59 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

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: 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...

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...

Data from: Phylogenomic resolution of the cetacean tree of life using target sequence capture

Michael McGowen, Georgia Tsagkogeorga, Sandra Álvarez-Carretero, Mario Dos Reis, Monika Struebig, Rob Deaville, Paul Jepson, Simon Jarman, Andrea Polanowski, Phillip Morin & Stephen Rossiter
The evolution of the cetaceans, from their early transition to an aquatic lifestyle to their subsequent diversification, has been the subject of numerous studies. However, while the higher-level relationships among cetacean families have been largely settled, several aspects of the systematics within these groups remain unresolved. Problematic clades include the oceanic dolphins (37 spp.), which have experienced a recent rapid radiation, and the beaked whales (22 spp.), which have not been investigated in detail using...

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: Next-generation sequencing for molecular ecology: a caveat regarding pooled samples

Eric C. Anderson, Hans J. Skaug & Daniel J. Barshis
We develop a model based on the Dirichlet-compound multinomial distribution (CMD) and Ewens sampling formula to predict the fraction of SNP loci that will appear fixed for alternate alleles between two pooled samples drawn from the same underlying population. We apply this model to next-generation sequencing (NGS) data from Baltic Sea herring recently published by (Corander et al., , Molecular Ecology, 2931–2940), and show that there are many more fixed loci than expected in the...

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 & 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: 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: 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: 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: Discovery and characterization of single nucleotide polymorphisms in two anadromous alosine fishes of conservation concern

Diana S. Baetscher, Daniel J. Hasselman, Kerry Reid, Eric P. Palkovacs & John Carlos Garza
Freshwater habitat alteration and marine fisheries can affect anadromous fish species, and populations fluctuating in size elicit conservation concern and coordinated management. We describe the development and characterization of two sets of 96 single nucleotide polymorphism (SNP) assays for two species of anadromous alosine fishes, alewife and blueback herring (collectively known as river herring), that are native to the Atlantic coast of North America. We used data from high-throughput DNA sequencing to discover SNPs and...

Data from: Genetic and individual assignment of tetraploid green sturgeon with SNP assay data

Eric C. Anderson, Thomas C. Ng, Eric D. Crandall & John Carlos Garza
Polyploid organisms pose substantial obstacles to genetic analysis, as molecular assay data are usually difficult to evaluate in a Mendelian framework. Green sturgeon (Acipenser medirostris) is a tetraploid species and is facing significant conservation challenges, including bycatch in ocean fisheries. We present here novel molecular genetic assays and analytical methodology for green sturgeon that allow discrimination of fish from the two visually indistinguishable distinct population segments (DPSs), and also provide individual-specific genetic tags. We show...

Data from: Integrating lipid storage into general representations of fish energetics

Benjamin T. Martin, Ron Heintz, Eric M. Danner & Roger M. Nisbet
Fish, even of the same species, can exhibit substantial variation in energy density (energy per unit wet weight). Most of this variation is due to differences in the amount of storage lipids. In addition to their importance as energy reserves for reproduction and for survival during unfavourable conditions, the accumulation of lipids represents a large energetic flux for many species, so figuring out how this energy flux is integrated with other major energy fluxes (growth,...

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: 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: 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: 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: Colonizing the wild west: low diversity of complete mitochondrial genomes in western North Pacific killer whales suggests a founder effect

Olga A. Filatova, Ekaterina A. Borisova, Ilya G. Meshchersky, Maria D. Logacheva, Nataliia V. Kuzkina, Olga V. Shpak, Phillip A. Morin, Erich Hoyt, Olga V Shpak, Ilya G Meschersky, Maria D Logacheva, Olga A Filatova, Ekaterina A Borisova, Nataliia V Kuzkina & Phillip A Morin
In the North Pacific, fish-eating R-type “resident” and mammal-eating T-type “transient” killer whales do not interbreed and differ in ecology and behavior. Full-length mitochondrial genomes (about 16.4 kbp) were sequenced and assembled for 12 R-type and 14 T-type killer whale samples from different areas of the western North Pacific. All R-type individuals had the same haplotype, previously described for R-type killer whales from both eastern and western North Pacific. However, haplotype diversity of R-type killer...

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 & T. Todd Jones
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: Circumpolar diversity and geographic differentiation of mtDNA in the critically endangered Antarctic blue whale (Balaenoptera musculus intermedia)

Angela L. Sremba, Brittany Hancock-Hanser, Trevor A. Branch, Rick L. LeDuc & C. Scott Baker
The Antarctic blue whale (Balaenoptera musculus intermedia) was hunted to near extinction between 1904 and 1972, declining from an estimated initial abundance of more than 250,000 to fewer than 400. Here, we describe mtDNA control region diversity and geographic differentiation in the surviving population of the Antarctic blue whale, using 218 biopsy samples collected under the auspices of the International Whaling Commission (IWC) during research cruises from 1990–2009. Microsatellite genotypes and mtDNA sequences identified 166...

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: Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

Diana S. Baetscher, Anthony J. Clemento, Thomas C. Ng, Eric C. Anderson & John C. Garza
The accelerating rate at which DNA sequence data is now generated by high-throughput sequencing instruments provides both opportunities and challenges for population genetic and ecological investigations of animals and plants. We show here how the common practice of calling genotypes from a single SNP per sequenced region ignores substantial additional information in the phased short-read sequences that are provided by high-throughput sequencing instruments. We target sequenced regions with multiple SNPs in kelp rockfish (Sebastes atrovirens)...

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...

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