56 Works

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: 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....

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: 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: 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...

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: 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: 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: 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...

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,...

Endangered predators and endangered prey: seasonal diet of Southern Resident killer whales

Michael Ford, M. Bradley Hanson, Candice Emmons, Meredith Everett, Kim Parsons, Linda Park, Jennifer Hempelmann, Donald Van Doornik, Gregory Schorr, Jeffrey Jacobsen, Mark Sears, Maya Sears, John Sneva, Robin Baird & Lynne Barre
Understanding diet is critical for conservation of endangered predators. The Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily in the west coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of the whales’ seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook...

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...

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: 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: 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: 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: 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...

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...

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: Titmice are a better indicator of bird density in Northern European than in Western European forests

Mira H. Kajanus, Jukka T. Forsman, Maximilian G. R. Vollstädt, Vincent Devictor, Merja Elo, Aleksi Lehikoinen, Mikko Mönkkönen, James T. Thorson & Sami M. Kivelä
Population sizes of many birds are declining alarmingly and methods for estimating fluctuations in species’ abundances at a large spatial scale are needed. The possibility to derive indicators from the tendency of specific species to co-occur with others has been overlooked. Here we tested whether the abundance of resident titmice can act as a general ecological indicator of forest bird density in European forests. Titmice species are easily identifiable and have a wide distribution, which...

Data from: Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Hollis Dahn, Jacquelyn Mountcastle, Jennifer Balacco, Sylke Winkler, Iliana Bista, Anthony Schmitt, Olga Vinnere Pettersson, Giulio Formenti, Karen Oliver, Michelle Smith, Wenhua Tan, Anne Kraus, Stephen Mac, Lisa Komoroske, Tanya Lama, Andrew Crawford, Robert Murphy, Samara Brown, Alan Scott, Phillip Morin, Erich Jarvis & Olivier Fedrigo
Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different...

Data from: Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation

Joseph I Hoffman, Kanchon Dasmahapatra, William Amos, Caleb Phillips, Tom Gelatt & John Bickham
Many studies use genetic markers to explore population structure and variability within species. However, only a minority use more than one type of marker and, despite increasing evidence of a strong link between heterozygosity and individual fitness, few ask whether diversity correlates with population trajectory. To address these issues, we analysed data from the Steller's sea lion, Eumetiopias jubatus, where three stocks are distributed over a vast geographic range and where both genetic samples and...

Data from: Spatial distribution, movements, and geographic range of Steller sea lions (Eumetopias jubatus) in Alaska

Lauri A. Jemison, Grey W. Pendleton, Kelly K. Hastings, John M. Maniscalco & Lowell W. Fritz
The two stocks of Steller sea lions (Eumetopias jubatus) in Alaska include an endangered western stock, recently recovering in parts of its range following decades of decline, and an eastern stock which was removed from the U.S. Endangered Species List in 2013 following increasing numbers since the 1970s. Information on overlapping distributions of eastern and western sea lions is needed for management considerations. We analyzed >30,000 sightings collected from 2000-2014 of 2,385 sea lions that...

Data from: Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?

Matthew R. Walsh, Kelsey Biles, Frank Cooley & Stephan B. Munch
Much work has shown that the environment can induce non-genetic changes in phenotype that span multiple generations. Theory predicts that predictable environmental variation selects for both increased within- and across-generation responses. Yet, to the best of our knowledge, there are no empirical tests of this prediction. We explored the relationship between within- versus across-generation plasticity by evaluating the influence of predator cues on the life-history traits of Daphnia ambigua. We measured the duration of predator-induced...

Ocean acidification alters properties of the exoskeleton in adult tanner crabs, Chionoecetes bairdi

Gary Dickinson, Shai Bejerano, Trina Salvador, Christine Makdisi, Shrey Patel, W. Christopher Long, Katherine Swiney, Robert Foy, Brittan Steffel, Kathryn Smith & Richard Aronson
Ocean acidification can affect the ability of calcifying organisms to build and maintain mineralized tissue. In decapod crustaceans, the exoskeleton is a multilayered structure composed of chitin, protein, and mineral, predominately magnesian calcite or amorphous calcium carbonate (ACC). We investigated the effects of acidification on the exoskeleton of mature (post-terminal-molt) female southern Tanner crabs, Chionoecetes bairdi. Crabs were exposed to one of three pH levels—8.1, 7.8, or 7.5—for two years. Reduced pH led to a...

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Affiliations

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