Is a robust phylogeny of the enterobacterial plant pathogens attainable?

Cladistics

Volumn 27, Issue 1, 2011, Pages 80-93

  Naum, Marianna ^a,b   Brown, Eric W ^b   Mason Gamer, Roberta J ^a  

^a UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^b CENTER FOR DRUG EVALUATION AND RESEARCH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; EVOLUTIONARY BIOLOGY; MAXIMUM LIKELIHOOD ANALYSIS; PARSIMONY ANALYSIS; PHYLOGENETICS; PHYLOGENY;

BACTERIA (MICROORGANISMS); BRENNERIA; ENTEROBACTERIACEAE; ERWINIA; PANTOEA; PECTOBACTERIUM;

EID: 78650800243     PISSN: 07483007     EISSN: 10960031     Source Type: Journal    
DOI: 10.1111/j.1096-0031.2010.00313.x     Document Type: Article

References (55)

1. Allard, M.W., Farris, J.S., Carpenter, J., 1999. Congruence among mammalian mitochondrial genes. Cladistics 15, 75-84.
2. Brenner, D.J., Falkow, F., 1971. Molecular relationships among members of the Enterobacteriaceae. Adv. Genet. 16, 81-118.
3. Brochier, C., Bapteste, E., Moreira, D., Philippe, H., 2002. Eubacterial phylogeny based on transfational apparatus proteins. Trends Genet. 18, 1-5.
4. Brown, E.W., Davis, R.M., Gouk, C., van der Zwet, T., 2000. Phylogenetic relationships of necrogenic Erwinia and Brenneria species as revealed by glyceraldehyde-3-phosphate dehydrogenase gene sequences. Int. J. Syst. Evol. Microbiol. 50, 2057-2068.
5. Brown, E.W., Kotewicz, M.L., Cebula, T.A., 2002. Detection of recombination among Salmonella enterica strains using the incongruence length difference test. Mol. Phylogenet. Evol. 24, 102-120.
6. Brown, E.W., Mammel, M.K., LeClerc, J.E., Cebula, T.A., 2003. Limited boundaries for extensive horizontal gene transfer among Salmonella pathogens. Proc. Natl Acad. Sci. USA 100, 15676-15681.
7. Charlebois, R.L., Beiko, R.G., Ragan, M.A., 2003. Microbial phylogenomics: branching out. Nature 421, 217.
8. Christensen, H., Kuhnert, P., Olsen, J.E., Bisgaard, M., 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, 1601-1609.
9. Clarke, G.D.P., Beiko, R.G., Ragan, M.A., Charlebois, R.L., 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, 2072-2080.
10. Cohan, F., 1996. The role of genetic exchange in bacterial evolution. ASM News 62, 631-636.
11. Cohan, F.M., 2001. Bacterial species and speciation. Syst. Biol. 50, 513-524.
12. Comas, I., Moya, A., Azad, R.K., Lawrence, J.G., Gonzalez-Candelas, F., 2006. The evolutionary origin of Xanthomonadales genomes and the nature of the horizontal gene transfer process. Mol. Biol. Evol. 23, 2049-2057.
13. Dauga, C., 2002. Evolution of the gyrB gene and the molecular phylogeny of Enterobactericaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol. 52, 531-547.
14. Doolittle, W.F., 1999. Phylogenetic classification and the universal tree. Science 284, 2124-2128.
15. Dye, D.W., 1968. A taxonomic study of the genus Erwinia I: the 'amylovora' group. NZ J. Sci. 11, 590-607.
16. Dye, D.W., 1969a. A taxonomic study of the genus Erwinia II: the 'carotovora' group. NZ J. Sci. 12, 81-97.
17. Dye, D.W., 1969b. A taxonomic study of the genus Erwinia III: the 'herbicola' group. NZ J. Sci. 12, 223-236.
18. Dye, D.W., 1969c. A taxonomic study of the genus Erwinia IV: the atypical Erwinias. NZ J. Sci. 12, 833-839.
19. Dykhuizen, D.E., Green, L., 1991. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173, 7257-7268.
20. Ehrlich, H.A., Gelford, D., Snisky, J.J., 1991. Recent advances in the polymerase chain reaction. Science 252, 1643.
21. Farris, J.S., Kallersjo, M., Kluge, A.G., Bult, C., 1995. Testing significance of incongruence. Cladistics 10, 315-319.
22. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
23. Fessehaie, A., De Boer, S., Levesque, C., 2002. Molecular characterization of DNA encoding 16S-23S rRNA intergenic spaces regions and 16S rRNA of pectolytic Erwinia species. Can. J. Microbiol. 48, 387-398.
24. Frati, F., Simon, C., Sullivan, J., Swofford, D.L., 1997. Evolution of the mitochondrial cytochrome oxidase II gene in Collembola. J. Mol. Evol. 44, 145-158.
25. Gavini, F.J., Mergaert, A., Beji, C., Mielcarek, D., Izard, K.K., DeLey, J., 1989. Transfer of Enterobacter agglomerans (Beijerinck 1888) Ewing and Fife 1972 to Pantoea gen. nov. as Pantoea agglomerans comb. nov. and description of Pantoea dispersa sp. nov. Int. J. Syst. Bacteriol. 39, 337-345.
26. Hauben, L., Moore, E.R.B., Vauterin, L., Steenackers, L., Mergaert, J., Verdonck, L., Swings, J., 1998. Phylogenetic position of phytopathogens within the Enterobacteriaceae. Syst. Appl. Microbiol. 21, 384-397.
27. Huelsenbeck, P.H., Ronquist, F., 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
28. Lan, R.T., Reeves, P.R., 2000. Intraspecies variation in bacterial genomes: the need for a species genome concept. Trends Microbiol. 8, 1911-1921.
29. Lan, R., Reeves, P.R., 2001. When does a clone deserve a name? A perspective on bacterial species based on population genetics. Trends Microbiol. 9, 419-424.
30. Lawrence, J.G., Ochman, H., Hartl, D.L., 1991. Molecular and evolutionary relationships among enteric bacteria. Journal of Genetic Microbiology 137, 1911-1921.
31. Lelliott, R.A., Dickey, R.S. (eds) 1985. Genus VII. Erwinia. Williams and Wilkins, New York. pp. 469-476.
32. Linz, S., Radtke, A., von Haeseler, A., 2007. A likelihood framework to measure horizontal gene transfer. Mol. Biol. Evol. 24, 1312-1319.
33. Maddison, W.P., Maddison, D.R., 2000. MacClade. Sinauer, Sunderland, MA.
34. Maniatis, T., Fritsch, E., Sambrook, J., 1982. Molecular Cloning: A Laboratory Manual. Cold Springs Harbor Laboratory, Cold Spring Harbor, New York.
35. Mason-Gamer, R.J., 2004. Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Syst. Biol. 53, 25-37.
36. Mergaert, J., Verdonck, L., Kersters, K., 1993. Transfer of Erwinia ananas and Erwinia stewartii to the genus Pantoea and description of Pantoea stewartii ssp. indologenes. Int. J. Syst. Bacteriol. 43, 162-173.
37. Naum, M., Mason-Gamer, R.J., Brown, E.W., 2008. Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the Enterobacteriaceae? J. Mol. Evol. 66, 630-642.
38. Nelson, K., Whittam, T.S., Selander, R.K., 1991. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl Acad. Sci. USA 88, 6667-6671.
39. Nesbo, C.L., Boucher, Y., Doolittle, W.F., 2001. Defining the core nontransferable prokaryotic genes: the euryachaeal core. J. Mol. Evol. 53, 340-350.
40. Ochman, H., Lawrence, J.G., Groisman, E.A., 2000. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299-304.
41. Sproer, C., Mendrock, U., Swiderski, J., Lang, E., Stackenbrandt, E., 1999. The phylogenetic position of Serratia, Buttiauxella and some other genera of the family Enterobacteriaceae. Int. J. Syst. Bacteriol. 49, 1433-1438.
42. Starr, M.P., Chatterjee, A.K., 1972. The genus Erwinia: enterobacteria pathogenic to plants and animals. Annu. Rev. Microbiol. 26, 389-426.
43. Struck, T.H., Purschke, G., Halanych, K.M., 2006. Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach. Syst. Biol. 55, 1-20.
44. Sullivan, J., Markert, J.A., Kilpatrick, C.W., 1997. Phylogeography and molecular systematics of the Peromyscus aztecus species group (Rodentia: Muridae) inferred using parsimony and likelihood. Syst. Biol. 46, 426-440.
45. Swofford, D.L., 2001. PAUP. *Phylogenetic Analysis Using Parsimony (*and Other Methods), V. 4b10. Sinauer, Sunderland, MA.
46. Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M., 1996. Phylogenetic Inference. In: Hillis, D.M., Moritz, C. (Eds), Phylogenetic Inference. Sinaur, Sunderland, MA, pp. 407-414.
47. Thompson, J.D., Higgins, D., Gibson, T.J., 1992. CLUSTAL version W: a novel multiple sequence alignment program. Nucleic Acids Res. 22, 4673-4680.
48. Toth, I.K., Pritchard, L., Birch, P.R.J., 2006. Comparative genomics reveals what makes an enterobacterial plant pathogen. Annu. Rev. Phytopathol. 44, 305-336.
49. Waldee, E.L., 1945. Comparative studies of some peritrichous phytopathogenic bacteria. Iowa State Coll. J. Sci. 19, 435-484.
50. Wertz, J.E., Goldstone, G., Gordon, D.M., Riley, M.A., 2003. A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J. Evol. Biol. 16, 1236-1248.
51. Winslow, C.E., Broadhurst, J., Buchanan, R.E., 1920. The families and genera of the bacteria Erwiniae. J. Bacteriol. 5, 209.
52. Yang, Z., Goldman, N., Friday, A., 1995. Maximum-likelihood trees from DNA sequences: a peculiar statistical estimation problem. Syst. Biol. 44, 384-399.
53. Young, J.M., 2001. Implications of alternative classifications and horizontal gene transfer for bacterial taxonomy. Int. J. Syst. Evol. Microbiol. 51, 945-953.
54. Young, J.M., Park, D.C., 2007. Relationships of plant pathogenic enterobacteria based on partial atpD, carA, and recA as individual and concatenated nucleotide and peptide sequences. Syst. Appl. Microbiol. 30, 343-354.
55. Zwickl, D., 2006. Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion., Genetic Algorithm Approaches for the Phylogenetic Analysis of Large Biological Sequence Datasets Under the Maximum Likelihood Criterion. University of Texas, Austin.