Evolution and development of the chordates: collagen and pharyngeal cartilage

Chordates evolved a unique body plan within deuterostomes and are considered to share five morphological characters, a muscular postanal tail, a notochord, a dorsal neural tube, an endostyle, and pharyngeal gill slits. The phylum Chordata typically includes three subphyla, Cephalochordata, Vertebrata, and Tunicata, the last showing a chordate body plan only as a larva. Hemichordates, in contrast, have pharyngeal gill slits, an endostyle, and a postanal tail but appear to lack a notochord and dorsal neural tube. Because hemichordates are the sister group of echinoderms, the morphological features shared with the chordates must have been present in the deuterostome ancestor. No extant echinoderms share any of the chordate features, so presumably they have lost these structures evolutionarily. We review the development of chordate characters in hemichordates and present new data characterizing the pharyngeal gill slits and their cartilaginous gill bars. We show that hemichordate gill bars contain collagen and proteoglycans but are acellular. Hemichordates and cephalochordates, or lancelets, show strong similarities in their gill bars, suggesting that an acellular cartilage may have preceded cellular cartilage in deuterostomes. Our evidence suggests that the deuterostome ancestor was a benthic worm with gill slits and acellular gill cartilages.     

Chordate evolution and the three-phylum system

Traditional metazoan phylogeny classifies the Vertebrata as a subphylum of the phylum Chordata, together with two other subphyla, the Urochordata (Tunicata) and the Cephalochordata. The Chordata, together with the phyla Echinodermata and Hemichordata, comprise a major group, the Deuterostomia. Chordates invariably possess a notochord and a dorsal neural tube. Although the origin and evolution of chordates has been studied for more than a century, few authors have intimately discussed taxonomic ranking of the three chordate groups themselves. Accumulating evidence shows that echinoderms and hemichordates form a clade (the Ambulacraria), and that within the Chordata, cephalochordates diverged first, with tunicates and vertebrates forming a sister group. Chordates share tadpole-type larvae containing a notochord and hollow nerve cord, whereas ambulacrarians have dipleurula-type larvae containing a hydrocoel. We propose that an evolutionary occurrence of tadpole-type larvae is fundamental to understanding mechanisms of chordate origin. Protostomes have now been reclassified into two major taxa, the Ecdysozoa and Lophotrochozoa, whose developmental pathways are characterized by ecdysis and trochophore larvae, respectively. Consistent with this classification, the profound dipleurula versus tadpole larval differences merit a category higher than the phylum. Thus, it is recommended that the Ecdysozoa, Lophotrochozoa, Ambulacraria and Chordata be classified at the superphylum level, with the Chordata further subdivided into three phyla, on the basis of their distinctive characteristics.     

Development and evolution of chordate cartilage

Deuterostomes are a monophyletic group of animals containing vertebrates, lancelets, tunicates, hemichordates, echinoderms, and xenoturbellids. Four out of these six extant groups-vertebrates, lancelets, tunicates, and hemichordates-have pharyngeal gill slits. All groups of deuterostome animals that have pharyngeal gill slits also have a pharyngeal skeleton supporting the pharyngeal openings, except tunicates. We previously found that pharyngeal cartilage in hemichordates and cephalochordates contains a fibrillar collagen protein similar to vertebrate type II collagen, but unlike vertebrate cartilage, the invertebrate deuterostome cartilages are acellular. We found SoxE and fibrillar collagen expression in the pharyngeal endodermal cells adjacent to where the cartilages form. These same endodermal epithelial cells also express Pax1/9, a marker of pharyngeal endoderm in vertebrates, lancelets, tunicates, and hemichordates. In situ experiments with a cephalochordate fibrillar collagen also showed expression in pharyngeal endoderm, as well as the ectoderm and the mesodermal coelomic pouches lining the gill bars. These results indicate that the pharyngeal endodermal cells are responsible for secretion of the cartilage in hemichordates, whereas in lancelets, all the pharyngeal cells surrounding the gill bars, ectodermal, endodermal, and mesodermal may be responsible for cartilage formation. We propose that endoderm secretion was primarily the ancestral mode of making pharyngeal cartilages in deuterostomes. Later the evolutionary origin of neural crest allowed co-option of the gene network for the secretion of pharyngeal cartilage matrix in the new migratory neural crest cell populations found in vertebrates.     

Expression pattern of the Brachyury gene in the arrow worm paraspadella gotoi (chaetognatha)

Arrow worms (the phylum Chaetognatha), which are among the major marine planktonic animals, are direct developers and exhibit features characteristic of both deuterostomes and protostomes. In particular, the embryonic development of arrow worms appears to be of the deuterostome type. Brachyury functions critically in the formation of the notochord in chordates, whereas the gene is expressed in both the blastopore and stomodeum invagination regions in embryos of hemichordates and echinoderms. Here we analyzed the expression of Brachyury (Pg-Bra) in the arrow worm Paraspadella gotoi and showed that Pg-Bra is expressed in the blastopore region and the stomodeum region in the embryo and then around the mouth opening region at the time of hatching. The expression of Pg-Bra in the embryo resembles that of Brachyury in embryos of hemichordates and echinoderms, whereas that in the mouth opening region in the hatchling appears to be novel.     

Structure of the caudal neural tube in an ascidian larva: vestiges of its possible evolutionary origin from a ciliated band.

Ultrastructural analysis and differential immunocytochemical staining with two antitubulin monoclonal antibodies were used to reexamine the organization and development of the neural tube in the larva of an ascidian, Ciona intestinalis, in appraisal of a theory that the dorsal tubular nervous system of the chordates evolved from two halves of a ciliated band in an auricularia-like larva of the kind found in echinoderms and hemichordates. One of the antibodies stained cilia in the nervous system and elsewhere; the other reacted primarily with neuronal axons. The caudal neural tube consists of four rows of large ciliated ependymal-glial cells enclosing an axial neural canal into which their single cilia extend. Two ventrolateral nerve tracts, containing axons, arise in the posterior brain region and extend along the length of the caudal tube, partially surrounded by the ependymal cells. The nonnervous, ciliated, ependymal neural tube of the ascidian larva with its two associated nerve tracts survives as a primitive early condition that could result from a ciliated band transformation. Tissues in the distal-most part of the ascidian larval tail have cell lineage origins that indicate an evolutionary history different from those in the proximal majority of the tail. The ependymal cells in this presumed later addition to the tail are not ciliated, although all of the others in the caudal ependymal tube appear to be.     

Structure of the caudal neural tube in an ascidian larva: Vestiges of its possible evolutionary origin from a ciliated band

Ultrastructural analysis and differential immunocytochemical staining with two antitubulin monoclonal antibodies were used to reexamine the organization and development of the neural tube in the larva of an ascidian, Ciona intestinalis, in appraisal of a theory that the dorsal tubular nervous system of the chordates evolved from two halves of a ciliated band in an auricularia-like larva of the kind found in echinoderms and hemichordates. One of the antibodies stained cilia in the nervous system and elsewhere; the other reacted primarily with neuronal axons. The caudal neural tube consists of four rows of large ciliated ependymal-glial cells enclosing an axial neural canal into which their single cilia extend. Two ventrolateral nerve tracts, containing axons, arise in the posterior brain region and extend along the length of the caudal tube, partially surrounded by the ependymal cells. The nonnervous, ciliated, ependymal neural tube of the ascidian larva with its two associated nerve tracts survives as a primitive early condition that could result from a ciliated band transformation. Tissues in the distal-most part of the ascidian larval tail have cell lineage origins that indicate an evolutionary history different from those in the proximal majority of the tail. The ependymal cells in this presumed later addition to the tail are not ciliated, although all of the others in the caudal ependymal tube appear to be.     

The origins of graptolites and other pterobranchs: a journey from ‘Polyzoa’

The graptolites, known only from fossils, have been convincingly allied to the pterobranch hemichordates, a group of tiny, mostly colonial marine invertebrates bearing feeding arms. The phylogenetic position of pterobranchs has been subject to debate and revision for over a century. Their colonial lifestyle and feeding arms were originally seen as evidence placing them among the bryozoans, until later and more careful anatomical studies revealed more characters in common with acorn worms. Pterobranchs and acorn worms are now grouped as the phylum Hemichordata. For many decades, it was thought that pterobranchs were closer to the ancestral form of hemichordates, particularly because ‘lophophorate’ invertebrates also possess feeding arms, notably the phoronids and bryozoans, as do crinoid echinoderms. This traditional view has been challenged by recent molecular evidence. First, there is strong molecular evidence to indicate that lophophorates are very distant from hemichordates and echinoderms, in a different major branch of the animal phylogenetic tree. Therefore, similarities between the feeding structures must be due to convergent evolution. Second, there is strong evidence that hemichordates and echinoderms form a clade (Ambulacraria) within the deuterostomes, rather than hemichordates being closer to chordates. Third, there is weaker evidence that pterobranchs may be derived from acorn worms, and hence that the vermiform body plan may be ancestral within hemichordates. This suggestion warrants further testing. Here we review the evidence for these conclusions, highlight strengths and weaknesses in the data and analyses, and consider the implications for the origins of pterobranchs and graptolites.     

Origins of radial symmetry identified in an echinoderm during adult development and the inferred axes of ancestral bilateral symmetry

How the radial body plan of echinoderms is related to the bilateral body plan of their deuterostome relatives, the hemichordates and the chordates, has been a long-standing problem. Now, using direct development in a sea urchin, I show that the first radially arranged structures, the five primary podia, form from a dorsal and a ventral hydrocoele at the oral end of the archenteron. There is a bilateral plane of symmetry through the podia, the mouth, the archenteron and the blastopore. This adult bilateral plane is thus homologous with the bilateral plane of bilateral metazoans and a relationship between the radial and bilateral body plans is identified. I conclude that echinoderms retain and use the bilateral patterning genes of the common deuterostome ancestor. Homologies with the early echinoderms of the Cambrian era and between the dorsal hydrocoele, the chordate notochord and the proboscis coelom of hemichordates become evident.     

Apluteal development of the sea urchin Holopneustes purpurescens Agassiz (Echinodermata: Echinoidea: Euechinoidea)

The external features of a shortened, apluteal development (lacking a pluteus larva) are described. Some features are unusual for echinoids. The large egg is distinctively marked by dark and pale coloured yolk. The sperm entry point is marked by a dark yolk spot and the first cleavage plane in most embryos is through the meridian on which the sperm entry point lies. Dark yolk in the animal hemisphere segregates largely to one blastomere in the two-cell embryo and pale yolk segregates to the other as a result of yolk movements during the first cell cycle. Progeny of the pale-yolk blastomere form adult oral structures and progeny of the dark-yolk blastomere form adult aboral structures. There is no feeding planktonic pluteus larva. The gastrula develops into a demersal vestibula larva with bilateral symmetry. The plane of symmetry is coincident with the Carpenter axis that defines a plane of symmetry through the madreporite in adult echinoderms. The coincidence shows that the anterior ambulacrum is vegetal with respect to egg polarity and the interradius originating at the madreporite is animal. The bilateral symmetry of the vestibula offers insight into the origin of radial symmetry in echinoderms and the body plan of an echinoderm ancestor.     

Ontogeny of the holothurian larval nervous system: evolution of larval forms

Echinoderm larvae share numerous features of neuroanatomy. However, there are substantial differences in specific aspects of neural structure and ontogeny between the dipleurula-like larvae of asteroids and the pluteus larvae of echinoids. To help identify apomorphic features, we have examined the ontogeny of the dipleurula-like auricularia larva of the sea cucumber, Holothuria atra. Neural precursors arise in the apical ectoderm of gastrulae and appear to originate in bilateral clusters of cells. The cells differentiate without extensive migration, and they align with the developing ciliary bands and begin neurogenesis. Neurites project along the ciliary bands and do not appear to extend beneath either the oral or aboral epidermis. Apical serotonergic cells are associated with the preoral loops of the ciliary bands and do not form a substantial commissure. Paired, tripartite connectives form on either side of the larval mouth that connect the pre-oral, post-oral, and lateral ciliary bands. Holothurian larvae share with hemichordates and bipinnariae a similar organization of the apical organ, suggesting that the more highly structured apical organ of the pluteus is a derived feature. However, the auricularia larva shares with the pluteus larva of echinoids several features of neural ontogeny. Both have a bilateral origin of neural precursors in ectoderm adjacent to presumptive ciliary bands, and the presumptive neurons move only a few cell diameters before undergoing neurogenesis. The development of the holothurian nervous systems suggests that the extensive migration of neural precursors in asteroids is a derived feature. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Deuterostome phylogeny and the sister group of the chordates: evidence from molecules and morphology

Complete coding regions of the 18S rRNA gene of an enteropneust hemichordate and an echinoid and ophiuroid echinoderm were obtained and aligned with 18S rRNA gene sequences of all major chordate clades and four outgroups. Gene sequences were analyzed to test morphological character phylogenies and to assess the strength of the signal. Maximum- parsimony analysis of the sequences fails to support a monophyletic Chordata; the urochordates form the sister taxon to the hemichordates, and together this clade plus the echinoderms forms the sister taxon to the cephalochordates plus craniates. Decay, bootstrap, and tree-length distribution analyses suggest that the signal for inference of dueterostome phylogeny is weak in this molecule. Parsimony analysis of morphological plus molecular characters supports both monophyly of echinoderms plus enteropneust hemichordates and a sister group relationship of this clade to chordates. Evolutionary parsimony does not support chordate monophyly. Neighbor-joining, Fitch-Margoliash, and maximum-likelihood analyses support a chordate lineage that is the sister group to an echinoderm-plus-hemichordate lineage. The results illustrate both the limitations of the 18S rRNA molecule alone for high- level phylogeny inference and the importance of considering both molecular and morphological data in phylogeny reconstruction.      

Fossil sister group of craniates: predicted and found

This study investigates whether the recently described Cambrian fossil Haikouella (and the very similar Yunnanozoon) throws light on the longstanding problem of the origin of craniates. In the first rigorous cladistic analysis of the relations of this animal, we took 40 anatomical characters from Haikouella and other taxa (hemichordates, tunicates, cephalochordates, conodont craniates and other craniates, plus protostomes as the outgroup) and subjected these characters to parsimony analysis. The characters included several previously unrecognized traits of Haikouella, such as upper lips resembling those of larval lampreys, the thick nature of the branchial bars, a mandibular branchial artery but no mandibular branchial bar, muscle fibers defining the myomeres, a dark fibrous sheath that defines the notochord, conclusive evidence for paired eyes, and a large hindbrain and diencephalon in the same positions as in the craniate brain. The cladistic analysis produced this tree: (protostomes, hemichordates (tunicates, (cephalochordates, (Haikouella, (conodonts + other craniates))))), with the "Haikouella + craniate" clade supported by bootstrap values that ranged from 81-96%, depending on how the analysis was structured. Thus, Haikouella is concluded to be the sister group of the craniates. Alternate hypotheses that unite Haikouella with hemichordates or cephalochordates, or consider it a basal deuterostome, received little or no support. Although it is the sister group of craniates, Haikouella is skull-less and lacks an ear, but it does have neural-crest derivatives in its branchial bars. Its craniate characters occur mostly in the head and pharynx; its widely spaced, robust branchial bars indicate it ventilated with branchiomeric muscles, not cilia. Despite its craniate mode of ventilation, Haikouella was not a predator but a suspension feeder, as shown by its cephalochordate-like endostyle, and tentacles forming a screen across the mouth. Haikouella was compared to pre-craniates predicted by recent models of craniate evolution and was found to fit these predictions closely. Specifically, it fits Northcutt and Gans' prediction that the change from ciliary to muscular ventilation preceded the change from suspension feeding to predatory feeding; it fits Butler's claim that vision was the first craniate sense to start elaborating; it is consistent with the ideas of Donoghue and others about the ancestor of conodont craniates; and, most strikingly, it resembles Mallatt's prediction of the external appearance of the ancestral craniate head. By contrast, Haikouella does not fit the widespread belief that ancestral craniates resembled hagfishes, because it has no special hagfish characters. Overall, Haikouella agrees so closely with recent predictions about pre-craniates that we conclude that the difficult problem of craniate origins is nearly solved.     

The neural tube/notochord complex is necessary for vertebral but not limb and body wall striated muscle differentiation.

The aim of this work was to investigate the role played by the axial organs, neural tube and notochord, on the differentiation of muscle cells from the somites in the avian embryo. Two of us have previously shown that neuralectomy and notochordectomy is followed by necrosis of the somites and consecutive absence of vertebrae and of most muscle cells derived from the myotomes while the limbs develop normally with muscles. Here we have focused our attention on muscle cell differentiation by using the 13F4 mAb that recognizes a cytoplasmic antigen specific of all types of muscle cells. We show that differentiation of muscle cells of myotomes can occur in the absence of notochord and neural tube provided that the somites from which they are derived have been in contact with the axial organs for a defined period of time, about 10 hours for the first somites formed at the cervical level, a duration that progressively reduces caudalward (i.e. for thoracic and lumbar somites). Either one or the other of the two axial organs, the neural tube or the notochord can prevent somitic cell death and fulfill the requirements for myotomal muscle cell differentiation. Separation of the neural tube/notochord complex from the somites by a surgical slit on one side of the embryo gave the same results as extirpation of these organs and provided a perfect control on the non-operated side. A striking finding was that limb and body wall muscles, although derived from the somites, differentiated in the absence of the axial organs. However, limb muscles that develop after excision of the neural tube started to degenerate from E10 onward due to lack of innervation. In vitro explantation of somites from different axial levels confirmed and defined precisely the chronology of muscle cell commitment in the myotomes as revealed by the in vivo experiments.     

The Origin of the Chordates

The study of development and comparisons of the adult structures of the several groups of protochordate animals reveals something of their interrelationships and origin. The hemichordates are perhaps closer to the echinoderms than to the chordates, but these groups appear to have been derived from a bilaterally symmetrical dipleurula ancestor, not from a sessile pterobranch-like form. The origin of the chordates is speculative but the idea of a prototunicate stage is rejected. The tunicate is viewed as a highly modified end product, with fewer similarities to the ancestral form than amphioxus. Amphioxus is quite suggestive of the vertebrate, yet it is more like the tunicate in the details of its embryology and along with that rather extreme peripheral group is best thought of as constituting a subphylum, the Acraniata. The idea of the early vertebrate as a filter feeder must be rejected since it is assumed here that perfection of that function led to a sessile or inactive way of life (as in the acraniates or lamprey larva) and failed to lead to the active creature with highly developed sensory, neural, and locomotor systems identified here as the protovertebrate. Further, the muscular plastic pharynx and moveable mouth of the protovertebrate suggest feeding on larger organisms, predation, and the abandonment of ciliary water-current feeding.     

Hemichordates and deuterostome evolution: robust molecular phylogenetic support for a hemichordate + echinoderm clade

SUMMARY Hemichordates were traditionally allied to the chordates, but recent molecular analyses have suggested that hemichordates are a sister group to the echinoderms, a relationship that has important consequences for the interpretation of the evolution of deuterostome body plans. However, the molecular phylogenetic analyses to date have not provided robust support for the hemichordate + echinoderm clade. We use a maximum likelihood framework, including the parametric bootstrap, to reanalyze DNA data from complete mitochondrial genomes and nuclear 18S rRNA. This approach provides the first statistically significant support for the hemichordate + echinoderm clade from molecular data. This grouping implies that the ancestral deuterostome had features that included an adult with a pharynx and a dorsal nerve cord and an indirectly developing dipleurula-like larva.     

Distinct Neuronal Lineages of the Ascidian Embryo Revealed by Expression of a Sodium Channel Gene

The ascidian larva contains tubular neural tissue, one of the prominent anatomical features of the chordates. The cell-cleavage pattern and cell maps of the nervous system have been described in the ascidian larva in great detail. Cell types in the neural tube, however, have not yet been defined due to the lack of a suitable molecular marker. In the present work, we identified neuronal cells in the caudal neural tube of theHalocynthiaembryo by utilizing a voltage-gated Na⁺channel gene, TuNa I, as a molecular marker. Microinjection of a lineage tracer revealed that TuNa I-positive neurons in the brain and in the trunk epidermis are derived from the a-line of the eight-cell embryo, which includes cell fates to epidermal and neural tissue. On the other hand, TuNa I-positive cells in the more caudal part of the neural tissue were not stained by microinjection into the a-line. These neurons are derived from the A-line, which contains fates of notochord and muscle, but not of epidermis. Electron microscopic observation confirmed that A-line-derived neurons consist of motor neurons innervating the dorsal and ventral muscle cells. Isolated A-line blastomeres have active membrane excitability distinct from those of the a-line-derived neuronal cells after culture under cleavage arrest, suggesting that the A-line gives rise to a neuronal cell distinct from that of the a-lineage. TuNa I expression in the a-line requires signals from another cell lineage, whereas that in the A-line occurs without tight cell contact. Thus, there are at least two distinct neuronal lineages with distinct cellular behaviors in the ascidian larva: the a-line gives rise to numerous neuronal cells, including sensory cells, controlled by a mechanism similar to vertebrate neural induction, whereas A-line cells give rise to motor neurons and ependymal cells in the caudal neural tube that develop in close association with the notochord or muscle lineage, but not with the epidermal lineage.     

Specification of ectoderm restricts the size of the animal plate and patterns neurogenesis in sea urchin embryos

The animal plate of the sea urchin embryo becomes the apical organ, a sensory structure of the larva. In the absence of vegetal signaling, an expanded and unpatterned apical organ forms. To investigate the signaling that restricts the size of the animal plate and patterns neurogenesis, we have expressed molecules that regulate specification of ectoderm in embryos and chimeras. Enhancing oral ectoderm suppresses serotonergic neuron differentiation, whereas enhancing aboral or ciliary band ectoderm increases differentiation of serotonergic neurons. In embryos in which vegetal signaling is blocked, Nodal expression does not reduce the size of the thickened animal plate; however, almost no neurons form. Expression of BMP in the absence of vegetal signaling also does not restrict the size of the animal plate, but abundant serotonergic neurons form. In chimeras in which vegetal signaling is blocked in the entire embryo, and one half of the embryo expresses Nodal, serotonergic neuron formation is suppressed in both halves. In similar chimeras in which vegetal signaling is blocked and one half of the embryo expresses Goosecoid (Gsc), serotonergic neurons form only in the half of the embryo not expressing Gsc. We propose that neurogenesis is specified by a maternal program that is restricted to the animal pole by signaling that is dependent on nuclearization of beta-catenin and specifies ciliary band ectoderm. Subsequently, neurogenesis in the animal plate is patterned by suppression of serotonergic neuron formation by Nodal. Like other metazoans, echinoderms appear to have a phase of neural development during which the specification of ectoderm restricts and patterns neurogenesis.     

Building divergent body plans with similar genetic pathways

Deuterostome animals exhibit widely divergent body plans. Echinoderms have either radial or bilateral symmetry, hemichordates include bilateral enteropneust worms and colonial pterobranchs, and chordates possess a defined dorsal-ventral axis imposed on their anterior-posterior axis. Tunicates are chordates only as larvae, following metamorphosis the adults acquire a body plan unique for the deuterostomes. This paper examines larval and adult body plans in the deuterostomes and discusses two distinct ways of evolving divergent body plans. First, echinoderms and hemichordates have similar feeding larvae, but build a new adult body within or around their larvae. In hemichordates and many direct-developing echinoderms, the adult is built onto the larva, with the larval axes becoming the adult axes and the larval mouth becoming the adult mouth. In contrast, indirect-developing echinoderms undergo radical metamorphosis where adult axes are not the same as larval axes. A second way of evolving a divergent body plan is to become colonial, as seen in hemichordates and tunicates. Early embryonic development and gastrulation are similar in all deuterostomes, but, in chordates, the anterior-posterior axis is established at right angles to the animal-vegetal axis, in contrast to hemichordates and indirect-developing echinoderms. Hox gene sequences and anterior-posterior expression patterns illuminate deuterostome phylogenetic relationships and the evolution of unique adult body plans within monophyletic groups. Many genes that are considered vertebrate 'mesodermal' genes, such as nodal and brachyury T, are likely to ancestrally have been involved in the formation of the mouth and anus, and later were evolutionarily co-opted into mesoderm during vertebrate development.     

The evolution of the hedgehog gene family in chordates: insights from amphioxus hedgehog

 The hedgehog family of intercellular signalling molecules have essential functions in patterning both Drosophila and vertebrate embryos. Drosophila has a single hedgehog gene, while vertebrates have evolved at least three types of hedgehog genes (the Sonic, Desert and Indian types) by duplication and divergence of a single ancestral gene. Vertebrate Sonic-type genes typically show conserved expression in the notochord and floor plate, while Desert- and Indian-type genes have different patterns of expression in vertebrates from different classes. To determine the ancestral role of hedgehog in vertebrates, I have characterised the hedgehog gene family in amphioxus. Amphioxus is the closest living relative of the vertebrates and develops a similar body plan, including a dorsal neural tube and notochord. A single amphioxus hedgehog gene, AmphiHh, was identified and is probably the only hedgehog family member in amphioxus, showing the duplication of hedgehog genes to be specific to the vertebrate lineage. AmphiHh expression was detected in the notochord and ventral neural tube, tissues that express Sonic-type genes in vertebrates. This shows that amphioxus probably patterns its ventral neural tube using a molecular pathway conserved with vertebrates. AmphiHh was also expressed on the left side of the pharyngeal endoderm, reminiscent of the left-sided expression of Sonic hedgehog in chick embryos which forms part of a pathway controlling left/right asymmetric development. These data show that notochord, floor plate and possibly left/right asymmetric expression are ancestral sites of hedgehog expression in vertebrates and amphioxus. In vertebrates, all these features have been retained by Sonic-type genes. This may have freed Desert-type and Indian-type hedgehog genes from selective constraint, allowing them to diverge and take on new roles in different vertebrate taxa. Received: 20 July 1998 / Accepted: 23 September 1998