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Imputing Supertrees and Supernetworks from Quartets


Holland, BR and Conner, G and Huber, K and Moulton, V, Imputing Supertrees and Supernetworks from Quartets, Systematic Biology, 56, (1) pp. 57-67. ISSN 1063-5157 (2007) [Refereed Article]

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DOI: doi:10.1080/10635150601167013


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.

Item Details

Item Type:Refereed Article
Keywords:Consensus networks; consensus trees; genome phylogeny; phylogenetic networks; phylogenetic trees; supernetworks; supertrees
Research Division:Mathematical Sciences
Research Group:Applied mathematics
Research Field:Biological mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the mathematical sciences
UTAS Author:Holland, BR (Professor Barbara Holland)
ID Code:62980
Year Published:2007
Web of Science® Times Cited:30
Deposited By:Mathematics
Deposited On:2010-03-31
Last Modified:2010-04-30

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