Wolbachia pipientis is associated with different mitochondrial haplotypes in natural populations of Drosophila willistoni

[Display omitted] ► Drosophila willistoni is a species recently infected with Wolbachia. Wolbachia may effect mitochondrial genetic diversity of host population. ► We evaluated infection in D. willistoni populations of the Atlantic Forest. ► No decrease in haplotype diversity of the mtCOI was detected. ► Wolbachia was seen to be associated to different mitochondria. The prevalence of the endosymbiont Wolbachia pipientis and its effects on mitochondrial genetic diversity were analyzed in natural populations of Drosophila willistoni, a neotropical species recently infected. Total infection rate was 55% and no evidence was found that the Wolbachia infection decreased the diversity of mtDNA. Wolbachia was seen to be associated with different mitochondria, suggesting multiple horizontal transmission events and/or transmission paternal leakage of mitochondrial and/or Wolbachia. These hypotheses are evaluated in the context of the present study and other research.