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For: Achaz G, Rodriguez-Verdugo A, Gaut BS, Tenaillon O. The reproducibility of adaptation in the light of experimental evolution with whole genome sequencing. Adv Exp Med Biol 2014;781:211-31. [PMID: 24277302 DOI: 10.1007/978-94-007-7347-9_11] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Number Cited by Other Article(s)
1
Eccleston RC, Manko E, Campino S, Clark TG, Furnham N. A computational method for predicting the most likely evolutionary trajectories in the stepwise accumulation of resistance mutations. eLife 2023;12:e84756. [PMID: 38132182 PMCID: PMC10807863 DOI: 10.7554/elife.84756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/21/2023] [Indexed: 12/23/2023]  Open
2
Baquero F, Martínez JL, F. Lanza V, Rodríguez-Beltrán J, Galán JC, San Millán A, Cantón R, Coque TM. Evolutionary Pathways and Trajectories in Antibiotic Resistance. Clin Microbiol Rev 2021;34:e0005019. [PMID: 34190572 PMCID: PMC8404696 DOI: 10.1128/cmr.00050-19] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
3
Behdenna A, Godfroid M, Petot P, Pothier J, Lambert A, Achaz G. A minimal yet flexible likelihood framework to assess correlated evolution. Syst Biol 2021;71:823-838. [PMID: 34792608 DOI: 10.1093/sysbio/syab092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 11/14/2022]  Open
4
Lambros M, Pechuan-Jorge X, Biro D, Ye K, Bergman A. Emerging Adaptive Strategies Under Temperature Fluctuations in a Laboratory Evolution Experiment of Escherichia Coli. Front Microbiol 2021;12:724982. [PMID: 34745030 PMCID: PMC8569431 DOI: 10.3389/fmicb.2021.724982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022]  Open
5
Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A 2021;118:2016886118. [PMID: 33441451 DOI: 10.1073/pnas.2016886118] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
6
Meroz N, Tovi N, Sorokin Y, Friedman J. Community composition of microbial microcosms follows simple assembly rules at evolutionary timescales. Nat Commun 2021;12:2891. [PMID: 33976223 PMCID: PMC8113234 DOI: 10.1038/s41467-021-23247-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/20/2021] [Indexed: 12/14/2022]  Open
7
Desjardins E, Kurtz J, Kranke N, Lindeza A, Richter SH. Beyond Standardization: Improving External Validity and Reproducibility in Experimental Evolution. Bioscience 2021. [DOI: 10.1093/biosci/biab008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
8
Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types. PLoS Comput Biol 2021;17:e1008596. [PMID: 33465077 PMCID: PMC7846111 DOI: 10.1371/journal.pcbi.1008596] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/29/2021] [Accepted: 12/01/2020] [Indexed: 11/19/2022]  Open
9
Hosseini SR, Diaz-Uriarte R, Markowetz F, Beerenwinkel N. Estimating the predictability of cancer evolution. Bioinformatics 2019;35:i389-i397. [PMID: 31510665 PMCID: PMC6612861 DOI: 10.1093/bioinformatics/btz332] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
10
Zhong Z, Liu CC. Probing pathways of adaptation with continuous evolution. CURRENT OPINION IN SYSTEMS BIOLOGY 2019;14:18-24. [PMID: 31608311 PMCID: PMC6788780 DOI: 10.1016/j.coisb.2019.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
11
Lumby CK, Nene NR, Illingworth CJR. A novel framework for inferring parameters of transmission from viral sequence data. PLoS Genet 2018;14:e1007718. [PMID: 30325921 PMCID: PMC6203404 DOI: 10.1371/journal.pgen.1007718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/26/2018] [Accepted: 09/26/2018] [Indexed: 11/18/2022]  Open
12
Dick C, Hinh J, Hayashi CY, Reznick DN. Convergent evolution of coloration in experimental introductions of the guppy (Poecilia reticulata). Ecol Evol 2018;8:8999-9006. [PMID: 30271561 PMCID: PMC6157698 DOI: 10.1002/ece3.4418] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/30/2018] [Accepted: 07/04/2018] [Indexed: 01/01/2023]  Open
13
Evolutionary constraints in fitness landscapes. Heredity (Edinb) 2018;121:466-481. [PMID: 29993041 DOI: 10.1038/s41437-018-0110-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/29/2022]  Open
14
Experimental evolution heals the scars of genome-scale recoding. Proc Natl Acad Sci U S A 2018. [PMID: 29514958 DOI: 10.1073/pnas.1801699115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
15
Westphal LL, Lau J, Negro Z, Moreno IJ, Ismail Mohammed W, Lee H, Tang H, Finkel SE, Kram KE. Adaptation of Escherichia coli to long-term batch culture in various rich media. Res Microbiol 2018;169:145-156. [PMID: 29454026 DOI: 10.1016/j.resmic.2018.01.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 12/22/2017] [Accepted: 01/23/2018] [Indexed: 12/29/2022]
16
Jahn LJ, Munck C, Ellabaan MMH, Sommer MOA. Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes. Front Microbiol 2017;8:816. [PMID: 28553265 PMCID: PMC5425606 DOI: 10.3389/fmicb.2017.00816] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/21/2017] [Indexed: 12/01/2022]  Open
17
Speed MP, Arbuckle K. Quantification provides a conceptual basis for convergent evolution. Biol Rev Camb Philos Soc 2017;92:815-829. [PMID: 26932796 PMCID: PMC6849873 DOI: 10.1111/brv.12257] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 01/28/2016] [Accepted: 02/02/2016] [Indexed: 12/26/2022]
18
Predicting evolution. Nat Ecol Evol 2017;1:77. [DOI: 10.1038/s41559-017-0077] [Citation(s) in RCA: 184] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 01/10/2017] [Indexed: 11/09/2022]
19
Matuszewski S, Ormond L, Bank C, Jensen JD. Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown. Virus Evol 2017;3:vex004. [PMID: 29977604 PMCID: PMC6007402 DOI: 10.1093/ve/vex004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
20
Nouhaud P, Tobler R, Nolte V, Schlötterer C. Ancestral population reconstitution from isofemale lines as a tool for experimental evolution. Ecol Evol 2016;6:7169-7175. [PMID: 27895897 PMCID: PMC5114691 DOI: 10.1002/ece3.2402] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 02/03/2023]  Open
21
Orgogozo V. Replaying the tape of life in the twenty-first century. Interface Focus 2015;5:20150057. [PMID: 26640652 PMCID: PMC4633862 DOI: 10.1098/rsfs.2015.0057] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
22
Elucidating the molecular architecture of adaptation via evolve and resequence experiments. Nat Rev Genet 2015;16:567-82. [PMID: 26347030 DOI: 10.1038/nrg3937] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
23
Blanquart F, Achaz G, Bataillon T, Tenaillon O. Properties of selected mutations and genotypic landscapes under Fisher's geometric model. Evolution 2014;68:3537-54. [PMID: 25311558 DOI: 10.1111/evo.12545] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 10/05/2014] [Indexed: 02/06/2023]
24
Tenaillon O. The Utility of Fisher's Geometric Model in Evolutionary Genetics. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2014;45:179-201. [PMID: 26740803 PMCID: PMC4699269 DOI: 10.1146/annurev-ecolsys-120213-091846] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
25
de Visser JAGM, Krug J. Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet 2014;15:480-90. [PMID: 24913663 DOI: 10.1038/nrg3744] [Citation(s) in RCA: 402] [Impact Index Per Article: 40.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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