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Groves of Phylogenetic Trees
C\'{e}cile An\'{e}1, Oliver Eulenstein2, Raul Piaggio-Talice2, and Michael J. Sanderson3
1Departments of Statistics and of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA
ane@stat.wisc.edu
2Department of Computer Science, Iowa State University, Ames, IA 50011-1041, USA
{oeulenst, rpiaggio}@cs.iastate.edu
3Department of Ecology and Evolutionary Biology, University of Arizona, Tucson 85721, USA
sanderm@email.arizona.edu
Annals of Combinatorics 13 (2) pp.139-167 June, 2009
AMS Subject Classification: 05C05, 68R10, 92D15
Abstract:
A major challenge in biological sciences is the reconstruction of the Tree of Life. To this effect, large genomic databases like GenBank and SwissProt are being mined for clusters from which phylogenies can be inferred. Systematists and comparative biologists commonly combine such phylogenies into informative supertrees that reveal information which was not explicitly displayed in any of the original phylogenies. However, whether a supertree is informative depends on particular overlap properties among the clusters from which it originates. In this work we formally introduce the concept of groves --- sets of clusters with the potential to construct informative supertrees. Thus maximal potential candidate clusters for informative supertree construction can be identified in large databases through groves, prior to inferring trees for each cluster. Groves also have the potential to lead to informative supermatrix construction. We developed methods that (i) efficiently identify particular types of groves and (ii) find lower and upper bounds on the minimal number of groves needed to cover all the trees or data sets in a database. Finally, we apply our methods to the green plant sequences from GenBank.
Keywords: supertree, supermatrix, triplets, clustering, evolution

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