Molecular dating in the evolution of vertebrate poxviruses

Intervirology

Volumn 54, Issue 5, 2011, Pages 253-260

  Babkin, Igor V ^a   Babkina, Irina N ^b  

^a INSTITUTE OF CHEMICAL BIOLOGY AND FUNDAMENTAL MEDICINE   (Russian Federation)

^b STATE RESEARCH CENTER OF VIROLOGY AND BIOTECHNOLOGY VECTOR   (Russian Federation)

Author keywords

Bayesian relaxed clock; DNA virus; Poxviridae; Viral evolution

Indexed keywords

ARTICLE; AT RICH SEQUENCE; CAPRIPOXVIRUS; FOWLPOX VIRUS; GENETIC CONSERVATION; GENUS; LEPORIPOXVIRUS; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; ORTHOPOXVIRUS; PHYLOGENY; POXVIRUS; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; VERTEBRATE; VIRUS GENE; VIRUS GENOME;

ANIMALS; CLUSTER ANALYSIS; DNA, VIRAL; EVOLUTION, MOLECULAR; HUMANS; PHYLOGENY; POXVIRIDAE; TIME FACTORS; VERTEBRATES;

AVIPOXVIRUS; CAPRIPOXVIRUS; DNA VIRUSES; LEPORIPOXVIRUS; ORTHOPOXVIRUS; POXVIRIDAE; SUIPOXVIRUS; VERTEBRATA; YATAPOXVIRUS;

EID: 84860390530     PISSN: 03005526     EISSN: 14230100     Source Type: Journal    
DOI: 10.1159/000320964     Document Type: Article

References (32)

1. Gubser C, Hue S, Kellam P, Smith GL: Poxvirus genomes: A phylogenetic analysis. J Gen Virol 2004; 85: 105-117.
2. Babkin IV, Shchelkunov SN: Molecular evolution of poxviruses. Genetika 2008; 44: 1029-1044.
3. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL-X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876-4882.
4. Huelsenbeck JP, Rannala B: Maximum likelihood estimation of phylogeny using stratigraphic data. Paleobiology 1997; 23: 174-180.
5. Posada D, Crandall KA: Modeltest: Testing the model of DNA substitution. Bioinformatics 1998; 14: 817-818.
6. Kumar S, Tamura K, Nei M: MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 2004; 5: 150-163.
7. Kishino H, Thorne JL, Bruno WJ: Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 2001; 18: 352-361.
8. Upton C, Slack S, Hunter AL, Ehlers A, Roper RL: Poxvirus orthologous clusters: Toward defining the minimum essential poxvirus genome. J Virol 2003; 77: 7590-7600.
9. Lefkowitz EJ, Wang C, Upton C: Poxviruses: Past, present and future. Virus Res 2006; 117: 105-118.
10. McLysaght A, Baldi PF, Gaut BS: Extensive gene gain associated with adaptive evolution of poxviruses. Proc Natl Acad Sci USA 2003; 100: 15655-15660.
11. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope M J: Universal trees based on large combined protein sequence data sets. Nat Genet 2001; 28: 281-285.
12. Anderson FE, Swofford DL: Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. Mol Phylogenet Evol 2004; 33: 440-451.
13. Shackelton LA, Holmes EC: The evolution of large DNA viruses: Combining genomic information of viruses and their hosts. Trends Microbiol 2004; 12: 458-465.
14. Condit RC, Niles EG: Regulation of viral transcription elongation and termination during vaccinia virus infection. Biochim Biophys Acta 2002; 1577: 325-336.
15. Broyles SS: Vaccinia virus transcription. J Gen Virol 2003; 84: 2293-2303.
16. Shchelkunov SN, Marennikova SS, Moyer RW: Orthopoxviruses Pathogenic for Humans. Berlin, Springer, 2005.
17. Traktman P: Poxvirus DNA replication; in Depamphilis ML (ed): DNA Replication in Eukaryotic Cells. Cold Spring Harbor, Cold Spring Harbor Laboratory, 1996, pp 775- 798.
18. Moss B: Poxviridae: The viruses and their replication; in Knipe DM, Howley PM (eds): Fields Virology. Philadelphia, Lippincott- Raven, 2001, pp 2849-2884.
19. Senkevich TG, White CL, Koonin EV, Moss B: Complete pathway for protein disulfide bond formation encoded by poxviruses. Proc Natl Acad Sci USA 2002; 99: 6667-6672.
20. Babkin IV, Shchelkunov SN: The time scale in poxvirus evolution. Mol Biol (Mosk) 2006; 40: 20-24.
21. Hughes AL, Irausquina S, Friedman R: The evolutionary biology of poxviruses. Infect Genet Evol 2010; 10: 50-59.
22. Babkina IN, Babkin IV, Li Y, Ropp S, Kline R, Damon IK, Esposito JJ, Sandakhchiev LS, Shchelkunov SN: Phylogenetic comparison of the genomes of different strains of variola virus. Dokl Biochem Biophys 2004; 398: 316-319.
23. Fenner F, Henderson DA, Arita I, Jezek Z, Ladnyi ID: Smallpox and Its Eradication. Geneva, WHO, 1988.
24. Gubser C, Smith GL: The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox. J Gen Virol 2002; 83: 855-872.
25. Institute of Medicine (USA): Committee on the Assessment of Future Scientific Needs for Live Variola Virus: Assessment of Future Scientific Needs for Live Variola Virus. Washington, National Academies Press, 1999.
26. Margoliash E: Primary structure and evolution of cytochrome C. Proc Natl Acad Sci USA 1965; 50: 672-679.
27. Drummond AJ, Ho SY, Phillips MJ, Rambaut A: Relaxed phylogenetics and dating with confidence. PLoS Biol 2006; 4:e88.
28. Li Y, Carroll DS, Gardner SN, Walsh MC, Vitalis EA, Damon IK: On the origin of smallpox: Correlating variola phylogenics with historical smallpox records. Proc Natl Acad Sci USA 2007; 104: 15787-15792.
29. Chang BSW, Donoghue MJ: Recreating ancestral proteins. Trends Ecol Evol 2000; 15: 109-114.
30. Esposito JJ, Sammons SA, Frace AM, Osborne JD, Glsen-Rasmussen M, Zhang M, Govil D, Damon IK, Kline R, et al: Genome sequence diversity and clues to the evolution of variola (smallpox) virus. Science 2006; 313: 807-812.
31. Jenkins GM, Rambaut A, Pybus OG, Holmes EC: Rates of molecular evolution in RNA viruses: A quantitative phylogenetic analysis. J Mol Evol 2002; 54: 156-165.
32. Kumar S, Hedges SB: A molecular timescale for vertebrate evolution. Nature 1998; 392: 917-920.