© 2007 Society of Systematic Biologists
Experimental Design Criteria in Phylogenetics: Where to Add Taxa
1 Laboratory of Plant Systematics K. U. Leuven, Belgium
2 EMBL-European Bioinformatics Institute Hinxton, United Kingdom
3 Department of Biosystems K. U. Leuven, Belgium
4 Nationaal Herbarium Nederland, Universiteit Leiden Branch Leiden, The Netherlands
Edited by Olivier Gascuel: Associate Editor
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Abstract |
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Accurate phylogenetic inference is a topic of intensive research and debate and has been studied in response to many different factors: for example, differences in the method of reconstruction, the shape of the underlying tree, the substitution model, and varying quantities and types of data. Investigating whether the conditions used might lead to inaccurate inference has been attempted through elaborate data exploration but less attention has been given to creating a unified methodology to enable experimental designs in phylogenetic analysis to be improved and so avoid suboptimal conditions. Experimental design has been part of the field of statistics since the seminal work of Fisher in the early 20th century and a large body of literature exists on how to design optimum experiments. Here we investigate the use of the Fisher information matrix to decide between candidate positions for adding a taxon to a fixed topology, and introduce a parameter transformation that permits comparison of these different designs. This extension to Goldman (1998. Proc. R. Soc. Lond. B. 265: 1779–1786) thus allows investigation of "where to add taxa" in a phylogeny. We compare three different measures of the total information for selecting the position to add a taxon to a tree. Our methods are illustrated by investigating the behavior of the three criteria when adding a branch to model trees, and by applying the different criteria to two biological examples: a simplified taxon-sampling problem in the balsaminoid Ericales and the phylogeny of seed plants.
Keywords: A-optimality; D-optimality; E-optimality; experimental design; Fisher information; phylogenetics; taxon sampling
Received October 12, 2006; Revised January 29, 2007; Accepted April 8, 2007
5 Present Address: Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, USA; E-mail: koen.geuten{at}yale.edu
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