Does a tree-like phytogeny only exist at the tips in the prokaryotes?

Proceedings of the Royal Society B: Biological Sciences

Volumn 271, Issue 1557, 2004, Pages 2551-2558

  Creevey, Christopher J ^a   Fitzpatrick, David A ^a   Philip, Gayle K ^a   Kinsella, Rhoda J ^a   O'Connell, Mary J ^a   Pentony, Melissa M ^a   Travers, Simon A ^a   Wilkinson, Mark ^b   McInerney, James O ^a,b  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^b DEPARTMENT OF LIFE SCIENCES   (United Kingdom)

Author keywords

Molecular evolution; Phylogenetic supertrees; Phylogenomics; Prokaryotic phylogeny; Taxonomic congruence

Indexed keywords

PHYLOGENY; PROKARYOTE;

ARTICLE; COHESIVE GENOMIC SIGNAL; DATA BASE; EVOLUTION; GAMMAPROTEOBACTERIA; GENOME; GENOMIC INSTABILITY; HORIZONTAL GENE TRANSFER; NONHUMAN; PARALOGY; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; PROTEOBACTERIA; TAXON; BACTERIAL GENOME; BACTERIUM; BIOLOGICAL MODEL; CLASSIFICATION; COMPARATIVE STUDY; GENETICS; METHODOLOGY; STATISTICAL MODEL;

BACTERIA; CLASSIFICATION; GENE TRANSFER, HORIZONTAL; GENOME, BACTERIAL; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; PHYLOGENY;

EID: 16644395866     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2004.2864     Document Type: Article

References (31)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Asai, T., Zaporjets, D., Squires, C. & Squires, C. L. 1999 An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria. Proc. Natl Acad. Sci. USA 96, 1971-1976.
3. Baum, B. R. 1992 Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon. 41, 3-10.
4. Blattner, F. R. (and 16 others) 1997 The complete genome sequence of Escherichia coli K-12. Science 277, 1453-1474.
5. Brown, J. R. 2001 Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst. Biol. 50, 497-512.
6. Canback, B., Tamas, I. & Andersson, S. G. 2004 A phylogenomic study of endosymbiotic bacteria. Mol. Biol. Evol. 21, 1110-1122.
7. Curtis, T. P., Sloan, W. T. & Cannell, J. W. 2002 From the cover: estimating prokaryotic diversity and its limits. Proc. Natl Acad. Sci. USA 99, 10494-10499.
8. Daubin, V., Gouy, M. & Perriere, G. 2001 Bacterial molecular phylogeny using supertree approach. Genome Res. 12, 155-164.
9. Faith, D. P. & Cranston, P. S. 1991 Could a cladogram this short have arisen by chance alone? On permutation tests for cladistic structure. Cladistics 7, 1-28.
10. Felsenstein, J. 1993 PHYLIP: Phylogeny Inference package. Seattle, WA: distributed by author.
11. Hayashi, T. (and 21 others) 2001 Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8, 11-22.
12. Jain, R., Rivera, M. C. & Lake, J. A. 1999 Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA. 96, 3801-3806.
13. Jones, D. T., Taylor, W. R. & Thornton, J. M. 1994 A mutation data matrix for transmembrane proteins. FEBS Lett. 339, 269-275.
14. Kurland, C. G., Canback, B. & Berg, O. G. 2003 Horizontal gene transfer: a critical review. Proc. Natl Acad. Sci. USA 100, 9658-9662.
15. Lake, J. A. & Rivera, M. C. 2004 Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol. 21, 81-690.
16. Lapointe, F.-J. & Cucumel, G. 1997 The average consensus procedure: combination of weighted trees of containing identical or overlapping sets of taxa. Syst. Biol. 46, 306-312.
17. Lerat, E., Daubin, V. & Moran, N. A. 2003 From gene trees to organismal phylogeny in prokaryotes: the case of the γ-proteobacteria. PLoS Biol. 1, 1, 101-109.
18. Nakhleh, L., Warnow, T. & Linder, C.R. 2004 Reconstructing reticulate evolution in species-theory and practice. In Proceedings of the eighth annual conference on research in computational molecular biology, pp. 337-346. San Diego, CA: ACM Press
19. Philippe, H. & Germot, A. 2000 Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of sequence evolution. Mol. Biol. Evol. 17, 830-834.
20. Pisani, D., Yates, A. M., Langer, M. C. & Benton, M. J. 2002 A genus-level supertree of the Dinosauria. Proc. R. Soc. Lond. B 269, 915-921. (doi:10.1098/rspb.2001.1942)
21. Purvis, A. 1995 A composite estimate of primate phylogeny. Trans. R. Soc. Lond. B 348, 405-421.
22. Schmidt, H. A., Strimmer, K., Vingron, M. & von Haeseler, A. 2002 TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502-504.
23. Semple, C. & Steel, M. 2000 A supertree method for rooted trees. Discrete Appl. Math. 105, 147-158.
24. Swofford, D. L. 2002 PAUP*. Phylogenetic Analysis Using Parsimony (*and other methods), v.4. Sunderland, MA: Sinauer Associates.
25. Thompson, J. D., Higgins, D. G. & Gibson, T. J. 1994 CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
26. Thorley, J. L. & Wilkinson M. (2003) A view of supertree methods. In Bioconsensus. DIMACS series in discrete mathemetics and theoretical computer science, vol. 61 (ed. F.S. Roberts), pp. 185-194. New York: The American Mathematical Society.
27. Welch, R. A. (and 18 others) 2002 Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl Acad. Sci. USA 99, 17 020-17 024.
28. Whelan, S. & Goldman, N. 2001 A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18, 691-699.
29. Wilkinson, M. 1998 Split support and split conflict randomization tests in phylogenetic inference. Syst. Biol. 47, 673-695.
30. Wilkinson, M., Thorley, J. L., Littlewood, D. T. J. & Bray, R. A. 2001 Towards a phylogenetic supertree of Platyhelminthes? In Interrelationships of the Platyhelminthes (ed. R. A. Bray), pp. 292-301. London: Taylor and Francis.
31. Woese, C. R. 2002 On the evolution of cells. Proc. Natl Acad. Sci. USA 99, 8742-8747.