Assessing thermal adaptation using family‐based association and F ST outlier tests in a threatened trout species

Physiological and genomic signatures of evolutionary thermal adaptation in redband trout from extreme climates

(2018) Zhongqi Chen et al.   Evolutionary Applications

Tolerance traits related to climate change resilience are independent and polygenic

(2018) Timothy M. Healy et al.   GLOBAL CHANGE BIOLOGY

Accurate genomic predictions for BCWD resistance in rainbow trout are achieved using low-density SNP panels: Evidence that long-range LD is a major contributing factor

(2018) Roger L. Vallejo et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow

(2018) Susanne P Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Trophic Ecology of Lahontan Cutthroat Trout: Historical Predator-Prey Interaction Supports Native Apex Predator in a Unique Desert Lake

(2018) Nicholas A. Heredia et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish

(2017) Charles Perrier et al.   MOLECULAR ECOLOGY

Thermal tolerance in the keystone species Daphnia magna -a candidate gene and an outlier analysis approach

(2017) M. Jansen et al.   MOLECULAR ECOLOGY

Return of a giant: DNA from archival museum samples helps to identify a unique cutthroat trout lineage formerly thought to be extinct

(2017) Mary M. Peacock et al.   Royal Society Open Science

The evolutionary basis of premature migration in Pacific salmon highlights the utility of genomics for informing conservation

(2017) Daniel J. Prince et al.   Science Advances

The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes

(2016) R. J. Scott McCairns et al.   Evolutionary Applications

Conservation of Native Pacific Trout Diversity in Western North America

(2016) Brooke E. Penaluna et al.   FISHERIES

Climate variables explain neutral and adaptive variation within salmonid metapopulations: the importance of replication in landscape genetics

(2016) Brian K. Hand et al.   MOLECULAR ECOLOGY

pcadapt: anRpackage to perform genome scans for selection based on principal component analysis

(2016) Keurcien Luu et al.   Molecular Ecology Resources

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

A single generation of domestication heritably alters the expression of hundreds of genes

(2016) Mark R. Christie et al.   Nature Communications

Transcriptomic response to heat stress among ecologically divergent populations of redband trout

(2015) Shawn R Narum et al.   BMC GENOMICS

Anadromy and residency in steelhead and rainbow trout (Oncorhynchus mykiss): a review of the processes and patterns

(2015) Neala W. Kendall et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genome-Wide Scan for Adaptive Divergence and Association with Population-Specific Covariates

(2015) M. Gautier   GENETICS

Differential Expression of Genes that Control Respiration Contribute to Thermal Adaptation in Redband Trout ( Oncorhynchus mykiss gairdneri )

(2015) Michael R. Garvin et al.   Genome Biology and Evolution

Identification of Multiple QTL Hotspots in Sockeye Salmon (Oncorhynchus nerka) Using Genotyping-by-Sequencing and a Dense Linkage Map

(2015) Wesley A. Larson et al.   JOURNAL OF HEREDITY

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

Environmental adaptation in Chinook salmon (Oncorhynchus tshawytscha) throughout their North American range

(2015) Benjamin C. Hecht et al.   MOLECULAR ECOLOGY

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab et al.   MOLECULAR ECOLOGY

Genomic resources and their influence on the detection of the signal of positive selection in genome scans

(2015) S. Manel et al.   MOLECULAR ECOLOGY

The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

(2015) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

The past, present and future of genomic scans for selection

(2015) Jeffrey D. Jensen et al.   MOLECULAR ECOLOGY

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

(2015) Nicola J. Barson et al.   NATURE

Piezo1 regulates mechanotransductive release of ATP from human RBCs

(2015) Eyup Cinar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Response to Acute Thermal Exposure in Juvenile Chinook Salmon Determined by RNAseq

(2015) Katharine M. H. Tomalty et al.   G3-Genes Genomes Genetics

Population structure, inbreeding and local adaptation within an endangered riverine specialist: the nase (Chondrostoma nasus)

(2014) Alan G. Hudson et al.   CONSERVATION GENETICS

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

Life-history diversity and its importance to population stability and persistence of a migratory fish: steelhead in two large North American watersheds

(2014) Jonathan W. Moore et al.   JOURNAL OF ANIMAL ECOLOGY

Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar)

(2014) Susan E. Johnston et al.   MOLECULAR ECOLOGY

Genome-wide single-generation signatures of local selection in the panmictic European eel

(2014) J. M. Pujolar et al.   MOLECULAR ECOLOGY

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

Genome scan methods against more complex models: when and how much should we trust them?

(2014) Pierre de Villemereuil et al.   MOLECULAR ECOLOGY

Ecological and evolutionary patterns of freshwater maturation in Pacific and Atlantic salmonines

(2014) Matthew R. Sloat et al.   REVIEWS IN FISH BIOLOGY AND FISHERIES

Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Conserving marine biodiversity: insights from life-history trait candidate genes in Atlantic cod (Gadus morhua)

(2013) Jakob Hemmer-Hansen et al.   CONSERVATION GENETICS

Transcriptomic responses to high water temperature in two species of Pacific salmon

(2013) Ken M. Jeffries et al.   Evolutionary Applications

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Variation in temperature tolerance among families of Atlantic salmon (Salmo salar) is associated with hypoxia tolerance, ventricle size and myoglobin level

(2013) K. Anttila et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

(2013) Paul A. Hohenlohe et al.   MOLECULAR ECOLOGY

Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

(2013) Charles Perrier et al.   MOLECULAR ECOLOGY

Genotyping-by-sequencing in ecological and conservation genomics

(2013) Shawn R. Narum et al.   MOLECULAR ECOLOGY

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

The Past as Prelude to the Future for Understanding 21st-Century Climate Effects on Rocky Mountain Trout

(2012) Daniel J. Isaak et al.   FISHERIES

Population genomics based on low coverage sequencing: how low should we go?

(2012) C. Alex Buerkle et al.   MOLECULAR ECOLOGY

Effect of Brook Trout Removal from a Spawning Stream on an Adfluvial Population of Lahontan Cutthroat Trout

(2012) G. Gary Scoppettone et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Harnessing genomics for delineating conservation units

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

Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka)

(2012) Ken M. Jeffries et al.   Ecology and Evolution

PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs

(2011) H. E. L. Lischer et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Potential climate change impacts on thermal habitats of Pacific salmon (Oncorhynchus spp.) in the North Pacific Ocean and adjacent seas

(2011) Omar I. Abdul-Aziz et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genomic toolboxes for conservation biologists

(2011) Francesco Angeloni et al.   Evolutionary Applications

Genetics of local adaptation in salmonid fishes

(2011) C R Primmer   HEREDITY

A conserved haplotype controls parallel adaptation in geographically distant salmonid populations

(2011) MICHAEL R. MILLER et al.   MOLECULAR ECOLOGY

Application of SNPs for population genetics of nonmodel organisms: new opportunities and challenges

(2011) S. J. HELYAR et al.   Molecular Ecology Resources

Comparison ofFSToutlier tests for SNP loci under selection

(2011) SHAWN R. NARUM et al.   Molecular Ecology Resources

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

(2011) PAUL A. HOHENLOHE et al.   Molecular Ecology Resources

Genetic adaptation to captivity can occur in a single generation

(2011) M. R. Christie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flow regime, temperature, and biotic interactions drive differential declines of trout species under climate change

(2011) S. J. Wenger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differences in Thermal Tolerance Among Sockeye Salmon Populations

(2011) E. J. Eliason et al.   SCIENCE

Climate change impacts on the biophysics and economics of world fisheries

(2011) U. Rashid Sumaila et al.   Nature Climate Change

Adaptation of redband trout in desert and montane environments

(2010) SHAWN R. NARUM et al.   MOLECULAR ECOLOGY

Multiple approaches to detect outliers in a genome scan for selection in ocellated lizards (Lacerta lepida) along an environmental gradient

(2010) VERA L. NUNES et al.   MOLECULAR ECOLOGY

Temperature and length-dependent modulation of the MH class IIβ gene expression in brook charr (Salvelinus fontinalis) by a cis-acting minisatellite

(2010) Sébastien Croisetière et al.   MOLECULAR IMMUNOLOGY

Genomics and the future of conservation genetics

(2010) Fred W. Allendorf et al.   NATURE REVIEWS GENETICS

Conservation genetics in transition to conservation genomics

(2010) N. Joop Ouborg et al.   TRENDS IN GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

LOSITAN: A workbench to detect molecular adaptation based on a Fst-outlier method

(2008) Tiago Antao et al.   BMC BIOINFORMATICS

SYNTHESIS: Evolutionary history of Pacific salmon in dynamic environments

(2008) Robin S. Waples et al.   Evolutionary Applications

A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms

(2008) Xiaoyi Gao et al.   GENETIC EPIDEMIOLOGY

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

(2008) M. Foll et al.   GENETICS

Fulton's body condition factor K correlates with survival time in a thermal challenge experiment in juvenile Lahontan cutthroat trout (Oncorhynchus clarki henshawi)

(2008) M.L. Robinson et al.   JOURNAL OF THERMAL BIOLOGY

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

genepop’007: a complete re-implementation of the genepop software for Windows and Linux

(2007) FRANÇOIS ROUSSET   Molecular Ecology Resources