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An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees

  • Yufeng Wu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7821)

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.

Keywords

Gene Tree Optimal Network Tree Node Phylogenetic Network Hybridization Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Albrecht, B., Scornavacca, C., Cenci, A., Huson, D.H.: Fast computation of minimum hybridization networks. Bioinformatics 28, 191–197 (2012)CrossRefGoogle Scholar
  2. 2.
    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)Google Scholar
  3. 3.
    Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combinatorics 8, 409–423 (2004)MathSciNetzbMATHCrossRefGoogle Scholar
  4. 4.
    Bordewich, M., Semple, C.: Computing the minimum number of hybridization events for a consistent evolutionary history. Discrete Applied Mathematics 155, 914–928 (2007)MathSciNetzbMATHCrossRefGoogle Scholar
  5. 5.
    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)CrossRefGoogle Scholar
  6. 6.
    Gusfield, D.: Optimal, efficient reconstruction of Root-Unknown phylogenetic networks with constrained and structured recombination. J. Comp. Sys. Sci. 70, 381–398 (2005)MathSciNetzbMATHCrossRefGoogle Scholar
  7. 7.
    Hein, J., Jiang, T., Wang, L., Zhang, K.: On the complexity of comparing evolutionary trees. Discrete Appl. Math. 71, 153–169 (1996)MathSciNetzbMATHCrossRefGoogle Scholar
  8. 8.
    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)CrossRefGoogle Scholar
  9. 9.
    Huson, D., Rupp, R., Gambette, P., Paul, C.: Computing galled networks from real data. Bioinformatics 25, i85–i93 (2009); Bioinformatics Suppl., Proceedings of ISMB 2009Google Scholar
  10. 10.
    Huson, D.H., Rupp, R., Scornavacca, C.: Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, Cambridge (2010)CrossRefGoogle Scholar
  11. 11.
    Morrison, D.A.: Introduction to Phylogenetic Networks. RJR Productions, Uppsala (2011)Google Scholar
  12. 12.
    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)Google Scholar
  13. 13.
    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)CrossRefGoogle Scholar
  14. 14.
    Semple, C.: Hybridization networks. In: Gascuel, O., Steel, M. (eds.) Reconstructing Evolution: New Mathematical and Computational Advances, Oxford, pp. 277–309 (2007)Google Scholar
  15. 15.
    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)CrossRefGoogle Scholar
  16. 16.
    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)CrossRefGoogle Scholar
  17. 17.
    Wu, Y.: A practical method for exact computation of subtree prune and regraft distance. Bioinformatics 25, 190–196 (2009)CrossRefGoogle Scholar
  18. 18.
    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)Google Scholar
  19. 19.
    Wu, Y.: Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution 66, 763–775 (2012)CrossRefGoogle Scholar
  20. 20.
    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)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Yufeng Wu
    • 1
  1. 1.Department of Computer Science and EngineeringUniversity of ConnecticutStorrsU.S.A.

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