Comparative genomics provides a timeframe for Wolbachia evolution and exposes a recent biotin synthesis operon...

The genus Wolbachia (Alphaproteobacteria) comprises the most abundant inherited intracellular bacteria¹. Despite their relevance as manipulators of human pathogen transmission² and arthropod reproduction³, many aspects of their evolutionary history are not well understood⁴. In arthropods, Wolbachia infections are typically transient on evolutionary timescales^5,6 and co-divergence between hosts and Wolbachia is supposedly rare. Consequently, much of our knowledge of Wolbachia genome evolution derives from very recently diverged strains, and a timescale for Wolbachia is lacking. Here, we investigated the genomes of four Wolbachia strains that have persisted within and co-diverged with their host lineage for ∼2 million years. Although the genomes showed very little evolutionary change on a nucleotide level, we found evidence for a recent lateral transfer of a complete biotin synthesis operon that has the potential to transform Wolbachia-host relationships⁷. Furthermore, this evolutionary snapshot enabled us to calibrate the divergence times of the supergroup A and B Wolbachia lineages using genome-wide data sets and relaxed molecular clock models. We estimated the origin of Wolbachia supergroups A and B to be ∼200 million years ago (Ma), which is considerably older than previously appreciated. This age coincides with the diversification of many insect lineages⁸ that represent most of Wolbachia's host spectrum.