Variation in core genes

I ended my talk at the CIfAR Integrated Microbial Diversity meeting by asking how much variation we should expect in 'core' bacterial genes within a single species, and I considered this more at lab meeting yesterday.  We see a lot of variation in competence phenotypes, due, we assume, to variation in the corresponding genes.  But we don't know if this variation is telling us something particular about how selection acts on DNA uptake and transformation, or is just 'normal'.

The variation could accumulate because loss of competence is sometimes a good thing, at least in the short term, but it could also be accumulate just because mildly deleterious changes are only slowly eliminated by selection.  This is especially likely to be true for genes that are only expressed occasionally.

So the variation in competence might mean that cells only need DNA uptake occasionally.  It would really help if we know more about when cells develop competence int heir natural environment...