Although dating bacterial divergences is highly problematic, the most recent common ancestor of H. influenzae and P. multocida, and thus of the Hin-subclade in Fig. 1, has been estimated to have lived about 270 million years ago (mya), and last common ancestor of the entire family must be older still [ 30, 31].
Bacterial community divergence in the mesocosms was quantified using a Euclidean-based divergence metric.
Still, at least one other group of cyclic parthenogens, aphids, has been shown to undergo a very rapid adaptive radiation as evidenced by modelling bacterial endosymbiont divergence.
To determine if these commonly used measures of bacterial sequence divergence - K16S, Ks, and Ka - increase in a correlated manner across all organisms (and thus provide largely consistent measurements of divergence times), we plotted their values against one another for the 42 genome-pairs.
This pattern of bacterial genetic divergence is in line with recent theoretical results indicating that genotypic clusters can arise and be maintained in the absence of selection or physical isolation when the recombination rate is a negative log-linear function of genetic distance [ 52, 53] and the effective population size (Ne) is extremely large [ 54].
Although the standard MLST scheme based on housekeeping genes enables estimates of recombination and mutation rates as well as intraspecific phylogenies (2, 5 ), our approach of including plasmidborne loci under positive selection helped identify the selective causes of bacterial lineage divergence.
A more realistic model is where GluRS(C) was appended to GluRS(N) before bacterial phylum-divergence but because the acquired GluRS(C) was non-functional, it was lost and regained several times, probably via intra-bacterial HGT, before becoming functionally compatible with GluRS(N) in a synchronous way [ 26, 27].
In the vast majority of bacterial genomes, the divergence between 16S rRNA gene sequence copies is <1% [45].
Because the housekeeping genes are recognized as the stable core of the bacterial genome, this divergence further shows the emergence of a new virulent ST.
