  Wolbachia are maternally-inherited symbiotic bacteria commonly found in
arthropods, which are able to manipulate the reproduction of their host in
order to maximise their transmission. Here we use whole genome resequencing
data from 290 lines of Drosophila melanogaster from North America, Europe and
Africa to predict Wolbachia infection status, estimate cytoplasmic genome copy
number, and reconstruct Wolbachia and mtDNA genome sequences. Complete
Wolbachia and mitochondrial genomes show congruent phylogenies, consistent with
strict vertical transmission through the maternal cytoplasm and imperfect
transmission of Wolbachia. Bayesian phylogenetic analysis reveals that the most
recent common ancestor of all Wolbachia and mitochondrial genomes in D.
melanogaster dates to around 8,000 years ago. We find evidence for a recent
incomplete global replacement of ancestral Wolbachia and mtDNA lineages, which
is likely to be one of several similar incomplete replacement events that have
occurred since the out-of-Africa migration that allowed D. melanogaster to
colonize worldwide habitats.
