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.

@article{Filliol2006GlobalPO,
  title={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.},
  author={Ingrid Filliol and Alifiya S. Motiwala and Magali Cavatore and Weihong Qi and Manzour Hernando Hazb{\'o}n and Miriam Bobadilla del Valle and Janet Fyfe and Lourdes Garc{\'i}a-Garc{\'i}a and Nalin Rastogi and Christophe Sola and Thierry Zozio and Marta In{\'i}rida Guerrero and Clara In{\'e}s Le{\'o}n and Jonathan Crabtree and Sam Angiuoli and K. D. Eisenach and Riza Durmaz and Moses Joloba and Adrian Rendon and Jos{\'e} Sifuentes-Osornio and Alfredo Ponce de Le{\'o}n and M. D. Cave and Robert Fleischmann and Thomas S. Whittam and David Alland},
  journal={Journal of bacteriology},
  year={2006},
  volume={188 2},
  pages={
          759-72
        }
}
We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace… CONTINUE READING

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