Analysis of host-parasite incongruence in papillomavirus evolution using importance sampling

Molecular Biology and Evolution

Volumn 27, Issue 6, 2010, Pages 1301-1314

  Shah, Seena D ^a   Doorbar, John ^a   Goldstein, Richard A ^a  

^a NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

Bayesian analysis; Host transfer; Importance sampling; Papillomavirus; Phylogenetic incongruence; Relaxed clock models

Indexed keywords

ARTICLE; BAYES THEOREM; EVOLUTION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC RECOMBINATION; HOST; HOST PARASITE INTERACTION; HUMAN; MOLECULAR CLOCK; NONHUMAN; PAPILLOMA VIRUS; PHYLOGENY; PORCUPINE; PRIMATE; SAMPLING; TIME PERCEPTION; VIRUS GENE;

ALPHAPAPILLOMAVIRUS; ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; GENES, VIRAL; HOST-PATHOGEN INTERACTIONS; HUMANS; MAMMALS; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINATION, GENETIC;

HYSTRICOGNATHI; MAMMALIA; PAPILLOMAVIRIDAE; PRIMATES;

EID: 77952862896     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq015     Document Type: Article

References (62)

1. Angulo M, Carvajal-Rodriguez A. 2007. Evidence of recombination within human alpha-papillomavirus. Virol J. 4:33.
2. Antonsson A, Hansson BG. 2002. Healthy skin of many animal species harbors papillomaviruses which are closely related to their human counterparts. J Virol. 76:12537-12542.
3. Antonsson A, McMillan NA. 2006. Papillomavirus in healthy skin of Australian animals. J Gen Virol. 87:3195-3200.
4. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. 2005. GenBank. Nucleic Acids Res. 33:D34-D38.
5. Bernard H-U. 1994. Coevolution of papillomaviruses with human populations. Trends Microbiol. 2:140-143.
6. Bininda-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. 2007. The delayed rise of present-day mammals. Nature 446:507-512.
7. Bloch N, Breen M, Spradbrow PB. 1994. Genomic sequences of bovine papillomaviruses in formalin-fixed sarcoids from Australian horses revealed by polymerase chain reaction. Vet Microbiol. 41:163-172.
8. Bogaert L, Martens A, Van Poucke M, Ducatelle R, De Cock H, Dewulf J, De Baere C, Peelman L, Gasthuys F. 2008. High prevalence of bovine papillomaviral DNA in the normal skin of equine sarcoid-affected and healthy horses. Vet Microbiol. 129:58-68.
9. Boshart M, Gissmann L, Ikenberg H, Kleinheinz A, Scheurlen W, zur Hausen H. 1984. A new type of papillomavirus DNA, its presence in genital cancer biopsies and in cell lines derived from cervical cancer. EMBO J. 3:1151-1157.
10. Bravo IG, Alonso A. 2004. Mucosal human papillomaviruses encode four different E5 proteins whose chemistry and phylogeny correlate with malignant or benign growth. J Virol. 78:13613-13626.
11. Bravo IG, Alonso A. 2007. Phylogeny and evolution of papilloma-viruses based on the E1 and E2 proteins. Virus Genes. 34:249-262.
12. Brooks DR. 1981. Hennig's parasitological method: a proposed solution. Syst Zool. 30:229-249.
13. Campo MS. 2002. Animal models of papillomavirus pathogenesis. Virus Res. 89:249-261.
14. Carvajal-Rodriguez A. 2008. Detecting recombination and diversifying selection in human alpha-papillomavirus. Infect Genet Evol. 8:689-692.
15. Castoe TA, de Koning AP, Kim HM, Gu W, Noonan BP, Naylor G, Jiang ZJ, Parkinson CL, Pollock DD. 2009. Evidence for an ancient adaptive episode of convergent molecular evolution. Proc Natl Acad Sci USA. 106:8986-8991.
16. Chambers G, Ellsmore VA, O'Brien PM, Reid SW, Love S, Campo MS, Nasir L. 2003. Association of bovine papillomavirus with the equine sarcoid. J Gen Virol. 84:1055-1062. (Pubitemid 36592596)
17. Chan S-Y, Bernard H-U, Ong C-K, Chan S-P, Hofmann B, Delius H. 1992. Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses. J Virol. 66:5714-5725.
18. Chan S-Y, Bernard H-U, Ratterree M, Birkebak TA, Faras AJ, Ostrow RS. 1997. Genomic diversity and evolution of papil-lomaviruses in rhesus monkeys. J Virol. 71:4938-4943.
19. Chan S-Y, Delius H, Halpern AL, Bernard H-U. 1995. Analysis of genomic sequences of 95 papillomavirus types: uniting typing, phylogeny, and taxonomy. J Virol. 69:3074-3083.
20. Chan S-Y, Ostrow RS, Faras AJ, Bernard H-U. 1997. Genital papillomaviruses (PVs) and epidermodysplasia verruciformis PVs occur in the same monkey species: implications for PV evolution. Virology 228:213-217.
21. Charleston MA. 1998. Jungles: a new solution to the host/parasite phylogeny reconciliation problem. Math Biosci. 149:191-223.
22. Danos O, Katinka M, Yaniv M. 1982. Human papillomavirus 1a complete DNA sequence: a novel type of genome organization among papovaviridae. EMBO J. 1:231-236.
23. de Villiers EM, Fauquet C, Broker TR, Bernard HU, zur Hausen H. 2004. Classification of papillomaviruses. Virology 324:17-27.
24. Doorbar J. 2005. The papillomavirus life cycle. J Clin Virol. 32(1 Suppl):S7-S15.
25. Doorbar J. 2006. Molecular biology of human papillomavirus infection and cervical cancer. Clin Sci (Lond). 110:525-541.
26. Drummond AJ, Ho SY, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88.
27. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
28. Drummond AJ, Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 7:214.
29. Durst M, Gissmann L, Ikenberg H, zur Hausen H. 1983. A papillomavirus DNA from a cervical carcinoma and its prevalence in cancer biopsy samples from different geographic regions. Proc Natl Acad Sci USA. 80:3812-3815.
30. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
31. Ferenczy A, Franco E. 2002. Persistent human papillomavirus infection and cervical neoplasia. Lancet Oncol. 3:11-16.
32. Garcia-Vallve S, Alonso A, Bravo IG. 2005. Papillomaviruses: different genes have different histories. Trends Microbiol. 13:514-521.
33. Gottschling M, Kohler A, Stockfleth E, Nindl I. 2007. Phylogenetic analysis of beta-papillomaviruses as inferred from nucleotide and amino acid sequence data. Mol Phylogenet Evol. 42:213-222.
34. Gottschling M, Stamatakis A, Nindl I, Stockfleth E, Alonso A, Bravo IG. 2007. Multiple evolutionary mechanisms drive papillomavirus diversification. Mol Biol Evol. 24:1242-1258.
35. Herbst LH, Lenz J, Van Doorslaer K, Chen Z, Stacy BA, Wellehan JF Jr., Manire CA, Burk RD. 2009. Genomic characterization of two novel reptilian papillomaviruses, Chelonia mydas papillomavirus 1 and Caretta caretta papillomavirus 1. Virology 383:131-135.
36. Ho GY, Burk RD, Klein S, Kadish AS, Chang CJ, Palan P, Basu J, Tachezy R, Lewis R, Romney S. 1995. Persistent genital human papillomavirus infection as a risk factor for persistent cervical dysplasia. J Natl Cancer Inst. 87:1365-1371.
37. Huelsenbeck JP, Bull JJ. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst Biol. 45:92-98.
38. Huelsenbeck JP, Rannala B, Yang Z. 1997. Statistical tests of host-parasite cospeciation. Evolution 51:410-419.
39. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
40. Huson DH, Bryant D. 2006. Application of phylogenetic networks in evolutionary studies. Mol Biol Evol. 23:254-267.
41. Legendre P, Desdevises Y, Bazin E. 2002. A statistical test for host-parasite coevolution. Syst Biol. 51:217-234.
42. Narechania A, Chen Z, DeSalle R, Burk RD. 2005. Phylogenetic incongruence among oncogenic genital alpha human papil-lomaviruses. J Virol. 79:15503-15510.
43. Ong CK, Chan SY, Campo MS, Fujinaga K, Mavromara-Nazos P, Labropoulou V, Pfister H, Tay SK, ter Meulen J, Villa LL. 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.
44. Otten N, von Tscharner C, Lazary S, Antczak DF, Gerber H. 1993. DNA of bovine papillomavirus type 1 and 2 in equine sarcoids: PCR detection and direct sequencing. Arch Virol. 132:121-131.
45. Page RDM. 1994. Parallel phylogenies: reconstructing the history of host-parasite assemblages. Cladistics 10:155-173.
46. Pfister H. 2003. Chapter 8: Human papillomavirus and skin cancer. J Natl Cancer Inst Monogr. 31:52-56.
47. Rector A, Lemey P, Tachezy R, et al. (15 co-authors). 2007. Ancient papillomavirus-host co-speciation in Felidae. Genome Biol. 8:R57.
48. Rector A, Stevens H, Lacave G, et al. (13 co-authors). 2008. Genomic characterization of novel dolphin papillomaviruses provides indications for recombination within the Papillomaviridae. Virology 378:151-161.
49. Rous P, Beard JW. 1935. The progression to carcinoma of virus-induced rabbit papillomas (Shope). J Exp Med. 62:523-554.
50. Sanderson MJ. 2003. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19:301-302.
51. Schiffman M, Herrero R, Desalle R, et al. (18 co-authors). 2005. The carcinogenicity of human papillomavirus types reflects viral evolution. Virology 337:76-84.
52. Srinivasan R. 2002. Importance sampling: applications in communications and detection. Berlin (Germany): Springer-Verlag.
53. Suyama M, Torrents D, Bork P. 2006. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34:W609-W612.
54. Tachezy R, Duson G, Rector A, Jenson AB, Sundberg JP, Van Ranst M. 2002. Cloning and genomic characterization of Felis domesticus papillomavirus type 1. Virology 301:313-321.
55. Tachezy R, Rector A, Havelkova M, Wollants E, Fiten P, Opdenakker G, Jenson B, Sundberg J, Van Ranst M. 2002. Avian papillomaviruses: the parrot Psittacus erithacus papillomavirus (PePV) genome has a unique organization of the early protein region and is phylogenetically related to the chaffinch papillomavirus. BMC Microbiol. 2:19.
56. Van Ranst M, Kaplan JB, Sundberg JP, Burk RD. 1995. Molecular evolution of the human papillomaviruses. In: Gibbs AJ, Calisher CH, Garcia-Arenal F, editors. Molecular basis of virus evolution. Cambridge: Cambridge University Press. p. 455-476.
57. Varsani A, van der Walt E, Heath L, Rybicki EP, Williamson AL, Martin DP. 2006. Evidence of ancient papillomavirus recombination. J Gen Virol. 87:2527-2531.
58. Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
59. Yang Z. 2006. Computational molecular evolution. Oxford: Oxford University Press.
60. Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 24:1586-1591
61. zur Hausen H. 1989. Papillomaviruses as carcinomaviruses. Adv Viral Oncol. 8:26.
62. zur Hausen H. 2000. Papillomaviruses causing cancer: evasion from host-cell control in early events in carcinogenesis. J Natl Cancer Inst. 92:690-698.