Phylogenetic invariants for genome rearrangements

Journal of Computational Biology

Volumn 6, Issue 3-4, 1999, Pages 431-445

  Blanchette, Mathieu ^b   Sankoff, David ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b University of Washington   (United States)

Author keywords

Breakpoints; Jukes Cantor semigroup; Metazoan phylogeny; Mitochondrial genome; Sorting by reversals

Indexed keywords

CONFERENCE PAPER; DNA TRANSPOSITION; GENE REARRANGEMENT; GENE SEQUENCE; GENE STRUCTURE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

ALGORITHMS; ANIMALS; EVOLUTION, MOLECULAR; GENE REARRANGEMENT; INVERTEBRATES; MODELS, GENETIC; MODELS, STATISTICAL; PHYLOGENY; SENSITIVITY AND SPECIFICITY;

ANIMALIA; INVERTEBRATA; METAZOA;

EID: 0032700064     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652799318373     Document Type: Conference Paper

References (73)

1. Aguinaldo, A.M.A., Turbeville, J.M., Linford, L.S., Rivera, M.C., Garey, J.R., Raff, R.A., and Lake, J.A. 1997. Evidence for a clade of nematodes, arthropods and other moulting animals. Nature (London) 387, 489-493.
2. Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H.L., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J.H., Staden, R., and Young, I.G. 1981. Sequence and organization of the human mitochondrial genome. Nature (London) 290, 457-465.
3. Asakawa, S., Himeno, H., Miura, K., and Watanabe, K. 1993. Nucleotide sequence and gene organization of the starfish Asterna pectinifera mitochondrial genome. Unpublished.
4. Bafna., V., and Pevzner, P.A. 1995. Sorting by transpositions, 614-623. In Galil, Z., and Ukkonen, E., eds., Proceedings of the Sixth Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science 937. Springer-Verlag, New York.
5. Bafna, V., and Pevzner, P.A. 1996. Genome rearrangements and sorting by reversals. SIAM J. Comput. 25, 272-289.
6. Berman, P., and Hannenhalli, S. 1996. Fast sorting by reversal, 168-185. In Hirschberg, D., and Myers, G., eds., Proceedings of the Seventh Symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science 1075. Springer-Verlag, New York.
7. Blanchette, M., Kunisawa, T., and Sankoff, D. 1996. Parametric genome rearrangement. Gene 172, GC 11-17.
8. Blanchette, M., Bourque, G., and Sankoff, D. 1997. Breakpoint phylogenies, 25-34. In Miyano, S., and Takagi, T., eds., Genome Informatics 1997. Universal Academy Press, Tokyo.
9. Blanchette, M., Kunisawa, T., and Sankoff, D. 1999. Gene order breakpoint evidence in animal mitochondrial phylogeny. J. Mol. Evol. 49, 193-203.
10. Boore, J.L., and Brown, W.M. 1994. Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata. Genetics 138, 423-443.
11. Boore, J.L., and Brown, W.M. 1995. Complete sequence of the mitochondrial DNA of the annelid worm Lumbricus terrestris. Genetics 141, 305-319.
12. Brusca, R.C., and Brusca, G.J. 1990. Invertebrates. Sinauer, Sunderland, MA.
13. Bryant, D., Deneault, M., and Sankoff, D. 1999. The breakpoint median problem. Manuscript, Centre de recherches mathématiques, Université de Montréal.
14. Caprara, A. 1997. Sorting by reversals is difficult, 75-83. In Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB 97). ACM, New York.
15. Caprara, A. 1999. Formulations and hardness of multiple sorting by reversals, 84-93. In Istrail, S., Pevzner, P., and Waterman, M., eds., Proceedings of the Third Annual International Conference on Computational Molecular Biology (RECOMB 99). ACM, New York.
16. Castresana, J., Feldmaier-Fuchs, G., and Paabo, S. 1998. Codon reassignment and amino acid composition in hemichordate mitochondria. Proc. Natl. Acad. Sci. U.S.A. 95, 3703-3707.
17. Cavender, J.A. 1989. Mechanized derivation of linear invariants. Mol. Biol. Evol. 6, 301-316.
18. Cavender, J.A., and Felsenstein, J. 1987. Invariants of phylogenies: Simple case with discrete states. J. Class. 4, 57-71.
19. Christofferson, M.L., and Araújo-de-Almeida, E.A. 1994. A phylogenetic framework of the enterocoela (Metameria: Coelomata). Rev. Norest. Biol. (Brazil) 9, 172-208.
20. Clary, D.O., and Wolstenholme, D.R. 1985. The mitochondrial DNA molecular of Drosophila yakuba: Nucleotide sequence, gene organization, and genetic code. J. Mol. Evol. 22, 252-271.
21. Dalkie, K.-S. 1998. Analysis of breakpoints for genome rearrangement. Honours essay, Department of Mathematics, University of Canterbury, New Zealand.
22. Drolet, S., and Sankoff, D. 1990. Quadratic invariants for multivalued characters. J. Theoret. Biol. 144, 117-129.
23. Eernisse, D.J., Albert, J.S., and Anderson, F.E. 1992. Annelida and Arthropoda are not sister taxa. A phylogenetic analysis of spiralian metazoan morphology. Syst. Biol. 41, 305-330.
24. Evans, S.N., and Speed, T.P. 1993. Invariants of some probability models used in phylogenetic inference. Ann. Stat. 21 355-377.
25. Evans, S.N., and Zhou, X. 1998. Constructing and counting phylogenetic invariants. J. Comp. Biol. 5, 713-724.
26. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410.
27. Felsenstein, J. 1991. Counting phylogenetic invariants in some simple cases. J. Theoret. Biol. 152, 357-376.
28. Ferretti, V., and Sankoff, D. 1993. The empirical discovery of phylogenetic invariants. Adv. Appl. Prob. 25, 290-302.
29. Ferretti, V., and Sankoff, D. 1995. Phylogenetic invariants for more general evolutionary models. J. Theoret. Biol. 173, 147-162.
30. Ferretti, V., and Sankoff, D. 1996. A remarkable nonlinear invariant for evolution with heterogeneous rates. Math. Biosci. 134, 71-83.
31. Ferretti, V., Lang, B.F., and Sankoff, D. 1994. Skewed base compositions, asymmetric transition matrices and phylogenetic invariants. J. Comput. Biol. 1, 77-92.
32. Fu, Y.X. 1995. Linear invariants under Jukes' and Cantor's one-parameter model. J. Theoret. Biol. 173, 339-352.
33. Gallut, C. 1998. Codage de l'ordre des gènes du génome mitochondrial animal en vue d'une analyse phylogénétique. Mémoire de DEA, Université Paris VI Pierre & Marie Curie.
34. Giribet, G., and Ribera, C. 1998. The position of Arthropods in the animal kingdom: A search for a reliable outgroup for internal arthropod phylogeny. Mol. Phylogenet. Evol. 9, 481-488.
35. Gu, Q.-P., Iwata, K., Peng, S., and Chen, Q.-M. 1997. A heuristic algorithm for genome rearrangements, 268-269. In Miyano, S., and Takagi, T., eds., Genome Informatics 1997. Universal Academy Press, Tokyo.
36. Hagedorn, T.R. 1999. On the number and structure of phylogenetic invariants. Advances in Applied Mathematics. In press.
37. Hagedorn, T.R., and Landweber, L.F. 1999. Phylogenetic invariants and geometry. Manuscript, College of New Jersey and Princeton University.
38. Hannenhalli, S., and Pevzner, P.A. 1995. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals), 178-189. In Proceedings of the 27th Annual ACM-SIAM Symposium on the Theory of Computing. ACM, New York.
39. Hannenhalli, S., Chappey, C., Koonin, E.V., and Pevzner, P.A. 1995. Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics 30, 299-311.
40. Hasegawa, M., Kishino, H., and Yano, T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol Evol. 22, 160-174.
41. Hendy, M.D., and Penny, D. 1996. Complete families of linear invariants for some stochastic models of sequence evolution, with and without the molecular clock assumption. J. Comp. Biol. 3, 19-31.
42. Jin, L., and Nei, M. 1990. Limitations of the evolutionary parsimony method of phylogenetic analysis. Mol. Biol. Evol. 7, 82-102.
43. Jukes, T.H., and Cantor, C.R. 1969. Evolution of protein molecules 21-132. In Munro, H.N., ed., Mammalian Protein Metabolism. Academic Press, New York.
44. Kaplan, H., Shamir, R., and Tarjan, R.E. 1997. Faster and simpler algorithm for sorting signed permutations by reversals 344-351. In Proceedings of the 8th Annual ACM-SIAM Symposium on Discrete Algorithms. ACM, New York.
45. Kececioglu, J., and Sankoff, D. 1994. Efficient bounds for oriented chromosome reversal distance, 307-325. In Crochemore, M., and Gusfield, D., eds., Proceedings of the Fifth Symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science 807. Springer-Verlag, New York.
46. Kececioglu, J., and Sankoff, D. 1995. Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. Algorithmica 13, 180-210.
47. Kimura, M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120.
48. Kimura, M. 1981. Estimation of evolutionary sequences between homologous nucleotide sequences. Proc. Natl. Acad. Sci. U.S.A. 78, 454-458.
49. Lake, J.A. 1987. A rate-independent technique for analysis of nucleic acid sequences: Evolutionary parsimony. Mol. Biol. Evol. 4, 167-191.
50. Maddison, D., and Maddison, W. 1995. Tree of Life metazoa page, http://phylogeny.arizona.edu/tree/eukaryotes/animals/ animals.html.
51. Nadeau, J.H., and Sankoff, D. 1998. Counting on comparative maps. Trends Genet. 14, 495-501.
52. Nguyen, T., and Speed, T.P. 1992. A derivation of all linear invariants for a nonbalanced trans version model. J. Mol. Evol. 35, 60-76.
53. Pe'er, I., and Shamir, R. 1998. The median problems for breakpoints are NP-complete. Electronic Colloquium on Computational Complexity Technical Report 98-071, http://www.eccc.uni-trier.de/eccc.
54. Rouse, G.W., and Fauchald, K. 1995. The articulation of annelids. Zool. Scripta 24, 269-301.
55. Ruppert, E.E., and Barnes, B.D. 1994. Invertebrate Zoology. Saunders, Philadelphia.
56. Sankoff, D. 1990. Designer invariants for large phylogenies. Mol. Biol. Evol. 7, 255-269.
57. Sankoff, D. 1992. Edit distance for genome comparison based on non-local operations, 121-135. In Apostolico, A., Crochemore, M., Galil, Z., and Manber, U., eds., Proceedings of the Third Symposium on Combinatorial Pattern Matching. Lecture Notes in Computer Science 644. Springer-Verlag, New York.
58. Sankoff, D. 1999. Comparative mapping and genome rearrangement, 124-134. In Dekkers, J.C.M., Lamont, S.J., and Rothschild, M.F., eds., From Jay Lush to Genomics: Visions for Animal Breeding and Genetics. Ames, Iowa, Iowa State University, and AgBiotechNet 1, http://agbio.cabweb.org/conference/index.html.
59. Sankoff, D., and Blanchette, M. 1997. The median problem for breakpoints in comparative genomics, 251-263. In Jiang, T., and Lee, D.T., eds., Computing and Combinatorics, Proceedings of COCOON '97. Lecture Notes in Computer Science 1276. Springer-Verlag, New York.
60. Sankoff, D., and Blanchette, M. 1998a. Multiple genome rearrangement and breakpoint phylogeny. J. Camp. Biol. 5, 555-570.
61. Sankoff, D., and Blanchette, M. 1998b. Phylogenetic invariants for metazoan mitochondrial genome evolution, 22-31. In Miyano, S., and Takagi, T., eds., Genome Informatics 1998. Universal Academy Press, Tokyo.
62. Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B.F, and Cedergren, R.J. 1992. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. U.S.A. 89, 6575-6579.
63. Sankoff, D., Sundaram, G., and Kececioglu, J. 1996. Steiner points in the space of genome rearrangements. Int. J. Found. Comput. Sci. 7, 1-9.
64. Steel, M.A. 1994. Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett. 7, 19-23.
65. Steel, M.A., and Fu, Y.X. 1995. Classifying and counting linear phylogenetic invariants for the Jukes-Cantor model. J. Comp. Biol. 2, 39-47.
66. Steel, M. A., Szekeley, L.A., Erdos, P.L., and Waddell, P. 1993. A complete family of phylogenetic invariants for any number of taxa under Kimura's 3ST model. NZ J. Bot. 31, 289-296.
67. Szekeley, L.A., Steel, M.A., and Erdos, P.L. 1993. Fourier calculus on evolutionary trees. Adv. Appl. Math. 14, 200-216.
68. Tajima, F., and Nei, M. 1984. Estimation of evolutionary distance between nucleotide sequences. Mol. Biol. Evol. 1, 269-285.
69. Tamura, K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Mol. Biol. Evol. 9, 678-687.
70. Tamura, K., and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
71. Valentine, J.W. no date. University of California Museum of Paleontology Metazoa Systematics Page, http://www. ucmp.berkeley.edu/phyla/metazoasy.html.
72. Wada, H., and Satoh, N. 1994. Details of the evolutionary history from invertebrates to vertebrates, as deduced from the sequences of 18S rDNA. Proc. Natl. Acad. Sci. U.S.A. 91, 1801-1804.
73. Watterson, G.A., Ewens, W.J., Hall, T.E., and Morgan, A. 1982. The chromosome inversion problem. J. Theoret. Biol. 99, 1-7.