Can the experimental evolution programme help us elucidate the genetic basis of adaptation in nature?

The fitness effect of mutations across environments: Fisher's geometrical model with multiple optima

(2015) Guillaume Martin et al.   EVOLUTION

Simple Phenotypic Sweeps Hide Complex Genetic Changes in Populations

(2015) Ram P. Maharjan et al.   Genome Biology and Evolution

Synonymous Genetic Variation in Natural Isolates ofEscherichia coliDoes Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment

(2015) Rohan Maddamsetti et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Effect of Selection Environment on the Probability of Parallel Evolution

(2015) Susan F. Bailey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian inference of selection in a heterogeneous environment from genetic time-series data

(2015) Zachariah Gompert   MOLECULAR ECOLOGY

Local interspecies introgression is the main cause of extreme levels of intraspecific differentiation in mussels

(2015) Christelle Fraïsse et al.   MOLECULAR ECOLOGY

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

RAD mapping reveals an evolving, polymorphic and fuzzy boundary of a plant pseudoautosomal region

(2015) S. Qiu et al.   MOLECULAR ECOLOGY

Targeted capture in evolutionary and ecological genomics

(2015) Matthew R. Jones et al.   MOLECULAR ECOLOGY

Selection on noise constrains variation in a eukaryotic promoter

(2015) Brian P. H. Metzger et al.   NATURE

Evolution of Darwin’s finches and their beaks revealed by genome sequencing

(2015) Sangeet Lamichhaney et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

Experimental evolution reveals hidden diversity in evolutionary pathways

(2015) Peter A Lind et al.   eLife

Effects of new mutations on fitness: insights from models and data

(2014) Thomas Bataillon et al.   Annals of the New York Academy of Sciences

The Utility of Fisher's Geometric Model in Evolutionary Genetics

(2014) O. Tenaillon   Annual Review of Ecology Evolution and Systematics

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance

(2014) Gunther Jansen et al.   DRUG RESISTANCE UPDATES

Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance

(2014) Jessica MA Blair et al.   Future Microbiology

Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat

(2014) Stéphanie Thépot et al.   GENETICS

Signatures of Sex-Antagonistic Selection on Recombining Sex Chromosomes

(2014) Mark Kirkpatrick et al.   GENETICS

A Bayesian MCMC Approach to Assess the Complete Distribution of Fitness Effects of New Mutations: Uncovering the Potential for Adaptive Walks in Challenging Environments

(2014) C. Bank et al.   GENETICS

The Impact of Macroscopic Epistasis on Long-Term Evolutionary Dynamics

(2014) B. H. Good et al.   GENETICS

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinaster Aiton, Pinaceae)

(2014) J.-P. Jaramillo-Correa et al.   GENETICS

Balancing Selection in Species with Separate Sexes: Insights from Fisher's Geometric Model

(2014) T. Connallon et al.   GENETICS

Standing Genetic Variation Drives Repeatable Experimental Evolution in Outcrossing Populations of Saccharomyces cerevisiae

(2014) Molly K. Burke 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

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

(2014) Michael J. Harms et al.   NATURE

Mainstreaming Caenorhabditis elegans in experimental evolution

(2014) J. C. Gray et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli

(2014) J. Plucain et al.   SCIENCE

Not Just a Theory—The Utility of Mathematical Models in Evolutionary Biology

(2014) Maria R. Servedio et al.   PLOS BIOLOGY

Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes

(2014) Yuheng Huang et al.   PLoS Genetics

Background Selection as Baseline for Nucleotide Variation across the Drosophila Genome

(2014) Josep M. Comeron   PLoS Genetics

Approximation to the Distribution of Fitness Effects across Functional Categories in Human Segregating Polymorphisms

(2014) Fernando Racimo et al.   PLoS Genetics

Assessing when chromosomal rearrangements affect the dynamics of speciation: implications from computer simulations

(2014) Jeffrey L. Feder et al.   Frontiers in Genetics

Detecting Natural Selection in Genomic Data

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

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

(2013) Ryan T. Hietpas et al.   EVOLUTION

PHENOTYPIC AND GENOTYPIC CONVERGENCES ARE INFLUENCED BY HISTORICAL CONTINGENCY AND ENVIRONMENT IN YEAST

(2013) Aymé Spor et al.   EVOLUTION

TEMPORAL VARIATION FAVORS THE EVOLUTION OF GENERALISTS IN EXPERIMENTAL POPULATIONS OFDROSOPHILA MELANOGASTER

(2013) Catriona Condon et al.   EVOLUTION

RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

(2013) L. Perfeito et al.   EVOLUTION

A Comparison of Models to Infer the Distribution of Fitness Effects of New Mutations

(2013) A. Kousathanas et al.   GENETICS

Robust Identification of Local Adaptation from Allele Frequencies

(2013) T. Gunther et al.   GENETICS

Inference of Natural Selection from Interspersed Genomic Elements Based on Polymorphism and Divergence

(2013) Ilan Gronau et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Carotenoids in unexpected places: Gall midges, lateral gene transfer, and carotenoid biosynthesis in animals

(2013) Cassidy Cobbs et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide signatures of convergent evolution in echolocating mammals

(2013) Joe Parker et al.   NATURE

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria

(2013) Frédéric Ariey et al.   NATURE

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

(2013) Matthew D. Herron et al.   PLOS BIOLOGY

Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels

(2013) Li Jiang et al.   PLoS Genetics

Spatial Structure of Ecological Opportunity Drives Adaptation in a Bacterium

(2012) Susan F. Bailey et al.   AMERICAN NATURALIST

ADAPTATION AND MALADAPTATION IN SELFING AND OUTCROSSING SPECIES: NEW MUTATIONS VERSUS STANDING VARIATION

(2012) Sylvain Glémin et al.   EVOLUTION

Evolutionary insight from whole-genome sequencing of experimentally evolved microbes

(2012) JEREMY R. DETTMAN et al.   MOLECULAR ECOLOGY

Genomic analysis of a key innovation in an experimental Escherichia coli population

(2012) Zachary D. Blount et al.   NATURE

Host-pathogen coevolution in human tuberculosis

(2012) S. Gagneux   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli

(2012) M. Le Gac et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The probability of genetic parallelism and convergence in natural populations

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

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Parallel Molecular Evolution in an Herbivore Community

(2012) Y. Zhen et al.   SCIENCE

Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda

(2012) J. R. Meyer et al.   SCIENCE

Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data

(2012) Art F. Y. Poon et al.   PLoS Computational Biology

Genomic Data Reveal a Complex Making of Humans

(2012) Isabel Alves et al.   PLoS Genetics

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

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

Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa

(2012) Alex Wong et al.   PLoS Genetics

Increased Fitness and Alteration of Metabolic Pathways during Bacillus subtilis Evolution in the Laboratory

(2011) Heather Maughan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Adaptive Introgression of Anticoagulant Rodent Poison Resistance by Hybridization between Old World Mice

(2011) Ying Song et al.   CURRENT BIOLOGY

ADAPTIVE LANDSCAPES IN EVOLVING POPULATIONS OF PSEUDOMONAS FLUORESCENS

(2011) Anita H. Melnyk et al.   EVOLUTION

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

(2011) Matthew V. Rockman   EVOLUTION

THE LENGTH OF ADAPTIVE WALKS IS INSENSITIVE TO STARTING FITNESS IN ASPERGILLUS NIDULANS

(2011) Danna R. Gifford et al.   EVOLUTION

CONVERGENCE, ADAPTATION, AND CONSTRAINT

(2011) Jonathan B. Losos   EVOLUTION

Stickbreaking: A Novel Fitness Landscape Model That Harbors Epistasis and Is Consistent with Commonly Observed Patterns of Adaptive Evolution

(2011) Anna C. Nagel et al.   GENETICS

Fitness Landscapes: An Alternative Theory for the Dominance of Mutation

(2011) Federico Manna et al.   GENETICS

Cost of Adaptation and Fitness Effects of Beneficial Mutations inPseudomonas fluorescens

(2011) Thomas Bataillon et al.   GENETICS

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

Revealing the genetic structure of a trait by sequencing a population under selection

(2011) L. Parts et al.   GENOME RESEARCH

Diversification in temporally heterogeneous environments: effect of the grain in experimental bacterial populations

(2011) P. A. VENAIL et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Parallel evolution and local differentiation in quinolone resistance in Pseudomonas aeruginosa

(2011) A. Wong et al.   MICROBIOLOGY-SGM

Joint analysis of demography and selection in population genetics: where do we stand and where could we go?

(2011) JUNRUI LI et al.   MOLECULAR ECOLOGY

The coupling hypothesis: why genome scans may fail to map local adaptation genes

(2011) NICOLAS BIERNE et al.   MOLECULAR ECOLOGY

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterozygote advantage as a natural consequence of adaptation in diploids

(2011) D. Sellis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations

(2011) G. G. Perron et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

FISHER'S MODEL AND THE GENOMICS OF ADAPTATION: RESTRICTED PLEIOTROPY, HETEROGENOUS MUTATION, AND PARALLEL EVOLUTION

(2010) Luis-Miguel Chevin et al.   EVOLUTION

Many Possible Worlds: Expanding the Ecological Scenarios in Experimental Evolution

(2010) Sinéad Collins   Evolutionary Biology

Inferences About the Distribution of Dominance Drawn From Yeast Gene Knockout Data

(2010) A. F. Agrawal et al.   GENETICS

Using Environmental Correlations to Identify Loci Underlying Local Adaptation

(2010) G. Coop et al.   GENETICS

Molecular Footprints of Local Adaptation in Two Mediterranean Conifers

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

Escherichia coli rpoB Mutants Have Increased Evolvability in Proportion to Their Fitness Defects

(2010) J. E. Barrick et al.   MOLECULAR BIOLOGY AND EVOLUTION

Next-generation sequencing as a tool to study microbial evolution

(2010) MICHAEL A. BROCKHURST et al.   MOLECULAR ECOLOGY

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Antagonistic coevolution accelerates molecular evolution

(2010) Steve Paterson et al.   NATURE

What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?

(2010) P. D. Keightley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs

(2009) Joe Hereford   AMERICAN NATURALIST

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

(2009) Daniel L. Halligan et al.   Annual Review of Ecology Evolution and Systematics

ADAPTATION TO DIFFERENT RATES OF ENVIRONMENTAL CHANGE INCHLAMYDOMONAS

(2009) Sinéad Collins et al.   EVOLUTION

Adaptive Divergence in Experimental Populations of Pseudomonas fluorescens. IV. Genetic Constraints Guide Evolutionary Trajectories in a Parallel Adaptive Radiation

(2009) M. J. McDonald et al.   GENETICS

Transcription, Translation, and the Evolution of Specialists and Generalists

(2009) S. Zhong et al.   MOLECULAR BIOLOGY AND EVOLUTION

Targets of Balancing Selection in the Human Genome

(2009) A. M. Andres et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Beagle in a bottle

(2009) Angus Buckling et al.   NATURE

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

The Properties of Adaptive Walks in Evolving Populations of Fungus

(2009) Sijmen E. Schoustra et al.   PLOS BIOLOGY

Pervasive Natural Selection in the Drosophila Genome?

(2009) Guy Sella et al.   PLoS Genetics

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

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

HOW REPEATABLE IS ADAPTIVE EVOLUTION? THE ROLE OF GEOGRAPHICAL ORIGIN AND FOUNDER EFFECTS IN LABORATORY ADAPTATION

(2008) Pedro Simões et al.   EVOLUTION

Selective Sweep at a Quantitative Trait Locus in the Presence of Background Genetic Variation

(2008) Luis-Miguel Chevin et al.   GENETICS

The Distribution of Beneficial and Fixed Mutation Fitness Effects Close to an Optimum

(2008) Guillaume Martin et al.   GENETICS

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Decay of unused characters by selection and drift

(2008) A. R. HALL et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Antagonistic Pleiotropy Involving Promoter Sequences in a Virus

(2008) John B. Presloid et al.   JOURNAL OF MOLECULAR BIOLOGY

Beneficial Fitness Effects Are Not Exponential for Two Viruses

(2008) Darin R. Rokyta et al.   JOURNAL OF MOLECULAR EVOLUTION

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

A Meta-Analysis of Local Adaptation in Plants

(2008) Roosa Leimu et al.   PLoS One

Regulatory Genes Control a Key Morphological and Ecological Trait Transferred Between Species

(2008) M. Kim et al.   SCIENCE

Adaptation from standing genetic variation

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