I am planning to test the co-diversification hypothesis between a host and its bacterial symbiont, demonstrating that both topologies and divergence times of the phylogenetic trees are congruent. I have robust estimations of the divergence dates of the hosts' species, but I was wondering if there is a way to calibrate the bacterial symbiont phylogeny calculated with bacterial sequences of quickly-evolving genes (rpoB/gyrB) obtained through amplicon sequencing.
Thank you in advance for any comment.