P. Roumagnac, F. Weill, C. Dolecek, S. Baker, and S. Brisse, Evolutionary History of Salmonella Typhi, Science, vol.314, issue.5803, pp.1301-1304, 2006.
DOI : 10.1126/science.1134933

R. Brosch, S. Gordon, M. Marmiesse, P. Brodin, and C. Buchrieser, complex, Proceedings of the National Academy of Sciences, vol.99, issue.6, pp.3684-3689, 2002.
DOI : 10.1073/pnas.052548299

K. Brudey, J. Driscoll, L. Rigouts, W. Prodinger, and A. Gori, Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology, BMC Microbiology, vol.6, issue.1, p.23, 2006.
DOI : 10.1186/1471-2180-6-23

I. Filliol, A. Motiwala, M. Cavatore, W. Qi, and M. Hazbon, Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set, Journal of Bacteriology, vol.188, issue.2, pp.759-772, 2006.
DOI : 10.1128/JB.188.2.759-772.2006

R. Frothingham and W. Meeker-o-'connell, Genetic diversity in the Mycobacterium tuberculosis complex based on variable numbers of tandem DNA repeats, Microbiology, vol.144, issue.5, pp.1189-1196, 1998.
DOI : 10.1099/00221287-144-5-1189

P. Groenen, A. Bunschoten, D. Van-soolingen, and J. Van-embden, Nature of DNA polymorphism in the direct repeat cluster of Mycobacterium tuberculosis; application for strain differentiation by a novel typing method, Molecular Microbiology, vol.85, issue.5, pp.1057-1065, 1993.
DOI : 10.1016/0923-2508(92)90104-V

M. Gutacker, J. Smoot, C. Migliaccio, S. Ricklefs, and S. Hua, Genome-wide analysis of synonymous single nucleotide polymorphisms in Mycobacterium tuberculosis complex organisms: resolution of genetic relationships among closely related microbial strains, Genetics, vol.162, pp.1533-1543, 2002.

S. Sreevatsan, X. Pan, K. Stockbauer, N. Connell, and B. Kreiswirth, Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination, Proceedings of the National Academy of Sciences, vol.94, issue.18, pp.9869-9874, 1997.
DOI : 10.1073/pnas.94.18.9869

P. Supply, E. Mazars, S. Lesjean, V. Vincent, and B. Gicquel, Variable human minisatellite-like regions in the Mycobacterium tuberculosis genome, Molecular Microbiology, vol.59, issue.3, pp.762-771, 2000.
DOI : 10.1046/j.1365-2958.2000.01905.x

X. Liu, M. Gutacker, J. Musser, and Y. Fu, Evidence for Recombination in Mycobacterium tuberculosis, Journal of Bacteriology, vol.188, issue.23, pp.8169-8177, 2006.
DOI : 10.1128/JB.01062-06

V. Rosas-magallanes, P. Deschavanne, L. Quintana-murci, R. Brosch, and B. Gicquel, Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis, Molecular Biology and Evolution, vol.23, issue.6, pp.1129-1135, 2006.
DOI : 10.1093/molbev/msj120

D. Vultos, T. Blazquez, J. Rauzier, J. Matic, I. Gicquel et al., Identification of Nudix Hydrolase Family Members with an Antimutator Role in Mycobacterium tuberculosis and Mycobacterium smegmatis, Journal of Bacteriology, vol.188, issue.8, pp.3159-3161, 2006.
DOI : 10.1128/JB.188.8.3159-3161.2006

M. Rad, P. Bifani, C. Martin, K. Kremer, and S. Samper, Mutations in putative mutator genes of Mycobacterium tuberculosis strains of the W-Beijing family, Emerg Infect Dis, vol.9, pp.838-845, 2003.

V. Mizrahi and S. Andersen, DNA repair in Mycobacterium tuberculosis. What have we learnt from the genome sequence?, Molecular Microbiology, vol.29, issue.6, pp.1331-1339, 1998.
DOI : 10.1093/emboj/17.6.1829

H. Bandelt, P. Forster, and A. Rohl, Median-joining networks for inferring intraspecific phylogenies, Molecular Biology and Evolution, vol.16, issue.1, pp.37-48, 1999.
DOI : 10.1093/oxfordjournals.molbev.a026036
URL : http://mbe.oxfordjournals.org/cgi/content/short/16/1/37

M. Hanekom, G. Van-der-spuy, E. Streicher, S. Ndabambi, and C. Mcevoy, A Recently Evolved Sublineage of the Mycobacterium tuberculosis Beijing Strain Family Is Associated with an Increased Ability to Spread and Cause Disease, Journal of Clinical Microbiology, vol.45, issue.5, pp.1483-1490, 2007.
DOI : 10.1128/JCM.02191-06

J. Eisen and P. Hanawalt, A phylogenomic study of DNA repair genes, proteins, and processes, Mutation Research/DNA Repair, vol.435, issue.3, pp.171-213, 1999.
DOI : 10.1016/S0921-8777(99)00050-6

B. Tye, J. Chien, I. Lehman, B. Duncan, and H. Warner, Uracil incorporation: A source of pulse-labeled DNA fragments in the replication of the Escherichia coli chromosome, Proceedings of the National Academy of Sciences, vol.75, issue.1, pp.233-237, 1978.
DOI : 10.1073/pnas.75.1.233

E. Rocha, J. Smith, L. Hurst, M. Holden, and J. Cooper, Comparisons of dN/dS are time dependent for closely related bacterial genomes, Journal of Theoretical Biology, vol.239, issue.2, pp.226-235, 2006.
DOI : 10.1016/j.jtbi.2005.08.037

R. Nielsen, Molecular Signatures of Natural Selection, Annual Review of Genetics, vol.39, issue.1, pp.197-218, 2005.
DOI : 10.1146/annurev.genet.39.073003.112420

E. Denamur and I. Matic, Evolution of mutation rates in bacteria, Molecular Microbiology, vol.21, issue.4, pp.820-827, 2006.
DOI : 10.1099/mic.0.27230-0

T. Tonjum and E. Seeberg, Microbial fitness and genome dynamics, Trends in Microbiology, vol.9, issue.8, pp.356-358, 2001.
DOI : 10.1016/S0966-842X(01)02099-6

S. Kumar, K. Tamura, and M. Nei, MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment, Briefings in Bioinformatics, vol.5, issue.2, pp.150-163, 2004.
DOI : 10.1093/bib/5.2.150

J. Rozas, J. Sanchez-delbarrio, X. Messeguer, and R. Rozas, DnaSP, DNA polymorphism analyses by the coalescent and other methods, Bioinformatics, vol.19, issue.18, pp.2496-2497, 2003.
DOI : 10.1093/bioinformatics/btg359