Reconstruction of reticulate networks from gene trees

Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science)

Volumn 3500, Issue , 2005, Pages 233-249

  Huson, Daniel H ^a   Klöpper, Tobias ^a   Lockhart, Pete J ^b   Steel, Mike A ^c  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b MASSEY UNIVERSITY   (New Zealand)

^c UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ERROR ANALYSIS; GENES; GENETIC ALGORITHMS; STATISTICAL METHODS; COMPUTATIONAL METHODS; EVOLUTIONARY ALGORITHMS; GRAPH THEORY; MOLECULAR STRUCTURE; NUMERICAL ANALYSIS; ROBUSTNESS (CONTROL SYSTEMS);

EVOLUTIONARY MODELS; INCOMPATIBILITY GRAPH; PHYLOGENETIC TREE;

MOLECULAR BIOLOGY; GENETIC ENGINEERING;

HYBRIDIZATION; MOLECULAR EVOLUTION; PHYLOGENETIC TREES; RETICULATE NETWORKS;

EID: 26444512722     PISSN: 03029743     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/11415770_18     Document Type: Conference Paper

References (27)

1. Holland, B., Huber, K., Moulton, V., Lockhart, P.J.: Using consensus networks to visualize contradictory evidence for species phylogeny. Molecular Biology and Evolution 21 (2004) 1459-1461
2. Rieseberg, L.H., Raymond, O., Rosenthal, D.M., Lai, Z., Livingstone, K., Nakazato, T., Durphy, J.L., Schwarzbach, A.E., Donovan, L.A., Lexer, C.: Major ecological transitions in annual sunflowers facilitated by hybridization. Science 301 (2003) 1211-1216
3. Hein, J.: Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. (1990) 185-200
4. Hein, J.: A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36 (1993) 396-405
5. Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. Journal of Computational Biology 8 (2001) 69-78
6. Gusfield, D., Eddhu, S., Langley, C.: Efficient reconstruction of phylgenetic networks with constrained recombination. In: Proceedings of the 2003 IEEE CSB Bioinformatics Conference. (2003)
7. D. Gusfield, S.E., Langley, C.: The fine structure of galls in phylogenetic networks, to appear in: INFORMS J. of Computing Special Issue on Computational Biology (2004)
8. Nakhleh, L., Warnow, T., Linder, C.R.: Reconstructing reticulate evolution in species - theory and practice. RECOMB'04 (2004) 337-346
9. Hudson, R.R., Kaplan, N.L.: Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111 (1985) 147-164
10. Myers, S.R., Griffiths, R.C.: Bounds on the minimal number of recombination events in a sample history. Genetics 163 (2003) 375-394
11. Bafna, V., Bansal, V.: The number of recombination events in a sample history: conflict graph and lower bounds. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1 (2004) 78-90
12. Bandelt, H.J., Dress, A.W.M.: A canonical decomposition theory for metrics on a finite set. Advances in Mathematics 92 (1992) 47-105
13. Dress, A.W.M., Huson, D.H.: Constructing splits graphs. IEEE/ACM Transactions in Computational Biology and Bioinformatics 1 (2004) 109-115
14. Gusfield, D., Bansal, V.: A fundamental decomposition theory for phylogenetic networks and incompatible characters. To appear in: Proceedings of RECOMB'2005 (2004)
15. Huson, D.H., Bryant, D.: Estimating phylogenetic trees and networks using SplitsTree 4. Manuscript in preparation, software available from www-ab.informatik.uni-tuebingen.de/software (2004)
16. Lockhart, P.J., McLenachan, P.A., Havell, D., Glenny, D., Huson, D.H., Jensen, U.: Phylogeny, dispersal and radiation of New Zealand alpine buttercups: molecular evidence under split decomposition. Ann Missouri Bot Gard 88 (2001) 458-477
17. Kreitman, M.: Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Genetics 11 (1985) 147-164
18. Semple, C., Steel, M.A.: Phylogenetics. Oxford University Press (2003)
19. Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In Munro, H.N., ed.: Mammalian Protein Metabolism. Academic Press (1969) 21-132
20. Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46 (1997) 523-536
21. Baroni, M., Semple, C., Steel, M.A.: A framework for representing reticulate evolution. Annals of Combinatorics (In press)
22. Huson, D.H., Dezulian, T., Kloepper, T., Steel, M.A.: Phylogenetic super-networks from partial trees. IEEE/ACM Transactions in Computational Biology and Bioinformatics, in press (2004)
23. Rosenberg, N.A.: The probability of topological concordance of gene trees and species trees. Theor. Pop. Biol. 61 (2002) 225-247
24. Sang, T., Zhong, Y.: Testing hybrization hypotheses based on incongruent gene trees. System. Biol. 49 (2000) 422-424
25. Steel, M.A., Lockhart, P., Penny, D.: Confidence in evolutionary trees from biological sequence data. Nature 364 (1993) 440-442
26. Tajima, F.: Evolutionary relationships of DNA sequences in finite populations. Genetics 105 (1983) 437-460
27. Alon, N., Spencer, J.H.: The Probabilistic Method. 2nd edn. John Wiley, (2000)