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Science 3 March 2006:
Vol. 311. no. 5765, pp. 1283 - 1287
DOI: 10.1126/science.1123061
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Reports

Toward Automatic Reconstruction of a Highly Resolved Tree of Life

Francesca D. Ciccarelli,1,2,3* Tobias Doerks,1* Christian von Mering,1 Christopher J. Creevey,1 Berend Snel,4 Peer Bork1,5{dagger}

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of {delta}-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.

1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany.
2 Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milan, Italy.
3 Institute of Molecular Oncology Foundation, Fondazione Italiana per la Ricerca sul Cancro, Via Adamello 16, 20139 Milan, Italy.
4 Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Center, Toernooiveld 1, 6525 ED, Nijmegen, Netherlands.
5 Max Delbrück Centrum, 13092 Berlin-Buch, Germany.

* These authors contributed equally to this work.

{dagger} To whom correspondence should be addressed. E-mail: peer.bork{at}embl.de

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