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For: Sanjuán R, Moya A, Elena SF. The contribution of epistasis to the architecture of fitness in an RNA virus. Proc Natl Acad Sci U S A 2004;101:15376-15379. [PMID: 15492220 PMCID: PMC524436 DOI: 10.1073/pnas.0404125101] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 09/09/2004] [Indexed: 02/07/2023]  Open
Number Cited by Other Article(s)
1
Feng Z, Huang J, Baboo S, Diedrich JK, Bangaru S, Paulson JC, Yates JR, Yuan M, Wilson IA, Ward AB. Structural and Functional Insights into the Evolution of SARS-CoV-2 KP.3.1.1 Spike Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.10.627775. [PMID: 39713475 PMCID: PMC11661143 DOI: 10.1101/2024.12.10.627775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
2
Herrera-Martí DA. Error thresholds in the presence of epistatic interactions. Phys Rev E 2024;110:054412. [PMID: 39690608 DOI: 10.1103/physreve.110.054412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 10/15/2024] [Indexed: 12/19/2024]
3
Shimagaki KS, Barton JP. Efficient epistasis inference via higher-order covariance matrix factorization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618287. [PMID: 39464126 PMCID: PMC11507688 DOI: 10.1101/2024.10.14.618287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
4
Holmes EC, Krammer F, Goodrum FD. Virology-The next fifty years. Cell 2024;187:5128-5145. [PMID: 39303682 PMCID: PMC11467463 DOI: 10.1016/j.cell.2024.07.025] [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: 02/29/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 09/22/2024]
5
Schwab B, Yin J. Computational multigene interactions in virus growth and infection spread. Virus Evol 2023;10:vead082. [PMID: 38361828 PMCID: PMC10868543 DOI: 10.1093/ve/vead082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/29/2023] [Accepted: 12/19/2023] [Indexed: 02/17/2024]  Open
6
Cotto O, Day T. A null model for the distribution of fitness effects of mutations. Proc Natl Acad Sci U S A 2023;120:e2218200120. [PMID: 37252948 PMCID: PMC10266029 DOI: 10.1073/pnas.2218200120] [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: 10/25/2022] [Accepted: 04/28/2023] [Indexed: 06/01/2023]  Open
7
Whitlock AOB, Bird BH, Ghersi B, Davison AJ, Hughes J, Nichols J, Vučak M, Amara E, Bangura J, Lavalie EG, Kanu MC, Kanu OT, Sjodin A, Remien CH, Nuismer SL. Identifying the genetic basis of viral spillover using Lassa virus as a test case. ROYAL SOCIETY OPEN SCIENCE 2023;10:221503. [PMID: 36968239 PMCID: PMC10031424 DOI: 10.1098/rsos.221503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
8
Shchur V, Spirin V, Sirotkin D, Burovski E, De Maio N, Corbett-Detig R. VGsim: Scalable viral genealogy simulator for global pandemic. PLoS Comput Biol 2022;18:e1010409. [PMID: 36001646 PMCID: PMC9447924 DOI: 10.1371/journal.pcbi.1010409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 09/06/2022] [Accepted: 07/18/2022] [Indexed: 11/24/2022]  Open
9
Johnson MS, Desai MM. Mutational robustness changes during long-term adaptation in laboratory budding yeast populations. eLife 2022;11:76491. [PMID: 35880743 PMCID: PMC9355567 DOI: 10.7554/elife.76491] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/25/2022] [Indexed: 11/13/2022]  Open
10
Barnes JE, Miller CR, Ytreberg FM. Searching for a mechanistic description of pairwise epistasis in protein systems. Proteins 2022;90:1474-1485. [DOI: 10.1002/prot.26328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 11/05/2021] [Accepted: 02/22/2022] [Indexed: 11/09/2022]
11
Yépez Y, Marcano-Ruiz M, Bezerra RS, Fam B, Ximenez JPB, Silva WA, Bortolini MC. Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm. Genet Mol Biol 2022;45:e20210309. [PMID: 35266951 PMCID: PMC8908351 DOI: 10.1590/1678-4685-gmb-2021-0309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 12/11/2022]  Open
12
Shchur V, Spirin V, Sirotkin D, Burovski E, De Maio N, Corbett-Detig R. VGsim: scalable viral genealogy simulator for global pandemic. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.21.21255891. [PMID: 33948608 PMCID: PMC8095227 DOI: 10.1101/2021.04.21.21255891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
13
Merleau NSC, Pénisson S, Gerrish PJ, Elena SF, Smerlak M. Why are viral genomes so fragile? The bottleneck hypothesis. PLoS Comput Biol 2021;17:e1009128. [PMID: 34237053 PMCID: PMC8291636 DOI: 10.1371/journal.pcbi.1009128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/20/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022]  Open
14
Intra-Population Competition during Adaptation to Increased Temperature in an RNA Bacteriophage. Int J Mol Sci 2021;22:ijms22136815. [PMID: 34202838 PMCID: PMC8268601 DOI: 10.3390/ijms22136815] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 01/21/2023]  Open
15
Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Phys Life Rev 2021;38:55-106. [PMID: 34088608 DOI: 10.1016/j.plrev.2021.03.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
16
Villa TG, Abril AG, Sánchez S, de Miguel T, Sánchez-Pérez A. Animal and human RNA viruses: genetic variability and ability to overcome vaccines. Arch Microbiol 2021;203:443-464. [PMID: 32989475 PMCID: PMC7521576 DOI: 10.1007/s00203-020-02040-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/29/2020] [Accepted: 09/12/2020] [Indexed: 02/06/2023]
17
Szilágyi A, Kovács VP, Szathmáry E, Santos M. Evolution of linkage and genome expansion in protocells: The origin of chromosomes. PLoS Genet 2020;16:e1009155. [PMID: 33119583 PMCID: PMC7665907 DOI: 10.1371/journal.pgen.1009155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 11/13/2020] [Accepted: 09/24/2020] [Indexed: 11/18/2022]  Open
18
Van Leuven JT, Ederer MM, Burleigh K, Scott L, Hughes RA, Codrea V, Ellington AD, Wichman HA, Miller CR. ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome Biol Evol 2020;13:5921183. [PMID: 33045052 PMCID: PMC7881332 DOI: 10.1093/gbe/evaa214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 12/11/2022]  Open
19
Zhang TH, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. PLoS Genet 2020;16:e1009009. [PMID: 33085662 PMCID: PMC7605711 DOI: 10.1371/journal.pgen.1009009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 11/02/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]  Open
20
Tekin E, Diamant ES, Cruz‐Loya M, Enriquez V, Singh N, Savage VM, Yeh PJ. Using a newly introduced framework to measure ecological stressor interactions. Ecol Lett 2020;23:1391-1403. [DOI: 10.1111/ele.13533] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 02/13/2020] [Accepted: 04/16/2020] [Indexed: 12/30/2022]
21
Agostini ML, Pruijssers AJ, Chappell JD, Gribble J, Lu X, Andres EL, Bluemling GR, Lockwood MA, Sheahan TP, Sims AC, Natchus MG, Saindane M, Kolykhalov AA, Painter GR, Baric RS, Denison MR. Small-Molecule Antiviral β-d-N4-Hydroxycytidine Inhibits a Proofreading-Intact Coronavirus with a High Genetic Barrier to Resistance. J Virol 2019;93:e01348-19. [PMID: 31578288 PMCID: PMC6880162 DOI: 10.1128/jvi.01348-19] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 09/24/2019] [Indexed: 12/22/2022]  Open
22
Fraïsse C, Welch JJ. The distribution of epistasis on simple fitness landscapes. Biol Lett 2019;15:20180881. [PMID: 31014191 DOI: 10.1098/rsbl.2018.0881] [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: 01/08/2023]  Open
23
Johnson MS, Martsul A, Kryazhimskiy S, Desai MM. Higher-fitness yeast genotypes are less robust to deleterious mutations. Science 2019;366:490-493. [PMID: 31649199 PMCID: PMC7204892 DOI: 10.1126/science.aay4199] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
24
Kemble H, Nghe P, Tenaillon O. Recent insights into the genotype-phenotype relationship from massively parallel genetic assays. Evol Appl 2019;12:1721-1742. [PMID: 31548853 PMCID: PMC6752143 DOI: 10.1111/eva.12846] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022]  Open
25
Jacquot M, Rao PP, Yadav S, Nomikou K, Maan S, Jyothi YK, Reddy N, Putty K, Hemadri D, Singh KP, Maan NS, Hegde NR, Mertens P, Biek R. Contrasting selective patterns across the segmented genome of bluetongue virus in a global reassortment hotspot. Virus Evol 2019;5:vez027. [PMID: 31392031 PMCID: PMC6680063 DOI: 10.1093/ve/vez027] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
26
Xie L, Yuan AE, Shou W. Simulations reveal challenges to artificial community selection and possible strategies for success. PLoS Biol 2019;17:e3000295. [PMID: 31237866 PMCID: PMC6658139 DOI: 10.1371/journal.pbio.3000295] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/25/2019] [Accepted: 05/13/2019] [Indexed: 02/04/2023]  Open
27
Existing Host Range Mutations Constrain Further Emergence of RNA Viruses. J Virol 2019;93:JVI.01385-18. [PMID: 30463962 DOI: 10.1128/jvi.01385-18] [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: 08/16/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023]  Open
28
Shim H. Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network. Evol Bioinform Online 2019;15:1176934318821072. [PMID: 30692845 PMCID: PMC6335656 DOI: 10.1177/1176934318821072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]  Open
29
Bera S, Fraile A, García-Arenal F. Analysis of Fitness Trade-Offs in the Host Range Expansion of an RNA Virus, Tobacco Mild Green Mosaic Virus. J Virol 2018;92:e01268-18. [PMID: 30257999 PMCID: PMC6258955 DOI: 10.1128/jvi.01268-18] [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: 07/20/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022]  Open
30
Mauck KE, Chesnais Q, Shapiro LR. Evolutionary Determinants of Host and Vector Manipulation by Plant Viruses. Adv Virus Res 2018;101:189-250. [PMID: 29908590 DOI: 10.1016/bs.aivir.2018.02.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
31
Akand EH, Downard KM. Identification of epistatic mutations and insights into the evolution of the influenza virus using a mass-based protein phylogenetic approach. Mol Phylogenet Evol 2018;121:132-138. [PMID: 29337273 DOI: 10.1016/j.ympev.2018.01.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 12/11/2017] [Accepted: 01/10/2018] [Indexed: 12/27/2022]
32
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]
33
Schoustra S, Hwang S, Krug J, de Visser JAGM. Diminishing-returns epistasis among random beneficial mutations in a multicellular fungus. Proc Biol Sci 2017;283:rspb.2016.1376. [PMID: 27559062 PMCID: PMC5013798 DOI: 10.1098/rspb.2016.1376] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/01/2016] [Indexed: 12/29/2022]  Open
34
Cervera H, Lalić J, Elena SF. Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations. Proc Biol Sci 2017;283:rspb.2016.0984. [PMID: 27534955 DOI: 10.1098/rspb.2016.0984] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/26/2016] [Indexed: 12/25/2022]  Open
35
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]
36
A Selective Bottleneck Shapes the Evolutionary Mutant Spectra of Enterovirus A71 during Viral Dissemination in Humans. J Virol 2017;91:JVI.01062-17. [PMID: 28931688 DOI: 10.1128/jvi.01062-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/14/2017] [Indexed: 12/15/2022]  Open
37
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
38
Djidjou-Demasse R, Moury B, Fabre F. Mosaics often outperform pyramids: insights from a model comparing strategies for the deployment of plant resistance genes against viruses in agricultural landscapes. THE NEW PHYTOLOGIST 2017;216:239-253. [PMID: 28776688 DOI: 10.1111/nph.14701] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 06/13/2017] [Indexed: 06/07/2023]
39
Minicka J, Elena SF, Borodynko-Filas N, Rubiś B, Hasiów-Jaroszewska B. Strain-dependent mutational effects for Pepino mosaic virus in a natural host. BMC Evol Biol 2017;17:67. [PMID: 28264646 PMCID: PMC5339997 DOI: 10.1186/s12862-017-0920-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/20/2017] [Indexed: 11/10/2022]  Open
40
Morley VJ, Turner PE. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change. Evolution 2017;71:872-883. [PMID: 28121018 PMCID: PMC5382103 DOI: 10.1111/evo.13193] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022]
41
Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016;1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
42
Palmer BA, Fanning LJ. Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness. PLoS One 2016;11:e0167089. [PMID: 27880830 PMCID: PMC5120871 DOI: 10.1371/journal.pone.0167089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022]  Open
43
Jochumsen N, Marvig RL, Damkiær S, Jensen RL, Paulander W, Molin S, Jelsbak L, Folkesson A. The evolution of antimicrobial peptide resistance in Pseudomonas aeruginosa is shaped by strong epistatic interactions. Nat Commun 2016;7:13002. [PMID: 27694971 PMCID: PMC5494192 DOI: 10.1038/ncomms13002] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/24/2016] [Indexed: 11/25/2022]  Open
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Arribas M, Cabanillas L, Kubota K, Lázaro E. Impact of increased mutagenesis on adaptation to high temperature in bacteriophage Qβ. Virology 2016;497:163-170. [PMID: 27471955 DOI: 10.1016/j.virol.2016.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 07/05/2016] [Indexed: 02/05/2023]
45
Blanquart F, Bataillon T. Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fisher's Geometric Model? Genetics 2016;203:847-62. [PMID: 27052568 PMCID: PMC4896198 DOI: 10.1534/genetics.115.182691] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 03/25/2016] [Indexed: 01/06/2023]  Open
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du Plessis L, Leventhal GE, Bonhoeffer S. How Good Are Statistical Models at Approximating Complex Fitness Landscapes? Mol Biol Evol 2016;33:2454-68. [PMID: 27189564 PMCID: PMC4989103 DOI: 10.1093/molbev/msw097] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]  Open
47
Agudo R, de la Higuera I, Arias A, Grande-Pérez A, Domingo E. Involvement of a joker mutation in a polymerase-independent lethal mutagenesis escape mechanism. Virology 2016;494:257-66. [PMID: 27136067 PMCID: PMC7111656 DOI: 10.1016/j.virol.2016.04.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 02/05/2023]
48
Cervera H, Elena SF. Genetic variation in fitness within a clonal population of a plant RNA virus. Virus Evol 2016;2:vew006. [PMID: 27774299 PMCID: PMC4989883 DOI: 10.1093/ve/vew006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 02/11/2016] [Accepted: 02/16/2016] [Indexed: 01/01/2023]  Open
49
Wu NC, Du Y, Le S, Young AP, Zhang TH, Wang Y, Zhou J, Yoshizawa JM, Dong L, Li X, Wu TT, Sun R. Coupling high-throughput genetics with phylogenetic information reveals an epistatic interaction on the influenza A virus M segment. BMC Genomics 2016;17:46. [PMID: 26754751 PMCID: PMC4710013 DOI: 10.1186/s12864-015-2358-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/28/2015] [Indexed: 12/15/2022]  Open
50
Bernet GP, Elena SF. Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus. BMC Evol Biol 2015;15:274. [PMID: 26643527 PMCID: PMC4672503 DOI: 10.1186/s12862-015-0555-2] [Citation(s) in RCA: 14] [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: 09/30/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022]  Open
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