Modeling bacterial evolution with comparative-genome-based marker systems: Application to Mycobacterium tuberculosis evolution and pathogenesis

David Alland, Thomas S. Whittam, Megan B. Murray, M. Donald Cave, Manzour H. Hazbon, Kim Dix, Mark Kokoris, Andreas Duesterhoeft, Jonathan A. Eisen, Claire M. Fraser, Robert D. Fleischmann

Research output: Contribution to journalArticle

87 Scopus citations

Abstract

The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared "reference strains." Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI "C" strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.

Original languageEnglish (US)
Pages (from-to)3392-3399
Number of pages8
JournalJournal of bacteriology
Volume185
Issue number11
DOIs
StatePublished - Jun 1 2003

    Fingerprint

All Science Journal Classification (ASJC) codes

  • Microbiology
  • Molecular Biology

Cite this

Alland, D., Whittam, T. S., Murray, M. B., Cave, M. D., Hazbon, M. H., Dix, K., Kokoris, M., Duesterhoeft, A., Eisen, J. A., Fraser, C. M., & Fleischmann, R. D. (2003). Modeling bacterial evolution with comparative-genome-based marker systems: Application to Mycobacterium tuberculosis evolution and pathogenesis. Journal of bacteriology, 185(11), 3392-3399. https://doi.org/10.1128/JB.185.11.3392-3399.2003