In this analysis the relaxed-clock provided a better fit to the data than the strict-clock (see Table S4) as evidenced by the values obtained for the standard deviation of the uncorrelated relaxed-clock that returned a mean of 0.46 across the independent runs (ranging from 0.36 to 0.60) indicating a relatively high degree of rate variation among lineages.
In addition, the degree of rate variation across sites was modulated by using several values of α, the shape parameter of the gamma distribution.
The seven closely related Bacillus genomes in the Bc group were analyzed separately and, as expected, a high degree of rate variation was observed (data not shown).
There is a high degree of rate variation for gene insertions/deletions, since the rate variation parameter α is 0.37; indicating that there is a small subset of genes with rapid gene turn-over.
Closely related groups tend to have a higher degree of rate variation for gene insertions/deletions among genes, while distantly related groups tend to have a lower level of rate variation for gene insertions/deletions.
Furthermore, different cutoffs used in identifying informational genes only resulted in variation of the number of informational genes but did not affect the degree of rate variation for insertions/deletions in non-informational genes (Additional file 10).
Even though informational genes are less likely to be laterally transferred than non-informational genes, the degree of rate variation for insertions/deletions did not change dramatically and remained high even when informational genes were excluded from the study.
However, there is no evidence found in this study that the degree of rate variation for gene insertions/deletions across genes is associated with genome size (data not shown).
To explore the sensitivity of the method to the strength of the temporal selection shift, I vary the degree of rate variation (smaller α implies greater rate variation) and the fraction of sites θ experiencing a selection shift across the divergence point.
The results reveal that rate variation of gene insertions/deletions is much more complex than simply a difference between informational genes and operational genes; instead, a high degree of rate variation for insertions/deletions remains among both informational genes and among non-informational genes.
