The Drosophila compound eye is specified by the concerted action of seven n
uclear factors that include Eyeless/Pax6. These factors have been called "m
aster control" proteins because loss-of-function mutants lack eyes and ecto
pic expression can direct ectopic eye development. However, inactivation of
these genes does not cause the presumptive eye to change identity. Surpris
ingly, we find that several of these eye specification genes are not coexpr
essed in the same embryonic cells-or even in the presumptive eye. We demons
trate that the EGF Receptor and Notch signaling pathways have homeotic func
tions that are genetically upstream of the eye specification genes, and sho
w that specification occurs much later than previously thought-not during e
mbryonic development but in the second larval stage.