Beyond Bioinformatics

Title

New measures of topological stability in phylogenetic trees – Taking taxon composition into account

Authors

Dirk Krüger ^{1 ,2,*}, Andrea Gargas ¹

Affiliation

¹University of Wisconsin, Botany Department, 430 Lincoln Drive, Madison, WI 53706, USA, ² Current Address: University of Wisconsin, Department of Soil Science, 1525 Observatory Drive, Madison, WI 53706, USA

Email

dirkkrueger@wisc.edu; * Corresponding author

Article Type

Prediction Model

Date

received December 27, 2006; accepted December 28, 2006; published online December 28, 2006

Abstract

In phylogenetic trees the addition and removal of taxa has large effects on tree topology, hence measures of branch support and tree stability should account for taxonomic composition. Currently no comprehensive system of composition-dependent parameters exists in any cladistic or phenetic strategy. We introduce several values and indices based on a modification of the original jackknife resampling. Their advantage is a complete evaluation and optimization of taxon composition in phylogenetic data. While related to the Jackknife Monophyly Index (JMI), our system of support measures expands beyond parsimony analyses, and includes indices estimating support for the entire phylogenetic tree based on individual branch supports.

Keywords

phylogeny; tree topology; taxon composition; jackknife

Citation

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics Publishing Group

Copyright

Publisher

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.