Constructing phylogenies from quartets: Elucidation of Eutherian superordinal relationships

Journal of Computational Biology

Volumn 5, Issue 3, 1998, Pages 377-390

  Ben Dor, Amir ^a,c   Chor, Benny ^a   Graur, Dan ^b   Ophir, Ron ^b   Pelleg, Dan ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b TEL AVIV UNIVERSITY   (Israel)

^c University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGY; CLUSTER ANALYSIS; COMPUTER PROGRAM; CONFERENCE PAPER; DATA ANALYSIS; DNA SEQUENCE; GEOMETRY; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; PHYLOGENY; PRIORITY JOURNAL; TAXONOMY;

EID: 0031721805     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.1998.5.377     Document Type: Conference Paper

References (43)

1. Agarwala, R., Bafna, V., Farach, M., Narayanan, B., Paterson, M., and Thorup, M. On the approximability of numerical taxonomy (fitting distances by tree metrics). In Proceedings of the Seventh Annual ACM-SIAM Symposium on Discrete Algorithms. 28-30 January 1996, ACM/SIAM, New York/Philadelphia, pp. 365-372.
2. Bandelt, H.-J., and Dress, A. 1986. Reconstructing the shape of a tree from observed dissimilarity data. Advances in Applied Mathematics 7:309-343.
3. Berry, V., and Gascuel, O. Inferring evolutionary trees with strong combinatorial evidence. Research Report CS-RR-341, Department of Computer Science, University of Warwick, Coventry, UK, March 1998. http://www.dcs. warwick.ac.uk/pub/reports/rr/341.html.
4. Bodlaender, H.L., Fellows, M.R., and Warnow, T. 1992. Two strikes against perfect phylogeny. In Kuich, W., ed. Automata, Languages and Programming, 19th International Colloquium, Volume 623 of Lecture Notes in Computer Science, 273-283.
5. Bourgain, J. 1985. On Lipschitz embedding of finite metric spaces in Hilbert space. Israel Jour. Math. 52, 46-52.
6. Buneman, P. 1971. The recovery of trees from measures of dissimilarity. In Hodson, F.R., Kendall, D.G., and Tautu, P., eds. Anglo-Romanian Conference on Mathematics in the Archaeological and Historical Sciences, Edinburgh University Press, Mamaia, Romania, pp. 387-395.
7. Cohen, J., and Farach, M. Numerical taxonomy on data: Experimental results. In Proceedings of the Eighth Annual ACM-SIAM Symposium on Discrete Algorithms, New Orleans, Louisiana, 5-7 January, 1997, pp. 410-417.
8. Day, W.H.E. 1983. Computationally difficult parsimony problems in phylogenetic systematics. J. Theoret. Biol., 103, 429-438.
9. Day, W.H.E., and Sankoff, D. 1986. Computational complexity of inferring phylogenies by compatibility. Syst. Zoology, 35, 224-229.
10. Duret, L., Mouchirod, D., and Gouy, M. 1994. HOVERGEN: A database of homologous vertebrate genes. Nucleic Acids Res. 22, 2360-2365.
11. Erdös, P., Mike Steel, M., Székely, L.A., and Warnow, T. 1997. Constructing big trees from short sequences. In Degano, P., Gorrieri, R., and Marchetti-Spaccamela, A., eds. Automata, Languages and Programming, 24th International Colloquium, Volume 1256 of Lecture Notes in Computer Science, 827-837.
12. Farach, M., Kannan, S., and Warnow, T. 1995. A robust model for finding optimal evolutionary trees. Algorithmica 13(1/2), 155-179.
13. Felsenstein, J. 1978. The number of evolutionary trees. Syst. Zool. 27, 27-33.
14. Felsenstein, J. 1985a. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 164-166.
15. Felsenstein, J. 1985b. PHYLIP - Phylogenetic inference package, version 3.4. Cladistics 5, 164-166.
16. Foulds, L.R., and Graham, R.L. 1982. The steiner problem in phylogeny is NP-complete. Advances in Applied Math. 3, 43-49.
17. Fitch, W.M. 1978. Towards defining the course of evolution: Minimum change for a specified tree topology. Sys. Zoology 20, 406-416.
18. Fitch, W.M. 1981. A non-sequential method for constructing trees and hierarchical classifications. J. Mol. Evol. 18(1), 30-37.
19. Fitch, W.M., and Margolaish, E. 1967. Construction of phylogenetic trees. Science 155, 279-284.
20. Fujisawa, K., Kojima, M., and Nakata, K. 1996. SDPA User's Manual, Tokyo Institute of Technology, Tokyo (ftp.is.titech.ac.jp/pub/OpRes/software/SDPA).
21. Gascuel, O. 1997. BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol. 14(7), 685.
22. Goemans, M.X., and Williamson, D.P. 1995. Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming. J. of the ACM 42(6), 1115-1145, Nov.
23. Gower, J., and Ross, G. 1969. Minimum spanning trees and single linkage cluster analysis. Applied Statistics 18, 54-64.
24. Graur, D. 1993. Towards a molecular resolution of the ordinal phylogeny of the eutherian mammals. FEBS Lett. 325, 152-159.
25. Graur, D. 1996. Mammalian phylogeny: Using every available molecule. Proceedings of the Training Course in Molecular Evolution. CIHEAM, Bari, Italy, pp. 6-8.
26. Graur, D., Duret, L., and Gouy, M. 1996. Phylogenetic position of the order Lagomorpha (rabbits, hares, and allies). Nature 379, 333-335.
27. Graur, D., Gouy, M., and Duret, L. 1997. Evolutionary affinities of the order Perissodactyla and the phylogenetic status of the superordinal taxa Ungulata and Altungulata. Mol. Phylogenet. Evol. 7, 195-200.
28. Grötschel, M., Lovász, L., and Schrijver, A. 1987. Geometric Algorithms and Combinatorial Optimization. Springer-Verlag, Berlin.
29. Gusfield, D. 1984. The steiner tree problem in phylogeny. Technical Report 334, Yale University, New Haven.
30. Hartigan, J.A. 1973. Minimum mutation fits to a given tree. Biometrics 29, 53-65.
31. Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, p. 75.
32. Krettek, A., Gullberg, A., and Arnason, U. 1995. Sequence analysis of the complete mitochondrial DNA molecule of the hedgehog, Erinaceus europaeus, and the phylogenetic position of he Lipotyphla. J. Mol. Evol. 41, 952-957.
33. Linial, N., Magen, A., and Saks, M. 1998. Trees and euclidean metrics, Proceedings of the Thirtieth Annual ACM Symposium on Theory of Computing, Dallas, Texas, 23-26 May, 1998, pp. 169-175.
34. Pelleg, D. 1998. Algorithms for constructing phylogenies from quartets, M.Sc. thesis, Dept. of Computer Science, Technion, IIT. http://www.cs.technion.ac.ril/Labs/cbl/publication.html
35. Phillips, C., and Warnow, T.J. 1996. The asymmetric median tree - a new model for building consensus trees. Discrete Applied Math. 71 (1-3), 311.
36. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
37. Sokal, R.R., and Sneath, P.H.A. 1963. Principles of Numerical Taxonomy. A Series of books in biology. W.H. Freeman, San Francisco.
38. Springer, M.S., Cleven, G.C., Madsen, O., de Jong, W.W., Waddell, V.G., Amrine, H.M., and Stanhope, M.J. 1997. Endemic African mammals shake the phylogenetic tree. Nature 388, 61-64.
39. Steel, M. 1992. The complexity of reconstructing trees from qualitative characters and subtrees. J. of Classification 9, 91-116.
40. Strimmer, K., and von Haeseler, A. 1996. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13(7), 964. Software available at ftp://ftp.ebi.ac.uk/pub/software/ unix/puzzle/.
41. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalty and weight matrix choice. Nucleic Acids Res. 22, 4673-4780.
42. Warnow, T. 1998. Some combinatorial optimization problems in phylogenetics. Unpublished manuscript.
43. Waterman, M.S., Smith, T.F., Singh, M., and Beyer, W.A. 1977. Additive evolutionary trees. J. Theoret. Biol. 64, 199-213.