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ä Plots: A Tool for Analyzing Phylogenetic Distance Data

Citation

Holland, BR and Huber, KT and Dress, A and Moulton, V, a Plots: A Tool for Analyzing Phylogenetic Distance Data, Molecular Biology and Evolution, 19, (12) pp. 2051-2059. ISSN 0737-4038 (2002) [Refereed Article]


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The definitive publisher-authenticated version is available online at: www.oxfordjournals.org

DOI: doi:10.1093/oxfordjournals.molbev.a004030

Abstract

A method is described that allows the assessment of treelikeness of phylogenetic distance data before tree estimation. This method is related to statistical geometry as introduced by Eigen, Winkler-Oswatitsch, and Dress (1988 [Proc. Natl. Acad. Sci. USA. 85:5913–5917]), and in essence, displays a measure for treelikeness of quartets in terms of a histogram that we call a plot. This allows identification of nontreelike data and analysis of noisy data sets arising from processes such as, for example, parallel evolution, recombination, or lateral gene transfer. In addition to an overall assessment of treelikeness, individual taxa can be ranked by reference to the treelikeness of the quartets to which they belong. Removal of taxa on the basis of this ranking results in an increase in accuracy of tree estimation. Recombinant data sets are simulated, and the method is shown to be capable of identifying single recombinant taxa on the basis of distance information alone, provided the parents of the recombinant sequence are sufficiently divergent and the mixture of tree histories is not strongly skewed toward a single tree. Plots and taxon rankings are applied to three biological data sets using distances derived from sequence alignment, gene order, and fragment length polymorphism.

Item Details

Item Type:Refereed Article
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:62971
Year Published:2002
Web of Science® Times Cited:53
Deposited By:Mathematics
Deposited On:2010-03-31
Last Modified:2010-04-29
Downloads:0

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