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Journal of Bacteriology, April 2002, p. 2072-2080, Vol. 184, No. 8
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.8.2072-2080.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Inferring Genome Trees by Using a Filter To Eliminate Phylogenetically Discordant Sequences and a Distance Matrix Based on Mean Normalized BLASTP Scores

G. D. Paul Clarke,1 Robert G. Beiko,2 Mark A. Ragan,3,4* and Robert L. Charlebois1,2,4

NeuroGadgets Inc., Ottawa, Ontario K1G 4B5,,1 Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada, and,2 The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia,3 Program in Evolutionary Biology, Canadian Institute for Advanced Research,4

Received 31 October 2001/ Accepted 14 January 2002

Darwin's paradigm holds that the diversity of present-day organisms has arisen via a process of genetic descent with modification, as on a bifurcating tree. Evidence is accumulating that genes are sometimes transferred not along lineages but rather across lineages. To the extent that this is so, Darwin's paradigm can apply only imperfectly to genomes, potentially complicating or perhaps undermining attempts to reconstruct historical relationships among genomes (i.e., a genome tree). Whether most genes in a genome have arisen via treelike (vertical) descent or by lateral transfer across lineages can be tested if enough complete genome sequences are used. We define a phylogenetically discordant sequence (PDS) as an open reading frame (ORF) that exhibits patterns of similarity relationships statistically distinguishable from those of most other ORFs in the same genome. PDSs represent between 6.0 and 16.8% (mean, 10.8%) of the analyzable ORFs in the genomes of 28 bacteria, eight archaea, and one eukaryote (Saccharomyces cerevisiae). In this study we developed and assessed a distance-based approach, based on mean pairwise sequence similarity, for generating genome trees. Exclusion of PDSs improved bootstrap support for basal nodes but altered few topological features, indicating that there is little systematic bias among PDSs. Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree.

* Corresponding author. Mailing address: The Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld 4072, Australia. Phone: 61-7-3365-1160. Fax: 61-7-3365-4388. E-mail: m.ragan{at}imb.uq.edu.au.

Journal of Bacteriology, April 2002, p. 2072-2080, Vol. 184, No. 8
0021-9193/02/$04.00+0     DOI: 10.1128/JB.184.8.2072-2080.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



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