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

 Previous Article  |  Next Article 

Journal of Bacteriology, February 2005, p. 1305-1316, Vol. 187, No. 4
0021-9193/05/$08.00+0     doi:10.1128/JB.187.4.1305-1316.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Weighted Genome Trees: Refinements and Applications

Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University Halifax, Nova Scotia,¹ NeuroGadgets Inc., Ottawa, Ontario, Canada²

Received 13 April 2004/ Accepted 4 November 2004

There are many ways to group completed genome sequences in hierarchical patterns (trees) reflecting relationships between their genes. Such groupings help us organize biological information and bear crucially on underlying processes of genome and organismal evolution. Genome trees make use of all comparable genes but can variously weight the contributions of these genes according to similarity, congruent patterns of similarity, or prevalence among genomes. Here we explore such possible weighting strategies, in an analysis of 142 prokaryotic and 5 eukaryotic genomes. We demonstrate that alternate weighting strategies have different advantages, and we propose that each may have its specific uses in systematic or evolutionary biology. Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution.

Supplemental material for this article may be found at http://jb.asm.org/.

This article has been cited by other articles:

• 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]  
• Mongodin, E. F., Nelson, K. E., Daugherty, S., DeBoy, R. T., Wister, J., Khouri, H., Weidman, J., Walsh, D. A., Papke, R. T., Sanchez Perez, G., Sharma, A. K., Nesbo, C. L., MacLeod, D., Bapteste, E., Doolittle, W. F., Charlebois, R. L., Legault, B., Rodriguez-Valera, F. (2005). The genome of Salinibacter ruber: Convergence and gene exchange among hyperhalophilic bacteria and archaea. Proc. Natl. Acad. Sci. USA 102: 18147-18152 [Abstract] [Full Text]  
• Konstantinidis, K. T., Tiedje, J. M. (2005). Towards a Genome-Based Taxonomy for Prokaryotes. J. Bacteriol. 187: 6258-6264 [Abstract] [Full Text]  
• van Passel, M. W. J., Bart, A., van der Ende, A. (2005). Default taxonomy and the genomics era. Microbiology 151: 2818-2820 [Full Text]