32 Works

Data from: Mapping and expression of candidate genes for development rate in rainbow trout (Oncorhynchus mykiss)

Matthew C. Hale, John A. Colletti, Scott A. Gahr, Julie Scardina, Frank P. Thrower, Matthew Harmon, Megan Carter, Ruth B. Phillips, Gary H. Thorgaard, Caird E. Rexroad & Krista M. Nichols
Development rate has important implications for individual fitness and physiology. In salmonid fishes, development rate correlates with many traits later in life, including life history diversity, growth, and age and size at sexual maturation. In rainbow trout (Oncorhynchus mykiss), a Quantitative Trait Locus (QTL) for embryonic development rate has been detected on chromosome 5 across populations. However, few candidate genes have been identified within this region. In this study, we use gene mapping, gene expression,...

North Pacific harbor porpoise SNP and microhaplotype genotypes, mitochondrial control region haplotype sequences

Phillip Morin, Brenna Forester, Karin Forney, Carla Crossman, Brittany Hancock-Hanser, Kelly Robertson, Lance Barrett-Lennard, Robin Baird, John Calambokidis, Pat Gearin, Bradley Hanson, Cassie Schumacher, Timothy Harkins, Michael Fontaine, Barbara Taylor & Kim Parsons
Harbor porpoises in the North Pacific are found in coastal waters from southern California to Japan, but population structure is poorly known outside of a few local areas. We used multiplexed amplicon sequencing of 292 loci and genotyped clusters of SNPs as microhaplotypes (N=271 samples) in addition to mtDNA sequence data (N=413 samples), to examine the genetic structure from samples collected along the Pacific coast and inland waterways from California to southern British Columbia. We...

Data from: Satellite tracking reveals novel migratory patterns and the importance of seamounts for endangered South Pacific humpback whales

Claire Garrigue, Phillip J. Clapham, Amy S. Kennedy & Alexandre N. Zerbini
The humpback whale population of New Caledonia appears to display a novel migratory pattern characterized by multiple directions, long migratory paths and frequent pauses over seamounts and other shallow geographical features. Using satellite-monitored radio tags, we tracked 34 whales for between 5 and 110 days, travelling between 270 and 8540 km on their southward migration from a breeding ground in southern New Caledonia. Mean migration speed was 3.53±2.22 km h−1, while movements within the breeding...

From pup to predator; generalized hidden Markov models reveal rapid development of movement strategies in a naïve long‐lived vertebrate

Matt I. D. Carter, Brett T. McClintock, Clare B. Embling, Kimberley A. Bennett, Dave Thompson & Debbie J. F. Russell
Rapid development of a successful foraging strategy is critical for juvenile survival, especially for naïve animals that receive no parental guidance. However, this process is poorly understood for many species. Although observation of early-life movements is increasingly possible with miniaturisation of animalborne telemetry devices, analytical limitations remain. Here, we tracked 29 recently-weaned, grey seal Halichoerus grypus pups from colonies in two geographically distinct regions of the United Kingdom. We analysed at-sea movements of pups throughout...

Adaptations of fish and fishing communities to rapid climate change

Doug McCauley
Climate change presents a profound challenge to the sustainability of coastal systems. Most research has overlooked the important coupling between human responses to climate effects and the cumulative impacts of these responses on ecosystems. Fisheries are a prime example of this feedback: climate changes cause shifts in species distributions and abundances, and fisheries adapt to these shifts. However, changes in the location and intensity of fishing also have major ecosystem impacts. This project's goal is...

Data from: Crossing to safety: Dispersal, colonization and mate choice in evolutionarily distinct populations of Steller sea lions, Eumetopias jubatus.

Gregory O’Corry-Crowe, Tom Gelatt, Lorrie Rea, Carolina Bonin, Michael Rehberg & Greg O'Corry-Crowe
Population growth typically involves range expansion and establishment of new breeding sites, while the opposite occurs during declines. Although density-dependence is widely invoked in theoretical studies of emigration and colonization in expanding populations, few empirical studies have documented the mechanisms. Still fewer have documented the direction and mechanisms of individual transfer in declining populations. Here we screen large numbers of pups sampled on their natal rookeries for variation in mtDNA (n=1,106) and 16 microsatellite loci...

Supplemental material for Climate forcing by battered-and-breaded fillets and crab-flavored sticks from Alaska pollock

Brandi McKuin, Jordan Watson, Alan Haynie & J. Elliott Campbell
Detailed supplemental datasets: inputs and output information and emission factors for ingredients, non-ingredient materials, and embodied energy of pollock products.

Data and code for simulation study and case study in \"A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity\"

Rahel Sollmann, Mitchell Eaton, William Link, Paul Mulondo, Samuel Ayebare, Sarah Prinsloo & Devin Johnson
This dataset contains the R and JAGS code underlying the simulation study, as well as the data and code underlying the case study on bird occurrence in Murchison Falls National Park, presented in the paper "A Bayesian Dirichlet process community occupancy model to estimate community structure and species similarity".

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: Bias correction of bounded location errors in presence-only data

Trevor J. Hefley, Brian M. Brost & Mevin B. Hooten
1. Location error occurs when the true location is different than the reported location. Because habitat characteristics at the true location may be different than those at the reported location, ignoring location error may lead to unreliable inference concerning species-habitat relationships. 2. We explain how a transformation known in the spatial statistics literature as a change of support (COS) can be used to correct for location errors when the true locations are points with unknown...

Results of the acoustic trawl survey of walleye pollock (Gadus chalcogrammus) in the Gulf of Alaska, June August 2017 (DY2017-06)

D. T. Jones, N. (Nathan) Lauffenburger, K. Williams & Alex De Robertis
AFSC processed report ; 2019-08

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: Broad-scale trophic shift in the pelagic North Pacific revealed by an oceanic seabird

Peggy H. Ostrom, Anne E. Wiley, Helen F. James, Sam Rossman, William A. Walker, Elise F. Zipkin & Yoshito Chikaraishi
Human-induced ecological change in the open oceans appears to be accelerating. Fisheries, climate change and elevated nutrient inputs are variously blamed, at least in part, for altering oceanic ecosystems. Yet it is challenging to assess the extent of anthropogenic change in the open oceans, where historical records of ecological conditions are sparse, and the geographical scale is immense. We developed millennial-scale amino acid nitrogen isotope records preserved in ancient animal remains to understand changes in...

Data from: Potentially adaptive mitochondrial haplotypes as a tool to identify divergent nuclear loci

Michael R. Garvin, William D. Templin, Anthony J. Gharrett, Nick DeCovich, Christine M. Kondzela, Jeffrey R. Guyon & Megan V. McPhee
1. Genetic tools are commonly used for conservation and management of at-risk species. Individuals are often sampled from mixtures composed of many populations, which creates a need to assign individuals to their source. This can be problematic when the genetic divergence among source populations is weak but can be improved using adaptive genetic loci, which should show stronger levels of divergence. 2. We previously reported a signature of positive selection in the mitochondrial-encoded ND5 subunit...

Data from: Taxonomy-based hierarchical analysis of natural mortality: polar and sub-polar phocid seals

Irina S. Trukhanova, Paul B. Conn & Peter L. Boveng
Knowledge of life‐history parameters is frequently lacking in many species and populations, often because they are cryptic or logistically challenging to study, but also because life‐history parameters can be difficult to estimate with adequate precision. We suggest using hierarchical Bayesian analysis (HBA) to analyze variation in life‐history parameters among related species, with prior variance components representing shared taxonomy, phenotypic plasticity, and observation error. We develop such a framework to analyze U‐shaped natural mortality patterns typical...

Data to replicate: Forecasting community reassembly using climate-linked spatio-temporal ecosystem models

James Thorson, Mayumi Arimitsu, Lewis Barnett, Wei Cheng, Lisa Eisner, Alan Haynie, Albert Hermann, Kirstin Holsman, David Kimmel, Mike Lomas, Jon Richar & Elizabeth Siddon
Ecosystems are increasingly impacted by human activities, altering linkages among physical and biological components. Spatial community reassembly occurs when these human impacts modify the spatial overlap between system components, and there is need for practical tools to forecast spatial community reassembly at landscape scales using monitoring data. To illustrate a new approach, we extend a generalization of empirical orthogonal function (EOF) analysis, which involves a spatio-temporal ecosystem model that approximates coupled physical, biological, and human...

Data from: Fine-scale population dynamics in a marine fish species inferred from dynamic state-space models

Lauren A. Rogers, Geir O. Storvik, Halvor Knutsen, Esben M. Olsen & Nils Chr. Stenseth
Identifying the spatial scale of population structuring is critical for the conservation of natural populations and for drawing accurate ecological inferences. However, population studies often use spatially aggregated data to draw inferences about population trends and drivers, potentially masking ecologically relevant population sub-structure and dynamics. The goals of this study were to investigate how population dynamics models with and without spatial structure affect inferences on population trends and the identification of intrinsic drivers of population...

Data from: Population assignment and local adaptation along an isolation-by-distance gradient in Pacific cod (Gadus macrocephalus)

Daniel P. Drinan, Kristen M. Gruenthal, Michael F. Canino, Dayv Lowry, Mary C. Fisher & Lorenz Hauser
The discernment of populations as management units is a fundamental prerequisite for sustainable exploitation of species. A lack of clear stock boundaries complicates not only the identification of spatial management units, but also the assessment of mixed fisheries by population assignment and mixed stock analysis. Many marine species, such as Pacific cod, are characterized by isolation-by-distance, showing significant differentiation but no clear stock boundaries. Here, we used restriction-site associated DNA (RAD) sequencing to investigate population...

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...

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: Spatio-temporal models reveal subtle changes to demersal communities following the Exxon Valdez oil spill

Andrew O. Shelton, Mary E. Hunsicker, Eric J. Ward, Blake E. Feist, Rachael Blake, Colette L. Ward, Benjamin C. Williams, Janet T. Duffy-Anderson, Anne B. Hollowed & Alan C. Haynie
Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez...

Data from: Assessing bottom-trawling impacts based on the longevity of benthic invertebrates

Jan Geert Hiddink, Simon Jennings, Marija Sciberras, Stefan Bolam, Giulia Cambie, Robert McConnaughey, Tessa Mazor, Ray Hilborn, Jeremy Collie, C. Roland Pitcher, Ana Parma, Petri Suuronen, Michel Kaiser, Adriaan Rijnsdorp, Jeremy S. Collie, Michel J. Kaiser, Adriaan D. Rijnsdorp & Robert A. McConnaughey
1. Bottom trawling is the most widespread human activity directly affecting seabed habitats. Assessment and effective management of the effects of bottom trawling at the scale of fisheries requires an understanding of differences in sensitivity of biota to trawling. Responses to disturbance are expected to depend on the intrinsic rate of increase of populations (r), which is expected to be linearly related to the reciprocal of longevity. 2. We examine the relationship between the longevity...

Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

James T. Thorson, Mayumi L. Arimitsu, Taal Levi & Gretchen H. Roffler
Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as...

Developing a Multi-Regional Social Accounting Matrix (MRSAM) for Southwest Alaska Fisheries

C. K. Seung, E. Waters & M. Taylor
NOAA technical memorandum NMFS-AFSC ; 399

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