothy L. King at the Leetown Science Center.

Razorback sucker (Xyrauchen texanus). Photo credit: Provided courtesy of Chester Figiel, U.S. Fish and Wildlife Service

Sperm from endangered razorback suckers stained with eosin nigrosin. Photo credit: Provided courtesy of Chester Figiel, U.S. Fish and Wildlife Service

• National Wetlands Research Center (NWRC) has partnered with U.S. Fish and Wildlife Service (USFWS), WRD, and National Park Service (NPS) in Nevada in examining the reproductive health of the endangered razorback sucker, common carp (Cyprinus carpio), and largemouth bass (Micropterus salmoides) in Lake Mead by comparing sperm quality in fish collected from waters dominated by municipal wastewater effluents in Las Vegas Bay with fish from reference sites.  The reproductive endpoints focus on the condition of the spermatozoa, including DNA quality.  Lowered quality in cells from experimental sites would likely reflect a reduction in reproductive capacity.  Andrology endpoints measured include:

  sperm counts DNA integrity spermatogenic stage viability mitochondrial function morphology apoptosis osmolality motility by computer assisted semen analysis

For more information contact Jill A. Jenkins, National Wetlands Research Center.

Shortnose Sturgeon (Acipenser brevirostrum). Photo credit: Noel Burkhead

Shortnose sturgeons, Acipenser brevirostrum, are protected by federal law (Endangered) and determining the status of the species in all Atlantic coast rivers is a priority of the Recovery Plan.  In some rivers, shortnose sturgeon survived the damming, overharvest, and pollution of the late 19th and early 20th Century, but in other rivers, the species was extirpated.  There are important rivers, like the Potomac River, where the status is unknown, although there have been reports of fish captured in recent years.  Efforts to capture, tag, and track adult shortnose sturgeon from winter refugia to spawning locations were successful in 2005 and 2006 with two female shortnose sturgeon captured near Craney Island on the Potomac River.  Leetown Science Center geneticists have  documented the presence of shortnose sturgeon in the Potomac River, developed nuclear DNA genetic markers to examine shortnose sturgeon populations, and investigated genetic diversity and phylogeographic structure throughout the species’ range. Polyploidy in sturgeon (4n-8n-16n) presents a challenge to investigation of evolutionary processes shaping the nuclear genome.  Although it is assumed that extant sturgeon species are functionally diploid, the degree to which the nuclear genome exhibits disomic inheritance is unknown.  Microsatellite markers are needed for genotyping of Potomac River shortnose sturgeon to distinguish among the genetic stocks that may be present. The genetic-based objectives of this study included: 1) development of microsatellite DNA markers for A. brevirostrum; 2) characterization of the genetic diversity of Potomac River A. brevirostrum; and 3) conduct a phylogeographic (range-wide) comparison of sturgeon sampled throughout the species’ range.   This study has identified five distinct population segments among the 19 rivers known to have reproducing populations.  Microsatellite DNA markers have determined that shortnose sturgeon migrate among adjacent river systems.  These comparisons assisted in determining whether Potomac River A. brevirostrum represented a natal stock or was colonized by migrants from adjacent populations (Delaware and Hudson River).

For more information contact Timothy L. King at the Leetown Science Center.