Hemichordates are a deuterostome phylum, the sister group to
echinoderms, and closely related to chordates. They have thus
been used to gain insights into the origins of deuterostome and
chordate body plans. Developmental studies of this group have
a long and distinguished history. Recent improvements in animal
husbandry, functional tool development and genomic resources
have resulted in novel developmental data from several species
in this group. In this Primer, we introduce representative
hemichordate species with contrasting modes of development
and summarize recent findings that are beginning to yield
important insights into deuterostome
Key words: Body plan, Deuterostome, Evolution, Hemichordata
Hemichordates are a phylum belonging to the major bilaterian
lineage called the deuterostomes (see Glossary, Box 1; Fig. 1A).
Hemichordates are exclusively marine organisms and are divided
into two major groups (Fig. 1B): the solitary enteropneust worms
(the acorn worms) and the colonial and tube-dwelling pterobranchs
(Hyman, 1959). Interest in this group of animals has been largely
based on their proposed morphological affinities and close
phylogenetic relationship to chordates (Brown et al., 2008; Lowe,
2008), making them an informative group with which to gain
insights into the early origins of the chordate body plan. Although
the composition of phyla that make up the deuterostomes and their
phylogenetic relationships have been revised many times
(Schaeffer, 1987; Turbeville et al., 1994; Wada and Satoh, 1994;
Halanych, 1995; Bourlat et al., 2006; Philippe et al., 2011),
zoologists have long proposed potential morphological affinities
between hemichordates and chordates, and these similarities have
formed the bases for numerous comparative morphological and
developmental studies since the 1800s. Hemichordates have thus
been influential in the formulation of a range of hypotheses on the
origins of chordates (Bateson, 1886; Garstang, 1894; Berrill, 1955;
Bone, 1960; Nielsen, 1999; Gerhart et al., 2005; Lacalli, 2005;
Brown et al., 2008).
The defining early studies of the developmental biology of
enteropneusts were carried out by two pioneers of developmental
biology: William Bateson and Thomas Hunt Morgan (Bateson,
1884b; Bateson, 1885; Morgan, 1891; Morgan, 1894). Pterobranchs
were first defined as a class in 1877 (Harmer, 1887), but it was not
until they were first found in shallow waters that the details of their
development were comprehensively described (Stebbing, 1970;
Dilly, 1973; Lester, 1988b; Lester, 1988a; Sato et al., 2008).
Bateson originally considered enteropneusts to be primitive
chordates and therefore informative for understanding the origin of
the vertebrates (Bateson, 1886). It was not until much later that the
reclassification of hemichordates into their own phylum was
widely accepted. Early studies from Metschnikoff (Metschnikoff,
1881) noted close morphological similarities between the early
larvae of enteropneusts and echinoderms (see Glossary, Box 1), but
the significance of this observation was not fully appreciated until
a series of molecular datasets, including Hox gene complements to
molecular phylogenetics, robustly supported the sister grouping of
hemichordates and echinoderms (Turbeville et al., 1994; Wada and
Satoh, 1994; Bromham and Degnan, 1999; Cameron et al., 2000;
Furlong and Holland, 2002; Bourlat et al., 2006; Dunn et al., 2008;
Swalla and Smith, 2008; Philippe et al., 2011). The profound
changes in phylogenetic relationships of the deuterostome phyla
are now leading to new testable hypotheses about the early
evolution of the lineage and the origins of chordates. An
Development 139, 2463-2475 (2012) doi:10.1242/dev.066712
© 2012. Published by The Company of Biologists Ltd
Evolutionary crossroads in developmental biology:
Eric Röttinger1and Christopher J. Lowe2,*
1Kewalo Marine Laboratory, Pacific Biosciences Research Center (PBRC), University
of Hawaii, 41 Ahui Street, Honolulu, HI 96734, USA. 2Hopkins Marine Station,
Department of Biology, Stanford University, 120 Oceanview Boulevard, Pacific
Grove, CA 93950, USA.
*Author for correspondence (firstname.lastname@example.org)
PRIMER SERIES PRIMER
Box 1. Glossary
Collar. A distinct body region between the proboscis and the trunk
that is attached to the proboscis on a medio-dorsal stalk. The
ventral mouth opens anterior to the collar.
Deuterostomes. A bilaterian lineage of animals classically defined
by the formation of mouth and anus: the blastoporal opening (site
of gastrulation) becomes the anus and the mouth forms
secondarily, later in development.
Direct development. Development to an adult body plan without
an intervening larval stage with a distinct body plan.
Echinoderm. Member of a phylum of marine invertebrates
comprising echinoids (sea urchins), asteroids (sea stars), crinoids (sea
lillies), holothuroids (sea cucumbers) and ophiuroids (brittle stars).
See also McClay (McClay, 2011) for a Development Primer on sea
Enterocoely. An embryonic phenomenon, during which
mesodermal coeloms form by out-pocketing of a part of the
Gonochoric. Having only one, male or female, set of reproductive
Holoblastic cleavage. The cleavage furrow extends through the
entire egg or blastomere, resulting in a complete cleavage.
Indirect development. Development to an adult body plan via a
distinct larval body plan followed by metamorphosis into an adult.
Lecithotrophic. Having a swimming, non-feeding larva that derives
its nutrition from maternally provisioned yolk.
Notochord. An embryonic rod-like structure that is located on the
dorsal part of the developing animal and is essential for initiating
the differentiation of the adult nervous system.
Proboscis. The highly contractile and expandable anteriormost part
of a hemichordate that is used for burrowing and locomotion.
Radial cleavage. After cleavage, the daughter blastomeres are
either perpendicular or parallel to each other. This type of cleavage
is characteristic of deuterostomes.
Zooid. A single animal that is part of a colonial structure.
understanding of these phylogenetic relationships also facilitates
the mapping of developmental genetic traits onto the new tree to
investigate the evolution of deuterostome developmental
mechanisms. New developmental studies in enteropneust and
pterobranch hemichordates have begun to focus on mechanisms of
early axial patterning and germ layer establishment in order to
make comparisons with the abundant developmental data from
larval echinoderms (Lapraz et al., 2009; Peter and Davidson, 2010;
Angerer et al., 2011) and chordates (Jessell, 2000; Gerhart, 2001;
Joubin and Stern, 2001; Kiecker and Lumsden, 2005; De Robertis,
2006; Kimelman, 2006; Dequeant and Pourquie, 2008; Tschopp
and Duboule, 2011).
Hemichordates and echinoderms are sister taxa and together
form a clade called the Ambulacraria (Metschnikoff, 1881), which
is closely related to chordates (Fig. 1A). In many comparative
studies of bilaterian development, deuterostomes are represented
almost exclusively by chordates. Despite many comprehensive
studies of early echinoid (sea urchin) development, echinoderms
have largely been excluded from broad body plan comparisons
owing to the difficulties of establishing a rigorous basis for
comparisons of their penta-radial adult body plan with that of other
bilaterians. However, echinoderm larvae are bilaterally symmetric
and exhibit compelling patterning similarities with chordates in
early endomesoderm specification and axis patterning (Lapraz et
al., 2009; Peter and Davidson, 2010; Angerer et al., 2011)
facilitating direct body plan comparisons with other phyla.
Nonetheless, a phylogenetically denser sampling of deuterostomes
is needed to make more rigorous comparisons with protostomes
and prebilaterians in order to test hypotheses of early bilaterian
evolution and development. Hemichordates share numerous
developmental similarities with both chordates and echinoderms
and hold great promise for providing insights into the early origins
of both chordate and deuterostome development.
In this Primer, we introduce the main hemichordate species used
for developmental studies, which represent different lineages and
contrasting early life history strategies, and we describe their basic
biology and early development. We then highlight significant and
recent findings from developmental genetic studies of
hemichordates, and conclude by discussing the promises of future
work that will make full use of the comprehensive genomic
resources and functional tools that have been developed.
Hemichordates, along with echinoderms and chordates, are
robustly supported within the deuterostomes (Fig. 1A) on both
morphological and molecular criteria (Schaeffer, 1987;
Turbeville et al., 1994; Bromham and Degnan, 1999; Cameron
et al., 2000; Furlong and Holland, 2002). Recent phylogenomic
studies have supported the addition of two phyla to the
deuterostomes: Xenoturbellida (Bourlat et al., 2003; Bourlat et
al., 2006) and Acoelomorpha (Philippe et al., 2011), together
termed xenacoelomorphs, which are small simple worms with no
through gut and a simple nervous system. However, both these
groups have long and problematic histories of phylogenetic
Development 139 (14)
e.g. R. compacta
e.g. S. kowalevskii
A Deuterostome phylogeny
B Hemichordata phylogeny
e.g. P. flava
e.g. T. baldwinae
e.g. G. hacksi
Fig. 1. Deuterostome and hemichordate phylogenies. (A)Hemichordates and their sister group the echinoderms make up the Ambulacraria
clade and are closely related to chordates. Recent phylogenomic studies have also placed acoelomorphs and xenoturbella, together termed
xenacoelomorphs, as a sister group to hemichordates and echinoderms (Philippe et al., 2011), although their position within deuterostomes
remains controversial (as indicated by a dashed line). (B)Hemichordate phylogeny with limited representation of the pterobranchs and
enteropneusts, showing the relationships between lineages containing the most commonly studied hemichordates, Ptychodera flava
(Ptychoderidae), Saccoglossus kowalevskii (Harrimaniidae) and Rhabdopleura compacta (Pterobranchia), along with the deep sea family
Torquaratidae [based on published data (Cameron et al., 2000; Winchell et al., 2002; Cannon et al., 2009; Osborn et al., 2012)].
Development 139 (14)
placement, and their position as the sister group to the
hemichordates and echinoderms remains controversial (Hejnol
et al., 2009; Lowe and Pani, 2011).
The phylogenetic relationships within hemichordates, and most
importantly the placement of pterobranchs, are a critical issue.
There is strong support for the placement of pterobranchs as a sister
group to the Harrimaniidae, making enteropneusts paraphyletic
(Cameron et al., 2000; Cameron, 2005; Cannon et al., 2009) (Fig.
1B). The significance of this finding for developmental biology is
that it suggests that studies from enteropneusts might be the most
informative for reconstructing ancestral developmental strategies
for this phylum (Brown et al., 2008). However, other studies have
either placed pterobranchs at the most basal position in the clade
(Winchell et al., 2002) or have failed to resolve their position
(Osborn et al., 2012). Further studies with additional genes will be
required to address this critical question (Cannon et al., 2009).
Enteropneusts are divided into four groups: Harrimaniidae,
Spengelidae, Torquaratoridae and Ptychoderidae (Cannon et al.,
2009; Osborn et al., 2012). The harrimanids and pterobranchs are
largely characterized by direct development (see Glossary, Box 1),
whereas the ptychoderids and spengelids exhibit indirect
development (see Glossary, Box 1), with a feeding larva and an
extended planktonic period. Little is known about the development
of the Torquaratoridae as they are deep-water species, although one
described species has large eggs suggesting that they might be
direct developers (Osborn et al., 2012). It is generally proposed that
the echinoderm dipleurula-type larva and hemichordate larvae are
homologous (Strathmann and Bonar, 1976; Nielsen, 2001),
suggesting that indirect development is a basal developmental
strategy for hemichordates, although there are dissenting views
(Nezlin, 2000). Most of the research on hemichordate development
has been carried out on two species of enteropneust worms:
Ptychodera flava (Fig. 2A) from the Ptychoderidae and
Saccoglossus kowalevskii (Fig. 2B) from the Harrimaniidae.
However, more recently, pterobranchs (Fig. 2C) as represented by
Rhabdopleura compacta and
enteropneusts such as Balanoglossus
Balanoglossus simodensis are being developed as valuable
additional models, ensuring that, in the future, no one species is
over emphasized in comparative analyses (Sato and Holland, 2008;
Ikuta et al., 2009; Sato et al., 2009; Miyamoto et al., 2010;
Miyamoto and Saito, 2010).
General morphology and habitat
Enteropneusts (acorn worms)
Acorn worms are benthic marine animals that are distributed
worldwide. They range in size from a few centimeters up to a
meter, and they are found in depths ranging from the intertidal to
the deep sea (Holland et al., 2005; Cannon et al., 2009; Osborn et
al., 2012). They display a tripartite body organization with an
anterior prosome (also called the proboscis; see Glossary, Box 1),
a mesosome (or collar; see Glossary, Box 1), and a posterior
metasome or trunk (Fig. 2D,E). The dorsoventral (DV) axis is
largely defined by the position of the mouth on the ventral side and
gill slits on the dorsal side. Most acorn worms use their proboscis
to burrow through sand using peristaltic movements, and they feed
either by deposit feeding, trapping detritus and sediments in mucus
secreted from the proboscis, or by filter feeding (Cameron, 2002;
Gonzalez and Cameron, 2009). Their mouth opens on the ventral
side, at the base of the proboscis, and the gut runs through to a
terminal anus in adults (Fig. 2D,E). The anterior, pharyngeal gut is
perforated by paired cartilaginous gill slits that bear a strong
morphological and molecular resemblance to those of the basal
chordate, amphioxus (Rychel et al., 2006; Rychel and Swalla,
A Ptychodera flava
B Saccoglossus kowalevskii
C Cephalodiscus sp.
1.5 cm1 mm
Fig. 2. General hemichordate
photographs of the enteropneusts P.
flava (A) and S. kowalevskii (B). (C)A
photomicrograph of a pterobranch
zooid of Cephalodiscus sp. (image
reproduced with kind permission
from K. Halanych). (D)Schematic
representation of a longitudinal
section of an enteropneust worm,
showing the structure and
composition of anterior structures
(blue, ectoderm; yellow, endoderm;
red, mesoderm). (E) The main body
structures of an adult enteropneust
and a pterobranch.
2007; Gillis et al., 2011). At the very anterior end of the gut, the
endoderm projects into the proboscis forming the stomochord (Fig.
2D), which is a supportive structure for the heart/kidney complex
(Balser and Ruppert, 1990) and has been proposed to be
homologous to the chordate notochord (see Glossary, Box 1)
(Bateson, 1886; Morgan, 1894). Currently, there is no molecular
support for this homology (Peterson et al., 1999) and it
consequently awaits further analysis.
The nervous system of adult enteropneusts comprises a broad
epithelial nerve plexus, which is most concentrated in the
proboscis, and two nerve cords: one dorsal and one ventral. The
dorsal nerve cord is superficial in the trunk, but in the collar is
internalized by a process that resembles neurulation in chordates
(Bateson, 1884a; Bateson, 1886; Brown et al., 2008;
Nomaksteinsky et al., 2009; Kaul and Stach, 2010), which has been
used as evidence to suggest that this structure shares homology
with the chordate dorsal nerve cord. Unlike chordates,
enteropneusts also possess a ventral nerve cord that starts in the
anterior trunk and extends posteriorly (Bullock, 1945; Knight-
Jones, 1952; Dilly et al., 1970).
Enteropneusts are characterized by separate sexes and in most
species oocytes can be clearly seen through the ectoderm. Gametes
are free-spawned and fertilization occurs externally.
By contrast, pterobranchs are small (several millimeters to
centimeters long), generally colonial, filter-feeding animals that
live in secreted tubes (collectively, a coenecium) (Sato et al.,
2008). Their feeding apparatus – the lophophore – is an
extension of the mesosome/collar (Fig. 2E), and their digestive
tract is U-shaped, juxtaposing the mouth and the anus near to the
tube opening (Dawydoff, 1948). Pterobranchs are mainly found
on the surfaces of rocks or shells where they can form dense
aggregates. Their colonies are usually hermaphroditic, but
individual zooids (Fig. 2C; see Glossary, Box 1) may be
gonochoric (see Glossary, Box 1).
Despite rather obvious morphological differences, enteropneusts
and pterobranchs share a similar body plan organization and several
unifying characters: the stomochord, described previously (Fig. 2D),
and a single pair of gill slits in Cephalodiscus but not in
Rhabdopleura. The pterobranch Rhabdopleura compacta, which can
be found off the south coast of England, is an emerging organism for
developmental studies (Stebbing, 1970; Dilly, 1973; Sato et al.,
2008). A related species, Rhabdopleura normani, is found in shallow
waters off Bermuda (Lester, 1988b; Lester, 1988a).
Life cycle and embryology
The enteropneust worm S. kowalevskii is a direct-developing
hemichordate (Fig. 3) that has a broad distribution along the eastern
seaboard of the USA (Lowe et al., 2004). Gravid individuals can
be collected in spring and late summer. Oocytes are induced to
spawn by temperature shock (Colwin and Colwin, 1962); each
female will release on average between 200 and 1000 oocytes,
which are ~300 m in diameter and can be fertilized in vitro with
a dilute sperm suspension. Early observers carefully described
normal development from fertilization through to hatching
(Bateson, 1884a; Bateson, 1885; Colwin and Colwin, 1953).
Following fertilization, a thick vitelline membrane is raised, similar
to that observed in sea urchins, and the embryo undergoes radial,
holoblastic cleavage (see Glossary, Box 1) to produce a hollow
blastula that is slightly thickened at the vegetal pole (Fig. 4A,A?).
Gastrulation occurs by circumferential invagination of the vegetal
endomesoderm (Fig. 4B-C?). Following gastrulation, the blastopore
closes and the embryo begins to elongate along the anteroposterior
(AP) axis (Fig. 4C,C?). At this time, the mesoderm forms by
enterocoely (see Glossary, Box 1) following contact with the
ectoderm: the proboscis mesoderm forms first, followed by two
pairs of lateral enterocoels in the prospective trunk and prospective
collar. Two days following fertilization, two circumferential
grooves become apparent in the ectoderm, dividing the animal into
the prosome, mesosome and metasome (Fig. 4D,D?). Around the
same time, the mouth perforates on the ventral side, but the anus
does not perforate until later (Fig. 4E,E?). The first pair of gill pores
is apparent by day 4, and the animal hatches after ~5 days of
development, at which point it resembles a small adult (Fig. 4F,F?).
Hatched juveniles are briefly pelagic (see Fig. 3) then begin to
burrow in sand and actively feed. Later development primarily
involves extension of the trunk and addition of gill slits, and both
of these processes appear to continue throughout life.
As an experimental benefit, the rapid pace of S. kowalevskii
development makes it possible to assess the effects of embryonic
experimental manipulations on development and organization of
the adult body plan, which can be technically more challenging in
animals with prolonged larval development, such as Ptychodera
P. flava is an indirect-developing enteropneust that is easily
obtained in shallow waters surrounding the Hawaiian Islands and
is also common on shallow reef flats through the Indo-Pacific
region (Lowe et al., 2004). Developmental work on P. flava has
been mostly carried out in Hawaii, and sexual reproduction is
restricted primarily to the months of December and January
(Hadfield, 1975; Tagawa et al., 1998a). During this time, adults
spawn hundreds of thousands of oocytes (~120 m in diameter)
into the water column and fertilization occurs externally. The
pelagic tornaria larvae feed in the plankton for several months
before settling and metamorphosing into benthic juveniles (Fig. 3).
Despite the difference in developmental modes, the early
development of P. flava and S. kowalevskii is similar; cleavage in P.
flava is radial (see Glossary, Box 1) and holoblastic and gives rise to
a hollow blastula (Fig. 4H) (Hadfield, 1975; Tagawa et al., 1998b).
The presumptive endomesoderm is located in the vegetal plate of the
blastula (Henry et al., 2001), a region that thickens prior to the
initiation of gastrulation and formation of the embryonic archenteron
(Fig. 4I). Toward the end of gastrulation, the anterior mesoderm
forms by enterocoely as the protocoel pinches off from the anterior
end of the archenteron and elongates asymmetrically towards the
dorsal ectoderm, where it fuses to form the hydropore (a pore that
connects the anterior mesoderm to the external environment) (Fig.
4J). A few hours later, the archenteron bends toward the ventral
ectoderm where it fuses with the stomodeum to form the mouth (Fig.
4K). The posterior mesoderm forms much later in development,
close to metamorphosis, which constitutes a distinct difference from
sea urchins and S. kowalevskii.
After hatching, the free-swimming tornaria larvae possess a
tripartite gut composed of a pharynx, stomach, intestine, a
protocoel (anterior mesoderm) and the apical plate (Fig. 4K). The
hatched larvae feed and grow in the water column for several
months, undergoing progressive morphological modifications (Fig.
4L) prior to metamorphosis (Fig. 4M,N) (Hadfield, 1975; Tagawa
et al., 1998b; Nielsen and Hay-Schmidt, 2007). Competent larvae
are composed mainly of anterior structures and can be collected by
Development 139 (14)
Development 139 (14)
plankton tow during the months of April and May in Hawaii.
Metamorphosis into the adult form occurs rapidly and can be
induced by the collection process. During metamorphosis, the
posterior of the larva rapidly proliferates and extends, which
contrasts with the early specification of the posterior structures in
Another indirect-developing hemichordate, Balanoglossus
simodensis, has also been successfully reared through metamorphosis
under laboratory conditions (Miyamoto and Saito, 2007) and thus
might provide an additional species for future comparative studies.
Pterobranchs are not as common as enteropneusts and generally
live in cold or deep waters. It was not until their discovery in
shallow waters that their development was thoroughly
characterized (Stebbing, 1970; Dilly, 1973; Lester, 1988b; Lester,
1988a). Recently, Sato and colleagues have begun to develop the
pterobranch Rhabdopleura compacta as an important new
hemichordate species that is amenable to developmental studies
(Sato et al., 2008; Sato and Holland, 2008; Sato et al., 2009).
How and when fertilization occurs remains unknown,
but developing larvae of this species can be observed year
round, with a peak between April and July. Development is direct
and lecithotrophic (see Glossary, Box 1) and larvae are ciliated and
pigmented. They are initially brooded inside the coenecium (Fig.
2E, Fig. 3C) and then released as swimming larvae.
Experimental approaches in hemichordates
Hemichordates are amenable to many descriptive and experimental
techniques, ranging from classic embryology to modern reverse
In vivo cell labeling (lineage tracing)
Fluorescent, cell-tracing dyes have successfully been injected into
individual cells or applied to membranes of cleaving hemichordate
embryos to allow researchers to track the fates of single
e.g. P. flava
e.g. S. kowalevskii
(early brooder, late pelagic)
e.g. R. compacta
A Indirect development
B Direct development
C Direct development
Fig. 3. Hemichordate life cycles. The life cycles of (A) indirect- or (B) direct-developing enteropneust hemichordates and (C) direct-developing
pterobranchs. The dashed line indicates the transition from benthos to pelagos. (A)Adult ptychoderid enteropneusts (e.g. P. flava) spawn eggs and
sperm into the water column, where external fertilization occurs. After hatching, the tornaria larva remains in the pelagic zone for several months,
undergoing slight morphological modifications before metamorphosing into and settling as a benthic juvenile. (B)Fertilization of the direct-
developing enteropneust S. kowalevskii occurs externally, inducing the formation of a thick vitelline membrane within which early development
occurs. Five days after fertilization, the embryos hatch and, after a very brief swimming phase, the juveniles begin to burrow in sand. (C)Little is
known about fertilization and the developmental stages of breeding pterobranchs (e.g. R. compacta), although it is known that ciliated and
pigmented larvae develop inside the coenecium. Developmental stages are indicated below each illustration and the internal organization of the
germ layers is indicated (blue, ectoderm; yellow, endoderm; red, mesoderm).
blastomeres for several weeks or more. These cell-labeling
approaches have been successfully carried out in S. kowalevskii
(Colwin and Colwin, 1951; Darras et al., 2011) and P. flava (Henry
et al., 2001) (Fig. 5A) and demonstrate that the cleavage patterns,
as well as the early fate maps of direct- and indirect-developing
hemichordates, are similar to those of indirect-developing
echinoids (Colwin and Colwin, 1951; Cameron et al., 1987;
Cameron et al., 1989; Cameron and Davidson, 1991; Henry et al.,
2001) (Fig. 6). In S. kowalevskii, direct injection of lysinated
fluorescent dextrans into single cells is possible up to the 132-cell
stage; descendants of injected cells can be imaged both in live
animals and in fixed specimens at high resolution (Fig. 5B). Clonal
descendants of injected cells inside the yolky embryos can be
readily imaged in fixed, optically cleared animals even after in situ
hybridization. Injections into blastomeres can also be used to target
reverse-genetic manipulations to specific regions of the embryo.
Other lineage-tracing approaches using light-activated fluorescent
molecules have also been used successfully to visualize cell
lineages in live animals. Photoactivatable GFP protein (Patterson
and Lippincott-Schwartz, 2002) and kaede mRNA (Ando et al.,
2002) (J. Gray and M. Kirschner, unpublished observations) can be
injected into oocytes and fluorescence can be activated in specific
regions with a confocal microscope at any point in development
The ability to produce large numbers of synchronously developing
embryos by in vitro fertilization facilitates the use of biochemical
pathway antagonists (Darras et al., 2011; Röttinger and Martindale,
2011) and recombinant proteins to manipulate large numbers of
embryos in both indirect- and direct-developing hemichordate
species (Lowe et al., 2006). However, these approaches are limited
in indirect-developing species that have feeding larvae owing to the
relatively slow larval development and the need to maintain
embryos in larger volumes of seawater. In S. kowalevskii, specific
gene knockdown and overexpression approaches have been
developed using microinjection into fertilized oocytes or
blastomeres. Overexpression using capped mRNA, as well as gene
knockdown by synthetic siRNA, have proven to be successful for
numerous genes (Fig. 5D) (Lowe et al., 2006; Darras et al., 2011).
Transient transgenic approaches remain to be developed for these
organisms, and forward-genetic approaches are unlikely to be
practical owing to the long generation times.
Gene expression analyses
In situ hybridizations and immunocytochemistry (Fig. 5E) are now
routine in all of the hemichordates discussed here. In S.
kowalevskii, fluorescent in situ protocols have also been developed,
allowing detailed examination of the relative expression patterns of
several genes (Pani et al., 2012) (Fig. 5F).
Early studies established the promise of S. kowalevskii for
embryological experiments (Colwin and Colwin, 1950). Recently,
Darras and colleagues (Darras et al., 2011) have built on this work
and combined embryological manipulations with molecular
analyses to investigate the inductive capacities of endomesoderm
in S. kowalevskii. At cleavage stages, blastomeres can be separated
Development 139 (14)
4 hpm 5 dpm
Fig. 4. Embryonic development of the commonly studied hemichordates. (A-G? ?) Direct development of S. kowalevskii. Each stage of
development (A-G) is also represented schematically (A?-G?), indicating the internal organization of the germ layers (blue, ectoderm; yellow,
endoderm; red, mesoderm). Axis orientation is given in A?,B?,D?. B is reproduced with permission (Ettensohn et al., 2004). G is reproduced with
permission (Lowe et al., 2003). (H-N)Indirect development of P. flava. The white square indicates the position of the hydropore, the asterisk
indicates the position of the mouth, the white arrowhead indicates the apical plate and the star indicates the protocoel. Below is indicated the
timescale of development from egg to juvenile: 7 days for S. kowalevskii and 2-4 months for P. flava. a, animal; ve, vegetal; an, anterior; po,
posterior; v, ventral; d, dorsal; l, left; r, right; hpf/mpf, hours/months post-fertilization; hpm/dpm, hours/days post-metamorphosis.
Development 139 (14)
and reared independently and, at later stages, embryos can be cut
and pieces of tissue grafted onto other embryos (Darras et al., 2011;
Colwin and Colwin, 1950). When combined with knockdown and
overexpression approaches, this is a powerful tool to test for
inductive interactions between different tissues, as has been used
to great effect in other developmental model organisms.
Key recent findings and their impact on the field
Basic body plan comparisons
During AP axis specification, there are close similarities between
S. kowalevskii and vertebrates in their relative spatial deployment
of transcription factors that are involved in ectodermal patterning,
including Hox genes, six3, foxG, distalless, nkx2-1, barH,
engrailed and pax2/5/8 (Lowe et al., 2003; Aronowicz and Lowe,
2006; Lemons et al., 2010; Pani et al., 2012). In vertebrates, the
expression of many of these genes is restricted to the CNS, whereas
in S. kowalevskii they are often expressed in circumferential rings
in the ectoderm during early development, possibly reflecting the
broad distribution of neurons at these stages of development.
Epidermal expression of Hox genes is also detected in amphioxus
and ascidians, suggesting that this might be an ancestral
deuterostome feature that is modified in vertebrates (Holland,
2005; Keys et al., 2005).
These similarities between hemichordate and chordate AP
patterning mechanisms provide a molecular basis for establishing
general regional homologies between the vertebrate and
enteropneust body plans, which has been challenging and
contentious based on morphological comparisons alone. Additional
investigations of gene expression and function in adult
hemichordates might be highly informative in the future. Notably,
the embryonic and juvenile proboscis ectoderm shares many
patterning similarities with the vertebrate forebrain, the collar
shares similarities with the midbrain, and the trunk shares
similarities with the hindbrain and spinal cord (Lowe et al., 2003).
More recent work has revealed striking developmental genetic
similarities between hemichordate ectodermal and vertebrate late
neural plate patterning events. In all vertebrates, local signaling
centers in the neural plate, characterized by expression of
secreted ligands in predictable AP positions within a conserved
transcriptional map, act to divide the brain into discrete regions
(Wurst and Bally-Cuif, 2001; Echevarria et al., 2003; Wilson and
Houart, 2004; Kiecker and Lumsden, 2005). Although some of
the transcriptional signatures associated with vertebrate signaling
centers are present in invertebrate chordates (Holland, 2009;
Irimia et al., 2010), in most instances the signaling ligands that
define the organizing abilities of these centers in vertebrates are
not expressed in the corresponding AP positions in the
amphioxus and ascidian nervous systems or general ectoderm.
These data have been used to support the plausible hypothesis
that most vertebrate brain signaling centers were sequentially
assembled during chordate evolution. In this scenario, the
recruitment of signaling ligands to these centers was the final
step achieved in stem vertebrates (Holland, 2009; Irimia et al.,
2010). However, ectodermal signaling centers that might be
homologous to three of those found in vertebrate brains have
now been described in S. kowalevskii (Pani et al., 2012),
suggesting that these developmental programs predate chordate
origins and were first assembled independently of the vertebrate
brain. These findings then suggest that the transcriptional
similarities and limited complements of signaling ligands in
amphioxus and ascidians, rather than representing partially
assembled signaling centers, are instead a result of secondary
simplification. This work suggests that, although by virtually any
morphological criterion vertebrates share many more similarities
with amphioxus than with hemichordates, molecular outgroup
data from hemichordates are also key for testing hypotheses of
the origins of vertebrate developmental mechanisms.
Antagonism between bone morphogenetic protein (Bmp), which is
the diffusible extracellular ligand of the transforming growth factor
(Tgf) family, and its specific antagonist Chordin plays a central
role in the establishment of the bilaterian DV axis (Holley and
Ferguson, 1997). These proteins have also been proposed to play
conserved roles in the specification of bilaterian CNS (Arendt and
Nubler-Jung, 1996; De Robertis and Sasai, 1996). Gene expression
analyses (Fig. 7) and functional studies show that these proteins are
also involved in DV patterning in hemichordates. In S. kowalevskii,
Bmp genes (Fig. 7A) are expressed on the prospective dorsal side
and chordin (Fig. 7B) on the ventral side during gastrulation and
early development (Lowe et al., 2006). After 3 days of
development, neurons are broadly distributed throughout the
ectoderm, including the dorsal midline where Bmp genes are
expressed. Manipulation of bmp2/4 levels by overexpression or
knockdown results in dorsalized or ventralized embryos,
Fig. 5. Experimental techniques available in
hemichordates. (A)Cell labeling using DiI (red) in P. flava.
Labeling of a single blastomere at the 8-cell stage gives rise to
stained cells in the ventral ectoderm, as well as in the protocoel
of a tornaria larva (Henry et al., 2001). (B)Cell labeling using
fluorescent dextran (green) in S. kowalevskii. Microinjection into
one blastomere at the 132-cell stage labels the daughter cells in
the proboscis (image provided by A. M. Pani). (C)In vivo
photoconversion of photoactivatable GFP protein for cell-
lineage tracing in S. kowalevskii (image provided by Rachael
Norris). (D)Microinjection of mRNA encoding -catenin:GFP
leads to staining of the vegetal pole of S. kowalevskii (Darras et
al., 2011). vv, vegetal view. (E)Anti-histone (magenta)
immunocytochemistry in P. flava (image provided by Eric
Röttinger). (F)Double fluorescence in situ hybridization of pax6
(red) and engrailed (cyan) in S. kowalevskii (image provided by
A. M. Pani).
respectively, indicating the importance of these genes for DV
patterning (Lowe et al., 2006). However, overactivating Bmp
signaling (by treatment with recombinant zebrafish Bmp4 protein)
does not repress early neural fates, suggesting that, despite playing
conserved roles in basic DV patterning, Bmps are not involved in
repressing neural fates in all bilaterians.
In P. flava, bmp2/4 and chordin are also expressed in the dorsal
and ventral ectoderm, respectively (Fig. 7H,I), suggesting that they
might play similar DV patterning roles in indirect-developing
hemichordates (Harada et al., 2002; Röttinger and Martindale,
2011). Treatment with NiCl2, a potent ventralizing agent used in
the manipulation of echinoderms (Hardin et al., 1992), has a strong
effect exclusively on patterning of the DV axis of P. flava and S.
kowalevskii embryos. The link between the NiCl2-sensitive
ventralizing signal and dorsalizing Bmp signal, as well as the
degree of conservation with the molecular mechanism underlying
echinoderm DV patterning, remain unclear.
Comparison with a limited number of other genes expressed
along the DV axis in Ambulacraria (Fig. 7) reveals both
conservation and divergence; bmp2/4 is expressed on the dorsal
side in both hemichordate species studied to date, but is expressed
in the ventral ectoderm in echinoids. Despite this spatial difference,
in both taxa Bmp signaling is required to specify dorsal fates
(Angerer et al., 2000; Duboc et al., 2004; Lowe et al., 2006).
Evolution of a posterior organizer
In chordates, the blastoporal organizer is involved in the initial
axial patterning of the AP axis and provides posteriorizing signals
to the embryo (Gerhart, 2001; Joubin and Stern, 2001; Holland,
2002). Unraveling the mechanistic basis of organizer function in
vertebrates is complex owing to its simultaneous roles in patterning
the DV and AP axes: any manipulation of the organizer results in
both AP and DV defects, often making it challenging to interpret
experimental results. Recent studies in S. kowalevskii highlight
some of the advantages of this organism for dissecting the genetic
mechanisms of early axial patterning. Unlike chordates, the early
molecular mechanisms of DV and AP axis specification are mostly
independent of one another in S. kowalevskii, although many
orthologous genes are involved (Lowe et al., 2006). The highly
conserved signaling and transcriptional network involved in the
early ectodermal patterning of S. kowalevskii and chordates raises
the possibility that these networks are regulated by homologous
A recent study of the early function of -catenin/Wnt signaling
in S. kowalevskii has indicated that this pathway plays a key role
in specifying endomesoderm and in establishing a posterior
organizer (Darras et al., 2011). The role of -catenin in the
specification of the endomesoderm is likely to be broadly
conserved in metazoans and has been documented in sea urchins
Development 139 (14)
Anterior ectodermPosterior ectoderm EndomesodermEndodermMesoderm
Fig. 6. Comparison of ambulacrarian (hemichordate and echinoderm) fate maps. Schematic representations of fate maps in (A-G) the direct-
developing hemichordate S. kowalevskii, (H-N) the indirect-developing hemichordate P. flava and (O-U) a generic, indirect-developing echinoid.
Ectoderm (light and dark blue) arises from the animalmost cells and endomesoderm (orange) is specified in the vegetal pole of all Ambulacraria.
However, the timing of endoderm and mesoderm segregation remains unclear in hemichordates. Anterior ectoderm is formed by the animalmost
blastomeres (dark blue) and posterior ectoderm arises from the macromeres (light blue) in hemichordates. The terms anterior versus posterior are
not normally used in the commonly studied echinoderms and the term ventral is often replaced by oral and dorsal by aboral. See Fig. 4 legend for
Development 139 (14)
(Logan et al., 1999), cnidarians (Wikramanayake et al., 2003;
Momose and Houliston, 2007) and nemerteans (Henry et al., 2008).
Embryological experiments in S. kowalevskii have demonstrated
that the establishment of the embryonic posterior domain is
dependent on the -catenin-mediated induction of endomesoderm
(Fig. 8A). The animal ectoderm in early blastulae will adopt
anterior fates if isolated from posteriorizing signals emanating from
the vegetal pole (Colwin and Colwin, 1953; Sive et al., 1989;
Darras et al., 2011), although these posteriorizing remain to be
characterized. This is very similar to the situation in vertebrates
(Sive et al., 1989) and sea urchins (Hörstadius, 1973), and Wnt/-
catenin signaling is involved in this process in both cases
(Hörstadius, 1973; Kiecker and Niehrs, 2001; Niehrs, 2010;
Angerer et al., 2011).
Morphological homologies with chordates
Classical morphological comparisons have raised hypotheses of
homologies between several structures in chordates and
hemichordates. Molecular genetic data can help test some of these
hypotheses; if the two proposed homologous structures share
substantial similarities in the genetic bases of their morphogenesis,
then this can add support to hypotheses of morphological
homology (Abouheif et al., 1997).
In hemichordates, the dorsal nerve cord has long been compared
to the dorsal CNS of chordates (Knight-Jones, 1952), although the
relationships between these structures remain uncertain. The
hemichordate dorsal nerve cord extends from the proboscis to the
anus along the dorsal midline and is superficial along most of its
length. However, the collar nerve cord is internalized into a
subepithelial, hollow structure through a process that strongly
resembles chordate neurulation (Bateson, 1884a; Brown et al.,
2008; Kaul and Stach, 2010). Early reports disagreed on the neural
composition of this cord, with Bullock (Bullock, 1945) arguing that
it was a largely through-conduction tract of axons without
associated cell bodies, whereas Knight-Jones (Knight-Jones, 1952)
argued for homology with the chordate dorsal nerve cord. Recent
analyses clearly show an agglomeration of cell bodies in the
hemichordate dorsal collar cord with an associated underlying
neuropil (Brown et al., 2008; Nomaksteinsky et al., 2009).
However, the internalized portion of the dorsal nerve cord is only
a small part of the nervous system, and much less is known about
nervous system patterning and organization in the rest of the
animal. In particular, there are no available data on the molecular
regionalization of the ventral nerve cord, which extends from the
posterior collar down the length of the animal, and of the extensive
nerve plexus of the proboscis and collar. Further work is required
to test whether any region(s) of the hemichordate nervous system
show the conserved mediolateral or DV axis patterning
mechanisms described in more conventionally centralized nervous
systems, such as those of annelids (Denes et al., 2007) and
chordates (Jessell, 2000; Holland, 2009).
The dorsolateral gill slits that perforate the pharynx in all
enteropneusts and some pterobranchs have close morphological
and functional similarities to chordate gill slits (Rychel and Swalla,
2007; Gonzalez and Cameron, 2009). Homology of deuterostome
gills has been further supported by reports of stem echinoderm
fossils with gills (Jefferies, 1986; Dominguez et al., 2002). Early
molecular analyses in hemichordates also demonstrated gill pore
expression of the transcription factor pax1/9, which has key roles
in chordate gill morphogenesis (Holland et al., 1995; Ogasawara et
al., 1999; Okai et al., 2000). A recent study also revealed that a
suite of transcription factors with conserved roles in the early
development of chordate endodermal pharyngeal out-pockets and
vertebrate gill slits is also expressed in out-pocketing hemichordate
gill pouches (Gillis et al., 2011), providing robust support for the
proposed homology of deuterostome gill pouches.
Fig. 7. Comparison of spatial gene expression in hemichordates and echinoderms. Spatial gene expression patterns analyzed by whole-
mount in situ hybridization at late gastrula stages in (A-G) the direct-developing hemichordate S. kowalevskii and (H-N) the indirect-developing
hemichordate P. flava. The corresponding echinoid gene expression patterns at the late gastrula stage are illustrated (O-U). A-G provided by J.
Gerhart, C. J. Lowe and A. M. Pani; H-N are reproduced with permission (Röttinger and Martindale, 2011); O-U are based on published data: O
(Angerer et al., 2000; Harada et al., 2001), P (Duboc et al., 2004; Bradham et al., 2009), Q (Croce et al., 2001), R (Oliveri et al., 2006), S (Howard-
Ashby et al., 2006), T (Croce et al., 2006), U (Yaguchi et al., 2008). dv, dorsal view.
Limitations and future directions
The most significant limitation with all the hemichordates that have
been studied so far is that they have limited reproductive periods.
One of the biggest challenges is to extend the experimental period
by determining cues that induce gametogenesis. The generation
times are not known for any enteropneusts, but are likely to be too
long to make forward genetics a practical strategy for functional
Hemichordate developmental research is just beginning to reap
the benefits of substantial progress in the development of genomics
resources. Development and refinement of new functional
approaches, together with the availability of new genomic datasets,
provide the essential resources with which to address a wide range
of key questions in developmental and evolutionary biology. The
genomics resources for S. kowalevskii are well developed and
include an extensive EST collection for a range of developmental
stages and adult tissues (Freeman et al., 2008), and an EST
resource is currently being developed for P. flava (Röttinger and
Martindale, 2011). In addition, the genomes for both species have
been sequenced and are currently in the process of being assembled
and annotated. A high-quality assembly of the S. kowalevskii
genome is available in GenBank. Developing methods for transient
transgenesis will be the next step in genetic techniques in
hemichordates, which will allow functional testing of cis-regulatory
Hemichordates have already revealed many important
developmental insights into early deuterostome and chordate
evolution. Previously, reconstructing ancestral developmental
strategies of deuterostomes has been challenging owing to the often
contrasting development strategies of chordates and echinoderms.
For example, mesoderm induction in chordates is mediated by a
variety of different signaling ligands that are not involved in
specifying larval sea urchin mesoderm. Considering vertebrates,
Nodal signaling is important in mesoderm induction in Xenopus
and zebrafish and in primitive streak formation of mouse (Conlon
et al., 1994; Feldman et al., 1998; Agius et al., 2000; Kimelman,
2006), and FGF signaling is key throughout vertebrate
development (Amaya et al., 1991; Amaya et al., 1993; Ciruna and
Rossant, 2001; Fletcher et al., 2006). Nodal is not involved in
mesoderm induction in the invertebrate chordates (Onai et al.,
2010) or sea urchins (Duboc et al., 2004; Lapraz et al., 2009), so
this developmental role is likely to have evolved in early
vertebrates. In ascidians, FGF signals are also important for
mesoderm development (Imai et al., 2002; Imai et al., 2003), and
in amphioxus FGF signals are important for the development of
anterior, but not posterior, somites (Bertrand et al., 2011). In sea
urchins, mesoderm is induced by Notch signaling (Sherwood and
McClay, 1999; Sweet et al., 2002) without any obvious role of
Nodal and only a limited influence by ERK, as one potential
cytoplasmic downstream FGF effector in the MAPK pathway
(Röttinger et al., 2004). Hemichordate functional developmental
data for mesoderm induction will be necessary to reconstruct
ancestral deuterostome mechanisms.
Comparative data from within the phylum will facilitate some of
the first comprehensive developmental investigations between two
species with similar adult body plans but contrasting life history
strategies. The difficulties of making broad bilaterian
developmental comparisons between species with contrasting life
histories are rarely considered, but can be a significant confounding
factor in comparisons between groups given the different life
histories of many organisms. Furthermore, comparisons of
developmental mechanisms between anatomically similar P. flava
and echinoderm larvae will help to address long-standing questions
of whether bilaterian, feeding primary larvae are homologous
(Davidson et al., 1995) or whether they have evolved convergently
in response to similar selective pressures (Sly et al., 2003).
Hemichordates also have the potential to become compelling
models for studying regeneration. The ability to regenerate is
widely distributed and occurs to some extent in most of the animal
phyla. In vertebrates (i.e. axolotl salamanders), regeneration is
limited to regrowth of particular body structures (reviewed by
Antos and Tanaka, 2010; Nacu and Tanaka, 2011), whereas certain
invertebrates are able to restore large parts of their bodies (Bely and
Nyberg, 2010). However, the developmentally simplest and most
intensely studied model systems for regenerative medicine are
phylogenetically very distant from chordates. The close
relationship of hemichordates and chordates suggests that a
molecular characterization of regeneration in hemichordates might
be very revealing. Enteropneusts have excellent regenerative
capacities (Tweedell, 1961; Packard, 1968; Rychel and Swalla,
2008; Humphreys et al., 2010; Miyamoto and Saito, 2010), and
impressive anterior and posterior regeneration has been reported in
several ptychoderids (Rao, 1955; Rychel and Swalla, 2008;
Humphreys et al., 2010) as well as reproduction by fission
(Packard, 1968; Miyamoto and Saito, 2010).
Although the potential of hemichordates to improve our
understanding of chordate and deuterostome body plan evolution
has its historical roots as far back as the early 1800s, the
morphological disparities between deuterostome body plans made
progress difficult. The recent application of experimental
approaches and the availability of genomic resources have enabled
molecular developmental studies of germ layer specification and
axial patterning in hemichordates. These studies are revealing
highly conservative developmental programs that are facilitating
unprecedented insights into early deuterostome body plan
Development 139 (14)
A Anteroposterior patterning
B Dorsoventral patterning
Fig. 8. Current model of hemichordate endomesoderm
specification and early axis patterning. (A)AP patterning. At the
blastula stage, accumulation of -catenin is required to specify
endomesoderm (orange), which in turn signals to the overlying
ectoderm (blue) to specify posterior ectoderm via as yet
uncharacterized signals (Darras et al., 2011). AP patterning is refined by
additional signals at later stages. (B)DV patterning. Bmp signaling in
the dorsal ectoderm is required to specify dorsal ectoderm and pattern
the DV axis (Lowe et al., 2006) and an as yet unidentified (question
mark) NiCl2-sensitive signal specifies ventral fates (Röttinger and
Martindale, 2011). Dark blue, anterior ectoderm; gray, collar ectoderm;
light blue, posterior ectoderm. See Fig. 4 legend for abbreviations.
Development 139 (14)
evolution. Future work will further test for developmental
similarities and differences with chordates and echinoderms to
determine ancestral deuterostome strategies. Furthermore, the
completed genomes for two species will encourage novel
comparative approaches and further functional tool development.
The ability to compare the development of both larval and direct-
developing species within the same group will provide valuable
data that are likely to make a key contribution to furthering our
understanding of the evolution of life history and the origins of
We thank Ariel Pani and Kevin Uhlinger in the C.J.L. laboratory for comments
on drafts of the manuscript; Atsuko Sato, Jessica Gray, Marc Kirschner,
Laurinda Jaffe and John Gerhart for giving permission to show unpublished
data; and Ken Halanych for the image of Cephalodiscus and Ariel Pani and
Rachael Norris for the images of S. kowalevskii.
C.J.L. was supported by the National Science Foundation and E.R. by the
Hawaii Community Foundation.
Competing interests statement
The authors declare no competing financial interests.
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