TY - JOUR T1 - Population genomics of <em>Wolbachia</em> and mtDNA in <em>Drosophila simulans</em> from California JF - bioRxiv DO - 10.1101/174375 SP - 174375 AU - Sarah Signor Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/08/11/174375.abstract N2 - 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 I 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. I find reduced diversity relative to expectation in both Wolbachia and mtDNA, but only mtDNA shows evidence of a recent selective sweep or population bottleneck. I find that all individuals in the population are infected, and we estimate Wolbachia and mtDNA titre in each genotype. I 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 derived from a single origin. Using Wolbachia and mtDNA titre as a phenotype, I 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. ER -