We also estimated the Slatkin's R ST [ 36] based on the variance in allele sizes to verify the contribution of stepwise-like mutations to genetic diversity and test the hypothesis that F ST = R ST using the software SPAGeDi 1.4 [ 37].
The long evolutionary history allowed this species to accumulate not only mutations relative to diversity, but also high differentiation between regions.
Taken together, these findings advance our understanding of mycobacterial evolution, contribute to a systems level understanding of this important human pathogen, and more broadly demonstrate the application of state-of-the-art techniques to provide novel insight into mechanisms by which intergenic and silent mutations contribute to diversity.
By comparing the human and chimpanzee genome sequences we identify and characterize genes with PTCs, in order to understand the contribution of these mutations to the transcriptome diversity between the species.
PCR using the FailSafe PCR System (Epicentre Biotechnologies) produces both transition (purine-to-purine) and transversion (purine-to-pyrimidine) mutations to generate a greater diversity of amino acid substitution mutations than transition mutations alone (Ivey et al. 2010).
If beneficial mutations under strong selection occur rarely, we would expect selective sweeps to drive these mutations to fixation, resulting in low diversity and a linear evolution pattern.
Once cells became strong citrate utilizers, the initial gltA mutation became deleterious driving the evolution of a diversity of secondary mutations to compensate for its cost.
In terms of the relative contribution of recombination versus mutation to WSP genetic diversity (Fig. 4B), it is notable that in half of the recombinant cases detected (9/18) recombination introduced more than 10 amino acid changes.
Although our data may not be robust owing to the small sample sizes, the relative contribution of recombination and point mutation to the genetic diversity of the mcy genes may be comparable to that of various genes of other highly recombinogenic bacteria, such as Helicobacter pylori and Streptococcus pneumoniae [ 37].
Population genetic theories predict that the slightly deleterious mutations contribute diversity to the population for a short while, but that they are selected against over long timescales and are prevented from becoming fixed (Kimura 1983).
