Whole genome resequencing identifies local adaptation associated with environmental variation for redband trout

Building a Bridge Between Adaptive Capacity and Adaptive Potential to Understand Responses to Environmental Change

(2021) Travis Seaborn et al.   GLOBAL CHANGE BIOLOGY

Heterogeneous genetic basis of age at maturity in salmonid fishes

(2021) Charles D. Waters et al.   MOLECULAR ECOLOGY

A long reads-based de-novo assembly of the genome of the Arlee homozygous line reveals chromosomal rearrangements in rainbow trout

(2021) Guangtu Gao et al.   G3-Genes Genomes Genetics

A beginner's guide to low‐coverage whole genome sequencing for population genomics

(2021) Runyang Nicolas Lou et al.   MOLECULAR ECOLOGY

Contribution of warm habitat to cold‐water fisheries

(2021) Nick Hahlbeck et al.   CONSERVATION BIOLOGY

Applying genomics in assisted migration under climate change: Framework, empirical applications, and case studies

(2021) Zhongqi Chen et al.   Evolutionary Applications

Influence of environmental conditions at spawning sites and migration routes on adaptive variation and population connectivity in Chinook salmon

(2021) Yara A. Alshwairikh et al.   Ecology and Evolution

Implications of Large-Effect Loci for Conservation: A Review and Case Study with Pacific Salmon

(2021) Robin S Waples et al.   JOURNAL OF HEREDITY

Validation and association of candidate markers for adult migration timing and fitness in Chinook Salmon

(2020) Ilana J. Koch et al.   Evolutionary Applications

Steelhead ( Oncorhynchus mykiss ) lineages and sexes show variable patterns of association of adult migration‐timing and age‐at‐maturity traits with two genomic regions

(2020) Stuart C. Willis et al.   Evolutionary Applications

Estimating the genome-wide contribution of selection to temporal allele frequency change

(2020) Vince Buffalo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Distribution of genetic variation underlying adult migration timing in steelhead of the Columbia River basin

(2020) Erin E. Collins et al.   Ecology and Evolution

The Gill‐Oxygen Limitation Theory and size at maturity/maximum size relationships for salmonid populations occupying flowing waters

(2020) Kevin A. Meyer et al.   JOURNAL OF FISH BIOLOGY

Whole genome resequencing reveals genomic regions associated with thermal adaptation in redband trout

(2020) Zhongqi Chen et al.   MOLECULAR ECOLOGY

Aquatic Landscape Genomics and Environmental Effects on Genetic Variation

(2019) Jared A. Grummer et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2018) Zhongqi Chen et al.   Evolutionary Applications

Comparing methods for detecting multilocus adaptation with multivariate genotype-environment associations

(2018) Brenna R. Forester et al.   MOLECULAR ECOLOGY

Mechanisms of thermal adaptation and evolutionary potential of conspecific populations to changing environments

(2018) Zhongqi Chen et al.   MOLECULAR ECOLOGY

The genomics of climate change

(2018) Mark J. Fitzpatrick et al.   SCIENCE

Global Warming of Salmon and Trout Rivers in the Northwestern U.S.: Road to Ruin or Path Through Purgatory?

(2018) Daniel J. Isaak et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations

(2018) Tasha Q. Thompson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Socioeconomic Pathways and their energy, land use, and greenhouse gas emissions implications: An overview

(2017) Keywan Riahi et al.   GLOBAL ENVIRONMENTAL CHANGE-HUMAN AND POLICY DIMENSIONS

WorldClim 2: new 1-km spatial resolution climate surfaces for global land areas

(2017) Stephen E. Fick et al.   INTERNATIONAL JOURNAL OF CLIMATOLOGY

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Landscape features along migratory routes influence adaptive genomic variation in anadromous steelhead (Oncorhynchus mykiss )

(2017) Steven J. Micheletti et al.   MOLECULAR ECOLOGY

Accounting for linkage disequilibrium in genome scans for selection without individual genotypes: The local score approach

(2017) María Inés Fariello et al.   MOLECULAR ECOLOGY

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

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Data-driven hypothesis weighting increases detection power in genome-scale multiple testing

(2016) Nikolaos Ignatiadis et al.   NATURE METHODS

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

Reliable Detection of Loci Responsible for Local Adaptation: Inference of a Null Model through Trimming the Distribution of FST

(2015) Michael C. Whitlock et al.   AMERICAN NATURALIST

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

The cold-water climate shield: delineating refugia for preserving salmonid fishes through the 21st century

(2015) Daniel J. Isaak et al.   GLOBAL CHANGE BIOLOGY

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

(2015) Nicola J. Barson et al.   NATURE

Status and Conservation of Interior Redband Trout in the Western United States

(2015) Clint C. Muhlfeld et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Dietary methionine availability affects the main factors involved in muscle protein turnover in rainbow trout (Oncorhynchus mykiss)

(2014) Ikram Belghit et al.   BRITISH JOURNAL OF NUTRITION

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

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

Population Origin and Water Temperature Affect Development Timing in Embryonic Sockeye Salmon

(2014) C. K. Whitney et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Adaptive potential of a Pacific salmon challenged by climate change

(2014) Nicolas J. Muñoz et al.   Nature Climate Change

Thermal adaptation and acclimation of ectotherms from differing aquatic climates

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

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Smoltification in an Impounded, Adfluvial Redband Trout Population Upstream from an Impassable Dam: Does It Persist?

(2012) Dean E. Holecek et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler 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

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

Influences of Habitat and Hybridization on the Genetic Structure of Redband Trout in the Upper Snake River Basin, Idaho

(2011) Christine C. Kozfkay et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Molecular characterization of the MuRF genes in rainbow trout: Potential role in muscle degradation

(2010) Jiannan Wang et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Biotic and Abiotic Factors Related to Redband Trout Occurrence and Abundance in Desert and Montane Streams

(2010) Kevin A. Meyer et al.   WESTERN NORTH AMERICAN NATURALIST

Differential gene expression after total replacement of dietary fish meal and fish oil by plant products in rainbow trout (Oncorhynchus mykiss) liver

(2009) S. Panserat et al.   AQUACULTURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS