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Selecting taxa to save or sequence : desirable criteria and a greedy solution.

Bordewich, M. and Rodrigo, A. G. and Semple, C. (2008) 'Selecting taxa to save or sequence : desirable criteria and a greedy solution.', Systematic biology., 57 (6). pp. 825-834.

Abstract

Three desirable properties for any method of selecting a subset of evolutionary units (EUs) for conservation or for genomic sequencing are discussed. These properties are spread, stability, and applicability. We are motivated by a practical case in which the maximization of phylogenetic diversity (PD), which has been suggested as a suitable method, appears to lead to counterintuitive collections of EUs and does not meet these three criteria. We define a simple greedy algorithm (GreedyMMD) as a close approximation to choosing the subset that maximizes the minimum pairwise distance (MMD) between EUs. GreedyMMD satisfies our three criteria and may be a useful alternative to PD in real-world situations. In particular, we show that this method of selection is suitable under a model of biodiversity in which features arise and/or disappear during evolution. We also show that if distances between EUs satisfy the ultrametric condition, then GreedyMMD delivers an optimal subset of EUs that maximizes both the minimum pairwise distance and the PD. Finally, because GreedyMMD works with distances and does not require a tree, it is readily applicable to many data sets.

Item Type:Article
Keywords:Biodiversity conservation, Greedy algorithm, Phylogenetic diversity.
Full text:Full text not available from this repository.
Publisher Web site:http://dx.doi.org/10.1080/10635150802552831
Record Created:21 Dec 2009 16:05
Last Modified:19 Aug 2010 14:38

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