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MBE Advance Access published online on October 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl140
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted September 29, 2006

Research Article

Rooting the Tree of Life Using Non-ubiquitous Genes

James A. Lake 1 *, Craig W. Herbold 2, Maria C. Rivera 3, Jacqueline A. Servin 2, and Ryan G. Skophammer 3

1 Department of MCD Biology, University of California, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, CA 90095, USA; UCLA NASA Astrobiology Institute, University of California, Los Angeles, CA 90095, USA
2 Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA; UCLA NASA Astrobiology Institute, University of California, Los Angeles, CA 90095, USA
3 Department of MCD Biology, University of California, Los Angeles, CA 90095, USA; UCLA NASA Astrobiology Institute, University of California, Los Angeles, CA 90095, USA

* To whom correspondence should be addressed.
James A. Lake, E-mail: Lake{at}mbi.ucla.edu


  Abstract

Insertion and deletion (indel) based analyses have great potential for rooting the tree of life, but their use has been limited because they require ubiquitous sequences that have not been horizontally/laterally transferred. Very few such sequences exist. Here we describe and demonstrate a new algorithm that can use non-ubiquitous sequences for rooting. This algorithm, top-down indel rooting, uses the traditional logical framework of indel rooting, but by considering gene gains and losses in addition to indel gains and losses it is able to analyze incomplete data sets. The method is demonstrated using theoretical examples, and incomplete gene sets. In particular, it is applied to the well studied Hsp70/MreB indel, a sequence set thought to have been compromised by gene transfers from firmicutes to archaebacteria. By sequentially assigning all observable character states, including gene absences, to the questionable archaebacterial Hsp70- and MreB-sequences, we demonstrate that this gene set robustly excludes the root of the tree of life from the Gram negative, double membrane prokaryotes independently of the archaeal character states. There are very few ubiquitous paralog gene sets, and most of them contain compromised data. The ability of top-down rooting to use incomplete and/or compromised gene sets promises to make rooting analyses more robust and to greatly increase the number of useful indel sets.

Keywords: Tree of life; Root; Indels; Cenancestor; Double Membrane Prokaryotes.
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