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Imputing Supertrees and Supernetworks from Quartets
journal contribution
posted on 2023-05-17, 02:19 authored by Barbara HollandBarbara Holland, Conner, G, Huber, K, Moulton, VInferring 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.
History
Publication title
Systematic BiologyVolume
56Pagination
57-67ISSN
1063-5157Department/School
School of Natural SciencesPublisher
Oxford University PressPlace of publication
Oxford, EnglandRights statement
The definitive publisher-authenticated version is available online at: www.oxfordjournals.orgRepository Status
- Restricted