87 Works

Community Sustainability Cooperatives in central California: Continued fishery participation through quota share holdings in the Pacific Coast groundfish fishery

Aaron Mamula & Rosemary Kosaka
NOAA technical memorandum NMFS-SWFSC ; 620

2017 Trinational Sardine and Small Pelagics Forum

Stephanie R. Flores
Administrative report LJ ; 19-02

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: 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: 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: 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...

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: 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...

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: 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: 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: Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)

Ying Zhen, Ryan J. Harrigan, Kristen C. Ruegg, Eric C. Anderson, Thomas C. Ng, Sirena Lao, Kirk E. Lohmueller & Thomas B. Smith
The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioural divergence across rainforest–savannah transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modelling make it possible to...

Data from: Genetic structure of Pacific trout at the extreme southern end of their native range

Alicia Abadía-Cardoso, John Carlos Garza, Richard L. Mayden & Francisco Javier García De León
Salmonid fishes are cold water piscivores with a native distribution spanning nearly the entire temperate and subarctic northern hemisphere. Trout in the genus Oncorhynchus are the most widespread salmonid fishes and are among the most important fish species in the world, due to their extensive use in aquaculture and valuable fisheries. Trout that inhabit northwestern Mexico are the southernmost native salmonid populations in the world, and the least studied in North America. They are unfortunately...

Data from: Limited trophic partitioning among sympatric delphinids off a tropical oceanic atoll

Hillary Young, Katherine Nigro, Douglas J. McCauley, Lisa T. Ballance, Erin M. Oleson & Simone Baumann-Pickering
Understanding trophic relationships among marine predators in remote environments is challenging, but it is critical to understand community structure and dynamics. In this study, we used stable isotope analysis of skin biopsies to compare the isotopic, and thus, trophic niches of three sympatric delphinids in the waters surrounding Palmyra Atoll, in the Central Tropical Pacific: the melon-headed whale (Peponocephala electra), Gray’s spinner dolphin (Stenella longirostris longirostris), and the common bottlenose dolphin (Tursiops truncatus). δ15N values...

Data from: DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus)

John R. Hyde, Karen E. Underkoffler & Meagan A. Sundberg
The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome...

Data from: Familial social structure and socially-driven genetic differentiation in Hawaiian short-finned pilot whales

Amy M. Van Cise, Karen. K. Martien, Sabre D. Mahaffy, Robin W. Baird, Daniel L. Webster, James H. Fowler, Erin M. Oleson & Phillip A. Morin
Social structure can have a significant impact on divergence and evolution within species, especially in the marine environment, which has few environmental boundaries to dispersal. On the other hand, genetic structure can affect social structure in many species, through an individual preference toward associating with relatives. One social species, the short-finned pilot whale (Globicephala macrorhynchus), has been shown to live in stable social groups for periods of at least a decade. Using mitochondrial control sequences...

Data from: Population differentiation of 2 forms of Bryde’s whales in the Indian and Pacific Oceans

Francine Kershaw, Matthew S. Leslie, Tim Collins, Rubaiyat M. Mansur, Brian D. Smith, Gianna Minton, Robert Baldwin, Richard G. LeDuc, R. Charles Anderson, & Howard C. Rosenbaum
Accurate identification of units for conservation is particularly challenging for marine species as obvious barriers to gene flow are generally lacking. Bryde’s whales (Balaenoptera spp.) are subject to multiple human-mediated stressors, including fisheries bycatch, ship strikes, and scientific whaling by Japan. For effective management, a clear understanding of how populations of each Bryde’s whale species/subspecies are genetically structured across their range is required. We conducted a population-level analysis of mtDNA control region sequences with 56...

Assessing the population level impacts of North Pacific Loggerhead and western Pacific Leatherback interactions in the Hawaii-based shallow set fishery

Summer L. Martin, Zachary Siders, Tomoharu Eguchi, Brian J. Langseth, Annie Yau, Jason Daniel Baker, Robert Ahrens & Timothy Todd Jones
NOAA technical memorandum NMFS-PIFSC ; 95

Report on the Summer 2019 California Current Ecosystem Survey (1907RL), 13 June to 9 September 2019, conducted aboard NOAA Ship Reuben Lasker, Fishing Vessels Lisa Marie and Long Beach Carnage, and three unmanned sailboats

Kevin L. Stierhoff, Juan P. Zwolinski, Josiah S. Renfree, Gabriel E. Johnson, Scott A. Mau, David W. Murfin, Thomas S. Sessions & David A. (David Arthur) Demer
NOAA technical memorandum NMFS NOAA-TM-NMFS-SWFSC ; 625

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

Matching Vessel Monitoring System data to trawl logbook and fish ticket data for the Pacific groundfish fishery

Aaron Mamula, Alice Thomas-Smyth, Cameron L. Speir, Rosemary Kosaka & Donald E. (Donald Edgar) Pearson
NOAA-TM-NMFS-SWFSC ; 623

Data from: Structure and phylogeography of two tropical predators, spinner (Stenella longirostris) and pantropical spotted (S attenuata) dolphins, from SNP data

Matthew S. Leslie & Phillip A. Morin
Little is known about global patterns of genetic connectivity in pelagic dolphins, including how circumtropical pelagic dolphins spread globally following the rapid and recent radiation of the subfamily delphininae. In this study, we tested phylogeographic hypotheses for two circumtropical species, the spinner dolphin (Stenella longirostris) and the pantropical spotted dolphin (Stenella attenuata), using >3,000 nuclear DNA single nucleotide polymorphisms (SNPs) in each species. Analyses for population structure indicated significant genetic differentiation between almost all subspecies...

Data from: Interpreting the FLOCK algorithm from a statistical perspective

Eric C. Anderson & Patrick D. Barry
We show that the algorithm in the program FLOCK (Duchesne & Turgeon 2009) can be interpreted as an estimation procedure based on a model essentially identical to the STRUCTURE (Pritchard et al. 2000) model with no admixture and non-correlated allele frequency priors. Rather than using MCMC, the FLOCK algorithm searches for the maximum-a-posteriori estimate of this STRUCTURE model via a simulated annealing algorithm with a rapid cooling schedule (namely, the exponent on the objective function...

Data from: Potential limitations of behavioral plasticity and the role of egg relocation in climate change mitigation for a thermally-sensitive endangered species

Michael J. Liles, Tarla Rai Peterson, Jeffrey A. Seminoff, Alexander R. Gaos, Eduardo Altamirano, Ana V. Henríquez, Velkiss Gadea, Sofía Chavarría, José Urteaga, Bryan P. Wallace & Markus J. Peterson
Anthropogenic climate change is widely considered a major threat to global biodiversity, such that the ability of a species to adapt will determine its likelihood of survival. Egg-burying reptiles that exhibit temperature-dependent sex determination, such as critically endangered hawksbill turtles (Eretmochelys imbricata), are particularly vulnerable to changes in thermal regimes because nest temperatures affect offspring sex, fitness, and survival. It is unclear whether hawksbills possess sufficient behavioral plasticity of nesting traits (i.e., redistribution of nesting...

Registration Year

  • 2022
    2
  • 2021
    9
  • 2020
    12
  • 2019
    5
  • 2018
    8
  • 2017
    13
  • 2016
    6
  • 2015
    10
  • 2014
    7
  • 2013
    6

Resource Types

  • Dataset
    79
  • Text
    8

Affiliations

  • Southwest Fisheries Science Center
    87
  • University of California, Santa Cruz
    17
  • National Marine Fisheries Service
    10
  • University of California System
    9
  • Alaska Fisheries Science Center
    7
  • Cascadia Research
    7
  • Oregon State University
    6
  • University of California, San Diego
    6
  • Pacific Islands Fisheries Science Center
    5
  • National Oceanic and Atmospheric Administration
    5