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Systematic Biology 2007 56(1):57-67; doi:10.1080/10635150601167013
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© 2007 Society of Systematic Biologists

Imputing Supertrees and Supernetworks from Quartets

B. Holland1, Glenn Conner2, Katharina Huber3 and V. Moulton3

1 Allan Wilson Centre for Molecular Ecology and Evolution, Massey University Palmerston North, New Zealand E-mail: B.R.Holland{at}massey.ac.nz
2 Massey University Palmerston North, New Zealand
3 School of Computing Sciences, Untiversity of East Anglia Norwich, UK

Edited by Rod Page: Associate Editor


  Abstract

Inferring species phylogenies is an important part of understanding molecular evolution. Even so, it is well known that an accurate phylogenetic tree reconstruction for a single gene does not always necessarily correspond to the species phylogeny. One commonly accepted strategy to cope with this problem is to sequence many genes; the way in which to analyze the resulting collection of genes is somewhat more contentious. Supermatrix and supertree methods can be used, although these can suppress conflicts arising from true differences in the gene trees caused by processes such as lineage sorting, horizontal gene transfer, or gene duplication and loss. In 2004, Huson et al. (IEEE/ACM Trans. Comput. Biol. Bioinformatics 1:151–158) presented the Z-closure method that can circumvent this problem by generating a supernetwork as opposed to a supertree. Here we present an alternative way for generating supernetworks called Q-imputation. In particular, we describe a method that uses quartet information to add missing taxa into gene trees. The resulting trees are subsequently used to generate consensus networks, networks that generalize strict and majority-rule consensus trees. Through simulations and application to real data sets, we compare Q-imputation to the matrix representation with parsimony (MRP) supertree method and Z-closure, and demonstrate that it provides a useful complementary tool.

Keywords: Consensus networks; consensus trees; genome phylogeny; phylogenetic networks; phylogenetic trees; supernetworks; supertrees

Received April 5, 2006; Revised June 14, 2006; Accepted August 25, 2006
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J. B. Whitfield, S. A. Cameron, D. H. Huson, and M. A. Steel
Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees
Syst Biol, December 1, 2008; 57(6): 939 - 947.
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