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For: Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ. Exceptional convergent evolution in a virus. Genetics 1997;147:1497-507. [PMID: 9409816 PMCID: PMC1208326 DOI: 10.1093/genetics/147.4.1497] [Citation(s) in RCA: 263] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
Number Cited by Other Article(s)
1
Ahlawat N, Mahilkar A, Saini S. Resource presentation dictates genetic and phenotypic adaptation in yeast. BMC Ecol Evol 2025;25:33. [PMID: 40234742 PMCID: PMC11998346 DOI: 10.1186/s12862-025-02361-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2024] [Accepted: 03/05/2025] [Indexed: 04/17/2025]  Open
2
Anderson NW, Kirk L, Schraiber JG, Ragsdale AP. A path integral approach for allele frequency dynamics under polygenic selection. Genetics 2025;229:1-63. [PMID: 39531638 DOI: 10.1093/genetics/iyae182] [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: 09/16/2024] [Revised: 10/11/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024]  Open
3
Silvestro D, Latrille T, Salamin N. Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation. Syst Biol 2024;73:789-806. [PMID: 38916476 PMCID: PMC11639169 DOI: 10.1093/sysbio/syae029] [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: 09/12/2023] [Revised: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 06/26/2024]  Open
4
Kunisch F, Campobasso C, Wagemans J, Yildirim S, Chan BK, Schaudinn C, Lavigne R, Turner PE, Raschke MJ, Trampuz A, Gonzalez Moreno M. Targeting Pseudomonas aeruginosa biofilm with an evolutionary trained bacteriophage cocktail exploiting phage resistance trade-offs. Nat Commun 2024;15:8572. [PMID: 39362854 PMCID: PMC11450229 DOI: 10.1038/s41467-024-52595-w] [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: 05/29/2023] [Accepted: 09/12/2024] [Indexed: 10/05/2024]  Open
5
Castiglioni VG, Olmo-Uceda MJ, Martín S, Félix MA, González R, Elena SF. Experimental evolution of an RNA virus in Caenorhabditis elegans. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024;123:105623. [PMID: 38901623 DOI: 10.1016/j.meegid.2024.105623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/02/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
6
Anderson NW, Kirk L, Schraiber JG, Ragsdale AP. A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599114. [PMID: 38915613 PMCID: PMC11195211 DOI: 10.1101/2024.06.14.599114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
7
Zion S, Katz S, Hershberg R. Escherichia coli adaptation under prolonged resource exhaustion is characterized by extreme parallelism and frequent historical contingency. PLoS Genet 2024;20:e1011333. [PMID: 38885285 PMCID: PMC11213340 DOI: 10.1371/journal.pgen.1011333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 06/28/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024]  Open
8
Greenrod STE, Cazares D, Johnson S, Hector TE, Stevens EJ, MacLean RC, King KC. Warming alters life-history traits and competition in a phage community. Appl Environ Microbiol 2024;90:e0028624. [PMID: 38624196 PMCID: PMC11107170 DOI: 10.1128/aem.00286-24] [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: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/17/2024]  Open
9
Bailes CL, Biggs KRH, Scott L, Wichman HA, Schwartz EJ. Genetic and functional basis of the reduction effect in bacteriophage ΦX174. Virology 2023;588:109905. [PMID: 39492403 DOI: 10.1016/j.virol.2023.109905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 11/05/2024]
10
Jewel D, Pham Q, Chatterjee A. Virus-assisted directed evolution of biomolecules. Curr Opin Chem Biol 2023;76:102375. [PMID: 37542745 PMCID: PMC10870257 DOI: 10.1016/j.cbpa.2023.102375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 08/07/2023]
11
Geiler-Samerotte K, Lang GI. Best Practices in Microbial Experimental Evolution. J Mol Evol 2023;91:237-240. [PMID: 37209159 PMCID: PMC10885815 DOI: 10.1007/s00239-023-10119-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
12
Martínez AA, Lang GI. Identifying Targets of Selection in Laboratory Evolution Experiments. J Mol Evol 2023;91:345-355. [PMID: 36810618 PMCID: PMC11197053 DOI: 10.1007/s00239-023-10096-2] [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: 12/07/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023]
13
Cano AV, Gitschlag BL, Rozhoňová H, Stoltzfus A, McCandlish DM, Payne JL. Mutation bias and the predictability of evolution. Philos Trans R Soc Lond B Biol Sci 2023;378:20220055. [PMID: 37004719 PMCID: PMC10067271 DOI: 10.1098/rstb.2022.0055] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023]  Open
14
Lyberger K, Schoener TW. Differential genotype response to increased resource abundance helps explain parallel evolution of Daphnia populations in the wild. Ecol Evol 2023;13:e9896. [PMID: 36937075 PMCID: PMC10015367 DOI: 10.1002/ece3.9896] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/17/2023]  Open
15
Lippi G, Henry BM, Plebani M. A Simple Epidemiologic Model for Predicting Impaired Neutralization of New SARS-CoV-2 Variants. Vaccines (Basel) 2023;11:128. [PMID: 36679973 PMCID: PMC9863154 DOI: 10.3390/vaccines11010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023]  Open
16
Jagdish T, Nguyen Ba AN. Microbial experimental evolution in a massively multiplexed and high-throughput era. Curr Opin Genet Dev 2022;75:101943. [PMID: 35752001 DOI: 10.1016/j.gde.2022.101943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/11/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022]
17
Boezen D, Ali G, Wang M, Wang X, van der Werf W, Vlak JM, Zwart MP. Empirical estimates of the mutation rate for an alphabaculovirus. PLoS Genet 2022;18:e1009806. [PMID: 35666722 PMCID: PMC9203023 DOI: 10.1371/journal.pgen.1009806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 06/16/2022] [Accepted: 04/27/2022] [Indexed: 01/02/2023]  Open
18
Amicone M, Borges V, Alves MJ, Isidro J, Zé-Zé L, Duarte S, Vieira L, Guiomar R, Gomes JP, Gordo I. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evol Med Public Health 2022;10:142-155. [PMID: 35419205 PMCID: PMC8996265 DOI: 10.1093/emph/eoac010] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/08/2022] [Indexed: 01/13/2023]  Open
19
Genetic engineering of marine cyanophages reveals integration but not lysogeny in T7-like cyanophages. THE ISME JOURNAL 2022;16:488-499. [PMID: 34429521 PMCID: PMC8776855 DOI: 10.1038/s41396-021-01085-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 08/02/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023]
20
Soares ADA, Wardil L, Klaczko LB, Dickman R. Hidden role of mutations in the evolutionary process. Phys Rev E 2021;104:044413. [PMID: 34781575 DOI: 10.1103/physreve.104.044413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022]
21
Horton JS, Flanagan LM, Jackson RW, Priest NK, Taylor TB. A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes. Nat Commun 2021;12:6092. [PMID: 34667151 PMCID: PMC8526746 DOI: 10.1038/s41467-021-26286-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 09/28/2021] [Indexed: 11/08/2022]  Open
22
Madgwick PG, Kanitz R. Evolution of resistance under alternative models of selective interference. J Evol Biol 2021;34:1608-1623. [PMID: 34449949 PMCID: PMC9293239 DOI: 10.1111/jeb.13919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 01/19/2023]
23
Biggs KRH, Bailes CL, Scott L, Wichman HA, Schwartz EJ. Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage. Viruses 2021;13:1389. [PMID: 34372595 PMCID: PMC8310164 DOI: 10.3390/v13071389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 01/15/2023]  Open
24
Bailey SF, Alonso Morales LA, Kassen R. Effects of synonymous mutations beyond codon bias: The evidence for adaptive synonymous substitutions from microbial evolution experiments. Genome Biol Evol 2021;13:6300525. [PMID: 34132772 PMCID: PMC8410137 DOI: 10.1093/gbe/evab141] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/22/2022]  Open
25
Law A, Solano O, Brown CJ, Hunter SS, Fagnan M, Top EM, Stalder T. Biosolids as a Source of Antibiotic Resistance Plasmids for Commensal and Pathogenic Bacteria. Front Microbiol 2021;12:606409. [PMID: 33967971 PMCID: PMC8098119 DOI: 10.3389/fmicb.2021.606409] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/09/2021] [Indexed: 12/05/2022]  Open
26
Ramazzotti D, Angaroni F, Maspero D, Gambacorti-Passerini C, Antoniotti M, Graudenzi A, Piazza R. VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. PATTERNS (NEW YORK, N.Y.) 2021;2:100212. [PMID: 33728416 PMCID: PMC7953447 DOI: 10.1016/j.patter.2021.100212] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/30/2020] [Accepted: 01/22/2021] [Indexed: 12/22/2022]
27
Bons E, Leemann C, Metzner KJ, Regoes RR. Long-term experimental evolution of HIV-1 reveals effects of environment and mutational history. PLoS Biol 2020;18:e3001010. [PMID: 33370289 PMCID: PMC7793244 DOI: 10.1371/journal.pbio.3001010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 01/08/2021] [Accepted: 11/30/2020] [Indexed: 11/21/2022]  Open
28
Hill T, Unckless RL. Recurrent evolution of high virulence in isolated populations of a DNA virus. eLife 2020;9:e58931. [PMID: 33112738 PMCID: PMC7685711 DOI: 10.7554/elife.58931] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 10/28/2020] [Indexed: 12/30/2022]  Open
29
Hossain MT, Yokono T, Kashiwagi A. The Single-Stranded RNA Bacteriophage Qβ Adapts Rapidly to High Temperatures: An Evolution Experiment. Viruses 2020;12:v12060638. [PMID: 32545482 PMCID: PMC7354602 DOI: 10.3390/v12060638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/10/2020] [Indexed: 11/22/2022]  Open
30
The developing toolkit of continuous directed evolution. Nat Chem Biol 2020;16:610-619. [DOI: 10.1038/s41589-020-0532-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/27/2020] [Indexed: 12/14/2022]
31
Finally, a Role Befitting Astar: Strongly Conserved, Unessential Microvirus A* Proteins Ensure the Product Fidelity of Packaging Reactions. J Virol 2020;94:JVI.01593-19. [PMID: 31666371 DOI: 10.1128/jvi.01593-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/24/2019] [Indexed: 12/14/2022]  Open
32
Dreier C, Resa-Infante P, Thiele S, Stanelle-Bertram S, Walendy-Gnirß K, Speiseder T, Preuss A, Müller Z, Klenk HD, Stech J, Gabriel G. Mutations in the H7 HA and PB1 genes of avian influenza a viruses increase viral pathogenicity and contact transmission in guinea pigs. Emerg Microbes Infect 2020;8:1324-1336. [PMID: 31503518 PMCID: PMC6746284 DOI: 10.1080/22221751.2019.1663131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
33
Jack BR, Boutz DR, Paff ML, Smith BL, Wilke CO. Transcript degradation and codon usage regulate gene expression in a lytic phage. Virus Evol 2019;5:vez055. [PMID: 31908847 PMCID: PMC6938266 DOI: 10.1093/ve/vez055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
34
Wasik BR, Voorhees IEH, Barnard KN, Alford-Lawrence BK, Weichert WS, Hood G, Nogales A, Martínez-Sobrido L, Holmes EC, Parrish CR. Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation. J Virol 2019;93:e01039-19. [PMID: 31511393 PMCID: PMC6854484 DOI: 10.1128/jvi.01039-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/09/2019] [Indexed: 12/19/2022]  Open
35
Kang M, Kim K, Choe D, Cho S, Kim SC, Palsson B, Cho BK. Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution. Front Microbiol 2019;10:1845. [PMID: 31474949 PMCID: PMC6706779 DOI: 10.3389/fmicb.2019.01845] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 07/26/2019] [Indexed: 01/09/2023]  Open
36
Bertels F, Leemann C, Metzner KJ, Regoes R. Parallel evolution of HIV-1 in a long-term experiment. Mol Biol Evol 2019;36:2400-2414. [PMID: 31251344 PMCID: PMC6805227 DOI: 10.1093/molbev/msz155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/06/2019] [Accepted: 06/22/2019] [Indexed: 12/15/2022]  Open
37
Bons E, Regoes RR. Virus dynamics and phyloanatomy: Merging population dynamic and phylogenetic approaches. Immunol Rev 2019;285:134-146. [PMID: 30129202 DOI: 10.1111/imr.12688] [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] [Indexed: 12/18/2022]
38
Blount ZD, Lenski RE, Losos JB. Contingency and determinism in evolution: Replaying life’s tape. Science 2018;362:362/6415/eaam5979. [DOI: 10.1126/science.aam5979] [Citation(s) in RCA: 263] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
39
Enav H, Kirzner S, Lindell D, Mandel-Gutfreund Y, Béjà O. Adaptation to sub-optimal hosts is a driver of viral diversification in the ocean. Nat Commun 2018;9:4698. [PMID: 30409965 PMCID: PMC6224464 DOI: 10.1038/s41467-018-07164-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/22/2018] [Indexed: 12/16/2022]  Open
40
A decade of genome sequencing has revolutionized studies of experimental evolution. Curr Opin Microbiol 2018;45:149-155. [DOI: 10.1016/j.mib.2018.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 03/02/2018] [Accepted: 03/07/2018] [Indexed: 11/20/2022]
41
Schönherz AA, Forsberg R, Guldbrandtsen B, Buitenhuis AJ, Einer-Jensen K. Introduction of Viral Hemorrhagic Septicemia Virus into Freshwater Cultured Rainbow Trout Is Followed by Bursts of Adaptive Evolution. J Virol 2018;92:e00436-18. [PMID: 29643236 PMCID: PMC5974487 DOI: 10.1128/jvi.00436-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 03/20/2018] [Indexed: 12/25/2022]  Open
42
Lázaro E, Arribas M, Cabanillas L, Román I, Acosta E. Evolutionary adaptation of an RNA bacteriophage to the simultaneous increase in the within-host and extracellular temperatures. Sci Rep 2018;8:8080. [PMID: 29795535 PMCID: PMC5967308 DOI: 10.1038/s41598-018-26443-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/11/2018] [Indexed: 01/09/2023]  Open
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Obolski U, Ram Y, Hadany L. Key issues review: evolution on rugged adaptive landscapes. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018;81:012602. [PMID: 29051394 DOI: 10.1088/1361-6633/aa94d4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
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Structural changes of tailless bacteriophage ΦX174 during penetration of bacterial cell walls. Proc Natl Acad Sci U S A 2017;114:13708-13713. [PMID: 29229840 DOI: 10.1073/pnas.1716614114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
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Miller CR, Van Leuven JT, Wichman HA, Joyce P. Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theor Popul Biol 2017;122:97-109. [PMID: 29198859 DOI: 10.1016/j.tpb.2017.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 10/18/2022]
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Stoltzfus A, McCandlish DM. Mutational Biases Influence Parallel Adaptation. Mol Biol Evol 2017. [PMID: 28645195 PMCID: PMC5850294 DOI: 10.1093/molbev/msx180] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
47
Additive Phenotypes Underlie Epistasis of Fitness Effects. Genetics 2017;208:339-348. [PMID: 29113978 DOI: 10.1534/genetics.117.300451] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/03/2017] [Indexed: 11/18/2022]  Open
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Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y. J Virol 2017;91:JVI.00690-17. [PMID: 28592544 PMCID: PMC5533922 DOI: 10.1128/jvi.00690-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 11/20/2022]  Open
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Warsi OM, Dykhuizen DE. Evolutionary implications of Liebig's law of the minimum: Selection under low concentrations of two nonsubstitutable nutrients. Ecol Evol 2017;7:5296-5309. [PMID: 28770068 PMCID: PMC5528229 DOI: 10.1002/ece3.3096] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/09/2017] [Accepted: 04/25/2017] [Indexed: 11/05/2022]  Open
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Stern A, Yeh MT, Zinger T, Smith M, Wright C, Ling G, Nielsen R, Macadam A, Andino R. The Evolutionary Pathway to Virulence of an RNA Virus. Cell 2017;169:35-46.e19. [PMID: 28340348 DOI: 10.1016/j.cell.2017.03.013] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 01/03/2017] [Accepted: 03/06/2017] [Indexed: 12/31/2022]
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