A survey of methods and tools to detect recent and strong positive selection

Genetic diversity and population structure ofSorghum mosaic virusinfectingSaccharumspp. hybrids

(2016) Q. Luo et al.   ANNALS OF APPLIED BIOLOGY

SweepFinder2: increased sensitivity, robustness and flexibility

(2016) Michael DeGiorgio et al.   BIOINFORMATICS

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

The Argonaute-binding platform of NRPE1 evolves through modulation of intrinsically disordered repeats

(2016) Joshua T. Trujillo et al.   NEW PHYTOLOGIST

An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster

(2016) Ana Catalán et al.   PLoS Genetics

Natural Selection and Genetic Diversity in the Butterfly Heliconius melpomene

(2016) Simon H. Martin et al.   GENETICS

Scalable linkage-disequilibrium-based selective sweep detection: a performance guide

(2016) Nikolaos Alachiotis et al.   GigaScience

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

(2015) Valeria Montano et al.   GENETICS

Positive Selection at the Polyhomeotic Locus Led to Decreased Thermosensitivity of Gene Expression in Temperate Drosophila melanogaster

(2015) Susanne Voigt et al.   GENETICS

Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems

(2015) Jorge Gonzalez-Dominguez et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Inference of Gorilla Demographic and Selective History from Whole-Genome Sequence Data

(2015) Kimberly F. McManus et al.   MOLECULAR BIOLOGY AND EVOLUTION

Methods to characterize selective sweeps using time serial samples: an ancient DNA perspective

(2015) Anna-Sapfo Malaspinas   MOLECULAR ECOLOGY

The consequences of not accounting for background selection in demographic inference

(2015) Gregory B. Ewing et al.   MOLECULAR ECOLOGY

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

(2015) Stefan Laurent et al.   MOLECULAR ECOLOGY

Evidence of long-term gene flow and selection during domestication from analyses of Eurasian wild and domestic pig genomes

(2015) Laurent A F Frantz et al.   NATURE GENETICS

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

Worldwide Population Structure, Long-Term Demography, and Local Adaptation of Helicobacter pylori

(2015) Valeria Montano et al.   GENETICS

Positive Selection at the Polyhomeotic Locus Led to Decreased Thermosensitivity of Gene Expression in Temperate Drosophila melanogaster

(2015) Susanne Voigt et al.   GENETICS

Demographic history and gene flow during silkworm domestication

(2014) Shao-Yu Yang et al.   BMC EVOLUTIONARY BIOLOGY

Human-induced evolution caught in action: SNP-array reveals rapid amphi-atlantic spread of pesticide resistance in the salmon ecotoparasite Lepeophtheirus salmonis

(2014) Francois Besnier et al.   BMC GENOMICS

On Detecting Incomplete Soft or Hard Selective Sweeps Using Haplotype Structure

(2014) Anna Ferrer-Admetlla et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the unfounded enthusiasm for soft selective sweeps

(2014) Jeffrey D Jensen   Nature Communications

Fine-Mapping and Selective Sweep Analysis of QTL for Cold Tolerance in Drosophila melanogaster

(2014) R. Wilches et al.   G3-Genes Genomes Genetics

Detecting Natural Selection in Genomic Data

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

SweeD: Likelihood-Based Detection of Selective Sweeps in Thousands of Genomes

(2013) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans

(2013) Marc Pybus et al.   NUCLEIC ACIDS RESEARCH

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

The impact of equilibrium assumptions on tests of selection

(2013) Jessica L. Crisci et al.   Frontiers in Genetics

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets

(2012) N. Alachiotis et al.   BIOINFORMATICS

EVIDENCE OF ADAPTATION FROM ANCESTRAL VARIATION IN YOUNG POPULATIONS OF BEACH MICE

(2012) Vera S. Domingues et al.   EVOLUTION

Limited Evidence for Classic Selective Sweeps in African Populations

(2012) J. M. Granka et al.   GENETICS

A Critical Assessment of Storytelling: Gene Ontology Categories and the Importance of Validating Genomic Scans

(2012) Pavlos Pavlidis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide patterns of standing genetic variation in a marine population of three-spined sticklebacks

(2012) PHILINE G. D. FEULNER et al.   MOLECULAR ECOLOGY

Loss and Gain of Function in SERPINB11: An Example of a Gene under Selection on Standing Variation, with Implications for Host-Pathogen Interactions

(2012) Susana Seixas et al.   PLoS One

Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation

(2012) Benjamin M. Peter et al.   PLoS Genetics

Genome-wide Comparison of African-Ancestry Populations from CARe and Other Cohorts Reveals Signals of Natural Selection

(2011) Gaurav Bhatia et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Inference of seed bank parameters in two wild tomato species using ecological and genetic data

(2011) A. Tellier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analytical results on the neutral non-equilibrium allele frequency spectrum based on diffusion theory

(2011) Daniel Živković et al.   THEORETICAL POPULATION BIOLOGY

FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

(2010) Stephanie Zierke et al.   BMC BIOINFORMATICS

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

(2010) K. Lin et al.   GENETICS

Searching for Footprints of Positive Selection in Whole-Genome SNP Data From Nonequilibrium Populations

(2010) P. Pavlidis et al.   GENETICS

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

A New Test for Detecting Recent Positive Selection that is Free from the Confounding Impacts of Demography

(2010) H. Li   MOLECULAR BIOLOGY AND EVOLUTION

Genetic hitchhiking versus background selection: the controversy and its implications

(2010) W. Stephan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identifying Signatures of Natural Selection in Tibetan and Andean Populations Using Dense Genome Scan Data

(2010) Abigail Bigham et al.   PLoS Genetics

The Impact of Sampling Schemes on the Site Frequency Spectrum in Nonequilibrium Subdivided Populations

(2009) T. Stadler et al.   GENETICS

Signals of recent positive selection in a worldwide sample of human populations

(2009) J. K. Pickrell et al.   GENOME RESEARCH

A flexible forward simulator for populations subject to selection and demography

(2008) R. D. Hernandez   BIOINFORMATICS

Linkage Disequilibrium Under Genetic Hitchhiking in Finite Populations

(2008) P. Pfaffelhuber et al.   GENETICS

Evidence that strong positive selection drives neofunctionalization in the tandemly duplicated polyhomeotic genes in Drosophila

(2008) S. Beisswanger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA