Synapomorphies of Craniata:

• Head
  • Sensory capsules: olfactory, eyes, and otic (organs of balance, and later hearing)
  • Expanded neurocranium (braincase) surrounding cranial nerves and thickened anterior neural tube (i.e., brain)
• Neural Crest
  • New germ cell layer, making craniates effectively "tetrablastic"
  • Appears dorsal and lateral to the neural tube and which contributes to a great variety of adult tissues and structures including: sensory neurons (nerve cells), some skeletal and connective tissues in the skull, and some pigment containing cells and other integumentary tissues. In the skull, the neural crest cells give rise to the brachial arches, jaws and parts of the braincase floor. In the gnathostomes and a number of fossil jawless vertebrates, the neural crest cells are also involved in the formation of the dermal skeleton (scales, teeth, and dermal bones).
• Mouth, with more specialized mouth parts
  • Pharynx with gills, used for both feeding and respiration
  • Branchial apparatus supported by cartiligenous brachial arches (gill bars) external to hemibranchs
  • Pharyngeal muscular pump (hypomeres)
• Caudal fin stregthened by cartiligenous radials
• Larval endostyle transforms into adult thyroid gland
• Gut
  • Liver and pancreas present (formed through endoderm-mesoderm induction)
  • Digestive system invested with smooth muscular lining (rather than cilia)
• Circulatory System
  • Two chambered heart
  • Hemoglobin for oxygen transport
  • Erythrocytes to contain hemoglobin
• Increased size (an order of magnitude)
• Cartilaginous endoskeleton: including fin rays and brachial arches

In terms of metabolic rate and aerobic capacity, only cephalopod mollusks and some arthropods are comparable to craniates.

Living jawless craniates include Myxinoidea (aka Hyperotreti, aka hagfish) and Petromyzontida (aka Hyperoartei, aka lampreys). Together were once called Cyclostomata or Agnatha, but are almost certainly paraphyletic.

Myxinoidea seem to be basal to all other craniates, living or fossil. Myxinoids have tentacles, and (at least the living ones) have large ventrolateral slime glands, esophago-cutaneous duct on the left side, and elongate body shape. Primitive condition is several pairs of small gill openings. Primitive features relative to vertebrates:

• Body fluid content (more than 10%, whereas it is less than 10% in all other craniates)
• Low oxygen affinity of their blood cells
• Lack of cardiac innervation
• Multiple veinous hearts
• Lack of sensory-line neuromasts (although they have acoustico-lateral nerve fibres)
• Comparitively simple pituitary gland
• Lack of muscles in caudal fin web
• Single loop to their semicircular canals (organs of balance)

Only fossil record of hagfish is from Mazon Creek, but some possible Chenjiang forms, including Haikouella (actual specimens here) and Myllokunmingia may represent other types of basal non-vertebrate craniates.

Vertebrata, characterized by:

• Metamerically arranged endoskeletal elements flanking the spinal cord (aka vertebrae)
• Extrinsic eye muscles, allowing eye movements
• Radial muscles in fins
• At least two vertical semicircular canals in the labyrinth
• True neuromasts in the sensory-line system

Only living jawless vertebrates are petromyzontids. They are characterized by a large sucker surrounding the mouth, strengthened by annular cartilage and by pine-shaped processes on gill arches. Also, they unique among extant vertebrates in having a median dorsal "nostril" (the nasohypophysial opening), but some other fossil vertebrates also display the same structure. All fossil lampreys are Mazon Creek forms.

Another possible basal vertebrate is Haikouichtys (Chengjiang Fm.).

A problematic group of basal craniates, probably basal vertebrates: Euconodonta

• Range from Middle Cambrian to the end of the Triassic
• Once lumped with protoconodonts (probably chaetognath jaws) and paraconodonts (uncertain affinity)
• Known primarily from isolated elements composed of calcium phosphate (and may actually be bone, dentine, and enamel!)
  • Elements divided into coniform, ramiform, and platform morphologies
• Animal itself is elongate, has a notochord, chevron-shaped myomeres, a postanal tail, dorsal fin and caudal fin radials, and possible extrinsic eye muscles
• Elements are mouthparts:
  • Coniform and ramiform are graspers
  • Platform are crushers
• Seem to have been pelagic predators a few cm long

Presence of a phosphatic hard parts suggests that they are closer to the "ostracoderms" and gnathostomes than are petromyzontids; however, some dispute claim that conodont elements are true bone, dentine, and enamel

"Ostracoderms": paraphyletic grade of armored jawless vertebrates. "Ostracoderms" share with gnathostomes:

• Mineralized exoskeleton (i.e., a dermal skeleton), including the hard tissues dentine, bone, and enamel
• Sensory-line canals and grooves

An Upper Cambrian form (Anatolepis) is known from bony plates, but the morphology of the whole animal is not known.

Many clades of "ostracoderms" (see here, and websites linked therein, for an extensive overview). "Ostracoderm"-grade vertebrates common in Ordovician through Late Devonian strata.

Some major groups and trends of "ostracoderms"

• Basal condition (including evolution of a rigid dermal skeleton head shield) seen in Pteraspidomorphi (Early Ordovician-Late Devonian), most famously Sacabambaspis (Ordovician of Bolivia) and Astraspis of Ordovician of North America
• Heterostraci (Early Silurian-Late Devonian), a diverse clade characterized by a single branchial exhalent opening on each side of the head armor
• Lightly armored Anaspida (Silurian), with a round mouth (like lampreys) and paired ventral fin-folds
• Galeaspida (Silurian-Devonian), with endochondral bone for neurocranium (shared with Osteostraci and Gnathostomata) and large inhalent nasopharyngeal opening
• Evolution of paired fins (and additional midline fins) for control in swimming (as in Osteostraci (Early Silurian-Late Devonian), also called "cephalaspids". Osteostracans have "cephalic fields" of unknown function (sensory, most likely) and ventrally-facing mouths.

However, as long as jawless, gills had to serve "double duty": as organs of feeding and of respiration.

One unusual "ostracoderm" group, the Thelodonti (?Late Ordovician-Late Devonian), had scales with hollow pulp cavity, which resemble the dermal scales of sharks and the teeth of gnathostomes. Some of these scales even wrap into the mouth of thelodonts. Proto-teeth? Perhaps, but general anatomy doesn't suggest that they were particularly close to the origin of gnathostomes.

Origin of the head
What do all of these taxa have in common that the outgroup (Cephalochordata) lacks? Heads! What phenomena are implicated in the sudden appearance of this complex structure?

• Homeobox (aka Homeotic, aka Hox) genes control segmentation and fundamental orientation of embryo. They are conservative gene clusters found throughout the animal realm. Besides controlling orientation and segmentation, each gene influences a specific region of the body.

• Gene transcription errors have profound effects. One common consequence of such errors is the gene duplication event, in which two paralogous copies of a gene are generated. Once present, they may each evolve independently and ultimately code for different proteins. For example, the lamprey has a single globin molecule, coded for by a single gene. In contrast, mammals have four globin molecules, each coded for by separate genes thought to have originated in at least three duplication events.

• Putting it together.
  
  1. The subjects of homeobox genes, gene duplication, and the origin of the craniate head come together in the "new head" model of craniate evolution
     
  2. Recall that craniates possess some unique tissues, not found in Branchiostoma, that generate many structures of head
     
     1. epidermal placodes - precursor to cranial structures including the lens of eye.
     2. hypomere - precursor to pharyngeal muscles
     3. neural crest - precursor to many things, including all bone, and cartilage of anterior cranium and gill arches.
  3. These special tissues are coded for by homeobox genes.
  4. The homeobox genes of craniates differ from those of Branchiostoma in one important respect: Rather than having one homeobox gene cluster, craniates all have at least two, arguably the result of a gene duplication event.
     
  5. The upshot is that the appearance of a complex head and branchial skeleton may have been the result of Hox gene duplication and the subsequent independent evolution of the resulting gene clusters. This introduces an interesting variation on the traditional gradualist view of evolution. Quite possibly, the material that natural selection shaped into the head appeared all at once, as the result of a one-time occurance - the duplication of a group of genes.