Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Comment
. 2006 Sep;2(9):e98.
doi: 10.1371/journal.ppat.0020098.

A re-evaluation of M. prototuberculosis

Noel H Smith
Comment

A re-evaluation of M. prototuberculosis

Noel H Smith. PLoS Pathog. 2006 Sep.
No abstract available

PubMed Disclaimer

Conflict of interest statement

Competing interests. The author has declared that no competing interests exist.

Figures

Figure 1
Figure 1. The Distribution of Mean Divergence and Maximum and Minimum Estimates of Divergence for Pairwise Comparisons of Alleles
Frequency in 1,000 trials plotted against percentage divergence. (A) All alleles (representing MTBC versus smooth). (B) Recombinant alleles only (representing smooth). Percentage divergence is the equivalent of percentage divergence at synonymous sites. The simulation started with an ancestral sequence of 800 base pairs (bp), representing the synonymous sites in the 3.4 Kb of sequence presented by Gutierrez et al. [1]. This was used to generate two independent populations with eight derived sequences following three bouts of binary replication. At each replication, a randomly selected bp was chosen and, to simulate mutations, changed with probability of 0.5. This generated, on average, 15 polymorphic sites in the entire dataset of 16 derived sequences, which approximates the number of polymorphic sites in the clonal frame of the dataset presented by Gutierrez et al. [1]. To compare differences arising from recombination, only one of the two independent populations (described above) was allowed to undergo recombination. To simulate this, sets of bp were changed in proportion to the observed recombinant segments shown boxed in Figure 3 of Gutierrez et al. [1]. For example, in four randomly selected sequences, the same 5 bp were simultaneously changed to simulate the recombinant segment in katG. Recombinant segments did not overlap. The above simulation was run for 1,000 independent trials; starting from the same ancestral sequence and the average pairwise diversity, the maximum and the minimum pairwise diversity were recorded for each population, for each trial.
See this image and copyright information in PMC

Comment in

Comment on

References

    1. Gutierrez MC, Brisse S, Brosch R, Fabre M, Omais B, et al. Ancient origin and gene mosaicism of the progenitor of Mycobacterium tuberculosis. . PLoS Pathog. 2005;1((1)):e5. DOI: 10.1371/journal.ppat.0010005. - DOI - PMC - PubMed
    1. Cohan FM. What are bacterial species? Annu Rev Microbiol. 2002;56:457–487. - PubMed
    1. Godreuil S, Cohan F, Shah H, Tibayrenc M. Which species concept for pathogenic bacteria? An E-debate. Infect Genet Evol. 2005;5:375–387. - PubMed
    1. Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, et al. Opinion: Re-evaluating prokaryotic species. Nat Rev Microbiol. 2005;3:733–739. - PubMed
    1. Smith NH, Kremer K, Inwald J, Dale J, Driscoll JR, et al. Ecotypes of the Mycobacterium tuberculosis complex. J Theor Biol. 2006;239:220–225. - PubMed

Publication types

Substances