Chordata

Chordata (from the Latin chorda, "cord") is the phylum of deuterostome bilaterian animals that includes all vertebrates (Vertebrata)—jawless cyclostomes, cartilaginous fishes (Chondrichthyes), ray-finned fishes (Actinopterygii), lobe-finned fishes (Sarcopterygii), amphibians, reptiles (Sauropsida), birds (Aves), and mammals (Mammalia)—together with two marine invertebrate subphyla: Cephalochordata (lancelets or amphioxus) and Tunicata (Urochordata: sea squirts, salps, and larvaceans). Comprising approximately 70,000 described extant species, chordates occupy ecological niches ranging from deep-sea hydrothermal vents and abyssal trenches to terrestrial deserts, forest canopies, and high-altitude airspace.

Within the superphylum Deuterostomia, Chordata is the sister clade to Ambulacraria (Echinodermata + Hemichordata), from which it diverged during the Ediacaran Period (~560–540 million years ago) prior to the appearance of Early Cambrian stem-chordates and early vertebrates in the Chengjiang Biota (~518 Ma, such as Yunnanozoon, Haikouichthys, and Myllokunmingia) and the Burgess Shale (~508 Ma, Pikaia gracilens and Metaspriggina).

Although an adult sessile sea squirt (Ciona), a burrowing lancelet (Branchiostoma), and a blue whale (Balaenoptera musculus) differ widely in adult body form, every chordate exhibits five shared derived anatomical structures (synapomorphies) during embryonic, larval, or adult life:

1. The Notochord (Chorda Dorsalis): A flexible, hydrostatic axial rod situated between the dorsal nerve cord and the ventral digestive tract, derived embryonically from chordamesoderm. The notochord consists of a core of large, turgid vacuolated cells (inflated by lysosome-related osmotic vacuoles pressurized up to ~1–2 atmospheres) wrapped inside a tough, helically wound collagenous and elastin extracellular sheath (principally type II and type XI collagen). Because the fibrous sheath prevents radial ballooning while allowing lateral bending, the notochord functions as an incompressible antagonistic axial skeleton: when segmented lateral body-wall muscles (myomeres) contract on one side, the body bends laterally into propulsive S-shaped swimming waves rather than telescoping shorter. In Cephalochordata and jawless Cyclostomata, the notochord persists throughout life as the primary axial support; in Gnathostomata, it acts as the essential embryonic signaling center (secreting Sonic hedgehog [Shh] to pattern the neural tube floor plate and sclerotome) before being surrounded and largely replaced by cartilaginous or bony vertebral centra, surviving in adult mammals as the gelatinous nucleus pulposus at the center of each intervertebral disc.
2. Dorsal Hollow Nerve Cord (Neural Tube): Whereas protostome invertebrates (Arthropoda, Annelida, Mollusca) possess a solid, paired ventral nerve cord located below the gut, chordates possess a single, hollow, fluid-filled neural tube located dorsal to the notochord. It forms during embryogenesis via neurulation: the dorsal ectoderm overlying the notochord—where Chordin, Noggin, and Follistatin secreted by the Spemann–Mangold organizer inhibit epidermal Bone Morphogenetic Protein (BMP4) signaling—thickens into the neural plate, elevates lateral neural folds, and rolls up into a hollow tube lined by ciliated ependymal cells circulating cerebrospinal fluid.
3. Pharyngeal Gill Slits (Pharyngeal Pouches): Series of lateral openings or endodermal outpocketings (pharyngeal pouches) that perforate the wall of the anterior pharynx behind the mouth, connecting the pharyngeal cavity to the exterior water. Originally evolved in Cambrian deuterostomes (shared with Hemichordata) as a ciliated mucociliary suspension-feeding sieve rather than a respiratory organ, the pharyngeal bars were later vascularized with capillary beds and supported by cartilaginous/bony branchial arches in fishes to serve as respiratory gills. In terrestrial tetrapods, the embryonic pharyngeal pouches never perforate into open gill slits; instead, they remodel during development into the Eustachian tube and middle-ear cavity (pouch 1), the palatine tonsil crypts (pouch 2), the thymus and inferior parathyroid glands (pouch 3), and the superior parathyroid and calcitonin-secreting ultimobranchial bodies (pouch 4).
4. Endostyle or Thyroid Gland: A ciliated, glandular groove running longitudinally along the ventral floor of the pharynx in lancelets, tunicates, and larval lampreys (ammocoetes). The endostyle secretes a continuous net of iodinated mucoproteins (driven across the pharyngeal gill bars by cilia to trap suspended food particles) and expresses the transcription factors Nkx2-1 (TTF-1), Pax8, and FoxE along with thyroid peroxidase (TPO)—covalently binding iodine to tyrosine residues to synthesize monoiodotyrosine, diiodotyrosine, and thyroid hormones (thyroxine T₄ and triiodothyronine T₃). During lamprey metamorphosis and in all jawed vertebrates, the pharyngeal endostyle closes off from the gut lumen to form the follicular endocrine thyroid gland.
5. Post-Anal Muscular Tail: A posterior extension of the body, supported by the notochord or vertebral column and flanked by segmented chevron-shaped myomeres, that extends behind the anus (in contrast to non-chordate worms such as annelids and nematodes, whose terminal anus sits at the posterior tip of the body).

For more than a century of classical morphology, zoologists grouped Cephalochordata and Vertebrata together as sister clades ("Euchordata" or "Myomerozoa") based on their shared fish-like myomeres and persistent notochords, placing sessile adult Tunicata at the base of the phylum. In 2006, phylogenomic analyses of hundreds of nuclear protein-coding genes by Frédéric Delsuc, Hervé Philippe, Blair Hedges, and colleagues overturned this textbook tree:

One of the deepest insights of evolutionary developmental biology (evo-devo)—originally proposed on anatomical grounds by Étienne Geoffroy Saint-Hilaire in 1822 and proven molecularly by Detlev Arendt, Katharina Nübler-Jung (1994), and Edward M. De Robertis and Yoshiki Sasai (1996)—is that the chordate body plan is dorso-ventrally inverted relative to protostomes and basal deuterostomes:

• In protostomes (Drosophila, Platynereis) and acorn worms (Hemichordata), the bone morphogenetic protein BMP4 / Decapentaplegic (Dpp) is expressed on the dorsal side (specifying dorsal non-neural epidermis), while its secreted antagonist Chordin / Short gastrulation (Sog) is expressed on the ventral side (where the ventral nerve cord forms), and the heart pumps blood forward along the dorsal vessel.
• In Chordata, this entire signaling axis flipped 180°: Chordin is expressed on the dorsal side (inducing the dorsal hollow neural tube above the notochord), while BMP4 is expressed on the ventral side (where the ventral chambered heart forms!).

What do the Cambrian fossils Pikaia gracilens, Metaspriggina, and Haikouichthys reveal about the origin of chordates?

In the Early Cambrian Chengjiang Lagerstätte of Yunnan, China (~518 Ma) and the Middle Cambrian Burgess Shale of British Columbia (~508 Ma), soft-bodied fossils preserve the step-by-step assembly of the chordate and vertebrate body plan:

• Pikaia gracilens (~508 Ma, Burgess Shale, re-analyzed by Simon Conway Morris and Jean-Bernard Caron, 2012) exhibits a dorsal axial organ/notochord and ~100 sigmoidal myomeres for lateral undulatory swimming;
• Haikouichthys ercaicunensis (~518 Ma, Chengjiang) and Metaspriggina walcotti (~508 Ma, Burgess Shale, Conway Morris & Caron, 2014) already possess paired camera-type eyes, nasal capsules, cartilaginous arcualia flanking the notochord, W-shaped myomeres, and seven pairs of bipartite pharyngeal gill bars—demonstrating that true stem-vertebrates swam in Early Cambrian seas more than 515 million years ago.

Why do chordates and only a few other organisms require dietary iodine?

Across the animal kingdom, almost all invertebrates use brominated or chlorinated tyrosines exclusively as structural cross-links in cuticular scleroproteins. In the ancestor of Chordata (and baseline deuterostomes), the pharyngeal endostyle evolved a specialized peroxidase-catalyzed iodination system to synthesize the signaling hormone triiodothyronine (T₃) and thyroxine (T₄), which bind nuclear thyroid hormone receptors (TRα/TRβ) to orchestrate chordate metamorphosis (triggering the transition from filter-feeding larva to adult in amphioxus, ascidians, lampreys, flatfishes, and amphibian tadpoles) and later regulating endothermic basal metabolic rate in birds and mammals.

1. Arendt, D., & Nübler-Jung, K. (1994). Inversion of dorsoventral axis? Nature, 371(6492), 26. doi:10.1038/371026a0
2. De Robertis, E. M., & Sasai, Y. (1996). A common plan for dorsoventral patterning in Bilateria. Nature, 380(6569), 37–40. doi:10.1038/380037a0
3. Delsuc, F., Brinkmann, H., Chourrout, D., & Philippe, H. (2006). Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature, 439(7079), 965–968. doi:10.1038/nature04336
4. Putnam, N. H., Butts, T., Ferrier, D. E. K., Furlong, R. F., Hellsten, U., Kawashima, T., ... & Rokhsar, D. S. (2008). The amphioxus genome and the evolution of the chordate karyotype. Nature, 453(7198), 1064–1071. doi:10.1038/nature06967
5. Conway Morris, S., & Caron, J.-B. (2014). A primitive fish from the Cambrian of North America. Nature, 512(7515), 419–422. doi:10.1038/nature13414
6. Satoh, N. (2016). Chordate Origins and Evolution: The Molecular Evolutionary Road to Vertebrates. Academic Press. doi:10.1016/C2015-0-00321-5