This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Clarke, G. D. P.
Right arrow Articles by Charlebois, R. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Clarke, G. D. P.
Right arrow Articles by Charlebois, R. L.

 Previous Article  |  Next Article 

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.



This article has been cited by other articles:

  • Beiko, R. G., Doolittle, W. F., Charlebois, R. L. (2008). The Impact of Reticulate Evolution on Genome Phylogeny. Syst Biol 57: 844-856 [Abstract] [Full Text]  
  • Wellner, A., Gophna, U. (2008). Neutrality of Foreign Complex Subunits in an Experimental Model of Lateral Gene Transfer. Mol Biol Evol 25: 1835-1840 [Abstract] [Full Text]  
  • Papadopoulos, J. S., Agarwala, R. (2007). COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics 23: 1073-1079 [Abstract] [Full Text]  
  • Fukami-Kobayashi, K., Minezaki, Y., Tateno, Y., Nishikawa, K. (2007). A Tree of Life Based on Protein Domain Organizations. Mol Biol Evol 24: 1181-1189 [Abstract] [Full Text]  
  • Doolittle, W. F., Bapteste, E. (2007). Inaugural Article: Pattern pluralism and the Tree of Life hypothesis. Proc. Natl. Acad. Sci. USA 104: 2043-2049 [Abstract] [Full Text]  
  • Cavalier-Smith, T. (2006). Cell evolution and Earth history: stasis and revolution. Phil Trans R Soc B 361: 969-1006 [Abstract] [Full Text]  
  • Lienau, E. K., DeSalle, R., Rosenfeld, J. A., Planet, P. J. (2006). Reciprocal Illumination in the Gene Content Tree of Life. Syst Biol 55: 441-453 [Abstract] [Full Text]  
  • Lebrun, E., Santini, J. M., Brugna, M., Ducluzeau, A.-L., Ouchane, S., Schoepp-Cothenet, B., Baymann, F., Nitschke, W. (2006). The Rieske Protein: A Case Study on the Pitfalls of Multiple Sequence Alignments and Phylogenetic Reconstruction. Mol Biol Evol 23: 1180-1191 [Abstract] [Full Text]  
  • Kunin, V., Goldovsky, L., Darzentas, N., Ouzounis, C. A. (2005). The net of life: Reconstructing the microbial phylogenetic network. Genome Res 15: 954-959 [Abstract] [Full Text]  
  • Gu, X., Huang, W., Xu, D., Zhang, H. (2005). GeneContent: software for whole-genome phylogenetic analysis. Bioinformatics 21: 1713-1714 [Abstract] [Full Text]  
  • Gophna, U., Doolittle, W. F., Charlebois, R. L. (2005). Weighted Genome Trees: Refinements and Applications. J. Bacteriol. 187: 1305-1316 [Abstract] [Full Text]  
  • Kunin, V., Ahren, D., Goldovsky, L., Janssen, P., Ouzounis, C. A. (2005). Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res 33: 616-621 [Abstract] [Full Text]  
  • Yang, S., Doolittle, R. F., Bourne, P. E. (2005). Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. USA 102: 373-378 [Abstract] [Full Text]  
  • Charlebois, R. L., Doolittle, W. F. (2004). Computing prokaryotic gene ubiquity: Rescuing the core from extinction. Genome Res 14: 2469-2477 [Abstract] [Full Text]  
  • Novichkov, P. S., Omelchenko, M. V., Gelfand, M. S., Mironov, A. A., Wolf, Y. I., Koonin, E. V. (2004). Genome-Wide Molecular Clock and Horizontal Gene Transfer in Bacterial Evolution. J. Bacteriol. 186: 6575-6585 [Abstract] [Full Text]  
  • Gu, X., Zhang, H. (2004). Genome Phylogenetic Analysis Based on Extended Gene Contents. Mol Biol Evol 21: 1401-1408 [Abstract] [Full Text]  
  • Teeling, H., Lombardot, T., Bauer, M., Ludwig, W., Glockner, F. O. (2004). Evaluation of the phylogenetic position of the planctomycete 'Rhodopirellula baltica' SH 1 by means of concatenated ribosomal protein sequences, DNA-directed RNA polymerase subunit sequences and whole genome trees. Int. J. Syst. Evol. Microbiol. 54: 791-801 [Abstract] [Full Text]  
  • Lynn, D. J., Singer, G. A. C., Hickey, D. A. (2002). Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 30: 4272-4277 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»