Visualizing and assessing phylogenetic congruence of core gene sets: A case study of the γ-proteobacteria

Molecular Biology and Evolution

Volumn 23, Issue 5, 2006, Pages 1019-1030

  Susko, E ^a   Leigh, J ^b   Doolittle, W F ^b   Bapteste, E ^c  

^a DALHOUSIE UNIVERSITY   (Canada)

^b DALHOUSIE UNIVERSITY   (Canada)

^c NONE

Author keywords

proteobacteria; Congruence; Heat map; Phylogeny

Indexed keywords

ANALYTIC METHOD; ARTICLE; CLUSTER ANALYSIS; GAMMAPROTEOBACTERIA; GENE MAPPING; GENE SEQUENCE; GENE TRANSFER; GENETIC ANALYSIS; GENOME ANALYSIS; HUMAN; HUMAN CELL; INHERITANCE; PHYLOGENY; PROTEOBACTERIA; RISK ASSESSMENT; SEQUENCE ALIGNMENT;

DATA INTERPRETATION, STATISTICAL; EVOLUTION; EVOLUTION, MOLECULAR; GAMMAPROTEOBACTERIA; GENE TRANSFER, HORIZONTAL; GENES, BACTERIAL; GENETICS; GENOME, BACTERIAL; GENOMICS; HEAT; MODELS, GENETIC; PHYLOGENY;

GAMMAPROTEOBACTERIA;

EID: 33646584164     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msj113     Document Type: Article

References (46)

1. Alon, U., Barkai, N., Notterman, D. A., Gish, K., Ybarra, S., Mack, D., and A. J. Levine. 1999. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745-6750.
2. Baldauf, S. L., A. J. Roger, I. Wenk-Siefert, and W. F. Doolittle. 2000. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science 290:972-977.
3. Bapteste, E., Y. Boucher, J. Leigh, and W. F. Doolittle. 2004. Phylogenetic reconstruction and lateral gene transfer. Trends Microbiol. 12:406-411.
4. Bapteste, E., H. Brinkmann, J. A. Lee et al. (11 co-authors). 2002. The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba. Proc. Natl. Acad. Sci. USA 99:1414-1419.
5. Bapteste, E., E. Susko, J. Leigh, D. MacLeod, R. L. Charlebois, and W. F. Doolittle. 2005. Do orthologous gene phylogenies really support tree-thinking? BMC Evol. Biol. 5:33.
6. Brochier, C., E. Bapteste, D. Moreira, and H. Philippe. 2002. Eubacterial phylogeny based on translational apparatus proteins. Trends Genet. 18:1-5.
7. Brown, J. R., and C. Volker. 2004. Phylogeny of gamma-proteobacteria: resolution of one branch of the universal tree? Bioessays 26:463-468.
8. Calinski, R. B., and J. Harabasz. 1974. A dendrite method for cluster analysis. Commun. Stat. 3:1-27.
9. Creevey, C. J., D. A. Fitzpatrick, G. K. Philip, R. J. Kinsella, M. J. O'Connell, M. M. Pentony, S. A. Travers, M. Wilkinson, and J. O. McInerney. 2004. Does a tree-like phylogeny only exist at the tips in the prokaryotes? Proc. R. Soc. Lond. B Biol. Sci. 271:2551-2558.
10. Darwin, C. 1859. On the origin of species. John Murray, London.
11. Deppenmeier, U., A. Johann, T. Hartsch, et al. (20 co-authors). 2002. The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J. Mol. Microbiol. Biotechnol. 4:453-461.
12. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
13. Feyerabend, P. 1975. Against method. Verso, London.
14. Flintoft, L. 2003. Family tree for gamma-proteobacteria. Nat. Rev. Microbiol. 1:1.
15. Getz, G., H. Gal, I. Kela, D. A. Notterman, and E. Domany. 2003. Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data. Bioinformatics 19:1079-1089.
16. Getz, G., E. Levine, and E. Domany. 2000. Coupled two-way clustering analysis of gene microarray data. Proc. Natl. Acad. Sci. USA 97:12079-12084.
17. Gordon, A. 1999. Classification. Chapman-Hall, London.
18. Grassly, N. C., J. Adachi, and A. Rambaut. 1997. PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:559-560.
19. Harris, J. K., S. T. Kelley, G. B. Spiegelman, and N. R. Pace. 2003. The genetic core of the universal ancestor. Genome Res. 13:407-412.
20. Jain, R., M. C. Rivera, and J. A. Lake. 1999. Horizontal gene transfer among genomes: The complexity hypothesis. Proc. Natl. Acad. Sci. USA 96:3801-3806.
21. Krzankowski, W. J., and Y. T. Lai. 1985. A criterion for determining the number of groups in a data set using sum of squares clustering. Biometrics 44:22-34.
22. Kuhn, T. 1962. The structure of scientific revolutions. University of Chicago Press, Chicago, Ill.
23. Kumar, S., and A. Rzhetsky. 1996. Evolutionary relationships of eukaryotic kingdoms. J. Mol. Evol. 42:183-193.
24. Kurland, C. G., B. Canback, and O. G. Berg. 2003. Horizontal gene transfer: a critical view. Proc. Natl. Acad. Sci. USA 100:9658-9662.
25. Lake, J. A., and M. C. Rivera. 2004. Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction. Mol. Biol. Evol. 21:681-690.
26. Lerat, E., V. Daubin, and N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-proteobacteria. PLoS Biol. 1:E19.
27. MacLeod, D., R. L. Charlebois, F. Doolittle, and E. Bapteste. 2005. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. BMC Evol. Biol. 5:27.
28. Mardia, K. V., J. T. Kent, and J. M. Bibby. 1979. Multivariate analysis. Academic Press, London.
29. Matte-Tailliez, O., C. Brochier, P. Forterre, and H. Philippe. 2002. Archaeal phylogeny based on ribosomal proteins. Mol. Biol. Evol. 5:631-639.
30. Milligan, G. W., and M. C. Cooper. 1985. An examination of procedures for determining the number of clusters in a data set. Psychometrika 50:159-179.
31. Nelson, K. E., R. A. Clayton, S. R. Gill, et al. (20 co-authors). 1999. Evidence for lateral gene transfer between archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329.
32. Nesbo, C. L., Y. Boucher, and W. F. Doolittle. 2001. Defining the core of nontransferable prokaryotic genes: the euryarchaeal core. J. Mol. Evol. 53:340-350.
33. Philippe, H. 1993. MUST, a computer package of management utilities for sequences and trees. Nucleic Acids Res. 21:5264-5272.
34. Philippe, H., and C. J. Douady. 2003. Horizontal gene transfer and phylogenetics. Curr. Opin. Microbiol. 6:498-505.
35. Raymond, J., O. Zhaxybayeva, J. P. Gogarten, S. Y. Gerdes, and R. E. Blankenship. 2002. Whole-genome analysis of photosynthetic prokaryotes. Science 298:1616-1620.
36. Schmidt, H. A., K. Strimmer, M. Vingron, and A. von Haeseler. 2002. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504.
37. Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492-508.
38. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116.
39. Shimodaira, H., and M. Hasegawa. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
40. Snel, B., M. A. Huynen, and B. E. Dutilh. 2005. Genome trees and the nature of genome evolution. Annu Rev Microbiol 59:191-209.
41. Somogyi, R., S. Fuhrman, G. Anderson, C. Madill, L. D. Greller, and B. Chang. 2004. Systematic exploration and mining of gene expression data provides evidence for higher-order, modular regulation. Pp. 202-221 in Ga G. P. W. Schlosser, ed. Modularity in development and evolution. University of Chicago Press, Chicago.
42. Teichmann, S. A., and G. Mitchison. 1999. Is there a phylogenetic signal in prokaryote proteins? J. Mol. Evol. 49:98-107.
43. Tibshirani, R., G. Walther, and T. Hastie. 2001. Estimating the number of clusters in a data set via the gap statistic. J. R. Stat. Soc. B:411-423.
44. Venables, W. N., and B. D. Ripley. 2002. Modern applied statistics with S-PLUS. Springer-Verlag, New York.
45. Wertz, J. E., C. Goldstone, D. M. Gordon, and M. A. Riley. 2003. A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J. Evol. Biol. 16:1236-1248.
46. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.