An exact nonparametric method for inferring mosaic structure in sequence triplets

Genetics

Volumn 176, Issue 2, 2007, Pages 1035-1047

  Boni, Maciej F ^a,b   Posada, David ^c   Feldman, Marcus W ^b  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b STANFORD UNIVERSITY   (United States)

^c UNIVERSITY OF VIGO   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DATA ANALYSIS; GENETIC RECOMBINATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; PARENT; PRIORITY JOURNAL; REPRODUCTION; STATISTICS;

ADULT; CHILD; FEMALE; HUMANS; LINKAGE DISEQUILIBRIUM; MALE; MODELS, GENETIC; MOSAICISM; MUTATION; RECOMBINATION, GENETIC; STATISTICS, NONPARAMETRIC; TRIPLETS; VARIATION (GENETICS);

EID: 34250757252     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.106.068874     Document Type: Article

References (73)

1. ARDLIE, K. G., L. KRUGLYAK and M. SEIELSTAD, 2002 Patterns of linkage disequilbrium in the human genome. Nat. Rev. Genet. 3: 299-309.
2. AWADALLA, P., 2003 The evolutionary genomics of pathogen recombination. Nat. Rev. Genet. 4: 50-60.
3. AWADALLA, P., A. EYRE-WALKER and J. MAYNARD SMITH, 1999 Linkage disequilibrium and recombination in hominid mitochondrial DNA. Science 286: 2524-2525.
4. BALDING, D. J., R. A. NICHOLS and D. M. HUNT, 1992 Detecting gene conversion: primate visual pigment genes. Proc. R. Soc. Lond. Ser. B 249: 275-280.
5. BARTON, D. E., and C. L. MALLOWS, 1965 Some aspects of the random sequence. Ann. Math. Stat. 36: 236-260.
6. BONI, M. F., 2007 Vaccination and antigenic drift in influenza. Vaccine (in press).
7. BROWN, C., E. C. GARNER, A. K. DUNKER and P. JOYCE, 2001 The power to detect recombination using the coalescent. Mol. Biol. Evol. 18: 1421-1424.
8. BRUEN, T. C., H. PHILIPPE and D. BRYANT, 2006 A simple and robust statistical test detecting the presence of recombination. Genetics 172: 2665-2681.
9. CARVAJAL-RODRÍGUEZ, A., K. A. CRANDALL and D. POSADA, 2006 Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method. Mol. Biol. Evol. 23: 817-826.
10. CRANDALL, K. A., and A. R. TEMPLETON, 1999 Statistical methods for detecting recombination, pp. 153-176 in The Evolution of HIV, edited by K. A. Crandall. Johns Hopkins University Press, Baltimore.
11. FELLER, W., 1957 An Introduction to Probability Theory and Its Applications, Vol. I. John Wiley & Sons, New York.
12. FELSENSTEIN, J., and G. A. CHURCHILL, 1996 A hidden Markov model approach to variation among sites in rate of evolution. Mol. Biol. Evol. 13: 93-104.
13. FITCH, W. M., and E. MARKOWITZ, 1970 An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4: 579-593.
14. GABRIEL, S. B., S. F. SCHAFFNER, H. NGUYEN, J. M. MOORE, J. ROY et al., 2002 The structure of haplotype blocks in the human genome. Science 296: 2225-2229.
15. GIBBS, M. J., J. S. ARMSTRONG and A. J. GIBBS, 2000 Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics 16: 573-582.
16. GIBBS, M. J., J. S. ARMSTRONG and A. J. GIBBS, 2001 Recombination in the hemagglutinin gene of the 1918 "Spanish flu." Science 293: 1842-1845.
17. GOSS, P. J. E., and R. C. LEWONTIN, 1996 Detecting heterogeneity of substitution along DNA and protein sequences. Genetics 143: 589-602.
18. GRASSLY, N. C., and E. C. HOLMES, 1997 A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol. 14: 239-247.
19. GRASSLY, N. C., P. H. HARVEY and E. C. HOLMES, 1999 Population dynamics of HIV-1 inferred from gene sequences. Genetics 151: 427-438.
20. HALKETT, F., J.-C. SIMON and F. BALLOUX, 2005 Tackling the population genetics of clonal and partially clonal organisms. Trends Ecol. Evol. 20: 194-201.
21. HOGAN, M. L., and D. SIEGMUND, 1986 Large deviations for the maxima of some random fields. Adv. Appl. Math. 7: 2-22.
22. HOLMES, E. C., M. WOROBEY and A. RAMBAUT, 1999 Phylogenetic evidence for recombination in dengue virus. Mol. Biol. Evol. 16: 405-409.
23. HOLMES, E. C., E. GHEDIN, N. MILLER, J. TAYLOR, Y. BAO et al., 2005 Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses. PLoS Biol. 3: e300.
24. HUDSON, R. R., and N. L. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
25. HUSMEIER, D., and G. MCGUIRE, 2003 Detecting recombination in 4-taxa DNA sequence alignments with Bayesian hidden Markov models and Markov chain Monte Carlo. Mol. Biol. Evol. 20: 315-337.
26. JAKOBSEN, I. B., and S. EASTEAL, 1996 A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences. Comput. Appl. Biosci 12: 291-295.
27. KARLIN, S., and V. BRENDEL, 1992 Chance and statistical significance in protein and DNA sequence analysis. Science 257: 39-49.
28. KARLIN, S., and A. DEMBO, 1992 Limit distributions of maximal segmental score among Markov-dependent partial sums. Adv. Appl. Probab. 24: 113-140.
29. KARLIN, S., A. DEMBO and T. KAWABATA, 1990 Statistical composition of high-scoring segments from molecular sequences. Ann. Stat. 18: 571-581.
30. KHATCHIKIAN, D., M. ORLICH and R. ROTT, 1989 Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the hemagglutinin gene of an influenza virus. Nature 340: 156-157.
31. KILBOURNE, E. D., 1978 Molecular epidemiology - influenza as archetype. Harvey Lect. 73: 225-258.
32. KIVISILD, T., P. SHEN, D. P. WALL, B. DO, R. SUNG et al., 2006 The role of selection in the evolution of human mitochondrial genomes. Genetics 172: 373-387.
33. LOLE, K. S., R. C. BOLLINGER, R. S. PARANJAPE, D. GADKARI, S. S. KULKARNI et al., 1999 Full-length immunodeficiency virus type 1 genomes from subtype c-infected seroconverters in india, with evidence of intersubtype recombination. J. Virol. 73: 152-160.
34. LOPEZ, P., D. CASANE and H. PHILIPPE, 2002 Heterotachy, an important process of protein evolution. Mol. Biol. Evol. 19: 1-7.
35. MARTIN, D., and E. RYBICKI, 2000 RDP: detection of recombination amongst aligned sequences. Bioinformatics 16: 562-563.
36. MARTIN, D. P., D. POSADA, K. A. CRANDALL and C. WILLIAMSON, 2005 A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints. AIDS Res. Hum. Retroviruses 21: 98-102.
37. MAYNARD SMITH, J., 1992 Analyzing the mosaic structure of genes. J. Mol. Evol. 34: 126-129.
38. MAYNARD SMITH, J., 1999 The detection and measurement of recombination from sequence data. Genetics 153: 1021-1027.
39. MAYNARD SMITH, J., and N. H. SMITH, 1998 Detecting recombination from gene trees. Mol. Biol. Evol. 15: 590-599.
40. MAYNARD SMITH, J., N. H. SMITH, M. O'ROURKE and B. G. SPRATT, 1993 How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90: 4384-4388.
41. MOYA, A., E. C. HOLMES and F. GONZÁLEZ- CANDELAS, 2004 The population genetics and evolutionary epidemiology of RNA viruses. Nat. Rev. Microbiol. 2: 279-288.
42. NELSON, M. I., L. SIMONSEN, C. VIBOUD, M. A. MILLER, J. TAYLOR et al., 2006 Stochastic processes are key determinants of the short-term evolution of influenza A virus. PLoS Pathog. 2: e125.
43. ORLICH, M., H. GOTTWALD and R. ROTT, 1994 Nonhomologous recombination between the hemagglutinin gene and the nucleoprotein gene of an influenza virus. Virology 204: 462-465.
44. PIGANEAU, G., and A. EYRE-WALKER, 2004 A reanalysis of the indirect evidence for recombination in human mitochondrial DNA. Heredity 92: 282-288.
45. PIGANEAU, G., M. GARDNER and A. EYRE- WALKER, 2004 A broad survey of recombination in animal mitochondria. Mol. Biol. Evol. 21: 2319-2325.
46. POSADA, D., 2002 Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol. Biol. Evol. 19: 708-717.
47. POSADA, D., and K. A. CRANDALL, 2001 Evaluation of methods for detecting recombination from DNA: computer simulations. Proc. Natl. Acad. Sci. USA 98: 13757-13762.
48. POSADA, D., K. A. CRANDALL and E. C. HOLMES, 2002 Recombination in evolutionary genomics. Annu. Rev. Genet. 36: 75-97.
49. PRITCHARD, J. K., and M. PRZEWORSKI, 2001 Linkage disequilibrium in humans: models and data. Am. J. Hum. Genet. 69: 1-14.
50. ROBERTSON, D. L., B. H. HAHN and P. M. SHARP, 1995 Recombination in AIDS viruses. J. Mol. Evol. 40: 249-259.
51. SALMINEM, M. O., J. K. CARR, D. S. BURKE and F. E. MCCUTCHAN, 1995 Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning. AIDS Res. Hum. Retroviruses 11: 1423-1425.
52. SAWYER, S., 1989 Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6: 526-538.
53. SCHIERUP, M. H., C. H. MORDHORST, C. P. MULLER and L. S. CHRISTENSEN, 2005 Evidence of recombination among early-vaccination era measles virus strains. BMC Evol. Biol. 5: 52.
54. SIEGMUND, D., 1986 Boundary crossing probabilities and statistical applications. Ann. Stat. 14: 361-404.
55. SIEGMUND, D., 1988 Approximate tail probabilities for the maxima of some random fields. Ann. Probab. 16: 487-501.
56. SIEPEL, A. C., A. L. HALPERN, C. MACKEN and B. T. M. KORBER, 1995 A computer program designed to screen rapidly for HIV type 1 intersubtype recombinant sequences. AIDS Res. Hum. Retroviruses 11: 1413-1416.
57. SNEATH, P. H. A., 1995 The distribution of the random division of a molecular sequence. Binary Comput. Microbiol. 7: 148-152.
58. SNEATH, P. H. A., 1998 The effect of evenly spaced constant sites on the distribution of the random division of a molecular sequence. Bioinformatics 14: 608-616.
59. 2 method of detecting recombination. Bioinformatics 19:1368-1370.
60. STEPHENS, J. C., 1985 Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2: 539-556.
61. STRIMMER, K., K. FORSLUND, B. HOLLAND and V. MOULTON, 2003 A novel exploratory method for visual recombination detection. Genome Biol. 4: R33.
62. STUMPF, M. P. H., and G. A. T. MCVEAN, 2003 Estimating recombination rates from population-genetic data. Nat. Rev. Genet. 4:959-968.
63. SUAREZ, D. L., D. A. SENNE, J. BANKS, I. H. BROWN, S. C. ESSEN et al., 2004 Recombination resulting in virulence shift in avian influenza outbreak, Chile. Emerg. Infect. Dis. 10: 693-699.
64. TAKAHATA, N., 1994 Comments on the detection of reciprocal recombination or gene conversion. Immunogenetics 39: 146-149.
65. WALL, J. D., 1999 Recombination and the power of statistical tests of neutrality. Genet. Res. 74: 65-79.
66. WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
67. WHITWORTH, W. A., 1901 Choice and Chance, Ed. 5. Hafner Publishing, New York.
68. WILSON, D. J., D. FALUSH and G. MCV EAN, 2005 Germs, genomes, and genealogies. Trends Ecol. Evol. 20: 39-45.
69. WIUF, C., T. CHRISTENSEN and J. HEIN, 2001 A simulation study of the reliability of recombination detection methods. Mol. Biol. Evol. 18: 1929-1939.
70. WOROBEY, M., 2001 A novel approach to detecting and measuring recombination: new insights into evolution of viruses, bacteria, and mitochondria. Mol. Biol. Evol. 18: 1425-1434.
71. WOROBEY, M., A. RAMBAUT, O. G. PYBUS and D. L. ROBERTSON, 2002 Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science 296: 211a.
72. YANG, Z., 1996 Among-site variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11: 367-371.
73. ZHOU, J., and B. G. SPRATT, 1992 Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis: interspecies recombination within the argF gene. Mol. Microbiol. 6: 2135-2146.