Abstract
Phylogenetic network is a model for reticulate evolution. Hybridization network is one type of phylogenetic network for a set of discordant gene trees, and “displays” each gene tree. A central computational problem on hybridization networks is: given a set of gene trees, reconstruct the minimum (i.e. most parsimonious) hybridization network that displays each given gene tree. This problem is known to be NP-hard, and existing approaches for this problem are either heuristics or make simplifying assumptions (e.g. work with only two input trees or assume some topological properties). In this paper, we develop an exact algorithm (called PIRN C ) for inferring the minimum hybridization networks from multiple gene trees. The PIRN C algorithm does not rely on structural assumptions. To the best of our knowledge, PIRN C is the first exact algorithm for this formulation. When the number of reticulation events is relatively small (say four or fewer), PIRN C runs reasonably efficient even for moderately large datasets. For building more complex networks, we also develop a heuristic version of PIRN C called PIRN CH . Simulation shows that PIRN CH usually produces networks with fewer reticulation events than those by an existing method.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Albrecht, B., Scornavacca, C., Cenci, A., Huson, D.H.: Fast computation of minimum hybridization networks. Bioinformatics 28, 191–197 (2012)
Bordewich, M., Linz, S., John, K.S., Semple, C.: A reduction algorithm for computing the hybridization number of two trees. Evolutionary Bioinformatics 3, 86–98 (2007)
Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combinatorics 8, 409–423 (2004)
Bordewich, M., Semple, C.: Computing the minimum number of hybridization events for a consistent evolutionary history. Discrete Applied Mathematics 155, 914–928 (2007)
Chen, Z., Wang, L.: Algorithms for reticulate networks of multiple phylogenetic trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9(2), 372–384 (2012)
Gusfield, D.: Optimal, efficient reconstruction of Root-Unknown phylogenetic networks with constrained and structured recombination. J. Comp. Sys. Sci. 70, 381–398 (2005)
Hein, J., Jiang, T., Wang, L., Zhang, K.: On the complexity of comparing evolutionary trees. Discrete Appl. Math. 71, 153–169 (1996)
Huson, D.H., Klöpper, T.H.: Beyond Galled Trees - Decomposition and Computation of Galled Networks. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 211–225. Springer, Heidelberg (2007)
Huson, D., Rupp, R., Gambette, P., Paul, C.: Computing galled networks from real data. Bioinformatics 25, i85–i93 (2009); Bioinformatics Suppl., Proceedings of ISMB 2009
Huson, D.H., Rupp, R., Scornavacca, C.: Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, Cambridge (2010)
Morrison, D.A.: Introduction to Phylogenetic Networks. RJR Productions, Uppsala (2011)
Nakhleh, L.: Evolutionary phylogenetic networks: models and issues. In: Heath, L., Ramakrishnan, N. (eds.) The Problem Solving Handbook for Computational Biology and Bioinformatics, pp. 125–158. Springer (2010)
Park, H.J., Nakhleh, L.: MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds.) ISBRA 2012. LNCS, vol. 7292, pp. 213–224. Springer, Heidelberg (2012)
Semple, C.: Hybridization networks. In: Gascuel, O., Steel, M. (eds.) Reconstructing Evolution: New Mathematical and Computational Advances, Oxford, pp. 277–309 (2007)
van Iersel, L., Keijsper, J., Kelk, S., Stougie, L., Hagen, F., Boekhout, T.: Constructing Level-2 Phylogenetic Networks from Triplets. In: Vingron, M., Wong, L. (eds.) RECOMB 2008. LNCS (LNBI), vol. 4955, pp. 450–462. Springer, Heidelberg (2008)
Whidden, C., Zeh, N.: A Unifying View on Approximation and FPT of Agreement Forests. In: Salzberg, S.L., Warnow, T. (eds.) WABI 2009. LNCS, vol. 5724, pp. 390–402. Springer, Heidelberg (2009)
Wu, Y.: A practical method for exact computation of subtree prune and regraft distance. Bioinformatics 25, 190–196 (2009)
Wu, Y.: Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees. Bioinformatics (Supplement Issue for ISMB 2010 Proceedings) 26, 140–148 (2010)
Wu, Y.: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66, 763–775 (2012)
Wu, Y., Wang, J.: Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In: Borodovsky, M., Gogarten, J.P., Przytycka, T.M., Rajasekaran, S. (eds.) ISBRA 2010. LNCS, vol. 6053, pp. 203–214. Springer, Heidelberg (2010)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Wu, Y. (2013). An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_29
Download citation
DOI: https://doi.org/10.1007/978-3-642-37195-0_29
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-37194-3
Online ISBN: 978-3-642-37195-0
eBook Packages: Computer ScienceComputer Science (R0)