Exceptional convergent evolution in a virus

Genetics

Volumn 147, Issue 4, 1997, Pages 1497-1507

  Bull, J J ^a,b   Badgett, M R ^a   Wichman, H A ^b   Huelsenbeck, J P ^c   Hillis, D M ^a,d   Gulati, A ^a   Ho, C ^a   Molineux, I J ^a  

^a Department of Zoology ^*

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c UNIVERSITY OF IDAHO   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIOPHAGE; EVOLUTION; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; PHYLOGENY; PRIORITY JOURNAL; VIRAL GENETICS; VIRUS GENOME; VIRUS REPLICATION;

BACTERIOPHAGE PHI X 174; DIRECTED MOLECULAR EVOLUTION; GENOME, VIRAL; MODELS, GENETIC; PHYLOGENY;

COLIPHAGE PHIX174;

EID: 0030823001     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (38)

1. BEINTEMA, J. J., V?. GAASTRA, J. A. LENSTRA, G. W. WELLING and W. M. FITCH, 1977 The molecular evolution of pancreatic ribonuclease.J. Mol. Evol. 10: 49-71.
2. BORMAN, A. M., S. PAULOUS and F. CLAVEL, 1996 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. 77: 419-426.
3. BULL.J.J., C.W. CUNXINGIIAM, I.J. MOLINEUX, M. R. BADGETT and D. M. HILLIS, 1993 Experimental molecular evolution of bacteriophage T7. Evolution 47: 993-1007.
4. CROW, J. F., and KIMURA, M., 1970 An Introduction to Population Genetics Theory. Harper and Row, New York.
5. CUNNINGHA-M, C. W., K.JENG.J. HUSTI, M. BADGETT, I.J. MOLINEUX et al., 1997 Parallel molecular evolution of deletions and nonsense mutations in bacteriophage T7. Mol. Biol. Evol. 14: 113116.
6. DOOLITTLE, R. F., 1994 Convergent evolution: the need to be explicit. Trends Biochem. Sci. 19: 15-18.
7. DO-WELL, C. E., 1980 Growth of bacteriophage φX 174 at elevated temperatures. J. Gen. Virol. 49: 41-50.
8. DYKHUIZEN, D., 1993 Chemostats used for studying natural selection and adaptive evolution. Methods Enzymol. 224: 613-631.
9. FELSENSTEIN, J., 1978 Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27: 401-410.
10. FELSENSTEIN, J. 1993 PHYLIP (Phytogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
11. FUNATSU, G., and H. G. WITTMANN, 1972 Ribosomal proteins. 33. Location of amino-acid replacements in protein S12 isolated from Escherichia coli mutants resistant to streptomycin. J. Mol. Biol. 68: 547-550.
12. GODSON, G. N., 1978 The other isomeric phages, pp. 103-112 in The Single-Stranded DA'A Phages, edited by D. T. DENHARDT, D. DRESSLER and D. S. RAY. Cold Spring Harbor Laboratory, New York.
13. HASEGAWA, M., H. KISIIINO and T.A. YANO, 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 22: 160-174.
14. HEDGES, S.B., and L. R. MAXSON, 1996 Molecules and morphology in amniote phylogeny. Mol. Phylogenet. Evol. 6:312-314.
15. HEISIG, P., 1995 Genetic evidence for a role of parC mutations in development of high-level fluoroquinoline resistance in Escherichia coli. Antimicrob. Agents Chemother. 40: 879-885.
16. HILUS, D. M., J.J. BULL, M. E. WHITE, M. R. BADGETT and I.J. MOLINEUX, 1992 Experimental phylogenetics: laboratory construction of a known phylogeny. Science 255: 589-592.
17. HILLIS, D. M.J. P.HUELSENBECKandC. W.CUNNINGIIAM,1694 Application and accuracy of molecular phytogenies. Science 264: 671 677.
18. INCARDONA, N. L., and U. R. MüLLER, 1985 Eclipse kinetics as a probe of quaternary structure in bacteriophage øX 174. J. Mol. Biol. 181: 479-486.
19. KORONA, R., C. H. NAKATSU, L.J. FoRNEYand R. LENSKI, 1994 Evidence for multiple adaptive peaks from populations of bacteria evolving in a structured habitat. Proc. Natl. Acad. Sci. USA 91:9037-9041.
20. LANDE R., 1983 The response to selection on major and minor affecting a metrical trait. Heredity 50: 47-65.
21. LI, W-H., 1997 Molecular Evolution. Sinauer, Sunderland, MA.
22. MOLLA, A., M. KORXEYEVA, Q. GAO, S. VASAVANONDA, P. J. SCHIPPER et al., 1996 Ordered accumulation of mutations in HIV protease confers resistance to ritonavir. Nature Med. 2: 760-766.
23. MOLLER, U. R., and R. D. WELLS, 1980 Intercistronic regions in φX 174 DNA II. Biochemical and biological analysis of mutants with altered intercistronic regions between genes J and F. J. Mol. Biol. 141: 25-41.
24. PEACOCK, D., and D. BOULTER, 1975 Use of amino acid sequence data in phylogeny and evaluation of methods using computer simulation. J. Mol. Biol. 95: 513-527.
25. ROMERO-HERRERA, A. E., N. LlESKA, M. GOODMAN and E. L. Sl.MONS, 1979 The use of amino acid sequence analysis in assessing evolution. Biochimie 61: 767-779.
26. SANDERSON, M.J., and M.J. DONOGHUE, 1996 The relationship between homoplasy and confidence in a phylogenetic tree, pp. 6789 in Homoplasy: The Recurrence of Similarity in Evolution, edited by M.J. SANDERSON and L. HUFFORD. Academic Press, New York.
27. SäNGER, F., G. M. AIR, B. G. BARRELL, N. L. BROIVN, A. R. COULSO.V et al., 1977 Nucleotide sequence of bacteriophage φX 174 DNA. Nature 265: 687-695.
28. SCHRäG, S.J., and V. PERROT, 1996 Reducing antibiotic resistance. Nature 381: 120-121.
29. SWOFFORD, D. L., 1997 PAUP: Phylogenetic Analysis Using Parsimony ( and other methods ), version 4.0. Sinauer Associates, Sunderland, MA.
30. VlZAN, J. L., C. HERNANDEZ-ClIICO, I. DEL CASTILLO and F. MORENO, 1991 The peptide antibiotic microcin B17 induces doublestrand cleavage of DNA mediated by E. coli DNA gyrase. EMBO J. 10: 467-476.
31. WEISBLUM, B., 1995 Erythromycin resistance by ribosome modification. Antimicrob. Agents Chemother. 39: 577-585.
32. WELLS, R. S., 1996 Excessive homoplasy in an evolutionarily constrained protein. Proc. R. Soc. Lond. B 263: 393-400.
33. YANG, Z, 1993 Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10: 1396-1401.
34. YANG, Z, 1994 Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-314.
35. YANG, Z., 1996a Phylogenetic Analysis by Maximum Likelihood (PAML), version 1.2. Department of Integrative Biology, University of California, Berkeley.
36. YANG, Z., 1996b Among site rate variation and its impact on phylogenetic analysis. TREE 11: 367-372.
37. YIN. J., 1993 Evolution of bacteriophage T7 in a growing plaque. J. Bacteriol. 175: 1272-1277.
38. YOSHIDA, H., M. NAKA.MURA, M. BOGAKI, H. ITO, T. KOJIMA et al. 1993 Mechanism of action of quinolones against Eslierichia coli DNA gyrase. Antimicrob. Agents Chemother. 37: 839-845.