Analysis of the Evolutionary Relationships of HIV-1 and SIVcpz Sequences Using Bayesian Inference: Implications for the Origin of HIV-1

Molecular Biology and Evolution

Volumn 20, Issue 12, 2003, Pages 1986-1996

  Paraskevis, D ^a   Lemey, P ^a   Salemi, M ^a   Suchard, M ^b   Van De Peer, Y ^c   Vandamme, A M ^a  

^a REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

Author keywords

Bayesian inference; Evolution; HIV; SIVcpz

Indexed keywords

ANALYTIC METHOD; ARTICLE; BAYES THEOREM; BAYESIAN INFERENCE; BAYESIAN MULTIPLE CHANGE POINT MODEL; BAYESIAN SCANNING; BOOTSCANNING ANALYSIS; CROSSING OVER; GENETIC RECOMBINATION; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PAN TROGLODYTES; SIMIAN IMMUNODEFICIENCY VIRUS; STATISTICAL MODEL; VIRUS ISOLATION; VIRUS STRAIN;

ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; HIV-1; LIKELIHOOD FUNCTIONS; MODELS, BIOLOGICAL; MULTIGENE FAMILY; PAN TROGLODYTES; PHYLOGENY; RECOMBINATION, GENETIC; SIMIAN IMMUNODEFICIENCY VIRUS;

HUMAN IMMUNODEFICIENCY VIRUS; HUMAN IMMUNODEFICIENCY VIRUS 1; PAN TROGLODYTES; PAN TROGLODYTES TROGLODYTES; RNA VIRUSES; SIMIAE; SIMIAN IMMUNODEFICIENCY VIRUS; TROGLODYTES; TROGLODYTES TROGLODYTES;

EID: 0346095401     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msg207     Document Type: Article

References (36)

1. Bailes, E., F. Gao, F. Bibollet-Ruche, V. Courgnard, M. Peeters, P. A. Marx, B. H. Hahn, and P. M. Sharp. 2003. Hybrid origin of SIV in chimpanzees. Science 300:1713.
2. Beer, B. E., E. Bailes, G. Dapolito, et al. (12 co-authors). 2000. Patterns of genomic sequence diversity among their simian immunodeficiency viruses suggest that L'Hoest monkeys (Cercopithecus lhoesti) are a natural lentivirus reservoir. J. Virol. 74:3892-3898.
3. Beer, B. E., B. T. Foley, C. L. Kuiken, Z. Tooze, R. M. Goeken, C. R. Brown, J. Hu, M. S. Claire, B. T. Korber, and V. M. Hirsch. 2001. Characterization of novel simian immunodeficiency viruses from red-capped mangabeys from Nigeria (SIVrcmNG409 and -NG411). J. Virol. 75:12014-12027.
4. Bibollet-Ruche, F., A. Galat-Luong, G. Cuny, P. Sarni-Manchado, G. Galat, J. P. Durand, X. Pourrut, and F. Veas. 1996. Simian immunodeficiency virus infection in a patas monkey (Erythrocebus patas): evidence for cross-species transmission from African green monkeys (Cercopithecus aethiops sabaeus) in the wild. J. Gen. Virol. 77:773-781.
5. Chen, Z., P. Telfier, A. Gettie, P. Red, L. Zhang, D. D. Ho, and P. A. Marx. 1996. Genetic characterization of new West African simian immunodeficiency virus SIVsm: geographic clustering of household-derived SIV strains with human immunodeficiency virus type 2 subtypes and genetically diverse viruses from a single feral sooty mangabey troop. J. Virol. 70:3617-3627.
6. Corbet, S., M. C. Müller-Trutwin, P. Versmisse, et al. (12 co-authors). 2000. env sequences of simian immunodeficiency viruses from chimpanzees in Cameroon are strongly related to those of human immunodeficiency virus group N from the same geographic area. J. Virol. 74:529-534.
7. Courgnaud, V., M. Salemi, X. Pourrut, et al. (11 co-authors). 2002. Characterization of a novel simian immunodeficiency virus with a vpu gene from greater spot-nosed monkeys (Cercopithecus nictitans) provides new insights into simian/ human immunodeficiency virus phylogeny. J. Virol. 76:8298-8309.
8. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17:368-376.
9. -. 1984. Distance methods for inferring phylogenies: a justification. Evolution 38:16-24.
10. Gao, F., E. Bailes, D. L. Robertson, et al. (12 co-authors). 1999. Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature 397:436-441.
11. Goldman, N. 1993. Statistical tests of models of DNA substitution. J. Mol. Evol. 36:182-198.
12. Hahn, B. H., G. M. Shaw, K. M. De Cock, and P. M. Sharp. 2000. AIDS as a zoonosis: scientific and public health implications. Science 287:607-614.
13. Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
14. Husmeier D., and F. Wright. 2001. Detection of recombination in DNA multiple alignments with hidden Markov models. J. Computat. Biol. 8:401-427.
15. -. 2002. A Bayesian approach to discriminate between alternative DNA sequence segmentations. Bioinformatics 18:226-234.
16. Husmeier, D., and G. McGuire. 2002. Detecting recombination with MCMC. Bioinformatics 18:S345-S353.
17. Jin, M. J., H. Hui, D. L. Robertson, M. C. Muller, F. Barre-Sinoussi, V. M. Hirsch, J. S. Allan, G. M. Shaw, P. M. Sharp, and B. H. Hahn. 1994. Mosaic genome structure of simian immunodeficiency virus from West African green monkeys. EMBO J. 13:2935-2947.
18. Kuiken, C., B. Foley, B. Hahn, P. Marx, F. McCutchan, J. Mellors, S. Wolinsky, and B. Korber. HIV Sequence Compendium 2001. Published by Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, N. Mex.
19. McGuire G., F. Wright, and M. J. Prentice. 2000. A Bayesian model for detecting past recombination events in DNA multiple alignments. J. Comp. Biol. 7:159-170.
20. Peeters, M., V. Courgnaud, P. Abela et al. (14 co-authors). 2002. Risk to human health from a plethora of simian immunodeficiency viruses in primate bushmeat. Emerg. Infect. Dis. 8:451-457.
21. Peeters, M., K. Fransen, E. Delaporte, M. Van der Haesevelde, G. M. Geshry-Damet, L. Kestens, G. Van der Groen, and P. Piot. 1992. Isolation and characterization of a new chimpanzee lentivirus (simian immunodeficiency virus isolate cpz-ant) from a wild-captured chimpanzee. AIDS 6:447-451.
22. Peeters, M., C. Honore, T. Huet, L. Bedjabaga, S. Ossari, P. Bussi, R. W. Cooper, and E. Delaporte. 1989. Isolation and partial characterization of an HIV-related virus occurring naturally in chimpanzees in Gabon. AIDS 3:625-630.
23. Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
24. Prince, A. M., B. Brotman, D. H. Lee, L. Andrus, J. Valinsky, and P. Marx. 2002. Lack of evidence for HIV type 1-related SIVcpz infection in captive and wild chimpanzees (Pan troglodytes verus) in West Africa. AIDS Res. Hum. Retroviruses 18:657-660.
25. Santiago, M. L., F. Bibollet-Ruche, E. Bailes et al. (13 co-authors). 2003. Amplification of a complete simian immunodeficiency virus genome from fecal RNA of a wild chimpanzee. J. Virol. 77:2233-2242.
26. Santiago, M. L., C. M. Rodenburg, S. Kamenya et al. (24 co-authors). 2002. SIVcpz in wild chimpanzees. Science 295:465.
27. Sharp, P. M., E. Bailes, R. R. Chaudhuri, C. M. Rodenburg, M. O. Santiago, and B. H. Hahn, 2001. The origins of acquired immune deficiency syndrome viruses: where and when? Philos. Trans. R. Soc. Lond. Ser. B. Biol. Sci. 356:867-876.
28. Sharp, P. M., E. Bailes, F. Gao, B. E. Beer, V. M. Hirsch, and B. H. Hahn. 2000. Origins and evolution of AIDS viruses: estimating the time scale. Biochem. Soc. Trans. 28:275-282.
29. Shimodaira, H. 2000. Another calculation of the p-value for the problem of regions using the scaled bootstrap resamplings. Technical Report No. 2000-2035. Stanford University, Stanford, Calif.
30. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
31. Simon, F., P. Mauclere, P. Roque, I. Loussert-Ajaka, M. C. Müller-Trutwin, S. Saragosti, M. C. Georges-Courbot, F. Barre-Sinoussi, and F. Brun-Vezinet. 1998. Identification of a new human immunodeficiency virus type 1 distinct from group M and group O. Nat. Med. 4:1032-1037.
32. Suchard, M. A., R. E. Weiss, K. S. Dorman, and J. S. Sinsheimer. 2002. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst. Biol. 51:715-728.
33. -. 2003. Inferring spatial phylogenetic variation along nucleotide sequences: a multiple change-point model. J. Am. Stat. Assoc. (in press).
34. Swofford, D. L. 1998. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Mass.
35. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
36. Weiss, R. A., and R. W. Wrangham. 1999. From pan to pandemic. Nature 397:385-386.