The general consensus from broad genomic comparisons is that developmental enhancers are reasonably well conserved between species within phyla with the same body plan, but not conserved between individuals from different phyla with distinct body plans.
Our previous work has defined conservation of the regulatory network involved in defining regions of the A/P axis in the vertebrate nervous system and the ectoderm of hemichordates. The conservation extends to the deployment of local signaling centers with key roles in regionalization of the vertebrate brain in early development. We are searching for the possibility that some of this regulatory conservation shared between hemichordates and vertebrates may extend to enhancer conservation. Our preliminary studies have revealed the conservation of a developmental enhancer involved in the secretion of the developmental ligand hedgehog (hh). Reciprocal transgenic enhancer swap experiments between hemichordates and vertebrates reveal that despite 600 million years of independent evolution, this enhancer is conserved between the two groups. We are further developing this work to investigate the extent of enhancer conservation between vertebrates and hemichordates.