Wolbachia-mediated persistence of mtDNA from a potentially extinct species KELLY A. DYER,* CRISTA BURKE†‡ and JOHN JAENIKE† *Department of Genetics, University of Georgia, Athens, GA 30602, USA, †Department of Biology, University of Rochester, Rochester, NY 14627, USA Abstract Drosophila quinaria is polymorphic for infection with Wolbachia, a maternally transmitted endosymbiont. Wolbachia-infected individuals carry mtDNA that is only distantly related to the mtDNA of uninfected individuals, and the clade encompassing all mtDNA haplotypes within D. quinaria also includes the mtDNA of several other species of Drosophila. Nuclear gene variation reveals no difference between the Wolbachia-infected and uninfected individuals of D. quinaria, indicating that they all belong to the same interbreeding biological species. We suggest that the Wolbachia and the mtDNA with which it is associated were derived via interspecific hybridization and introgression. The sequences in the Wolbachia and the associated mtDNA are ‡6% divergent from those of any known Drosophila species. Thus, in spite of nearly complete species sampling, the sequences from which these mitochondria were derived remain unknown, raising the possibility that the donor species is extinct. The association between Wolbachia infection and mtDNA type within D. quinaria suggests that Wolbachia may be required for the continued persistence of the mtDNA from an otherwise extinct Drosophila species. We hypothesize that pathogen-protective effects conferred by Wolbachia operate in a negative frequency-dependent manner, thus bringing about a stable polymorphism for Wolbachia infection. Keywords: Drosophila quinaria, introgression, mtDNA, MLST, phylogenetics Received 27 December 2010; revision revised 7 April 2011; accepted 18 April 2011 Introduction Wolbachia may be the most widespread endosymbiont in terrestrial ecosystems, infecting perhaps two-thirds of present-day insect species, as well as a substantial frac- tion of species in other arthropod groups (Stouthamer et al. 1999; Hilgenboecker et al. 2008). In many host species, Wolbachia spread and persist by manipulating host reproduction in ways such as cytoplasmic incom- patibility and male-killing, which enhance the relative fitness of infected cytoplasmic lineages, even though such tactics can exact a severe demographic and genetic toll on the host population (Engelsta¨dter & Hurst 2009). Wolbachia, however, are not invariably parasitic: several recent reports indicate that some strains are beneficial to their hosts, boosting fertility (Dedeine et al. 2001), fecundity (Weeks et al. 2007; Brownlie et al. 2009), and resistance to pathogens and parasites (Hedges et al. 2008; Teixeira et al. 2008; Kambris et al. 2009). Regardless of their fitness effects, the sojourn times of Wolbachia within host lineages are typically short on an evolutionary time scale, as phylogenetic analy- ses reveal very few examples of codivergence of insect host species and their associated Wolbachia (Werren et al. 1995; but see Raychoudhury et al. 2009; Stahlhut et al. 2010). Such patterns indicate that there must be relatively high rates of Wolbachia colonization of new host species, as well as high rates of extinction of Wolbachia from infected species, although the mecha- nisms by which these processes occur are largely unknown. Correspondence: Kelly A. Dyer, E-mail: kdyer@uga.edu; John Jaenike, E-mail: john.jaenike@rochester.edu ‡Present address: Crista Burke, Department of Biology, Tufts University, Medford, MA 02155, USA. E-mail: crista.burke@ tufts.edu Ó 2011 Blackwell Publishing Ltd Molecular Ecology (2011) 20, 2805–2817 doi: 10.1111/j.1365-294X.2011.05128.x