Revisiting the Design of the Long-Term Evolution Experiment with Escherichia coli

[1]  M. Burke.  Embracing Complexity: Yeast Evolution Experiments Featuring Standing Genetic Variation , 2023, Journal of molecular evolution.

[2]  E. Callaway.  Legendary bacterial evolution experiment enters new era , 2022, Nature.

[3]  R. Lenski,et al.  Experimental Test of the Contributions of Initial Variation and New Mutations to Adaptive Evolution in a Novel Environment , 2022, bioRxiv.

[4]  Jeffrey E. Barrick,et al.  A road map for in vivo evolution experiments with blood‐borne parasitic microbes , 2022, Molecular ecology resources.

[5]  W. Ratcliff,et al.  Experimental evolution is not just for model organisms , 2022, PLoS biology.

[6]  Jeffrey E. Barrick,et al.  High-throughput characterization of mutations in genes that drive clonal evolution using multiplex adaptome capture sequencing. , 2021, Cell systems.

[7]  Jeffrey E. Barrick,et al.  Insertion-sequence-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria , 2021, Nature Communications.

[8]  Richard E. Lenski,et al.  Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection , 2019, bioRxiv.

[9]  Jean C. C. Vila,et al.  On the deformability of an empirical fitness landscape by microbial evolution , 2018, Proceedings of the National Academy of Sciences.

[10]  Benjamin H. Good,et al.  The Dynamics of Molecular Evolution Over 60,000 Generations , 2017, Nature.

[11]  R. Lenski,et al.  Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection , 2017, bioRxiv.

[12]  R. Lenski.  What is adaptation by natural selection? Perspectives of an experimental microbiologist , 2017, PLoS Genetics.

[13]  R. Lenski.  Convergence and Divergence in a Long-Term Experiment with Bacteria* , 2017, The American Naturalist.

[14]  Richard E. Lenski,et al.  Tempo and mode of genome evolution in a 50,000-generation experiment , 2016, Nature.

[15]  T. Cooper,et al.  Constraints on adaptation of Escherichia coli to mixed‐resource environments increase over time , 2015, Evolution; international journal of organic evolution.

[16]  Richard E. Lenski,et al.  Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population , 2015, bioRxiv.

[17]  J. Fox,et al.  From Here to Eternity—The Theory and Practice of a Really Long Experiment , 2015, PLoS biology.

[18]  U. Riebesell,et al.  Experimental evolution gone wild , 2015, Journal of The Royal Society Interface.

[19]  Jeffrey E. Barrick,et al.  Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli , 2015, Genetics.

[20]  Nicholas Leiby,et al.  Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli , 2014, PLoS biology.

[21]  Daniel E. Deatherage,et al.  Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.

[22]  Michael J. Wiser,et al.  Long-Term Dynamics of Adaptation in Asexual Populations , 2013, Science.

[23]  David L. Stern,et al.  The genetic causes of convergent evolution , 2013, Nature Reviews Genetics.

[24]  Michael M. Desai,et al.  Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations , 2013, Nature.

[25]  Jeffrey E. Barrick,et al.  Genomic Analysis of a Key Innovation in an Experimental E. coli Population , 2012, Nature.

[26]  Otto X. Cordero,et al.  Population Genomics of Early Events in the Ecological Differentiation of Bacteria , 2012, Science.

[27]  Kevin R. Thornton,et al.  Genome-wide analysis of a long-term evolution experiment with Drosophila , 2010, Nature.

[28]  Olivier Tenaillon,et al.  The population genetics of commensal Escherichia coli , 2010, Nature Reviews Microbiology.

[29]  R. Lenski,et al.  Experimental evolution with E. coli in diverse resource environments. I. Fluctuating environments promote divergence of replicate populations , 2010, BMC Evolutionary Biology.

[30]  R. Lenski,et al.  Identification and dynamics of a beneficial mutation in a long-term evolution experiment with Escherichia coli , 2009, BMC Evolutionary Biology.

[31]  R. Lenski,et al.  Tracing ancestors and relatives of Escherichia coli B, and the derivation of B strains REL606 and BL21(DE3). , 2009, Journal of molecular biology.

[32]  R. Lenski,et al.  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, Journal of molecular biology.

[33]  Jeffrey E. Barrick,et al.  Genome evolution and adaptation in a long-term experiment with Escherichia coli , 2009, Nature.

[34]  Jeffrey E. Barrick,et al.  Genome-wide mutational diversity in an evolving population of Escherichia coli. , 2009, Cold Spring Harbor symposia on quantitative biology.

[35]  R. Lenski,et al.  Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli , 2008 .

[36]  T. Cooper.  Recombination Speeds Adaptation by Reducing Competition between Beneficial Mutations in Populations of Escherichia coli , 2007, PLoS biology.

[37]  F. Moore,et al.  Tempo and constraint of adaptive evolution in Escherichia coli (Enterobacteriaceae, Enterobacteriales) , 2006 .

[38]  Dominique Schneider,et al.  Tests of parallel molecular evolution in a long-term experiment with Escherichia coli. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Richard E. Lenski,et al.  Rates of DNA Sequence Evolution in Experimental Populations of Escherichia coli During 20,000 Generations , 2003, Journal of Molecular Evolution.

[40]  R. Lenski,et al.  Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Lurias,et al.  MUTATIONS OF BACTERIA FROM VIRUS SENSITIVITY TO VIRUS RESISTANCE’-’ , 2003 .

[42]  R. Lenski,et al.  The population genetics of ecological specialization in evolving Escherichia coli populations , 2000, Nature.

[43]  Alyssa C. Bumbaugh,et al.  Parallel evolution of virulence in pathogenic Escherichia coli , 2000, Nature.

[44]  R. Lenski,et al.  Pervasive compensatory adaptation in Escherichia coli , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[45]  Daniel E Rozen,et al.  Long‐Term Experimental Evolution in Escherichia coli. VIII. Dynamics of a Balanced Polymorphism , 2000, The American Naturalist.

[46]  W Arber,et al.  Genomic evolution during a 10,000-generation experiment with bacteria. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Lenski,et al.  Diminishing returns from mutation supply rate in asexual populations. , 1999, Science.

[48]  N. W. Davis,et al.  The complete genome sequence of Escherichia coli K-12. , 1997, Science.

[49]  R. Lenski,et al.  Evolution of high mutation rates in experimental populations of E. coli , 1997, Nature.

[50]  S. Elena,et al.  FREQUENCY‐DEPENDENT SELECTION IN A MAMMALIAN RNA VIRUS , 1997, Evolution; international journal of organic evolution.

[51]  R. Lenski,et al.  Long-term experimental evolution in , 1997 .

[52]  M Travisano,et al.  Long-term experimental evolution in Escherichia coli. IV. Targets of selection and the specificity of adaptation. , 1996, Genetics.

[53]  A. F. Bennett,et al.  EVOLUTIONARY ADAPTATION TO TEMPERATURE. IV. ADAPTATION OF ESCHERICHIA COLI AT A NICHE BOUNDARY , 1996, Evolution; international journal of organic evolution.

[54]  A. F. Bennett,et al.  Experimental tests of the roles of adaptation, chance, and history in evolution. , 1995, Science.

[55]  Richard E. Lenski,et al.  Long-Term Experimental Evolution in Escherichia coli. II. Changes in Life-History Traits During Adaptation to a Seasonal Environment , 1994, The American Naturalist.

[56]  R. Lenski,et al.  Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[57]  A F Bennett,et al.  Temperature acclimation and competitive fitness: an experimental test of the beneficial acclimation assumption. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[58]  A. F. Bennett,et al.  EVOLUTIONARY ADAPTATION TO TEMPERATURE II. THERMAL NICHES OF EXPERIMENTAL LINES OF ESCHERICHIA COLI , 1993, Evolution; international journal of organic evolution.

[59]  R. Lenski,et al.  Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations , 1991, The American Naturalist.

[60]  Michael R Rose,et al.  LABORATORY EVOLUTION OF POSTPONED SENESCENCE IN DROSOPHILA MELANOGASTER , 1984, Evolution; international journal of organic evolution.

[61]  C. Paquin,et al.  Relative fitness can decrease in evolving asexual populations of S. cerevisiae , 1983, Nature.

[62]  B. Bachmann,et al.  Linkage map of Escherichia coli K-12, edition 6 , 1980 .

[63]  J. Lederberg,et al.  Gene Recombination in Escherichia Coli , 1946, Nature.