Recombination estimation under complex evolutionary models with the coalescent composite-likelihood method

Molecular Biology and Evolution

Volumn 23, Issue 4, 2006, Pages 817-827

  Carvajal Rodríguez, Antonio ^a,b   Crandall, Keith A ^a   Posada, David ^b  

^a BRIGHAM YOUNG UNIVERSITY   (United States)

^b UNIVERSITY OF VIGO   (Spain)

Author keywords

Coalescent; Complex models; Composite likelihood; HIV 1; Recombination

Indexed keywords

ALLELE; ARTICLE; DEMOGRAPHY; EVOLUTION; GENE FREQUENCY; GENE MUTATION; GENETIC ANALYSIS; GENETIC HETEROGENEITY; GENETIC MODEL; GENETIC RECOMBINATION; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; POPULATION GROWTH; POPULATION STRUCTURE; SIMULATION;

ALLELES; CODON; COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE PRODUCTS, ENV; GENETICS, POPULATION; HIV-1; HUMANS; LIKELIHOOD FUNCTIONS; LONGITUDINAL STUDIES; MODELS, GENETIC; RECOMBINATION, GENETIC; SELECTION (GENETICS); SELECTION, GENETIC;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 33644911496     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj102     Document Type: Article

References (57)

1. Anderson, J. P., A. G. Rodrigo, G. H. Learn, Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood, and J. I. Mullins. 2001. Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. J. Mol. Evol. 53:55-68.
2. Anisimova, M., R. Nielsen, and Z. Yang. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236.
3. Awadalla, P. 2003. The evolutionary genomics of pathogen recombination. Nat. Rev. Genet. 4:50-60.
4. Barton, N. H., and A. M. Etheridge. 2004. The effect of selection on genealogies. Genetics 166:1115-1131.
5. Buendia, P., and G. Narasimhan. 2004. MinPD: distance-based phylogenetic analysis and recombination detection of serially-sampled HIV quasispecies. Proceedings of the IEEE Computer Society Bioinformatics Conference, Stanford, Calif.
6. Crandall, K. A., C. R. Kelsey, H. Imamichi, C. H. Lane, and N. P. Salzman. 1999. Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol. Biol. Evol. 16:372-382.
7. Crow, J. F., and M. Kimura. 1970. An introduction to population genetics theory. Harper & Row, New York.
8. Drummond, A., G. Nicholls, A. G. Rodrigo, and W. Solomon. 2002. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320.
9. Fearnhead, P., and P. Donnelly. 2001. Estimating recombination rates from population genetic data. Genetics 159: 1299-1318.
10. Fu, Y.-X. 2001. Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol. Biol. Evol. 18:620-626.
11. Golding, G. B. 1997. The effect of purifying selection on genealogies. Pp. 271-285 in P. Donnelly and S. Tavaré, ed. Progress in population genetics and human evolution. Springer-Verlag, New York.
12. Goldman, N., and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
13. Griffiths, R. C., and P. Marjoram. 1996. Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol. 3:479-502.
14. Griffiths, R. C., and S. Tavare. 1994. Sampling theory for neutral alleles in a varying environment. Phil. Trans. R. Soc. Lond. B 344:403-410.
15. Hudson, R. R. 1983. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23:183-201.
16. _. 2001. Two-locus sampling distributions and their application. Genetics 159:1805-1817.
17. Hudson, R. R., D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Mol. Biol. Evol. 9:138-151.
18. Hudson, R. R., M. Slatkin, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132:583-589.
19. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pp. 21-132 in H. M. Munro, ed. Mammalian protein metabolism. Academic Press, New York.
20. Kuhner, M. K., J. Yamato, and J. Felsenstein. 2000. Maximum likelihood estimation of recombination rates from population data. Genetics 156:1393-1401.
21. Leitner, T., S. Kumar, and J. Albert. 1997. Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol. 71:4761-4770.
22. Liu, Y., D. C. Nickle, D. Shriner, M. A. Jensen, H. Gerald, J. Learn, J. E. Mittler, and J. I. Mullins. 2004. Molecular clock-like evolution of human immunodeficiency virus type 1. Virology 329:101-108.
23. McVean, G. A. T. 2002. A genealogical interpretation of linkage disequilibrium. Genetics 162:987-991.
24. McVean, G. A. T., P. Awadalla, and P. Fearnhead. 2002. A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160:1231-1241.
25. Neuhauser, C., and S. M. Krone. 1997. The genealogy of samples in models with selection. Genetics 145:519-534.
26. Nielsen, R., and Z. Yang. 1998. Likelihood methods for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936.
27. Posada, D., and K. A. Crandall. 2001a. Selecting models of nucleotide substitution: an application to human immunodeficiency virus 1 (HIV-1). Mol. Biol. Evol. 18:897-906.
28. Posada, D., and K. A. Crandall. 2001b. Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl. Acad. Sci. USA 98:13757-13762.
29. Posada, D., and K. A. Crandall. 2002. The effect of recombination on the accuracy of phylogeny estimation. J. Mol. Evol. 54:396-402.
30. Posada, D., K. A. Crandall, and E. C. Holmes. 2002. Recombination in evolutionary genomics. Annu. Rev. Genet. 36:75-97.
31. Przeworski, M., B. Charlesworth, and J. D. Wall. 1999. Genealogies and weak purifying selection. Mol. Biol. Evol. 16:246-252.
32. Pybus, O. G., E. C. Holmes, and P. H. Harvey. 1999. The mid-depth method and HIV-1: a practical approach for testing hypotheses of viral epidemic history. Mol. Biol. Evol. 16:953-959.
33. Rambaut, A., D. Posada, K. A. Crandall, and E. C. Holmes. 2004. The causes and consequences of HIV evolution. Nat. Rev. Genet. 5:52-61.
34. Rodrigo, A. G., and J. Felsenstein. 1999. Coalescent approaches to HIV population genetics. Pp. 233-272 in K. A. Crandall, ed. Evolution of HIV. Johns Hopkins University Press, Baltimore, Md.
35. Rodríguez, F., J. F. Oliver, A. Marín, and J. R. Medina. 1990. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142:485-501.
36. Ross, H. A., and A. G. Rodrigo. 2002. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. J. Virol. 76:11715-11720.
37. Schierup, M. H., and J. Hein. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156:879-891.
38. Seo, T.-K., J. L. Thorne, M. Hasegawa, and H. Kishino. 2002. Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics 160:1283-1293.
39. Shankarappa, R., P. Gupta, Learn, G. H. Jr, A. G. Rodrigo, Rinaldo, C. R. Jr, M. C. Gorry, J. I. Mullins, P. L. Nara, and G. D. Ehrlich. 1998. Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology 241:251-259.
40. Shankarappa, R., J. B. Margolick, S. J. Gange et al. (12 co-authors). 1999. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. J. Virol. 73:10489-10502.
41. Shriner, D., D. C. Nickle, M. A. Jensen, and J. I. Mullins. 2003. Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet. Res. 81:115-121.
42. Shriner, D., A. G. Rodrigo, D. C. Nickle, and J. I. Mullins. 2004. Pervasive genomic recombination of HIV-1 in vivo. Genetics 167:1573-1583.
43. Slatkin, M., and R. R. Hudson. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129:555-562.
44. Stephens, M., and P. Donnelly. 2000. Inference in molecular population genetics. J. R. Stat. Soc. Ser. B 62:605-655.
45. _. 2003. Ancestral inference in population genetics models with selection (with discussion). Aust. N. Z. J. Stat. 45:395-430.
46. Stumpf, M. P. H., and G. A. T. McVean. 2003. Estimating recombination rates from population-genetic data. Nat. Rev. Genet. 4:959-968.
47. Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Mass.
48. Templeton, A. R., R. A. Reichert, A. E. Weisstein, X.-F. Yu, and R. B. Markham. 2004. Selection in context: patterns of natural selection in the glycoprotein 120 region of human immunodeficiency virus 1 within infected individuals. Genetics 167:1547-1561.
49. Wall, J. D. 2000. A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17:156-163.
50. Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol. 7:256-276.
51. Weiss, K. M., and A. G. Clark. 2002. Linkage disequilibrium and the mapping of complex human traits. Trends Genet. 18:19-24.
52. Wilson, D. J., D. Falush, and G. McVean. 2005. Germs, genomes and genealogies. Trends Ecol. Evol. 20:39-45.
53. Wiuf, C., T. Christensen, and J. Hein. 2001. A simulation study of the reliability of recombination detection methods. Mol. Biol. Evol. 18:1929-1939.
54. Worobey, M. 2001. A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol. Biol. Evol. 18:1425-1434.
55. Yang, Z. 1993. Maximum likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol. Biol. Evol. 10:1396-1401.
56. _. 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39:306-314.
57. _. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.