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Imputing Supertrees and Supernetworks from Quartets
Citation
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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The definitive publisher-authenticated version is available online at: www.oxfordjournals.org
DOI: doi:10.1080/10635150601167013
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.
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 |
| Author: | Holland, BR (Associate Professor Barbara Holland) |
| ID Code: | 62980 |
| Year Published: | 2007 |
| Web of Science® Times Cited: | 28 |
| Deposited By: | Mathematics |
| Deposited On: | 2010-03-31 |
| Last Modified: | 2010-04-30 |
| Downloads: | 0 |
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