Research Article: Maximum Parsimony on Phylogenetic networks

Date Published: May 2, 2012

Publisher: BioMed Central

Author(s): Lavanya Kannan, Ward C Wheeler.

http://doi.org/10.1186/1748-7188-7-9

Abstract

Phylogenetic networks are generalizations of phylogenetic trees, that are used to model evolutionary events in various contexts. Several different methods and criteria have been introduced for reconstructing phylogenetic trees. Maximum Parsimony is a character-based approach that infers a phylogenetic tree by minimizing the total number of evolutionary steps required to explain a given set of data assigned on the leaves. Exact solutions for optimizing parsimony scores on phylogenetic trees have been introduced in the past.

In this paper, we define the parsimony score on networks as the sum of the substitution costs along all the edges of the network; and show that certain well-known algorithms that calculate the optimum parsimony score on trees, such as Sankoff and Fitch algorithms extend naturally for networks, barring conflicting assignments at the reticulate vertices. We provide heuristics for finding the optimum parsimony scores on networks. Our algorithms can be applied for any cost matrix that may contain unequal substitution costs of transforming between different characters along different edges of the network. We analyzed this for experimental data on 10 leaves or fewer with at most 2 reticulations and found that for almost all networks, the bounds returned by the heuristics matched with the exhaustively determined optimum parsimony scores.

The parsimony score we define here does not directly reflect the cost of the best tree in the network that displays the evolution of the character. However, when searching for the most parsimonious network that describes a collection of characters, it becomes necessary to add additional cost considerations to prefer simpler structures, such as trees over networks. The parsimony score on a network that we describe here takes into account the substitution costs along the additional edges incident on each reticulate vertex, in addition to the substitution costs along the other edges which are common to all the branching patterns introduced by the reticulate vertices. Thus the score contains an in-built cost for the number of reticulate vertices in the network, and would provide a criterion that is comparable among all networks. Although the problem of finding the parsimony score on the network is believed to be computationally hard to solve, heuristics such as the ones described here would be beneficial in our efforts to find a most parsimonious network.

Partial Text

Phylogenetic trees, or evolutionary trees, are the basic structures necessary to examine the relationships among organisms. Phylogenetic networks are generalizations of phylogenetic trees that are used to model evolutionary events when they are not only passed via vertical descent, but also by events such as horizontal exchange or recombination that cannot be modeled on a tree. Several different methods and criteria have been used to construct phylogenetic trees. The parsimony method is one such approach for inferring phylogenies, whose general idea was given in [1-3]. In this paper, our focus is on extending this approach to phylogenetic networks.

In the maximum parsimony problem, there are known character-states for a set of taxa (of the species) or Operational Taxonomic Units (OTUs). The problem is to find an order of branching and an ancestral configuration of character-states requiring the minimum number of character-state changes to account for the descent of the OTUs. Short of searching all possible networks, the problem is still in the early stage of being addressed. A more modest goal is to find maximum parsimony ancestral character-states for which both the current character-states and the network are known.

The authors declare that they have no competing interests.

WW conceived the study, and participated in its design and coordination, LK implemented the algorithms in OCAML. LK wrote the paper and WW proofread all versions of the manuscript during its preparation. All authors read and approved the final manuscript.

 

Source:

http://doi.org/10.1186/1748-7188-7-9

 

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