The origin and integration of novel traits are fundamental processes during the developmental evolution of complex organisms. Yet how novel traits integrate into pre-existing contexts remains poorly understood. Beetle horns represent a spectacular evolutionary novelty integrated within the context of the adult dorsal head, a highly conserved trait complex present since the origin of insects. We investigated whether
otd1/2
and
six3
, members of a highly conserved gene network that instructs the formation of the anterior end of most bilaterians, also play roles in patterning more recently evolved traits. Using ablation-based fate-mapping, comparative larval RNA interference (RNAi) and transcript sequencing, we found that
otd1/2
, but not
six3
, play a fundamental role in the post-embryonic formation of the adult dorsal head and head horns of
Onthophagus
beetles. By contrast, neither gene appears to pattern the adult head of
Tribolium
flour beetles even though all are expressed in the dorsal head epidermis of both
Onthophagus
and
Tribolium
. We propose that, at least in beetles, the roles of
otd
genes during post-embryonic development are decoupled from their embryonic functions, and that potentially non-functional post-embryonic expression in the dorsal head facilitated their co-option into a novel horn-patterning network during
Onthophagus
evolution.
Regulation of the retinal determination gene dachshund in the embryonic head and developing eye of Drosophila
