Cis-regulatory variation in the shavenbaby gene underlies intraspecific phenotypic variation, mirroring interspecific divergence in the same trait

Despite considerable progress in recent decades in dissecting the genetic causes of natural morphological variation, there is limited understanding of how variation within species ultimately contributes to species differences. We have studied patterning of the non-sensory hairs, commonly known as “trichomes,” on the dorsal cuticle of first-instar larvae of Drosophila. Most Drosophila species produce a dense lawn of trichomes, but a subset of dorsal trichomes were lost in D. sechellia and D. ezoana due entirely to regulatory evolution of the shavenbaby (svb) gene. Here we describe intraspecific variation in dorsal trichome patterns of first-instar larvae of D. virilis that is similar to the trichome pattern variation identified previously between species. We found that 67% of this difference is explained by a QTL that contains svb and that svb expression correlates with trichome variation within D. virilis . Despite using an experimental design with reasonable power to detect a second lo...