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MBE Advance Access originally published online on May 30, 2003
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Mol. Biol. Evol. 20(7):1036-1042. 2003
DOI: 10.1093/molbev/msg115
© 2003 by the Society for Molecular Biology and Evolution. ISSN: 0737-4038

Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases

Michael J. Sanderson*,, Amy C. Driskell*, Richard H. Ree{dagger}, Oliver Eulenstein{ddagger} and Sasha Langley*

* Section of Evolution and Ecology, University of California, Davis
{dagger} Botanical Garden and Centre for Plant Research, University of British Columbia
{ddagger} Department of Computer Science, Iowa State University

E-mail: mjsanderson{at}ucdavis.edu.

To improve the accuracy of tree reconstruction, phylogeneticists are extracting increasingly large multigene data sets from sequence databases. Determining whether a database contains at least k genes sampled from at least m species is an NP-complete problem. However, the skewed distribution of sequences in these databases permits all such data sets to be obtained in reasonable computing times even for large numbers of sequences. We developed an exact algorithm for obtaining the largest multigene data sets from a collection of sequences. The algorithm was then tested on a set of 100,000 protein sequences of green plants and used to identify the largest multigene ortholog data sets having at least 3 genes and 6 species. The distribution of sizes of these data sets forms a hollow curve, and the largest are surprisingly small, ranging from 62 genes by 6 species, to 3 genes by 65 species, with more symmetrical data sets of around 15 taxa by 15 genes. These upper bounds to sequence concatenation have important implications for building the tree of life from large sequence databases.

Key Words: biclique • NP-complete • sequence concatenation • phylogeny • optimization


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