Phylogenetic detection of recombination with a Bayesian prior on the distance between trees

PLoS ONE

Volumn 3, Issue 7, 2008, Pages

  de Oliveira Martins, Leonardo ^a   Leal, Élcio ^b   Kishino, Hirohisa ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b FEDERAL UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTICAL ERROR; ARTICLE; BAYES THEOREM; COMPUTER SIMULATION; CONTROLLED STUDY; GENE SEQUENCE; GENETIC DATABASE; GENETIC DISTANCE; GENETIC HETEROGENEITY; GENETIC RECOMBINATION; GENOME ANALYSIS; HUMAN IMMUNODEFICIENCY VIRUS 1; PHYLOGENY; SEQUENCE ANALYSIS; VIRUS GENOME; VIRUS RECOMBINATION;

BAYES THEOREM; GENETIC HETEROGENEITY; HIV-1; PHYLOGENY; RECOMBINATION, GENETIC;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 50349088009     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002651     Document Type: Article

References (63)

1. Posada D (2002) Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol 19: 708-717.
2. Posada D, Crandall KA, Holmes EC (2002) Recombination in evolutionary genomics. Annu Rev Genet 36: 75-97.
3. Awadalla P (2003) The evolutionary genomics of pathogen recombination. Nat Rev Genet 4: 50-60.
4. Fearnhead P, Harding RM, Schneider JA, Myers S, Donnelly P (2004) Application of coalescent methods to reveal fine-scale rate variation and recombination hotspots. Genetics 167: 2067-2081.
5. Golding GB (1984) The sampling distribution of linkage disequilibrium. Genetics 108: 257-274.
6. Griffiths RC (1981) Neutral two-locusmultiple allele models with recombination. Theor Popul Biol 19: 169-186.
7. Hey J, Wakeley J (1997) A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
8. Hudson RR (1985) The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109: 611-631.
9. Hudson RR. (2001) Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
10. Kuhner MK, Yamato J, Felsenstein J (2000) Maximum likelihood estimation of recombination rates from population data. Genetics 156: 1393-1401.
11. McVean G, Awadalla P, Fearnhead P (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
12. Nielsen R (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
13. Wiuf C, Posada D (2003) A coalescent model of recombination hotspots. Genetics 164: 407-417.
14. Siepel AC, Halperen AL, Macken C, Korber B (1995) A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res Hum Retroviruses 11: 1413-1416.
15. Salminen MO, Carr JK, Burke DS, McCutchan FE (1995) Identication of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res Hum Retroviruses 11: 1423-1425.
16. Weiller GF (1998) Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol Biol Evol 15: 326-335.
17. Grassly NC, Holmes EC (1997) A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol 14: 239-247.
18. Husmeier D, Wright F (2001) Probabilistic divergence measures for detecting interspecies recombination. Bioinformatics 17: S123-S131.
19. Husmeier D (2005) Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics 21 Suppl 2: ii166-172.
20. Husmeier D, Wright F (2001) Detection of recombination in DNA multiple alignments with hidden Markov models. J Comput Biol 8: 401-427.
21. Minin VN, Dorman KS, Fang F, Suchard MA (2005) Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics 21: 3034-3042.
22. Minin VN, Dorman KS, Fang F, Suchard MA (2007) Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes. Genetics 175: 1773-1785.
23. Sierra M, Thomson MM, Rios M, Casado G, Castro RO, et al. (2005) The analysis of near hill-length genome sequences of human immunodeficiency virus type 1 BF intersubtype recombinant viruses from Chile, Venezuela and Spain reveals their relationship to diverse lineages of recombinant viruses related to CRF12_BF. Infect Genet Evol 5: 209-217.
24. Hordijk W, Gascuel O (2005) Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics 21: 4338-4347.
25. Nakhleh L, Ruths D, Wang LS (2005) RIATA-HGT: A fast and accurate heuristic for reconstructing horizontal gene transfer. Computing and Combinatorics, Proceedings 3595: 84-93.
26. Suchard MA (2005) Stochastic models for horizontal gene transfer: taking a random walk through tree space. Genetics 170: 419-431.
27. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13: 555-556.
28. Fang F, Ding J, Minin VN, Suchard MA, Dorman KS (2007) cBrother: relaxing parental tree assumptions for Bayesian recombination detection. Bioinformatics 23: 507-508.
29. Chan CX, Beiko RG, Ragan MA (2006) Detecting recombination in evolving nucleotide sequences. BMC Bioinformatics 7: 412.
30. Rajaram ML, Minin VN, Suchard MA, Dorman KS (2007) Hot and Cold: Spatial Fluctuation in HIV-1 Recombination Rates. Bioinformatics and Bioengineering, 2007 BIBE 2007 Proceedings of the 7th IEEE International Conference on. pp 707-714.
31. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
32. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
33. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods) Version 4.0 b10. Sunderland, MA: Sinauer Associates.
34. Gelman A, Rubin DB (1992) Inference from Iterative Simulation Using Multiple Sequences. Statistical Science 7: 457-472.
35. Jotun Hein MHS (2005) Gene Genealogies, Variation and Evolution: A Primer in Coalescent Theory: Oxford University Press.
36. Song YS, Hein J (2005) Constructing minimal ancestral recombination graphs. J Comput Biol 12: 147-169.
37. Drummond AJ, Ho SY, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Biol 4: e88.
38. Kishino H, Thorne JL, Bruno WJ (2001) Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol Biol Evol 18: 352-361.
39. Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Syst Biol 51: 689-702.
40. Beiko RG, Hamilton N (2006) Phylogenetic identification of lateral genetic transfer events. BMC Evol Biol 6: 15.
41. Song YS (2003) On the Combinatorics of Rooted Binary Phylogenetic Trees. Annals of Combinatorics 7: 365-379.
42. Suchard MA, Weiss RE, Dorman KS, Sinsheimer JS (2003) Inferring spatial phylogenetic variation along nucleotide sequences: a multiple changepoint model. J Am Stat Assoc 98: 427-438.
43. Lefeuvre P, Lett JM, Reynaud B, Martin DP (2007) Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog 3(11): e181: doi:10.1371/journal.ppat.0030181.
44. Felsenstein J (2004) Inferring phylogenies. Sinauer Associates Sunderland, Mass., USA.
45. Allen BL, Steel MA (2001) Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics 5: 1-15.
46. Nakhleh L, Warnow T, Linder CR, St John K (2005) Reconstructing reticulate evolution in species-theory and practice. J Comput Biol 12: 796-811.
47. Beiko RG, Harlow TJ, Ragan MA (2005) Highways of gene sharing in prokaryotes. Proc Natl Acad Sci U S A 102: 14332-14337.
48. Ge F, Wang LS, Kim J (2005) The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. PLoS Biol 3: e316.
49. Hallett MT, Lagergren J (2001) Efficient algorithms for lateral gene transfer problems. Proc Fifth Ann Intl Conf Comput Biol. pp 149-156.
50. MacLeod D, Charlebois RL, Doolittle F, Bapteste E (2005) Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol Biol 5: 27.
51. Song YS, Hein J (2003) Parsimonious Reconstruction of Sequence Evolution and Haplotype Blocks: Finding the Minimum Number of Recombination Events. Algorithms in Bioinformatics: Third International Workshop, WABI 2003, Budapest, Hungary, September 15-20, 2003: Proceedings: pp 287-302.
52. Hein J (1990) Reconstructing evolution of sequences subject to recombination using parsimony. Math Biosci 98: 183-200.
53. Hein J (1993) A Heuristic Method to Reconstruct the History of Sequences Subject to Recombination. Journal of Molecular Evolution 36: 396-405.
54. Hickey G, Dehne F, Rau-Chaplin A, Blouin C (2008) SPR Distance Computation for Unrooted Trees. Evolutionary Bioinformatics 2008 4: 17-27.
55. Robinson DF, Foulds LR (1981) Comparison of phylogenetic trees. Math Biosci 53: 131-147.
56. Steel M, Warnow T (1993) Kaikoura Tree Theorems-Computing the Maximum Agreement Subtree. Information Processing Letters 48: 77-82.
57. Bryant D, Moulton V (2004) Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 21: 255-265.
58. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17: 368-376.
59. Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22: 160-174.
60. Altekar G, Dwarkadas S, Huelsenbeck JP, Ronquist F (2004) Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20: 407-415.
61. Al-Awadhi F, Hurn M, Jennison C (2004) Improving the acceptance rate of reversible jump MCMC proposals. Statistics & Probability Letters 69: 189-198.
62. DiMatteo I, Genovese CR, Kass RE (2001) Bayesian curve-fitting with free-knot splines. Biometrika 88: 1055-1071.
63. R Development Core Team (2008) R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing. ISBN 3-900051-07-0. Available http://www.R-project.org/. Accessed 22 May 2008.