Chapter 13 : Phylogenetic and Genomic Analysis

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This chapter briefly discusses the different steps in constructing evolutionary trees, including collecting data sets of homologous sequences, generating a multiple-sequence alignment, inferring tree topology, and assessing confidence in the tree. Multiple-sequence alignments are the essential prerequisite for most phylogenetic analyses. There are currently four primary methods for constructing phylogenies from protein and nucleic acid sequence alignments: the distance-based neighbor-joining (NJ) method and the character-based methods, including maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference. The major advantage of bootstrap technique is that it can be applied to basically all tree construction methods, although one has to keep in mind that applying the bootstrap method multiplies the computer time needed by the number of bootstrap samples requested. Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single phylogenetic marker, i.e., the 16S rRNA gene among bacteria. Given the vast number of genome sequences now available, it is possible to compute trees from whole genomes.

Citation: Gevers D, Coenye T. 2007. Phylogenetic and Genomic Analysis, p 157-168. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch13
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Comparison of phylogenetic trees based on 16S rRNA gene (right; scale bar indicates 1% sequence dissimilarity) and (left; scale bar indicates 5% sequence dissimilarity) sequences of a selection of species. Sequences were extracted from GenBank and were aligned by using BioNumerics 4.0 (Applied Maths, Sint-Martens-Latem, Belgium), and trees were constructed based on the NJ algorithm as implemented in BioNumerics 4.0.

Citation: Gevers D, Coenye T. 2007. Phylogenetic and Genomic Analysis, p 157-168. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch13
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1. Abascal, F.,, R. Zardoya, and, D. Posada. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 21042105.
2. Acinas, S. G.,, L. A. Marcelino,, V. Klepac-Ceraj, and, M. F. Polz. 2004. Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J. Bacteriol. 186: 26292635.
3. Adekambi, T.,, and M. Drancourt. 2004. Dissection of phylogenetic relationships among 19 rapidly growing Mycobacterium species by 16S rRNA, hsp65, sodA, recA and rpoB gene sequencing. Int. J. Syst. Evol. Microbiol. 54: 20952105.
4. Alsen, G. J.,, H. Matsuda,, R. Hagstrom, and, R. Overbeek. 1994. fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput. Appl. Biosci. 10: 4148.
5. Anderson, I.,, A. Sorokin,, V. Kapatral,, G. Reznik,, A. Bhattacharya,, N. Mikhailova,, H. Burd,, V. Joukov,, D. Kaznadzey,, T. Walunas,, M. d’Souza,, N. Larsen,, G. Pusch,, K. Liolios,, Y. Grechkin,, A. Lapidus,, E. Goltsman,, L. Chu,, M. Fonstein,, S. D. Ehrlich,, R. Overbeek,, N. Kyrpides, and, N. Ivanova. 2005. Comparative genome analysis of Bacillus cereus group genomes with Bacillus subtilis. FEMS Microbiol. Lett. 250: 175184.
6. Baldauf, S. L. 2003. Phylogeny for the faint of heart: a tutorial. Trends Genet. 19: 345351.
7. Bansal, A. K.,, and T. E. Meyer. 2002. Evolutionary analysis by whole genome comparisons. J. Bacteriol. 184: 22602272.
8. Benson, D. A.,, I. Karsch-Mizrachi,, D. J. Lipman,, J. Ostell, and, D. L. Wheeler. 2005. GenBank. Nucleic Acids Res. 33: D34D38.
9. Bern, M.,, and D. Goldberg. 2005. Automatic selection of representative proteins for bacterial phylogeny. BMC Evol. Biol. 5: 34.
10. Bininda-Emonds, O. R. 2005. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 6: 156.
11. Blackwood, K. S.,, C. He,, J. Gunton,, C. Y. Turenne,, J. Wolfe, and, A. M. Kabani. 2000. Evaluation of recA sequences for identification of Mycobacterium species. J. Clin. Microbiol. 38: 28462852.
12. Bodrossy, L.,, N. Stralis-Pavese,, J. C. Murrell,, S. Radajewski,, A. Weilharter, and, A. Sessitsch. 2003. Development and validation of a diagnostic microbial microarray for methanotrophs. Environ. Microbiol. 5: 566582.
13. Bos, D. H.,, and D. Posada. 2005. Using models of nucleotide evolution to build phylogenetic trees. Dev. Comp. Immunol. 29: 211227.
14. Boucher, Y.,, C. J. Douady,, A. K. Sharma,, M. Kamekura, and, W. F. Doolittle. 2004. Intragenomic heterogeneity and intergenomic recombination among haloarchaeal rRNA genes. J. Bacteriol. 186: 39803990.
15. Brown, J. R.,, C. J. Douady,, M. J. Italia,, W. E. Marshall, and, M. J. Stanhope. 2001. Universal trees based on large combined protein sequence data sets. Nat. Genet. 28: 281285.
16. Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17: 540552.
17. Chenna, R.,, H. Sugawara,, T. Koike,, R. Lopez,, T. J. Gibson,, D. G. Higgins, and, J. D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 34973500.
18. Cho, J. C.,, and J. M. Tiedje. 2001. Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl. Environ. Microbiol. 67: 36773682.
19. Christensen, H.,, P. Kuhnert,, J. E. Olsen, and, M. Bisgaard. 2004. Comparative phylogenies of the housekeeping genes atpD, infB and rpoB and the 16S rRNA gene within the Pasteurellaceae. Int. J. Syst. Evol. Microbiol. 54: 16011609.
20. Cladera, A. M.,, A. Bennasar,, M. Barcelo,, J. Lalucat, and, E. Garcia-Valdes. 2004. Comparative genetic diversity of Pseudomonas stutzeri genomovars, clonal structure, and phylogeny of the species. J. Bacteriol. 186: 52395248.
21. Clarke, G. D.,, R. G. Beiko,, M. A. Ragan, and, R. L. Charlebois. 2002. Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores. J. Bacteriol. 184: 20722080.
22. Clarridge, J. E., III. 2004. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin. Microbiol. Rev. 17: 840862.
23. Clayton, R. A.,, G. Sutton,, P. S. Hinkle, Jr.,, C. Bult, and, C. Fields. 1995. Intraspecific variation in small-subunit rRNA sequences in GenBank: why single sequences may not adequately represent prokaryotic taxa. Int. J. Syst. Bacteriol. 45: 595599.
24. Coenye, T.,, D. Gevers,, Y. Van de Peer,, P. Vandamme, and, J. Swings. 2005. Towards a prokaryotic genomic taxonomy. FEMS Microbiol. Rev. 29: 147167.
25. Coenye, T.,, and P. Vandamme. 2003. Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes. FEMS Microbiol. Lett. 228: 4549.
26. Coenye, T.,, and P. Vandamme. 2003. Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case. Microbiology 149: 35073517.
27. Coenye, T.,, P. Vandamme,, J. R. Govan, and, J. J. LiPuma. 2001. Taxonomy and identification of the Burkholderia cepacia complex. J. Clin. Microbiol. 39: 34273436.
28. Cole, J. R.,, B. Chai,, R. J. Farris,, Q. Wang,, S. A. Kulam,, D. M. McGarrell,, G. M. Garrity, and, J. M. Tiedje. 2005. The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res. 33: D294D296.
29. Dauga, C. 2002. Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol. 52: 531547.
30. de Queiroz, A.,, M. J. Donoghue, and, J. Kim. 1995. Separate versus combined analysis of phylogenetic evidence. Ann. Rev. Ecol. Syst. 26: 657681.
31. Driskell, A. C.,, C. Ane,, J. G. Burleigh,, M. M. McMahon,, B. C. O’Meara, and, M. J. Sanderson. 2004. Prospects for building the tree of life from large sequence databases. Science 306: 11721174.
32. Dror, O.,, H. Benyamini,, R. Nussinov, and, H. Wolfson. 2003. MASS: multiple structural alignment by secondary structures. Bioinformatics 19 (Suppl. 1) : i95i104.
33. Dutilh, B. E.,, M. A. Huynen,, W. J. Bruno, and, B. Snel. 2004. The consistent phylogenetic signal in genome trees revealed by reducing the impact of noise. J. Mol. Evol. 58: 527539.
34. Eisen, J. A. 1995. The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J. Mol. Evol. 41: 11051123.
35. Felsenstein, J. 1985. Confidence-limits on phylogenies—an approach using the bootstrap. Evolution 39: 783791.
36. Felsenstein, J.,, and H. Kishino. 1993. Is there something wrong with the bootstrap on phylogenies—a reply. Syst. Biol. 42: 193200.
37. Feng, D. F.,, and R. F. Doolittle. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25: 351360.
38. Fitch, W. M. 2000. Homology: a personal view on some of the problems. Trends Genet. 16: 227231.
39. Fitzgerald, J. R.,, and J. M. Musser. 2001. Evolutionary genomics of pathogenic bacteria. Trends Microbiol. 9: 547553.
40. Fitz-Gibbon, S. T.,, and C. H. House. 1999. Whole genome-based phylogenetic analysis of free-living microorganisms. Nucleic Acids Res. 27: 42184222.
41. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496512.
42. Forslund, K.,, D. H. Huson, and, V. Moulton. 2004. VisRD—visual recombination detection. Bioinformatics 20: 36543655.
43. Fox, G. E.,, J. D. Wisotzkey, and, P. Jurtshuk, Jr. 1992. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int. J. Syst. Bacteriol. 42: 166170.
44. Frishman, D.,, and P. Argos. 1995. Knowledge-based protein secondary structure assignment. Proteins 23: 566579.
45. Garrity, G. M.,, and J. G. Holt. 2001. The road map to the Manual, p. 119–166. In D. R. Boone and, R. W. Castenholz (ed.), Bergey’s Manual of Systematic Bacteriology. Springer-Verlag, New York, N.Y.
46. Gevers, D.,, F. M. Cohan,, J. G. Lawrence,, B. G. Spratt,, T. Coenye,, E. J. Feil,, E. Stackebrandt,, Y. Van de Peer,, P. Vandamme,, F. L. Thompson, and, J. Swings. 2005. Opinion: re-evaluating prokaryotic species. Nat. Rev. Microbiol. 3: 733739.
47. Godoy, D.,, G. Randle,, A. J. Simpson,, D. M. Aanensen,, T. L. Pitt,, R. Kinoshita, and, B. G. Spratt. 2003. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderfia mallei. J. Clin. Microbiol. 41: 20682079.
48. Gu, X.,, and H. Zhang. 2004. Genome phylogenetic analysis based on extended gene contents. Mol. Biol. Evol. 21: 14011408.
49. Hall, B. G. 2001. Phylogenetic Trees Made Easy: a How-To Manual for Molecular Biologists. Sinauer Associates, Inc., Sunderland, Mass.
50. Hallin, P. F.,, and D. W. Ussery. 2004. CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data. Bioinformatics 20: 36823686.
51. Harrington, C. S.,, and S. L. W. On. 1999. Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications. Int. J. Syst. Bacteriol. 49: 11711175.
52. Henz, S. R.,, D. H. Huson,, A. F. Auch,, K. Nieselt-Struwe, and, S. C. Schuster. 2004. Whole-genome prokaryotic phylogeny. Bioinformatics 21: 23292335.
53. Heringa, J. 1999. Two strategies for sequence comparison: profile-preprocessed and secondary structure-induced multiple alignment. Comput. Chem. 23: 341364.
54. Hillis, D. M.,, M. W. Allard, and, M. M. Miyamoto. 1993. Analysis of DNA sequence data: phylogenetic inference. Methods Enzymol. 224: 456487.
55. Holder, M.,, and P. O. Lewis. 2003. Phylogeny estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4: 275284.
56. Holmes, D. E.,, K. P. Nevin, and, D. R. Lovley. 2004. Comparison of 16S rRNA, nifD, recA, gyrB, rpoB and fusA genes within the family Geobacteraceae fam. nov. Int. J. Syst. Evol. Microbiol. 54: 15911599.
57. Horner, D. S.,, and G. Pesole. 2004. Phylogenetic analyses: a brief introduction to methods and their application. Expert Rev. Mol. Diagn. 4: 339350.
58. House, C. H.,, and S. T. Fitz-Gibbon. 2002. Using homolog groups to create a whole-genomic tree of free-living organisms: an update. J. Mol. Evol. 54: 539547.
59. Reference deleted.
60. Huelsenbeck, J. P. 1995. The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining. Mol. Biol. Evol. 12: 843849.
61. Huelsenbeck, J. P.,, F. Ronquist,, R. Nielsen, and, J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294: 23102314.
62. Huson, D. H. 1998. SplitsTree: analyzing and visualizing evolutionary data. Bioinformatics 14: 6873.
63. Huson, D. H.,, and M. Steel. 2004. Phylogenetic trees based on gene content. Bioinformatics 20: 20442049.
64. Huynen, M.,, T. Dandekar, and, P. Bork. 1998. Differential genome analysis applied to the species-specific features of Helicobacter pylori. FEBS Lett. 426: 15.
65. Huynen, M. A.,, and P. Bork. 1998. Measuring genome evolution. Proc. Natl. Acad. Sci. USA 95: 58495856.
66. Jensen, R. A. 2001. Orthologs and paralogs—we need to get it right. Genome Biol. 2:interactions1002.1–interactions1002.3.
67. Johnson, J. L. 1991. DNA reassociation experiments, p. 21–40. In E. Stackebrandt and, M. J. Goodfellow (ed.), Nucleic Acid Techniques in Bacterial Systematics. John Wiley & Sons Ltd., Chichester, United Kingdom.
68. Kabsch, W.,, and C. Sander. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 25772637.
69. Kanz, C.,, P. Aldebert,, N. Althorpe,, W. Baker,, A. Baldwin,, K. Bates,, P. Browne,, A. van den Broek,, M. Castro,, G. Cochrane,, K. Duggan,, R. Eberhardt,, N. Faruque,, J. Gamble,, F. G. Diez,, N. Harte,, T. Kulikova,, Q. Lin,, V. Lombard,, R. Lopez,, R. Mancuso,, M. McHale,, F. Nardone,, V. Silventoinen,, S. Sobhany,, P. Stoehr,, M. A. Tuli,, K. Tzouvara,, R. Vaughan,, D. Wu,, W. Zhu, and, R. Apweiler. 2005. The EMBL Nucleotide Sequence Database. Nucleic Acids Res. 33: D29D33.
70. Karlin, S.,, G. M. Weinstock, and, V. Brendel. 1995. Bacterial classifications derived from RecA protein sequence comparisons. J. Bacteriol. 177: 68816893.
71. Koizumi, Y.,, J. J. Kelly,, T. Nakagawa,, H. Urakawa,, S. El-Fantroussi,, S. Al-Muzaini,, M. Fukui,, Y. Urushigawa, and, D. A. Stahl. 2002. Parallel characterization of anaerobic toluene- and ethylbenzene-degrading microbial consortia by PCR-denaturing gradient gel electrophoresis, RNA-DNA membrane hybridization, and DNA microarray technology. Appl. Environ. Microbiol. 68: 32153225.
72. Kolaczkowski, B.,, and J. W. Thornton. 2004. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 431: 980984.
73. Korbel, J. O.,, B. Snel,, M. A. Huynen, and, P. Bork. 2002. SHOT: a web server for the construction of genome phylogenies. Trends Genet. 18: 158162.
74. Kunin, V.,, D. Ahren,, L. Goldovsky,, P. Janssen, and, C. A. Ouzounis. 2005. Measuring genome conservation across taxa: divided strains and united kingdoms. Nucleic Acids Res. 33: 616621.
75. Kwok, A. Y.,, and A. W. Chow. 2003. Phylogenetic study of Staphylococcus and Macrococcus species based on partial hsp60 gene sequences. Int. J. Syst. Evol. Microbiol. 53: 8792.
76. La Scola, B.,, Z. Zeaiter,, A. Khamis, and, D. Raoult. 2003. Gene-sequence-based criteria for species definition in bacteriology: the Bartonella paradigm. Trends Microbiol. 11: 318321.
77. Lerat, E.,, V. Daubin, and, N. A. Moran. 2003. From gene trees to organismal phylogeny in prokaryotes: the case of the γ-Proteobacteria. PLoS Biol. 1: E19.
78. Lilburn, T. G.,, and G. M. Garrity. 2004. Exploring prokaryotic taxonomy. Int. J. Syst. Evol. Microbiol. 54: 713.
79. Lin, J.,, and M. Gerstein. 2000. Whole-genome trees based on the occurrence of folds and orthologs: implications for comparing genomes on different levels. Genome Res. 10: 808818.
80. Lloyd, A. T.,, and P. M. Sharp. 1993. Evolution of the recA gene and the molecular phylogeny of bacteria. J. Mol. Evol. 37: 399407.
81. Loy, A.,, A. Lehner,, N. Lee,, J. Adamczyk,, H. Meier,, J. Ernst,, K. H. Schleifer, and, M. Wagner. 2002. Oligo-nucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68: 50645081.
82. Naser, S.,, F. L. Thompson,, B. Hoste,, D. Gevers,, K. Vandemeulebroecke,, I. Cleenwerck,, C. C. Thompson,, M. Vancanneyt, and, J. Swings. 2005. Phylogeny and identification of enterococci by atpA gene sequence analysis. J. Clin. Microbiol. 43: 22242230.
83. Naser, S. M.,, F. L. Thompson,, B. Hoste,, D. Gevers,, P. Dawyndt,, M. Vancanneyt, and, J. Swings. 2005. Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 151: 21412150.
84. Opperdoes, F. R. 2003. Phylogenetic analysis using protein sequences, p. 207–235. In M. Salemi and, A. M. Vandamme (ed.), The Phylogenetic Handbook: a Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge, United Kingdom.
85. Payne, G. W.,, P. Vandamme,, S. H. Morgan,, J. J. Lipuma,, T. Coenye,, A. J. Weightman,, T. H. Jones, and, E. Mahenthiralingam. 2005. Development of a recA gene-based identification approach for the entire Burkholderia genus. Appl. Environ. Microbiol. 71: 39173927.
86. Posada, D.,, and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14: 817818.
87. Priest, F. G.,, M. Barker,, L. W. Baillie,, E. C. Holmes, and, M. C. Maiden. 2004. Population structure and evolution of the Bacillus cereus group. J. Bacteriol. 186: 79597970.
88. Rasko, D. A.,, M. R. Altherr,, C. S. Han, and, J. Ravel. 2005. Genomics of the Bacillus cereus group of organisms. FEMS Microbiol. Rev. 29: 303329.
89. Rokas, A.,, and S. B. Carroll. 2005. More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol. Biol. Evol. 22: 13371344.
90. Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng. 12: 8594.
91. Salemi, M.,, and A. M. Vandamme (ed.). 2003. The Phylogenetic Handbook: a Practical Approach to DNA and Protein Phylogeny. Cambridge University Press, Cambridge, United Kingdom.
92. Santos, S. R.,, and H. Ochman. 2004. Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ. Microbiol. 6: 754759.
93. Sawa, G.,, J. Dicks, and, I. N. Roberts. 2003. Current approaches to whole genome phylogenetic analysis. Brief Bioinform. 4: 6374.
94. Schierup, M. H.,, and J. Hein. 2000. Consequences of recombination on traditional phylogenetic analysis. Genetics 156: 879891.
95. 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: 502504.
96. Simossis, V. A.,, and J. Heringa. 2005. PRALINE: a multiple sequence alignment toolbox that integrates homology-extended and secondary structure information. Nucleic Acids Res. 33: W289W294.
97. Snel, B.,, P. Bork, and, M. A. Huynen. 1999. Genome phylogeny based on gene content. Nat. Genet. 21: 108110.
98. Soler, L.,, M. A. Yanez,, M. R. Chacon,, M. G. Aguilera-Arreola,, V. Catalan,, M. J. Figueras, and, A. J. Martinez-Murcia. 2004. Phylogenetic analysis of the genus Aeromonas based on two housekeeping genes. Int. J. Syst. Evol. Microbiol. 54: 15111519.
99. Soltis, P. S.,, and D. E. Soltis. 2003. Applying the bootstrap in phylogeny reconstruction. Stat. Sci. 18: 256267.
100. Stackebrandt, E.,, W. Frederiksen,, G. M. Garrity,, P. A. Grimont,, P. Kampfer,, M. C. Maiden,, X. Nesme,, R. Rossello-Mora,, J. Swings,, H. G. Truper,, L. Vauterin,, A. C. Ward, and, W. B. Whitman. 2002. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int. J. Syst. Evol. Microbiol. 52: 10431047.
101. Stackebrandt, E.,, and B. M. Goebel. 1994. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846849.
102. Stevens, J. R.,, and C. J. Schofield. 2003. Phylogenetics and sequence analysis—some problems for the unwary. Trends Parasitol. 19: 582588.
103. Stralis-Pavese, N.,, A. Sessitsch,, A. Weilharter,, T. Reichenauer,, J. Riesing,, J. Csontos,, J. C. Murrell, and, L. Bodrossy. 2004. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ. Microbiol. 6: 347363.
104. Tanaoka, J. 1994. Determination of the DNA base composition, p. 463–470. In M. Goodfellow and, A. G. J. O’Donnell (ed.), Chemical Methods in Prokaryotic Systematics. John Wiley & Sons Ltd., Chichester, United Kingdom.
105. Tekaia, F.,, A. Lazcano, and, B. Dujon. 1999. The genomic tree as revealed from whole proteome comparisons. Genome Res. 9: 550557.
106. Thompson, C. C.,, F. L. Thompson,, K. Vandemeulebroecke,, B. Hoste,, P. Dawyndt, and, J. Swings. 2004. Use of recA as an alternative phylogenetic marker in the family Vibrionaceae. Int. J. Syst. Evol. Microbiol. 54: 919924.
107. Thompson, F. L.,, D. Gevers,, C. C. Thompson,, P. Dawyndt,, S. Naser,, B. Hoste,, C. B. Munn, and, J. Swings. 2005. Phylogeny and molecular identification of vibrios based on multilocus sequence analysis. Appl. Environ. Microbiol. 71: 51075115.
108. Thompson, F. L.,, T. Iida, and, J. Swings. 2004. Biodiversity of vibrios. Microbiol. Mol. Biol. Rev. 68: 403431.
109. Tortoli, E. 2003. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin. Microbiol. Rev. 16: 319354.
110. van Berkum, P.,, Z. Terefework,, L. Paulin,, S. Suomalainen,, K. Lindström, and, B. D. Eardly. 2003. Discordant phylogenies within the rrn loci of rhizobia. J. Bacteriol. 185: 29882998.
111. Vancanneyt, M.,, P. Vandamme, and, K. Kersters. 1995. Differentiation of Bordetella pertussis, B. parapertussis, and B. bronchiseptica by whole-cell protein electrophoresis and fatty-acid analysis. Int. J. Syst. Bacteriol. 45: 843847.
112. Vandamme, P.,, C. S. Harrington,, K. Jalava, and, S. L. On. 2000. Misidentifying helicobacters: the Helicobacter cinaedi example. J. Clin. Microbiol. 38: 22612266.
113. Vandamme, P.,, B. Pot,, M. Gillis,, P. Devos,, K. Kersters, and, J. Swings. 1996. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407438.
114. Vandamme, P. A. R. 2003. Taxonomy and classification of bacteria, p. 271–285. In P. R. Murray,, E. J. Baron,, J. H. Jorgensen,, M. A. Pfaller, and, R. H. Yolken (ed.), Manual of Clinical Microbiology, 8th ed. ASM Press, Washington, D.C.
115. Waddell, P. J.,, H. Kishino, and, R. Ota. 2000. Rapid evaluation of the phylogenetic congruence of sequence data using likelihood ratio tests. Mol. Biol. Evol. 17: 19881992.
116. Wayne, L. G.,, D. J. Brenner,, R. R. Colwell,, P. A. D. Grimont,, O. Kandler,, M. I. Krichevsky,, L. H. Moore,, W. E. C. Moore,, R. G. E. Murray,, E. Stackebrandt,, M. P. Starr, and, H. G. Truper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463464.
117. Weisburg, W. G.,, S. J. Giovannoni, and, C. R. Woese. 1989. The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction. Syst. Appl. Microbiol. 11: 128134.
118. Wernersson, R.,, and A. G. Pedersen. 2003. RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31: 35373539.
119. Whelan, S.,, P. Lio, and, N. Goldman. 2001. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17: 262272.
120. Willems, A.,, E. Falsen,, B. Pot,, E. Jantzen,, B. Hoste,, P. Vandamme,, M. Gillis,, K. Kersters, and, J. De Ley. 1990. Acidovorax, a new genus for Pseudomonas facilis, Pseudomonas delafieldii, E. Falsen (EF) group 13, EF group 16, and several clinical isolates, with the species Acidovorax facilis comb. nov., Acidovorax delafieldii comb. nov., and Acidovorax temperans sp. nov. Int. J. Syst. Bacteriol. 40: 384398.
121. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51: 221271.
122. Woese, C. R. 1991. The use of ribosomal RNA in reconstructing evolutionary relationships among bacteria, p. 1–24. In R. K. Selander,, A. G. Clark, and, T. S. Whittam (ed.), Evolution at the Molecular Level. Sinauer Associates, Inc., Sunderland, Mass.
123. Woese, C. R.,, E. Stackebrandt, and, W. Ludwig. 1985. What are mycoplasmas—the relationship of tempo and mode in bacterial evolution. J. Mol. Evol. 21: 305316.
124. Wolf, Y. I.,, S. E. Brenner,, P. A. Bash, and, E. V. Koonin. 1999. Distribution of protein folds in the three superkingdoms of life. Genome Res. 9: 1726.
125. Wolf, Y. I.,, I. B. Rogozin,, N. V. Grishin, and, E. V. Koonin. 2002. Genome trees and the tree of life. Trends Genet. 18: 472479.
126. Wuyts, J.,, G. Perriere, and, Y. Van De Peer. 2004. The European ribosomal RNA database. Nucleic Acids Res. 32: D101D103.
127. Yamamoto, S.,, H. Kasai,, D. L. Arnold,, R. W. Jackson,, A. Vivian, and, S. Harayama. 2000. Phylogeny of the genus Pseudomonas: intrageneric structure reconstructed from the nucleotide sequences of gyrB and rpoD genes. Microbiology 146: 23852394.
128. Yang, Q.,, and M. Blanchette. 2004. StructMiner: a tool for alignment and detection of conserved secondary structure. Genome Inform. Ser. Workshop Genome Inform. 15: 102111.
129. Yang, S.,, R. F. Doolittle, and, P. E. Bourne. 2005. Phylogeny determined by protein domain content. Proc. Natl. Acad. Sci. USA 102: 373378.
130. Ye, R. W.,, T. Wang,, L. Bedzyk, and, K. M. Croker. 2001. Applications of DNA microarrays in microbial systems. J. Microbiol. Methods 47: 257272.
131. Zeigler, D. R. 2003. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 53: 18931900.
132. Zhang, H.,, and X. Gu. 14 November 2004, posting date. Maximum likelihood for genome phylogeny on gene content. Stat. Appl. Genet. Mol. Biol. 3:no. 1, article 31. [Online.] http://www.bepress.com/sagmb/vol3/iss1/art31.

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