Differentiation and Phylogenetic Relationships in Mycobacterium Spp with Special Reference

Appendix

Differentiation and phylogenetic relationships in Mycobacterium spp with special reference to the RNase P RNA gene rnpB

Björn Herrmanna,*PelleStoltb, Guma Abdeldaima,c, Carl-Johan Rubina, Leif A. Kirsebomb,Mikael Thollessond

aSection of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden

bDepartment of Cell and Molecular Biology, Biomedical Centre, SE-751 24 Uppsala, Sweden

cNationalCenter for Diseases Control, Algeria street, P. O. Box 15038 Benghazi, Libya

dSystematic Biology, Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18D, Uppsala University, SE-752 36 Uppsala, Sweden

Additional information

Bacterial strains: Mycobacteria used in this study are listed in Table A1.

Phylogentic methods: The obtained alignments (individual genes and concatenated alignments) were used for phylogenetic inference using a Bayesian approach as implemented in MrBayes3.1.2 [1]. MrBayes uses Metropolis Coupled Markov Chain Monte Carlo methods to calculate the posterior probabilities for the parameters of interest. Each analysis was run for 1107 generations with four differently heated chains each in two independent chains; generations before convergence (as monitored on all continuous-valued parameters) were discarded as burn-in. Default, mainly non-informative, priors were used for all parameters.

To select an adequate model for the Bayesian analysis, we used an hierarchical likelihood ratio test (ηLRT) approach [2]. To do this, we used PAUP* 4.0b10; Macintosh versions [3] and the same test hierarchy (and thus model selection) as implemented in the program Modeltest[4]at p<0.01. Neighbour-Joining (NJ) trees under the Jukes-Cantor (JC) model were produced for each of the data sets/partitions separately as well as in combination, and the parameters and likelihood of each model were estimated using these trees.

References

1.Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001;17:754-5.

2.Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst. 1997;28:437-6

3.Swofford DL. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). 4 ed. Sunderland, Massachusetts: Sinauer Associates; 2003.

4.Posada D, Crandall KA (1998). MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.

Table A1. Strains, GenBank accession numbers of rnpB, 16S r RNA and hsp65 gene sequences and sources of strains used for rnpB analysis.

Genbank accession no

ATCC, American Type Culture Collection, Manassas, VA, U.S.A.; CCUG, Culture Collection University of Göteborg, Gothenburg, Sweden; SMI, Swedish Institute for Infectious Disease Control, Stockholm, Sweden.