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Systematic Biology Advance Access originally published online on September 21, 2009
Systematic Biology 2009 58(6):586-594; doi:10.1093/sysbio/syp058
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© The Author(s) 2009. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Taxon Selection under Split Diversity

Bui Quang Minh1,2,3,4, Steffen Klaere1,2,3,4,5,* and Arndt von Haeseler1,2,3,4

1 Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Dr.-Bohr-Gasse 9/6, 1030 Vienna, Austria
2 University of Vienna, Dr.-Bohr-Gasse 9/6, 1030 Vienna, Austria
3 Medical University of Vienna, Dr.-Bohr-Gasse 9/6, 1030 Vienna, Austria
4 Veterinary University of Vienna, Dr.-Bohr-Gasse 9/6, 1030 Vienna, Austria
5 Department of Mathematics, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand

* Correspondence to be sent to: Department of Mathematics, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand; E-mail: steffen.klaere{at}gmail.com.


  Abstract

The "phylogenetic diversity" (PD) measure of biodiversity is evaluated using a phylogenetic tree, usually inferred from morphological or molecular data. Consequently, it is vulnerable to errors in that tree, including those resulting from sampling error, model misspecification, or conflicting signals. To improve the robustness of PD, we can evaluate the measure using either a collection (or distribution) of trees or a phylogenetic network. Recently, it has been shown that these 2 approaches are equivalent but that the problem of maximizing PD in the general concept is NP-hard. In this study, we provide an efficient dynamic programming algorithm for maximizing PD when splits in the trees or network form a circular split system. We illustrate our method using a case study of game birds ("Galliformes") and discuss the different choices of taxa based on our approach and PD.

Keywords: Biodiversity conservation; dynamic programming; phylogenetic diversity; phylogenetic network; split diversity; split system

Received October 3, 2008; Revised January 21, 2009; Accepted August 10, 2009

Associate Editor: Lars Jermiin


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