ABSTRACT
Wolbachia pipientis is a widespread intracellular endosymbiont infecting many arthropods and filarial nematodes. Little is known about the short-term evolution of Wolbachia or its interaction with its host. Wolbachia is maternally inherited, resulting in co-inheritance of mitochondrial organelles such as mtDNA. Here we explore the short-term evolution of Wolbachia, and the relationship between Wolbachia and mtDNA, using a large inbred panel of Drosophila simulans infected with the Wolbachia strain wRi. We find reduced diversity relative to expectation in both Wolbachia and mtDNA, but only mtDNA shows evidence of a recent selective sweep or population bottleneck. We find that all individuals in the population are infected, and we estimate Wolbachia and mtDNA titre in each genotype. We find considerable variation in both phenotypes, despite low genetic diversity in Wolbachia and mtDNA. A phylogeny of Wolbachia and of mtDNA show that both trees are largely unresolved, suggesting a recent origin of the infection and a single origin. Using Wolbachia and mtDNA titre as a phenotype, we perform an association analysis with the nuclear genome and find several regions implicated in the phenotype, including one which contains four CAAX-box protein processing genes. CAAX-box protein processing can be an important part of host-pathogen interactions in other systems, suggesting interesting directions for future research.