Through the analysis of cytoplasmic incompatibility and similar mitochondrial DNA, it has been shown that D. simulans and D. mauritiana are more closely related to each other than to D. sechellia.

Cytoplasmic incompatibility causes egg and sperm cells to fail in creating viable offspring, a common feature in Wolbachia-infected D. simulans and D. mauritiana individuals.

Infections of Wolbachia, a commonly infectious strain of bacteria observed in many insects such as Trichogramma and Muscidifurax uniraptor wasps, are transmitted between generations of Drosophila simulans.

The infection is maintained through a process involving cytoplasmic incompatibility (CI) in which Wolbachia hinders uninfected individuals from producing offspring.

[9] While the mechanism for the decreased virus-induced mortality is still unknown, Wolbachia provides antiviral properties, potentially perpetuated by outcompeting the virus.

Such progeny often have reduced fitness due to increased genetic homozygosity leading to expression of deleterious recessive alleles.

Among Drosophila simulans inbred males, two fitness characteristics, fertility and attractiveness to females, are especially susceptible to inbreeding depression.