25 Works

Data from: Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon

Lisa W Seeb, William D Templin, Shunpei Sato, Syuiti Abe, Kenneth Warheit, Jung Youn Park & James E Seeb
Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometers, have become increasingly valuable in the presence of climate change, increasing hatchery production, and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive datasets from spawning populations originating from across the species? range....

Freshwater floodplain habitats buffer native food webs from negative effects of non-native centrarchids and bullfrogs

Meredith Holgerson, Martha Barnard, Byunghyun Ahn, Marc Hayes & Angela Strecker
Species introductions are common in freshwater environments, with the potential to transform community and ecosystem structure. Predatory fishes and American bullfrogs (Rana catesbeiana = Lithobates catesbeianus) are both widespread aquatic invaders implicated in native amphibian declines. In lowland ecosystems, co-occurrence between native and non-native fishes and larval amphibians appears more common than in high-elevation ecosystems, though community interactions there are poorly studied. In this study, we used stable isotope analysis of carbon (δ13C) and nitrogen...

Data from: Estimation of genotyping error rate from repeat genotyping, unintentional recaptures and known parent-offspring comparisons in 16 microsatellite loci for brown rockfish (Sebastes auriculatus)

Maureen A. Hess, James G. Rhydderch, Larry L. LeClair, Raymond M. Buckley, Mitsuhiro Kawase & Lorenz Hauser
Genotyping errors are present in almost all genetic data and can affect biological conclusions of a study, particularly for studies based on individual identification and parentage. Many statistical approaches can incorporate genotyping errors, but usually need accurate estimates of error rates. Here, we used a new microsatellite data set developed for brown rockfish (Sebastes auriculatus) to estimate genotyping error using three approaches: (i) repeat genotyping 5% of samples, (ii) comparing unintentionally recaptured individuals and (iii)...

Data from: Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha)

Michael J. Ford, Andrew Murdoch & Michael Hughes
We used parentage analysis based on microsatellite genotypes to measure rates of homing and straying of Chinook salmon (Oncorhynchus tshawytscha) among five major spawning tributaries within the Wenatchee River, Washington. Based on analysis of 2248 natural-origin and 11594 hatchery-origin fish, we estimated that the rate of homing to natal tributaries by natural-origin fish ranged from 0% to 99% depending on the tributary. Hatchery-origin fish released in one of the five tributaries homed to that tributary...

Data from: Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)

Daniel P. Drinan, Kristen M. Gruenthal, Michael F. Canino, Dayv Lowry, Mary C. Fisher & Lorenz Hauser
The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation-by-distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site associated DNA (RAD) sequencing to investigate population...

Endangered predators and endangered prey: seasonal diet of Southern Resident killer whales

Michael Ford, M. Bradley Hanson, Candice Emmons, Meredith Everett, Kim Parsons, Linda Park, Jennifer Hempelmann, Donald Van Doornik, Gregory Schorr, Jeffrey Jacobsen, Mark Sears, Maya Sears, John Sneva, Robin Baird & Lynne Barre
Understanding diet is critical for conservation of endangered predators. The Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily in the west coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of the whales’ seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook...

Data from: Signatures of natural selection among lineages and habitats in Oncorhynchus mykiss

Morten T. Limborg, Scott M. Blankenship, Sewall F. Young, Fred M. Utter, Lisa W. Seeb, Mette H. H. Hansen & James E. Seeb
Recent advances in molecular interrogation techniques now allow unprecedented genomic inference about the role of adaptive genetic divergence in wild populations. We used high-throughput genotyping to screen a genome-wide panel of 276 single nucleotide polymorphisms (SNPs) for the economically and culturally important salmonid Oncorhynchus mykiss. Samples included 805 individuals from 11 anadromous and resident populations from the northwestern United States and British Columbia, and represented two major lineages including paired populations of each life history...

Data from: Forty years of seagrass population stability and resilience in an urbanizing estuary

Andrew Olaf Shelton, Tessa B. Francis, Blake E. Feist, Gregory D. Williams, Adam Lindquist, Phillip S. Levin & Philip S. Levin
Coasts and estuaries contain among the most productive and ecologically important habitats in the world and face intense pressure from current and projected human activities, including coastal development. Seagrasses are a key habitat feature in many estuaries perceived to be in widespread decline owing to human actions. We use spatio-temporal models and a 41-year time series from 100s of km of shoreline which includes over 160 000 observations from Puget Sound, Washington, USA, to examine...

Data from: Genomewide association analyses of fitness traits in captive-reared Chinook salmon: applications in evaluating conservation strategies

Charles D. Waters, Jeffrey J. Hard, Marine S.O. Brieuc, David E. Fast, Kenneth I. Warheit, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish & Marine S. O. Brieuc
A novel application of genome-wide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus...

A novel method for detecting extra-home range movements (EHRMs) by animals and recommendations for future EHRM studies

Todd Jacobsen, Kevyn Wiskirchen & Stephen Ditchkoff
Infrequent, long-distance animal movements outside of typical home range areas provide useful insights into resource acquisition, gene flow, and disease transmission within the fields of conservation and wildlife management, yet understanding of these movements is still limited across taxa. To detect these extra-home range movements (EHRMs) in spatial relocation datasets, most previous studies compare relocation points against fixed spatial and temporal bounds, typified by seasonal home ranges (referred to here as the “Fixed-Period” method). However,...

rhinoceros auklet microsatellite data

Theresa Burg, Marie Prill, Katharine Studholme, Alice Domalik, Strahan Tucker, Catherine Jardine, Mark Maftei, Kenneth Wright, Jesse Beck, Russell Bradley, Ryan Carle, Thomas Good, Scott Hatch, Peter Hodum, Motohiro Ito, Scott Pearson, Nora Rojek, Leslie Slater, Yutaka Watanuki, Alexis Will, Aidan Bindoff, Glenn Crossin, Mark Drever & Mark Hipfner
We tested the hypothesis that segregation in wintering areas promotes population differentiation in a sentinel North Pacific seabird, the rhinoceros auklet (Cerorhinca monocerata). We collected tissue samples for genetic analyses on five breeding colonies in the western Pacific Ocean (Japan) and 13 in the eastern Pacific Ocean (California to Alaska), and deployed light-level geologgers on 12 eastern Pacific colonies to delineate wintering areas. Loggers were deployed previously on one colony in Japan. There was strong...

Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia

Cristian B. Canales-Aguirre, Wesley A. Larson, Garret J. McKinney, C. Eliza Claure, J. Dellis Rocha, Santiago G. Ceballos, Maria I. Cádiz, José M. Yáñez & Daniel Gómez-Uchida
Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this...

Data from: Evaluating DNA degradation rates in faecal pellets of the endangered pygmy rabbit

Stephanie M. DeMay, Penny A. Becker, Chad A. Eidson, Janet L. Rachlow, Timothy R. Johnson & Lisette P. Waits
Noninvasive genetic sampling of faecal pellets can be a valuable method for monitoring rare and cryptic wildlife populations, like the pygmy rabbit (Brachylagus idahoensis). To investigate this method’s efficiency for pygmy rabbit monitoring, we evaluated the effect of sample age on DNA degradation in faecal pellets under summer field conditions. We placed 275 samples from known individuals in natural field conditions for 1 to 60 days and assessed DNA quality by amplifying a 294 base...

Data from: Broodstock history strongly influences natural spawning success in hatchery steelhead (Oncorhynchus mykiss)

Michael J. Ford, Andrew R. Murdoch, Michael J. Hughes, Todd R. Seamons, Eric LaHood, Eric S. LaHood & Michael S. Hughes
We used genetic parentage analysis of 6200 potential parents and 5497 juvenile offspring to evaluate the relative reproductive success of hatchery and natural steelhead (Onchorhynchus mykiss) when spawning in the wild between 2008 and 2011 in the Wenatchee River, Washington. Hatchery fish originating from two prior generation hatchery parents had <20% of the reproductive success of natural origin spawners. In contrast, hatchery females originating from a cross between two natural origin parents of the prior...

Re-coding of the Dataset for Status of the European Green Crab, Carcinus maenas, in Oregon and Washington coastal Estuaries in 2019 and 2020

Kimberly Sims, Sylvia Behrens Yamada, Shon Schooler, Renee Heller, Luke Donaldson, Graham T Takacs, Andrea Randall & Chelsey Buffington
European green crab, Carcinus maenas, trapped and collected in coastal Oregon and Washington coastal estuaries during the 2019 and 2020. Data for individual crabs include: estuary, site, date of collection, sex, carapace width, weight, molt stage (color of abdomen), missing limbs, estimated year class, method of collection, and name of collector. This dataset has been re-coded for Kimberly Sims MNR capstone

Relative influences of microhabitat incubation conditions and genetic parentage effects on lake sturgeon (Acipenser fulvescens) offspring traits during early ontogeny (DATA)

Kari Dammerman
Knowledge on factors influencing traits during critical early growth periods is essential for predicting population persistence. Genetic effects and microhabitat stream conditions at female selected oviposition sites influence larval phenotypes. However, limited work has examined contributions of both factors across sequential ontogenetic stages for larvae of wild origin. Using a wild population of lake sturgeon (Acipenser fulvescens) from Black Lake, Michigan (USA), fertilized eggs were collected from stream substrate just prior to hatch at one-meter...

Dataset from: Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring

Sarah Bassing, Melia DeVivo, Taylor Ganz, Brian Kertson, Laura Prugh, Trent Roussin, Lauren Satterfield, Rebecca Windell, Aaron Wirsing & Beth Gardner
Estimating habitat and spatial associations for wildlife is common across ecological studies, and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inferences in...

Data from: Interactive effects of wildfires, season, and predator activity shape mule deer movements

Taylor R. Ganz, Melia DeVivo, Brian Kertson, Trent Roussin, Lauren Satterfield, Aaron Wirsing & Laura Prugh
Wildfires are increasing in size, frequency, and severity due to climate change and fire suppression, but the direct and indirect effects on wildlife remain largely unresolved. Fire removes forest canopy, which can improve forage for ungulates but also reduce snow interception, leading to a deeper snowpack and potentially increased vulnerability to predation in winter. If ungulates exhibit predator-mediated foraging, burns should generally be selected for in summer to access high-quality forage and avoided in winter...

Data from: Genetic assessment of a summer chum salmon metapopulation in recovery

Maureen P. Small, Thom H. Johnson, Cherril Bowman & Edith Martinez
Programs to rebuild imperiled wild fish populations often include hatchery-born fish derived from wild populations to supplement natural spawner abundance. These programs require monitoring to determine their demographic, biological, and genetic effects. In 1990s in Washington State, the Summer Chum Salmon Conservation Initiative developed a recovery program for the threatened Hood Canal summer chum salmon Evolutionarily Significant Unit (ESU) (the metapopulation) that used in-river spawners (wild fish) for each respective supplementation broodstock in six tributaries....

Data from: Forest cover mediates genetic connectivity of northwestern cougars

Matthew J. Warren, David O. Wallin, Richard A. Beausoleil & Kenneth I. Warheit
Population structure, connectivity, and dispersal success of individuals can be challenging to demonstrate for solitary carnivores with low population densities. Though the cougar (Puma concolor) is widely distributed throughout North America and is capable of dispersing long distances, populations can be geographically structured and genetic isolation has been documented in some small populations. We described genetic structure and explored the relationship between landscape resistance and genetic variation in cougars in Washington and southern British Columbia...

Data from: Landscape genetics of the nonnative red fox of California

Benjamin N. Sacks, Jennifer L. Brazeal, Jefferey C. Lewis & Jeffrey C. Lewis
Invasive mammalian carnivores contribute disproportionately to declines in global biodiversity. In California, nonnative red foxes (Vulpes vulpes) have significantly impacted endangered ground-nesting birds and native canids. These foxes derive primarily from captive-reared animals associated with the fur-farming industry. Over the past five decades, the cumulative area occupied by nonnative red fox increased to cover much of central and southern California. We used a landscape-genetic approach involving mitochondrial DNA (mtDNA) sequences and 13 microsatellites of 402...

Data from: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Charles D. Waters, Jeffrey J. Hard, Marine S. O. Brieuc, David E. Fast, Kenneth I. Warheit, Robin Waples, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish & Robin S. Waples
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal...

Data from: Consequences for conservation: population density and genetic effects on reproduction of an endangered lagomorph

Stephanie M. DeMay, Penny A. Becker, Lisette P. Waits, Timothy R. Johnson & Janet L. Rachlow
Understanding reproduction and mating systems is important for managers tasked with conserving vulnerable species. Genetic tools allow biologists to investigate reproduction and mating systems with high resolution and are particularly useful for species that are otherwise difficult to study in their natural environments. We conducted parentage analyses using 19 nuclear DNA microsatellite loci to assess the influence of population density, genetic diversity, and ancestry on reproduction, and to examine the mating system of pygmy rabbits...

Data from: Maintaining a wild phenotype in a conservation hatchery program for Chinook salmon: the effect of managed breeding on early male maturation

Donald A. Larsen, Deborah L. Harstad, Abby E. Fuhrman, Curtis M. Knudsen, Steven L. Schroder, William J. Bosch, Peter F. Galbreath, David E. Fast & Brian R. Beckman
In many salmonid species, age and size of maturation is plastic and influenced by the interaction between genetic and environmental factors. Hatchery reared salmon often mature at an earlier age and smaller size than wild fish. Modern salmon conservation efforts have focused on managing the level of gene flow between hatchery and natural origin fish to minimize potential genotypic and phenotypic change. In salmonids, maturation probability is dependent on exceeding a genetically set threshold in...

Data from: Simulating effects of fitness and dispersal on the use of Trojan sex chromosomes for invasive species management

Casey Day, Erin Landguth, Ryan Simmons, Bill Baker, Andrew Whiteley, Paul Lukacs & Andrew Bearlin
The use of Trojan Y Chromosomes (TYC) for controlling invasive species involves manipulating the sex chromosomes of captive-raised individuals. Once released, the offspring of these individuals consist of only one sex, thereby skewing the sex-ratio of the invasive population and potentially leading to eradication. Simulation models are needed that can inform managers on how to maximize the likelihood of species eradication, since implementation of this novel management approach in the field is still rare. Here,...

Registration Year

  • 2022
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  • 2020
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  • 2011

Resource Types

  • Dataset


  • Washington Department of Fish and Wildlife
  • University of Washington
  • Northwest Fisheries Science Center
  • National Oceanic and Atmospheric Administration
  • Oregon Department of Fish and Wildlife
  • University of Idaho
  • Western Washington University
  • University of Montana
  • Oregon State University
  • Columbia River Inter-Tribal Fish Commission