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Science 12 November 2004:
Vol. 306. no. 5699, pp. 1172 - 1174
DOI: 10.1126/science.1102036
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Reports

Prospects for Building the Tree of Life from Large Sequence Databases

Amy C. Driskell,1,2* Cécile Ané,1{dagger}{ddagger} J. Gordon Burleigh,1{dagger} Michelle M. McMahon,1{dagger} Brian C. O'Meara,2{dagger} Michael J. Sanderson1

We assess the phylogenetic potential of ~300,000 protein sequences sampled from Swiss-Prot and GenBank. Although only a small subset of these data was potentially phylogenetically informative, this subset retained a substantial fraction of the original taxonomic diversity. Sampling biases in the databases necessitate building phylogenetic data sets that have large numbers of missing entries. However, an analysis of two "supermatrices" suggests that even data sets with as much as 92% missing data can provide insights into broad sections of the tree of life.

1 Section of Evolution and Ecology, University of California, One Shields Avenue, Davis, CA 95616, USA.
2 Center for Population Biology, University of California, One Shields Avenue, Davis, CA 95616, USA.



{dagger} These authors contributed equally to this work.

{ddagger} Present address: Department of Statistics, University of Wisconsin, Medical Science Center, 1300 University Avenue, Madison, WI 53706, USA.

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

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