Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees

Journal of Molecular Evolution

Volumn 44, Issue 2, 1997, Pages 199-206

  Ong, Chi Keong ^a   Nee, Sean ^a   Rambaut, Andrew ^a   Bernard, Hans Ulrich ^b   Harvey, Paul H ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Molecular clock; Papillomaviruses; Phylogeny; Population history; Transmission dynamics

Indexed keywords

ARTICLE; DATA BASE; NONHUMAN; OPEN READING FRAME; PAPILLOMA VIRUS; PHYLOGENY; VIRUS TRANSMISSION;

CODON; DNA, VIRAL; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; MOUTH MUCOSA; OPEN READING FRAMES; PAPILLOMAVIRIDAE; PHYLOGENY; SKIN;

EID: 0031055633     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006136     Document Type: Article

References (40)

1. Archie JW (1989a) A randomisation test for phylogenetic data in systematic data. Syst Zool 38:239-252
2. Archie JW (1989b) Phylogenies in plant families: a demonstration of phylogenetic randomness in DNA sequence data derived from proteins. Evolution 43:1796-1800
3. Bernard HU, Chan SY, Delius H (1994a) Evolution of Papillomaviruses. Curr Top Microbiol Immunol 186:33-54
4. Bernard H-U, Chan SY, Manos MM, Ong CK, Villa LL, Delius H, Peyton CL, Bauer HM, Wheeler CM (1994b) Identification and assessment of known and novel human papillomaviruses by polymerase chain reaction, restriction digest fingerprinting, nucleotide sequence and phylogenetic algorithms. J Infect Dis 170:1077-1085
5. Campo MS, Moar MH, Jarrett WHF, Laird HM (1980) A new papillomavirus associated with alimentary cancer in cattle. Nature 286:180-182
6. Chan SY, Ho L, Ong CK, Chow V, Drescher B, Duerst M, ter Meulen J, Villa LL, Luande J, Mgaya HN, Bernard H-U (1992a) Molecular variants of human papillomavirus-type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind. J Virol 66:2057-2066
7. Chan SY, Bernard H-U, Ong CK, Chan SP, Hoffman B, Delius H (1992b) Phylogenetic analysis of 48 papillomaviruses and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses. J Virol 66:5714-5725
8. Chan SY, Delius H, Halpem AL, Bernard H-U (1995) Analysis of genomic sequences of 95 papillomavirus types: uniting typing, phylogeny, and taxonomy. J Virol 69:3074-3083
9. Cox DR, Lewis PAW (1966) The statistical analysis of series of events. Methuen, London
10. de Villiers E-M (1994) Human pathogenic papillomavirus types: an update. Curr Top Microbiol Immunol 186:1-12
11. Delius H, Hoffmann B (1994) Primer-directed sequencing of human papillomavirus types. Curr Top Microbiol Immunol 186:13-31
12. Faith DP, Cranston PS (1991) Could a cladogram this short have arisen by chance alone?: On a permutation test for cladistic structure. Cladistics 7:1-28
13. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368-376
14. Felsenstein J (1982) Numerical methods for inferring evolutionary trees. Q Rev Biol 57:379-404
15. Galloway DA (1994) Editorial: navigating the descent into papillomavirus hell. J Infect Dis 170:1075-1076
16. Goldman N (1993) Statistical tests of models of DNA substitution. J Mol Evol 36:182-198
17. Harvey PH (1996) Phylogenies for ecologists: the 1995 Tansley lecture. J Anim Ecol 65:255-263
18. Harvey PH, Holmes EC, Rambaut A, Nee S (1995) How to reveal viral population history from gene sequence data. In: Schwyzer M, Ackermann M (eds) Immunobiology of viral infections. Fondation Mérieux, pp 1-8
19. Hillis DM, Huelsenbeck JP (1992) Signal, noise, and reliability in molecular phylogenetic analyses. J Hered 83:189-195
20. Ho L, Tay SK, Chan SY, Bernard H-U (1993a) Sequence variants of human papillomavirus type 16 from couples suggest sexual transmission with low infectivity and polyclonality in genital neoplasia. J Infect Dis 168:803-809
21. Ho L, Chan SY, Burk RD, Das BC, Fujinaga K, Icenogle JP, Kahn T, Kiviat N, Lancaster W, Mavromara-Nazos P, Labropoulou V, Mitrani-Rosenbaum S, Norrild B, Pillai MR, Stoerker J, Syrjaenen K, Syrjaenen S, Tay SK, Villa LL, Wheeler CM, Williamson A-L, Bernard H-U (1993b) The genetic drift of human papillomavirus type 16 is a means of reconstructing prehistoric viral spread and the movement of ancient human populations. J Virol 67:6413-6423
22. Holmes EC, Nee S, Rambaut A, Garnett GP, Harvey PH (1995) Revealing the history of infectious disease epidemics through phylogenetic trees. Philos Trans R Soc Lond Biol 349:33-40
23. Myers G, Bernard H-U, Delius H, Favre M, Icenogle J, van Ranst M, Wheeler C (1994) Human papillomaviruses 1994. In: Wheeler C (ed) A compilation and analysis of nucleic and amino acid sequences. Los Alamos National Laboratory, Los Alamos, NM, pp III-3
24. Nee S, Holmes EC, Harvey PH (1995) Inferring population history from molecular phylogenies. Philos Trans R Soc Lond Biol 349:25-31
25. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) fastDNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10:41-48
26. Ong CK, Chan SY, Campo MS, Fujinaga K, Mavromara-Nazos P, Labropoulou V, Pfister H, Tay SK, ter Meulen J, Villa LL, Bernard H-U (1993) Evolution of human papillomavirus type 18: an ancient phylogenetic root in Africa and intratype diversity reflect coevolution with human ethnic groups. J Virol 67:6424-6431
27. Ong CK, Nee S, Rambaut A, Harvey PH (1996) Interring the population history of an epidemic from a phylogenetic tree. J Theor Biol 182:173-178
28. Orth (1994) Papillomaviruses- human. In: Webster RG, Granoff A (eds) Enclyclopedia of virology, vol 2. Academic Press, London, pp 1013-1021
29. Rambaut A, Harvey PH, Nee S (in press a) End-Epi: an application for reconstructing phylogenetic and population processes from molecular sequences. Comput Appl Biosci
30. Rambaut A, Grassly N, Nee S, Harvey PH (in press b) Bi-De: an application for simulating phylogenetic processes. Comput Appl Biosci
31. Shope RE, Hurst EW (1933) Infectious papillomatosis of rabbits. J Exp Med 68:607-624
32. Sundberg JP (1987) Papillomavirus infections in animals. In: Syrjaenen K, Gissmann L, Koss LG (eds) Papillomaviruses and human disease. Springer Verlag, Berlin, pp 40-103
33. Swofford DL (1993) Phylogenetic analysis using parsimony: PAUP, version 3.1. Illinois Natural History Survey, Champaign, IL
34. Syrjaenen KJ, Gissman L, Koss LG (1987) Papillomaviruses and human disease. Springer-Verlag, Berlin
35. van Ranst M, Kaplan JB, Burk RD (1992) Phylogenetic classification of human papillomaviruses: correlation with clinical manifestations. J Gen Virol 73:2653-1660
36. van Ranst M, Tachezy AR, Burk RD (1994) Human papillomavirus sequences: what is in stock? Papillomavirus Rep 5:65-75
37. Yang ZH, Goldman N, Friday A (1995a) Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst Biol 44:384-399
38. Yang ZH, Luder IJ, Lin HG (1995b) Molecular evolution of the Hepatitis B virus genome. J Mol Evol 41:587-596
39. Zanotto PM de A, Gould AG, Gao GF, Harvey PH, Holmes EC (1996) Population dynamics of flaviviruses revealed by molecular phylogenies. Proc Natl Acad Sci USA 93:548-553
40. zur Hausen H (1991) Viruses in human cancers. Science 254:1167-1173