A practical guide to environmental association analysis in landscape genomics

Detecting adaptive evolution based on association with ecological gradients: Orientation matters!

(2015) E Frichot et al.   HEREDITY

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

Genomic variation across landscapes: insights and applications

(2015) Jason G. Bragg et al.   NEW PHYTOLOGIST

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

Widespread Signals of Convergent Adaptation to High Altitude in Asia and America

(2014) Matthieu Foll et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

(2014) Jesse R. Lasky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-Tagged Amplification (GTA): a PCR-based method to prepare sample-tagged amplicons from hundreds of individuals for next generation sequencing

(2014) Thien Ho et al.   MOLECULAR BREEDING

Signatures of diversifying selection at EST-SSR loci and association with climate in naturalEucalyptuspopulations

(2014) Donna Bradbury et al.   MOLECULAR ECOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

Landscape genomics and a common garden trial reveal adaptive differentiation to temperature across Europe in the tree speciesAlnus glutinosa

(2014) Hanne De Kort 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

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

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

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

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

AFLPs and Mitochondrial Haplotypes Reveal Local Adaptation to Extreme Thermal Environments in a Freshwater Gastropod

(2014) María Quintela et al.   PLoS One

Microgeographic adaptation and the spatial scale of evolution

(2014) Jonathan L. Richardson et al.   TRENDS IN ECOLOGY & EVOLUTION

Advances and limits of using population genetics to understand local adaptation

(2014) Peter Tiffin et al.   TRENDS IN ECOLOGY & EVOLUTION

A Population Genetic Signal of Polygenic Adaptation

(2014) Jeremy J. Berg et al.   PLoS Genetics

INTEGRATING LANDSCAPE GENOMICS AND SPATIALLY EXPLICIT APPROACHES TO DETECT LOCI UNDER SELECTION IN CLINAL POPULATIONS

(2013) Matthew R. Jones et al.   EVOLUTION

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

(2013) Bourret Vincent et al.   EVOLUTION

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Community genetics in the time of next-generation molecular technologies

(2013) Felix Gugerli et al.   MOLECULAR ECOLOGY

Are adaptive loci transferable across genomes of related species? Outlier and environmental association analyses in Alpine Brassicaceae species

(2013) Deborah Zulliger 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

Genomic evidence for the parallel evolution of coastal forms in theSenecio lautuscomplex

(2013) Federico Roda 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

Population genomic footprints of selection and associations with climate in natural populations ofArabidopsis hallerifrom the Alps

(2013) Martin C. Fischer et al.   MOLECULAR ECOLOGY

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

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

(2013) Arthur Korte et al.   Plant Methods

Validation of SNP Allele Frequencies Determined by Pooled Next-Generation Sequencing in Natural Populations of a Non-Model Plant Species

(2013) Christian Rellstab et al.   PLoS One

Putting the landscape into the genomics of trees: approaches for understanding local adaptation and population responses to changing climate

(2013) V. L. Sork et al.   Tree Genetics & Genomes

Ten years of landscape genetics

(2013) Stéphanie Manel et al.   TRENDS IN ECOLOGY & EVOLUTION

Dismantling the Mantel tests

(2013) Gilles Guillot et al.   Methods in Ecology and Evolution

Detecting correlation between allele frequencies and environmental variables as a signature of selection. A fast computational approach for genome-wide studies

(2013) Gilles Guillot et al.   Spatial Statistics

Adaptive Genetic Variation on the Landscape: Methods and Cases

(2012) Sean D. Schoville et al.   Annual Review of Ecology Evolution and Systematics

Collinearity: a review of methods to deal with it and a simulation study evaluating their performance

(2012) Carsten F. Dormann et al.   ECOGRAPHY

An outlier locus relevant in habitat-mediated selection in an alpine plant across independent regional replicates

(2012) Dominique Buehler et al.   EVOLUTIONARY ECOLOGY

Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce ( Picea abies )

(2012) Jun Chen et al.   GENETICS

Parallel and lineage-specific molecular adaptation to climate in boreal black spruce

(2012) JULIEN PRUNIER et al.   MOLECULAR ECOLOGY

Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation

(2012) STÉPHANIE MANEL et al.   MOLECULAR ECOLOGY

The geographical and environmental determinants of genetic diversity for four alpine conifers of the European Alps

(2012) E. Mosca et al.   MOLECULAR ECOLOGY

Genome-wide patterns of latitudinal differentiation among populations ofDrosophila melanogasterfrom North America

(2012) Daniel K. Fabian et al.   MOLECULAR ECOLOGY

Characterizing genomic variation ofArabidopsis thaliana: the roles of geography and climate

(2012) JESSE R. LASKY et al.   MOLECULAR ECOLOGY

Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel

(2012) Matthew W Horton et al.   NATURE GENETICS

The nature of confounding in genome-wide association studies

(2012) Bjarni J. Vilhjálmsson et al.   NATURE REVIEWS GENETICS

Genomic consequences of multiple speciation processes in a stick insect

(2012) P. Nosil et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

What is needed for next-generation ecological and evolutionary genomics?

(2012) Scott A. Pavey et al.   TRENDS IN ECOLOGY & EVOLUTION

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

(2011) R. Kofler et al.   BIOINFORMATICS

Analysis of trematode parasite communities in fish eye lenses by pyrosequencing of naturally pooled DNA

(2011) Christian Rellstab et al.   INFECTION GENETICS AND EVOLUTION

Genetic analysis of differentiation among breeding ponds reveals a candidate gene for local adaptation in Rana arvalis

(2011) ALEX RICHTER-BOIX et al.   MOLECULAR ECOLOGY

Exome sequencing as a tool for Mendelian disease gene discovery

(2011) Michael J. Bamshad et al.   NATURE REVIEWS GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Molecular spandrels: tests of adaptation at the genetic level

(2011) Rowan D. H. Barrett et al.   NATURE REVIEWS GENETICS

What can patterns of differentiation across plant genomes tell us about adaptation and speciation?

(2011) J. L. Strasburg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Adaptations to Climate-Mediated Selective Pressures in Humans

(2011) Angela M. Hancock et al.   PLoS Genetics

Detecting Selection in Population Trees: The Lewontin and Krakauer Test Extended

(2010) Maxime Bonhomme et al.   GENETICS

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae)

(2010) A. J. Eckert et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

THE GENOTYPICAL RESPONSE OF THE PLANT SPECIES TO THE HABITAT

(2010) GÖTE TURESSON   HEREDITAS

Overview of techniques to account for confounding due to population stratification and cryptic relatedness in genomic data association analyses

(2010) M J Sillanpää   HEREDITY

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Using Population Genomics to Detect Selection in Natural Populations: Key Concepts and Methodological Considerations

(2010)   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Molecular Footprints of Local Adaptation in Two Mediterranean Conifers

(2010) D. Grivet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina

(2010) BÉNÉDICTE N. PONCET et al.   MOLECULAR ECOLOGY

INVITED REVIEW: Spatial modelling and landscape-level approaches for visualizing intra-specific variation

(2010) HENRI A. THOMASSEN et al.   MOLECULAR ECOLOGY

Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests

(2010) J. A. HOLLIDAY et al.   MOLECULAR ECOLOGY

Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina

(2010) S. MANEL et al.   MOLECULAR ECOLOGY

Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field

(2010) STÉPHANIE MANEL et al.   MOLECULAR ECOLOGY

Considering spatial and temporal scale in landscape-genetic studies of gene flow

(2010) COREY DEVIN ANDERSON et al.   MOLECULAR ECOLOGY

Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae)

(2010) ANDREW J. ECKERT et al.   MOLECULAR ECOLOGY

Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data

(2010) PIERRE LEGENDRE et al.   Molecular Ecology Resources

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Adaptation – not by sweeps alone

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

Adaptations to new environments in humans: the role of subtle allele frequency shifts

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

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Landscape genetics of plants

(2010) Rolf Holderegger et al.   TRENDS IN PLANT SCIENCE

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

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

Genomic signatures of local directional selection in a high gene flow marine organism; the Atlantic cod (Gadus morhua)

(2009) Einar E Nielsen et al.   BMC EVOLUTIONARY BIOLOGY

Association Genetics of Coastal Douglas Fir ( Pseudotsuga menziesii var. menziesii , Pinaceae). I. Cold-Hardiness Related Traits

(2009) Andrew J. Eckert et al.   GENETICS

Detecting loci under selection in a hierarchically structured population

(2009) L Excoffier et al.   HEREDITY

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

Spatial patterns of variation due to natural selection in humans

(2009) John Novembre et al.   NATURE REVIEWS GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Adaptation and colonization history affect the evolution of clines in two introduced species

(2009) Stephen R. Keller et al.   NEW PHYTOLOGIST

Land ahead: using genome scans to identify molecular markers of adaptive relevance

(2009) Rolf Holderegger et al.   Plant Ecology & Diversity

ECOLOGICAL GENETICS IN THE NORTH ATLANTIC: ENVIRONMENTAL GRADIENTS AND ADAPTATION AT SPECIFIC LOCI

(2008) Paul S. Schmidt et al.   ECOLOGY

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

(2008) M. Foll et al.   GENETICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Spatial analysis method (sam): a software tool combining molecular and environmental data to identify candidate loci for selection

(2008) STÉPHANE JOOST et al.   Molecular Ecology Resources

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders

(2008) Angela M. Hancock et al.   PLoS Genetics

Surfing during population expansions promotes genetic revolutions and structuration

(2008) Laurent Excoffier et al.   TRENDS IN ECOLOGY & EVOLUTION

Adaptation from standing genetic variation

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