VI.1 Tree of Life

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Peer Bork

Francesca Ciccarelli

Berend Snel

Chris Creevey

Christian Von Mering

This map by computational biologist Peer Bork, oncologist Francesca Ciccarelli, and bioinformatics researchers Chris Creevey, Berend Snel, and Christian von Mering shows the global phylogeny of 191 species whose genomes have been fully sequenced. The green subtree presents ‘Archaea,’ a group of single-celled microorganisms. Given in red are ‘Eukaryota’—organisms whose cells contain complex structures inside the membranes. ‘Bacteria’ are colored blue. Labels and color shadings indicate various frequently used subdivisions. The branch separating ‘Eukaryota’ and ‘Archaea’ from ‘Bacteria’ in this unrooted tree has been shortened for display purposes. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It was constructed using an automatic procedure that generates a tree with branch lengths comparable across all three domains. The result revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing the confirmation of accepted relationships and the resolution of disputed and preliminary classifications. An interactive tree of life application is at http://itol.embl.de.


References:

Ciccarelli, Francesca, Tobias Doerks, Christian Von Mering, Christopher J. Creevey, Berend Snel, Peer Bork. 2006. “Toward Automatic Reconstruction of a Highly Resolved Tree of Life.” Science 311 (5765): 1283-1287.

Bork, Peer, Francesca Ciccarelli, Berend Snel, Christian von Mering, and Chris Creevey. 2006. Tree of Life. Courtesy of European Molecular Biology Laboratory. In “6th Iteration (2009): Science Maps for Scholars,” Places & Spaces: Mapping Science, edited by Katy Börner and Elisha F. Hardy. http://scimaps.org

Acknowledgements: This exhibit is supported by the National Science Foundation under Grant No. IIS-0238261, CHE-0524661, IIS-0534909 and IIS-0715303, the James S. McDonnell Foundation; Thomson Reuters; the Cyberinfrastructure for Network Science Center, University Information Technology Services, and the School of Library and Information Science, all three at Indiana University. Some of the data used to generate the science maps is from the Web of Science by Thomson Reuters and Scopus by Elsevier. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.