Molecular basis of adaptive convergence in experimental populations of RNA viruses

Genetics

Volumn 162, Issue 2, 2002, Pages 533-542

  Cuevas, José M ^a   Elena, Santiago F ^a   Moya, Andrés ^a  

^a UNIVERSITY OF VALENCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; AMINO ACID SUBSTITUTION; ARTICLE; GENE SEQUENCE; GENETIC RECOMBINATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN RNA BINDING; RNA PURIFICATION; RNA VIRUS; SEQUENCE ANALYSIS; VESICULAR STOMATITIS VIRUS; VIRUS GENOME; VIRUS REPLICATION; GENETIC EPISTASIS; GENETICS; PHYLOGENY; POINT MUTATION; STATISTICAL MODEL;

PROKARYOTA; RNA VIRUSES; VESICULAR STOMATITIS VIRUS;

EPISTASIS, GENETIC; EVOLUTION, MOLECULAR; LIKELIHOOD FUNCTIONS; PHYLOGENY; POINT MUTATION; RNA VIRUSES;

EID: 0036811120     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (44)

1. Akaike, H., 1974 A new look at the statistical model identification. IEEE Trans. Autom. Contr. 19: 716-723.
2. Boucher, C. A. B., E. O'Sullivan, J. W. Mulder, C. Ramautarsing, P. Kellam et al., 1992 Ordered appearance of zidovudine resistance mutations during treatment of 18 human immunodeficiency virus-positive subjects. J. Infect. Dis. 165: 105-110.
3. Bracho, M. A., A. Moya and E. Barrio, 1998 Contribution of Taq polymerase-induced errors to the estimation of RNA virus diversity. J. Gen. Virol. 79: 2921-2928.
4. Bull, J. J., M. R. Badgett, H. A. Wichman, J. P. Huelsenbeck, D. M. Hillis et al., 1997 Exceptional convergent evolution in a virus. Genetics 147: 1497-1507.
5. Chao, L., 1988 Evolution of sex in RNA viruses. J. Theor. Biol. 133: 99-112.
6. Charlesworth, B., 1998 The effect of synergistic epistasis on the inbreeding load. Genet. Res. 71: 85-89.
7. Condra, J. H., D. J. Holder, W. A. Schleif, O. M. Blahy, R. M. Danovich et al., 1996 Genetic correlates of in vivo viral resistance to indinavir, a human immunodeficiency virus type 1 protease inhibitor. J. Virol. 70: 8270-8276.
8. Coyne, J. A., 1992 The genetics of speciation. Nature 355: 511-515.
9. de Visser, J. A. G. M., R. F. Hoekstra and H. van den Ende, 1997 Test of interaction between genetic markers that affect fitness in Aspergillus niger. Evolution 51: 1499-1505.
10. Elena, S. F., 1999 Little evidence for synergism among deleterious mutations in a nonsegmented RNA virus. J. Mol. Evol. 49: 703-707.
11. Elena, S. F., and R. E. Lenski, 1997 Test of synergistic interactions among deleterious mutations in bacteria. Nature 390: 395-398.
12. Elena, S. F., and A. Moya, 1999 Rate of deleterious mutation and the distribution of its effects on fitness in vesicular stomatitis virus. J. Evol. Biol. 12: 1078-1088.
13. Eyre-Walker, A., 1999 Evidence of selection on silent site base composition in mammals: Potential implications for the evolution of isochores and junk DNA. Genetics 152: 675-683.
14. Fares, M. A., A. Moya, C. Escarmis, E. Baranowski, E. Domingo et al., 2001 Evidence for positive selection in the capsid protein-coding region of the foot-and-mouth disease virus (FMDV) subjected to experimental passage regimens. Mol. Biol. Evol. 18: 10-21.
15. Fay, J. C., G. J. Wychkoff and C.-I Wu, 2001 Positive and negative selection on the human genome. Genetics 158: 1227-1234.
16. Gerrish, P. J., and R. E. Lenski, 1998 The fate of competing beneficial mutations in an asexual population. Genetica 102 (103): 127-144.
17. Hofmann-Lehmann, R., J. Vlasak, A. L. Chenine, P. L. Li, T. W. Baba et al., 2002 Molecular evolution of human immunodeficiency virus env in humans and monkeys: Similar patterns occur during natural disease progression or rapid virus passage. J. Virol. 76: 5278-5284.
18. Holland, J. J., J. C. de la Torre, D. K. Clarke and E. A. Duarte, 1991 Quantitation of relative fitness and great adaptability of clonal populations of RNA viruses. J. Virol. 65: 2960-2967.
19. Holmes, E. C., and A. Moya, 2002 Is the quasispecies concept relevant to RNA viruses? J. Virol. 76: 460-462.
20. Jenkins, G. M., M. Worobey, C. H. Woelk and E. C. Holmes, 2001 Nonquasispecies evidence for the evolution of RNA viruses. Mol. Biol. Evol. 18: 987-994.
21. Kellam, P., C. A. B. Boucher, J. M. G. H. Tijnagel and B. A. Larder, 1994 Zidovudine treatment results in the selection of human immunodeficiency virus type 1 variants whose genotypes confer increasing levels of drug resistance. J. Gen. Virol. 75: 341-351.
22. Kondrashov, A. S., 1985 Deleterious mutations as an evolutionary factor. II. Facultative apomixes and selfing. Genetics 111: 635-653.
23. Kondrashov, A. S., and J. F. Crow, 1991 Haploidy or diploidy: Which is better? Nature 351: 314-315.
24. Larder, B. A., K. E. Coates and S. D. Kemp, 1991 Zidovudine-resistant human immunodeficiency virus selected by passage in cell culture. J. Virol. 65: 5232-5236.
25. Lenski, R. E., V. Souza, L. P. Duong, Q. G. Phan, T. N. Nguyen et al., 1994 Epistatic effects of promoter and repressor functions of the Tn10 tetracycline-resistance operon of the fitness of Escherichia coli. Mol. Ecol. 3: 127-135.
26. Lewontin, R., 2000 Population genetics: problems, foundations, and historical perspectives, pp. 5-23 in Evolutionary Genetics: From Molecules to Morphology, edited by C. B. Krimbas and R. S. Singh. Cambridge University Press, Cambridge, UK.
27. Martínez-Picado, J., A. V. Savara, L. Sutton and R. T. D'Aquila, 1999 Replicative fitness of protease inhibitor-resistant mutants of human immunodeficiency virus type 1. J. Virol. 73: 3744-3752.
28. Martínez-Picado, J., M. P. DePasquale, N. Kartsonis, G. J. Hanna, J. Wong et al., 2000 Antiretroviral resistance during successful therapy of HIV type 1 infection. Proc. Natl. Acad. Sci. USA 97: 10948-10953.
29. McKnight, K. L., and S. M. Lemon, 1998 The rhinovirus type 14 genome contains an internally located RNA structure that is required for viral replication. RNA 4: 1569-1584.
30. Miralles, R., P. J. Gerrish, A. Moya and S. F. Elena, 1999 Clonal interference and the evolution of RNA viruses. Science 285: 1745-1747.
31. Miralles, R., A. Moya and S. F. Elena, 2000 Diminishing returns of population size in the rate of RNA virus adaptation. J. Virol. 74: 3566-3571.
32. Molla, A., M. Korneyeva, Q. Gao, S. Vasavanonda, P. J. Schipper et al., 1996 Ordered accumulation of mutations in HIV protease confers resistance to ritonavir. Nat. Med. 2: 760-766.
33. Nijhuis, M., R. Schuurman, D. de Jong, E. J. Rickson, E. Gustchina et al., 1999 Increased fitness of drug resistant HIV-1 protease as a result of acquisition of compensatory mutations during suboptimal therapy. AIDS 13: 2349-2359.
34. Ohta, T., 1973 Slightly deleterious mutant substitutions in evolution. Nature 246: 74-76.
35. Peck, J. R., and D. Waxman, 2000 Mutation and sex in a competitive world. Nature 406: 399-404.
36. Peters, A. D., and P. D. Keightley, 2000 A test for epistasis among induced mutations in Caenorhabditis elegans. Genetics 156: 1635-1647.
37. Phillips, P. C., S. P. Otto and M. C. Whitlock, 2000 Beyond the average: the evolutionary importance of gene interactions and variability of epistatic effects, pp. 20-38 in Epistasis and the Evolutionary Process, edited by J. B. Wolf, E. D. Brodie III and M. J. Wade. Oxford University Press, Oxford.
38. Shimodaira, H., and M. Hasegawa, 1999 Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16: 1114-1116.
39. Smallwood, S., and S. A. Moyer, 1993 Promoter analysis of the vesicular stomatitis virus RNA polymerase. Virology 192: 254-263.
40. Sokal, R. S., and F. J. Rohlf, 1995 Biometry. Ed. 3. W. H. Freeman, New York.
41. Stillman, E. A., and M. A. Whitt, 1997 Mutational analyses of the intergenic dinucleotide and the transcriptional start sequence of vesicular stomatitis virus (VSV) define sequences required for efficient termination and initiation of VSV transcripts. J. Virol. 71: 2127-2137.
42. Stillman, E. A., and M. A. Whitt, 1998 The length and sequence composition of vesicular stomatitis virus intergenic regions affect mRNA levels and the site of transcript initiation. J. Virol. 72: 5565-5572.
43. Wichman, H. A., M. R. Badgett, L. A. Scott, C. M. Boulianne and J. J. Bull, 1999 Different trajectories of parallel evolution during viral adaptation. Science 285: 422-424.
44. Wright, S., 1931 Evolution in Mendelian populations. Genetics 16: 97-159.