Genome dynamics during experimental evolution

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

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

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

(2013) Sean Michael Carroll et al.   PLoS Genetics

Genetic changes during a laboratory adaptive evolution process that allowed fast growth in glucose to an Escherichia coli strain lacking the major glucose transport system

(2012) César Aguilar et al.   BMC GENOMICS

The Evolution of Low Mutation Rates in Experimental Mutator Populations of Saccharomyces cerevisiae

(2012) Michael J. McDonald et al.   CURRENT BIOLOGY

Cancer in Light of Experimental Evolution

(2012) Kathleen Sprouffske et al.   CURRENT BIOLOGY

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

(2012) Zachary D. Blount et al.   NATURE

Genome Features of “Dark-Fly”, a Drosophila Line Reared Long-Term in a Dark Environment

(2012) Minako Izutsu et al.   PLoS One

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

Experimental evolution of multicellularity

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

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee 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

Drift-barrier hypothesis and mutation-rate evolution

(2012) W. Sung 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

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

(2012) J. R. Meyer et al.   SCIENCE

Experimental evolution

(2012) Tadeusz J. Kawecki et al.   TRENDS IN ECOLOGY & EVOLUTION

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

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

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

Whole-Genome Sequencing and Phenotypic Analysis of Bacillus subtilis Mutants following Evolution under Conditions of Relaxed Selection for Sporulation

(2011) Christopher T. Brown et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Balance Between Mutators and Nonmutators in Asexual Populations

(2011) Michael M. Desai et al.   GENETICS

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

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

Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture

(2011) R. Nahku et al.   MICROBIOLOGY-SGM

Microbial laboratory evolution in the era of genome-scale science

(2011) T. M. Conrad et al.   Molecular Systems Biology

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Standing Genetic Variation in Contingency Loci Drives the Rapid Adaptation of Campylobacter jejuni to a Novel Host

(2011) John P. Jerome et al.   PLoS One

Experimental selection of hypoxia-tolerant Drosophila melanogaster

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

Evolutionary dynamics of bacteria in a human host environment

(2011) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan 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

Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

(2011) Farren J. Isaacs et al.   SCIENCE

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

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

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

(2010) E. Crozat et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Measurements of spontaneous rates of mutations in the recent past and the near future

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

The population genetics of mutations: good, bad and indifferent

(2010) L. Loewe 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

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Adaptive Evolution of an sRNA That Controls Myxococcus Development

(2010) Y. T. N. Yu et al.   SCIENCE

Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome

(2010) D. G. Gibson et al.   SCIENCE

Experimental Evolution of a Plant Pathogen into a Legume Symbiont

(2010) Marta Marchetti et al.   PLOS BIOLOGY

Spontaneous Mutation Accumulation Studies in Evolutionary Genetics

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

Evolution at a High Imposed Mutation Rate: Adaptation Obscures the Load in Phage T7

(2009) R. Springman et al.   GENETICS

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

(2009) P. D. Keightley et al.   GENOME RESEARCH

Genomic Sequencing Reveals Regulatory Mutations and Recombinational Events in the Widely Used MC4100 Lineage of Escherichia coli K-12

(2009) T. Ferenci et al.   JOURNAL OF BACTERIOLOGY

Directed Evolution of Ionizing Radiation Resistance in Escherichia coli

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

Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E. coli B and K-12 Genomes

(2009) F. William Studier et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2009) Jeffrey E. Barrick et al.   NATURE

Fitness and its role in evolutionary genetics

(2009) H. Allen Orr   NATURE REVIEWS GENETICS

A genome-wide view of Caenorhabditis elegans base-substitution mutation processes

(2009) D. R. Denver et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Fitness Effects of Random Mutations in Single-Stranded DNA and RNA Bacteriophages

(2009) Pilar Domingo-Calap et al.   PLoS Genetics

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Experimental evolution and genome sequencing reveal variation in levels of clonal interference in large populations of bacteriophage φX174

(2008) Kim M Pepin et al.   BMC EVOLUTIONARY BIOLOGY

Death and cannibalism in a seasonal environment facilitate bacterial coexistence

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

Clonal Interference, Multiple Mutations and Adaptation in Large Asexual Populations

(2008) C. A. Fogle et al.   GENETICS

Neutralism and selectionism: a network-based reconciliation

(2008) Andreas Wagner   NATURE REVIEWS GENETICS

A genome-wide view of the spectrum of spontaneous mutations in yeast

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

Whole-genome mutational biases in bacteria

(2008) P. A. Lind 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