Reconstructing reticulate evolution in species - Theory and practice

Journal of Computational Biology

Volumn 12, Issue 6, 2005, Pages 796-811

  Nakhleh, Luay ^a   Warnow, Tandy ^b   Linder, C Randal ^c   St John, Katherine ^d  

^a Rice University   (United States)

^b University of Texas at Austin   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^d CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Hybrid speciation; Phylogenetic networks; Reticulate evolution

Indexed keywords

CONFERENCE PAPER; EVOLUTION; GENETIC ALGORITHM; HORIZONTAL GENE TRANSFER; HYBRID; PHYLOGENETIC TREE; PRIORITY JOURNAL; RETICULATE EVOLUTION; SPECIES DIFFERENTIATION; THEORY;

COMPUTER SIMULATION; EVOLUTION, MOLECULAR; GENE FREQUENCY; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; PHYLOGENY; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 23844438866     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.796     Document Type: Conference Paper

References (25)

1. Bafna, V., and Bansal, V. 2004. The number of recombination events in a sample history: Conflict graph and lower bounds. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1(2), 78-90.
2. Bandelt, H.J., and Dress, A.W.M. 1992. Split decomposition: A new and useful approach to phylogenetic analysis of distance data. Mol. Phyl. Evol. 1, 242-252.
3. Bender, M.A., and Farach-Colton, M. 2000 The LCA problem revisited. Latin American Theoretical INformatics, 88-94.
4. Bryant, D., and Moulton, V. 2002. NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. Proc. 2nd Workshop Algorithms in Bioinformatics (WABI '02), 375-391. vol. 2452 of Lecture Notes in Computer Science.
5. Day, W.H.E. 1985. Optimal algorithms for comparing trees with labeled leaves. J. Classification 2, 7-28.
6. Dress, A., and Huson, D. 1998. Computing phylogenetic networks from split systems. Manuscript.
7. Gabriel, S.B., Schaffner, S.F., Nguyen, H., Moore, J.M., Roy, J., Blumenstiel, B., Higgins, J., DeFelice, M., Lochner, A., Faggart, M., Liu-Cordero, S.N., Rotimi, C., Adeyemo, A., Cooper, R., Ward, R., Lander, E.S., Daly, M.J., and Altshuler, D. 2002. The structure of haplotype blocks in the human genome. Science 296(5576), 2225-2229.
8. Gusfield, D. 1991. Efficient algorithms for inferring evolutionary trees. Networks 21, 19-28.
9. Gusfield, D., Eddhu, S., and Langley, C. 2003. Efficient reconstruction of phylogenetic networks with constrained recombination. Proc. Computational Systems Bioinformatics (CSB '03).
10. Gusfield, D., and Hickerson, D. 2004. A new efficiently-computed lower bound on the number of recombinations needed in phylogentic networks. Technical Report CSE-2004-6, University of California, Davis.
11. Harel, D., and Tarjan, R.E. 1984. Fast algorithms for finding nearest common ancestors. SIAM J. Comput. 13(2), 338-355.
12. Lawrence, J.G., and Ochman, H. 2002. Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10, 1-4.
13. Maddison, W.P. 1997. Gene trees in species trees. Systematic Biol. 46(3), 523-536.
14. Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., and Timme, R. 2004. Phylogenetic networks: Modeling, reconstructibility, and accuracy. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1(1), 13-23.
15. Nakhleh, L., Clement, A., Warnow, T., Linder, C.R., and Moret, B.M.E. 2004. Quality measures for phylogenetic networks. Technical Report TR-CS-2004-06. University of New Mexico, Albuquerque, New Mexico.
16. Nakhleh, L., Sun, J., Warnow, T., Linder, C.R., Moret, B.M.E., and Tholse, A. 2003. Towards the development of computational tools for evaluating phylogenetic network reconstruction method. Proc. 8th Pacific Symp. on Biocomputing (PSB '03), 315-326.
17. Page, R., and Charleston, M.A. 1998. Trees within trees: Phylogeny and historical associations. Trends Ecol. Evol. 13, 356-359.
18. Posada, D., and Wiuf, C. 2003. Simulating haplotype blocks in the human genome. Bioinformatics 19(2), 289-290.
19. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
20. Shimodaira, H., and Hasegawa, M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16, 1114-1116.
21. Swofford, D.L. 1996. PAUP*: Phylogenetic analysis using parsimony (and other methods), version 4.0, Sinauer Associates, Underland, MA.
22. Wang, L., Zhang, K., and Zhang, L. 2001. Perfect phylogenetic networks with recombination. J. Comp. Biol. 8(1), 69-78.
23. Warnow, T. 1994. Tree compatibility and inferring evolutionary history. J. Algorithms 16, 388-407.
24. Zhang, K., and Jin, L. 2003. HaploBlockFinder: Haplotype block analyses. Bioinformatics 19(10), 1300-1301.
25. Zwickl, D., and Hillis, D. 2002. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biol. 51(4), 588-598.