I have been interested in bacterial pan genomes for some time: apart from acquiring mutations in genes shared between strains, bacteria are able to pick up genes (via several Lateral Gene Transfer processes), duplicate genes and also lose genes. These processes can take place rapidly, and could potentially have large effects on fitness. Together with Adam Eyre-Walker and several co-authors, I wrote an Opinion piece exploring both the rate at which these accessory genome changes can occur and their evolutionary fate (see this post). Earlier this year, I published a short meta-analysis with Nadia Andreani and Elze Hesse (see this post) explicitly demonstrating that species with genetically more diverse core genomes also have more diverse accessory genomes. This pattern is inconsistent with predominantly strongly deleterious effects and consistent with slightly deleterious or neutral fitness effects. A recent Opinion piece in Nature Microbiology by McInerney etal argued that most observed accessory genome changes are actually adaptive. This prompted Jesse Shapiro to write a short letter to Nature Microbiology contrasting these findings with ours, prompting Adam and myself to write a critique of the McInerney paper and McInerney to write a response. I feel that the evolution of accessory genomes is one of the least understood but most pressing issues in evolutionary microbiology. Hopefully the present discussion will help to stir up debate.
Prospective PhD’s: please see the blog post below!