Acquisition by -Clade Hosts and Transfer of Incompatibility Loci Between Distantly Related .

Maternally transmitted infect about half of insect species, yet the predominant mode(s) of acquisition remains uncertain. Species-specific associations could be old, with and hosts codiversifying (, cladogenic acquisition), or relatively young and acquired by horizontal transfer or introgression. The three -clade hosts [(, ) ] diverged ∼3 MYA and currently hybridize on the West African islands Bioko and São Tomé. Each species is polymorphic for nearly identical that cause weak cytoplasmic incompatibility (CI)-reduced egg hatch when uninfected females mate with infected males. -clade are closely related to Mel, globally polymorphic in We use draft and mitochondrial genomes to demonstrate that -clade phylogenies for and mitochondria tend to follow host nuclear phylogenies. However, roughly half of individuals, sampled both inside and outside of the São Tomé hybrid zone, have introgressed mitochondria. Both mitochondria and possess far more recent common ancestors than the bulk of the host nuclear genomes, precluding cladogenic acquisition. General concordance of and mitochondrial phylogenies suggests that horizontal transmission is rare, but varying relative rates of molecular divergence complicate chronogram-based statistical tests. Loci that cause CI in Mel are disrupted in -clade ; but a second set of loci predicted to cause CI are located in the same WO prophage region. These alternative CI loci seem to have been acquired horizontally from distantly related , with transfer mediated by flanking -specific ISWpi1 transposons.