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May 2003 Applying the Bootstrap in Phylogeny Reconstruction
Pamela S. Soltis, Douglas E. Soltis
Statist. Sci. 18(2): 256-267 (May 2003). DOI: 10.1214/ss/1063994980


With the increasing emphasis in biology on reconstruction of phylogenetic trees, questions have arisen as to how confident one should be in a given phylogenetic tree and how support for phylogenetic trees should be measured. Felsenstein suggested that bootstrapping be applied across characters of a taxon-by-character data matrix to produce replicate "bootstrap data sets," each of which is then analyzed phylogenetically, with a consensus tree constructed to summarize the results of all replicates. The proportion of trees/replicates in which a grouping is recovered is presented as a measure of support for that group. Bootstrapping has become a common feature of phylogenetic analysis. However, the interpretation of bootstrap values remains open to discussion, and phylogeneticists have used these values in multiple ways. The usefulness of phylogenetic bootstrapping is potentially limited by a number of features, such as the size of the data matrix and the underlying assu! mptions of the phylogeny reconstruction program. Recent studies have explored the application of bootstrapping to large data sets and the relative performance of bootstrapping and jackknifing.


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Pamela S. Soltis. Douglas E. Soltis. "Applying the Bootstrap in Phylogeny Reconstruction." Statist. Sci. 18 (2) 256 - 267, May 2003.


Published: May 2003
First available in Project Euclid: 19 September 2003

zbMATH: 1331.62441
MathSciNet: MR2026084
Digital Object Identifier: 10.1214/ss/1063994980

Keywords: bootstrap , jackknife , phylogeny , Support

Rights: Copyright © 2003 Institute of Mathematical Statistics


Vol.18 • No. 2 • May 2003
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