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Systematic Biology 2006 55(5):769-773; doi:10.1080/10635150600981604
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© 2006 Society of Systematic Biologists

Phylogenetic Diversity within Seconds

Bui Quang Minh, Steffen Klaere and Arndt von Haeseler

Center for Integrative Bioinformatics, Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Veterinary University of Vienna Dr.-Bohr-Gasse 9/6, A-1030, Vienna, Austria E-mail: arndt.von.haeseler{at}univie.ac.at (A.v.H.)

Edited by Mike Steel: Associate Editor


  Abstract

We consider a (phylogenetic) tree with n labeled leaves, the taxa, and a length for each branch in the tree. For any subset of k taxa, the phylogenetic diversity is defined as the sum of the branch-lengths of the minimal subtree connecting the taxa in the subset. We introduce two time-efficient algorithms (greedy and pruning) to compute a subset of size k with maximal phylogenetic diversity in O(n log k) and O[n + (n–k) log (n–k)] time, respectively. The greedy algorithm is an efficient implementation of the so-called greedy strategy (Steel, 2005; Pardi and Goldman, 2005), whereas the pruning algorithm provides an alternative description of the same problem. Both algorithms compute within seconds a subtree with maximal phylogenetic diversity for trees with 100,000 taxa or more.

Keywords: Biodiversity conservation; Comparative genomics; Greedy algorithm; Phylogenetic diversity; Phylogenetic tree; Pruning algorithm

Received March 7, 2006; Revised April 21, 2006; Accepted June 15, 2006
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