Lampreys and hagfish, which together are known as the
cyclostomes or ‘agnathans’, are the only surviving lineages of
jawless fish. They diverged early in vertebrate evolution,
before the origin of the hinged jaws that are characteristic of
gnathostome (jawed) vertebrates and before the evolution of
paired appendages. However, they do share numerous
characteristics with jawed vertebrates. Studies of cyclostome
development can thus help us to understand when, and how,
key aspects of the vertebrate body evolved. Here, we
summarise the development of cyclostomes, highlighting the
key species studied and experimental methods available. We
then discuss how studies of cyclostomes have provided
important insight into the evolution of fins, jaws, skeleton and
Key words: Cyclostome, Evolution, Gnathostome, Hagfish,
Lampreys and hagfish are unusual animals, and you are not likely
to forget them if you have seen them. Most lampreys are
ectoparasites on fish, using a circular, sucker-like mouth to clamp
onto their hosts. Rasping, tooth-like structures then grind into host
flesh for feeding. Hagfish, by contrast, are typically deep-sea
scavengers, feeding on sunken carcasses by burrowing inside via
an orifice or wound. They lack clear vertebrae allowing them to tie
their body in a knot, and they can produce huge quantities of slime
when provoked. Together, lampreys and hagfish are usually
referred to as the cyclostomes, ‘agnathans’ or jawless vertebrates
(see Glossary, Box 1), and, as these names imply, they lack the
hinged jaws characteristic of other living vertebrates. The latter are
accordingly known as jawed vertebrates, or gnathostomes (see
Glossary, Box 1), and several other characteristics support this
separation, perhaps most notably the presence of paired fins/limbs
and a mineralised skeleton in the gnathostomes and their absence
Although there is general consensus that living gnathostomes
comprise a clade (Fig. 1), the precise relationship between the
lamprey, hagfish and jawed vertebrate lineages has been more
controversial. Three arrangements of these lineages are possible,
and two have been widely championed in recent years. One places
lampreys as most closely related to jawed vertebrates in the clade
Vertebrata (see Glossary, Box 1), with hagfish more distantly
related; all three together then comprise Craniata (see Glossary,
Box 1). This phylogenetic scheme is commonly seen in text books
and is appealing because it implies a gradual assembly of vertebrate
characters, and supports the hagfish and lampreys as experimental
models for distinct craniate and vertebrate evolutionary grades (i.e.
perceived ‘stages’ in evolution). However, only comparative
morphology provides support for this phylogenetic hypothesis. The
competing hypothesis, which unites lampreys and hagfish as sister
taxa in the clade Cyclostomata, thus equally related to
gnathostomes, has enjoyed unequivocal support from phylogenetic
analyses of protein-coding sequence data (e.g. Delarbre et al., 2002;
Furlong and Holland, 2002; Kuraku et al., 1999). Support for
cyclostome theory is now overwhelming, with the recognition of
novel families of non-coding microRNAs that are shared
exclusively by hagfish and lampreys (Heimberg et al., 2010).
Perhaps most significantly, contradictory morphological evidence
has eroded, particularly through new insights into hagfish
development, which have demonstrated that they have lost, not
primitively lacked, many of the characteristics [e.g. vertebrae (Ota
et al., 2011)] used previously to diagnose a lamprey-gnathostome
clade. A monophyletic cyclostome clade thus provides two
experimental models that, in contrast with gnathostomes, can reveal
the nature of the ancestral vertebrate. However, this clade implies
a phenotypically complex ancestral vertebrate, broadening the gulf
in bodyplan organisation distinguishing vertebrates from their
spineless invertebrate relatives, and making the challenge of
explaining its origin in developmental evolution all the more
The immediate invertebrate relatives of vertebrates are also
chordates: the Urochordata (ascidians and other tunicates; see
Glossary, Box 1) and the Cephalochordata (amphioxus and allies;
see Glossary, Box 1), both of which have been the subject of other
articles in this Evolutionary crossroads in development biology
series (Bertrand and Escriva, 2011; Lemaire, 2011). Phylogenomic
(see Glossary, Box 1) data convincingly place the Urochordata, not
Cephalochordata, as more closely related to Vertebrata (Delsuc et
al., 2006). Hence, from the perspective of living taxa, a whole suite
of characteristics unite Vertebrata, including an axial skeleton, brain
complexity, cranial sensory complexity, neural crest cells (see
Glossary, Box 1) and their many derivatives, and perhaps also a
predatory (as opposed to a filter feeding) lifestyle. This can give
the appearance of a step-wise change in complexity at this point in
evolutionary history. However, the vertebrates also have a rich
fossil record (Fig. 1) with many well-defined lineages, allowing the
point at which certain characteristics appeared to be understood
relatively well. Their study instead points to a more gradual
acquisition of vertebrate complexity. This in turn has important
implications for interpreting molecular and developmental studies
of cyclostomes, as we discuss below.
A final characteristic that unites gnathostomes is genome
duplication: all living gnathostomes appear to have evolved from
an ancestral lineage that experienced two rounds of whole genome
duplication, commonly known as ‘1R’ and ‘2R’ (see Glossary, Box
1), and this explains the relative complexity and redundancy of
Development 139, 2091-2099 (2012) doi:10.1242/dev.074716
© 2012. Published by The Company of Biologists Ltd
Evolutionary crossroads in developmental biology:
cyclostomes (lamprey and hagfish)
Sebastian M. Shimeld1,* and Phillip C. J. Donoghue2
1Department of Zoology, University of Oxford, The Tinbergen Building, South Parks
Road, Oxford OX1 3PS, UK. 2School of Earth Sciences, University of Bristol, Wills
Memorial Building, Queens Road, Bristol BS8 1RJ, UK.
*Author for correspondence (email@example.com)
many developmental gene families in vertebrate model species
compared with invertebrate models, such as Drosophila. The 1R
ploidy event demonstrably post-dated the divergence of the
vertebrate, amphioxus and urochordate lineages (Dehal and Boore,
2005), but the timing of the 2R ploidy event with respect to
cyclostome-gnathostome divergence is less clear. Received wisdom
has it that 2R occurred within the gnathostome stem lineage (see
Glossary, Box 1) after cyclostome divergence; however, molecular
phylogenetic analyses of individual gene families are often unclear
on this (Kuraku et al., 2009). Thus, it remains possible that both 1R
and 2R occurred in the vertebrate stem lineage, or that extra
cyclostome genes are derived from independent duplications, or a
mixture of shared and independent duplications.
As we discuss below, despite recent advances neither lampreys
nor hagfish are easy systems to work with compared with model
vertebrates. Their attraction stems from where they branch in
animal phylogeny. As the only surviving lineages from a once
diverse and disparate evolutionary grade of jawless fishes, they
provide an experimental window into the developmental biology
and genomic constitution of the ancestral vertebrate. It is important
to note, however, that neither lampreys nor hagfish can be taken as
literal proxies for the ancestral vertebrate: both lineages have
acquired characteristics specific to cyclostomes, and both have
transformed or lost ancestral vertebrate characters. However, in
comparison to vertebrate outgroups, such as the urochordates, and
ingroups, such as sharks and bony fishes, lampreys and hagfish can
provide insights into the molecular and genomic changes that
underlie the assembly and subsequent evolution of the vertebrate
and gnathostome bodyplans.
Model species and life cycles
Neither lampreys nor hagfish are speciose taxa, with 38 and 60
species defined, respectively (Hardisty, 2006). Both have habitats or
life cycles that render them relatively difficult model systems for
developmental biology, though notable progress has been made on
this front in recent years. The stages in typical lamprey and hagfish
life cycles are shown in Fig. 2. Two lamprey species, Petromyzon
marinus and Lethenteron japonicum, account for the majority of
published lamprey studies, although other species such as Lampetra
fluviatilis and Lampetra planeri are also studied. Adult lampreys are
usually ectoparasites and many are marine. However, when ready to
breed they enter river systems and swim upriver, spawning on the
gravel bottom of relatively fast-flowing river sections. Here, they
clear stones using their sucker-like mouth, creating a small
depression into which eggs are deposited and males add sperm. The
embryos develop in the gravel, initially in a chorion, before hatching
and continuing to develop until they reach a feeding larval stage
known as an ammocoete, which is similar to the adult but lacks the
characteristic feeding apparatus and some other structures. The
ammocoete buries itself in mud on the river bottom and lives as a
filter feeder for several years before undergoing metamorphosis into
the adult. Adults usually migrate to the sea, although in some species,
such as L. planeri, they may proceed directly to reproduction without
further feeding, and notably in the Great Lakes in North America the
invasive population of P. marinus spends its adult phase in the fresh
water of the Lakes.
To our knowledge, lampreys have never been taken through a
complete life cycle in captivity, and developmental studies are
based on wild-caught specimens. Fertilised eggs can be collected
from spawning sites and easily cultured. Gravid adults can also
be collected and held for some time in cool fresh water, before
strip-spawning and in vitro fertilisation. For a methodological
description, see Nikitina et al. (Nikitina et al., 2009). In vitro
development has allowed the establishment of staging series,
including one for P. marinus (Piavis, 1971) and Lampetra
reissneri (Tahara, 1988), although as there are few differences
between species, these stagings are often used for other lamprey
Development 139 (12)
Box 1. Glossary
1R/2R. Shorthand for the whole genome duplication events that
occurred early in vertebrate evolution.
Agnathan (Agnatha). Literally meaning ‘lacking jaws’ this refers
to the jawless fish including lampreys and hagfish. It is an
evolutionary grade, not a clade, although it is sometimes
inappropriately used as a synonym of ‘cyclostomes’.
Cephalochordata. A clade of invertebrate chordates commonly
known as the ‘lancelet’ or ‘amphioxus’. For more information, see
Bertrand and Escriva (Bertrand and Escriva, 2011).
Conserved noncoding elements (CNEs). Regions of a genome
that show atypically high levels of sequence similarity, implying
selective constraint, and that do not encode protein.
Craniate (Craniata). The chordate clade, named after the cranium
or skeletal braincase, that includes hagfishes, lampreys and
gnathostomes. Assuming cyclostome monophyly, it is equivalent to
the vertebrate clade and is, therefore, defunct.
Crown group. A clade circumscribed by its living members and
their last common ancestor, including all the extinct species that
also share this same common ancestor.
Cyclostome (Cyclostomata). Literally meaning ‘circular mouth’,
this refers to the clade of jawless hagfishes and lampreys, but not
the extinct skeletonised jawless vertebrates that are more related to
Gnathostome (Gnathostomata). The clade encompassing living
jawed vertebrates. Importantly, it might not include all jawed
vertebrates because the extinct placoderms are considered by some
to be a sister clade to Gnathostomata.
Neural crest. A population of cells that emerge from the neural
tube and migrate to the periphery where they differentiate into one
or more of a characteristic suite of cell types, including neurons,
glia, pigment cells, osteocytes, chondrocytes, odontocytes and
Osteostracans. An extinct clade of jawless fishes, more closely
related to jawed vertebrates than any other such clade.
Pharyngeal. Pertaining to the pharynx, which is a chamber at the
anterior end of the digestive tract.
Phylogenomic. Assessment of phylogenetic relationships using
large quantities of sequence data.
Placoderms. An extinct clade or grade of jawed vertebrates,
considered either to be the sister lineage of living jawed vertebrates
or to include the members of the ancestral lineages of living jawed
vertebrates plus chondrichthyans and osteichthyans.
Somites. Embryonic paired segmental masses of mesoderm that
occur lateral to the neural tube and that differentiate into
sclerotome (forming vertebrae), dermatome (dermis) and myotome
Stem group/lineage. Extinct members of an extant evolutionary
lineage that fall outside the crown group to which they are more
Stem-gnathostomes. Extinct vertebrates more closely related to
living jawed vertebrates than to living cyclostomes.
Urochordata. A clade of invertebrate chordates commonly known
as the ‘tunicates’ or ‘sea squirts’. For more information, see Lemaire
The chordate clade comprising cyclostomes,
gnathostomes, their last common ancestor and all of its
descendents, living and extinct.
Development 139 (12)
Lampreys have proven to be tricky developmental models, but
hagfish are harder still. Finding eggs in slime is relatively common,
although they are invariably unfertilised; where and how hagfish
fertilise then lay their eggs in the wild is unknown (Gorbman, 1997).
The only sizeable collections of hagfish embryos are those of the
Pacific hagfish Eptatretus stoutii which were made in the late 19th
and early 20th centuries (Conel, 1931; Dean, 1898; Doflein, 1898;
Price, 1896). The eggs were recovered by fishermen in Monterey
Bay, California, captured in the slime extruded by the animals. The
Atlantic hagfish Myxine glutinosa is known from studies of only
three embryos (Fernholm, 1969; Holmgren, 1946). In all instances,
these early studies of hagfish embryology were limited to
morphology and classical histology.
Recently, however, research groups in Japan and Taiwan have
succeeded in getting captive hagfish of the species Eptatretus
burgeri to produce fertilised eggs in aquaria (Ota et al., 2007). This
has allowed the application of molecular developmental methods
for the first time to hagfish and promises to re-invigorate research
in this area (Ota and Kuratani, 2007; Ota and Kuratani, 2008).
Techniques for investigating lamprey and hagfish
The methods used to investigate lamprey and hagfish
development are summarised in Table 1. For hagfish, these
methods are currently limited to descriptive studies of gene
expression. The study of lampreys is more advanced and
includes numerous gene expression studies on a range of species
and several methods of embryo manipulation. Perhaps the most
effective of these has been the injection of antisense morpholino
oligonucleotides for gene knockdown in P. marinus (McCauley
and Bronner-Fraser, 2006), which has been used for the detailed
dissection of the neural crest gene regulatory network (GRN), as
discussed in detail below. Despite these advances, however, the
long life cycle and difficult culture of these species means that
genetic and germ line transgenesis methods are unlikely to be
Key findings and impact on the field
The study of lamprey and hagfish development is motivated
principally by the phylogenetic position of these organisms; they
provide a window into understanding the developmental processes
present in early vertebrates and, hence, a key to understanding what
has changed during the evolution of novel structures, such as fins
and jaws. This is not to say that either lampreys or hagfish are
directly representative of the common ancestor; both lineages have
their own suites of specialisations and indeed the living cyclostome
and gnathostome lineages have been diverging for exactly the same
length of time. However, the cyclostomes are an outgroup to the
gnathostomes. Outgroups are fundamentally important for
phylogenetic inference in comparative biology and, in this case,
comparison between cyclostomes and gnathostomes can reveal
what is shared between them, and hence ancestral, and therefore
also what is derived. Below, we review a selection of recent
advances in this vein. We also discuss recent advances in our
understanding of the genome-level similarities and differences
between cyclostome and gnathostome development.
CambrianOrd.Sil. Devonian Carbonif. Permian Triassic Jurassic Cretaceous
Time in millions of years before present (Ma)
Fig. 1. Phylogeny of living and a representative selection of extinct chordates within the context of geological time. The 1R whole
genome duplication event occurred in the vertebrate stem lineage, but it is unclear whether the 2R event occurred in the vertebrate or
gnathostome stem lineages. Relationships are based on Delsuc et al. (Delsuc et al., 2006), Donoghue et al. (Donoghue et al., 2000) and Brazeau
(Brazeau, 2009). The spindles (dark grey) on the living lineages reflect the timing of origin of their respective crown groups (see Glossary, Box 1):
amphioxus (Nohara et al., 2004); tunicates (Swalla and Smith, 2008); hagfishes and lampreys (Kuraku and Kuratani, 2006); chondrichthyans (Inoue
et al., 2010); actinopterygians (Inoue et al., 2003). Geological timescale from Ogg et al. (Ogg et al., 2008). Ord., Ordovician; Sil., Silurian; Carbonif.,
Carboniferous; Pg, Paleogene; Ng, Neogene.
The evolution of paired appendages
All living gnathostomes (excluding lineages in which secondary loss
has occurred, such as snakes and eels) have paired pelvic and
pectoral appendages. These form fins in cartilaginous and bony fish,
and are modified into limbs in tetrapods. Both hagfish and lampreys
lack paired appendages and so it is clear that these structures evolved
in the gnathostome lineage after it separated from cyclostomes.
Paired bodywall outgrowths were widespread among extinct stem-
gnathostomes (see Glossary, Box 1) (Wilson et al., 2007), but
unequivocal homologues are first manifested in the pectoral position
in the jawless osteostracans (see Glossary, Box 1). Pelvic appendages
are first encountered in the earliest jawed vertebrates, the placoderms
(see Glossary, Box 1) (Young, 2010).
Appendage development has been studied intensively in model
vertebrates for many years and, more recently, some authors have
begun to explore the molecular control of appendage development
in cartilaginous fish (Dahn et al., 2007; Freitas et al., 2006).
Comparisons of model vertebrates and cartilaginous fish have
helped to reveal the likely ground plan for gnathostome appendage
development, which includes a role for Hox genes, retinoic acid
(RA), Hedgehog (Hh) and fibroblast growth factor (FGF)
signalling, T-box (Tbx) genes, and a mode of muscularisation
(Freitas et al., 2006; Gillis et al., 2009; Neyt et al., 2000).
As cyclostomes lack paired appendages, how can they be studied
experimentally to understand appendage evolution? Freitas et al.
(Freitas et al., 2006) took the approach of trying to define the origin
of the molecular circuitry controlling the development of paired
appendages. They showed that features of paired and median fin
development, including Hox and Tbx expression, are shared in the
catshark. Lampreys also develop a continuous medial fin, and Freitas
et al. (Freitas et al., 2006) showed that the development of this fin
was also marked by Hox and Tbx gene expression. This suggests that
aspects of paired appendage developmental control were co-opted
from the medial fin, which is a primitive feature of chordates. Other
Development 139 (12)
3 4 5 6 7
Fig. 2. Lamprey and hagfish adults and embryos. (A)Ventral view of the head of an adult lamprey, Petromyzon marinus. Note the circular
mouth and arrangement of tooth-like structures. (B)Spawning behaviour in the brook lamprey Lampetra planeri in a stream in southern England.
The adults clear a small area of gravel, creating a pit-like nest into which the eggs are laid. (C)Developing embryos of L. planeri collected from a
nest. At this stage, equivalent to about stage 24-25 of Tahara (Tahara, 1988), the embryo head has extended away from the yolk. Most embryos
are still within their chorion; however, the one marked with an asterisk is in the process of hatching. (D)Very early ammocoete larva of L. planeri in
lateral view with anterior to the left. The pigmented eye is visible (arrow), as are numerous pigmented melanocytes (brown). The upper lip (Ul) and
lower lip (Ll) are marked, and posterior to these come the seven pharyngeal slits (numbered), the heart (h) and the gut (g), which contains the
remaining yolk. A prominent notochord (n) serves as an axial skeleton, above which is the CNS. (E)Ventral view of the head of an adult hagfish,
Eptatretus burgeri, showing the circular mouth and anterior tentacles. (F)Eggs of E. burgeri. Note the small terminal hooks, which act to connect
eggs into strings. (G)Close up of an E. burgeri fertilised egg showing the developing embryo and associated vasculature, plus the terminal hooks.
(H)Head of the developing embryo of E. burgeri, with anterior to the right. Note the very large quantity of yolk. For more details on hagfish
embryology and anatomy the reader is referred to a recent review on the subject (Ota and Kuratani, 2008). The image in A was reproduced with
kind permission from Lyman Thorsteinson, courtesy of USGS (United States Geological Survey); C was reproduced with kind permission from
Ricardo Lara-Ramirez; E-H were reproduced with kind permission from Kinya G. Ota.
Development 139 (12)
aspects of paired appendage development in gnathostomes have not
been identified in lamprey median fin development, including Hh
signalling and a role for RA. However, Hh and RA signalling occurs
in gnathostome gill arches (Gillis et al., 2009), structures also found
in cyclostomes. The development of gill arches has not been well
studied in cyclostomes, but it is known that the lamprey pharynx is
affected by RA exposure (Kuratani et al., 1998) and that expression
of the Hh receptor Patched
developmental regulation of these gill arches is likely (Hammond et
al., 2009). Overall, this suggests that the evolution of paired
appendages occurred via co-option of the molecular circuitry
regulating primitive chordate structures, prior to the divergence of
cyclostomes and gnathostomes (Fig. 3A). Dissection of the
regulatory interactions between key genes in cyclostome
development would clarify this further.
indicates that Hh-mediated
The origin of articulated jaws
Articulated jaws are a diagnostic characteristic of gnathostomes
and are often postulated to have allowed a more active predatory
life history (Gans and Northcutt, 1983). It has also been considered
that the evolution of jaws allowed jawed vertebrates to outcompete
jawless fish, leaving just the relict lineages of lampreys and
hagfish, although the timing of jawless fish lineage extinction
shows that, in reality, their extinction was much more complex than
this (Purnell, 2001).
Nearly a decade ago, a number of studies (e.g. Horigome et al.,
1999; Kuratani et al., 1999; Neidert et al., 2001; Shigetani et al.,
2002) started to address jaw evolution at the level of gene
expression. These studies revealed a high level of similarity
between lamprey and gnathostome pharyngeal (see Glossary, Box
1) patterning in terms of the expression of transcription factor
genes, such as those of the distal-less (Dlx), muscle segment
homeobox (Msx) and Hand families (Fig. 3B), and the position and
function of signalling pathways. These data, coupled with analyses
of neural crest cell migration, led Shigetani et al. (Shigetani et al.,
2002) to propose that changes in the interaction between neural
crest populations and pharyngeal tissues might underlie jaw
evolution. More recently, these studies have been extended and,
although still confirming much similarity in gene expression, have
revealed what might be a key difference between lampreys and
gnathostomes. The lamprey first arch lacks the focal expression of
the homebox-containing transcription factor Bapx1 (Nkx3.2) and
the Transforming growth factor (TGF)- signalling molecule
Gdf5/6/7 that, in gnathostomes, pattern the jaw joint (Cerny et al.,
2010; Kuraku et al., 2010). These results suggest a model (Fig. 3B)
in which the extensive existing pattern in the first arch of the
vertebrate ancestor has been subtly adapted in the gnathostome
lineage by acquisition of a focused patterning system specifying a
joint, a requirement for hinged jaws. How this might have occurred
is unknown and other explanations remain possible.
Somites and skeletons
The somites (see Glossary, Box 1) of jawed vertebrates are
patterned into compartments that give rise to distinct tissues: the
sclerotome, dermatome and myotome, which form axial skeleton,
dermis and muscle, respectively. In model vertebrates, the
mechanisms controlling this are quite well understood and involve
initial signalling from the notochord, neural tube and more lateral
mesoderm to subdivide the somite (Bothe et al., 2007). Lamprey
somites appear to be essentially the same as this, and a small
sclerotome forms the axial cartilaginous nodules that are
homologous to vertebrae (Tretjakoff, 1926). Hagfish have been
considered historically to lack similar structures. Recently,
however, it has become clear that they do develop a sclerotome
compartment that gives rise to small axial cartilaginous elements
(Ota et al., 2011).
Table 1. Summary of experimental methods applied to lamprey and hagfish embryos
Species Summary Selected references
(Boorman and Shimeld, 2002;
Derobert et al., 2002;
Murakami et al., 2001;
Neidert et al., 2001;
Ogasawara et al., 2000; Ota
et al., 2007; Swain et al.,
Standard whole-mount in situ hybridisation
techniques work well, though can be
difficult on early developmental stages.
This method has also been adapted for
gene expression in the adult lamprey
microRNA visualisation Lamprey:
Analysis via locked nucleic acid probes as for
microRNA visualisation in other species
(Pierce et al., 2008)
Methods reported include lineage tracing via
injection of markers dyes, and ablation
(Langille and Hall, 1988;
McCauley and Bronner-
Fraser, 2006; Shigetani et
Morpholino oligonucleotide methods are
well described and very effective at early
(McCauley and Bronner-
Fraser, 2006; Sauka-
Spengler et al., 2007)
Expression of plasmid-based reporter genes
used to express GFP from a strong
promoter (CMV) and gene-specific
(Kusakabe et al., 2003)
L. japonica Use of cyclopamine to inhibit Hh signalling
and SU5402 to inhibit FGF signalling.
Retinoic acid has also been applied
(Murakami et al., 2004;
Sugahara et al., 2011)
Gnathostomes also develop an extensive dermal skeleton, which
is usually mineralised and is derived primarily from neural crest
cells (Donoghue et al., 2008). This is generally confined to the head
in amniotes; however, non-tetrapod vertebrates and, in particular,
fossil data show that extensive dermal armour evolved early in the
gnathostome lineage after its separation from cyclostomes. It is also
clear from the paleontological record that the dermal mineralised
skeleton significantly pre-dates the origin of a mineralised vertebral
skeleton, which is first encountered in the earliest jawed vertebrates
(Donoghue and Sansom, 2002).
How and when did skeletal tissues and their mineralisation
evolve? As lampreys and hagfish have cranial neural crest-derived
and axial sclerotome-derived skeletons, both these pre-date the
radiation of living vertebrates. Studies in lampreys, hagfish and
amphioxus have suggested that cartilage in all three taxa is
molecularly similar to that of jawed vertebrates, both with respect
to the proteins forming the cartilaginous matrix itself and to the
transcription factor genes that mark their differentiation, such as the
Runt-related (Runx) and Sry-related (SoxD and SoxE) transcription
factors (Cattell et al., 2011; Hecht et al., 2008; Kaneto and Wada,
2011; McCauley and Bronner-Fraser, 2006; Ohtani et al., 2008;
Wada, 2010; Zhang and Cohn, 2006; Zhang et al., 2006). However,
a recent detailed study of lamprey cartilage has suggested that such
generalisations should be treated with caution: lampreys are known
to have several structurally distinct cartilages, and Cattell et al.
(Cattell et al., 2011) found that these cartilage types display
considerable diversity in cartilage gene expression. Based on this,
they proposed a complex multistep model for the evolution of
cartilage diversity in vertebrates. Testing this model will require
deconstruction of regulatory interactions in at least jawed
vertebrates and lampreys, and possibly also in amphioxus.
The development of the neural crest
The neural crest is an enigmatic tissue, attracting attention from
evolutionary biologists because of its often-hypothesised specificity
to vertebrates and significant contribution to the cranial complexity
that separates vertebrates from other animals. Lampreys have a
neural crest that is very similar to that of gnathostomes, including
an ability to differentiate into a wide range of tissues, and hagfish,
although less well studied, are likely to be similar (Ota et al., 2007).
There are also data suggesting that neural crest might pre-date
vertebrate origins (Donoghue et al., 2008) as some urochordates
possess migratory cells with similar properties (Jeffery et al., 2004).
Recent studies have used gene knockdown strategies to dissect
carefully the gene regulatory interactions controlling lamprey
neural crest (Nikitina et al., 2008; Sauka-Spengler et al., 2007).
Such experiments can be hard to interpret in gnathostome models,
in which developmental speed could mask direct and indirect
interactions. However, in lampreys, experiments of this nature can
be conducted with high fidelity, as the very slow pace of
development allows detailed dissection of both the relative timing
of normal gene expression and the impact of gene knockdown on
putative target genes. The combined data from these experiments
has allowed the construction of a detailed GRN model of lamprey
neural crest development, defining genes at different tiers in the
progression from dorsoventral epidermal patterning and neural
plate specification to the cell biology of neural crest migration
(Sauka-Spengler and Bronner-Fraser, 2008; Sauka-Spengler et al.,
In turn, this has allowed the inference of key differences between
vertebrates and invertebrate chordates, particularly amphioxus (Yu
et al., 2008). Some aspects of development, including neural
dorsoventral patterning, appear to be conserved between these
Development 139 (12)
in midline fin
in midline fins
in midline fin
Hox, Tbx, Hh, RA
in paired fins
Bapx, Gdf5 in jaw
Gsc, Hand in
Fig. 3. Models of vertebrate jaw and paired fin evolution. (A)Modern gnathostomes (top, represented by a shark) and cyclostomes (bottom,
represented by a lamprey) both use Hedgehog (Hh) and retinoic acid (RA) in patterning the pharynx, and Hox and Tbx in patterning midline fins. This
allows us to infer that both were present in the common ancestor (centre). A hypothesis for paired fin evolution in the jawed vertebrates is shown in red,
and involves co-option of these patterning mechanisms into new sites of fin development on the flank. Many other changes would also have been
required, including the evolution of muscularisation and associated innervation. (B)Modern gnathostomes and cyclostomes [both represented by stylised
diagrams, with the anterior and mouth (m) to the left] use similar suites of genes to pattern the dorsoventral (DV) axis of the pharyngeal arches
(numbered), including Dlx, Msx, Gsc and Hand genes (Cerny et al., 2010; Kuraku et al., 2010). A difference, shown in red, is the use of Bapx and
Gdf5/6/7 by gnathostomes to pattern a joint in the skeletal elements of the first arch. This is hypothesised to have been required for forming hinged jaws.
Development 139 (12)
groups. However, a key difference is the absence of expression in
amphioxus of some genes involved in specifying the neural-
epidermal border region (where the crest will arise) and of genes
responsible for delamination of crest cells and their subsequent
migration (Yu et al., 2008). These data suggest that the neural crest
evolved by adding a new regulatory tier under pre-existing
mechanisms for dorsoventral neural patterning.
Genome-level insights into vertebrate development and
Many genes classically considered to be ‘developmental’, such as
those encoding transcription factors and proteins involved in cell
signalling, are duplicated in jawed vertebrates, in comparison to
amphioxus and urochordates. These so-called ‘transdev’ genes are
often multi-copy in lampreys too. As discussed above, the
additional paralogues in jawed vertebrates are usually derived from
whole genome duplications, and a simple explanation for this is
that cyclostomes and jawed vertebrates share these genome
duplications. Molecular phylogenetics have, however, been unclear
on this issue, often showing different topologies for different gene
families when shared ancestry of genome duplication would predict
shared topologies (Kuraku et al., 2009). A possible explanation for
this is that genome duplication occurred shortly before the
separation of the cyclostome and jawed vertebrate lineages, as this
could allow insufficient time for resolution of paralagous genes
and, hence, confused molecular phylogenies. A good cyclostome
genome assembly would probably resolve this. Alternatively,
incongruous topologies among gene families might reflect the
dramatic editing that occurs in the genome of somatic cell lineages
in lampreys and, perhaps, hagfishes (Smith et al., 2009). This is a
potential problem because the lamprey genome sequencing project
is based on somatic cells.
Various authors have also linked gene and genome duplication
to the evolution of morphological complexity, with the underlying
assumption that duplicate genes provide extra genetic material that
is freed from purifying selection by redundancy and is, hence, free
to evolve new functions that guide evolutionary innovation. There
are a few good examples of this, including the functional
diversification of globin proteins, which emerged as paralogues
from 1R and 2R whole genome duplication events in early
vertebrate evolution, to perform specialised roles in oxidative
metabolism (Hoffmann et al., 2011). However, many of these
examples describe neofunctionalisation or instances of
complementary degeneracy within derived vertebrate clades. There
is little evidence of whole genome duplications having effected
vertebrate, or indeed, gnathostome, innovations. The gradual
accumulation of vertebrate and gnathostome characteristics over
considerable evolutionary time, evidenced by the fossil record
(Donoghue and Purnell, 2005), coupled with the frequent re-use of
existing genetic circuitry in vertebrate evolution discussed above,
argue against such an interpretation. It is likely that the
evolutionary consequences of whole genome duplication are more
intricate and are realised over a more prolonged period than has
A better case can perhaps be made for the role of the non-coding
trans-acting regulatory microRNAs in early vertebrate evolution.
A combination of genome resources and small RNA library
sequencing has revealed a fundamental episode of microRNA
innovation in the lineage leading to vertebrates after its separation
from the tunicate lineage. The rate of innovation of novel
microRNA families is higher in this interval of vertebrate evolution
than in any other interval in animal evolution. This phenomenon
pre-dated, and is not a consequence of, whole genome duplication,
as lampreys possess multiple paralogues within these microRNA
families (Heimberg et al., 2008). Furthermore, as lampreys share
duplicated microRNAs with mouse and human, this evidence
implies that both the 1R and 2R whole genome duplication events
occurred before living vertebrates diverged. Deep sequencing of
organ-specific small RNA libraries from lamprey has revealed that
vertebrate-specific microRNAs are expressed in vertebrate
innovations and elaborations. As lampreys exhibit expression
profiles in these organs that are comparable to both fish and mouse,
it appears that these were established in the last common ancestor
of vertebrates and were subsequently conserved (Heimberg et al.,
2010). However, analysis of the role of microRNAs in cyclostome
development has not yet extended beyond expression analyses
using RNA probes (e.g. Pierce et al., 2008).
The development of numerous vertebrate genome sequences has
also allowed the evolution of other non-coding sequences to be
assessed. Jawed vertebrate transdev genes are associated with an
exceptional density of conserved non-coding elements (CNEs; see
Glossary, Box 1), which, where studied, are usually regulatory
(Woolfe et al., 2005). Extension of these studies to lamprey and
amphioxus data reveals a surprising pattern. Although the drop off
in the number and length of CNEs observed with increasing
phylogenetic distance is to be expected, the degree of change is not.
Lampreys have a reasonable number of conserved sequences, at
least as far as has been assessed to date (McEwen et al., 2009).
However, amphioxus shares only a handful of such sequences with
vertebrates (Putnam et al., 2008). One interpretation of these data
is that early vertebrate evolution saw considerable flexibility in
gene regulatory interactions, followed by a ‘locking-in’ effect, such
that many regulatory sequences came under purifying selection,
fixing them as the CNEs we observe when comparing the genomes
of living gnathostomes.
Evolution of the vertebrate adaptive immune system(s)
As recently as 2009, the immune system was marshalled as evidence
for the ultimately fallacious hypothesis that lampreys are closer
relatives of gnathostomes than are hagfish (Nicholls, 2009). Hagfish
have long been considered to lack lymphocytes and the adaptive
immune system shared by lampreys and gnathostomes. However,
over the past decade it has emerged gradually that the adaptive
immune system of lampreys is distinct from the immunoglobulin, T
cell receptor (TCR)-, antibody- and recombination activating gene
(RAG)-based system of gnathostomes, and instead it appears to be
based on variable lymphocyte receptors (VLRs) (Pancer et al., 2004).
Furthermore, hagfish share this VLR-based system all the way down
to the VLR-encoding paralogues (Pancer et al., 2005; Rogozin et al.,
2007) that, in lampreys, exhibit expression patterns specific to
distinct cell lineages that might be equivalent to gnathostome T and
B cells (Guo et al., 2009). VLRs, like TCRs, are assembled by
somatic rearrangement of distinct gene segments, notably the
leucine-rich repeat regions that bestow the physical diversity of the
encoded proteins. However, this is achieved not by RAG, which is
absent in cyclostomes, but, at least in part, by VLR-specific cytosine
deaminases (CDAs) (Rogozin et al., 2007) at sites specific to the T-
like and B-like lymphocytes (Bajoghli et al., 2011). VLRB- and
CDA2-expressing B-like lymphocytes occur and, therefore, appear
to develop in the typhlosole and kidneys. Lampreys have long been
considered to lack a thymus, the site of T lymphocyte development
in gnathostomes. However, VLRA- and CDA1-expressing T-like
lymphocytes have been identified in, and therefore appear to develop
in, the tissues comprising the tips of gill filaments, which have now
been dubbed ‘thymoids’ (Bajoghli et al., 2011). Thus, distinct T and
B lymphocytes might be primitive to the vertebrate common
ancestor, but adaptive immunity with a comparable repertoire of
immune responses appears to have evolved independently in the
cyclostome and gnathostome lineages. As such, cyclostomes provide
a unique perspective on the evolution of the adaptive immune
system, and auto immunity, that is enjoyed by all other vertebrates.
Limitations and future directions
The major limitation for studying both lampreys and hagfish is
most likely to be the availability of embryos, coupled with the
difficulty of long-term culture. Although some populations of
lampreys are amenable to study, these are geographically confined
and long distance transportation of adults to host laboratories is
usually necessary. Breeding seasons are also limited. The
prolonged larval stage prior to metamorphosis in lampreys pushes
many features of evolutionary interest that are confined to the adult
out of experimental reach. For hagfish, the severe restriction of
embryo availability will probably continue, confining the study of
these species to specialised laboratories. This will also hinder the
development of embryo manipulation methods.
Despite this, we can predict advances on several fronts over the
next few years. The current lack of comprehensive genome data for
lampreys and hagfish is unlikely to be long term. Well-assembled
genomes should address questions concerning the timing of 2R and
help define orthological relationships between cyclostome and
gnathostome genes more fully. This, in turn, will aid interpretation
of comparative gene expression and function. It will also allow
more comprehensive analysis of the non-coding genome:
microRNAs, other non-coding RNAs, and regulatory elements, for
The successful adaptation of morpholino-based gene knockdown
and other gene manipulation methods to lampreys means that gene
regulatory interactions can be dissected in these species. Most
studies of cyclostomes to date have been descriptive and, although
these yield significant insight, understanding developmental
mechanisms and hence the mechanistic basis of evolutionary
change often requires functional analysis. Such studies have the
potential to reveal how key vertebrate specific characteristics
We thank Kinya G. Ota, Ricardo Lara-Ramirez and the United States Geological
Survey (USGS) for images.
Work in the authors’ laboratories is funded by the Royal Society,
Biotechnology and Biological Sciences Research Council (BBSRC) and Japan
Society for the Promotion of Science (JSPS) [S.M.S.]; and by BBSRC and Natural
Environment Research Council (NERC) [P.C.J.D.].
Competing interests statement
The authors declare no competing financial interests.
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