The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.
Speciation in sexual organisms is defined as the inability of two populations to get viable offspring. Speciation in asexual, obligate endosymbionts is thought to be an indirect consequence of host-specialization. An important question is if divergent endosymbionts would start blending if the host barrier isolating them were removed. Here, we have studied Wolbachia, an abundant group of bacteria in the insect world. Wolbachia is classified into supergroups based on multi-locus sequence typing. We have sequenced the genomes from the Wolbachia strains wNo and wHa. These are particularly interesting since they belong to different supergroups yet co-occur as a double-infection in natural populations of Drosophila simulans. A comparative genomics study showed that wHa and wNo contain no uniquely shared genes. Instead, each strain shares unique gene functions with members of the same supergroup that infect other hosts. This unexpected finding suggests an alternative means of ecological speciation, indicating that speciation is not restricted to host-specialization but rather that related endosymbionts can coexist as separate species in the same host. Our study sheds light on the genomic divergence between different partners inhabiting the intracellular niche of the same host organism.