WT, mcm7 -ts, and pol2 -12 did not produce any clusters, while the other mutator genomes contained between one and nine mutation clusters.
But these mutation clusters can also randomly diminish and even die out, if the mutated lineages differentiate and terminate these lineages.
We now discuss two examples of mutation clusters.
Recently, Wagner proposed a method to detect such mutation clusters.
Second, we tested whether mutation clusters were associated predominantly with specific secondary structure motifs.
By and large, we have found that mutation clusters are not particularly common.
Local minima in the Q-landscape correspond to potential mutation clusters.
Therefore, secondary structure composition does not seem to affect the location of mutation clusters.
This result agrees with our hypothesis that solvent exposure can lead to spurious mutation clusters.
Supplementary Tables S1, S2, and S3 list the significant mutation clusters in the three species groups.
We have used this method to search for mutation clusters in bacteria, fly, and mammals.
