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Systematic Biology 2007 56(3):431-444; doi:10.1080/10635150701411279
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© 2007 Society of Systematic Biologists

Resource-Aware Taxon Selection for Maximizing Phylogenetic Diversity

Fabio Pardi and Nick Goldman

EMBL—European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK E-mail: pardi{at}ebi.ac.uk (F.P.)

Edited by Mike Steel: Associate Editor


  Abstract

Phylogenetic diversity (PD) is a useful metric for selecting taxa in a range of biological applications, for example, bioconservation and genomics, where the selection is usually constrained by the limited availability of resources. We formalize taxon selection as a conceptually simple optimization problem, aiming to maximize PD subject to resource constraints. This allows us to take into account the different amounts of resources required by the different taxa. Although this is a computationally difficult problem, we present a dynamic programming algorithm that solves it in pseudo-polynomial time. Our algorithm can also solve many instances of the Noah's Ark Problem, a more realistic formulation of taxon selection for biodiversity conservation that allows for taxon-specific extinction risks. These instances extend the set of problems for which solutions are available beyond previously known greedy-tractable cases. Finally, we discuss the relevance of our results to real-life scenarios.

Keywords: Biodiversity conservation; comparative genomics; dynamic programming; phylogenetic diversity; Noah's Ark Problem; species choice; taxon selection

Received September 21, 2006; Revised November 16, 2006; Accepted December 29, 2006
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B. Q. Minh, S. Klaere, and A. von Haeseler
Taxon Selection under Split Diversity
Syst Biol, December 1, 2009; 58(6): 586 - 594.
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