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MBE Advance Access published online on May 30, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg115
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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Accepted January 29, 2003
© 2003 Society for Molecular Biology and Evolution

Original Articles

Obtaining Maximal Concatenated Phylogenetic Data Sets from Large Sequence Databases

Michael J. Sanderson 1*, Amy C. Driskell 1, Richard H. Ree 1, Oliver Eulenstein 2, Sasha Langley 1

1 Section of Evolution and Ecology, University of California, Davis, California, 95616 USA
2 Department of Computer Science, Iowa State University, Ames, IA 50011, USA

* To whom correspondence should be addressed. E-mail: mjsanderson{at}ucdavis.edu.


  Abstract

To improve the accuracy of tree reconstruction, phylogeneticists are extracting increasingly large multi-gene 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 multi-gene 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 multi-gene 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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