Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies

Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America

(2017) Shawn R. Narum et al.   Evolutionary Applications

Harnessing the Power of Genomics to Secure the Future of Seafood

(2017) Louis Bernatchez et al.   TRENDS IN ECOLOGY & EVOLUTION

Evaluating the benefit of captive breeding and reintroductions to endangered Sonoran pronghorn

(2016) Jon S. Horne et al.   BIOLOGICAL CONSERVATION

Genomic signatures amongOncorhynchus nerkaecotypes to inform conservation and management of endangered Sockeye Salmon

(2016) Krista M. Nichols et al.   Evolutionary Applications

It’s a bear market: evolutionary and ecological effects of predation on two wild sockeye salmon populations

(2016) J E Lin et al.   HEREDITY

Decision forest: Twenty years of research

(2016) Lior Rokach   Information Fusion

From population genomics to conservation and management: a workflow for targeted analysis of markers identified using genome-wide approaches in Atlantic salmonSalmo salar

(2016) T. Aykanat et al.   JOURNAL OF FISH BIOLOGY

Saving the spandrels? Adaptive genomic variation in conservation and fisheries management

(2016) D. E. Pearse   JOURNAL OF FISH BIOLOGY

On the maintenance of genetic variation and adaptation to environmental change: considerations from population genomics in fishes

(2016) L. Bernatchez   JOURNAL OF FISH BIOLOGY

Specific alleles at immune genes, rather than genome-wide heterozygosity, are related to immunity and survival in the critically endangered Attwater's prairie-chicken

(2016) Zachary W. Bateson et al.   MOLECULAR ECOLOGY

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Genetic basis of adult migration timing in anadromous steelhead discovered through multivariate association testing

(2016) Jon E. Hess et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

(2016) Brittany A. Garner et al.   TRENDS IN ECOLOGY & EVOLUTION

RAD Sequencing Highlights Polygenic Discrimination of Habitat Ecotypes in the Panmictic American Eel

(2015) Scott A. Pavey et al.   CURRENT BIOLOGY

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

(2015) Charles D. Waters et al.   Evolutionary Applications

Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

(2015) Benjamin Hornoy et al.   Genome Biology and Evolution

Spatio-temporal variation in fish condition is not consistently explained by density, temperature, or season for California Current groundfishes

(2015) JT Thorson   MARINE ECOLOGY PROGRESS SERIES

RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

(2015) M. Laporte et al.   MOLECULAR ECOLOGY

Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

(2015) Marine S. O. Brieuc et al.   MOLECULAR ECOLOGY

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

(2015) Laura Benestan et al.   MOLECULAR ECOLOGY

An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

(2015) G. J. McKinney et al.   Molecular Ecology Resources

Sex-dependent dominance at a single locus maintains variation in age at maturity in salmon

(2015) Nicola J. Barson et al.   NATURE

A Synthesis of Findings from an Integrated Hatchery Program after Three Generations of Spawning in the Natural Environment

(2015) David E. Fast et al.   NORTH AMERICAN JOURNAL OF AQUACULTURE

Genomics and the challenging translation into conservation practice

(2015) Aaron B.A. Shafer et al.   TRENDS IN ECOLOGY & EVOLUTION

A random forest approach to capture genetic effects in the presence of population structure

(2015) Johannes Stephan et al.   Nature Communications

Spatio-temporal variation in fish condition is not consistently explained by density, temperature, or season for California Current groundfishes

(2015) JT Thorson   MARINE ECOLOGY PROGRESS SERIES

Detection and mapping of QTL for temperature tolerance and body size in Chinook salmon (Oncorhynchus tshawytscha) using genotyping by sequencing

(2014) Meredith V. Everett et al.   Evolutionary Applications

Using genomics to characterize evolutionary potential for conservation of wild populations

(2014) Katherine A. Harrisson et al.   Evolutionary Applications

On the reproductive success of early-generation hatchery fish in the wild

(2014) Mark R. Christie et al.   Evolutionary Applications

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates

(2014) Camille Berthelot et al.   Nature Communications

Genome-wide association study of coronary and aortic calcification implicates risk loci for coronary artery disease and myocardial infarction

(2013) Jessica van Setten et al.   ATHEROSCLEROSIS

Adaptive genetic markers discriminate migratory runs of Chinook salmon (Oncorhynchus tshawytscha) amid continued gene flow

(2013) Kathleen G. O'Malley et al.   Evolutionary Applications

Microevolution in time and space: SNP analysis of historical DNA reveals dynamic signatures of selection in Atlantic cod

(2013) Nina O. Therkildsen et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Temporal variation in selection on body length and date of return in a wild population of coho salmon, Oncorhynchus kisutch

(2012) Miyako Kodama et al.   BMC EVOLUTIONARY BIOLOGY

Evaluating Alternative Strategies for Minimizing Unintended Fitness Consequences of Cultured Individuals on Wild Populations

(2012) MARISSA L. BASKETT et al.   CONSERVATION BIOLOGY

Correction for population stratification in random forest analysis

(2012) Yang Zhao et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Adaptive evolution: evaluating empirical support for theoretical predictions

(2012) Carrie F. Olson-Manning et al.   NATURE REVIEWS GENETICS

Harnessing genomics for delineating conservation units

(2012) W. Chris Funk et al.   TRENDS IN ECOLOGY & EVOLUTION

Depletion of the novel protein PHACTR-1 from human endothelial cells abolishes tube formation and induces cell death receptor apoptosis

(2011) Rafika Jarray et al.   BIOCHIMIE

Hatcheries, Conservation, and Sustainable Fisheries—Achieving Multiple Goals: Results of the Hatchery Scientific Review Group's Columbia River Basin Review

(2011) P. J. Paquet et al.   FISHERIES

An Emerging Role of Zoos to Conserve Biodiversity

(2011) D. A. Conde et al.   SCIENCE

Random Forests for Genetic Association Studies

(2011) Benjamin A Goldstein et al.   Statistical Applications in Genetics and Molecular Biology

Genotype by environment interactions for growth in European seabass (Dicentrarchus labrax) are large when growth rate rather than weight is considered

(2010) Mathilde Dupont-Nivet et al.   AQUACULTURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Factors influencing the relative fitness of hatchery and wild spring Chinook salmon (Oncorhynchus tshawytscha) in the Wenatchee River, Washington, USA

(2010) Kevin S. Williamson et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Adaptation – not by sweeps alone

(2010) Jonathan K. Pritchard et al.   NATURE REVIEWS GENETICS

Behavior and Breeding Success of Wild and First-Generation Hatchery Male Spring Chinook Salmon Spawning in an Artificial Stream

(2010) Steven L. Schroder et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The effects of captive experience on reintroduction survival in carnivores: A review and analysis

(2008) Kristen R. Jule et al.   BIOLOGICAL CONSERVATION

Captive Breeding, Reintroduction, and the Conservation of Amphibians

(2008) RICHARD A. GRIFFITHS et al.   CONSERVATION BIOLOGY

SYNTHESIS: A review of quantitative genetic components of fitness in salmonids: implications for adaptation to future change

(2008) Stephanie M. Carlson et al.   Evolutionary Applications

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Modulation of the Neural Glutamate Transporter EAAC1 by the Addicsin-interacting Protein ARL6IP1

(2008) Saori Akiduki et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Run Timing, Spawn Timing, and Spawning Distribution of Hatchery- and Natural-Origin Spring Chinook Salmon in the Imnaha River, Oregon

(2008) Timothy L. Hoffnagle et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

Breeding Success of Wild and First-Generation Hatchery Female Spring Chinook Salmon Spawning in an Artificial Stream

(2008) Steven L. Schroder et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Migration Timing of Columbia River Spring Chinook Salmon: Effects of Temperature, River Discharge, and Ocean Environment

(2008) Matthew L. Keefer et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Genetic adaptation to captivity in species conservation programs

(2007) RICHARD FRANKHAM   MOLECULAR ECOLOGY