Maximum Parsimony on Phylogenetic networks

作者：Lavanya Kannan, Ward C. Wheeler · 发表于：Algorithms for Molecular Biology · 年份：2012 · DOI：10.1186/1748-7188-7-9 · 被引用次数：112 · 研究领域：Genomics and Phylogenetic Studies、Evolution and Paleontology Studies、Genome Rearrangement Algorithms

BACKGROUND: 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. RESULTS: 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. CONCLUSION: The parsimony score we define here does not directly reflect the cost of the best tree in the n...