68 Works

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...

Larval fish abundances off southern California from 1951 to 2016

Andrew Thompson
The 2014-2016 Northeast Pacific Marine Heatwave (MHW) induced the warmest 3-year period on record in the California Current Ecosystem. We tested whether larval fish assemblage structure, phenology and diversity dynamics were comparable to past warming events from 1951-2013. First, we hypothesized, based on past observations of biological effect of warming, that mesopelagic species with southern distributions relative to southern California and Pacific sardine Sardinops sagax (a coastal pelagic species) would increase during the MHW while...

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: Applying empirical dynamic modeling to distinguish abiotic and biotic drivers of population fluctuations in sympatric fishes

Ben Wasserman, Tanya Rogers, Stephan Munch & Eric Palkovacs
Fluctuations in the population abundances of interacting species are widespread. Such fluctuations could be a response to abiotic factors, biotic interactions, or a combination of the two. Correctly identifying the drivers are critical for effective population management. However, such effects are not always static in nature. Nonlinear relationships between abiotic factors and biotic interactions make it difficult to parse true effects. We used a type of nonlinear forecasting, empirical dynamic modeling, to investigate the context-dependent...

Using seabird and whale distribution models to estimate spatial consumption of krill to inform fishery management

Victoria Warwick-Evans, Natalie Kelly, Luciano Dalla Rosa, Ari Friedlaender, Jefferson Hinke, Jeong-Hoon Kim, Nobuo Kokubun, Jarrod Santora, Eduardo Secchi, Elisa Seyboth & Philip Trathan
Ecosystem dynamics at the north-west Antarctic Peninsula are driven by interactions between physical and biological processes. For example, baleen whale populations are recovering from commercial harvesting against the backdrop of rapid climate change, including reduced sea-ice extent and changing ecosystem composition. Concurrently, the commercial harvesting of Antarctic krill is increasing, with the potential to increase the likelihood for competition with and between krill predators and the fishery. However, understanding the ecology, abundance, and spatial distribution...

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....

EnKF Analyses and Forecasts of Hurricane Harvey (2017)

Y. Zhang, S.B. Sieron, Y. Lu, X. Chen, R.G. Nystrom, M. Minamide, M. Chan, C.M. Hartman, Z. Yao, J.H. Ruppert, A. Okazaki, S.J. Greybush & E.E. Clothiaux
Ensemble-based data assimilation of radar observations across inner-core regions of tropical cyclones (TCs) in tandem with satellite all-sky infrared radiances across the TC domain improves TC track and intensity forecasts. This study further investigates potential enhancements in TC track, intensity, and rainfall forecasts via assimilation of all-sky microwave radiances using Hurricane Harvey (2017) as an example. Assimilating GPM constellation all-sky microwave radiances in addition to GOES-16 all-sky infrared radiances reduces the forecast errors in the...

Information on marine management policies for invasive lionfish in the Western Atlantic Ocean and Mediterranean Sea

Allison C. Candelmo, Aylin Ulman, Fadilah Z. Ali, Stephen R. Gittings, Summer R. Huber, Lauryn E. Magno, Kaylin R. Clements, Burak Ali Çiçek, Jennifer K. Chapman, Fabian C. Kyne, Michel Bariche, Kimani Kitson-Walters, Francesco Tiralongo, Demetris Kletou, Taner Yildiz, Nir Stern, Sara A.A. Al Mabruk, Mohammed Adel, Nejmeddine Bradai, Shevy B.S. Rothman, Vasileios Minasidis, Stephanie J. Green, Jennifer N. Solomon, Holden E. Harris, Philip E. Karp … & James V Hart
The invasion of lionfish (Pterois volitans and P. miles) in the Western Atlantic is perhaps the best studied marine fish invasion to date; meanwhile another lionfish invasion is rapidly evolving in the Mediterranean. We reviewed lionfish management policies from several decades in the Western Atlantic to suggest policy recommendations for the Mediterranean. These strategic recommendations are synthesized in our corresponding manuscript titled: “Lessons from the Western Atlantic lionfish invasion can inform policy and management strategies...

Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

Halvor Knutsen, Diana Catarino, Lauren Rogers, Marte Sodeland, Morten Mattingsdal, Marlene Jahnke, Jeffrey Hutchings, Ida Mellerud, Sigurd Espeland, Kerstin Johanneson, Olivia Roth, Michael Hansen, Sissel Jentoft, Carl Andre & Per Erik Jorde
Gene flow shapes spatial genetic structure as well as the potential for local adaptation of populations. Among marine animals with non-migratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats will influence the distribution of biological populations and their pattern of gene flow. We used whole genome sequencing to...

Data from: Network analysis of sea turtle movements and connectivity: a tool for conservation prioritization

Connie Y. Kot, Susanne Åkesson, Joanna Alfaro-Shigueto, Diego Fernando Amorocho Llanos, Marina Antonopoulou, George H. Balazs, Warren R. Baverstock, Janice M. Blumenthal, Annette C. Broderick, Ignacio Bruno, Ali Fuat Canbolat, Paolo Casale, Daniel Cejudo, Michael S. Coyne, Corrie Curtice, Sarah DeLand, Andrew DiMatteo, Kara Dodge, Daniel C. Dunn, Nicole Esteban, Angela Formia, Mariana M. P. B. Fuentes, Ei Fujioka, Julie Garnier, Matthew H. Godfrey … & Patrick N. Halpin
Aim: Understanding the spatial ecology of animal movements is a critical element in conserving long-lived, highly mobile marine species. Analysing networks developed from movements of six sea turtle species reveals marine connectivity and can help prioritize conservation efforts. Location: Global. Methods: We collated telemetry data from 1,235 individuals and reviewed the literature to determine our dataset’s representativeness. We used the telemetry data to develop spatial networks at different scales to examine areas, connections, and their...

Neutral and adaptive loci reveal fine-scale population structure in Eleginops maclovinus from North Patagonia

Cristian B. Canales-Aguirre, Wesley A. Larson, Garret J. McKinney, C. Eliza Claure, J. Dellis Rocha, Santiago G. Ceballos, Maria I. Cádiz, José M. Yáñez & Daniel Gómez-Uchida
Patagonia is an understudied area, especially when it comes to population genomic studies with relevance to fishery management. However, the dynamic and heterogeneous landscape in this area can harbor important but cryptic genetic population structure. Once such information is revealed, it can be integrated into the management of infrequently investigated species. Eleginops maclovinus is a protandrous hermaphrodite species with economic importance for local communities that is currently managed as a single genetic unit. In this...

University of Colorado Institute of Arctic and Alpine Research (INSTAAR) Flask-Air Sample Measurements of Stable Isotopic Composition of Atmospheric Methane (dCH4-13C) at NOAA GML Global and Regional Background Sites, 1998-Present

Sylvia Michel, Bruce Vaughn, Justin Reid Clark, &
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 ESRL/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: Sperm whale population structure in the eastern and central North Pacific inferred by the use of single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial DNA

Sarah L. Mesnick, Barbara L. Taylor, Frederick I Archer, Karen K Martien, Sergio Escorza Treviño, Brittany L. Hancock-Hanser, Sandra Carolina Moreno Medina, Victoria L Pease, Kelly M Robertson, Janice M Straley, Robin W Baird, John Calambokidis, Gregory S. Schorr, Paul Wade, Vladimir Burkanov, Chris R. Lunsford, Luke Rendell & Phillip A Morin
We use mitochondrial DNA (400bp), six microsatellites and 36 single nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate population structure of sperm whales (Physeter macrocephalus) in the eastern and central North Pacific. SNP markers, reproducible across technologies and laboratories, are ideal for long-term studies of globally distributed species such as sperm whales, a species of conservation concern due to both historical and contemporary impacts. We estimate genetic differentiation among three strata in the...

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...

Data from: Assessing thermal adaptation using family-based association and FST-outlier tests in a threatened trout

Stephen J. Amish, Omar Ali, Mary Peacock, Michael Miller, Morgan Robinson, Seth Smith, Gordon Luikart & Helen Neville
Discovering genetic markers associated with phenotypic or ecological characteristics can improve our understanding of adaptation and guide conservation of key evolutionary traits. The Lahontan cutthroat trout (Oncorhynchus clarkii henshawi) of the northern Great Basin Desert, USA, demonstrated exceptional tolerance to high temperatures in the desert lakes where it resided historically. This trait is central to a conservation hatchery effort to protect the genetic legacy of the nearly extinct lake ecotype. We genotyped full‐sibling families from...

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