Controlling false discoveries in genome scans for selection

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

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

(2015) M. Gautier   GENETICS

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

(2015) E Frichot et al.   HEREDITY

A practical guide to environmental association analysis in landscape genomics

(2015) Christian Rellstab 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

TESS3: fast inference of spatial population structure and genome scans for selection

(2015) Kevin Caye et al.   Molecular Ecology Resources

A new FST-based method to uncover local adaptation using environmental variables

(2015) Pierre de Villemereuil 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

Ecological genomics meets community-level modelling of biodiversity: mapping the genomic landscape of current and future environmental adaptation

(2014) Matthew C. Fitzpatrick et al.   ECOLOGY LETTERS

Fast and Efficient Estimation of Individual Ancestry Coefficients

(2014) Eric Frichot et al.   GENETICS

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Keeping It Local: Evidence for Positive Selection in Swedish Arabidopsis thaliana

(2014) Christian D. Huber et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Advances and limits of using population genetics to understand local adaptation

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

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

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

(2013) Matthew R. Jones 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

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

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

Adaptive Genetic Variation on the Landscape: Methods and Cases

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

Quantifying the roles of ecology and geography in spatial genetic divergence

(2012) Ian J. Wang et al.   ECOLOGY LETTERS

Forecasting changes in population genetic structure of alpine plants in response to global warming

(2012) FLORA JAY et al.   MOLECULAR ECOLOGY

The nature of confounding in genome-wide association studies

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

Correcting Away the Hidden Heritability

(2011) Scott M. Williams et al.   ANNALS OF HUMAN GENETICS

Comparison ofFSToutlier tests for SNP loci under selection

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

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

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

(2010) Maxime Bonhomme et al.   GENETICS

Likelihood-Free Inference of Population Structure and Local Adaptation in a Bayesian Hierarchical Model

(2010) E. Bazin et al.   GENETICS

Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading

(2010) A. Platt et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Genetic Variations in Tibetan Populations and High-Altitude Adaptation at the Himalayas

(2010) Y. Peng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

New approaches to population stratification in genome-wide association studies

(2010) Alkes L. Price et al.   NATURE REVIEWS GENETICS

Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency

(2010) A. M. Hancock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correction for hidden confounders in the genetic analysis of gene expression

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

Genetic Evidence for High-Altitude Adaptation in Tibet

(2010) T. S. Simonson et al.   SCIENCE

Approximate Bayesian Computation (ABC) in practice

(2010) Katalin Csilléry et al.   TRENDS IN ECOLOGY & EVOLUTION

Who believes in whole-genome scans for selection?

(2009) J Hermisson   HEREDITY

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

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

A Genealogical Interpretation of Principal Components Analysis

(2009) Gil McVean   PLoS Genetics

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

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

(2008) M. Foll et al.   GENETICS

How to Interpret a Genome-wide Association Study

(2008) Thomas A. Pearson   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Adaptations to Climate in Candidate Genes for Common Metabolic Disorders

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