Tunicata

Phylum Chordata—the deuterostome clade uniting vertebrates (Craniata) with two subphyla of marine invertebrate suspension feeders, Cephalochordata (lancelets or amphioxus, ~35 species) and Tunicata (formerly Urochordata: ascidian sea squirts, pelagic thaliaceans, and appendicularian larvaceans, ~3,000 species)—is defined by five canonical developmental synapomorphies present at least during embryonic or larval life:

1. A pressurized axial skeletal rod—the notochord (expressing the T-box transcription factor Brachyury and FoxA2)—situated between the digestive gut and the nerve cord;
2. A single dorsal hollow nerve cord formed by rolling or folding of the dorsal neuroectodermal plate (neurulation);
3. Pharyngeal gill slits (perforating the lateral walls of the pharynx for mucociliary filter feeding and gas exchange);
4. A ventral glandular groove on the floor of the pharynx—the endostyle (expressing Nkx2-1/TTF-1 and Pax8, which concentrates iodine and secretes iodinated mucoproteins and tyrosine derivatives, and is directly homologous to the vertebrate thyroid gland); and
5. A muscular post-anal tail driven by chevron-shaped or flanking myotomal muscle blocks.

From the mid-19th century (when Alexander Kowalevsky in 1866–1867 discovered that sessile adult sea squirts hatch from a microscopic, free-swimming chordate tadpole larva possessing a notochord and dorsal neural tube) until 2006, virtually every zoology textbook grouped Cephalochordata + Vertebrata into a clade called "Euchordata" or "Myomerozoa" because lancelets (Branchiostoma) look strikingly like miniature, translucent, headless fish throughout their entire life cycle.

In 2006, Frédéric Delsuc, Henner Brinkmann, Daniel Chourrout, and Hervé Philippe analyzed 146 nuclear protein-coding genes across deuterostomes and discovered that the textbook tree was inverted by long-branch attraction (LBA):

• Why Tunicates Were Misplaced at the Base of Chordata: Tunicates (Ciona, Oikopleura) have undergone a 2-to-3-fold acceleration in molecular evolutionary rate alongside severe genome compaction, whereas cephalochordates (Branchiostoma floridae) have the slowest amino-acid substitution rate of any chordate (slower even than jawed vertebrates!). In early single-gene 18S rRNA trees, the long branch of Tunicata was artificially pulled toward the distant echinoderm/hemichordate outgroups, leaving slow-evolving amphioxus with vertebrates by default.
• The Olfactores Clade (Tunicata + Vertebrata): When analyzed with site-heterogeneous CAT-GTR models and corroborated by shared microRNA families, rare domain rearrangements, and embryonic cell-lineage tracing (Putnam et al., 2008), Cephalochordata is the basal sister group to all other chordates, while Tunicata and Vertebrata form the clade Olfactores (named by Richard Jefferies in 1991 for improved anterior chemosensory/placodal structures).

Because Branchiostoma floridae evolved so slowly and never underwent the two rounds of whole-genome duplication (2R-WGD) that occurred at the base of Vertebrata, its 520 Mb genome (sequenced by Nicholas H. Putnam, Daniel S. Rokhsar, Linda Z. Holland, Peter W. H. Holland, and colleagues in 2008) preserves the 17 ancestral chordate linkage groups in near-ancestral synteny:

• Unbroken 15-Gene Hox and 3-Gene ParaHox Clusters: Whereas mammals have 39 Hox genes split across four paralogous chromosomal clusters (HoxA, HoxB, HoxC, HoxD), amphioxus possesses a single, contiguous 470-kb Hox cluster containing 15 genes (AmphiHox1 through AmphiHox15) alongside an intact 3-gene ParaHox cluster (Gsx–Pdx/Xlox–Cdx)—proving that a single 4-fold duplication (1 → 4) created the vertebrate genome.
• Why Amphioxus Is Called Cephalochordata: Unlike tunicates (where the notochord is restricted to the larval tail) and vertebrates (where the notochord ends beneath the midbrain behind the pituitary, allowing neural crest and placodes to build a pre-chordal head), the amphioxus notochord extends all the way to the anterior tip of the snout ahead of the cerebral vesicle. Furthermore, amphioxus notochord cells are actually specialized striated muscle cells innervated by dorsal nerve cord projections: contracting the notochordal actin-myosin filaments increases the stiffness of the hydrostatic rod during high-speed burrowing into coarse marine sand.

Despite their sessile adult morphology, tunicates display three remarkable developmental and biochemical features that illuminate vertebrate origins:

1. Horizontal Acquisition of Bacterial Cellulose Synthase (CesA): Tunicates are the only animals on Earth capable of synthesizing crystalline cellulose (tunicin), which forms the tough protective external tunic surrounding the adult sea squirt and the intricate microfluidic mucus-and-cellulose filtration house of Oikopleura. Genomic analysis of Ciona intestinalis (Dehal et al., 2002; Matthysse et al., 2004) revealed that the common ancestor of all tunicates (~530 Ma) acquired a functional cellulose synthase + glycosylhydrolase fusion gene (Ci-CesA) via horizontal gene transfer from a marine Streptomyces-like actinobacterium or cyanobacterium.
2. Miniature Invariant Tadpole Larva (Ciona): The swimming tadpole larva of Ciona intestinalis develops from an invariant cleavage lineage (mapped by Edwin Grant Conklin in 1905 and Patrick Lemaire) comprising only ~2,600 total cells, including precisely 40 vacuolated notochord cells stacked in a single-file "coin-roll" column, 36 tail muscle cells, and a miniature central nervous system of only ~330 cells (177 neurons, whose complete connectome was reconstructed by Kerrianne Ryan and Ian Meinertzhagen in 2016).
3. Shared Cardiopharyngeal Mesoderm and Proto-Neural Crest: As demonstrated by Lionel Christiaen, Michael Levine, and colleagues, the trunk ventral cells (TVCs) of the Ciona embryo express a conserved gene regulatory cascade (Mesp → Ets1/2 → FoxF → Gata4/5/6 + Nk4/Nkx2-5 + Tbx1/10 + Islet) that gives rise to both the first and second heart fields and the branchiomeric (siphon) pharyngeal muscles—a shared cardiopharyngeal developmental module unique to Olfactores (Tunicata + Vertebrata) and absent in amphioxus. Simultaneously, the lateral neural plate border of Ciona (the a9.49 lineage) forms migratory-capable pigment cells (the otolith and ocellus) alongside paired Six1/2⁺/Eya⁺ proto-placodes, confirming the shared developmental ground plan of Olfactores.

Why does the sea squirt Ascidia or Phallusia accumulate vanadium to 10 million times the concentration of seawater?

Many phlebobranch ascidians (Ascidia sydneiensis, Phallusia mammillata, Ciona) absorb dissolved vanadate (V^VO₄³⁻, ~35 nM in seawater) across their branchial sac, transport it via vanabins (vanadium-binding metallochaperones), and reduce it via NADPH/glutathione inside specialized signet-ring blood cells (vanadocytes) into vanadyl (V^IV) and trivalent vanadium (V^III) stored in acidic vacuoles (pH 1.9–2.4, acidified by V-ATPase with sulfate counterions) at concentrations up to 350 mM (10⁷-fold bioconcentration), functioning as a potent chemical deterrent against fish and fouling epibionts.

How do pelagic salps (Thaliacea) impact the global oceanic carbon sink?

When coastal or Southern Ocean phytoplankton blooms occur, pelagic salps (Salpa thompsoni, Pegea) reproduce asexually by budding long chains of hundreds of filter-feeding blastozooids, doubling their population biomass in days. Because salps pump water continuously through a fine pharyngeal mucus net by muscular jet propulsion, they package picoplankton and diatoms into dense, fast-sinking fecal pellets that sink at 500 to 1,500 meters per day—exporting massive pulses of particulate organic carbon directly into the deep-ocean biological carbon pump.

1. 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
2. Putnam, N. H., Butts, T., Ferrier, D. E., 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
3. Dehal, P., Satou, Y., Campbell, R. K., Chapman, J., Degnan, B., De Tomaso, A., ... & Rokhsar, D. S. (2002). The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science, 298(5601), 2157–2167. doi:10.1126/science.1080049
4. Ryan, K., Lu, Z., & Meinertzhagen, I. A. (2016). The CNS connectome of a tadpole larva of Ciona intestinalis (L.) highlights sidedness in the brain of a chordate sibling. eLife, 5, e16962. doi:10.7554/eLife.16962