MBE Advance Access originally published online on October 5, 2006
Molecular Biology and Evolution 2007 24(1):130-136; doi:10.1093/molbev/msl140
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Research Articles |
Rooting the Tree of Life Using Nonubiquitous Genes
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* Department of MCD Biology, University of California
Molecular Biology Institute, University of California
Department of Human Genetics, University of California
UCLA NASA Astrobiology Institute, University of California
E-mail: lake{at}mbi.ucla.edu.
Accepted for publication September 29, 2006.
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 nonubiquitous 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.
Key Words: tree of life • root • indels • cenancestor • double-membrane prokaryotes
Martin Embley, Associate Editor
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