An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees
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.
KeywordsGene Tree Optimal Network Tree Node Phylogenetic Network Hybridization Network
Unable to display preview. Download preview PDF.
- 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
- 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
- 11.Morrison, D.A.: Introduction to Phylogenetic Networks. RJR Productions, Uppsala (2011)Google Scholar
- 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
- 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
- 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