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)


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.


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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© 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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