44 Works

Data from: Deepwater Horizon oil spill impacts on sea turtles could span the Atlantic

Nathan F. Putman, F. Alberto Abreu-Grobois, Iñaky Iturbe-Darkistade, Emily M. Putman, Paul M. Richards & Philippe Verley
We investigated the extent that the 2010 Deepwater Horizon oil spill potentially affected oceanic-stage sea turtles from populations across the Atlantic. Within an ocean-circulation model, particles were backtracked from the Gulf of Mexico spill site to determine the probability of young turtles arriving in this area from major nesting beaches. The abundance of turtles in the vicinity of the oil spill was derived by forward-tracking particles from focal beaches and integrating population size, oceanic-stage duration...

Data from: Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago

Jean-Baptiste Jouffray, Magnus Nyström, Albert V. Norström, Ivor D. Williams, Lisa M. Wedding, John N. Kittinger & Gareth J. Williams
Loss of coral reef resilience can lead to dramatic changes in benthic structure, often called regime shifts, which significantly alter ecosystem processes and functioning. In the face of global change and increasing direct human impacts, there is an urgent need to anticipate and prevent undesirable regime shifts and, conversely, to reverse shifts in already degraded reef systems. Such challenges require a better understanding of the human and natural drivers that support or undermine different reef...

Data from: Local adaptation in transgenerational responses to predators

Matthew R. Walsh, Todd Castoe, Julian Holmes, Michelle Packer, Kelsey Biles, Melissa Walsh, Stephan B. Munch & David M. Post
Environmental signals can induce phenotypic changes that span multiple generations. Along with phenotypic responses that occur during development (i.e., ‘within-generation’ plasticity), such ‘transgenerational plasticity’ (TGP) has been documented in a diverse array of taxa spanning many environmental perturbations. New theory predicts that temporal stability is a key driver of the evolution of TGP. We tested this prediction using natural populations of zooplankton from lakes in Connecticut that span a large gradient in the temporal dynamics...

Data from: Influence of environmental parameters on movements and habitat utilization of humpback whales (Megaptera novaeangliae) in the Madagascar breeding ground

Laurène Trudelle, Salvatore Cerchio, Alexandre N. Zerbini, Ygor Geyer, Francois-Xavier Mayer, Jean-Luc Jung, Maxime R. Hervé, Stéphane Pous, Jean-Baptiste Sallée, Howard C. Rosenbaum, Olivier Adam & Jean-Benoit Charrassin
Assessing the movement patterns and key habitat features of breeding humpback whales is a prerequisite for the conservation management of this philopatric species. To investigate the interactions between humpback whale movements and environmental conditions off Madagascar, we deployed 25 satellite tags in the northeast and southwest coast of Madagascar. For each recorded position, we collated estimates of environmental variables and computed two behavioural metrics: behavioural state of ‘transiting’ (consistent/directional) versus ‘localized’ (variable/non-directional), and active swimming...

Data from: Genetic variation in blue whales in the eastern Pacific: implication for taxonomy and use of common wintering grounds

Richard G. LeDuc, F.I. Archer, Aimee R. Lang, Karen K. Martien, Brittany Hancock-Hanser, Juan P. Torres-Florez, Rodrigo Hucke-Gaete, Howard C. Rosenbaum, Koen Van Waerebeek, Robert L. Brownell, Barbara L. Taylor & F. I. Archer
Many aspects of blue whale biology are poorly understood. Some of the gaps in our knowledge, such as those regarding their basic taxonomy and seasonal movements, directly affect our ability to monitor and manage blue whale populations. As a step towards filling in some of these gaps, microsatellite and mtDNA sequence analyses were conducted on blue whale samples from the Southern Hemisphere, the eastern tropical Pacific (ETP), and the northeast Pacific. The results indicate that...

Historical dynamics of the demersal fish community in the East and South China Seas

Jin Gao, James Thorson, Cody Szuwalski & Hui-Yu Wang
Taiwan has a long history of fishery operations and contributes significantly to global fishery harvest. The East and South China seas are important fishing grounds with very limited public data. More efforts are needed to digitize and analyze historical catch rate data to illuminate species and community changes in this region. In this study, we digitize historical records of catch and effort from government fishery reports for nine commercial species caught by otter trawl, reported...

Data from: Behavioral responses of individual blue whales (Balaenoptera musculus) to mid-frequency military sonar

Brandon L. Southall, Stacy L. DeRuiter, Ari Friedlaender, Alison K. Stimpert, Jeremy A. Goldbogen, Elliott Hazen, Caroline Casey, Selene Fregosi, David E. Cade, Ann N. Allen, Catriona M. Harris, Greg Schorr, David Moretti, Shane Guan & John Calambokidis
This study measured the degree of behavioral responses in blue whales (Balaenoptera musculus) to controlled noise exposure off the southern California coast. High-resolution movement and passive acoustic data were obtained from non-invasive archival tags (n=42) while surface positions were obtained with visual focal follows. Controlled exposure experiments (CEEs) were used to obtain direct behavioral measurements before, during, and after simulated and operational military mid-frequency active sonar (MFAS), pseudorandom noise (PRN), and controls (no noise exposure)....

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: 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...

Cold call: the acoustic repertoire of Ross Sea killer whales (Orcinus orca, Type C) in McMurdo Sound, Antarctica

Rebecca Wellard, Robert Pitman, John Durban & Christine Erbe
Killer whales (Orcinus orca) are top marine predators occurring globally. In Antarctic waters, five ecotypes have been described, with Type C being the smallest form of killer whale known. Acoustic recordings of nine encounters of Type C killer whales were collected in 2012 and 2013 in McMurdo Sound, Ross Sea. In a combined 3.5 hours of recordings, 6386 killer whale vocalisations were detected and graded based on their signal-to-noise ratio. Spectrograms of the highest-quality calls...

Changes in dive patterns of leatherback turtles with sea surface temperature and potential foraging habitats

Junichi Okuyama, Scott Benson, Jeffrey Seminoff & Peter Dutton
Marine mesotherms are able to occupy broader thermal niches than ectotherms; however, this means they must exhibit greater tolerance to diverse environmental conditions across the ocean. Knowledge remains limited about how differences in environmental conditions within occupied habitats affect the bioenergetics of mesotherms and associated ecological traits. Here, we report that leatherback turtles (Dermochelys coriacea) migrating across the North Pacific changed their dive behavior regionally, possibly in response to changes in sea surface temperature and...

Data from: Avoiding tipping points in fisheries management through Gaussian process dynamic programming

Carl Boettiger, Marc Mangel & Stephan Munch
Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some...

Data from: Natal and breeding philopatry of female Steller sea lions in southeastern Alaska

Kelly K. Hastings, Lauri A. Jemison, Grey W. Pendleton, Kimberly L. Raum-Suryan & Kenneth W. Pitcher
Information on drivers of dispersal is critical for wildlife conservation but is rare for long-lived marine mammal species with large geographic ranges. We fit multi-state mark-recapture models to resighting data of 369 known-aged Steller sea lion (Eumetopias jubatus) females marked as pups on their natal rookeries in southeastern Alaska from 1994-2005 and monitored from 2001-15. We estimated probabilities of females being first observed parous at their natal site (natal philopatry), and of not moving breeding...

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: Water, water everywhere: environmental DNA can unlock population structure in elusive marine species

Kim M. Parsons, Meredith Everett, Marilyn Dahlheim & Linda Park
Determining management units for natural populations is critical for effective conservation and management. However, collecting the requisite tissue samples for population genetic analyses remains the primary limiting factor for a number of marine species. The harbor porpoise (Phocoena phocoena), one of the smallest cetaceans in the Northern Hemisphere, is a primary example. These elusive, highly mobile small animals confound traditional approaches of collecting tissue samples for genetic analyses, yet their nearshore habitat makes them highly...

Data from: Genetic diversity of white sharks, Carcharodon carcharias, in the northwest Atlantic and southern Africa

Shannon J. O'Leary, Kevin A. Feldheim, Andrew T. Fields, Lisa J. Natanson, Sabine Wintner, Nigel Hussey, Mahmood S. Shivji & Demian D. Chapman
The white shark, Carcharodon carcharias, is both one of the largest apex predators in the world and among the most heavily protected marine fish. Population genetic diversity is in part shaped by recent demographic history and can thus provide information complementary to more traditional population assessments, which are difficult to obtain for white sharks and have at times been controversial. Here, we use the mitochondrial control region and 14 nuclear-encoded microsatellite loci to assess white...

Data from: Effective population sizes of a major vector of human diseases, Aedes aegypti

Norah P. Saarman, Andrea Gloria-Soria, Eric C. Anderson, Benjamin R. Evans, Evlyn Pless, Luciano V. Cosme, Cassandra Gonzalez-Acosta, Basile Kamgang, Dawn M. Wesson & Jeffrey R. Powell
The effective population size (Ne) is a fundamental parameter in population genetics that determines the relative strength of selection and random genetic drift, the effect of migration, levels of inbreeding, and linkage disequilibrium. In many cases where it has been estimated in animals, Ne is on the order of 10-20% of the census size. In this study, we use 12 microsatellite markers and 14,888 single nucleotide polymorphisms (SNPs) to empirically estimate Ne in Aedes aegypti,...

Data from: Sex change and effective population size: implications for population genetic studies in marine fish

Ilaria Coscia, Julien Chopelet, Robin S. Waples, Bruce Mann & Stefano Mariani
Large variance in reproductive success is the primary factor that reduces effective population size (Ne) in natural populations. In sequentially hermaphroditic (sex-changing) fish, the sex ratio is typically skewed and biased towards the 'first' sex, while reproductive success increases considerably after sex change. Therefore, sex-changing fish populations are theoretically expected to have lower Ne than gonochorists (separate sexes), assuming all other parameters are essentially equal. In this study, we estimate Ne from genetic data collected...

Data from: Genome-wide SNP data suggests complex ancestry of sympatric North Pacific killer whale ecotypes

Andrew D. Foote & Phillip A. Morin
Three ecotypes of killer whale occur in partial sympatry in the North Pacific. Individuals assortatively mate within the same ecotype, resulting in correlated ecological and genetic differentiation. A key question is whether this pattern of evolutionary divergence is an example of incipient sympatric speciation from a single panmictic ancestral population, or whether sympatry could have resulted from multiple colonisations of the North Pacific and secondary contact between ecotypes. Here, we infer multilocus coalescent trees from...

Data from: Predator-driven brain size evolution in natural populations of Trinidadian killifish (Rivulus hartii)

Matthew R. Walsh, Whitnee Broyles, Shannon M. Beston & Stephan B. Munch
Vertebrates exhibit extensive variation in relative brain size. It has long been assumed that this variation is the product of ecologically driven natural selection. Yet, despite more than 100 years of research, the ecological conditions that select for changes in brain size are unclear. Recent laboratory selection experiments showed that selection for larger brains is associated with increased survival in risky environments. Such results lead to the prediction that increased predation should favour increased brain...

Data from: Discovery and characterization of single nucleotide polymorphisms in Chinook salmon, Oncorhynchus tshawytscha

Anthony J. Clemento, Alicia Abadía-Cardoso, Hilary A. Starks & John C. Garza
Molecular population genetics of non-model organisms has been dominated by the use of microsatellite loci over the last two decades. The availability of extensive genomic resources for many species is contributing to a transition to the use of single nucleotide polymorphisms (SNPs) for the study of many natural populations. Here we describe the discovery of a large number of SNPs in Chinook salmon, one of the world’s most important fishery species, through large-scale Sanger sequencing...

Data from: Does mating behaviour affect connectivity in marine fishes? Comparative population genetics of two protogynous groupers (Family Serranidae)

David S. Portnoy, Christopher M. Hollenbeck, Mark A. Renshaw, Nancie J. Cummings & John R. Gold
Pelagic larval duration (PLD) has been hypothesized to be the primary predictor of connectivity in marine fishes; however, few studies have examined the effects that adult reproductive behaviour may have on realized dispersal. We assessed gene flow (connectivity) by documenting variation in microsatellites and mitochondrial DNA sequences in two protogynous species of groupers, the aggregate spawning red hind, Epinephelus guttatus, and the single-male, harem-spawning coney, Cephalopholis fulva, to ask if reproductive strategy affects connectivity. Samples...

Data from: Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure

Kristen Ruegg, Howard C. Rosenbaum, Eric C. Anderson, Marcia Engel, Anna Rothschild, C. Scott Baker & Stephen R. Palumbi
Once hunted to the brink of extinction, humpback whales (Megaptera novaeangliae) in the North Atlantic have recently been increasing in numbers. However, uncertain information on past abundance makes it difficult to assess the extent of the recovery in this species. While estimates of pre-exploitation abundance based upon catch data suggest the population might be approaching pre-whaling numbers, estimates based on mtDNA genetic diversity suggest they are still only a fraction of their past abundance levels....

Selection of indicators for assessing and managing the impacts of bottom trawling on seabed habitats

Jan Geert Hiddink, Michel Kaiser, Marija Sciberras, Robert McConnaughey, Tessa Mazor, Ray Hilborn, Jeremy Collie, C. Roland Pitcher, Ana Parma, Petri Suuronen, Adriaan Rijnsdorp & Simon Jennings
1. Bottom-trawl fisheries are the most-widespread source of anthropogenic physical disturbance to seabed habitats. Development of fisheries-, conservation- and ecosystem-based management strategies requires the selection of indicators of the impact of bottom trawling on the state of benthic biota. Many indicators have been proposed, but no rigorous test of a range of candidate indicators against 9 commonly-agreed criteria (concreteness, theoretical basis, public awareness, cost, measurement, historical data, sensitivity, responsiveness, specificity) has been performed. 2. Here,...

Data from: Effects of distance on detectability of Arctic waterfowl using double-observer sampling during helicopter surveys

Ray T Alisauskas & Paul B Conn
Aerial survey is an important, widely employed approach for estimating free‐ranging wildlife over large or inaccessible study areas. We studied how a distance covariate influenced probability of double‐observer detections for birds counted during a helicopter survey in Canada’s central Arctic. Two observers, one behind the other but visually obscured from each other, counted birds in an incompletely shared field of view to a distance of 200 m. Each observer assigned detections to one of five...

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Resource Types

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Affiliations

  • National Marine Fisheries Service
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  • Oregon State University
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