Site stripping based on likelihood ratio reduction is a useful tool to evaluate the impact of non-clock-like behavior on viral phylogenetic reconstructions

FEMS Immunology and Medical Microbiology

Volumn 39, Issue 2, 2003, Pages 125-132

  Lemey, Philippe ^a   Salemi, Marco ^a   Wang, Bin ^b   Duffy, Margaret ^c   Hall, William H ^c   Saksena, Nitin K ^b   Vandamme, Anne Mieke ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b UNIVERSITY OF SYDNEY   (Australia)

^c UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

Dating; Evolutionary rate; Hepatitis C virus; Human immunodeficiency virus; Molecular clock; TipDate

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENETIC VARIABILITY; HEPATITIS C VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE CONSTRUCTION METHOD; PRIORITY JOURNAL; UNINDEXED SEQUENCE; VIRAL GENETICS; VIRUS STRAIN; VIRUS TRANSMISSION;

EID: 0242475196     PISSN: 09288244     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0928-8244(03)00239-6     Document Type: Article

References (34)

1. Zuckerland, E. and Pauling, L. (1962) Molecular disease, evolution, and genetic heterogeneity. In: Horizons in Biochemistry (Kasha, M. and Pullman, B., Eds.), pp. 189-225. Academic Press, New York.
2. Gillespie, J.H. (1991) The Causes of Molecular Evolution. Oxford University Press, Oxford.
3. Ohta T., Kimura M. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1:1971;18-25.
4. Langley, C.H. and Fitch, W.M. (1973) The constancy of evolution: a statistical analysis of a and b haemoglobins, cytochrome c, and fibrinopeptide A. In: Genetic Structure of Populations (Morton, N.E., Ed.), pp. 246-262. University of Hawaii Press, Honolulu, HI.
5. Takezaki N., Rzhetsky A., Nei M. Phylogenetic test of the molecular clock and linearized trees. Mol. Biol. Evol. 12:1995;823-833.
6. Korber B., Theiler J., Wolinsky S. Limitations of a molecular clock applied to considerations of the origin of HIV-1. Science. 280:1998;1868-1871.
7. Rodriguez-Trelles F., Tarrio R., Ayala F.J. Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH. Proc. Natl. Acad. Sci. USA. 98:2001;11405-11410.
8. Goudsmit J., Lukashov V.V. Dating the origin of the HIV-1 subtypes. Nature. 400:1999;325-326.
9. Schierup M.H., Hein J. Recombination and the molecular clock. Mol. Biol. Evol. 17:2000;1578-1579.
10. Korber B., Muldoon M., Theiler J., Gao F., Gupta R., Lapedes A., Hahn B.H., Wolinsky S., Bhattacharya T. Timing the ancestor of the HIV-1 pandemic strains. Science. 288:2000;1789-1796.
11. Sharp P.M., Bailes E., Gao F., Beer B.E., Hirsch V.M., Hahn B.H. Origins and evolution of AIDS viruses: estimating the time-scale. Biochem. Soc. Trans. 28:2000;275-282.
12. Salemi M., Strimmer K., Hall W.W., Duffy M., Delaporte E., Mboup S., Peeters M., Vandamme A.M. Dating the common ancestor of SIVcpz and HIV-1 group M and the origin of HIV-1 subtypes using a new method to uncover clock-like molecular evolution. FASEB J. 15:2001;276-278.
13. Sharp P.M., Bailes E., Chaudhuri R.R., Rodenburg C.M., Santiago M.O., Hahn B.H. The origins of acquired immune deficiency syndrome viruses: where and when? Phil. Trans. R. Soc. Lond. B Biol. Sci. 356:2001;867-876.
14. Gojobori T., Moriyama E.N., Kimura M. Molecular clock of viral evolution, and the neutral theory. Proc. Natl. Acad. Sci. USA. 87:1990;10015-10018.
15. Suzuki Y., Yamaguchi-Kabata Y., Gojobori T. Nucleotide substitution rates of HIV-1. Aids Res. 2:2000;39-47.
16. Jenkins G.M., Rambaut A., Pybus O.G., Holmes E.C. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J. Mol. Evol. 54:2002;156-165.
17. Rambaut A. Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies. Bioinformatics. 16:2000;395-399.
18. Yoder A.D., Yang Z. Estimation of primate speciation dates using local molecular clocks. Mol. Biol. Evol. 17:2000;1081-1090.
19. Soltis P.R., Soltis D.E., Savolainen V., Crane P.R., Barraclough T.G. Rate heterogeneity among lineages of tracheophytes: Integration of molecular and fossil data and evidence for molecular living fossils. Proc. Natl. Acad. Sci. USA. 82:2002;4430-4435.
20. Sanderson M. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14:1997;1218-1231.
21. Rambaut A., Bromham L. Estimating divergence dates from molecular sequences. Mol. Biol. Evol. 15:1998;442-448.
22. Thorne J.L., Kishino H., Painter I.S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1998;1647-1657.
23. Huelsenbeck J.P., Larget B., Swofford D. A compound poisson process for relaxing the molecular clock. Genetics. 154:2000;1879-1892.
24. Masciotra S., Owen S.M., Rudolph D., Yang C., Wang B., Saksena N., Spira T., Dhawan S., Lal R.B. Temporal relationship between V1V2 variation, macrophage replication, and coreceptor adaptation during HIV-1 disease progression. AIDS. 16:2002;1887-1898.
25. McAllister J., Casino C., Davidson F., Power J., Lawlor E., Yap P.L., Simmonds P., Smith D.B. Long-term evolution of the hypervariable region of hepatitis C virus in a common-source-infected cohort. J. Virol. 72:1998;4893-4905.
26. Duffy M., Salemi M., Sheehy N., Vandamme A.-M., Hegarty J., Curry M., Nolan N., Kelleher D., McKiernan S., Hall W.W. Comparative rates of nucleotide sequence variation in the hypervariable region of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection. Virology. 302:2002;354-364.
27. Casino C., McAllister J., Davidson F., Power J., Lawlor E., Yap P.L., Simmonds P., Smith D.B. Variation of hepatitis C virus following serial transmission: multiple mechanisms of diversification of the hypervariable region and evidence for convergent genome evolution. J. Gen. Virol. 80:1999;717-725.
28. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
29. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:1998;817-818.
30. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:1997;555-556.
31. Yang Z., Nielsen R., Goldman N., Pedersen A.M. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics. 155:2000;431-449.
32. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. Mol. Evol. 17:1981;368-376.
33. Wu C.I., Li W.H. Evidence for higher rates of nucleotide substitution in rodents than in man. Proc. Natl. Acad. Sci. USA. 82:1985;1741-1745.
34. Bromham L., Penny D., Rambaut A., Hendy M.D. The power of relative rates tests depends on the data. J. Mol. Evol. 5:2000;296-301.