Congruence of evolutionary relationships inside the Leuconostoc–Oenococcus–Weissella clade assessed by phylogenetic analysis of the 16S rRNA gene, dnaA, gyrB, rpoC and dnaK

References

1. Adékambi T., Drancourt M. 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 54:2095–2105 [CrossRef]
   [Google Scholar]
2. Alfaro M. E., Zoller S., Lutzoni F. 2003; Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol Biol Evol 20:255–266 [CrossRef]
   [Google Scholar]
3. Antunes A., Rainey F. A., Nobre M. F., Schumann P., Ferreira A. M., Ramos A., Santos H., da Costa M. S. 2002; Leuconostoc ficulneum sp. nov., a novel lactic acid bacterium isolated from a ripe fig, and reclassification of Lactobacillus fructosus as Leuconostoc fructosum comb. nov. Int J Syst Evol Microbiol 52:647–655
   [Google Scholar]
4. Brandley M. C., Schmitz A., Reeder T. W. 2005; Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst Biol 54:373–390 [CrossRef]
   [Google Scholar]
5. Bull J. J., Huelsenbeck J. P., Cunningham C. W., Swofford D. L., Waddell P. J. 1993; Partitioning and combining data in phylogenetic analysis. Syst Biol 42:384–397 [CrossRef]
   [Google Scholar]
6. Castoe T. A., Doan T. M., Parkinson C. L. 2004; Data partitions and complex models in Bayesian analysis: the phylogeny of gymnophtalmid lizards. Syst Biol 53:448–469 [CrossRef]
   [Google Scholar]
7. Collins M. D., Rodrigues U., Aguirre M., Farrow J., Martinez-Murcia A., Phillips B., Williams A., Wallbanks S. 1991; Phylogenetic analysis of the genus Lactobacillus and related lactic acid bacteria as determined by reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 77:5–12 [CrossRef]
   [Google Scholar]
8. Collins M. D., Samelis J., Metaxopoulos J., Wallbanks S. 1993; Taxonomic studies on some leuconostoc-like organisms from fermented sausages: description of a new genus Weissella for the Leuconostoc paramesenteroides group of species. J Appl Bacteriol 75:595–603 [CrossRef]
   [Google Scholar]
9. Dicks L. M. T., Dellaglio F. E., Collins M. D. 1995; Proposal to reclassify Leuconostoc oenos as Oenococcus oeni gen. nov., comb. nov.. Int J Syst Bacteriol 45:395–397 [CrossRef]
   [Google Scholar]
10. Felsenstein J. 1978; Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410 [CrossRef]
    [Google Scholar]
11. Felsenstein J. 2002 phylip (phylogenetic inference package), version 3.6a. Distributed by the author. Department of Genome Sciences University of Washington; Seattle, USA:
    [Google Scholar]
12. Garvie E. I. 1976; Hybridization between the deoxyribonucleic acids of some strains of heterofermentative lactic acid bacteria. Int J Syst Bacteriol 26:116–122 [CrossRef]
    [Google Scholar]
13. Garvie E. I. 1981; Sub-divisions within the genus Leuconostoc as shown by RNA/DNA hybridization. J Gen Microbiol 127:209–212
    [Google Scholar]
14. Goldman N., Anderson J. P., Rodrigo A. G. 2000; Likelihood-based tests of topologies in phylogenetics. Syst Biol 49:652–670 [CrossRef]
    [Google Scholar]
15. Hall B. G. 2004 Phylogenetic Trees Made Easy: a How-To Manual for Molecular Biologists , 2nd edn. Sunderland, MA: Sinauer Associates;
    [Google Scholar]
16. 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 12:843–849
    [Google Scholar]
17. Huelsenbeck J. P., Hillis D. M. 1993; Success of phylogenetic methods in the four-taxon case. Syst Biol 42:247–264 [CrossRef]
    [Google Scholar]
18. Huelsenbeck J. P., Ronquist F. R. 2001; MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755 [CrossRef]
    [Google Scholar]
19. Kandler O., Weiss N. 1986; Regular, nonsporing gram-positive rods. In Bergey's Manual of Systematic Bacteriology vol 2 pp  1208–1234 Edited by Sneath P. H. A., Mair N. S., Sharpe M. E., Holt J. G. Baltimore: Williams & Wilkins;
    [Google Scholar]
20. Konstantinidis K. T., Tiedje J. M. 2005; Towards a genome-based taxonomy for prokaryotes. J Bacteriol 187:6258–6264 [CrossRef]
    [Google Scholar]
21. Lanave C., Preparata G., Saccone C., Serio G. 1984; A new method for calculating evolutionary substitution rates. J Mol Evol 20:86–93 [CrossRef]
    [Google Scholar]
22. Marchuk D., Drumm M., Saulino A., Collins F. 1991; Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products. Nucleic Acids Res 19:1154 [CrossRef]
    [Google Scholar]
23. Martinez-Murcia A. J., Collins M. D. 1990; A phylogenetic analysis of the genus Leuconostoc based on reverse transcriptase sequencing of 16S rRNA. FEMS Microbiol Lett 70:73–84 [CrossRef]
    [Google Scholar]
24. Martinez-Murcia A. J., Harland N. M., Collins M. D. 1993; Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: assessment of congruence of small- and large-subunit rRNA derived trees. J Appl Bacteriol 74:532–541
    [Google Scholar]
25. Mills D. A., Rawsthorne H., Parker C., Tamir D., Makarova K. 2005; Genomic analysis of Oenococcus oeni PSU-1 and its relevance to winemaking. FEMS Microbiol Rev 29:465–475
    [Google Scholar]
26. Morse R., Collins M. D., O'Hanlon K., Wallbanks S., Richardson P. T. 1996; Analysis of the beta subunit of DNA-dependent RNA polymerase does not support the hypothesis inferred from 16S rRNA analysis that Oenococcus oeni (formerly Leuconostoc oenos ) is a tachytelic (fast-evolving) bacterium. Int J Syst Bacteriol 46:1004–1009 [CrossRef]
    [Google Scholar]
27. Morse R., O'Hanlon K., Collins M. D. 2002; Phylogenetic, amino acid content and indel analyses of the β subunit of DNA-dependent RNA polymerase of Gram-positive and Gram-negative bacteria. Int J Syst Evol Microbiol 52:1477–1484 [CrossRef]
    [Google Scholar]
28. Philippe H., Zhou Y., Brinkmann H., Rodrigue N., Delsuc F. 2005; Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol 5:50 [CrossRef]
    [Google Scholar]
29. Pitcher D. G., Sanders N. A., Owen R. J. 1989; Rapid extraction of bacterial genomic DNA with guanidium thiocyanate. Lett Appl Microbiol 8:151–156 [CrossRef]
    [Google Scholar]
30. Posada D., Crandall K. A. 1998; Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818 [CrossRef]
    [Google Scholar]
31. Shimodaira H., Hasegawa M. 1999; Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114–1116 [CrossRef]
    [Google Scholar]
32. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. other authors 2002; Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047 [CrossRef]
    [Google Scholar]
33. Swofford D. L. 2003 paup*. Phylogenetic Analysis Using Parsimony (*and other methods), version 4.0b10 Sunderland, MA: Sinauer Associates;
    [Google Scholar]
34. Tamura K., Nei M. 1993; Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 10:512–526
    [Google Scholar]
35. 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 [CrossRef]
    [Google Scholar]
36. Yamamoto S., Harayama S. 1995; PCR amplification and direct sequencing of gyrB genes with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104–1109
    [Google Scholar]
37. Yamamoto S., Harayama S. 1998; Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB , rpoD and 16S rRNA genes. Int J Syst Bacteriol 48:813–819 [CrossRef]
    [Google Scholar]
38. Yang Z. 1996; Maximum-likelihood models for combined analyses of multiple sequence data. J Mol Evol 42:587–596 [CrossRef]
    [Google Scholar]
39. Yang D., Woese C. R. 1989; Phylogenetic structure of the “leuconostocs”: an interesting case of a rapidly evolving organism. Syst Appl Microbiol 12:145–149 [CrossRef]
    [Google Scholar]