The tunicate (sea squirt) Ciona intestinalis spends its adult life anchored to a hard substrate, filter feeding and releasing gametes (eggs and sperm) into the surrounding sea water. For a fleeting day or two of its life, however, the larva of C. intestinalis adopts a tadpole morphology (Figure 1A). This morphology provides hints as to the origins of the chordates (see Box 1 for a glossary of specialist terms used in this article), including that of the most successful chordate clade, the vertebrates. In 1866, the Russian biologist Alexander Kowalevsky observed the ascidian tadpole and noted the presence of a dorsal nervous system and prominent notochord, two defining features of chordates (Kowalevsky, 1866). Prior to this, the chordate features of tunicates had not been described and, in fact, a century earlier the taxonomy of Carl Linnaeus placed C. intestinalis and other ascidians (see Glossary) within the molluscs, based on their adult form (Linné, 1767).

Figure 1

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Today, due to its unique evolutionary position, and ease of use, C. intestinalis is the model organism of choice for many labs that aim to uncover the mechanisms that drive embryonic development and morphogenesis. In the era of recombinant DNA and genomics, many standard tools are available to the C. intestinalis researcher, including a well-annotated genome, methods to manipulate gene function and to create mutant strains and reporter lines, and techniques for expressing engineered DNA (Satoh, 2014). Additionally, many resources have been built thanks to the cooperative efforts of C. intestinalis investigators (see Box 2).

Unlike researchers working on more common model organisms, those working on C. intestinalis rely on wild-caught specimens. The large-scale culturing of C. intestinalis is limited to only a few laboratories that have marine facilities, and attempts to establish an inbred laboratory strain of C. intestinalis for widespread use have not yet been successful. Researchers should be aware that differences between isolates (for example, in their geography, ecology, and life history), while potentially confounding, might also lead to new insights regarding regional adaptation and variation, and dispersal.

C. intestinalis is a member of the Tunicata (see Glossary). The Tunicata include the sessile ascidians, like C. intestinalis, as well as the free floating (pelagic) thaliaceans and larvaceans (see Glossary). Together with vertebrates and cephalochordates (see Glossary), tunicates make up the chordates. The defining feature of Chordata is the notochord, an anterior-to-posterior oriented rod of cells, which lies just below the spinal cord. In the first chordates, the notochord was likely to have conferred a biomechanical advantage to swimming larvae by providing them with stiffness and turgor, as it does for the C. intestinalis larva. Within the vertebrates, the notochord has an added role, acting as a signaling center for neighboring tissues of the developing embryo. Other morphological features uniting C. intestinalis (and other tunicates) to the chordates include a dorsal, hollow nervous system and a muscular post-anal tail (the anus of most ascidians, however, is re-positioned from the tail to the head in adult life).

Chordate phylogeny has been recently reordered (Delsuc et al., 2006; Singh et al., 2009), with tunicates and vertebrates now grouped as sister taxa within the chordates, where previously cephalochordates (e.g., amphioxus) and vertebrates were long thought to share a more-recent common ancestor (see for example, Schaeffer, 1987; Nielsen, 1995). This re-ordering has yielded new insights into the timing of the appearance of characters once believed to be unique to vertebrates. For example, neurogenic placodes (see Glossary), which in vertebrates give rise to the sensory structures of the head, including the olfactory and auditory systems, and neural crest cells (see Glossary), a key innovation in the elaboration of vertebrate cephalic structures (Gans and Northcutt, 1983), are both believed to have morphological antecedents in tunicates (Manni et al., 2001; Jeffery et al., 2004), indicating that these structures predate the divergence of tunicate and vertebrate lineages. Cephalochordates, by contrast, apparently lack neural crest-like cells or placode-like structures and may represent the basal chordate state, before these innovations occurred. Although some authors maintain that true placodes and neural crest remain vertebrate inventions (Schlosser et al., 2014), the newer phylogeny has highlighted the relevance of C. intestinalis in providing a window on the evolution of such traits.

Despite these conserved structures that unite the chordates, tunicates have several morphological features that diverge radically from their vertebrate cousins, including the adult body form, the absence of somites (see Glossary), hermaphroditic reproduction, and, curiously, the ability to synthesize cellulose (Kimura and Itoh, 1996; Matthysse et al., 2004; Nakashima et al., 2004). Cellulose production is thought to derive from the horizontal transfer of a prokaryotic cellulose synthase gene; the tunicate ancestor appears to have cobbled together the remainder of the cellulose biosynthetic pathway from its existing gene complement, as no other known plant or prokaryotic cellulose biosynthetic components have been identified in any tunicate. It has long been debated whether these divergent features were primitive (i.e., representative of the last common chordate ancestor) or derived (i.e., unique to tunicates). The finding that tunicates and vertebrates form a clade, with cephalochordates as the out-group, has shed new light on this issue. Cephalochordates lack the ability to make cellulose, have somites, and do not undergo a metamorphosis like most tunicates, arguing that many of the unique features of tunicates are derived (Swalla, 2006; Swalla and Smith, 2008). Likewise some tunicate genomic anomalies, such as degenerate Hox clusters (see Glossary), also appear to be derived (Ikuta et al., 2004).

In the wild, C. intestinalis is a member of the marine biofouling (see Glossary) community, lining the hulls of boats and crowding the underwater surfaces of buoys and docks. It thrives even in the presence of the anthropogenic insults generated in a marina setting, such as effluent from boats, surface petroleum slicks and organic waste. C. intestinalis is cosmopolitan in distribution, found on both sides of the Atlantic and Pacific Oceans, and it has been reported in the oceans off Australia and South Africa (Therriault and Herborg, 2008b).

Two varieties of C. intestinalis, Type A and Type B, have been described. Type A is found on both sides of the Pacific, the Mediterranean and North Atlantic, and off the coasts of South Africa; Type B is found off the Atlantic coasts of Europe and North America (Caputi et al., 2007). The two types are known to overlap only in the English Channel and off the northern coast of France (Caputi et al., 2007; Nydam and Harrison, 2007; Sato et al., 2012). Reproductive barriers exist between the two, and attempts to rear fertile hybrids in the lab have been unsuccessful (Caputi et al., 2007); these facts alone suggest that A and B may, in fact, be properly viewed as two distinct species, not merely as sub-species. Nonetheless (and in apparent contradiction to laboratory observations), evidence of intermixing from the wild population within the shared range of A and B types shows that this reproductive isolation is not complete (Nydam and Harrison, 2011a). We therefore prefer to view A and B as sub-species even though they may be, at the same time, species in the making. This population provides a natural laboratory to investigate the mechanisms of speciation in action. For example, the proteins that mediate sperm-egg recognition have been reported to have evolved more rapidly than have other C. intestinalis proteins within the area of overlap, but still no faster than the rate at which these gamete-recognition proteins have changed in areas where only a single type is found (Nydam and Harrison, 2011b). The factors that have contributed to the divergence of these lineages bear greater examination, including differences in both life history (see Box 3) and genetics. Investigations into their genetic differences will likely be facilitated by the availability of separate assemblies for the genomes of Type A and Type B (Tassy et al., 2010). The existence of these subtypes also underscores the need to precisely determine the taxonomic status of any model system in order to clarify which features vary or are shared within and between species subtypes, particularly in the case of an organism like C. intestinalis where researchers rely almost entirely on wild-caught specimens.

Although the place of origin of C. intestinalis is a matter of speculation (Therriault and Herborg, 2008a), they are thought to have extended their range through human activity, for instance, by travelling on the hulls of boats or by being carried in ballast water that is later discharged into the ocean. C. intestinalis was first reported in 1917 on the west coast of North America (Ritter and Forsyth, 1917). While its hardiness and adaptability to man-made environments makes C. intestinalis a nuisance—for example, accumulation on boat surfaces may add weight and drag to a vessel, and competition for space and food may hinder aquaculture (Ramsay et al., 2009)—these traits render these animals easily collectable for research purposes. As an immobile, indiscriminate filter feeder, C. intestinalis would appear to be an easy target for its predators which include sea stars, crabs, shrimp, nudibranchs and fish (Gullikesen and Skjaeveland, 1973; Carver et al., 2003; Dumont et al., 2009). However, its tough cellulose-containing tunic provides a level of protection and we speculate that the accumulation of toxins, in particular vanadium, a metal known to be found in high concentrations in ascidians (Michibata et al., 1991), could also serve as a deterrent.

The early development of C. intestinalis, from zygote to swimming larva, has been well described (Hotta et al., 2007). The embryo undergoes a regular pattern of development within a protective chorion, surrounded on the exterior by the finger-like gelatinous projections of the follicle cells. About 40 min after an egg is fertilized, an invariant series of cell divisions begins. At 112 cells (4.5 hr post fertilization), the embryo undergoes gastrulation (see Glossary). Neurulation soon follows (see Glossary), with the formation of the chordate-specific hollow, dorsal nervous system. About 18 hr after fertilization, a C. intestinalis larva hatches from its chorion and begins to search for a suitable spot to attach, and then undergo metamorphosis. Sensing gravity and light with two pigmented sensory organs found in its brain, the otolith and ocellus, respectively (see Figure 1A), the C. intestinalis larva generally swims up and away from light. As a result, larvae often settle on the undersides of docks and boats (Figure 1C), ropes and buoys—often conveniently within arms' reach of the surface. Similarly in the lab, we find that C. intestinalis swimming larvae readily attach to the surface of plastic petri dishes; hundreds can attach to a single large dish, which can then be transferred to the controlled conditions of a marine facility for rearing. The long-term culture of C. intestinalis, over multiple generations, is still best accomplished in a marine lab setting with access to unfiltered sea water, which provides these animals with their natural food source. However, C. intestinalis has also been reared with some success in facilities supplied with artificial sea water and re-hydrated food (Veeman et al., 2011).

C. intestinalis attach to a surface via the adhesive palps at their rostral tip (see Figure 1A), initiating a radical metamorphosis, the first event of which—the complete resorption of the tail—deprives the animal of it most recognizable chordate features. In the hours after settling, the animal develops a stalk, or stolon, at its attachment point, and its viscera are re-oriented within the body. Within a few days, a beating heart becomes visible. The mouth also opens, channeling water from the outside to the pharynx, and then through gill slits to right and left atrial chambers, and then back out into the surrounding sea water. Food is filtered from the incoming water, trapped on the pharyngeal mucus, a product of the endostyle (an organ thought to be homologous to the thyroid), and then directed to the esophagus and gut. Based on conserved features of vertebrates and cephalochordates, we can assume that in the ancestral chordate, the exit point of the gut, the anus, was at the ventral side of the tail. Because C. intestinalis reabsorbs its tail at metamorphosis, it must re-route this exit point. It does so through one of the atrial siphon cavities, usually the left. While anatomical and molecular evidence suggest that the atrial siphon primordia share a common origin with the primordia of the vertebrate ear (Manni et al., 2004; Mazet et al., 2005; Kourakis and Smith, 2007), the functional role of the atrial siphon in adult C. intestinalis is as a cloaca, a common exit point for waste, filtered sea water, sperm and eggs. The final topology of the adult animal is attained when, after a few weeks time, right and left atrial siphons fuse at the dorsal midline, yielding an animal with a single atrial siphon for outward-current flow, and a single, larger oral siphon, for inward-current flow (Figure 1B). After a few months time, the animals will be sexually mature and will live for up to 6 months (Satoh, 1994); in captivity, we find they live for as long as a year and a half.

As an experimental organism, C. intestinalis has the advantage of being available and gravid year-round, although populations may wane during colder months (Berrill, 1937). At 3 months, individuals are typically 3–6 cm in length and are sexually mature. They are broadcast spawners, with several to hundreds of individuals simultaneously releasing eggs and sperm into the surrounding seawater, thereby increasing the chances of fertilization. Spawning occurs according to a light–dark cycle, cued by the arrival of daylight after several hours of darkness. We mimic this light–dark cycle in the lab for controlled spawning; C. intestinalis can be induced to spawn after less than 1 hr in darkness (Veeman et al., 2011).

C. intestinalis, like most other tunicates, are hermaphrodites, although recogniton molecules on the surface of the chorion limit the ability of animals to self-fertilize (Harada et al., 2008). While self-fertility is limited and not likely to play a large role in wild populations (Jiang and Smith, 2005), self-fertilization offers a convenient way for researchers to unmask recessive alleles responsible for developmentally noteworthy phenotypes. After eggs and sperm from a single individual are mixed, the resulting progeny can be screened during embryogenesis, larval life, or beyond, to identify morphological or behavioral variants (Sordino et al., 2008). In fact, wild C. intestinalis populations are a repository of genetic variability, so finding these mutants is not difficult. An analysis of Ciona savignyi, a closely related sister species to C. intestinalis that also has extensive polymorphism, has shown that its polymorphisms are not evenly distributed in the genome but are highest in intergenic regions and introns, as would be expected from purifying selection. It has been hypothesized that the high level of polymorphism is not due to an increased mutation rate, but rather to the large effective population size (Small et al., 2007).

The C. intestinalis genome has important differences compared to vertebrate genomes. In many cases, a developmental regulatory gene in C. intestinalis is represented by multiple orthologous genes from vertebrates. For example, the vertebrate genes fgf8, fgf17, and fgf18 all share orthology—similarity by common descent—with the single C. intestinalis gene fgf8/17/18. During the vertebrate radiation, two rounds of whole-genome duplication likely occurred, producing four vertebrate genes for every one C. intestinalis gene, followed by subsequent gene loss and duplication events (Kasahara, 2007). This can simplify the study of gene interactions in C. intestinalis and facilitate experimental perturbations, such as gene knock-down. However, when the whole genome is considered, current best estimates show that C. intestinalis has ∼90% of the number of protein-coding genes as that found in the human genome (17,000 in C. intestinalis vs 19,000 in humans) (Satou et al., 2005; Tassy et al., 2010; Ezkurdia et al., 2014; Cunningham et al., 2015). The total genome size of C. intestinalis, however, is less than one twenty-fifth that of the human genome because of the reduction in non-coding gene sequence, such as introns, and because of the organization of about one fifth of its genes into operons (see Glossary; Satou et al., 2008). This small, compact genome offers various advantages to the researcher (Wang and Christiaen, 2012; Irvine, 2013).

The tunicates—including C. intestinalis—are highly successful marine invertebrates. In most environments, C. intestinalis is considered to be invasive, and it can be so successful as to constitute a considerable fraction of the local biomass (Therriault and Herborg, 2008b; Ramsay et al., 2009). Many questions remain unanswered with regard to the sources and dates of its introduction, and regarding the relative contributions of human-mediated vs natural dispersion routes, and adaptations of various populations to local conditions (see also Box 3 for further outstanding questions). The widespread and easily collected populations of C. intestinalis, together with the genetic and genomic resources available for this organism, make this a ripe area for research.

The lifestyle adopted by the adult C. intestinalis, that of a sessile filter feeder, has served it well and has shaped its anatomy, physiology and embryology. Many of the features of C. intestinalis that at various times have been called primitive or basal, such as the simplicity of the embryo or the adult body form, are best seen as products of the animal's unique natural history. From a practical point of view, because of its inherently high levels of polymorphism and because of the many sites used to collect experimental animals worldwide, C. intestinalis researchers must remember that locally collected animals might be quite different to those used to generate the data found in C. intestinalis databases (see Box 2). With these unique features of C. intestinalis in mind, we can expect this relatively obscure marine model organism to contribute much to our understanding of basic chordate biology and to the history of the chordate clade.

1. Book

   1. Berrill NJ

   (1937)

   Culture methods for ascidians In: Culture Methods for invertebrate Animals

   Galtsoff PS, editors. Ithaca, New York: Comstock Publishing.

   • Google Scholar
2. 1. Caputi L
   2. Andreakis N
   3. Mastrototaro F
   4. Cirino P
   5. Vassillo M
   6. Sordino P

   (2007) Cryptic speciation in a model invertebrate chordate

   Proceedings of the National Academy of Sciences of USA 104:9364–9369.

   https://doi.org/10.1073/pnas.0610158104

   • Google Scholar
3. 1. Carver CE
   2. Chisholm A
   3. Mallet AL

   (2003)

   Strategies to mitigate the impact of Ciona intestinalis (L.) biofouling on shellfish production

   Journal of Shellfish Research 22:621–631.

   • Google Scholar
4. 1. Cunningham F
   2. Amode MR
   3. Barrell D
   4. Beal K
   5. Billis K
   6. Brent S
   7. Carvalho-Silva D
   8. Clapham P
   9. Coates G
   10. Fitzgerald S
   11. Gil L
   12. Giron CG
   13. Gordon L
   14. Hourlier T
   15. Hunt SE
   16. Janacek SH
   17. Johnson N
   18. Juettemann T
   19. Kahari AK
   20. Keenan S
   21. Martin FJ
   22. Maurel T
   23. McLaren W
   24. Murphy DN
   25. Nag R
   26. Overduin B
   27. Parker A
   28. Patricio M
   29. Perry E
   30. Pignatelli M
   31. Riat HS
   32. Sheppard D
   33. Taylor K
   34. Thormann A
   35. Vullo A
   36. Wilder SP
   37. Zadissa A
   38. Aken BL
   39. Birney E
   40. Harrow J
   41. Kinsella R
   42. Muffato M
   43. Ruffier M
   44. Searle SM
   45. Spudich G
   46. Trevanion SJ
   47. Yates A
   48. Zerbino DR
   49. Flicek P

   (2015) Ensembl 2015

   Nucleic Acids Research 43:D662–D669.

   https://doi.org/10.1093/nar/gku1010

   • Google Scholar
5. 1. Delsuc F
   2. Brinkmann H
   3. Chourrout D
   4. Philippe H

   (2006) Tunicates and not cephalochordates are the closest living relatives of vertebrates

   Nature 439:965–968.

   https://doi.org/10.1038/nature04336

   • Google Scholar
6. 1. Dumont CP
   2. Urriago JD
   3. Abarca A
   4. Gaymer CF
   5. Thiel M

   (2009) The native rock shrimp Rhynchocinetes typus as a biological control of fouling in suspended scallop cultures

   Aquaculture 292:74–79.

   https://doi.org/10.1016/j.aquaculture.2009.03.044

   • Google Scholar
7. 1. Ezkurdia I
   2. Juan D
   3. Rodriguez JM
   4. Frankish A
   5. Diekhans M
   6. Harrow J
   7. Vazquez J
   8. Valencia A
   9. Tress ML

   (2014) Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes

   Human Molecular Genetics 23:5866–5878.

   https://doi.org/10.1093/hmg/ddu309

   • Google Scholar
8. 1. Gans C
   2. Northcutt RG

   (1983) Neural crest and the origin of vertebrates: a new head

   Science 220:268–273.

   https://doi.org/10.1126/science.220.4594.268

   • Google Scholar
9. 1. Gullikesen B
   2. Skjaeveland SH

   (1973)

   The sea-star, Asteria rubens L., as predator on the ascidian, Ciona intestinalis (L.), in Borgenfjorden, North-Troendelag, Norway

   Sarsia 52:15–20.

   • Google Scholar
10. 1. Harada Y
    2. Takagaki Y
    3. Sunagawa M
    4. Saito T
    5. Yamada L
    6. Taniguchi H
    7. Shoguchi E
    8. Sawada H

    (2008) Mechanism of self-sterility in a hermaphroditic chordate

    Science 320:548–550.

    https://doi.org/10.1126/science.1152488

    • Google Scholar
11. 1. Hotta K
    2. Mitsuhara K
    3. Takahashi H
    4. Inaba K
    5. Oka K
    6. Gojobori T
    7. Ikeo K

    (2007) A web-based interactive developmental table for the ascidian Ciona intestinalis, including 3D real-image embryo reconstructions: I. From fertilized egg to hatching larva

    Developmental Dynamics 236:1790–1805.

    https://doi.org/10.1002/dvdy.21188

    • Google Scholar
12. 1. Ikuta T
    2. Yoshida N
    3. Satoh N
    4. Saiga H

    (2004) Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development

    Proceedings of the National Academy of Sciences of USA 101:15118–15123.

    https://doi.org/10.1073/pnas.0401389101

    • Google Scholar
13. 1. Irvine SQ

    (2013)

    Study of Cis-regulatory elements in the Ascidian Ciona intestinalis

    Current Genomics 14:56–67.

    • Google Scholar
14. 1. Jeffery WR
    2. Strickler AG
    3. Yamamoto Y

    (2004) Migratory neural crest-like cells form body pigmentation in a urochordate embryo

    Nature 431:696–699.

    https://doi.org/10.1038/nature02975

    • Google Scholar
15. 1. Jiang D
    2. Smith WC

    (2005) Self- and cross-fertilization in the solitary ascidian Ciona savignyi

    Biological Bulletin 209:107–112.

    https://doi.org/10.2307/3593128

    • Google Scholar
16. 1. Kasahara M

    (2007) The 2R hypothesis: an update

    Current Opinion in Immunology 19:547–552.

    https://doi.org/10.1016/j.coi.2007.07.009

    • Google Scholar
17. 1. Kimura S
    2. Itoh T

    (1996) New cellulose synthesizing complexes (terminal complexes) involved in animal cellulose biosynthesis in the tunicate Metandrocarpa uedai

    Protoplasma 194:151–163.

    https://doi.org/10.1007/BF01882023

    • Google Scholar
18. 1. Kourakis MJ
    2. Smith WC

    (2007) A conserved role for FGF signaling in chordate otic/atrial placode formation

    Developmental Biology 312:245–257.

    https://doi.org/10.1016/j.ydbio.2007.09.020

    • Google Scholar
19. 1. Kowalevsky AO

    (1866)

    Entwickungsgeschichte der einfachen Ascidien

    Mémoires de l'Académie Impériale des Sciences de St. Pétersbourg 10:1–19.

    • Google Scholar
20. 1. Linné CA

    (1767)

    Systema naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Uppsala

    • Google Scholar
21. 1. Manni L
    2. Lane NJ
    3. Burighel P
    4. Zaniolo G

    (2001) Are neural crest and placodes exclusive to vertebrates?

    Evolution & Development 3:297–298.

    https://doi.org/10.1046/j.1525-142X.2001.01040.x

    • Google Scholar
22. 1. Manni L
    2. Lane NJ
    3. Joly JS
    4. Gasparini F
    5. Tiozzo S
    6. Caicci F
    7. Zaniolo G
    8. Burighel P

    (2004) Neurogenic and non-neurogenic placodes in ascidians

    Journal of Experimental Zoology Part B, Molecular and Developmental Evolution 302:483–504.

    https://doi.org/10.1002/jez.b.21013

    • Google Scholar
23. 1. Matthysse AG
    2. Deschet K
    3. Williams M
    4. Marry M
    5. White AR
    6. Smith WC

    (2004) A functional cellulose synthase from ascidian epidermis

    Proceedings of the National Academy of Sciences of USA 101:986–991.

    https://doi.org/10.1073/pnas.0303623101

    • Google Scholar
24. 1. Mazet F
    2. Hutt JA
    3. Milloz J
    4. Millard J
    5. Graham A
    6. Shimeld SM

    (2005) Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes

    Developmental Biology 282:494–508.

    https://doi.org/10.1016/j.ydbio.2005.02.021

    • Google Scholar
25. 1. Michibata H
    2. Iwata Y
    3. Hirata J

    (1991) Isolation of highly acidic and vanadium-containing blood-cells from among several types of blood-cell from Ascidiidae species by density-gradient centrifugation

    Journal of Experimental Zoology 257:306–313.

    https://doi.org/10.1002/jez.1402570304

    • Google Scholar
26. 1. Nakashima K
    2. Yamada L
    3. Satou Y
    4. Azuma J
    5. Satoh N

    (2004) The evolutionary origin of animal cellulose synthase

    Development Genes and Evolution 214:81–88.

    https://doi.org/10.1007/s00427-003-0379-8

    • Google Scholar
27. Book

    1. Nielsen C

    (1995)

    Animal Evolution: Interrelationships of the Living Phyla

    Oxford University Press.

    • Google Scholar
28. 1. Nydam ML
    2. Harrison RG

    (2007) Genealogical relationships within and among shallow-water Ciona species (Ascidiacea)

    Marine Biology 151:1839–1847.

    https://doi.org/10.1007/s00227-007-0617-0

    • Google Scholar
29. 1. Nydam ML
    2. Harrison RG

    (2011a) Introgression despite substantial divergence in a broadcast spawning marine invertebrate

    Evolution 65:429–442.

    https://doi.org/10.1111/j.1558-5646.2010.01153.x

    • Google Scholar
30. 1. Nydam ML
    2. Harrison RG

    (2011b) Reproductive protein evolution in two cryptic species of marine chordate

    BMC Evolutionary Biology 11:18.

    https://doi.org/10.1186/1471-2148-11-18

    • Google Scholar
31. 1. Ramsay A
    2. Davidson J
    3. Bourque D
    4. Stryhn H

    (2009) Recruitment patterns and population development of the invasive ascidian Ciona intestinalis in Prince Edward Island, Canada

    Aquatic Invasions 9:169–176.

    https://doi.org/10.3391/ai.2009.4.1.17

    • Google Scholar
32. Book

    1. Ritter WE
    2. Forsyth RA

    (1917)

    Ascidians of the littoral zone of southern California

    University of California publications in Zoology.

    • Google Scholar
33. 1. Sasakura Y
    2. Nakashima K
    3. Awazu S
    4. Matsuoka T
    5. Nakayama A
    6. Azuma J
    7. Satoh N

    (2005) Transposon-mediated insertional mutagenesis revealed the functions of animal cellulose synthase in the ascidian Ciona intestinalis

    Proceedings of the National Academy of Sciences of USA 102:15134–15139.

    https://doi.org/10.1073/pnas.0503640102

    • Google Scholar
34. 1. Sato A
    2. Satoh N
    3. Bishop JDD

    (2012) Field identification of ‘types’ A and B of the ascidian Ciona intestinalis in a region of sympatry

    Marine Biology 159:1611–1619.

    https://doi.org/10.1007/s00227-012-1898-5

    • Google Scholar
35. 1. Satoh N

    (1994)

    Developmental biology of ascidians

    Developmental biology of ascidians, New York, Cambridge University Press, Cambridge England.

    • Google Scholar
36. Book

    1. Satoh N

    (2014)

    Developmental Genetics of Ascidians

    Hoboken, NJ, USA: Wiley-Blackwell.

    • Google Scholar
37. 1. Satou Y
    2. Kawashima T
    3. Shoguchi E
    4. Nakayama A
    5. Satoh N

    (2005) An integrated database of the ascidian, Ciona intestinalis: towards functional genomics

    Zoological Science 22:837–843.

    https://doi.org/10.2108/zsj.22.837

    • Google Scholar
38. 1. Satou Y
    2. Mineta K
    3. Ogasawara M
    4. Sasakura Y
    5. Shoguchi E
    6. Ueno K
    7. Yamada L
    8. Matsumoto J
    9. Wasserscheid J
    10. Dewar K
    11. Wiley GB
    12. Macmil SL
    13. Roe BA
    14. Zeller RW
    15. Hastings KE
    16. Lemaire P
    17. Lindquist E
    18. Endo T
    19. Hotta K
    20. Inaba K

    (2008) Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

    Genome Biology 9:R152.

    https://doi.org/10.1186/gb-2008-9-10-r152

    • Google Scholar
39. 1. Schaeffer B

    (1987)

    Deuterostome monophyly and phylogeny

    Evolution & Development 21:179–235.

    • Google Scholar
40. 1. Schlosser G
    2. Patthey C
    3. Shimeld SM

    (2014) The evolutionary history of vertebrate cranial placodes II. Evolution of ectodermal patterning

    Developmental biology 389:98–119.

    https://doi.org/10.1016/j.ydbio.2014.01.019

    • Google Scholar
41. 1. Singh TR
    2. Tsagkogeorga G
    3. Delsuc F
    4. Blanquart S
    5. Shenkar N
    6. Loya Y
    7. Douzery EJ
    8. Huchon D

    (2009) Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny

    BMC Genomics 10:534.

    https://doi.org/10.1186/1471-2164-10-534

    • Google Scholar
42. 1. Small KS
    2. Brudno M
    3. Hill MM
    4. Sidow A

    (2007) Extreme genomic variation in a natural population

    Proceedings of the National Academy of Sciences of USA 104:5698–5703.

    https://doi.org/10.1073/pnas.0700890104

    • Google Scholar
43. 1. Sordino P
    2. Andreakis N
    3. Brown ER
    4. Leccia NI
    5. Squarzoni P
    6. Tarallo R
    7. Alfano C
    8. Caputi L
    9. D'Ambrosio P
    10. Daniele P
    11. D'Aniello E
    12. D'Aniello S
    13. Maiella S
    14. Miraglia V
    15. Russo MT
    16. Sorrenti G
    17. Branno M
    18. Cariello L
    19. Cirino P
    20. Locascio A
    21. Spagnuolo A
    22. Zanetti L
    23. Ristoratore F

    (2008) Natural variation of model mutant phenotypes in Ciona intestinalis

    PLOS ONE 3:e2344.

    https://doi.org/10.1371/journal.pone.0002344

    • Google Scholar
44. 1. Swalla BJ

    (2006) Building divergent body plans with similar genetic pathways

    Heredity 97:235–243.

    https://doi.org/10.1038/sj.hdy.6800872

    • Google Scholar
45. 1. Swalla BJ
    2. Smith AB

    (2008) Deciphering deuterostome phylogeny: molecular, morphological and palaeontological perspectives

    Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 363:1557–1568.

    https://doi.org/10.1098/rstb.2007.2246

    • Google Scholar
46. 1. Tassy O
    2. Dauga D
    3. Daian F
    4. Sobral D
    5. Robin F
    6. Khoueiry P
    7. Salgado D
    8. Fox V
    9. Caillol D
    10. Schiappa R
    11. Laporte B
    12. Rios A
    13. Luxardi G
    14. Kusakabe T
    15. Joly JS
    16. Darras S
    17. Christiaen L
    18. Contensin M
    19. Auger H
    20. Lamy C
    21. Hudson C
    22. Rothbacher U
    23. Gilchrist MJ
    24. Makabe KW
    25. Hotta K
    26. Fujiwara S
    27. Satoh N
    28. Satou Y
    29. Lemaire P

    (2010) The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program

    Genome Research 20:1459–1468.

    https://doi.org/10.1101/gr.108175.110

    • Google Scholar
47. 1. Therriault T
    2. Herborg LM

    (2008a) Predicting the potential distribution of the vase tunicate Ciona intestinalis in Canadian waters: informing a risk assessment

    ICES Journal of Marine Science 65:788–794.

    https://doi.org/10.1093/icesjms/fsn054

    • Google Scholar
48. 1. Therriault T
    2. Herborg LM

    (2008b) A qualitative biological risk assessment for vase tunicate Ciona intestinalis in Canadian waters: using expert knowledge

    ICES Journal of Marine Science 65:781–787.

    https://doi.org/10.1093/icesjms/fsn059

    • Google Scholar
49. 1. Veeman MT
    2. Chiba S
    3. Smith WC

    (2011) Ciona genetics

    Methods in Molecular Biology 770:401–422.

    https://doi.org/10.1007/978-1-61779-210-6_15

    • Google Scholar
50. 1. Wang W
    2. Christiaen L

    (2012) Transcriptional enhancers in ascidian development

    Current Topics in Developmental Biology 98:147–172.

    https://doi.org/10.1016/B978-0-12-386499-4.00006-9

    • Google Scholar

Author details

1. Matthew J Kourakis

   Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States

   Contribution

   Matthew Kourakis and William Smith collaborated for this article. M.K. provided a first draft, while subsequent drafts were contributed to equally by both authors.

   Competing interests

   The authors declare that no competing interests exist.

2. William C Smith

   Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, United States

   Contribution

   Matthew Kourakis and William Smith collaborated for this article. M.K. provided a first draft, while subsequent drafts were contributed to equally by both authors.

   For correspondence

   w_smith@lifesci.ucsb.edu

   Competing interests

   The authors declare that no competing interests exist.

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