32 Works

Groundfish Expanded Mortality Multiyear (GEMM), 2002-18

Kayleigh A. Somers, Jason E. Jannot, Vanessa J. Tuttle, Kate Richerson, Neil Riley & Jon T. McVeigh
NWFSC data report ; 2020-01

Data from: Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Charles Waters, Jeffrey Hard, David Fast, Curtis Knudsen, William Bosch & Kerry-Ann Naish
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by...

Ecosystem Status Report of the California Current for 2019: A Summary of Ecosystem Indicators Compiled by the California Current Integrated Ecosystem Assessment Team (CCEIA)

Christopher James Harvey, Newell Garfield, Gregory D. (Gregory Dean) Williams, Nick Tolimieri, Isaac Schroeder, Kelly S. Andrews, Katie Barnas, Eric Peter Bjorkstedt, Steven J. Bograd, Richard D. Brodeur, Brian J. (Brian Joseph) Burke, Jason Marc Cope, Audrey Coyne, Lynn deWitt, Judy Dowell, Field, Fisher, Jennifer , Peter Frey, Thomas Good, Elliott Lee Hazen, Daniel S. Holland, Matthew Hunter, Kym Jacobson, Michael G. Jacox & Christy Juhasz
NOAA Technical Memorandum NMFS-NWFSC ; 149

Weighted Length Frequency Distributions for Pacific Halibut in U.S. West Coast Limited Entry and Catch Share Bottom Trawl and Pot Fisheries, 2004–18

Jason Earl Jannot, Kate E. Richerson, Kayleigh A. Somers & Jon McVeigh
NOAA data report NMFS NWFSC-DR ; 2019-03

Observed and Estimated Total Bycatch of Salmon in U.S. West Coast Fisheries, 2002–18

Richerson, Kate, Kayleigh A. Somers, Jannot, Jason Earl, Tuttle, Vanessa J., Riley, Neil B. & McVeigh, Jon
NOAA data report NMFS NWFSC DR ; 2019-02

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 & Andrew O. Shelton
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: 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: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A. Morin, Kim M. Parsons, Frederick I. Archer, María C. Ávila-Arcos, Lance G. Barrett-Lennard, Luciano Dalla Rosa, Sebastián Duchêne, John W. Durban, Graeme M. Ellis, Steven H. Ferguson, John K. Ford, Michael J. Ford, Cristina Gabrilao, M. Thomas P. Gilbert, Kristin Kaschner, Craig O. Matkin, Stephen D. Petersen, Kelly M. Robertson, Ingrid N. Visser, Paul R. Wade, Simon Y. W. Ho & Andrew D. Foote
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from...

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: Use of genotyping-by-sequencing data to develop a high-throughput and multi-functional SNP panel for conservation applications in Pacific lamprey

Jon E. Hess, Nathan R. Campbell, Margaret F. Docker, Cyndi Baker, Aaron Jackson, Ralph Lampman, Brian McIlraith, Mary L. Moser, David P. Statler, William P. Young, Andrew J. Wildbill & Shawn R. Narum
Next generation sequencing data can be mined for highly informative single nucleotide polymorphisms (SNPs) to develop high-throughput genomic assays for non-model organisms. However, choosing a set of SNPs to address a variety of objectives can be difficult because SNPs are often not equally informative. We developed an optimal combination of 96 high-throughput SNP assays from a total of 4,439 SNPs identified in a previous study of Pacific lamprey (Entosphenus tridentatus), and used them to address...

Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)

Eleni L. Petrou, Lorenz Hauser, Robin S. Waples, Jim E. Seeb, William D. Templin, Daniel Gomez-Uchida, Lisa W. Seeb, E. L. Petrou, L. Hauser, J. E. Seeb, D. Gomez-Uchida, L. W. Seeb, W. D. Templin & R. S. Waples
Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was...

Data from: Spatio-temporal models reveal subtle changes to demersal communities following the Exxon Valdez oil spill

Andrew O. Shelton, Mary E. Hunsicker, Eric J. Ward, Blake E. Feist, Rachael Blake, Colette L. Ward, Benjamin C. Williams, Janet T. Duffy-Anderson, Anne B. Hollowed, Alan C. Haynie, Andrew O Shelton, Eric J Ward, Blake E Feist, Mary E Hunsicker, Janet T Duffy-Anderson, Anne B Hollowed, Alan C Haynie, Benjamin C Williams & Colette L Ward
Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez...

Data from: Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon

Robin S. Waples, Anna Elz, Billy D. Arnsberg, James R. Faulkner, Jeffrey J. Hard, Emma Timmins-Schiffman & Linda K. Park
Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the U.S., have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In...

Data from: Genetic signatures of ecological diversity along an urbanization gradient

Ryan P. Kelly, James L. O'Donnell, Natalie C. Lowell, Andrew O. Shelton, Jameal F. Samhouri, Shannon M. Hennessey, Blake E. Feist & Gregory D. Williams
Despite decades of work in environmental science and ecology, estimating human influences on ecosystems remains challenging. This is partly due to complex chains of causation among ecosystem elements, exacerbated by the difficulty of collecting biological data at sufficient spatial, temporal, and taxonomic scales. Here, we demonstrate the utility of environmental DNA (eDNA) for quantifying associations between human land use and changes in an adjacent ecosystem. We analyze metazoan eDNA sequences from water sampled in nearshore...

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...

Data from: Model-based inference for estimating shifts in species distribution, area occupied and centre of gravity

James T. Thorson, Malin L. Pinsky & Eric J. Ward
Changing climate is already impacting the spatial distribution of many taxa, including bees, plants, birds, butterflies and fishes. A common goal is to detect range shifts in response to climate change, including changes in the centre of the population's distribution (the centre of gravity, COG), population boundaries and area occupied. Conventional estimators, such as the abundance-weighted average (AWA) estimator for COG, confound range shifts with changes in the spatial distribution of available survey data and...

Data from: Evaluating adaptive divergence between migratory and non-migratory ecotypes of a salmonid fish, Oncorhynchus mykiss

Matthew C. Hale, Frank P. Thrower, Ewann A. Berntson, Michael R. Miller & Krista M. Nichols
Next generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. Using the two approaches in parallel is an especially attractive approach in non-models organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a non-model fish species, rainbow...

Data from: Ontogenetic changes in embryonic and brain gene expression in progeny produced from migratory and resident Oncorhynchus mykiss

Garrett J. McKinney, Matthew C. Hale, Giles Goetz, Michael Gribskov, Frank P. Thrower & Krista M. Nichols
Little information has been gathered regarding the ontogenetic changes that contribute to differentiation between resident and migrant individuals, particularly before the onset of gross morphological and physiological changes in migratory individuals. The aim of this study was to evaluate gene expression during early development in Oncorhynchus mykiss populations with different life histories, in a tissue known to integrate environmental cues to regulate complex developmental processes and behaviours. We sampled offspring produced from migrant and resident...

Data from: Using time series analysis to characterize evolutionary and plastic responses to environmental change: a case study of a shift toward earlier migration date in sockeye salmon

Lisa G. Crozier, Mark D. Scheuerell & Richard W. Zabel
Environmental change can shift the phenotype of an organism through either evolutionary or nongenetic processes. Despite abundant evidence of phenotypic change in response to recent climate change, we typically lack sufficient genetic data to identify the role of evolution. We present a method of using phenotypic data to characterize the hypothesized role of natural selection and environmentally driven phenotypic shifts (plasticity). We modeled historical selection and environmental predictors of interannual variation in mean population phenotype...

Data from: Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Rebecca Hooper, Jaelle C. Brealey, Tom Van Der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul Wade, M Thomas P. Gilbert, Philip A. Morin, Jochen B.W. Wolf, Andrew D. Foote, Katerina Guschanski, Phillip A. Morin, M. Thomas P. Gilbert, M. Bradley Hanson & Jochen B. W. Wolf
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro‐organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies...

Data from: Increased natural reproduction and genetic diversity one generation after cessation of a steelhead trout (Oncorhynchus mykiss) conservation hatchery program

Barry A. Berejikian & Donald M. Van Doornik
Spatial and temporal fluctuations in productivity and abundance confound assessments of captive propagation programs aimed at recovery of Threatened and Endangered populations. We conducted a 17 year before-after-control-impact experiment to determine the effects of a conservation hatchery program for anadromous steelhead trout (Oncorhynchus mykiss) on a key indicator of natural reproduction (naturally produced nests or 'redds'). The supplemented population exhibited a significant (2.6-fold) increase in redd abundance in the generation following supplementation. Four non-supplemented (control)...

Data from: Genes predict long distance migration and large body size in a migratory fish, Pacific lamprey

Jon E. Hess, Christopher C. Caudill, Matthew L. Keefer, Brian J. McIlraith, Mary L. Moser & Shawn R. Narum
Elucidation of genetic mechanisms underpinning migratory behavior could help predict how changes in genetic diversity may affect future spatiotemporal distribution of a migratory species. This ability would benefit conservation of one such declining species, anadromous Pacific lamprey (Entosphenus tridentatus). Nonphilopatric migration of adult Pacific lamprey has homogenized population-level neutral variation but has maintained adaptive variation that differentiates groups based on geography, run-timing and adult body form. To investigate causes for this adaptive divergence, we examined...

Data from: Fine-scale local adaptation in an invasive freshwater fish has evolved in contemporary time

Peter A. H. Westley, Eric J. Ward, Ian A. Fleming, P. A. H. Westley, I. A. Fleming & E. J. Ward
Adaptive evolutionary change in only a few generations can increase the ability of non-native invasive species to spread, and yet adaptive divergence is rarely assessed in recently established populations. In this paper, we experimentally test for evidence of fine-scale local adaptation in juvenile survival and growth among three populations of an invasive freshwater fish with reciprocal transplants and common-garden experiments. Despite intrinsic differences in habitat quality, in two out of three populations we detected evidence...

Data from: Intermittent breeding and constraints on litter size: consequences for effective population size per generation (Ne) and per reproductive cycle (Nb)

Robin S. Waples & Tiago Antao
In iteroparous species, it is easier to estimate Nb = effective number of breeders in one reproductive cycle than Ne = effective population size per generation. Nb can be used as a proxy for Ne and also can provide crucial insights into eco-evolutionary processes that occur during reproduction. We used analytical and numerical methods to evaluate effects of intermittent breeding and litter/clutch size on inbreeding Nb and Ne. Fixed or random litter sizes ≥ 3...

Data from: The structure and distribution of benthic communities on a shallow seamount (Cobb Seamount, Northeast Pacific Ocean)

Cherisse Du Preez, Janelle M. R. Curtis & M. Elizabeth Clarke
Partially owing to their isolation and remote distribution, research on seamounts is still in its infancy, with few comprehensive datasets and empirical evidence supporting or refuting prevailing ecological paradigms. As anthropogenic activity in the high seas increases, so does the need for better understanding of seamount ecosystems and factors that influence the distribution of sensitive benthic communities. This study used quantitative community analyses to detail the structure, diversity, and distribution of benthic mega-epifauna communities on...

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