Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution

Evolution of mutualism from parasitism in experimental virus populations

(2018) Jason W. Shapiro et al.   EVOLUTION

Specific adaptation to strong competitors can offset the negative effects of population size reductions

(2018) Xin-Feng Zhao et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection

(2018) Rohan Maddamsetti et al.   PLoS Genetics

Co-evolution with Staphylococcus aureus leads to lipopolysaccharide alterations in Pseudomonas aeruginosa

(2017) Mikael Tognon et al.   ISME Journal

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein

(2017) Betül Kacar et al.   JOURNAL OF MOLECULAR EVOLUTION

Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria

(2017) Fen Peng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination Alters the Dynamics of Adaptation on Standing Variation in Laboratory Yeast Populations

(2017) Katya Kosheleva et al.   MOLECULAR BIOLOGY AND EVOLUTION

Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations

(2017) Toon Swings et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation-Driven Parallel Evolution during Viral Adaptation

(2017) Andrew M Sackman et al.   MOLECULAR BIOLOGY AND EVOLUTION

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Hitchhiking and epistasis give rise to cohort dynamics in adapting populations

(2017) Sean W. Buskirk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specificity of genome evolution in experimental populations ofEscherichia colievolved at different temperatures

(2017) Daniel E. Deatherage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR

(2017) Christian Sievert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

Sexual recombination and increased mutation rate expedite evolution of Escherichia coli in varied fitness landscapes

(2017) George L. Peabody V et al.   Nature Communications

Clonal Heterogeneity Influences the Fate of New Adaptive Mutations

(2017) Ignacio Vázquez-García et al.   Cell Reports

Widespread Genetic Incompatibilities between First-Step Mutations during Parallel Adaptation of Saccharomyces cerevisiae to a Common Environment

(2017) Jasmine Ono et al.   PLOS BIOLOGY

Phenotypic heterogeneity promotes adaptive evolution

(2017) Zoltán Bódi et al.   PLOS BIOLOGY

History of antibiotic adaptation influences microbial evolutionary dynamics during subsequent treatment

(2017) Phillip Yen et al.   PLOS BIOLOGY

Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coli

(2017) Toon Swings et al.   eLife

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

(2017) James P. J. Hall et al.   Nature Ecology & Evolution

Adaptive evolution by spontaneous domain fusion and protein relocalization

(2017) Andrew D. Farr et al.   Nature Ecology & Evolution

Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory

(2017) Andrea Wünsche et al.   Nature Ecology & Evolution

An in vivo system for directed experimental evolution of rabbit haemorrhagic disease virus

(2017) Robyn N. Hall et al.   PLoS One

Experimental Induction of Bacterial Resistance to the Antimicrobial Peptide Tachyplesin I and Investigation of the Resistance Mechanisms

(2016) Jun Hong et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

In VitroEmergence of High Persistence upon Periodic Aminoglycoside Challenge in the ESKAPE Pathogens

(2016) Joran Elie Michiels et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

De Novo Emergence of Genetically Resistant Mutants of Mycobacterium tuberculosis from the Persistence Phase Cells formed against Antituberculosis Drugs In Vitro

(2016) Jees Sebastian et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution

(2016) George Peabody et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Benzoate- and Salicylate-Tolerant Strains of Escherichia coli K-12 Lose Antibiotic Resistance during Laboratory Evolution

(2016) Kaitlin E. Creamer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Multi-host environments select for host-generalist conjugative plasmids

(2016) Anastasia Kottara et al.   BMC EVOLUTIONARY BIOLOGY

The stepwise evolution of the exome during acquisition of docetaxel resistance in breast cancer cells

(2016) Stine Ninel Hansen et al.   BMC GENOMICS

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Selection Maintains Apparently Degenerate Metabolic Pathways due to Tradeoffs in Using Methylamine for Carbon versus Nitrogen

(2016) Dipti D. Nayak et al.   CURRENT BIOLOGY

The ghosts of selection past reduces the probability of plastic rescue but increases the likelihood of evolutionary rescue to novel stressors in experimental populations of wild yeast

(2016) Pedram Samani et al.   ECOLOGY LETTERS

Adaptation ofEscherichia colito glucose promotes evolvability in lactose

(2016) Kelly N. Phillips et al.   EVOLUTION

Rapid multiple-level coevolution in experimental populations of yeast killer and nonkiller strains

(2016) Magdalena D. Pieczynska et al.   EVOLUTION

Iron availability shapes the evolution of bacteriocin resistance in Pseudomonas aeruginosa

(2016) R Fredrik Inglis et al.   ISME Journal

Evolution by flight and fight: diverse mechanisms of adaptation by actively motile microbes

(2016) Olaya Rendueles et al.   ISME Journal

Evolutionary convergence in experimental Pseudomonas populations

(2016) Peter A Lind et al.   ISME Journal

Rapid evolution of microbe-mediated protection against pathogens in a worm host

(2016) Kayla C King et al.   ISME Journal

Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection RequirescitTanddctA

(2016) Dustin J. Van Hofwegen et al.   JOURNAL OF BACTERIOLOGY

Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling

(2016) Kenneth M. Flynn et al.   JOURNAL OF BACTERIOLOGY

Escherichia colipopulations adapt to complex, unpredictable fluctuations by minimizing trade-offs across environments

(2016) S. M. Karve et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium

(2016) Deepa Agashe et al.   MOLECULAR BIOLOGY AND EVOLUTION

Host diversity limits the evolution of parasite local adaptation

(2016) Daniel Morley et al.   MOLECULAR ECOLOGY

Negative frequency‐dependent interactions can underlie phenotypic heterogeneity in a clonal microbial population

(2016) David Healey et al.   Molecular Systems Biology

Disentangling genetic and epigenetic determinants of ultrafast adaptation

(2016) Arne B Gjuvsland et al.   Molecular Systems Biology

Tempo and mode of genome evolution in a 50,000-generation experiment

(2016) Olivier Tenaillon et al.   NATURE

Sex speeds adaptation by altering the dynamics of molecular evolution

(2016) Michael J. McDonald et al.   NATURE

Compounds that select against the tetracycline-resistance efflux pump

(2016) Laura K Stone et al.   Nature Chemical Biology

Tumor cells can follow distinct evolutionary paths to become resistant to epidermal growth factor receptor inhibition

(2016) Aaron N Hata et al.   NATURE MEDICINE

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

Within-host evolution of bacterial pathogens

(2016) Xavier Didelot et al.   NATURE REVIEWS MICROBIOLOGY

Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness

(2016) Yinhua Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species

(2016) Ákos Nyerges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temperate phages both mediate and drive adaptive evolution in pathogen biofilms

(2016) Emily V. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species ofPseudomonas

(2016) T. Vogwill et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The genomic basis of adaptation to the fitness cost of rifampicin resistance inPseudomonas aeruginosa

(2016) Qin Qi et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

(2016) Tom Vogwill et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Host coevolution alters the adaptive landscape of a virus

(2016) Alita R. Burmeister et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Spatiotemporal microbial evolution on antibiotic landscapes

(2016) M. Baym et al.   SCIENCE

Ecological speciation of bacteriophage lambda in allopatry and sympatry

(2016) J. R. Meyer et al.   SCIENCE

Rhizosphere selection ofPseudomonas putidaKT2440 variants with increased fitness associated to changes in gene expression

(2016) José Miguel Quesada et al.   Environmental Microbiology Reports

The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is shaped by strong epistatic interactions

(2016) Nicholas Jochumsen et al.   Nature Communications

Rapid radiation in bacteria leads to a division of labour

(2016) Wook Kim et al.   Nature Communications

Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance

(2016) Kelley R. Healey et al.   Nature Communications

Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells

(2016) Michael Ramirez et al.   Nature Communications

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

(2016) Pedro Gómez et al.   Nature Communications

Adaptive evolution of complex innovations through stepwise metabolic niche expansion

(2016) Balázs Szappanos et al.   Nature Communications

Experimental evolution of the grain of metabolic specialization in yeast

(2016) Pedram Samani et al.   Ecology and Evolution

Within Host Evolution Selects for a Dominant Genotype of Mycobacterium tuberculosis while T Cells Increase Pathogen Genetic Diversity

(2016) Richard Copin et al.   PLoS Pathogens

Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat

(2016) Haeyoung Jeong et al.   Jove-Journal of Visualized Experiments

Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence

(2016) Bram Van den Bergh et al.   Nature Microbiology

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host

(2016) Elizabeth J. Klemm et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

High functional diversity stimulates diversification in experimental microbial communities

(2016) A. Jousset et al.   Science Advances

Trade-Offs of Escherichia coli Adaptation to an Intracellular Lifestyle in Macrophages

(2016) M. Azevedo et al.   PLoS One

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution

(2016) Denis Cottinet et al.   PLoS One

A Novel Point Mutation Promotes Growth Phase-Dependent Daptomycin Tolerance in Staphylococcus aureus

(2015) Lukas Mechler et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Acid-Adapted Strains of Escherichia coli K-12 Obtained by Experimental Evolution

(2015) Mark M. Harden et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Sulfur Isotope Fractionation during the Evolutionary Adaptation of a Sulfate-Reducing Bacterium

(2015) André Pellerin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Negative frequency-dependent selection is intensified at higher population densities in protist populations

(2015) Ewan J. A. Minter et al.   Biology Letters

Phenotypic convergence in bacterial adaptive evolution to ethanol stress

(2015) Takaaki Horinouchi et al.   BMC EVOLUTIONARY BIOLOGY

Parasite Exposure Drives Selective Evolution of Constitutive versus Inducible Defense

(2015) Edze R. Westra et al.   CURRENT BIOLOGY

Positively Frequency-Dependent Interference Competition Maintains Diversity and Pervades a Natural Population of Cooperative Microbes

(2015) Olaya Rendueles et al.   CURRENT BIOLOGY

Experimental evolution of the model eukaryote Saccharomyces cerevisiae yields insight into the molecular mechanisms underlying adaptation

(2015) Karin Voordeckers et al.   CURRENT OPINION IN MICROBIOLOGY

Microbial bet-hedging: the power of being different

(2015) Ard Jan Grimbergen et al.   CURRENT OPINION IN MICROBIOLOGY

Evolutionary rescue can be impeded by temporary environmental amelioration

(2015) Yi-Qi Hao et al.   ECOLOGY LETTERS

Character displacement and the evolution of niche complementarity in a model biofilm community

(2015) Crystal N. Ellis et al.   EVOLUTION

Populations adapt to fluctuating selection using derived and ancestral allelic diversity

(2015) Wei-Hsiang Lin et al.   EVOLUTION

Modeling and quantifying frequency-dependent fitness in microbial populations with cross-feeding interactions

(2015) Noah Ribeck et al.   EVOLUTION

Constraints on adaptation ofEscherichia colito mixed-resource environments increase over time

(2015) Rebecca S. Satterwhite et al.   EVOLUTION

The effects of spatial structure, frequency dependence and resistance evolution on the dynamics of toxin-mediated microbial invasions

(2015) Ben Libberton et al.   Evolutionary Applications

The Evolutionarily Stable Distribution of Fitness Effects

(2015) D. P. Rice et al.   GENETICS

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

(2015) Rohan Maddamsetti et al.   GENETICS

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

(2015) Aifen Zhou et al.   ISME Journal

Escherichia colipopulations in unpredictably fluctuating environments evolve to face novel stresses through enhanced efflux activity

(2015) S. M. Karve et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The impact of high-order epistasis in the within-host fitness of a positive-sense plant RNA virus

(2015) J. Lalić et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Experimental evolution in fluctuating environments: tolerance measurements at constant temperatures incorrectly predict the ability to tolerate fluctuating temperatures

(2015) T. Ketola et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Speed of evolution in large asexual populations with diminishing returns

(2015) Maria R. Fumagalli et al.   JOURNAL OF THEORETICAL BIOLOGY

Use of genome sequencing to assess nucleotide structure variation of Staphylococcus aureus strains cultured in spaceflight on Shenzhou-X, under simulated microgravity and on the ground

(2015) Jun Guo et al.   MICROBIOLOGICAL RESEARCH

Multiple Resistance at No Cost: Rifampicin and Streptomycin a Dangerous Liaison in the Spread of Antibiotic Resistance

(2015) Paulo Durão et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coevolution with Bacteriophages Drives Genome-Wide Host Evolution and Constrains the Acquisition of Abiotic-Beneficial Mutations

(2015) Pauline D. Scanlan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rampant Parasexuality Evolves in a Hospital Pathogen during Antibiotic Selection

(2015) Kathryn Beabout 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

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations

(2015) Sergio Pulido-Tamayo et al.   NUCLEIC ACIDS RESEARCH

Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects

(2015) Rebecca M. Lennen et al.   NUCLEIC ACIDS RESEARCH

Coupling of diversification and pH adaptation during the evolution of terrestrial Thaumarchaeota

(2015) Cécile Gubry-Rangin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid and widespread de novo evolution of kin discrimination

(2015) Olaya Rendueles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment withEscherichia coli

(2015) Richard E. Lenski et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

(2015) V.-P. Friman et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system

(2015) T. Hiltunen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Rate of novel host invasion affects adaptability of evolving RNA virus lineages

(2015) Valerie J. Morley et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system

(2015) Tiffany B. Taylor et al.   SCIENCE

Black Queen evolution: the role of leakiness in structuring microbial communities

(2015) J. Jeffrey Morris   TRENDS IN GENETICS

Collateral sensitivity of antibiotic-resistant microbes

(2015) Csaba Pál et al.   TRENDS IN MICROBIOLOGY

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

Bacteriophages Limit the Existence Conditions for Conjugative Plasmids

(2015) Ellie Harrison et al.   mBio

The reverse evolution from multicellularity to unicellularity during carcinogenesis

(2015) Han Chen et al.   Nature Communications

Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes

(2015) Adam C. Palmer et al.   Nature Communications

Low-Cost, High-Throughput Sequencing of DNA Assemblies Using a Highly Multiplexed Nextera Process

(2015) Elaine B. Shapland et al.   ACS Synthetic Biology

Evolution of mating behavior between two populations adapting to common environmental conditions

(2015) Margarida Bárbaro et al.   Ecology and Evolution

Experimental evolution reveals hidden diversity in evolutionary pathways

(2015) Peter A Lind et al.   eLife

Adaptive laboratory evolution of Escherichia coli K-12 MG1655 for growth at high hydrostatic pressure

(2015) Angeliki Marietou et al.   Frontiers in Microbiology

Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli

(2015) Rohan Maddamsetti et al.   GENETICS

Rapid evolution of silver nanoparticle resistance in Escherichia coli

(2015) Joseph L. Graves et al.   Frontiers in Genetics

The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm

(2015) Elizabeth B. Perry et al.   PLoS One

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

A Small-Volume, Low-Cost, and Versatile Continuous Culture Device

(2015) Dominick Matteau et al.   PLoS One

The Evolution of Bet Hedging in Response to Local Ecological Conditions

(2014) Etienne Rajon et al.   AMERICAN NATURALIST

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

(2014) Ryan A. LaCroix et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Identification, Characterization, and Natural Selection of Mutations Driving Airborne Transmission of A/H5N1 Virus

(2014) Martin Linster et al.   CELL

Evolution of Resistance to a Last-Resort Antibiotic in Staphylococcus aureus via Bacterial Competition

(2014) Gudrun Koch et al.   CELL

Delayed transmission selects for increased survival of vesicular stomatitis virus

(2014) Brian R. Wasik et al.   EVOLUTION

Understanding adaptation and diversification: Insights from the study of microbial experimental evolution

(2014) Britt Koskella   EVOLUTION

COEXISTENCE OF EVOLVING BACTERIA STABILIZED BY A SHARED BLACK QUEEN FUNCTION

(2014) J. Jeffrey Morris et al.   EVOLUTION

Hybridization facilitates evolutionary rescue

(2014) Rike B. Stelkens et al.   Evolutionary Applications

Role of pleiotropy during adaptation of TEM-1β-lactamase to two novel antibiotics

(2014) Martijn F. Schenk et al.   Evolutionary Applications

Increased survival of experimentally evolved antimicrobial peptide-resistantStaphylococcus aureusin an animal host

(2014) Adam J. Dobson et al.   Evolutionary Applications

The functional basis of adaptive evolution in chemostats

(2014) David Gresham et al.   FEMS MICROBIOLOGY REVIEWS

The Evolution of Phenotypic Switching in Subdivided Populations

(2014) Oana Carja et al.   GENETICS

The Fates of Mutant Lineages and the Distribution of Fitness Effects of Beneficial Mutations in Laboratory Budding Yeast Populations

(2014) Evgeni M. Frenkel et al.   GENETICS

Fitness Is Strongly Influenced by Rare Mutations of Large Effect in a Microbial Mutation Accumulation Experiment

(2014) K. Heilbron et al.   GENETICS

Genomics of Rapid Adaptation to Antibiotics: Convergent Evolution and Scalable Sequence Amplification

(2014) David Laehnemann et al.   Genome Biology and Evolution

The enduring utility of continuous culturing in experimental evolution

(2014) David Gresham et al.   GENOMICS

The spectrum of adaptive mutations in experimental evolution

(2014) Gregory I. Lang et al.   GENOMICS

Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms

(2014) Vaughn S. Cooper et al.   GENOMICS

Experimental evolution and the dynamics of genomic mutation rate modifiers

(2014) Y Raynes et al.   HEREDITY

Fundamental shift in vitamin B12 eco-physiology of a model alga demonstrated by experimental evolution

(2014) Katherine E Helliwell et al.   ISME Journal

Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance

(2014) Kanchana R. Kildegaard et al.   METABOLIC ENGINEERING

Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations

(2014) Troy E. Sandberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Molly K. Burke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Strength of Selection Pressure Is an Important Parameter Contributing to the Complexity of Antibiotic Resistance Evolution

(2014) Tugce Oz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Shaping Bacterial Symbiosis With Legumes by Experimental Evolution

(2014) Marta Marchetti et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Optimization of lag time underlies antibiotic tolerance in evolved bacterial populations

(2014) Ofer Fridman et al.   NATURE

Alternating antibiotic treatments constrain evolutionary paths to multidrug resistance

(2014) Seungsoo Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Refining a key metabolic innovation inEscherichia coli: Fig. 1.

(2014) Sergey Kryazhimskiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental evolution of prepared learning

(2014) A. S. Dunlap et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Importance of positioning for microbial evolution

(2014) W. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bet-hedging during bacterial diauxic shift

(2014) A. Solopova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Emergence of antibiotic resistance from multinucleated bacterial filaments

(2014) Julia Bos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental evolution of bet hedging under manipulated environmental uncertainty in Neurospora crassa

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

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

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

(2014) J. Plucain et al.   SCIENCE

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

On the unfounded enthusiasm for soft selective sweeps

(2014) Jeffrey D Jensen   Nature Communications

Adaptive synonymous mutations in an experimentally evolved Pseudomonas fluorescens population

(2014) Susan F. Bailey et al.   Nature Communications

Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol

(2014) Kian-Kai Cheng et al.   Nature Communications

Delayed bactericidal response of Mycobacterium tuberculosis to bedaquiline involves remodelling of bacterial metabolism

(2014) Anil Koul et al.   Nature Communications

Genome-wide analysis captures the determinants of the antibiotic cross-resistance interaction network

(2014) Viktória Lázár et al.   Nature Communications

Consumer co-evolution as an important component of the eco-evolutionary feedback

(2014) Teppo Hiltunen et al.   Nature Communications

Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs

(2014) Joanne L. Fothergill et al.   Nature Communications

A Low Cost, Customizable Turbidostat for Use in Synthetic Circuit Characterization

(2014) Chris N. Takahashi et al.   ACS Synthetic Biology

When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load: The Smile-Frown Transition

(2014) Rafael Pena-Miller et al.   PLOS BIOLOGY

Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments

(2014) Aaron M. New et al.   PLOS BIOLOGY

Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli

(2014) Nicholas Leiby et al.   PLOS BIOLOGY

Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer

(2014) Philippe Remigi et al.   PLOS BIOLOGY

The Genomic Landscape of Compensatory Evolution

(2014) Béla Szamecz et al.   PLOS BIOLOGY

Ex Uno Plures: Clonal Reinforcement Drives Evolution of a Simple Microbial Community

(2014) Margie Kinnersley et al.   PLoS Genetics

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

(2014) Jungeui Hong et al.   PLoS Genetics

Silencing by H-NS Potentiated the Evolution of Salmonella

(2014) Sabrina S. Ali et al.   PLoS Pathogens

Evolving a 24-hr oscillator in budding yeast

(2014) Gregg A Wildenberg et al.   eLife

Genetic Determinants forn-Butanol Tolerance in Evolved Escherichia coli Mutants: Cross Adaptation and Antagonistic Pleiotropy betweenn-Butanol and Other Stressors

(2013) Luis H. Reyes et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome-scale genetic engineering in Escherichia coli

(2013) Jaehwan Jeong et al.   BIOTECHNOLOGY ADVANCES

The cost of antibiotic resistance depends on evolutionary history in Escherichia coli

(2013) Daniel C Angst et al.   BMC EVOLUTIONARY BIOLOGY

Evolution of Escherichia coli rifampicin resistance in an antibiotic-free environment during thermal stress

(2013) Alejandra Rodríguez-Verdugo et al.   BMC EVOLUTIONARY BIOLOGY

A case of adaptation through a mutation in a tandem duplication during experimental evolution in Escherichia coli

(2013) Ram P Maharjan et al.   BMC GENOMICS

Sub-inhibitory concentrations of some antibiotics can drive diversification of Pseudomonas aeruginosa populations in artificial sputum medium

(2013) Elli A Wright et al.   BMC MICROBIOLOGY

Real-time microbial adaptive diversification in soil

(2013) Pedro Gómez et al.   ECOLOGY LETTERS

Comparative genomics and transcriptomics analysis of experimentally evolvedEscherichia coli MC1000 in complex environments

(2013) Pilar Eliana Puentes-Téllez et al.   ENVIRONMENTAL MICROBIOLOGY

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

(2013) Ryan T. Hietpas et al.   EVOLUTION

STOCHASTIC TEMPERATURES IMPEDE RNA VIRUS ADAPTATION

(2013) Barry W. Alto et al.   EVOLUTION

TEMPO AND MODE OF MULTICELLULAR ADAPTATION IN EXPERIMENTALLY EVOLVEDSACCHAROMYCES CEREVISIAE

(2013) William C. Ratcliff et al.   EVOLUTION

EVOLUTIONARY REVERSALS OF ANTIBIOTIC RESISTANCE IN EXPERIMENTAL POPULATIONS OFPSEUDOMONAS AERUGINOSA

(2013) Danna R. Gifford et al.   EVOLUTION

RATES OF FITNESS DECLINE AND REBOUND SUGGEST PERVASIVE EPISTASIS

(2013) L. Perfeito et al.   EVOLUTION

EPISTATIC INTERACTIONS DETERMINE THE MUTATIONAL PATHWAYS AND COEXISTENCE OF LINEAGES IN CLONALESCHERICHIA COLIPOPULATIONS

(2013) Ram Prasad Maharjan et al.   EVOLUTION

First steps in experimental cancer evolution

(2013) Tiffany B. Taylor et al.   Evolutionary Applications

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

(2013) Aifen Zhou et al.   ISME Journal

Rapid prey evolution can alter the structure of predator-prey communities

(2013) V.-P. Friman et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Statistical questions in experimental evolution

(2013) Michael M Desai   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Patterns of Epistasis between Beneficial Mutations in an Antibiotic Resistance Gene

(2013) Martijn F. Schenk et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bacterial evolution of antibiotic hypersensitivity

(2013) V. Lazar et al.   Molecular Systems Biology

Evolutionary potential, cross-stress behavior and the genetic basis of acquired stress resistance in Escherichia coli

(2013) M. Dragosits et al.   Molecular Systems Biology

Evolutionary rescue from extinction is contingent on a lower rate of environmental change

(2013) Haley A. Lindsey et al.   NATURE

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Building a morbidostat: an automated continuous-culture device for studying bacterial drug resistance under dynamically sustained drug inhibition

(2013) Erdal Toprak et al.   Nature Protocols

Evaluating evolutionary models of stress-induced mutagenesis in bacteria

(2013) R. Craig MacLean et al.   NATURE REVIEWS GENETICS

Genome dynamics during experimental evolution

(2013) Jeffrey E. Barrick et al.   NATURE REVIEWS GENETICS

A chemostat array enables the spatio-temporal analysis of the yeast proteome

(2013) N. Denervaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

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

Founder niche constrains evolutionary adaptive radiation

(2013) R. C. E. Flohr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

(2013) J. Schreiber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bounded population sizes, fluctuating selection and the tempo and mode of coexistence

(2013) X. Yi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation inEscherichia coli

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

Genome duplication and mutations in ACE2 cause multicellular, fast-sedimenting phenotypes in evolved Saccharomyces cerevisiae

(2013) B. Oud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A trade-off between oxidative stress resistance and DNA repair plays a role in the evolution of elevated mutation rates in bacteria

(2013) C. Torres-Barcelo et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Population genomics of rapid adaptation by soft selective sweeps

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

Population size and the rate of evolution

(2013) Robert Lanfear et al.   TRENDS IN ECOLOGY & EVOLUTION

Experimental evolution of an alternating uni- and multicellular life cycle in Chlamydomonas reinhardtii

(2013) William C. Ratcliff et al.   Nature Communications

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

(2013) Elza C de Bruin et al.   Genome Medicine

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

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

Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

(2013) Barbara Dunn et al.   PLoS Genetics

Whole Genome, Whole Population Sequencing Reveals That Loss of Signaling Networks Is the Major Adaptive Strategy in a Constant Environment

(2013) Daniel J. Kvitek et al.   PLoS Genetics

Evolution after Introduction of a Novel Metabolic Pathway Consistently Leads to Restoration of Wild-Type Physiology

(2013) Sean Michael Carroll et al.   PLoS Genetics

The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

(2013) Kenneth M. Flynn et al.   PLoS Genetics

The Genetic Basis of Escherichia coli Pathoadaptation to Macrophages

(2013) Migla Miskinyte et al.   PLoS Pathogens

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Improved use of a public good selects for the evolution of undifferentiated multicellularity

(2013) John H Koschwanez et al.   eLife

The Use of Chemostats in Microbial Systems Biology

(2013) Naomi Ziv et al.   Jove-Journal of Visualized Experiments

Design and Use of Multiplexed Chemostat Arrays

(2013) Aaron W. Miller et al.   Jove-Journal of Visualized Experiments

Extremely rapid acclimation ofEscherichia colito high temperature over a few generations of a fed-batch culture during slow warming

(2013) Stéphane Guyot et al.   MicrobiologyOpen

Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments

(2012) Pilar Eliana Puentes-Téllez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Epistasis between mutations is host-dependent for an RNA virus

(2012) J. Lalic et al.   Biology Letters

Multiple long-term, experimentally-evolved populations of Escherichia coli acquire dependence upon citrate as an iron chelator for optimal growth on glucose

(2012) Nicholas Leiby et al.   BMC EVOLUTIONARY BIOLOGY

Cancer in Light of Experimental Evolution

(2012) Kathleen Sprouffske et al.   CURRENT BIOLOGY

Effects of predation on real-time host-parasite coevolutionary dynamics

(2012) Ville-Petri Friman et al.   ECOLOGY LETTERS

THE EVOLUTION OF STRESS-INDUCED HYPERMUTATION IN ASEXUAL POPULATIONS

(2012) Yoav Ram et al.   EVOLUTION

Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1

(2012) Liat Avrahami-Moyal et al.   FEMS YEAST RESEARCH

Long-Term Diversity and Genome Adaptation of Acinetobacter baylyi in a Minimal-Medium Chemostat

(2012) Nadia Jezequel et al.   Genome Biology and Evolution

Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus

(2012) J Lalić et al.   HEREDITY

Harnessing recombination to speed adaptive evolution in Escherichia coli

(2012) James Winkler et al.   METABOLIC ENGINEERING

Visualizing evolution in real time to determine the molecular mechanisms of n-butanol tolerance in Escherichia coli

(2012) Luis H. Reyes et al.   METABOLIC ENGINEERING

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

(2012) Zachary D. Blount et al.   NATURE

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

Staphylococcus aureus in Continuous Culture: A Tool for the Rational Design of Antibiotic Treatment Protocols

(2012) Klas I. Udekwu et al.   PLoS One

FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations

(2012) Lon M. Chubiz et al.   PLoS One

Experimental evolution of multicellularity

(2012) W. C. Ratcliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance

(2012) K. Walkiewicz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

(2012) S. Wielgoss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections

(2012) C. C. Traverse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Molecular Diversity of Adaptive Convergence

(2012) O. Tenaillon et al.   SCIENCE

Real-Time Evolution of New Genes by Innovation, Amplification, and Divergence

(2012) J. Nasvall et al.   SCIENCE

Airborne Transmission of Influenza A/H5N1 Virus Between Ferrets

(2012) S. Herfst et al.   SCIENCE

The Potential for Respiratory Droplet-Transmissible A/H5N1 Influenza Virus to Evolve in a Mammalian Host

(2012) C. A. Russell et al.   SCIENCE

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

(2012) J. R. Meyer et al.   SCIENCE

The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation

(2012) J. M. Hughes et al.   mBio

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Optimization of Gene Expression through Divergent Mutational Paths

(2012) Hsin-Hung Chou et al.   Cell Reports

Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant

(2012) Sasha F. Levy et al.   PLOS BIOLOGY

Species Interactions Alter Evolutionary Responses to a Novel Environment

(2012) Diane Lawrence et al.   PLOS BIOLOGY

Evolution of Stress Response in the Face of Unreliable Environmental Signals

(2012) Markus Arnoldini et al.   PLoS Computational Biology

Repeated, Selection-Driven Genome Reduction of Accessory Genes in Experimental Populations

(2012) Ming-Chun Lee et al.   PLoS Genetics

Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum

(2012) Nigel F. Delaney et al.   PLoS Genetics

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

(2012) Alex Wong et al.   PLoS Genetics

Visualizing evolution in real-time method for strain engineering

(2012) Luis H. Reyes et al.   Frontiers in Microbiology

The multiplicity of divergence mechanisms in a single evolving population

(2012) Ram P Maharjan et al.   GENOME BIOLOGY

Experimental Evolution of a Facultative Thermophile from a Mesophilic Ancestor

(2011) Ian K. Blaby et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Host-parasite coevolutionary arms races give way to fluctuating selection

(2011) Alex R. Hall et al.   ECOLOGY LETTERS

EXPERIMENTAL EVOLUTION OF ULTRAVIOLET RADIATION RESISTANCE IN ESCHERICHIA COLI

(2011) Robert P. Goldman et al.   EVOLUTION

Measuring Selection Coefficients Below 10−3: Method, Questions, and Prospects

(2011) Romain Gallet et al.   GENETICS

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

(2011) Gregory I. Lang et al.   GENETICS

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

(2011) H. Bachmann et al.   GENOME RESEARCH

Laboratory Evolution and Multi-platform Genome Re-sequencing of the Cellulolytic ActinobacteriumThermobifida fusca

(2011) Yu Deng et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Insertion Sequence-Driven Evolution of Escherichia coli in Chemostats

(2011) Joël Gaffé et al.   JOURNAL OF MOLECULAR EVOLUTION

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

(2011) Jeremy J Minty et al.   Microbial Cell Factories

Cost of Antibiotic Resistance and the Geometry of Adaptation

(2011) Ana Sousa et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multihost Experimental Evolution of a Plant RNA Virus Reveals Local Adaptation and Host-Specific Mutations

(2011) S. Bedhomme et al.   MOLECULAR BIOLOGY AND EVOLUTION

Metabolic trade-offs and the maintenance of the fittest and the flattest

(2011) Robert E. Beardmore et al.   NATURE

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli

(2011) Dae-Hee Lee et al.   PLoS One

Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity

(2011) C. Auriol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exclusion rules, bottlenecks and the evolution of stochastic phenotype switching

(2011) E. Libby et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Modes of response to environmental change and the elusive empirical evidence for bet hedging

(2011) A. M. Simons   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Adaptation and Evolutionary Rescue in Metapopulations Experiencing Environmental Deterioration

(2011) G. Bell et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments

(2011) Q. Zhang et al.   SCIENCE

Rapid Acquisition of Gigapascal-High-Pressure Resistance by Escherichia coli

(2011) D. Vanlint et al.   mBio

Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape

(2011) Daniel J. Kvitek et al.   PLoS Genetics

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

(2011) Jared W. Wenger et al.   PLoS Genetics

Epistasis between Beneficial Mutations and the Phenotype-to-Fitness Map for a ssDNA Virus

(2011) Darin R. Rokyta et al.   PLoS Genetics

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

Selection of Resistant Bacteria at Very Low Antibiotic Concentrations

(2011) Erik Gullberg et al.   PLoS Pathogens

Experimental Adaptation of Burkholderia cenocepacia to Onion Medium Reduces Host Range

(2010) C. N. Ellis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploring the Low-Pressure Growth Limit: Evolution of Bacillus subtilis in the Laboratory to Enhanced Growth at 5 Kilopascals

(2010) W. L. Nicholson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations

(2010) Tim F Cooper et al.   BMC EVOLUTIONARY BIOLOGY

Transcriptome analysis of parallel-evolved Escherichia coli strains under ethanol stress

(2010) Takaaki Horinouchi et al.   BMC GENOMICS

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

Ecological drivers of the evolution of public-goods cooperation in bacteria

(2010) Michael A. Brockhurst et al.   ECOLOGY

NOVEL COOPERATION EXPERIMENTALLY EVOLVED BETWEEN SPECIES

(2010) William Harcombe   EVOLUTION

PARALLEL CHANGES IN HOST RESISTANCE TO VIRAL INFECTION DURING 45,000 GENERATIONS OF RELAXED SELECTION

(2010) Justin R. Meyer et al.   EVOLUTION

Diminishing Returns From Beneficial Mutations and Pervasive Epistasis Shape the Fitness Landscape for Rifampicin Resistance in Pseudomonas aeruginosa

(2010) R. C. MacLean et al.   GENETICS

Divergence Involving Global Regulatory Gene Mutations in an Escherichia coli Population Evolving under Phosphate Limitation

(2010) Lei Wang et al.   Genome Biology and Evolution

Shifts in the host range of a promiscuous plasmid through parallel evolution of its replication initiation protein

(2010) Masahiro Sota et al.   ISME Journal

Adaptive evolution of nontransgenic Escherichia coli KC01 for improved ethanol tolerance and homoethanol fermentation from xylose

(2010) Yongze Wang et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

The renaissance of continuous culture in the post-genomics age

(2010) Alan T. Bull   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Host Alternation of Chikungunya Virus Increases Fitness while Restricting Population Diversity and Adaptability to Novel Selective Pressures

(2010) L. L. Coffey et al.   JOURNAL OF VIROLOGY

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

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

Sublethal Antibiotic Treatment Leads to Multidrug Resistance via Radical-Induced Mutagenesis

(2010) Michael A. Kohanski et al.   MOLECULAR CELL

Regulatory and metabolic rewiring during laboratory evolution of ethanol tolerance in E. coli

(2010) Hani Goodarzi et al.   Molecular Systems Biology

Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli

(2010) Shota Atsumi et al.   Molecular Systems Biology

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

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli

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

The Repeatability of Adaptive Radiation During Long-Term Experimental Evolution of Escherichia coli in a Multiple Nutrient Environment

(2010) Gerda Saxer et al.   PLoS One

Rapid evolution of stability and productivity at the origin of a microbial mutualism

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

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Transition from Positive to Neutral in Mutation Fixation along with Continuing Rising Fitness in Thermal Adaptive Evolution

(2010) Toshihiko Kishimoto et al.   PLoS Genetics

Genetic Basis of Growth Adaptation of Escherichia coli after Deletion of pgi, a Major Metabolic Gene

(2010) Pep Charusanti et al.   PLoS Genetics

The impact of population size on the evolution of asexual microbes on smooth versus rugged fitness landscapes

(2009) Andreas Handel et al.   BMC EVOLUTIONARY BIOLOGY

Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli

(2009) Mark T Stanek et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary rescue can prevent extinction following environmental change

(2009) Graham Bell et al.   ECOLOGY LETTERS

ADAPTATION TO DIFFERENT RATES OF ENVIRONMENTAL CHANGE INCHLAMYDOMONAS

(2009) Sinéad Collins et al.   EVOLUTION

THE EFFECT OF ELEVATED MUTATION RATES ON THE EVOLUTION OF COOPERATION AND VIRULENCE OFPSEUDOMONAS AERUGINOSA

(2009) Daniel Racey et al.   EVOLUTION

Adaptive evolution in single species bacterial biofilms

(2009) Alison M. Kraigsley et al.   FEMS MICROBIOLOGY LETTERS

Episodic Selection and the Maintenance of Competence and Natural Transformation in Bacillus subtilis

(2009) P. J. Johnsen et al.   GENETICS

Quantitative phenotyping via deep barcode sequencing

(2009) A. M. Smith et al.   GENOME RESEARCH

Directed Evolution of Ionizing Radiation Resistance in Escherichia coli

(2009) D. R. Harris et al.   JOURNAL OF BACTERIOLOGY

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

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

(2009) Jeffrey E. Barrick et al.   NATURE

Global discovery of adaptive mutations

(2009) Hani Goodarzi et al.   NATURE METHODS

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

Spatial structure leads to ecological breakdown and loss of diversity

(2009) G. Saxer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Properties of Adaptive Walks in Evolving Populations of Fungus

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

E Unibus Plurum: Genomic Analysis of an Experimentally Evolved Polymorphism in Escherichia coli

(2009) Margie A. Kinnersley et al.   PLoS Genetics

Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS

(2009) Daniel M. Stoebel et al.   PLoS Genetics

Positive Epistasis Drives the Acquisition of Multidrug Resistance

(2009) Sandra Trindade et al.   PLoS Genetics

Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations

(2009) Tom M Conrad et al.   GENOME BIOLOGY

Aerobic Fermentation of D-Glucose by an Evolved Cytochrome Oxidase-Deficient Escherichia coli Strain

(2008) V. A. Portnoy et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Death and cannibalism in a seasonal environment facilitate bacterial coexistence

(2008) Daniel E. Rozen et al.   ECOLOGY LETTERS

Synergistic Fitness Interactions and a High Frequency of Beneficial Changes Among Mutations Accumulated Under Relaxed Selection in Saccharomyces cerevisiae

(2008) W. J. Dickinson   GENETICS

The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products

(2008) D. M. Stoebel et al.   GENETICS

Genetic Basis of Evolutionary Adaptation by Escherichia coli to Stressful Cycles of Freezing, Thawing and Growth

(2008) S. C. Sleight et al.   GENETICS

The pleiotropic cost of host-specialization in Tobacco etch potyvirus

(2008) Patricia Agudelo-Romero et al.   INFECTION GENETICS AND EVOLUTION

Evolution of Penicillin-Binding Protein 2 Concentration and Cell Shape during a Long-Term Experiment withEscherichia coli

(2008) Nadège Philippe et al.   JOURNAL OF BACTERIOLOGY

The rate of environmental change drives adaptation to an antibiotic sink

(2008) G. G. PERRON et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

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

(2008) Katy C Kao et al.   NATURE GENETICS

Heterogeneous Adaptive Trajectories of Small Populations on Complex Fitness Landscapes

(2008) Daniel E. Rozen et al.   PLoS One

Adaptation increases the likelihood of diversification in an experimental bacterial lineage

(2008) C. C. Spencer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arbovirus evolution in vivo is constrained by host alternation

(2008) L. L. Coffey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated evolution of resistance in multidrug environments

(2008) M. Hegreness et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bet-hedging and epigenetic inheritance in bacterial cell development

(2008) J.-W. Veening et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli

(2008) Z. D. Blount et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics

THE INTERACTIVE EFFECTS OF PARASITES, DISTURBANCE, AND PRODUCTIVITY ON EXPERIMENTAL ADAPTIVE RADIATIONS

(2007) Rebecca Benmayor et al.   EVOLUTION

The genetic basis of parallel and divergent phenotypic responses in evolving populations of Escherichia coli

(2007) E. A Ostrowski et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES