Initially, Deuterostomia included the phyla Brachiopoda,[6] Bryozoa,[7] Chaetognatha,[8] and Phoronida[6] based on morphological and embryological characteristics.

However, Deuterostomia was redefined in 1995 based on DNA molecular sequence analyses, leading to the removal of the lophophorates which was later combined with other protostome animals to form the superphylum Lophotrochozoa.

[10][11] Genetic studies have also revealed that deuterostomes have more than 30 genes not found in any other animal groups, but which yet are present in some marine algae and prokaryotes.

[12] A consensus phylogeny of the deuterostomes is:[citation needed] There is a possibility that Ambulacraria is the sister clade to Xenacoelomorpha, and could form the Xenambulacraria group.

Another feature present in both the Hemichordata and Chordata is pharyngotremy — the presence of spiracles or gill slits into the pharynx, which is also found in some primitive fossil echinoderms (mitrates).

[citation needed] The highly modified nervous system of echinoderms obscures much about their ancestry, but several facts suggest that all present deuterostomes evolved from a common ancestor that had pharyngeal gill slits, a hollow nerve cord, circular and longitudinal muscles and a segmented body.

[21][22] That implies that the protostome and deuterostome lineages split long before Kimberella appeared, and hence well before the start of the Cambrian 538.8 million years ago,[20] i.e. during the earlier part of the Ediacaran Period (circa 635-539 Mya, around the end of global Marinoan glaciation in the late Neoproterozoic).

It has been proposed that the ancestral deuterostome, before the chordate/ambulacrarian split, could have been a chordate-like animal with a terminal anus and pharyngeal openings but no gill slits, with active suspension feeding strategy.

[32] The Mid Cambrian fossil Rhabdotubus johanssoni has been interpreted as a pterobranch hemichordate,[33] whereas Spartobranchus is an acorn-worm from the Burgess Shale, providing proof that all main lineages were already well established 508 mya.

The ancestral deuterostome was most likely a benthic worm that possessed a cartilaginous skeleton, a central nervous system, and gill slits.