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Historical contingency in the evolution of antibiotic resistance after decades of relaxed selection.

Card KJ, LaBar T, Gomez JB, Lenski RE.

PLoS Biol. 2019 Oct 23;17(10):e3000397. doi: 10.1371/journal.pbio.3000397. eCollection 2019 Oct.


Changes in Intrinsic Antibiotic Susceptibility during a Long-Term Evolution Experiment with Escherichia coli.

Lamrabet O, Martin M, Lenski RE, Schneider D.

mBio. 2019 Mar 5;10(2). pii: e00189-19. doi: 10.1128/mBio.00189-19.


Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene.

Lamrabet O, Plumbridge J, Martin M, Lenski RE, Schneider D, Hindré T.

Mol Biol Evol. 2019 Jun 1;36(6):1121-1133. doi: 10.1093/molbev/msz042.


Contingency and determinism in evolution: Replaying life's tape.

Blount ZD, Lenski RE, Losos JB.

Science. 2018 Nov 9;362(6415). pii: eaam5979. doi: 10.1126/science.aam5979. Review.


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

Maddamsetti R, Lenski RE.

PLoS Genet. 2018 Jan 31;14(1):e1007199. doi: 10.1371/journal.pgen.1007199. eCollection 2018 Jan.


Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria.

Couce A, Caudwell LV, Feinauer C, Hindré T, Feugeas JP, Weigt M, Lenski RE, Schneider D, Tenaillon O.

Proc Natl Acad Sci U S A. 2017 Oct 24;114(43):E9026-E9035. doi: 10.1073/pnas.1705887114. Epub 2017 Oct 10.


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 KA, Dobson RCJ, Lenski RE, Cooper TF.

Mol Biol Evol. 2018 Jan 1;35(1):202-210. doi: 10.1093/molbev/msx279.


The dynamics of molecular evolution over 60,000 generations.

Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM.

Nature. 2017 Nov 2;551(7678):45-50. doi: 10.1038/nature24287. Epub 2017 Oct 18.


Evolution of organismal stoichiometry in a long-term experiment with Escherichia coli.

Turner CB, Wade BD, Meyer JR, Sommerfeld BA, Lenski RE.

R Soc Open Sci. 2017 Jul 19;4(7):170497. doi: 10.1098/rsos.170497. eCollection 2017 Jul.


Convergence and Divergence in a Long-Term Experiment with Bacteria.

Lenski RE.

Am Nat. 2017 Aug;190(S1):S57-S68. doi: 10.1086/691209. Epub 2017 Mar 1.


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

Lenski RE.

ISME J. 2017 Oct;11(10):2181-2194. doi: 10.1038/ismej.2017.69. Epub 2017 May 16. Review.


What is adaptation by natural selection? Perspectives of an experimental microbiologist.

Lenski RE.

PLoS Genet. 2017 Apr 20;13(4):e1006668. doi: 10.1371/journal.pgen.1006668. eCollection 2017 Apr. Review.


Core Genes Evolve Rapidly in the Long-term Evolution Experiment with Escherichia coli.

Maddamsetti R, Hatcher PJ, Green AG, Williams BL, Marks DS, Lenski RE.

Genome Biol Evol. 2017 Apr 4. doi: 10.1093/gbe/evx064. [Epub ahead of print]


Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures.

Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE.

Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1904-E1912. doi: 10.1073/pnas.1616132114. Epub 2017 Feb 15.


Ecological speciation of bacteriophage lambda in allopatry and sympatry.

Meyer JR, Dobias DT, Medina SJ, Servilio L, Gupta A, Lenski RE.

Science. 2016 Dec 9;354(6317):1301-1304. Epub 2016 Nov 24.


Host coevolution alters the adaptive landscape of a virus.

Burmeister AR, Lenski RE, Meyer JR.

Proc Biol Sci. 2016 Sep 28;283(1839). pii: 20161528.


Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment.

Großkopf T, Consuegra J, Gaffé J, Willison JC, Lenski RE, Soyer OS, Schneider D.

BMC Evol Biol. 2016 Aug 20;16(1):163. doi: 10.1186/s12862-016-0733-x.


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

Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE.

Nature. 2016 Aug 11;536(7615):165-70. Epub 2016 Aug 1.


You lookin' at me?

Bergstrom CT, Wasik BR, Lenski RE.

Br J Clin Pharmacol. 2016 Oct;82(4):1149. doi: 10.1111/bcp.13036. Epub 2016 Jul 14. No abstract available.


Sustained fitness gains and variability in fitness trajectories in the long-term evolution experiment with Escherichia coli.

Lenski RE, Wiser MJ, Ribeck N, Blount ZD, Nahum JR, Morris JJ, Zaman L, Turner CB, Wade BD, Maddamsetti R, Burmeister AR, Baird EJ, Bundy J, Grant NA, Card KJ, Rowles M, Weatherspoon K, Papoulis SE, Sullivan R, Clark C, Mulka JS, Hajela N.

Proc Biol Sci. 2015 Dec 22;282(1821):20152292. doi: 10.1098/rspb.2015.2292.


Replaying Evolution to Test the Cause of Extinction of One Ecotype in an Experimentally Evolved Population.

Turner CB, Blount ZD, Lenski RE.

PLoS One. 2015 Nov 18;10(11):e0142050. doi: 10.1371/journal.pone.0142050. eCollection 2015.


Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.

Maddamsetti R, Hatcher PJ, Cruveiller S, Médigue C, Barrick JE, Lenski RE.

Mol Biol Evol. 2015 Nov;32(11):2897-904. doi: 10.1093/molbev/msv161. Epub 2015 Jul 20.


From Here to Eternity--The Theory and Practice of a Really Long Experiment.

Fox JW, Lenski RE.

PLoS Biol. 2015 Jun 23;13(6):e1002185. doi: 10.1371/journal.pbio.1002185. eCollection 2015 Jun.


Genetically integrated traits and rugged adaptive landscapes in digital organisms.

Ostrowski EA, Ofria C, Lenski RE.

BMC Evol Biol. 2015 May 12;15:83. doi: 10.1186/s12862-015-0361-x.


A Comparison of Methods to Measure Fitness in Escherichia coli.

Wiser MJ, Lenski RE.

PLoS One. 2015 May 11;10(5):e0126210. doi: 10.1371/journal.pone.0126210. eCollection 2015.


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

Maddamsetti R, Lenski RE, Barrick JE.

Genetics. 2015 Jun;200(2):619-31. doi: 10.1534/genetics.115.176677. Epub 2015 Apr 24.


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

Ribeck N, Lenski RE.

Evolution. 2015 May;69(5):1313-20. doi: 10.1111/evo.12645. Epub 2015 Apr 29.


Coevolution drives the emergence of complex traits and promotes evolvability.

Zaman L, Meyer JR, Devangam S, Bryson DM, Lenski RE, Ofria C.

PLoS Biol. 2014 Dec 16;12(12):e1002023. doi: 10.1371/journal.pbio.1002023. eCollection 2014 Dec.


Does evolutionary theory need a rethink?

Laland K, Uller T, Feldman M, Sterelny K, Müller GB, Moczek A, Jablonka E, Odling-Smee J, Wray GA, Hoekstra HE, Futuyma DJ, Lenski RE, Mackay TF, Schluter D, Strassmann JE.

Nature. 2014 Oct 9;514(7521):161-4. doi: 10.1038/514161a. No abstract available.


Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli.

Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D.

mBio. 2014 Sep 9;5(5):e01377-14. doi: 10.1128/mBio.01377-14.


Coexistence of evolving bacteria stabilized by a shared Black Queen function.

Morris JJ, Papoulis SE, Lenski RE.

Evolution. 2014 Oct;68(10):2960-71. doi: 10.1111/evo.12485. Epub 2014 Aug 1.


Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

Plucain J, Hindré T, Le Gac M, Tenaillon O, Cruveiller S, Médigue C, Leiby N, Harcombe WR, Marx CJ, Lenski RE, Schneider D.

Science. 2014 Mar 21;343(6177):1366-9. doi: 10.1126/science.1248688. Epub 2014 Mar 6.


Long-term dynamics of adaptation in asexual populations.

Wiser MJ, Ribeck N, Lenski RE.

Science. 2013 Dec 13;342(6164):1364-7. doi: 10.1126/science.1243357. Epub 2013 Nov 14.


Genome dynamics during experimental evolution.

Barrick JE, Lenski RE.

Nat Rev Genet. 2013 Dec;14(12):827-39. doi: 10.1038/nrg3564. Epub 2013 Oct 29. Review.


Experiments on the role of deleterious mutations as stepping stones in adaptive evolution.

Covert AW 3rd, Lenski RE, Wilke CO, Ofria C.

Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):E3171-8. doi: 10.1073/pnas.1313424110. Epub 2013 Aug 5.


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

Wielgoss S, Barrick JE, Tenaillon O, Wiser MJ, Dittmar WJ, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):222-7. doi: 10.1073/pnas.1219574110. Epub 2012 Dec 17.


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

Blount ZD, Barrick JE, Davidson CJ, Lenski RE.

Nature. 2012 Sep 27;489(7417):513-8. doi: 10.1038/nature11514. Epub 2012 Sep 19.


Ontogeny tends to recapitulate phylogeny in digital organisms.

Clune J, Pennock RT, Ofria C, Lenski RE.

Am Nat. 2012 Sep;180(3):E54-63. doi: 10.1086/666984. Epub 2012 Jul 16.


Experimental evolution.

Kawecki TJ, Lenski RE, Ebert D, Hollis B, Olivieri I, Whitlock MC.

Trends Ecol Evol. 2012 Oct;27(10):547-60. doi: 10.1016/j.tree.2012.06.001. Epub 2012 Jul 21. Review.


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

Le Gac M, Plucain J, Hindré T, Lenski RE, Schneider D.

Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9487-92. doi: 10.1073/pnas.1207091109. Epub 2012 May 29.


The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss.

Morris JJ, Lenski RE, Zinser ER.

mBio. 2012 May 2;3(2). pii: e00036-12. doi: 10.1128/mBio.00036-12. Print 2012.


Repeatability and contingency in the evolution of a key innovation in phage lambda.

Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE.

Science. 2012 Jan 27;335(6067):428-32. doi: 10.1126/science.1214449.


Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli.

Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D.

G3 (Bethesda). 2011 Aug 1;1(3):183-186.


Chance and necessity in the evolution of a bacterial pathogen.

Lenski RE.

Nat Genet. 2011 Nov 28;43(12):1174-6. doi: 10.1038/ng.1011.


L'enfant terrible at 30: the maturation of evolutionary developmental biology.

Haag ES, Lenski RE.

Development. 2011 Jul;138(13):2633-7. doi: 10.1242/dev.066928.


Negative epistasis between beneficial mutations in an evolving bacterial population.

Khan AI, Dinh DM, Schneider D, Lenski RE, Cooper TF.

Science. 2011 Jun 3;332(6034):1193-6. doi: 10.1126/science.1203801.


Second-order selection for evolvability in a large Escherichia coli population.

Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE.

Science. 2011 Mar 18;331(6023):1433-6. doi: 10.1126/science.1198914.


Altered regulation of the OmpF porin by Fis in Escherichia coli during an evolution experiment and between B and K-12 strains.

Crozat E, Hindré T, Kühn L, Garin J, Lenski RE, Schneider D.

J Bacteriol. 2011 Jan;193(2):429-40. doi: 10.1128/JB.01341-10. Epub 2010 Nov 19.


Evolutionary dynamics, epistatic interactions, and biological information.

Strelioff CC, Lenski RE, Ofria C.

J Theor Biol. 2010 Oct 21;266(4):584-94. doi: 10.1016/j.jtbi.2010.07.025. Epub 2010 Jul 24.


Parallel changes in host resistance to viral infection during 45,000 generations of relaxed selection.

Meyer JR, Agrawal AA, Quick RT, Dobias DT, Schneider D, Lenski RE.

Evolution. 2010 Oct;64(10):3024-34. doi: 10.1111/j.1558-5646.2010.01049.x. Epub 2010 Aug 19.


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