Comparative developmental and genetic studies of these pharyngeal structures between hemichordates and urochordates have brought about important insights regarding the evolution of the deuterostome body plan.
Since sea urchins are deuterostomes, this suggests that the ancestral deuterostome shared its orientation with protostomes, and that dorsoventral inversion originated in some ancestral chordate.
If chaetognaths branched off from the protostomes before they evolved their distinctive protostome embryonic characters, they may have retained deuterostome characters inherited from early bilaterian ancestors.
The deuterostome affiliations were recently corroborated by studies that indicate a basal position of this phylum within the deuterostomes or a sister group relationship with the echinoderms and hemichordates.