Abstract
Phylogenetic reconstruction from gene-rearrangement data has seen increased attention over the last five years. Existing methods are limited computationally and by the assumption (highly unrealistic in practice) that all genomes have the same gene content. We have recently shown that we can scale our reconstruction tool, GRAPPA, to instances with up to a thousand genomes with no loss of accuracy and at minimal computational cost. Computing genomic distances between two genomes with unequal gene contents has seen much progress recently, but that progress has not yet been reflected in phylogenetic reconstruction methods. In this paper, we present extensions to our GRAPPA approach that can handle limited numbers of duplications (one of the main requirements for analyzing genomic data from organelles) and a few deletions. Although GRAPPA is based on exhaustive search, we show that, in practice, our bounding functions suffice to prune away almost all of the search space (our pruning rates never fall below 99.995%), resulting in high accuracy and fast running times. The range of values within which we have tested our approach encompasses mitochondria and chloroplast organellar genomes, whose phylogenetic analysis is providing new insights on evolution.
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References
Bader, D.A., Moret, B.M.E., Warnow, T., Wyman, S.K., Yan, M.: GRAPPA (Genome Rearrangements Analysis under Parsimony and other Phylogenetic Algorithms), www.cs.unm.edu/~moret/GRAPPA/
Bader, D.A., Moret, B.M.E., Yan, M.: A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8(5), 483–491 (2001); A preliminary version appeared in WADS 2001, pp. 365–376 (2001)
Bourque, G., Pevzner, P.: Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Research 12, 26–36 (2002)
Bryant, D.: The complexity of calculating exemplar distances. In: Sankoff, D., Nadeau, J. (eds.) Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics. Map Alignment, and the Evolution of Gene Families, pp. 207–212. Kluwer Academic Pubs., Dordrecht (2000)
Bryant, D.: A lower bound for the breakpoint phylogeny problem. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 235–247. Springer, Heidelberg (2000)
Caprara, A.: Sorting by reversals is difficult. In: Proc. 1st Int’l Conf. on Comput. Mol. Biol. RECOMB 1997, pp. 75–83. ACM Press, New York (1997)
Caprara, A.: Formulations and hardness of multiple sorting by reversals. In: Proc. 3rd Int’l Conf. on Comput. Mol. Biol. RECOMB 1999, pp. 84–93. ACM Press, New York (1999)
Caprara, A.: On the practical solution of the reversal median problem. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 238–251. Springer, Heidelberg (2001)
Cosner, M.E., Jansen, R.K., Moret, B.M.E., Raubeson, L.A., Wang, L.-S., Warnow, T., Wyman, S.K.: An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae. In: Sankoff, D., Nadeau, J. (eds.) Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families, pp. 99–121. Kluwer Academic Pubs., Dordrecht (2000)
Downie, S.R., Palmer, J.D.: Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In: Soltis, P., Soltis, D., Doyle, J.J. (eds.) Plant Molecular Systematics, pp. 14–35. Chapman and Hall, Boca Raton (1992)
El-Mabrouk, N.: Genome rearrangement by reversals and insertions/deletions of contiguous segments. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 222–234. Springer, Heidelberg (2000)
Hannenhalli, S., Pevzner, P.A.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Summer University of Southern Stockholm 1993, pp. 178–189. ACM Press, New York (1995)
Huson, D., Nettles, S., Rice, K., Warnow, T., Yooseph, S.: The hybrid tree reconstruction method. ACM J. Experimental Algorithmics 4(5) (1999), http://www.jea.acm.org/1999/HusonHybrid/
Huson, D., Nettles, S., Warnow, T.: Disk-covering, a fast converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6(3), 369–386 (1999)
Huson, D., Vawter, L., Warnow, T.: Solving large-scale phylogenetic problems using DCM-2. In: Proc. 7th Int’l Conf. on Intelligent Systems for Molecular Biology (ISMB 1999), pp. 118–129. AAAI Press, Menlo Park (1999)
Larget, B., Kadane, J.B., Simon, D.: A Markov chain Monte Carlo approach to reconstructing ancestral genome rearrangements. Technical report, Carnegie Mellon University, Pittsburgh, PA (2002), Available at www.stat.cmu.edu/tr/tr765/
Marron, M., Swenson, K.M., Moret, B.M.E.: Genomic distances under deletions and insertions. In: Warnow, T.J., Zhu, B. (eds.) COCOON 2003. LNCS, vol. 2697, Springer, Heidelberg (2003) (accepted, to appear)
Moret, B.M.E., Siepel, A.C., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 521–536. Springer, Heidelberg (2002)
Moret, B.M.E., Tang, J., Wang, L.-S., Warnow, T.: Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65(3), 508–525 (2002)
Olmstead, R.G., Palmer, J.D.: Chloroplast DNA systematics: a review of methods and data analysis. Amer. J. Bot. 81, 1205–1224 (1994)
Palmer, J.D.: Chloroplast and mitochondrial genome evolution in land plants. In: Herrmann, R. (ed.) Cell Organelles, pp. 99–133. Springer, Heidelberg (1992)
Pe’er, I., Shamir, R.: The median problems for breakpoints are NP-complete. Elec. Colloq. on Comput. Complexity 71 (1998)
Raubeson, L.A., Jansen, R.K.: Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255, 1697–1699 (1992)
Saitou, N., Nei, M.: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)
Sankoff, D.: Genome rearrangement with gene families. Bioinformatics 15(11), 909–917 (1999)
Sankoff, D., Blanchette, M.: Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5, 555–570 (1998)
Sankoff, D., Nadeau, J. (eds.): Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment, and the Evolution of Gene Families. Kluwer Academic Pubs., Dordrecht (2000)
Siepel, A.C., Moret, B.M.E.: Finding an optimal inversion median: Experimental results. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 189–203. Springer, Heidelberg (2001)
Tang, J., Moret, B.M.E.: Scaling up accurate phylogenetic reconstruction from gene-order data. In: Proc. 11th Int’l Conf. on Intelligent Systems for Molecular Biology (ISMB 2003). Bioinformatics, Suppl. 1, vol. 19, pp. 305–312. Oxford U. Press, Oxford (2003)
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Tang, J., Moret, B.M.E. (2003). Phylogenetic Reconstruction from Gene-Rearrangement Data with Unequal Gene Content. In: Dehne, F., Sack, JR., Smid, M. (eds) Algorithms and Data Structures. WADS 2003. Lecture Notes in Computer Science, vol 2748. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-45078-8_4
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DOI: https://doi.org/10.1007/978-3-540-45078-8_4
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