Sea squirts, lancelets and acorn worms

A sea squirt (Ciona intestinalis) - a member of Tunicata 
Wikimedia Commons uploaded by perezoso (GFDL)

Genomics has clarified our position in the tree of life. To explain this I need to define some taxonomic terms.

Phylum Chordata comprises three subphyla: Vertebrata (Craniata), Tunicata (Urochordata)and Cephalochordata. Tunicates include sea squirts  such as Ciona (pictured) above. A familiar cephalochordate is the lancelet Branchiostoma lanceolatum better known as Amphioxus (shown below).

Amphioxus or Branchiostoma lanceolatum
(c) Virginia Gewin here (CC-BY-SA 3.0)

Amphioxus has long been used to exemplify the general plan of chordate organization and lancelets used to be regarded as the closest relatives to vertebrates. The genomic evidence, however, has tunicates like the sea squirts as sister group to vertebrates with cephalochordates as a deeper branch. Additional support is given by conserved molecular signatures (here).

Chordates belong in the Superphylum Deuterostomia (brilliantly reviewed by Lowe et al. here) along with Phylum Hemichordata and Phylum Echinodermata. Echinoderms are richly represented in the fossil record and the five extant classes include sea urchins, sea cucumbers and starfish. Hemichordates include the acorn worms for which two genomes just became available (here and here).

Acorn Worms (Hemichordata: Enteropneusta)
from Spengel 1883 (public domain)

One of many findings was a cluster of six genes that are conserved across chordates and implicated in patterning of gill slits. This is significant because gill slits were an innovation in the deuterostome lineage (although secondarily lost in echinoderms).

Relationships between deuterostome phyla were largely worked out through their embryology, an example being the erection of Chordata by Haeckel. Understanding the genes involved in developmental processes remains a focus in working out our evolutionary history (see the review by Lowe et al. mentioned above).