Loss of segmentation would be an apomorphy in Urochordates by this hypothesis. Pay a visit to my lab if you'd like to pick up an article with this title. The early fossil record is full of segmented forms. E.g. trilobites are segmented stem arthropods present in the early Cambrian, the time when animal fossils first become prominent. Segmental body plans evolved very early in the history of metazoans, but the issue of controversy is whether it evolved independently in different lineages.
Homologous genes function in fly and fish segmentation.
These data arguably support homology of segmentation in chordates and arthropods, but the story is so fragmentary at the moment that convergent evolution of segmentation in these creatures seems really just as likely an explanation. The larval lamprey is our best fit among extant animals for what we think the adult ancestor looked like, way back when . Way back when is near the end of the Cambrian Period of the Paleozoic Era, ca. We are, at this time, some 10s of Myr more recent than the Burgess Shale, the resting ground of Pikaia and her diverse invertebrate relatives. And, from the fossils we learn something about MA that we did not predict at all, from either comparative anatomy of extant animals like the hagfish and lamprey or from observing what is developing in our generalized von Baerian pharyngula.