77 Works

Data from: Linking transcriptional responses to organismal tolerance reveals mechanisms of thermal sensitivity in a mesothermal endangered fish

Lisa M. Komoroske, Richard E. Connon, Kenneth M. Jeffries, Nann A. Fangue & Ken M. Jeffries
Forecasting species' responses to climate change requires understanding the underlying mechanisms governing environmental stress tolerance, including acclimation capacity and acute stress responses. Current knowledge of these physiological processes in aquatic ectotherms is largely drawn from eurythermal or extreme stenothermal species. Yet many species of conservation concern exhibit tolerance windows and acclimation capacities in between these extremes. We linked transcriptome profiles to organismal tolerance in a mesothermal endangered fish, the delta smelt (Hypomesus transpacificus), to quantify...

Data from: Genetic stock composition of marine bycatch reveals disproportional impacts on depleted river herring genetic stocks

Daniel J. Hasselman, Eric C. Anderson, Emily E. Argo, N. David Bethoney, Stephen R. Gephard, David M. Post, Bradley P. Schondelmeier, Thomas F. Schultz, Theodore V. Willis & Eric P. Palkovacs
Bycatch of mid-trophic level anadromous fishes that connect marine and freshwater ecosystems is a growing conservation concern. Anadromous alewife (Alosa pseudoharengus) and blueback herring (A. aestivalis) are important components of coastal freshwater and marine food webs, but have experienced dramatic declines in the abundances of spawning adults. Freshwater-focused restoration efforts have yielded few consistent signs of recovery; raising concerns that bycatch in Northwest Atlantic commercial fisheries may be negating these conservation actions. Using data from...

Data from: Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus.

Gregory O’Corry-Crowe, Tom Gelatt, Lorrie Rea, Carolina Bonin, Michael Rehberg & Greg O'Corry-Crowe
Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density-dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n=1,106) and 16 microsatellite loci...

Data from: A role for migration-linked genes and genomic islands in divergence of a songbird

Kristen Ruegg, Eric C. Anderson, Jason Boone, Jazz Pouls & Thomas B. Smith
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently there has been a debate around the role of “genomic islands of divergence” (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson’s thrush, Catharus ustulatus, is a migratory songbird with two genetically-distinct subspecies that differ in a number of traits known to be involved in reproductive isolation...

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: Trophic sensitivity of invasive predator and native prey interactions: integrating environmental context and climate change

Brian S. Cheng, Lisa M. Komoroske & Edwin D. Grosholz
Climate change is predicted to intensify the impacts of invasive species by enhancing their performance relative to their native counterparts. However, few studies have compared the performance of invasive predators and native prey, despite the fact that non-native predators are well known to disrupt native communities. The ‘trophic sensitivity hypothesis’ suggests that predators are less tolerant of increasing environmental stress than their prey, whereas the ‘tolerant invaders hypothesis’ suggests that invaders are more tolerant than...

Data from: Dispersal of a near-shore marine fish connects marine reserves and adjacent fished areas along an open coast

Diana Baetscher, Eric Anderson, Elizabeth Gilbert-Horvath, Daniel Malone, Emily Saarman, Mark Carr & John Garza
Marine species with pelagic larvae typically exhibit little population structure, suggesting long distance dispersal and high gene flow. Directly quantifying dispersal of marine fishes is challenging but important, particularly for design of marine protected areas (MPAs). Here, we studied kelp rockfish (Sebastes atrovirens) sampled along ~25 km of coastline in a boundary current-driven ecosystem and used genetic parentage analysis to identify dispersal events and characterize them, since the distance between sedentary parents and their settled...

Co-occurrence of beaked whale strandings and naval sonar in the Mariana Islands, Western Pacific

Anne Simonis, Robert Brownell, Bruce Thayre, Jennifer Trickey, Erin Oleson, Roderick Huntington & Simone Baumann-Pickering
Mid-frequency active sonar (MFAS), used for antisubmarine warfare (ASW), has been associated with multiple beaked whale (BW) mass stranding events. Multinational naval ASW exercises have utilized MFAS offshore of the Mariana Archipelago semi-annually since 2006. We report BW and MFAS acoustic activity near the islands of Saipan and Tinian from March 2010 through November 2014. Signals from Cuvier’s (Ziphius cavirostris) and Blainville’s beaked whales (Mesoplodon densirostris), and a third unidentified BW species were detected throughout...

Heterogeneous genetic basis of age at maturity in salmonid fishes

Charles Waters, Anthony Clemento, Tutku Aykanat, John Garza, Kerry-Ann Naish, Shawn Narum & Craig Primmer
Understanding the genetic basis of repeated evolution of the same phenotype across taxa is a fundamental aim in evolutionary biology and has applications to conservation and management. However, the extent to which interspecific life-history trait polymorphisms share evolutionary pathways remains under-explored. We address this gap by studying the genetic basis of a key life-history trait, age at maturity, in four species of Pacific salmon (genus Oncorhynchus) that exhibit intra- and interspecific variation in this trait...

Data from: Whole-body endothermy in a mesopelagic fish, the opah, Lampris guttatus

Nicholas C. Wegner, Owyn E. Snodgrass, Heidi Dewar & John R. Hyde
Endothermy (the metabolic production and retention of heat to warm body temperature above ambient) enhances physiological function, and whole-body endothermy generally sets mammals and birds apart from other animals. Here, we describe a whole-body form of endothermy in a fish, the opah (Lampris guttatus), that produces heat through the constant “flapping” of wing-like pectoral fins and minimizes heat loss through a series of counter-current heat exchangers within its gills. Unlike other fish, opah distribute warmed...

Data from: Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change?

Catherine R. M. Attard, Luciano B. Beheregaray, K. Curt S. Jenner, Peter C. Gill, Micheline- N. Jenner, Margaret G. Morrice, Kelly M. Robertson & Luciana M. Möller
Understanding the degree of genetic exchange between subspecies and populations is vital for the appropriate management of endangered species. Blue whales (Balaenoptera musculus) have two recognized Southern Hemisphere subspecies that show differences in geographic distribution, morphology, vocalizations and genetics. During the austral summer feeding season the pygmy blue whale (B. m. brevicauda) is found in temperate waters and the Antarctic blue whale (B. m. intermedia) in polar waters. Here we used genetic analyses to report...

Data from: Targeted multiplex next-generation sequencing: Advances in techniques of mitochondrial and nuclear DNA sequencing for population genomics

Brittany Hancock-Hanser, Amy Frey, Matthew S. Leslie, Peter H. Dutton, Frederick I. Archer, Phillip A. Morin & Brittany L. Hancock-Hanser
Next-generation sequencing (NGS) is emerging as an efficient and cost-effective tool in population genomic analyses of nonmodel organisms, allowing simultaneous resequencing of many regions of multi-genomic DNA from multiplexed samples. Here, we detail our synthesis of protocols for targeted resequencing of mitochondrial and nuclear loci by generating indexed genomic libraries for multiplexing up to 100 individuals in a single sequencing pool, and then enriching the pooled library using custom DNA capture arrays. Our use of...

Data from: Reconstructing the migratory behavior and long-term survivorship of juvenile Chinook salmon under contrasting hydrologic regimes

Anna M. Sturrock, J. D. Wikert, Timothy Heyne, Carl Mesick, Alan E. Hubbard, Travis M. Hinkelman, Peter K. Weber, George E. Whitman, Justin J. Glessner & Rachel C. Johnson
The loss of genetic and life history diversity has been documented across many taxonomic groups, and is considered a leading cause of increased extinction risk. Juvenile salmon leave their natal rivers at different sizes, ages and times of the year, and it is thought that this life history variation contributes to their population sustainability, and is thus central to many recovery efforts. However, in order to preserve and restore diversity in life history traits, it...

Data from: Calculating the ecological impacts of animal-borne instruments on aquatic organisms

T. Todd Jones, Kyle S. Van Houtan, Brian L. Bostrom, Peter Ostafichuk, Jon Mikkelsen, Emre Tezcan, Michael Carey, Brittany Imlach & Jeffrey A. Seminoff
1. Animal-borne instruments provide researchers with valuable data to address important questions on wildlife ecology and conservation. However, these devices have known impacts on animal behaviour and energetics. Tags deployed on migrating animals may reduce reproductive output through increased energy demands or cause phenological mismatches of foraging and nesting events. For marine organisms, the only tagging guidelines that exist are based on lift and thrust impacts on birds – concepts that do not translate well...

Data from: Large-scale parentage analysis reveals reproductive patterns and heritability of spawn timing in a hatchery population of steelhead (Oncorhynchus mykiss)

Alicia Abadía-Cardoso, Eric C. Anderson, Devon E. Pearse & John Carlos Garza
Understanding life history traits is an important first step in formulating effective conservation and management strategies. The use of artificial propagation and supplementation as such a strategy can have numerous effects on the supplemented natural populations and minimizing life history divergence is crucial in minimizing these effects. Here, we use single nucleotide polymorphism (SNP) genotypes for large-scale parentage analysis and pedigree reconstruction in a hatchery population of steelhead, the anadromous form of rainbow trout. Nearly...

Data from: Strong maternal fidelity and natal philopatry shape genetic structure in North Pacfic humpback whales

C. Scott Baker, Debbie Steel, John Calambokidis, Erin A. Falcone, Ursula Gozález-Peral, Jay Barlow, Alexander M. Burdin, Phillip J. Clapham, John K. B. Ford, Christine M. Gabriele, David Mattila, Janice M. Straley, Barbara L. Taylor, Jorge Urbán, Paul R. Wade, David Weller, Briana H. Witteveen, Manami Yamaguchi, CS Baker, BH Witteveen, E Falcone, BL Taylor, JKB Ford, AM Burdin, PJ Clapham … & JM Straley
We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds in humpback whales based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. For 2,193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions during the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. From sequences of the mtDNA...

Data from: Drifting to oblivion? Rapid genetic differentiation in an endangered lizard following habitat fragmentation and drought

Amy G. Vandergast, Dustin A. Wood, Andrew R. Thompson, Mark Fisher, Cameron W. Barrows & Tyler J. Grant
Aim: The frequency and severity of habitat alterations and disturbance are predicted to increase in upcoming decades, and understanding how disturbance affects population integrity is paramount for adaptive management. Although rarely is population genetic sampling conducted at multiple time points, pre- and post-disturbance comparisons may provide one of the clearest methods to measure these impacts. We examined how genetic properties of the federally threatened Coachella Valley fringe-toed lizard (Uma inornata) responded to severe drought and...

Data from: Phenomenological vs. biophysical models of thermal stress in aquatic eggs

Benjamin T. Martin, Andrew Pike, Sara N. John, Natnael Hamda, Jason Roberts, Steven T. Lindley & Eric M. Danner
Oxygen consumption before hatching of fish embryos as a function of egg sizeThis dataset contains information on the size (radius and volume), experimental temperature, and oxygen consumption rate (micrograms O2/hr) of embryos of 14 species of fish measure before hatching.NfuncRdatabaseFinalTableDRYAD.csv

Data from: Natal foraging philopatry in eastern Pacific hawksbill turtles

Alexander R. Gaos, Rebecca L. Lewison, Michael P. Jensen, Michael J. Liles, Ana Henriquez, Sofia Chavarria, Carlos Mario Pacheco, Melissa Valle, David Melero, Velkiss Gadea, Eduardo Altamirano, Perla Torres, Felipe Vallejo, Cristina Miranda, Carolina LeMarie, Jesus Lucero, Karen Oceguera, Didiher Chacón, Luis Fonseca, Marino Abrego, Jeffrey A. Seminoff, Eric E. Flores, Israel Llamas, Rodrigo Donadi, Bernardo Peña … & Daniela Alarcón Ruales
The complex processes involved with animal migration have long been a subject of biological interest and broad-scale movement patterns of many marine turtle populations still remain unresolved. While it is widely accepted that once marine turtles reach sexual maturity they home to natal areas for nesting or reproduction, the role of philopatry to natal areas during other life stages has received less scrutiny, despite widespread evidence across the taxa. Here we report on genetic research...

Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Ian R. Bradbury, Brendan F. Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J. Lehnert, Marie Clément, Eric C. Anderson, Nicholas W. Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson & Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci,...

Data from: Mesoscale activity facilitates energy gain in a top predator

Briana Abrahms, Kylie L. Scales, Elliott L. Hazen, Steven J. Bograd, Robert S. Schick, Patrick W. Robinson & Daniel P. Costa
How animal movement decisions interact with the distribution of resources to shape individual performance is a key question in ecology. However, links between spatial and behavioural ecology and fitness consequences are poorly understood because the outcomes of individual resource selection decisions, such as energy intake, are rarely measured. In the open ocean, mesoscale features (~10-100 km) such as fronts and eddies can aggregate prey and thereby drive the distribution of foraging vertebrates through bottom-up biophysical...

Data from: Physiological, morphological, and ecological tradeoffs influence vertical habitat use of deep-diving toothed-whales in the Bahamas

Trevor W. Joyce, John W. Durban, Diane E. Claridge, Charlotte A. Dunn, Holly Fearnbach, Kim M. Parsons, Russel D. Andrews & Lisa T. Ballance
Dive capacity among toothed whales (suborder: Odontoceti) has been shown to generally increase with body mass in a relationship closely linked to the allometric scaling of metabolic rates. However, two odontocete species tagged in this study, the Blainville’s beaked whale Mesoplodon densirostris and the Cuvier’s beaked whale Ziphius cavirostris, confounded expectations of a simple allometric relationship, with exceptionally long (mean: 46.1 min & 65.4 min) and deep dives (mean: 1129 m & 1179 m), and...

Data from: Habitat modeling of Irrawaddy dolphins (Orcaella brevirostris) in the eastern Gulf of Thailand

Justine Jackson-Ricketts, Chalatip Junchompoo, Ellen Hines, Elliot Hazen, Louisa Ponnampalam, Anoukchika Ilangakoon & Somchai Monanunsap
Aim: The Irrawaddy dolphin (Orcaella brevirostris) is an endangered cetacean found throughout Southeast Asia. The main threat to this species is human encroachment, led by entanglement in fishing gear. Information on this data-poor species’ ecology and habitat use is needed to effectively inform spatial management. Location: We investigated the habitat of a previously unstudied group of Irrawaddy dolphins in the eastern Gulf of Thailand, between the villages of Laem Klat and Khlong Yai, in Trat...

Winter-run Chinook salmon resource selection function 2020

Peter Dudley
We use historic aerial redd surveys of Sacramento River winter-run Chinook salmon, coupled with 2D hydraulic modeling, and apply multivariable polynomial, logistic regression to calculate spawning resource selection functions (RSFs) based on water velocity and depth, and examine their interactions with water temperature. Our methods resulted in univariate and multivariate resource selection functions with interactions between both velocity and depth preference with changing temperature. Preferred depth increased and preferred velocity decreased with increasing temperature.

Datasets supporting: Acute bottlenecks to the survival of juvenile Pygoscelis penguins occur immediately after fledging

Jefferson Hinke, George Watters, Christian Reiss, Jarrod Santora & Mercedes Santos
This data set contains a zipped file with 8 individual .csv files used to support the analysis of survival bottlenecks presented by Hinke et al.(2020), "Acute bottlenecks to the survival of juvenile Pygoscelis penguins occur immediately after fledging". Data include geographical position estimates from satellite telemetry studies on Adélie (Pygoscelis adeliae), chinstrap (P. antarctica), and gentoo (P. papua) penguins tracked from the Antarctic peninsula region, carcass counts from ship and beach surveys in the study...

Registration Year

  • 2022
  • 2021
  • 2020
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  • 2013

Resource Types

  • Dataset


  • Southwest Fisheries Science Center
  • University of California, Santa Cruz
  • University of California System
  • Alaska Fisheries Science Center
  • Oregon State University
  • University of California, San Diego
  • Cascadia Research
  • National Oceanic and Atmospheric Administration
  • Duke University
  • Pacific Islands Fisheries Science Center