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

Evolving New Skeletal Traits by cis -Regulatory Changes in Bone Morphogenetic Proteins

(2016) Vahan B. Indjeian et al.   CELL

Are heritability and selection related to population size in nature? Meta-analysis and conservation implications

(2016) Jacquelyn L. A. Wood et al.   Evolutionary Applications

Genomic tools for new insights to variation, adaptation, and evolution in the salmonid fishes: a perspective for charr

(2016) Kathryn R. Elmer   HYDROBIOLOGIA

The genetic consequences of selection in natural populations

(2016) Timothy J. Thurman et al.   MOLECULAR ECOLOGY

Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki)

(2016) Manuel Vera et al.   MOLECULAR ECOLOGY

Epigenetic divergence as a potential first step in darter speciation

(2016) Tracy A. Smith et al.   MOLECULAR ECOLOGY

The multivariate association between genomewide DNA methylation and climate across the range ofArabidopsis thaliana

(2016) Thomas E. Keller et al.   MOLECULAR ECOLOGY

Species-wide patterns of DNA methylation variation inQuercus lobataand their association with climate gradients

(2016) Paul F. Gugger et al.   MOLECULAR ECOLOGY

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

Parallel genetic divergence among coastal-marine ecotype pairs of European anchovy explained by differential introgression after secondary contact

(2016) A. Le Moan et al.   MOLECULAR ECOLOGY

Epigenetics in ecology and evolution: what we know and what we need to know

(2016) Koen J. F. Verhoeven et al.   MOLECULAR ECOLOGY

Causes of molecular convergence and parallelism in protein evolution

(2016) Jay F. Storz   NATURE REVIEWS GENETICS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Adaptation to Global Change: A Transposable Element–Epigenetics Perspective

(2016) Olivier Rey et al.   TRENDS IN ECOLOGY & EVOLUTION

Detecting Polygenic Evolution: Problems, Pitfalls, and Promises

(2016) Maren Wellenreuther et al.   TRENDS IN GENETICS

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

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

Population genomics of local adaptation versus speciation in coral reef fishes (Hypoplectrusspp, Serranidae)

(2016) Sophie Picq et al.   Ecology and Evolution

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

(2016) Jakob Hemmer-Hansen et al.   BIOLOGICAL BULLETIN

The Role of Standing Variation in Geographic Convergent Adaptation

(2015) Peter L. Ralph et al.   AMERICAN NATURALIST

Modern Approaches to Local Adaptation

(2015) Michael C. Whitlock   AMERICAN NATURALIST

Local Adaptation by Alleles of Small Effect

(2015) Sam Yeaman   AMERICAN NATURALIST

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

Population genomic evidence for adaptive differentiation in Baltic Sea three-spined sticklebacks

(2015) Baocheng Guo et al.   BMC BIOLOGY

Parallel evolution in Ugandan crater lakes: repeated evolution of limnetic body shapes in haplochromine cichlid fish

(2015) Gonzalo Machado-Schiaffino et al.   BMC EVOLUTIONARY BIOLOGY

Signatures of natural selection between life cycle stages separated by metamorphosis in European eel

(2015) J. M. Pujolar et al.   BMC GENOMICS

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

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

Similar plastic responses to elevated temperature among different-sized brook trout populations

(2015) Jacquelyn L. A. Wood et al.   ECOLOGY

Experimental evidence of genome-wide impact of ecological selection during early stages of speciation-with-gene-flow

(2015) Scott P. Egan et al.   ECOLOGY LETTERS

Emergence of long-term balanced polymorphism under cyclic selection of spatially variable magnitude

(2015) Davorka Gulisija et al.   EVOLUTION

Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)

(2015) Anne C. Dalziel et al.   EVOLUTION

Using neutral, selected, and hitchhiker loci to assess connectivity of marine populations in the genomic era

(2015) Pierre-Alexandre Gagnaire et al.   Evolutionary Applications

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

Genomic signatures of geographic isolation and natural selection in coral reef fishes

(2015) Michelle R. Gaither et al.   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

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

Population genomics of natural and experimental populations of guppies (Poecilia reticulata)

(2015) Bonnie A. Fraser et al.   MOLECULAR ECOLOGY

Detecting balancing selection in genomes: limits and prospects

(2015) Anna Fijarczyk 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

Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout

(2015) Melinda R. Baerwald et al.   MOLECULAR ECOLOGY

Population differentiation determined from putative neutral and divergent adaptive genetic markers in Eulachon (Thaleichthys pacificus, Osmeridae), an anadromous Pacific smelt

(2015) John R. Candy 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 new FST-based method to uncover local adaptation using environmental variables

(2015) Pierre de Villemereuil et al.   Methods in Ecology and Evolution

Towards the identification of the loci of adaptive evolution

(2015) Carolina Pardo-Diaz et al.   Methods in Ecology and Evolution

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs

(2015) Martin Laporte et al.   G3-Genes Genomes Genetics

Convergent Evolution During Local Adaptation to Patchy Landscapes

(2015) Peter L. Ralph et al.   PLoS Genetics

Do North Atlantic eels show parallel patterns of spatially varying selection?

(2014) Malene G Ulrik et al.   BMC EVOLUTIONARY BIOLOGY

So, you want to use next-generation sequencing in marine systems? Insight from the Pan-Pacific Advanced Studies Institute

(2014) DA Willette et al.   BULLETIN OF MARINE SCIENCE

Multilocus Adaptation Associated with Heat Resistance in Reef-Building Corals

(2014) Rachael A. Bay et al.   CURRENT BIOLOGY

Adaptations to local environments in modern human populations

(2014) Choongwon Jeong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Population genomic analyses of early-phase Atlantic Salmon (Salmo salar) domestication/captive breeding

(2014) Hannu Mäkinen et al.   Evolutionary Applications

Climate change, adaptation, and phenotypic plasticity: the problem and the evidence

(2014) Juha Merilä et al.   Evolutionary Applications

Environmental heat stress induces epigenetic transgenerational inheritance of robustness in parthenogenetic Artemia model

(2014) Parisa Norouzitallab et al.   FASEB JOURNAL

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

(2014) J. M. Pujolar 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

Footprints of Directional Selection in Wild Atlantic Salmon Populations: Evidence for Parasite-Driven Evolution?

(2014) Ksenia J. Zueva et al.   PLoS One

Applying evolutionary biology to address global challenges

(2014) S. P. Carroll et al.   SCIENCE

Stick Insect Genomes Reveal Natural Selection's Role in Parallel Speciation

(2014) V. Soria-Carrasco et al.   SCIENCE

The Population Genetics of Evolutionary Rescue

(2014) H. Allen Orr et al.   PLoS Genetics

Genomic Evidence of Rapid and Stable Adaptive Oscillations over Seasonal Time Scales in Drosophila

(2014) Alan O. Bergland et al.   PLoS Genetics

Evolutionary Rescue in Structured Populations

(2013) Hildegard Uecker et al.   AMERICAN NATURALIST

How epigenetic mutations can affect genetic evolution: Model and mechanism

(2013) Filippos D. Klironomos et al.   BIOESSAYS

Molecular consequences of animal breeding

(2013) Leif Andersson   CURRENT OPINION IN GENETICS & DEVELOPMENT

Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens)

(2013) Sébastien Bélanger-Deschênes et al.   ECOTOXICOLOGY

LANDSCAPE GENOMICS IN ATLANTIC SALMON (SALMO SALAR): SEARCHING FOR GENE-ENVIRONMENT INTERACTIONS DRIVING LOCAL ADAPTATION

(2013) Bourret Vincent et al.   EVOLUTION

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

(2013) Pierre-Alexandre Gagnaire et al.   EVOLUTION

Patterns of DNA Methylation Throughout a Range Expansion of an Introduced Songbird

(2013) A. L. Liebl et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

High degree of cryptic population differentiation in the Baltic Sea herringClupea harengus

(2013) Jukka Corander et al.   MOLECULAR ECOLOGY

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

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

(2013) C. R. Primmer et al.   MOLECULAR ECOLOGY

A genomic island linked to ecotype divergence in Atlantic cod

(2013) Jakob Hemmer-Hansen et al.   MOLECULAR ECOLOGY

Pervasive selection or is it…? why areFSToutliers sometimes so frequent?

(2013) Nicolas Bierne et al.   MOLECULAR ECOLOGY

Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations

(2013) Stéphane De Mita et al.   MOLECULAR ECOLOGY

Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

(2013) Stéphane Joost et al.   MOLECULAR ECOLOGY

A road map for molecular ecology

(2013) Rose L. Andrew et al.   MOLECULAR ECOLOGY

Genomic divergence between the migratory and stationary ecotypes of Atlantic cod

(2013) Bård O. Karlsen et al.   MOLECULAR ECOLOGY

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Evolutionary change during experimental ocean acidification

(2013) M. H. Pespeni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics of rapid adaptation by soft selective sweeps

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

Genome sequencing and population genomics in non-model organisms

(2013) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Predicting Adaptive Phenotypes From Multilocus Genotypes in Sitka Spruce ( Picea sitchensis ) Using Random Forest

(2013) Jason A. Holliday et al.   G3-Genes Genomes Genetics

Applying ecological and evolutionary theory to cancer: a long and winding road

(2012) Frédéric Thomas et al.   Evolutionary Applications

Random forests for genomic data analysis

(2012) Xi Chen et al.   GENOMICS

Oxidative phosphorylation gene transcription in whitefish species pairs reveals patterns of parallel and nonparallel physiological divergence

(2012) M. L. Evans et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genomic signatures of divergent selection and speciation patterns in a ‘natural experiment’, the young parallel radiations of Nicaraguan crater lake cichlid fishes

(2012) Andreas F. Kautt et al.   MOLECULAR ECOLOGY

Monitoring adaptive genetic responses to environmental change

(2012) MICHAEL M. HANSEN et al.   MOLECULAR ECOLOGY

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

Population genetics of the American eel (Anguilla rostrata):FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species

(2012) Caroline L. Côté et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

Adaptation ofDrosophilato a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles

(2012) PABLO OROZCO-terWENGEL et al.   MOLECULAR ECOLOGY

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

(2012) Jon E. Hess et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Epigenetics and the environment: emerging patterns and implications

(2012) Robert Feil et al.   NATURE REVIEWS GENETICS

The probability of genetic parallelism and convergence in natural populations

(2012) G. L. Conte et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

DNA methylation: A source of random variation in natural populations

(2011) Rachel Massicotte et al.   Epigenetics

THE QTN PROGRAM AND THE ALLELES THAT MATTER FOR EVOLUTION: ALL THAT'S GOLD DOES NOT GLITTER

(2011) Matthew V. Rockman   EVOLUTION

ESTABLISHMENT AND MAINTENANCE OF ADAPTIVE GENETIC DIVERGENCE UNDER MIGRATION, SELECTION, AND DRIFT

(2011) Sam Yeaman et al.   EVOLUTION

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Conciliation biology: the eco-evolutionary management of permanently invaded biotic systems

(2011) Scott P. Carroll   Evolutionary Applications

The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel ( Anguilla rostrata )

(2011) Pierre-Alexandre Gagnaire et al.   GENETICS

Ecologically and Evolutionarily Important SNPs Identified in Natural Populations

(2011) L. M. Williams et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparison ofFSToutlier tests for SNP loci under selection

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

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Industrial Melanism in British Peppered Moths Has a Singular and Recent Mutational Origin

(2011) A. E. van't Hof et al.   SCIENCE

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

Fast Transcriptional Responses to Domestication in the Brook Charr Salvelinus fontinalis

(2010) C. Sauvage et al.   GENETICS

Parallel Evolution of Opsin Gene Expression in African Cichlid Fishes

(2010) K. E. O'Quin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

(2010) BERNARD ANGERS et al.   MOLECULAR ECOLOGY

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

Adaptation – not by sweeps alone

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

On the origin of species: insights from the ecological genomics of lake whitefish

(2010) L. Bernatchez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Convergence in pigmentation at multiple levels: mutations, genes and function

(2010) M. Manceau et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Parallel adaptive evolution of Atlantic cod on both sides of the Atlantic Ocean in response to temperature

(2010) I. R. Bradbury et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Compromising genetic diversity in the wild: unmonitored large-scale release of plants and animals

(2010) Linda Laikre et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

The causes of repeated genetic evolution

(2009) Nicolas Gompel et al.   DEVELOPMENTAL BIOLOGY

Genetics of human height

(2009) Brian P. McEvoy et al.   Economics & Human Biology

EDITORIAL: Toward Darwinian fisheries management

(2009) Erin S. Dunlop et al.   Evolutionary Applications

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Independent Introduction of Two Lactase-Persistence Alleles into Human Populations Reflects Different History of Adaptation to Milk Culture

(2008) Nabil Sabri Enattah et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Signatures of selection in natural populations adapted to chronic pollution

(2008) Larissa M Williams et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary origins of invasive populations

(2008) Carol Eunmi Lee et al.   Evolutionary Applications

Speciation through sensory drive in cichlid fish

(2008) Ole Seehausen et al.   NATURE

Genetic basis of fitness differences in natural populations

(2008) Hans Ellegren et al.   NATURE

Heritability in the genomics era — concepts and misconceptions

(2008) Peter M. Visscher et al.   NATURE REVIEWS GENETICS

Genetic effects of harvest on wild animal populations

(2008) F ALLENDORF et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary change in human-altered environments

(2007) THOMAS B. SMITH et al.   MOLECULAR ECOLOGY

Speciation reversal and biodiversity dynamics with hybridization in changing environments

(2007) OLE SEEHAUSEN et al.   MOLECULAR ECOLOGY

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION