A graphical method for detecting recombination in phylogenetic data sets

Molecular Biology and Evolution

Volumn 14, Issue 11, 1997, Pages 1125-1131

  McGuire, Gráinne ^a,b   Wright, Frank ^a   Prentice, Michael J ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b Biomathematics Statistics Scotland   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA STRAND BREAKAGE; GENE SEQUENCE; GENETIC RECOMBINATION; MATHEMATICAL ANALYSIS; PHYLOGENY; TOPOGRAPHY;

EID: 0030732297     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.molbev.a025722     Document Type: Article

References (19)

1. BOLLYKY, P. L., A. RAMBAUT, P. H. HARVEY, and E. C. HOLMES. 1996. Recombination between sequences of hepatitis B virus from different genotypes. J. Mol. Evol. 42:92-102.
2. CAVALLI-SFORZA, L. L., and A. W. EDWARDS. 1967. Phylogenetic analysis: models and estimation procedures. Evolution 21:550-570.
3. FELSENSTEIN, J. 1993. PHYLIP. Version 3.5c. University of Washington, Seattle. http://evolution.genetics.washington.edu/phylip.html.
4. _. 1997. An alternating least squares approach to inferring phylogenies from pairwise distances. Syst. Biol. 46:101-111.
5. FITCH, W. M., and E. MARGOLIASH. 1967. Construction of phylogenetic trees. Science 155:279-284.
6. HEIN, J. 1993. A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36:396-405.
7. HUELSENBECK, J. P., and J. J. BULL. 1996. A likelihood ratio test to detect conflicting phylogenetic signal. Syst. Biol. 45:92-98.
8. HUELSENBECK, J. P., D. M. HILLIS, and R. JONES. 1996. Parametric bootstrapping in molecular phylogenetics: applications and performance. Pp. 19-45 in J. D. FERRARIS and S. R. PALUMBI, eds. Molecular zoology: advances, strategies and protocols. Wiley-Liss, New York.
9. JUKES, T. H., and C. R. CANTOR. 1969. Evolution of protein molecules. Pp. 21-132 in H. N. MUNRO, ed. Mammalian protein metabolism. Academic Press, New York.
10. KIMURA, M. 1980. A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16:111-120.
11. KISHINO, H., and M. HASEGAWA. 1989. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J. Mol. Evol. 29:170-179.
12. MAYNARD SMITH, J. 1992. Analyzing the mosaic structure of genes. J. Mol. Evol. 34:126-129.
13. ROBERTSON, D. L., P. M. SHARP, and B. M. HAHN. 1995. Recombination in HIV-1. Nature 374:124-126,
14. RYSAVY, F. R., M. J. BISHOP. G. P. GIBBS, and G. W. WILLIAMS. 1992. The UK Human Genome Mapping Project online computing service. Comput. Appl. Biosci. 8:149-154.
15. SALMINEN, M. O., J. K. CARR, D. S. BURKE, and F. E. MCCUTCHAN. 1995. Identirication of breakpoint in intergen- otypic recombinants of HIV type 1 by bootscanning. AIDs Res. Hum. Retroviruscs 11:1423-1425.
16. SAWYER, S. 1989. Statistical tests for detecting gene conversion. Mol. Biol. Evol. 6:526-538.
17. STEPHENS, J. C. 1985. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2:539-556.
18. THOMPSON, J. T., 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.
19. 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 agrF gene. Mol. Microbiol. 6:2135-2146.