Eagle Fish Genetics Laboratory

Eagle, ID, United States

Eagle Fish Genetics Laboratory

Eagle, ID, United States
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Hinrichsen R.A.,Hinrichsen Environmental Services | Steele C.A.,Pacific States Marine Fisheries Commission | Ackerman M.W.,Pacific States Marine Fisheries Commission | Campbell M.R.,Eagle Fish Genetics Laboratory | And 5 more authors.
Transactions of the American Fisheries Society | Year: 2016

Abstract: For salmon populations in the Columbia River and Snake River basins, many of which are listed under the U.S. Endangered Species Act of 1973, reliable estimates of the proportion of hatchery-origin adults in spawning areas (p) are needed to assess population status and the genetic and demographic interactions of hatchery- and natural-origin fish. Some hatchery fish receive visible marks, coded wire tags (CWTs), parentage-based tags (PBTs), or all three. This allows one to identify whether fish recovered after release are of hatchery origin. Parentage-based tagging involves genotyping hatchery broodstock and uses parentage assignments as “tags” that identify the origin and brood year of their progeny. We derived a maximum likelihood estimator of p and applied it to the 2012 and 2013 carcass survey data for spring–summer Chinook Salmon Oncorhynchus tshawytscha in the South Fork Salmon River, Idaho. Maximum likelihood estimation was also applied to CWT data and, for investigating the importance of expected tag recoveries on precision, to simulated PBT data for fall Chinook Salmon spawning in the Hanford Reach of the Columbia River. Precision of p from maximum likelihood estimation increased with the expected number of tag recoveries in a carcass survey, whether CWTs or PBTs. In the South Fork Salmon River application, there were 340% more PBT recoveries than CWT recoveries, leading to greater precision in release-specific values of p from maximum likelihood estimation. The maximum likelihood estimation procedure provides fisheries managers a method to design a tagging and sampling program aimed at estimating p, a valuable measure of the potential for interaction of wild- and hatchery-origin fish on the spawning grounds. To design a program for estimating p, we recommend selecting a target level of precision and then choosing a tagging fraction and sampling rate that delivers that precision in the most cost-effective way. Received August 21, 2015; accepted January 19, 2016 Published online April 27, 2016 © 2016, © American Fisheries Society 2016.


Ardren W.R.,U.S. Fish and Wildlife Service | DeHaan P.W.,U.S. Fish and Wildlife Service | Smith C.T.,U.S. Fish and Wildlife Service | Taylor E.B.,University of British Columbia | And 8 more authors.
Transactions of the American Fisheries Society | Year: 2011

The bull trout Salvelinus confluentus is a broadly distributed char in northwestern North America that has undergone significant population declines. This species is currently protected under the Endangered Species Act across its range in the coterminous United States. To clarify patterns of phylogenetic structure and to assist with identification of conservation units, we examined genetic variation within and among 75 representative bull trout populations sampled throughout the USA. Genealogies from a 520-base-pair portion of the mitochondrially encoded NADH dehydrogenase 1 gene (ND-1) revealed reciprocal monophyly between coastal and interior lineages that differed by 1.34% in DNA sequence. The geographic distribution of the two lineages was divided by the Cascade Mountains, a pattern that likely reflects postglacial dispersal from separate glacial refugia. Analysis of microsatellite variation revealed that 76% of populations had an estimated effective population size less than 50 and indicated high divergence among populations caused by genetic drift (average genetic differentiation index FST = 0.32) and mutation (average genetic differentiation index RST = 0.58). Concordant phylogeographic and phylogenetic patterns observed with microsatellite and mitochondrial DNA analyses provided evidence for two to six bull trout lineages that largely reflect historic patterns of gene flow and isolation among populations. These lineages can be further subdivided into finer-scale units due to the extremely low dispersal among populations and small effective population sizes. In fact, Bayesian analysis of population structure identified an optimal solution of 69 genetically different groups. Based on these results, we believe that conservation efforts should ideally be focused on the 118 bull trout core areas originally identified in the draft Endangered Species Act recovery plan, which are broadly defined as metapopulations.We provide examples of how other data, such as unique life history forms and ecological setting, can be used in combination with our genetic results to refine the U.S. Fish andWildlife Service's hierarchical conservation strategy for bull trout. © American Fisheries Society 2011.


Stark E.J.,Nampa Fisheries Research | Kozfkay C.C.,Eagle Fish Genetics Laboratory
Reviews in Fish Biology and Fisheries | Year: 2014

Captive rearing is a conservation strategy where juveniles are collected from the natural environment, reared to maturity in a hatchery environment, and then released back into the natural environment at maturity for volitional spawning. This strategy has been used to produce adult outplants for stock enhancement where natural escapement is poor or capture of adults is difficult. In both Idaho (Chinook salmon, Oncorhynchus tshawytscha) and Maine (Atlantic salmon, Salmo salar), captive rearing programs have been initiated as an experimental strategy to prevent cohort collapse and conserve genetic integrity of select depressed populations. In this paper, we provide an overview of these programs and describe some of the methods used to evaluate the effectiveness of this approach. Behaviors such as habitat selection, courting, and spawn timing were monitored. Data collected for both programs indicate that the captive fish display similar behaviors as their wild conspecifics in terms of habitat selection and spawning, although there were some differences in spawn timing. Evaluations of egg and fry production also indicate that captive-reared adults are successfully spawning and producing offspring. Each program is still waiting on final evaluations of reproductive success through genetic analyses of returning adults, but results so far indicate that this could be an additional captive propagation strategy for depressed populations. © 2014 Springer International Publishing Switzerland.


Draheim H.M.,Eagle Fish Genetics Laboratory | Lopez V.,Allegheny National Forest | Etter D.,562 E Stoll Road | Winterstein S.R.,Michigan State University | And 2 more authors.
Ursus | Year: 2015

Sampling bias can lead to erroneous interpretations of spatial genetic structure that can subsequently impact conservation efforts and management decisions. Genetic sampling of rare and elusive species can be challenging and, by necessity, samples are often collected opportunistically from multiple sources that could differ in spatial dispersion and timing of collection. Here we quantified the effects of timing of sample collection and sampling methods on spatial and temporal variability in sample dispersion and measures of American black bear (Ursus americanus) local spatial genetic structure. Hair (N = 890) and tissue (N = 1,017) samples were collected from Michigan's Northern Lower Peninsula (USA) during the summer using noninvasive (hair snares) and autumn harvest methods during 2003, 2005, and 2009. Point pattern analyses of sample dispersion revealed that sample density did not differ significantly between seasons or among years. Measures of spatial genetic structure (i.e., spatial autocorrelation) revealed significant positive genetic spatial structuring at distances of 0-10 km when samples were analyzed separately by year, season, and when temporally distinct samples were grouped. Local genetic spatial autocorrelation analyses revealed spatial genetic patterns over the entire study area were consistent across seasons and years. Spatial genetic structure is indicative of the extent of dispersal and gene flow, which is crucial for developing management plans for harvested species. Collectively, our data show that non-invasive and harvest collection methods similarly capture spatial genetic heterogeneity at the scale and spatial extent appropriate for management. © 2015 International Association for Bear Research and Management.


PubMed | Eagle Fish Genetics Laboratory and U.S. Department of Agriculture
Type: Journal Article | Journal: PloS one | Year: 2016

Among the many threats posed by invasions of nonnative species is introgressive hybridization, which can lead to the genomic extinction of native taxa. This phenomenon is regarded as common and perhaps inevitable among native cutthroat trout and introduced rainbow trout in western North America, despite that these taxa naturally co-occur in some locations. We conducted a synthetic analysis of 13,315 genotyped fish from 558 sites by building logistic regression models using data from geospatial stream databases and from 12 published studies of hybridization to assess whether environmental covariates could explain levels of introgression between westslope cutthroat trout and rainbow trout in the U.S. northern Rocky Mountains. A consensus model performed well (AUC, 0.78-0.86; classification success, 72-82%; 10-fold cross validation, 70-82%) and predicted that rainbow trout introgression was significantly associated with warmer water temperatures, larger streams, proximity to warmer habitats and to recent sources of rainbow trout propagules, presence within the historical range of rainbow trout, and locations further east. Assuming that water temperatures will continue to rise in response to climate change and that levels of introgression outside the historical range of rainbow trout will equilibrate with those inside that range, we applied six scenarios across a 55,234-km stream network that forecast 9.5-74.7% declines in the amount of habitat occupied by westslope cutthroat trout populations of conservation value, but not the wholesale loss of such populations. We conclude that introgression between these taxa is predictably related to environmental conditions, many of which can be manipulated to foster largely genetically intact populations of westslope cutthroat trout and help managers prioritize conservation activities.


Ackerman M.W.,University of Washington | Ackerman M.W.,Eagle Fish Genetics Laboratory | Templin W.D.,Alaska Department of Fish and Game | Seeb J.E.,University of Washington | Seeb L.W.,University of Washington
Conservation Genetics | Year: 2013

Identifying the spatial distribution of genetic variation across the landscape is an essential step in informing species conservation. Comparison of closely related and geographically overlapping species can be particularly useful in cases where landscape may similarly influence genetic structure. Congruent patterns among species highlight the importance that landscape heterogeneity plays in determining genetic structure whereas contrasting patterns emphasize differences in species-specific ecology and life-history or the importance of species-specific adaptation to local environments. We examined the interacting roles of demography and adaptation in determining spatial genetic structure in two closely related and geographically overlapping species in a pristine environment. Using single nucleotide polymorphism (SNP) loci exhibiting both neutral and putative adaptive variation, we evaluated the genetic structure of sockeye salmon in the Copper River, Alaska; these data were compared to existing data for Chinook salmon from the same region. Overall, both species exhibited patterns of isolation by distance; the spatial distribution of populations largely determined the distribution of genetic variation across the landscape. Further, both species exhibited largely congruent patterns of within- and among-population genetic diversity, highlighting the role that landscape heterogeneity and historical processes play in determining spatial genetic structure. Potential adaptive differences among geographically proximate sockeye salmon populations were observed when high FST outlier SNPs were evaluated in a landscape genetics context. Results were evaluated in the context of conservation efforts with an emphasis on reproductive isolation, historical processes, and local adaptation. © 2012 The Author(s).


Narum S.R.,Columbia River Inter Tribal Fish Commission | Campbell N.R.,Columbia River Inter Tribal Fish Commission | Kozfkay C.C.,Eagle Fish Genetics Laboratory | Meyer K.A.,414 East Locust Lane
Molecular Ecology | Year: 2010

Natural populations that evolve under extreme climates are likely to diverge because of selection in local environments. To explore whether local adaptation has occurred in redband trout (Oncorhynchus mykiss gairdneri) occupying differing climate regimes, we used a limited genome scan approach to test for candidate markers under selection in populations occurring in desert and montane streams. An environmental approach to identifying outlier loci, spatial analysis method and linear regression of minor allele frequency with environmental variables revealed six candidate markers (P < 0.01). Putatively neutral markers identified high genetic differentiation among desert populations relative to montane sites, likely due to intermittent flows in desert streams. Additionally, populations exhibited a highly significant pattern of isolation by temperature (P < 0.0001) and those adapted to the same environment had similar allele frequencies across candidate markers, indicating selection for differing climates. These results imply that many genes are involved in the adaptation of redband trout to differing environments, and selection acts to reinforce localization. The potential to predict genetic adaptability of individuals and populations to changing environmental conditions may have profound implications for species that face extensive anthropogenic disturbances. © 2010 Blackwell Publishing Ltd.


Steele C.A.,Pacific States Marine Fisheries Commission | Anderson E.C.,Southwest Fisheries Science Center | Ackerman M.W.,Pacific States Marine Fisheries Commission | Hess M.A.,Columbia River Inter tribal Fisheries Commission | And 3 more authors.
Canadian Journal of Fisheries and Aquatic Sciences | Year: 2013

Parentage-based tagging (PBT) is a promising alternative to traditional coded-wire tag (CWT) methodologies for monitoring and evaluating hatchery stocks. This approach involves the genotyping of hatchery broodstock and uses parentage assignments to identify the origin and brood year of their progeny. In this study we empirically confirmed that fewer than 100 single nucleotide polymorphisms (SNPs) were needed to accurately conduct PBT, we demonstrated that our selected panel of SNPs was comparable in accuracy to a panel of microsatellites, and we verified that stock assignments made with this panel matched those made using CWTs.Wealso demonstrated that when sampling of spawners was incomplete, an estimated PBT rate for the offspring could also be predicted with fewer than 100 SNPs. This study in the Snake River basin is one of the first large-scale implementations of PBT in salmonids and lays the foundation for adopting this technology more broadly in the region, thereby allowing the unprecedented ability to mark millions of smolts and an opportunity to address a variety of parentage-based research and management questions.


Bowersox B.,Clearwater Region | Wickersham T.,Eagle Fish Genetics Laboratory | Redfield L.,Eagle Fish Genetics Laboratory | Ackerman M.W.,Eagle Fish Genetics Laboratory
Transactions of the American Fisheries Society | Year: 2016

Big Bear Creek in the Potlatch River system, Idaho, contains an Endangered Species Act-listed wild population of steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) that is the focus of extensive habitat restoration actions intended to increase population abundance. Both anadromous and resident O. mykiss populations occur in the Big Bear Creek drainage; however, anadromous individuals are known to spawn and rear only in the lower drainage, whereas putative resident fish occur in the headwaters. Big Bear Falls is a potential upstream migration barrier that is located between the two populations. Oncorhynchus mykiss of unknown origin are present within 1 km above the falls. We used analyses of genetic diversity, structure, and sibship reconstruction to determine whether Big Bear Falls limited the movement of steelhead to headwater areas. Known resident O. mykiss were sampled in headwater areas, known anadromous adults were sampled at a weir in the lower drainage, and juveniles of unknown life history were collected from areas below and above the falls. Allele frequency data indicated that anadromous and headwater resident populations were highly differentiated and that exchange of genetic material between populations was limited. However, juvenile O. mykiss in the above-waterfall collection were found to be the offspring or recent descendants of steelhead that successfully navigated above Big Bear Falls, demonstrating that the falls is not a complete barrier. We also identified evidence of limited downstream gene flow, suggesting that resident fish contributed genetic material to the downstream anadromous population. This study documented the successful passage of adult steelhead above Big Bear Falls and the downstream movement of resident fish from the headwaters. However, uncertainties still exist regarding the annual variability in passage and the habitat limitations that impact O. mykiss utilization of areas immediately above the falls. Received March 14, 2015; accepted October 27, 2015 © 2016, © American Fisheries Society 2016.


Kalinowski S.T.,Montana State University | van Doornik D.M.,National Oceanic and Atmospheric Administration | Kozfkay C.C.,Eagle Fish Genetics Laboratory | Waples R.S.,National Oceanic and Atmospheric Administration
Conservation Genetics | Year: 2012

Snake River sockeye salmon spawning in Redfish Lake, Idaho are one of the most endangered taxa of Pacific salmon. The wild population nearly went extinct in the 1990s, and all surviving fish were incorporated into a captive broodstock program at that time. We used pedigree analysis to evaluate the effectiveness of the breeding program in retaining genetic variation from 1991 through 2008. Broodstock records document which males were crossed with which females, but fish from multiple crosses were frequently raised in the same tank so the exact pedigree of the population is unknown. Therefore, a simulation-based approach was used to estimate how much genetic diversity was retained by this breeding program. Results indicate that in 2008, after 5.5 generations of breeding, the average inbreeding coefficient was probably about 0.056. We estimated the inbreeding effective population size to be 41 over the entire program and 115 for the most recent generation. This amount of inbreeding is substantially less than has occurred in many high-profile captive breeding programs. Our results depend on several assumptions regarding the relatedness of fish in the breeding program, but simulations suggest our main results are relatively insensitive to these assumptions. © 2012 Springer Science+Business Media B.V.

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