83 Works

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

Distribution, Biomass, and Demography of Coastal Pelagic Fishes in the California Current Ecosystem During Summer 2019 Based on Acoustic-Trawl Sampling

Kevin L. Stierhoff, Juan P. Zwolinski & David A. (David Arthur) Demer
NOAA technical memorandum NMFS NOAA-TM-NMFS-SWFSC ; 626

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

Triennial migration and philopatry in the critically endangered soupfin shark (Galeorhinus galeus)

Andrew Nosal, Daniel Cartamil, Arnold Ammann, Lyall Bellquist, Noah Ben-Aderet, Kayla Blincow, Echelle Burns, Eric Chapman, Ryan Freedman, Peter Klimley, Ryan Logan, Christopher Lowe, Brice Semmens, Connor White & Philip Hastings
Globally, one-quarter of shark and ray species is threatened with extinction due to overfishing. Effective conservation and management can facilitate population recoveries; however, these efforts depend on robust data on movement patterns and stock structure, which are lacking for many threatened species, including the Critically Endangered soupfin shark (Galeorhinus galeus), a circumglobal coastal-pelagic species. Using passive acoustic telemetry, we continuously tracked 34 mature female soupfin sharks, surgically implanted with coded acoustic transmitters, for seven years...

Speciation in the abyss - genomics and morphology reveal a new species of beaked whale

Emma L. Carroll, Michael R. McGowen, Morgan L. McCarthy, Felix G. Marx, Natacha Aguilar De Soto, Merel L. Dalebout, Sascha Dreyer, Oscar E. Gaggiotti, Sabine S. Hansen, Anton Van Helden, Aubrie B. Onoufriou, Robin W. Baird, C. Scott Baker, Simon Berrow, Danielle Cholewiak, Diane Claridge, Rochelle Constantine, Nicholas J. Davison, Catarina Eira, R. Ewan Fordyce, John Gatesy, G. J. Greg Hofmeyr, Vidal Martin, James G. Mead, Antonio A. Mignucci-Giannoni … & Morten T. Olsen
Earth’s deep oceans remains less well understood than the surface of Mars. Beaked whales (ziphiids) are among the most visible inhabitants of the abyss, due to their large size and worldwide distribution, yet their diversity and ecology remain obscure. We combine genomic and morphometric analyses to reveal a new Southern Hemisphere ziphiid species, Ramari’s beaked whale, Mesoplodon eueu, whose name is linked to the Indigenous people of the lands from which the species holotype and...

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...

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.

Data From: Polygenic basis and the role of genome duplication in adaptation to similar selective environments

Matthew Campbell, Eric Anderson, John Carlos Garza & Devon Pearse
Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and...

Data from: A tradeoff between precopulatory and postcopulatory trait investment in male cetaceans

James P. Dines, Sarah L. Mesnick, Katherine Ralls, Laura J. May Collado, Ingi Agnarsson, Matthew D. Dean & Laura May-Collado
Mating with multiple partners is common across species, and understanding how individual males secure fertilization in the face of competition remains a fundamental goal of evolutionary biology. Game theory stipulates that males have a fixed budget for reproduction that can lead to a trade-off between investment in precopulatory traits like body size, armaments, and ornaments, and postcopulatory traits such as testis size and spermatogenic efficiency. Recent theoretical and empirical studies have shown that if males...

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
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...

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