© 2007 Society of Systematic Biologists
Conditioned Genome Reconstruction: How to Avoid Choosing the Conditioning Genome
1 Department of Mathematics and Statistics, Dalhousie University Halifax, Nova Scotia, B3H 3J5, Canada
2 Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia, B3H 4H7, Canada
3 Department of Mathematics, University of Auckland Private Bag 92019, Auckland, New Zealand
4 McGill Centre for Bioinformatics, McGill University 3775 University Street, Duff Medical Building, Montreal, Quebec, H3A 2B4, Canada
Edited by Olivier Gascuel: Associate Editors
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Abstract |
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Genome phylogenies can be inferred from data on the presence and absence of genes across taxa. Logdet distances may be a good method, because they allow expected genome size to vary across the tree. Recently, Lake and Rivera proposed conditioned genome reconstruction (calculation of logdet distances using only those genes present in a conditioning genome) to deal with unobservable genes that are absent from every taxon of interest. We prove that their method can consistently estimate the topology for almost any choice of conditioning genome. Nevertheless, the choice of conditioning genome is important for small samples. For real bacterial genome data, different choices of conditioning genome can result in strong bootstrap support for different tree topologies. To overcome this problem, we developed supertree methods that combine information from all choices of conditioning genome. One of these methods, based on the BIONJ algorithm, performs well on simulated data and may have applications to other supertree problems. However, an analysis of 40 bacterial genomes using this method supports an incorrect clade of parasites. This is a common feature of model-based gene content methods and is due to parallel gene loss.
Keywords: BIONJ; conditioned genome reconstruction; consistency; gene content; logdet; supertrees
Received January 18, 2006; Revised April 7, 2006; Accepted August 10, 2006
5 Current Address: School of Biological Sciences, University of Liverpool, Liverpool, L69 7ZB, UK; E-mail: m.spencer{at}liverpool.ac.uk
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