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Philosophical Transactions of the Royal Society B: Biological Sciences logoLink to Philosophical Transactions of the Royal Society B: Biological Sciences
. 2000 Nov 29;355(1403):1677–1684. doi: 10.1098/rstb.2000.0731

Experimental evolution recapitulates natural evolution.

H A Wichman 1, L A Scott 1, C D Yarber 1, J J Bull 1
PMCID: PMC1692893  PMID: 11127915

Abstract

Genomes of the closely related bacteriophages phiX174 and S13 are 5386 bases long and differ at 114 nucleotides, affecting 28 amino acids. Both parental phages were adapted to laboratory culture conditions in replicate lineages and analysed for nucleotide changes that accumulated experimentally Of the 126 experimental substitutions, 90% encoded amino-acid changes, and 62% of the substitutions occurred in parallel in more than one experimental line. Furthermore, missense changes at 12 of the experimental sites were at residues differing between the parental phages; in ten cases the phiX174 experimental lineages were convergent with the S13 parent, or vice versa, at both the nucleotide and amino-acid levels. Convergence at a site was even obtained in both directions in three cases. These results point to a limited number of pathways taken during evolution in these viruses, and also raise the possibility that much of the amino-acid variation in the natural evolution of these viruses has been selected.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Borman A. M., Paulous S., Clavel F. Resistance of human immunodeficiency virus type 1 to protease inhibitors: selection of resistance mutations in the presence and absence of the drug. J Gen Virol. 1996 Mar;77(Pt 3):419–426. doi: 10.1099/0022-1317-77-3-419. [DOI] [PubMed] [Google Scholar]
  2. Bull J. J., Badgett M. R., Wichman H. A., Huelsenbeck J. P., Hillis D. M., Gulati A., Ho C., Molineux I. J. Exceptional convergent evolution in a virus. Genetics. 1997 Dec;147(4):1497–1507. doi: 10.1093/genetics/147.4.1497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bush R. M., Bender C. A., Subbarao K., Cox N. J., Fitch W. M. Predicting the evolution of human influenza A. Science. 1999 Dec 3;286(5446):1921–1925. doi: 10.1126/science.286.5446.1921. [DOI] [PubMed] [Google Scholar]
  4. Crill W. D., Wichman H. A., Bull J. J. Evolutionary reversals during viral adaptation to alternating hosts. Genetics. 2000 Jan;154(1):27–37. doi: 10.1093/genetics/154.1.27. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cunningham C. W., Jeng K., Husti J., Badgett M., Molineux I. J., Hillis D. M., Bull J. J. Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. Mol Biol Evol. 1997 Jan;14(1):113–116. doi: 10.1093/oxfordjournals.molbev.a025697. [DOI] [PubMed] [Google Scholar]
  6. Drake J. W. A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci U S A. 1991 Aug 15;88(16):7160–7164. doi: 10.1073/pnas.88.16.7160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Ekechukwu M. C., Fane B. A. Characterization of the morphogenetic defects conferred by cold-sensitive prohead accessory and scaffolding proteins of phi X174. J Bacteriol. 1995 Feb;177(3):829–830. doi: 10.1128/jb.177.3.829-830.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fane B. A., Hayashi M. Second-site suppressors of a cold-sensitive prohead accessory protein of bacteriophage phi X174. Genetics. 1991 Aug;128(4):663–671. doi: 10.1093/genetics/128.4.663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fane B. A., Shien S., Hayashi M. Second-site suppressors of a cold-sensitive external scaffolding protein of bacteriophage phi X174. Genetics. 1993 Aug;134(4):1003–1011. doi: 10.1093/genetics/134.4.1003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ffrench-Constant R. H. The molecular and population genetics of cyclodiene insecticide resistance. Insect Biochem Mol Biol. 1994 Apr;24(4):335–345. doi: 10.1016/0965-1748(94)90026-4. [DOI] [PubMed] [Google Scholar]
  11. Fitch W. M., Bush R. M., Bender C. A., Cox N. J. Long term trends in the evolution of H(3) HA1 human influenza type A. Proc Natl Acad Sci U S A. 1997 Jul 22;94(15):7712–7718. doi: 10.1073/pnas.94.15.7712. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Huang W., Petrosino J., Hirsch M., Shenkin P. S., Palzkill T. Amino acid sequence determinants of beta-lactamase structure and activity. J Mol Biol. 1996 May 17;258(4):688–703. doi: 10.1006/jmbi.1996.0279. [DOI] [PubMed] [Google Scholar]
  13. Lau P. C., Spencer J. H. Nucleotide sequence and genome organization of bacteriophage S13 DNA. Gene. 1985;40(2-3):273–284. doi: 10.1016/0378-1119(85)90050-2. [DOI] [PubMed] [Google Scholar]
  14. McKenna R., Ilag L. L., Rossmann M. G. Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A. J Mol Biol. 1994 Apr 15;237(5):517–543. doi: 10.1006/jmbi.1994.1253. [DOI] [PubMed] [Google Scholar]
  15. Palzkill T., Botstein D. Probing beta-lactamase structure and function using random replacement mutagenesis. Proteins. 1992 Sep;14(1):29–44. doi: 10.1002/prot.340140106. [DOI] [PubMed] [Google Scholar]
  16. Ronen A., Rahat A. Mutagen specificity and position effects on mutation in T4rII nonsense sites. Mutat Res. 1976 Jan;34(1):21–34. doi: 10.1016/0027-5107(76)90258-x. [DOI] [PubMed] [Google Scholar]
  17. Sanger F., Air G. M., Barrell B. G., Brown N. L., Coulson A. R., Fiddes C. A., Hutchison C. A., Slocombe P. M., Smith M. Nucleotide sequence of bacteriophage phi X174 DNA. Nature. 1977 Feb 24;265(5596):687–695. doi: 10.1038/265687a0. [DOI] [PubMed] [Google Scholar]
  18. Stewart C. B., Wilson A. C. Sequence convergence and functional adaptation of stomach lysozymes from foregut fermenters. Cold Spring Harb Symp Quant Biol. 1987;52:891–899. doi: 10.1101/sqb.1987.052.01.097. [DOI] [PubMed] [Google Scholar]
  19. Treves D. S., Manning S., Adams J. Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. Mol Biol Evol. 1998 Jul;15(7):789–797. doi: 10.1093/oxfordjournals.molbev.a025984. [DOI] [PubMed] [Google Scholar]
  20. Wichman H. A., Badgett M. R., Scott L. A., Boulianne C. M., Bull J. J. Different trajectories of parallel evolution during viral adaptation. Science. 1999 Jul 16;285(5426):422–424. doi: 10.1126/science.285.5426.422. [DOI] [PubMed] [Google Scholar]

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