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Volume 8, Number 11—November 2002

Genomewide Pattern of Synonymous Nucleotide Substitution in Two Complete Genomes of Mycobacterium tuberculosis

Austin L. Hughes*Comments to Author , Robert Friedman*, and Megan B. Murray†
Author affiliations: *University of South Carolina, Columbia, South Carolina, USA; †Harvard School of Public Health, Boston, Massachusetts, USA;

Main Article

Table 1

Estimatesa of the divergence time of the H37Rv and CDC1551 genotypes of Mycobacterium tuberculosis

Reference No. loci Synomymous substitutions/site/yr Divergence time (H37Rv and CDC1551)
11 67 4.7 ± 0.2 X 10-9 34,900 ± 2,300 b (33,500–36,400) c
12 128 4.4 X 10-9 37,300 ± 2,500 b

aBased on synonymous substitutions between Escherichia coli and Salmonella typhimurium, assumed to have diverged 100 million years ago (13,14).
bEstimates are shown ± standard error, based on standard error of mean pS.
cRange based on standard error of rate estimate.

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  1. Kato-Maeda  M, Bifani  PJ, Kreiswirth  BN, Small  PN. The nature and consequence of genetic diversity within Mycobacterium tuberculosis. J Clin Invest. 2001;107:5337. DOIPubMedGoogle Scholar
  2. Sreevatsan  S, Pan  X, Stockbauer  KE, Connell  ND, Kreiswirth  BN, Whittam  TS, Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent dissemination. Proc Natl Acad Sci U S A. 1997;94:986974. DOIPubMedGoogle Scholar
  3. Kapur  V, Whittam  TS, Musser  JM. Is Mycobacterium tuberculosis 15,000 years old? J Infect Dis. 1994;170:13489.PubMedGoogle Scholar
  4. Betts  JC, Dodson  P, Quan  S, Lewis  AP, Thomas  PJ, Duncan  K, Comparison of the proteome of Mycobacterium tuberculosis strain H37Rv with clinical isolate CDC 1551. Microbiology. 2000;146:320516.PubMedGoogle Scholar
  5. Altschul  SF, Madden  TL, Schäffer  AA, Zhang  J, Zhang  Z, Miller  W, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389402. DOIPubMedGoogle Scholar
  6. Thompson  JD, Higgins  DG, Gibson  TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994;22:467380. DOIPubMedGoogle Scholar
  7. Nei  M, Gojobori  T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986;3:41826.PubMedGoogle Scholar
  8. Hughes  AL. Adaptive evolution of genes and genomes. New York: Oxford University Press; 1999.
  9. The International SNP Map Working Group. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001;409:92833. DOIPubMedGoogle Scholar
  10. Ochman  H, Elwyn  S, Moran  NA. Calibrating bacterial evolution. Proc Natl Acad Sci U S A. 1999;96:1263843. DOIPubMedGoogle Scholar
  11. Sharp  PM. Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium: codon usage, map position, and concerted evolution. J Mol Evol. 1991;33:2333. DOIPubMedGoogle Scholar
  12. Smith  NGC, Eyre-Walker  A. Nucleotide substitution rate estimation in enterobacteria: approximate and maximum-likelihood methods lead to similar conclusions. Mol Biol Evol. 2001;18:21246.PubMedGoogle Scholar
  13. Ochman  H, Wilson  AC. Evolution in bacteria: evidence for a universal substitution rate in cellular organisms. J Mol Evol. 1987;26:7486. DOIPubMedGoogle Scholar
  14. Doolittle  RF, Feng  D-F, Tsang  S, Cho  G, Little  E. Determining divergence times of the major kingdoms of living organisms with a protein clock. Science. 1996;271:4707. DOIPubMedGoogle Scholar
  15. Cole  ST, Brosch  R, Parkhill  J, Garnier  T, Churcher  C, Harris  D, Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 1998;393:53744. DOIPubMedGoogle Scholar
  16. Takahata  N, Nei  M. Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci. Genetics. 1990;124:96778.PubMedGoogle Scholar
  17. Le Dantec  C, Winter  N, Gicquel  B, Vincent  V, Picardeau  P. Genomic sequence and transcriptional analysis of a 23-kilobase mycobacterial linear plasmid: evidence for horizontal transfer and identification of plasmid maintenance systems. J Bacteriol. 2001;183:215764. DOIPubMedGoogle Scholar
  18. Stead  WW. The origin and erratic global spread of tuberculosis. How the past explains the present and is the key to the future. Clin Chest Med. 1997;18:6577. DOIPubMedGoogle Scholar
  19. Brosch  R, Gordon  SV, Marmiesse  M, Brodin  P, Buchrieser  C, Eiglmeier  K, A new evolutionary scenario for the Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A. 2002;99:36849. DOIPubMedGoogle Scholar
  20. Hughes  AL, Verra  F. Very large long-term effective population size in the virulent human malaria parasite Plasmodium falciparum. Proc R Soc Lond B Biol Sci. 2001;268:185560. DOIGoogle Scholar
  21. Mu  J, Duan  J, Makova  KD, Joy  DA, Huynh  CQ, Branch  OH, Chromosome-wide SNPs reveal an ancient origin for Plasmodium falciparum. Nature. 2002;418:3236. DOIPubMedGoogle Scholar
  22. Burnet  M. Natural history of infectious disease. Cambridge: Cambridge University Press; 1940.
  23. Read  TD, Salzberg  SL, Pop  M, Shumway  M, Umayam  L, Jiang  L, Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science. 2002;296:202833. DOIPubMedGoogle Scholar
  24. Fleischmann  RD, Alland  D, Eisen  JA, Carpenter  L, White  O, Peterson  J, Sequencing of the M. tuberculosis genome: comparison of a recent clinical isolate with the laboratory strain. J Bacteriol. 2002. In press.PubMedGoogle Scholar

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