44 Works

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
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: 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: 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
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...

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...

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

Data from: Estimation of a killer whale (Orcinus orca) population’s diet using sequencing analysis of DNA from feces

Michael J. Ford, Jennifer Hempelmann, M. Bradley Hanson, Katherine L. Ayres, Robin W. Baird, Candice K. Emmons, Jessica I. Lundin, Gregory S. Schorr, Samuel K. Wasser & Linda K. Park
Estimating diet composition is important for understanding interactions between predators and prey and thus illuminating ecosystem function. The diet of many species, however, is difficult to observe directly. Genetic analysis of fecal material collected in the field is therefore a useful tool for gaining insight into wild animal diets. In this study, we used high-throughput DNA sequencing to quantitatively estimate the diet composition of an endangered population of wild killer whales (Orcinus orca) in their...

Data from: Spatial variation buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon

James T. Thorson, Mark D. Scheuerell, Eric R. Buhle & Timothy Copeland
1. Spatial, phenotypic, and genetic diversity at relatively small scales can buffer species against large-scale processes such as climate change that tend to synchronize populations and increase temporal variability in overall abundance or production. This portfolio effect generally results in improved biological and economic outcomes for managed species. Previous evidence for the portfolio effect in salmonids has arisen from examinations of time series of adult abundance, but we lack evidence of spatial buffering of temporal...

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: 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...

Environmental DNA provides quantitative estimates of Pacific hake abundance and distribution in the open ocean.

Andrew Shelton, Ana Ramon-Laca, Abigail Wells, Julia Clemons, Dezhang Chu, Blake Feist, Ryan Kelly, Sandra Parker-Stetter, Rebecca Thomas, Krista Nichols & Linda Park
All species inevitably leave genetic traces in their environments, and the resulting environmental DNA (eDNA) reflects the species present in a given habitat. It remains unclear whether eDNA signals can provide quantitative metrics of abundance on which human livelihoods or conservation successes depend. Here, we report the results of a large eDNA ocean survey (spanning 86,000 km2 to depths of 500m) to understand the abundance and distribution of Pacific hake Merluccius productus, the target of...

North Pacific harbor porpoise SNP and microhaplotype genotypes, mitochondrial control region haplotype sequences

Phillip Morin, Brenna Forester, Karin Forney, Carla Crossman, Brittany Hancock-Hanser, Kelly Robertson, Lance Barrett-Lennard, Robin Baird, John Calambokidis, Pat Gearin, Bradley Hanson, Cassie Schumacher, Timothy Harkins, Michael Fontaine, Barbara Taylor & Kim Parsons
Harbor porpoises in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples) in addition to mtDNA sequence data (N=413 samples), to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We...

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...

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: 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: 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...

West Coast Fishing Communities Socio-Economic Data Model: technical documentation and guidelines for use

Aaron Mamula, Camille Kohler, Rosemary Kosaka, Anna Varney & Karma C. Norman
NOAA technical memorandum NMFS-SWFSC ; 621

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

, Kayleigh A. Somers, , , &
NOAA data report NMFS NWFSC DR ; 2019-02

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

Genotypes for herring samples collected from Chinook salmon gut contents

Eleni Petrou, Joshua Chamberlin, Will Duguid, Russel Barsh, Francis Juanes, Jessica Qualley & Lorenz Hauser
Dynamic prey resources influence foraging opportunities for consumers. In coastal food webs, forage fish abundance and seasonal reproduction mediate foraging opportunities for mobile consumers. Recent declines in Chinook salmon productivity have prompted efforts to determine whether poormarine survival is caused by limited feeding opportunities. To establish the importance of phenological diversity in Pacific herring for Chinook salmon, we used genetic stock identification to assign individual herring collected from the guts of juvenile and adult Chinook...

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: 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: 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: Rigorous monitoring of a large-scale marine stock enhancement program demonstrates the need for comprehensive management of fisheries and nursery habitat

Shuichi Kitada, Kaori Nakajima, Katsuyuki Hamasaki, Hirotoshi Shishidou, Robin S. Waples & Hirohisa Kishino
Release of captively-bred individuals into the wild is one of the most popular tools in fisheries, forestry, and wildlife management, and introgression of hatchery-reared animals into wild populations is of global concern. However, research and monitoring of impacts on wild populations are generally lacking, and the benefit of hatcheries for long-term fisheries and conservation goals is unclear. Using spatio-temporal genetic monitoring and a four-dacade time series of catch data, we quantified the effects on the...

Data from: The evolution of microendemism in a reef fish (Hypoplectrus maya)

Benjamin M. Moran, Kosmas Hench, Robin S. Waples, Marc P. Höppner, Carole C. Baldwin, W. Owen McMillan & Oscar Puebla
Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50-km segment of the Mesoamerican Barrier Reef System (MBRS)....

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
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...

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