55 Works

Supplementary Information: Antibiotic resistance in Vibrio-like bacteria is common on Cape Cod, MA beaches

Megan May & Rebecca J. Gast
Antibiotic resistance (AR) is a natural process, enhanced by anthropogenic antibiotic use. Natural environments, like the ocean, act as reservoirs of resistance; but until recently, little research has examined their dynamics. Six beaches on Cape Cod, MA, with varying human impacts, were sampled over one year on nine occasions. Vibrio-like bacteria were isolated from wet sand, dry sand, and water from each beach and tested for sensitivity to five antibiotics (amoxicillin/clavulanic acid, ciprofloxacin, doxycycline, oxytetracycline,...

University of Colorado Institute of Arctic and Alpine Research (INSTAAR) Flask-Air Sample Measurements of Stable Isotopic Composition of Atmospheric Carbon Dioxide (d18O-CO2) at NOAA GML Global and Regional Background Sites, 1990-Present

James White, Bruce Vaughn, Sylvia Michel, &
The CCGG cooperative air sampling network effort began in 1967 at Niwot Ridge, Colorado. Today, the network is an international effort which includes regular discrete samples from the NOAA GML baseline observatories, cooperative fixed sites, and commercial ships. Air samples are collected approximately weekly from a globally distributed network of sites. Samples are analyzed for Carbon Dioxide (CO2), Methane (CH4), Carbon Monoxide (CO), Hydrogen Gas (H2), Nitrous Oxide (N2O), and Sulfur Hexafluoride (SF6); and by...

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: Acquisition of obligate mutualist symbionts during the larval stage is not beneficial for a coral host

Aaron Hartmann, Kristen Marhaver, Anke Klueter, Michael Lovci, Collin Closek, Erika Diaz Almeyda, Valerie Chamberland, Frederick Archer, Dimitri Deheyn, Mark Vermeij & Monica Medina
Theory suggests that the direct transmission of endosymbionts from parents to offspring (vertical transmission) in animal hosts is advantageous and evolutionarily stable, yet many host species instead acquire their symbionts from the environment (horizontal acquisition). An outstanding question in marine biology is why some scleractinian corals do not provision their eggs and larvae with the endosymbiotic dinoflagellates that are necessary for a juvenile’s ultimate survival. We tested whether the acquisition of photosynthetic endosymbionts (family Symbiodiniaceae)...

Data from: Evaluating consumptive and nonconsumptive predator effects on prey density using field times series data

, Scott D. Peacor, David B. Bunnell, Henry A. Vanderploeg, Steve A. Pothoven, Ashley K. Elgin, James R. Bence, Jing Jiao, Edward L. Ionides, D.B. Bunnell, J.A. Marino, E.L. Ionides, S.A. Pothoven, A.K. Elgin, H.A. Vanderploeg, S.D. Peacor & J.R. Bence
Determining the degree to which predation affects prey abundance in natural communities constitutes a key goal of ecological research. Predators can affect prey through both consumptive effects (CEs) and nonconsumptive effects (NCEs), although the contributions of each mechanism to the density of prey populations remain largely hypothetical in most systems. Common statistical methods applied to time series data cannot elucidate the mechanisms responsible for hypothesized predator effects on prey density (e.g., differentiate CEs from NCEs),...

Data from: Age specific survival rates of Steller sea lions at rookeries with divergent population trends in the Russian Far East

Alexey V. Altukhov, Russel D. Andrews, Donald G. Calkins, Thomas S. Gelatt, Eliezer D. Gurarie, Thomas R. Loughlin, Evgeny G. Mamaev, Victor S. Nikulin, Peter A. Permyakov, Sergey D. Ryazanov, Vladimir V. Vertyankin & Vladimir N. Burkanov
After a dramatic population decline, Steller sea lions have begun to recover throughout most of their range. However, Steller sea lions in the Western Aleutians and Commander Islands are continuing to decline. Comparing survival rates between regions with different population trends may provide insights into the factors driving the dynamics, but published data on vital rates have been extremely scarce, especially in regions where the populations are still declining. Fortunately, an unprecedented dataset of marked...

Threatened salmon rely on a rare life history strategy in a warming landscape

Flora Cordoleani, Corey Phillis, Anna Sturrock, Alyssa FitzGerald, George Whitman, Anthony Malkassian, Peter Weber & Rachel Johnson
Rare phenotypes and behaviours within a population are often overlooked, yet they may serve a heightened role for species imperilled by rapid warming. In threatened spring-run Chinook salmon spawning at the southern edge of the species range, we show late-migrating juveniles are critical to cohort success in years characterized by droughts and ocean heatwaves. Late migrants rely on cool river temperatures over summer, increasingly rare due to the combined effects of warming and impassable dams....

Supplementary tropical-cyclone count data-set for ‘Stratified statistical models of North Atlantic basin-wide and regional tropical cyclone counts’ (Journal of Geophysical Research, Kozar et al. 2012)

M.E. Kozar, M.E. Mann, S.J. Camargo, J.P. Kossin & J.L. Evans
Using the historical Atlantic tropical cyclone record, this study examines the empirical relationships between climate state variables and Atlantic tropical cyclone counts. The state variables considered as predictors include indices of the El Niño/Southern Oscillation and Northern Atlantic Oscillation, and both “local” and “relative” measures of Main Development Region sea surface temperature. Other predictors considered include indices measuring the Atlantic Meridional Mode and the West African monsoon. Using all of the potential predictors in a...

Data from: Evidence for ship noise impacts on humpback whale foraging behaviour

Hannah B. Blair, Nathan D. Merchant, Ari S. Friedlaender, David N. Wiley & Susan E. Parks
Noise from shipping activity in North Atlantic coastal waters has been steadily increasing and is an area of growing conservation concern, as it has the potential to disrupt the behaviour of marine organisms. This study examines the impacts of ship noise on bottom foraging humpback whales (Megaptera novaeangliae) in the western North Atlantic. Data were collected from 10 foraging whales using non-invasive archival tags that simultaneously recorded underwater movements and the acoustic environment at the...

Data from: Extensive hybridization following a large escape of domesticated Atlantic salmon in the Northwest Atlantic

Brendan F. Wringe, Nicholas W. Jeffery, Ryan R.E. Stanley, Lorraine C. Hamilton, Eric C. Anderson, Ian A. Fleming, Carole Grant, J. Brian Dempson, Geoff Veinott, Steven J. Duffy & Ian R. Bradbury
SNP genotype dataSNP genotype data for 95 SNPs for juvenile and baseline samples.2014_2015_data.csvGeographic distance from escape event to each riverGeographic distance from escape event to each riverDistance_from_escape.csvRiver Axial Distances and Catch

Data from: Robust estimates of a high Ne/N ratio in a top marine predator, southern bluefin tuna

Robin S. Waples, Peter M. Grewe, Mark W. Bravington, Richard Hillarty & Pierre Feutry
Genetic studies of several marine species with high fecundity have produced “tiny” estimates (≤10−3) of the ratio of effective population size (Ne) to adult census size (N), suggesting that even very large populations might be at genetic risk. A recent study using close-kin mark-recapture methods estimated adult abundance at N ≈ 2 × 106 for southern bluefin tuna (SBT), a highly fecund top predator that supports a lucrative (~$1 billion/year) fishery. We used the same...

Data from: Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions

Michael G. Buhnerkempe, Katherine C. Prager, Christopher C. Strelioff, Denise J. Greig, Jeff L. Laake, Sharon R. Melin, Robert L. DeLong, Frances M. D. Gulland & James O. Lloyd-Smith
Identifying mechanisms driving pathogen persistence is a vital component of wildlife disease ecology and control. Asymptomatic, chronically infected individuals are an oft-cited potential reservoir of infection but demonstrations of the importance of chronic shedding to pathogen persistence at the population level remain scarce. Studying chronic shedding using commonly collected disease data is hampered by numerous challenges, including short-term surveillance that focuses on single epidemics and acutely ill individuals, the subtle dynamical influence of chronic shedding...

Zona pellucida (ZP3) sequence data from 230 Pacific cod (phased)

Ingrid Spies
Genetic differentiation has been observed in marine species even when no obvious barriers to gene flow exist, and understanding such differentiation is essential for effective fisheries management. Highly differentiated outlier loci can provide information on how genetic variation might contribute to local adaptation but may also be affected by historical demographic events. A locus which aligned to a predicted zona pellucida sperm-binding protein 3 gene (ZP3) in Atlantic cod (Gadus morhua) was previously identified as...

Pseudo-Precipitation: A Continuous Precipitation Variable

Huiling Yuan, Paul Schultz, Edward I. Tollerud, Dingchen Hou, Yuejian Zhu, Malequias Pena, Mike Charles & Zoltan Toth
NOAA Technical Memorandum OAR GSD ; 62

Data from: A global perspective on the trophic geography of sharks

Christopher Stephen Bird, Ana Veríssimo, Sarah Magozzi, Kátya G. Abrantes, Alex Aguilar, Hassan Al-Reasi, Adam Barnett, Dana M. Bethea, Gérard Biais, Asuncion Borrell, Marc Bouchoucha, Mariah Boyle, Edward J. Brooks, Juerg Brunnschweiler, Paco Bustamante, Aaron Carlisle, Diana Catarino, Stéphane Caut, Yves Cherel, Tiphaine Chouvelon, Diana Churchill, Javier Ciancio, Julien Claes, Ana Colaço, Dean L. Courtney … & Clive N. Trueman
Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits...

Data from: Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci

Ryan K. Waples, Wesley A. Larson & Robin S. Waples
Contemporary effective population size (Ne) can be estimated using linkage disequilibrium (LD) observed across pairs of loci presumed to be selectively neutral and unlinked. This method has been commonly applied to data sets containing 10–100 loci to inform conservation and study population demography. Performance of these Ne estimates could be improved by incorporating data from thousands of loci. However, these thousands of loci exist on a limited number of chromosomes, ensuring that some fraction will...

Data from: Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

Mark R. Christie, Melanie L. Marine, Rod A. French, Robin S. Waples & Michael S. Blouin
Many declining and commercially important populations are supplemented with captive-born individuals that are intentionally released into the wild. These supplementation programs often create large numbers of offspring from relatively few breeding adults, which can have substantial population-level effects. We examined the genetic effects of supplementation on a wild population of steelhead trout (Oncorhynchus mykiss) from the Hood River, Oregon, by matching 12 run-years of hatchery steelhead back to their broodstock parents. We show that the...

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: Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Charles D. Waters, Jeffrey J. Hard, Marine S. O. Brieuc, David E. Fast, Kenneth I. Warheit, Robin Waples, Curtis M. Knudsen, William J. Bosch, Kerry A. Naish & Robin S. Waples
Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal...

Data from: Maintaining a wild phenotype in a conservation hatchery program for Chinook salmon: the effect of managed breeding on early male maturation

Donald A. Larsen, Deborah L. Harstad, Abby E. Fuhrman, Curtis M. Knudsen, Steven L. Schroder, William J. Bosch, Peter F. Galbreath, David E. Fast & Brian R. Beckman
In many salmonid species, age and size of maturation is plastic and influenced by the interaction between genetic and environmental factors. Hatchery reared salmon often mature at an earlier age and smaller size than wild fish. Modern salmon conservation efforts have focused on managing the level of gene flow between hatchery and natural origin fish to minimize potential genotypic and phenotypic change. In salmonids, maturation probability is dependent on exceeding a genetically set threshold in...

Coral restoration – a systematic review of current methods, successes, failures and future directions

Lisa Boström-Einarsson, Russell C. Babcock, Elisa Bayraktarov, Daniela Ceccarelli, Nathan Cook, Sebastian C. A. Ferse, Boze Hancock, Peter Harrison, Margaux Hein, Elizabeth Shaver, Adam Smith, David Suggett, Phoebe J. Stewart-Sinclair, Tali Vardi & Ian M. McLeod
Coral reef ecosystems have suffered an unprecedented loss of habitat-forming hard corals in recent decades. While marine conservation has historically focused on passive habitat protection, demand for and interest in active restoration has been growing in recent decades. However, a disconnect between coral restoration practitioners, coral reef managers and scientists has resulted in a disjointed field where it is difficult to gain an overview of existing knowledge. To address this, we aimed to synthesise the...

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...

Lipid content and stable isotopes of zooplankton during five winters around the northern Antarctic Peninsula

Jennifer Walsh & Christian Reiss
The Southern Ocean zooplankton community is diverse, yet most species are understudied, especially with respect to their overwinter feeding ecologies. This dataset describes body condition and trophic biomarker data (lipid content and stable isotopes of carbon and nitrogen) from 19 zooplankton species collected over five consecutive winters (August and September 2012 – 2016) around the northern Antarctic Peninsula. To complement these data and provide context for interpretation, we report environmental data (percent sea-ice cover, sea-ice...

Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales

Eiren Jacobson, Charlotte Boyd, Tamara McGuire, Kim Shelden, Gina Himes Boor & André Punt
Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modelling (IPM) offers a mechanism for leveraging these datasets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can...

Phylogenomic discordance in the Eared Seals is best explained by incomplete lineage sorting following explosive radiation in the Southern Hemisphere

Fernando Lopes, Larissa Oliveira, Amanda Kessler, Yago Beux, Enrique Crespo, Susana Cárdenas-Alayza, Patricia Majluf, Maritza Sepulveda, , Valentina Franco-Trecu, Diego Paez-Rosas, Jaime Chaves, Carolina Loch, Bruce Robertson, Karina Acevedo-Whitehouse, Fernando Elorriaga-Verplancken, Stephen Kirkman, Claire Peart, Jochen Wolf & Sandro Bonatto
The phylogeny and systematics of fur seals and sea lions (Otariidae) have long been studied with diverse data types, including an increasing amount of molecular data. However, only a few phylogenetic relationships have reached acceptance pointing at strong gene-tree species tree discordance. Divergence times in the group also vary largely between studies. These uncertainties impeded the understanding of the biogeographical history of the group, such as when and how trans-equatorial dispersal and subsequent speciation events...

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