By Garstang's hypothesis, segmentation is derived in the clade that includes amphioxus and the vertebrates. Ascidians, even at the larval stage, do not have a prominent segmental body plan, as you see for yourself in this week's lab. An alternative hypothesis is that like MA the chordate ancestor was segmented. Loss of segmentation would be an apomorphy in Urochordates by this hypothesis. Like bilaterality this idea comes from ago, including ideas of Geoffroy Saint-Hilaire.
Homologous genes function in fly and fish segmentation.
If we take these data at face value, they argue for homology of body segmentation between protostomes and chordates. Accordingly we can propose that the chordate ancestor was segmented. 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.