Experimental evolution as a high-throughput screen for genetic adaptations

Mutations of bacteria from virus sensitivity to virus resistance

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The effect of linkage on limits to artificial selection

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Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations

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The effect of linkage on limits to artificial selection

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Phase and Antigenic Variation in Bacteria

van der Woude, M. W., & Bäumler, A. J. (2004) · Clinical Microbiology Reviews · doi:10.1128/cmr.17.3.581-611.2004 · Cited by 766 · see citing works

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

Toprak, E., Veres, A., Michel, J.-B., Chait, R., Hartl, D. L., & Kishony, R. (2012) · Nature Genetics · doi:10.1038/ng.1034 · Cited by 764 · see citing works

The dynamics of molecular evolution over 60,000 generations

Good, B. H., McDonald, M. J., Barrick, J. E., Lenski, R. E., & Desai, M. M. (2017) · Nature · doi:10.1038/nature24287 · Cited by 733 · see citing works

The fate of competing beneficial mutations in an asexual population

Gerrish, P. J., & Lenski, R. E. (1998) · Contemporary issues in genetics and evolution · doi:10.1007/978-94-011-5210-5_12 · Cited by 721 · see citing works

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

Lee, H., Popodi, E., Tang, H., & Foster, P. L. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210309109 · Cited by 681 · see citing works

Beneficial Mutation–Selection Balance and the Effect of Linkage on Positive Selection

Desai, M. M., & Fisher, D. S. (2007) · Genetics · doi:10.1534/genetics.106.067678 · Cited by 590 · see citing works

The fate of competing beneficial mutations in an asexual population.

Gerrish, P. J., & Lenski, R. E. (1998) · PubMed · Cited by 520 · see citing works

Quantitative evolutionary dynamics using high-resolution lineage tracking

Levy, S. F., Blundell, J. R., Venkataram, S., Petrov, D. A., Fisher, D. S., & Sherlock, G. J. (2015) · Nature · doi:10.1038/nature14279 · Cited by 461 · see citing works

Parallel changes in gene expression after 20,000 generations of evolution in <i>Escherichia</i> <i>coli</i>

Cooper, T. F., Rozen, D. E., & Lenski, R. E. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0334340100 · Cited by 440 · see citing works

Experimental evolution and the dynamics of adaptation and genome evolution in microbial populations

Lenski, R. E. (2017) · The ISME Journal · doi:10.1038/ismej.2017.69 · Cited by 367 · see citing works

Mechanisms Causing Rapid and Parallel Losses of Ribose Catabolism in Evolving Populations ofEscherichia coliB

Cooper, V. S., Schneider, D., Blot, M., & Lenski, R. E. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.9.2834-2841.2001 · Cited by 277 · see citing works

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

Hillesland, K. L., & Stahl, D. A. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0908456107 · Cited by 254 · see citing works

The fixation probability of beneficial mutations

Patwa, Z., & Wahl, L. M. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0248 · Cited by 232 · see citing works

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

King, K. C., Brockhurst, M. A., Vasieva, O., Paterson, S., Betts, A., Ford, S. A., Frost, C. L., Horsburgh, M. J., Haldenby, S. T., & Hurst, G. D. D. (2016) · The ISME Journal · doi:10.1038/ismej.2015.259 · Cited by 218 · see citing works

Experimental Evolution of a Plant Pathogen into a Legume Symbiont

Marchetti, M., Capela, D., Glew, M. D., Cruveiller, S., Chane-Woon-Ming, B., Gris-Liebe, C., Timmers, T., Poinsot, V., Gilbert, L. B., Heeb, P., et al. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000280 · Cited by 193 · see citing works

Surface sensing and lateral subcellular localization of WspA , the receptor in a chemosensory‐like system leading to c‐di‐ GMP production

O’Connor, J. R., Kuwada, N. J., Huangyutitham, V., Wiggins, P. A., & Harwood, C. S. (2012) · Molecular Microbiology · doi:10.1111/mmi.12013 · Cited by 166 · see citing works

Alternative Evolutionary Paths to Bacterial Antibiotic Resistance Cause Distinct Collateral Effects

Barbosa, C., Trebosc, V., Kemmer, C., Rosenstiel, P. C., Beardmore, R., Hinrich Schulenburg, Y., & Jansen, G. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx158 · Cited by 166 · see citing works

Experimental evolution reveals hidden diversity in evolutionary pathways

Lind, P. A., Farr, A. D., & Rainey, P. B. (2015) · eLife · doi:10.7554/elife.07074 · Cited by 162 · see citing works

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

McDonald, M. J., Gehrig, S. M., Meintjes, P., Zhang, X., & Rainey, P. B. (2009) · Genetics · doi:10.1534/genetics.109.107110 · Cited by 150 · see citing works

Long-Term Experimental Evolution inEscherichia coli.IX. Characterization of Insertion Sequence-Mediated Mutations and Rearrangements

Schneider, D., Duperchy, E., Coursange, E., Lenski, R. E., & Blot, M. (2000) · Genetics · doi:10.1093/genetics/156.2.477 · Cited by 138 · see citing works

Experimentally revised repertoire of putative contingency loci in Neisseria meningitidis strain MC58: evidence for a novel mechanism of phase variation

Martín, P., van de Ven, T., Mouchel, N. A. P., Jeffries, A. C., Hood, D. W., & Moxon, E. R. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03678.x · Cited by 102 · see citing works

Multihost Experimental Evolution of the Pathogen Ralstonia solanacearum Unveils Genes Involved in Adaptation to Plants

Guidot, A., Jiang, W., Ferdy, J., Thébaud, C., Barberis, P. A., Gouzy, J., & Genin, S. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu229 · Cited by 97 · see citing works

Rapid radiation in bacteria leads to a division of labour

Kim, W., Levy, S. B., & Foster, K. R. (2016) · Nature Communications · doi:10.1038/ncomms10508 · Cited by 82 · see citing works

Laboratory Evolution of Microbial Interactions in Bacterial Biofilms

Martin, M., Hölscher, T., Dragoš, A., Cooper, V. S., & Kovács, Á. T. (2016) · Journal of Bacteriology · doi:10.1128/jb.01018-15 · Cited by 82 · see citing works

Evolutionary reversion of live viral vaccines: Can genetic engineering subdue it?

Bull, J. J. (2015) · Virus Evolution · doi:10.1093/ve/vev005 · Cited by 82 · see citing works

Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri

Dillon, M. M., Sung, W., Sebra, R., Lynch, M., & Cooper, V. S. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw224 · Cited by 74 · see citing works

De novo evolved interference competition promotes the spread of biofilm defectors

Martin, M., Dragoš, A., Hölscher, T., Maróti, G., Bálint, B., Westermann, M., & Kovács, Á. T. (2017) · Nature Communications · doi:10.1038/ncomms15127 · Cited by 60 · see citing works

Host coevolution alters the adaptive landscape of a virus

Burmeister, A. R., Lenski, R. E., & Meyer, J. R. (2016) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2016.1528 · Cited by 59 · see citing works

Evolutionary convergence in experimental Pseudomonas populations

Lind, P. A., Farr, A. D., & Rainey, P. B. (2016) · The ISME Journal · doi:10.1038/ismej.2016.157 · Cited by 59 · see citing works

Parallel evolution of small colony variants in Burkholderia cenocepacia biofilms

Cooper, V. S., Staples, R. K., Traverse, C. C., et al. (2014) · Genomics · doi:10.1016/j.ygeno.2014.09.007 · Cited by 55 · see citing works

Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens

Gallie, J., Libby, E., Bertels, F., Remigi, P., Jendresen, C. B., Ferguson, G. C., Desprat, N., Buffing, M. F., Sauer, U., Beaumont, H. J. E., et al. (2015) · PLoS Biology · doi:10.1371/journal.pbio.1002109 · Cited by 55 · see citing works

Evolution of mutualism from parasitism in experimental virus populations

Shapiro, J. W., & Turner, P. E. (2018) · Evolution · doi:10.1111/evo.13440 · Cited by 52 · see citing works

Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria

Pankey, M. S., Foxall, R. L., Ster, I. M., Perry, L. A., Schuster, B. M., Donner, R. A., Coyle, M., Cooper, V. S., & Whistler, C. A. (2017) · eLife · doi:10.7554/elife.24414 · Cited by 51 · see citing works

FFPopSim: an efficient forward simulation package for the evolution of large populations

Zanini, F., & Neher, R. A. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts633 · Cited by 49 · see citing works

Interspecies Social Spreading: Interaction between Two Sessile Soil Bacteria Leads to Emergence of Surface Motility

McCully, L. M., Bitzer, A. S., Seaton, S. C., et al. (2019) · mSphere · doi:10.1128/msphere.00696-18 · Cited by 35 · see citing works

Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution

Cottinet, D., Condamine, F., Brémond, N., Griffiths, A. D., Rainey, P. B., de Visser, J. A. G. M., Baudry, J., & Bibette, J. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152395 · Cited by 31 · see citing works

There and back again: consequences of biofilm specialization under selection for dispersal

O’Rourke, D., FitzGerald, C., Traverse, C. C., et al. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00018 · Cited by 28 · see citing works

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

Peng, F., Widmann, S., Wünsche, A., Duan, K., Donovan, K. A., Dobson, R. C. J., Lenski, R. E., & Cooper, T. F. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx279 · Cited by 28 · see citing works

Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations

Dillon, M. M., Rouillard, N. P., van Dam, B., Gallet, R., & Cooper, V. S. (2016) · Evolution · doi:10.1111/evo.12868 · Cited by 26 · see citing works

The Fitness Effects of Spontaneous Mutations Nearly Unseen by Selection in a Bacterium with Multiple Chromosomes

Dillon, M. M., & Cooper, V. S. (2016) · Genetics · doi:10.1534/genetics.116.193060 · Cited by 22 · see citing works

How Do Microbial Populations and Communities Function as Model Systems?

O’Malley, M. A., Travisano, M., Velicer, G. J., & Bolker, J. A. (2015) · The Quarterly Review of Biology · doi:10.1086/682588 · Cited by 20 · see citing works

Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

Zhou, A., Lau, R., Baran, R., Ma, J., von Netzer, F., Shi, W., Gorman‐Lewis, D., Kempher, M. L., He, Z., Qin, Y., et al. (2017) · mBio · doi:10.1128/mbio.01780-17 · Cited by 19 · see citing works

Interspecies Social Spreading: Interaction between two sessile soil bacteria leads to emergence of surface motilityPreprint

McCully, L. M., Bitzer, A. S., Seaton, S. C., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/296814 · Cited by 4 · see citing works

Acquisition of cross-azole tolerance and aneuploidy in <i>Candida albicans</i> strains evolved to posaconazole

Kukurudz, R. J., Chapel, M., Wonitowy, Q., Adamu Bukari, A.-R., Sidney, B., Sierhuis, R., & Gerstein, A. C. (2022) · G3 · doi:10.1093/g3journal/jkac156 · Cited by 35 · see citing works

Evolutionary rescue of phosphomannomutase deficiency in yeast models of human disease

Vignogna, R. C., Allocca, M., Monticelli, M., Norris, J. W., Steet, R., Perlstein, E. O., Andreotti, G., & Lang, G. I. (2022) · eLife · doi:10.7554/elife.79346 · Cited by 15 · see citing works

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

Handel, A., & Rozen, D. E. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-236 · Cited by 43 · see citing works

Genetic Background Modifies the Topography of a Fitness Landscape, Influencing the Dynamics of Adaptive Evolution

Ogbunugafor, C. B., & Eppstein, M. J. (2019) · IEEE Access · doi:10.1109/access.2019.2935911 · Cited by 8 · see citing works

Mutational robustness changes during long-term adaptation in laboratory budding yeast populations

Johnson, M. S., & Desai, M. M. (2022) · eLife · doi:10.7554/elife.76491 · Cited by 21 · see citing works

Local Fitness Landscapes Predict Yeast Evolutionary Dynamics in Directionally Changing Environments

Gorter, F. A., Aarts, M. G. M., Zwaan, B. J., & de Visser, J. A. G. M. (2017) · Genetics · doi:10.1534/genetics.117.300519 · Cited by 31 · see citing works

Genotypic context modulates fitness landscapes: Effects on the speed and direction of evolution for antimicrobial resistancePreprint

Ogbunugafor, C. B., Guerrero, R. F., & Eppstein, M. J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/427328