Changes in cis -regulatory modules (CRMs) that control developmental gene expression patterns have been implicated in the evolution of animal morphology ^1-6 . However, the genetic mechanisms underlying complex morphological traits remain largely unknown. Here we investigated the molecular mechanisms that induce the pigmentation gene yellow ( y ) in a complex spot and shade pattern on the abdomen of the quinaria group species Drosophila guttifera . We show that the y expression pattern is controlled by only one CRM, which contains a stripe-inducing CRM at its core. We identified several developmental genes that may collectively interact with the CRM to orchestrate the patterning in the pupal abdomen of D. guttifera . We further show that the core CRM is conserved among D. guttifera and the closely related quinaria group species Drosophila deflecta , which displays a similarly spotted abdominal pigment pattern. Our data suggest that besides direct activation of patterns in distinct spots, abdominal spot patterns in Drosophila species may have evolved through partial repression of an ancestral stripe pattern, leaving isolated spots behind. Abdominal pigment patterns of extant quinaria group species support the partial repression hypothesis and further emphasize the modularity of the D. guttifera pattern.

To understand how novel animal patterning emerged, one needs to ask how the development of color patterns has changed among diverging species. Here we examine three species of fruit flies – Drosophila guttifera ( D. guttifera ), Drosophila palustris ( D. palustris ), and Drosophila subpalustris ( D. subpalustris ) – displaying a varying number of abdominal spot rows that were either gained or lost throughout evolutionary time. Through in situ hybridization, we examine the mRNA expression patterns for the pigmentation genes Dopa decarboxylase ( Ddc ), tan ( t ), and yellow ( y ) during pupal development. Our results show that Ddc , t , and y are co-expressed in identical patterns, each foreshadowing the adult abdominal spots in D. guttifera , D. palustris , and D. subpalustris .