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“Is histological development as complete a test of homology as morphological development?”
(Huxley, 18641]: 296)

The vertebrate skeletal system has paramount importance for analyses in evolutionary
biology. Because vertebrate skeletons can be viewed as aggregates of apparently discrete
units, namely bones, they have attracted the interest of comparative anatomists since
even before the dawn of the concept of evolution 2]. In addition, because bones can be preserved as fossils, comparative research can
include extinct vertebrates, thereby shedding light on evolutionary patterns and processes
(e.g., 3]). In addition, the vertebrate skeletal system is well suited to biomechanical analyses,
allowing both morphological and functional transitions throughout evolution to be
reconstructed (e.g., 4]).

In any comparative study, homology is a conceptual basis for comparing equivalent
units. There is, however, a difficulty in establishing homology—that is, “the apparent
loose relationship between morphological characters and their genetic basis” 5]. Incongruities between morphologies and their genetic bases may lead to errors when
homology is defined solely according to criteria of ontogeny.

Skeletal systems of vertebrates are intolerant of such incongruities (reviewed by
6]). Historical continuities of skeletal elements as step-wise morphological changes
along a phylogenic lineage are inferable from detailed comparative analyses. However,
within these continuities, discontinuities of genetic and developmental bases arise
in which morphologically homologous bones are produced through different developmental
processes 7],8].

Before the concept of evolution was established, two distinct types of bones were
recognized in vertebrate skeletons and were thought to reflect their embryonic development;
specifically, whether the bone arose from a cartilaginous precursor or not (e.g.,
9],10]). Bone arising from precursor cartilage develops not only on the surface of the cartilage
(perichondral ossification), but also within the cartilage mass as the cartilage template
becomes degraded (endochondral ossification), thereby distinguishing this type of
bone from that lacking a cartilaginous precursor in terms of developmental process,
or histogenesis. This line of demarcation in histogenesis was later considered to
reflect the evolutionary succession of bones. For example, Huxley (1864: 298) 1] wrote, “It is highly probable that, throughout the vertebrate series, certain bones
are always, in origin, cartilage bone, while certain others are always, in origin,
membrane bone.” In addition, differences in the cell type of the osteoblast precursors—either
mesodermal or neural crest cells—has historically been offered in support of the notion
that these two histogenetically distinct types of bone generally evolved separately.
However, here, we confirm, through a review of both classical and recent research,
that both histogenesis and cell lineage are decoupled with the two independent lineages
of skeletal systems, namely endo- and exoskeletons, the continuities of which are
inferable from comparative morphology.

In this review, we first summarize various evolutionary continuities of vertebrate
skeletal systems. We then describe their developmental bases at two hierarchal levels,
namely histogenesis and cell lineage, according to recent studies in developmental
biology. In light of this understanding, we discuss the loose relationship between
morphology and developmental basis and suggest that a frame shift in character identity
occurred across cell lineages during the evolution of vertebrate skeletal systems.

Morphological divisions—endoskeleton vs. exoskeleton

From the perspective of comparative morphology, including paleontology, it has been
suggested that two lineages of skeletal systems—the endoskeleton and exoskeleton—have
succeeded in vertebrate evolution (Figure 1, Table 1) 7],11]. This mode of classification is defined exclusively by phylogenetic continuities,
and thus differs from terminology based on ontogeny 7]. For example, the endoskeleton consists of bones preformed from cartilage and their
evolutionary derivatives, or homologues (Table 1) 7]. Most endoskeletal bones, such as those in the axial and limb skeletons, are located
together with muscles within a deep layer of the body. However, in the evolution toward
turtles, the thoracic axial skeleton was exposed, owing to loss of the dorsal axial
muscles, to form the carapace 12]. In this sense, the turtle carapace should be considered an “exposed endoskeleton.”
The distal tip of the distal (ungual) phalange is another example of an exposed endoskeleton
that is recognized in vertebrates 12].

Figure 1. Distribution of endoskeletons (endo) and exoskeletons (exo) in the vertebrate body.(A) Osteostracan Cephalaspis (redrawn from 13]). (B) Basal jawed vertebrate Compagopiscis (redrawn from 14]). (C) Temnospondyl tetrapod Dendrerpeton (redrawn from 15]).

Table 1. Classification of skeletal systems

There is convincing evidence that cartilaginously preformed bones changed during evolution
to become intramembranous bones. For example, the orbitosphenoid, a cranial skeletal
element, of the Amphisbaenia (Reptilia: Squamata) develops intramembranously, although
it clearly is homologous with the cartilaginously preformed orbitosphenoid of other
tetrapods 16]. Patterson (1977) 7] proposed calling such intramembranous bones “membrane bones” and discriminated them
from bones that developed within the dermis, or “dermal bone.” According Patterson’s
terminology, the endoskeleton consists of cartilage and membrane bones (Table 1: Note that the above-mentioned Huxley’s definition of “membrane bone” is different
from that used in this paper, as he did not distinguish dermal bones from other intramembranously
formed bones).

In contrast, the exoskeleton consists of dermal bones (sensu7]), which are homologous with bony armor and are often coated with enameloid or dentine
tissues in basal vertebrates (Figure 1, Table 1; 17]). Exoskeletal bones are located superficially in the body in ancestral conditions,
but some exoskeletal bones, such as the dentary and clavicle of mammals, have shifted
in their positions to a layer deeper than that of some muscles 18]-20]. In this sense, the dentary and clavicle might be referred to as “sunken exoskeleton.”

A possible intermediate condition between ancestral and sunken exoskeletons is represented
by the gastralia (Figure 2). The gastralia are a series of segmental rod-like bones that cover the ventral aspect
of the abdomen in crocodilians and the tuatara, among living forms. Based on fossil
evidence, the gastralia are thought to have evolved from exoskeletal bony scales and
thus are exoskeletal elements 21]. However, the gastralia embryonically develop in close association with the rectus
abdominis muscle in a deep layer, whereas other trunk exoskeletal elements develop
close to the epidermis 22],23] (see also Figure 2). Accordingly, Hay (1898) 22] distinguished the gastralia from other dermal bones and classified the gastralia
as “fascia bone.” Such a concept had been inherited in the distinction between “epithecal”
and “thecal” ossifications, as used by Völker (1913) 24] and Zangerl (1939) 25], which indicate outer and inner dermal layers of ossification, respectively.

Figure 2. Gastralia of the American alligator (Alligator mississippiensis). The embryos were staged according to Ferguson (1985) 26]. (A) Transverse section of the ventral trunk of an embryo at stage 17. Formation of the
gastralia begins with condensation of cells (arrows) in the dermis (drm). Alcian-blue,
hematoxylin and eosin stains; scale bar, 100 ?m. (B) Transverse section of the ventral trunk of an embryo at stage 19. The distance between
the primordial gastralia and the rectus abdominis muscle (ram) decreases. Alcian-blue,
hematoxylin and eosin stains; scale bar, 100 ?m. (C) Enlarged image of the primordial gastralia, showing the matrix that is stained with
Alcian blue (arrowhead), which appears transiently before the bony tissue is formed.
Alcian-blue, hematoxylin and eosin stains; scale bar, 50 ?m. (D) Transverse section of the ventral trunk of an embryo at stage 22. The gastralia contact
the rectus abdominis muscle. The ventral cutaneous branch of the intercostal nerve
(vcb) runs adjacent to the margin of the gastralium. Alcian-blue, hematoxylin, eosin
and immunohistochemistry with anti-acetylated tubulin antibody (T6793, Sigma-Aldrich)
stains; scale bar, 100 ?m. tvm, transversus ventralis muscle. (E) Ventral view of a stage 25 embryo. Alizarin red and Alcian blue stains; scale bar,
1 cm. (F) Enlarged image of E.

The previously mentioned evolutionary shifts in the topographic positions of exoskeletal
elements recalls the idea of Holmgren (1940) 27], who suggested that, in some cases, various exoskeletal elements evolved into endoskeleton
as the result of a topographic shift (delamination theory). However, studies of comparative
morphology provide no evidence of interchangeability between endo- and exoskeletons
7]; the two historical lines of endo- and exoskeletal systems are likely to have evolved
quite independently from each other. It is true that, in some cases, exposed endo-
and exoskeletal elements become fused into a single element during ontogeny, as seen
in the ontogenetic fusion between endoskeletal costal plates and exoskeletal peripherals
to form the carapace in turtles, and in the fusion between endoskeletal vertebrae
and exoskeletal osteoderms to form a tail club in ankylosaurid dinosaurs 28]. However, the ossification centers maintain their separate entities, implying incompatibility
between the endo- and exoskeletons. (Nevertheless, it is worth noting that a vestigial
component of the cleithrum (exoskeletal element) on the scapula (endoskeletal element)
in mammals has been suspected repeatedly 29],30]. This evolutionary change represents a “phylogenetic fusion” advocated by Patterson,
1977 7]).

Some skeletal elements cannot always be traced back to the ancestral endo- or exoskeleton.
There are some examples of newly acquired endo- or exoskeletons in various derived
taxa. In special cases, bones are sometimes produced within musculotendinous tissues
as neo-formations in specific taxa (e.g., the ossified tendon 31]; and sesamoid bones) or by pathologic ossification. Smith (1947) 32] called these bones “subdermal bones,” whereas Patterson (1977) 7] classified them as membrane bones and components of the endoskeleton (Table 1).

As another example of newly evolved endoskeletal bones, the baculum is a cartilage
bone that was newly acquired in the lineage of eutherian mammals 33]. Likewise, non-eutherian mammals have epipubic bones, which were newly acquired in
the more basal mammalian lineage and lost in the crown eutherians 34]. It remains uncertain whether the baculum evolved from the epipubic bone of non-eutherian
mammals 35], but examples of the baculum and epipubic bone are suggestive of a novel cartilage
bone (a component of the endoskeletal system) that was acquired as an autapomorphy
of a specific clade.

In addition, novel exoskeletal elements have been acquired in specific clades. The
predentary and rostral bones are examples of such exoskeletal elements 36],37]. Osteoderms (the bony plates covering body contours) occur recurrently throughout
vertebrate evolution 38]-40]. Although morphological traits are distributed intermittently along the phylogeny,
osteoderms are considered to share a developmental basis (“latent homology” sensu40]), perhaps illustrative of the historical continuity of these bony elements 39],40].

Histogenesis: endochondral and intramembranous ossifications

In contrast to the distinction of exo- and endoskeletons, adjectives such as ‘endochondral’,
‘dermal’ and ‘intramembranous’ are used exclusively for histogenetic aspects of skeletal
tissues, and primarily unrelated to skeletal morphological identities 11]. In many cases, endoskeletal bones develop in association with preexisting cartilage,
whereas exoskeletal bones develop solely intramembranously. However, some endoskeletal
bones develop solely intramembranously, without any association with cartilage (membrane
bones: Table 1), and some exoskeletal bones are likewise associated with cartilage. Comparative
morphology studies have shown that cartilaginously preformed bone in the ancestral
endoskeleton became intramembranously developed bone in derived taxa (e.g., the orbitosphenoid
of the Amphisbaenia 16]). In contrast, cartilage (secondary or adventitious cartilage) develops on the periphery
of exoskeletal bones that develops intramembranously, late in ontogeny of derived
clades 7],41]. Cartilage has even been identified in the exoskeletal armor of the trunk (placodont
sauropterygians 42]). Therefore, histogenetic modes with respect to the association of cartilage are
interchangeable throughout evolution, as once suggested by De Beer (1937) 43].

Cartilage-derived bone is produced through both intramembranous (perichondral) and
endochondral ossification. In perichondral ossification, the typical mode for periosteal
bone formation, osteoblasts are differentiated from the perichondrium/periosteum surrounding
the cartilage and subsequently produce the osteoid inside the periosteum. In the development
of the costal plate of the turtle carapace, the periosteum expanded outward; therefore,
osteoblasts produce outgrowths of the periosteal bone collar, or bony trabeculae 12].

Recent studies have shown that osteoblast cells derived from the perichondrium also
support endochondral ossification 44]. In the early phase of this developmental process, osteoblastic precursors differentiate
from perichondrial cells (Figure 3A) and subsequently migrate from surfaces in which the cartilage template is degraded
into the primary ossification center of the endochondral bone (Figure 3B). Typically, blood vessels invade the cartilage from entrances of osteoblastic precursors
and extend along their migration, suggesting intimate developmental relationship between
vascularization and endochondral ossification 44]. The osteoblast precursors mature into osteoblasts to form bony trabeculae inside
the cartilage (Figure 3C).

Figure 3. Process of endochondral ossification. (A) Differentiation of osteoblastic precursors from perichondrial cells. (B) Migration of osteoblastic precursors (C) Formation of bony trabeculae by mature osteoblasts.

According to histological analyses of fossils, perichondral ossification evolved in
the clade containing osteostracans and jawed vertebrates, whereas the endoskeletons
of galeaspids comprise calcified cartilages, not perichondral bones 45]. Endochondral ossification originated evolutionarily in osteichthyes—that is, later
than the emergence of perichondral ossification 46].

In the development of the cranial exoskeletal bones of extant osteichthyans, osteogenic
cells are differentiated from mesenchymal condensations in the dermis. During this
process of intramembranous ossification, osteoblasts mature from a specific transitional
cell type (chondrocyte-like osteoblast), which co-expresses both osteogenic and chondrogenic
marker genes 47].

Postcranial osteoderms (exoskeletal bones) develop in the dermis, presumably regulated
by an intimate interaction with the epidermis. For example, in armadillos, the osteoderm
is produced by osteoblasts that are differentiated from the condensation of dermal
cells, with the orientation of the primordial osteoderm parallel to that of the epidermis
48]. In contrast, the osteoderm of alligators develops beneath the keel of scutes, but
no osteoblasts are morphologically recognizable during this process 49]. There remains much room for investigation regarding the development of reptilian
osteoderms.

In some fishes, exoskeletal bones are coated with enameloid or dentine tissues, namely,
odontogenic components (reviewed by 50]). These enameloid- and dentine-coated bones occur widely among stem-osteichthyans,
and odontogenic components are present in chondrichthyans also. However, the odontogenic
components seen in chondrichthyans are believed to represent the vestige of the enameloid-
and dentine-coated bones of ancestral jawed vertebrates, in which the bony portion
was lost secondarily 51]—the exoskeleton of stem-gnathostomes likely was composed primarily of bone. This
view is supported by recent histological data from placoderms (a taxon of stem-gnathostomes),
indicating that the condition seen in extant chondrichthyans is derived. In placoderms,
bony components always contributed to the exoskeleton, whereas odontogenic components
did not always contribute to the exoskeleton 52],53], suggesting that odontogenic components were not prerequisite for exoskeletal development
in these taxa.

In addition to endochondral and intramembranous ossifications there is a disparate
mode of bone formation, namely metaplastic bone formation 54], the process by which preexisting tissues change directly (i.e., through metaplasia)
into bony tissues. Exposed endoskeleton 12],55],56] and exoskeleton 57] contain portions of metaplastic bone, in which the collagen fibers of the dermis
are engulfed.

Collectively, comparisons of histogenesis in living and fossil vertebrates suggest
the following scenario (Figure 4). In stem vertebrates basal to the clade of osteostracan-jawed vertebrates, the endoskeleton
was composed purely of cartilage (Figure 4A). Osteostracans and non-osteichthyes jawed vertebrates evolved ossified endoskeletons
(Figure 4B). In these animals, both endo- and exoskeletons developed purely through intramembranous
ossification, although the endoskeleton developed on the surface of cartilage (perichondral
ossification; as for perichondral ossification in chondrichthyes, see 58]). Osteichthyes acquired endochondral ossification, in which bony tissues are produced
within (as well as on top of) cartilage (Figure 4C). During evolution, cartilage structures were occasionally lost and replaced in
part by endoskeletal bones (membrane bones) and occasionally acquired in association
with exoskeletal bones (secondary cartilages). Exoskeletal bones might be coated with
enameloid and dentine tissues, but whether such a trait represents the ancestral or
derived state is equivocal, on the sole basis of histological data. Alternatively,
perhaps exoskeletal bones in the ancestral condition were not associated with enameloid
and dentine tissues.

Figure 4. Evolution of the endoskeleton. Phylogenetic framework was adopted from 59]. Asterisks indicate paraphyletic groups. (A) Endoskeleton composed purely of cartilage. (B) Endoskeleton with perichondral ossification. (C) Endoskeleton with peri- and endochondral ossifications.

Developmental origins and cell lineages—mesoderm and neural crest in the vertebrate
cranium

Developmentally, the skeletal tissues of vertebrates have dual origins—the mesoderm
and neural crest. Platt (1893) 60] suggested that the ectodermally derived mesenchyme (that is, ectomesenchyme) contributes
to the cranial skeleton in basal vertebrates. De Beer (1958, 1971) 61],62] later used Platt’s notion to refute von Baer’s germ layer theory 63], because mesoderm generally was believed to be the main source of skeletal tissue
in animals.

The origination of part of the vertebrate cranium from the neural crest has been exemplified
through several experimental embryologic analyses involving amphibian and avian models
in which neural crest grafting experiments are possible (reviewed by 64],65]). Even in non-model vertebrate species, including lampreys, similar results have
been obtained 66],67] (also see 68],69]). The use of transgenic techniques has revealed the contribution of the neural crest
to the skull in teleosts and mammals (Figure 5) 70]-73]. It was previously thought that the rostral neural crest (cephalic crest) yielded
mesenchymal tissue throughout the bodies of vertebrates, whereas the posterior portion
(that is, the trunk crest) typically gave rise to a more limited repertoire of tissues,
including melanocytes and the peripheral nervous system 74]-77]. In the head, it has generally been accepted that the visceral arch skeleton (see
below) is derived from the neural crest 78] (reviewed by 79]), which however, is not yet completely exemplified for some of the visceral dermal
bones at the genetic level in the mouse (reviewed by 8]; Figure 5C).

Figure 5. Developmental origins of the dermal skull roof.(A and B) Different views of the neural crest. Noden (1982, 1984) 80],81] placed the neural crest-mesodermal boudary in the dermal skull roof in the rostral
part of the avian frontal (A), whereas Couly at al. (1993) 82] reported that the entire dermal skull roof is derived from the neural crest. Note
that the occipital represents an endoskeletal vertebral element secondarily assimilated
to the cranium in gnathostomes. (C) Developmental origins of the dermal skull roof and the posterior cranium in the mouse,
based on transgenic approaches by 70],72],83],84]. Neural crest-mesoderm boundary is located at the boundary between the frontal and
parietal. (D–G) Neural crest- and mesodermal origins of the cranial elements in zebrafish based on
transgenic techniques by Kague et al. (2012) 73]. Names of the bones were revised based on comparative osteology by 85],86]. Dorsal view of the chondrocranium (D), and left lateral (E), dorsal (F), and ventral (G) views of adult zebrafish. In these views, the elements colored grey are of mesodermal
origin. Note tha the neural crest-mesodermal boundary of the dermal skull roof is
found in the frontal of this animal. Abbreviations: boc, basioccipital; bp, basal
plate; cl, cleithrum; co, coracoid; d, dentary; e, ethmoid; eoc, exoccipital; fr,
frontal; hm, hyomandibula; ia, intercalar; iop, interopercle; ip, interparietal; k,
kinethomoid; le, lateral ethmoid; mpt, metapterygoid; mx, maxilla; nas, nasal; nc,
notochord; oc, otic capsule; occ, occipital; op, opercle; os, orbitosphenoid; par,
parietal; pe, preethmoid; pm, premaxilla; po, periotic; pop, preopercle; pp, postparietal;
pro, prootic; ps, parasphenoid; pto, pterotic; pts, pterosphenoid; q, quadrate; se,
supraethmoid; soc, supraoccipital; so, supraorbital; soc, supraoccipital; sop, subopercle;
sph, sphenotic; sq, squamosal; st, supratemporal; tc, trabecula; tma, taenia marginalis
anterior; tmp, taenia marginalis posterior; Redrawn from 8](A–C) and from 73](D–G).

In the context of comparative embryology and morphology, the cranium traditionally
has been divided into several components, primarily the dorsal and ventral moieties
(the neurocrania and viscerocrania, respectively) 43],79],87]-94]. The neurocrania and viscerocrania are both recognized as endoskeletons over which
a dermal covering, the dermatocranium, develops to encapsulate the entire endocranium.
As noted earlier, the endocranium forms as a cartilage precursor and either ossifies
through endochondral ossification to be replaced by bone, or degenerates (in cases
in which dermal bones can perform the same functions). The cartilaginous skull roof
in elasmobranchs is complete, but in animals in which the dermal skull roof is well
developed that part of the cartilaginous neurocranium typically is absent.

Like the cranium, the dermatocranium can be divided into dorsal and ventral components
corresponding to its neural and visceral elements. The cartilaginous neurocranium
was initially recognized as a rostral continuation of the vertebral column, its elements
being united and expanded to hold the enlarged brain. In contrast, the viscerocranium
is composed of serial and metameric visceral arch skeletons surrounding the pharynx.
In jawed vertebrates, one of the rostral elements is enlarged and divided dorsoventrally
into the upper and lower jaws. The developmental origins of these cranial components
have been, and remain, the focus of much debate.

According to Noden (1988)’s scheme 78], the neural crest-derived ectomesenchyme resides predominantly within the ventral
part of the pharyngular head, in the region in which the craniofacial structures will
form, whereas the majority of the cranial mesoderm is found more dorsally, lateral
to the notochord and surrounding the brain primordium 78] (reviewed by 8]). This arrangement prompts the speculation that the distinction between neurocrania
and viscerocrania will correspond to that of their embryonic cell lineages, i.e.,
mesoderm and neural crest. This seems reasonable, given that, like that of trunk somites,
chondrification of the mesoderm is understood to require signals that emanate from
the notochord. In contrast, the skeletogenesis of neural crest cells differs from
that of the paraxial mesoderm, and is highly dependent on epithelial–mesenchymal interactions
82] (reviewed by 95]). Although this explanation holds true for part of the cranium, it is contradicted
elsewhere.

First, the so-called cranial base is not entirely made of mesodermal cells—its rostral
portion (rostral to the position of hypophysis) is preformed as paired rods of cartilages
called trabeculae, which are derived from the neural crest 71],82],96] (reviewed by 97]; Figures 5D, 6A–C). Comparative embryologists have suggested that this structure represents visceral
arch skeletons that had been ancestrally developing rostral to the mandibular arch
(reviewed by 97]-99]). Although trabeculae in the cyclostomes are not homologous with those in jawed vertebrates,
it is now generally accepted that the rostral part of the neurocranium originates
from the neural crest throughout the vertebrate species 79],100],101] (also see 68],102]). Therefore, in a developmental sense, the endoskeletal neurocranium is a composite
structure, derived from both the mesoderm and cephalic neural crest. Its posterior
part, which originates mainly from a pair of longitudinal plates called parachordals,
is a mesodermal structure, except for the otic capsule, which is derived partly from
the neural crest. The parachordals secondarily incorporate segmented somitic (vertebrae-like)
materials to complete the posteriormost portion, the occipital region 43],90],103]-106]. In the chicken, and in other sauropsids as well, this part of the neurocranium contains
five somites 43],82]. Therefore, as far as this portion is concerned, the vertebrate cranium—like the
vertebral column—is segmented, as suggested by transcendental morphologists 2],107],108] (also see 109]).

Figure 6. Neural crest mapping of the anuran cranium.(A-C) Mapping data in Bombina orientalis based on DiI injection onto the neural fold of the neurula (A). From an experiment performed by Olsson and Hanken (1996) 110]. Origins and differentiation of three crest cell streams are colored in the right
neural fold (A), and dorsal (B) and ventral (C) views of larval chondrocranium. Trigeminal crest cells are colored red, hyoid crest
cells yellow, and circumpharyngeal crest cells blue. Numbers on the left neural fold
indicate sites of injections. Note that the trabecular plate (tp in B), generally derived from the premandibular crest cells, is mapped on the hyoid crest
in Bombina. (D-F) Fate-mapping of adult Xenopus cranium. Dorsal (D), ventral (E) views. Hyoid crest cells are distributed extensively in the sphenethmoidal region
of the cranium. (F) Dorsal view of the lower jaw. Note that a part of the articular (proximal end of
the Meckel’s cartilage) contains hyoid crest cells. Abbreviations: ac, alary cartilage;
bh, basihyal; C, origin of circumpharyngeal crest cells; cb, ceratobranchials; ch,
ceratohyal; ct, cornu trabecula; H, origin of hyoid crest cells; ir, infrarostral;
mc, Meckel’s cartilage; ns, nasal septum; oc, otic capsule; obl, oblique cartilage;
pao, planum antorbitale; pep, pars externa plectri; pip, pars interna plectri; pmp,
pars media plectri; posmp, posterior maxillary process; pq, palatoquadrate; pt, pterygoid;
q, quadrate; sn, solum nasi; sr, suprarostral; T, origin of trigeminal crest cells;
tp, trabecular plate; tym, tympanic annulus; vlp, ventrolateral process. Redrawn from
111],112].

The developmental origins of the dermatocranium are more enigmatic, creating an obstacle
to the understanding of its evolution, and vice versa (Figures 5, 6 and 7). According to classical theory, transcendental morphologists and others believed
that the anteroposterior segmentation of the roof of the dermatocranium merely reflected
the pattern of cranial mesodermal segments of hypothetical ancestors (reviewed by
92],113],114]; Figure 7A). However, this conventional assumption, which was captured through morphological
comparisons (before evolution was conceptualized), is incompatible with our current
understanding of developmental origins. Again—in all vertebrate embryos examined so
far—the neural crest contributes to both the visceral part of the calvarium and the
neural components of the dermatocranium.

Figure 7. Evolution of dermatocranial elements.(A) Traditional scheme of the dermal skull roof, based on the head segmentation scheme
of Jollie (1981) 113]. (B) Schematized prototype of the arthrodire dermal skull roof as suggested by Heintz
(1932) 115]. Homologies between various dermal elements in B and F are indicated by color. (C-F) Dermatocranium of Eustenopteron(C and D) and Entelognathus(E and F), lateral (C and E) and dorsal (D and F) views. Thick red lines represent lateral lines that correspond to patterns of some
dermal elements. Presumed homologous dermal elements are shown in the same color in
C and E and the left halves of D and F. On the right side of D and F, neural crest- and mesoderm-derived elements are differently colored according to
assumptions that the crest–mesoderm interface is primarily found between the frontal
and parietal bones (as in the mouse) and that postparietal homologues are consistently
derived from the neural crest in sarcopterygians (including tetrapods). C-F, redrawn from 59].

The dermal elements of the calvarium are likely patterned according to the lateral
line system, and thus the homology of these elements is, in aquatic forms, based on
the homology of lateral lines (see 59],114] and references therein; Figure 7C–F). Although the patterns of dermal bones and lateral lines are coupled developmentally,
it is unclear whether the lateral line induces the dermal bones, or vice versa (see
116]). Presumably the typical dermal bones found in fishes (including placoderms) became
secondarily sunken exoskeletal elements concomitant with the shift in developmental
interactions to induce membranous ossification in a deeper layer of the dermis, as
found in amniotes. Questions remain regarding homologies (evolutionary continuities)
of the dermal elements (reviewed by 8]), as well as their early evolution. The pattern of the dermal skull roof perhaps
was first established in placoderms 59] (Figure 7B–F; also see 115]), in which the topographic relationship between dermal bones and lateral lines seen
in modern vertebrates is recognizable, at least in part. From lines of circumstantial
evidence regarding neural crest contribution and its putative relationship with lateral
lines, it is unlikely that the dermal skull roof elements represent segmental organization
of the vertebrate head. The lateral lines are not induced as primordia with any segmental
prepatterning (for the developmental pattern of the placodes, see 117] and references therein); therefore, the dermal skull roof elements may form independently
of any segmental prepattern.

By constructing chick–quail chimeras, Noden found that the rostral part of the dermal
skull roof is derived from the neural crest, whereas the posterior arises from the
mesoderm 80],81],118],119] (Figure 5A). The boundary between these two cell lineages lies in the frontal bone (for the
homology of the avian frontal bone, see 8]). Similar results from a similar experiment were obtained by Le Lièvre (1978) 120]. However, Couly et al. (1993) 82] showed that the entire dermis, as well as the dermatocranial elements, is exclusively
of neural crest origin (Figure 5B). To date, systematic fate mapping of the avian craniofacial structures has not
been completed; the explanation underlying these inconsistent results remains unclear,
but may involve contamination by non-crest tissues or incomplete postsurgical wound
healing (summarized by 8]).

Regardless, the views of Couly et al. (1993) 82] once prevailed among zoologists and carried the expectation that the entire exoskeleton
of vertebrates—head and trunk—would be of neural crest origin (reviewed by 121]). Another finding that appeared to strengthen this assumption was that the differentiation
repertoire of the neural crest is not entirely predetermined differentially along
the anteroposterior axis (head versus trunk); heterotopically transplanted trunk neural
crest can exhibit skeletogenic potency in the head environment of the embryo 122] (also see 123] for a similar experiment; also see 124]). It was thus speculated that the trunk neural crest is normally suppressed from
differentiating into the exoskeleton in animals that have lost most of the postcranial
exoskeleton, which, however, can be reactivated under specific circumstances. In fact,
all exoskeletal elements in vertebrates, including the dermal skull roof, teleost
scales, lepidotrichia, and the extensive head shield in some fossil lineages such
as osteostracans and placoderms, were expected to originate from the neural crest
17]—despite the lack of any supporting evidence for this notion. This overly simplified
prediction was further extended to postulate the involvement of the neural crest in
the turtle shell, which had often been interpreted erroneously as an exoskeletal element
(see 12]; see above). Here, the mesoderm-crest duality was related to an in–out topography
of endo/exoskeletal parts in the neurocranium, not along the dorsoventral axis.

New embryonic technologies have apparently dispelled the above unsubstantiated assumptions.
Shimada et al. (2013) 77], for example, performed transplantations of somites and neural crest in medaka embryos
and convincingly showed that the trunk scales of this fish originate from the mesoderm,
not the neural crest. Analyses of transgenic lines of zebrafish by several other groups
yielded similar results 75],125]. However, several groups suspect that the neural crest contributes to the exoskeleton
of the trunk, for example, to the lepidotrichia of the caudal and dorsal fins in zebrafishes
73] and the turtle plastron 124],126]. Furthermore, a recent study tracing the lineages of transgenic cells revealed that
trunk neural crest cells do not generate a skeletogenic tissue (that is, ectomesenchyme)
76] although they have skeletogenic potential in the developing head 122]. These lines of evidence, in combination with the fossil evidence from placoderms
52],53] (see above), suggest that the exoskeleton of the trunk develops from the mesoderm
in the ancestral condition in the jawed vertebrates and that accretions of the enameloid
and dentine tissues (i.e., odontogenic component) to the trunk exoskeleton occurred
in many lineages, distinct from what had previously been hypothesized (e.g., 127]).

Consequently, the interface between the neural crest- and mesoderm-derived parts of
the exoskeleton again appears to be somewhere in the skull roof, and different results
regarding its specific location have been obtained via different experimental methods
in embryos of different taxa (reviewed by 8]; Figure 5A, B). Our current understanding regarding the origin of vertebrate skull roof is
therefore confused.

Transgenic technology was used to label crest-derived ectomesenchyme and its derivatives
in mice (Figure 5C) 30],70],72],83]. In this model, the Wnt-1 promoter was used to drive Cre to activate a reporter gene as a marker for all neural crest cells. This methodology
resulted in labeling of the nasal, frontal, and interparietal regions in addition
to the more ventrally located dermal elements, and the signal distribution was complementary
to the pattern obtained by using Mesp1–Cre/R26R to label mesodermal cell lineages (see 72]). This result resembles those of Noden (1978, 1982, 1983, 1984) 80],81],118],128] and Le Lièvre (1978) 120] in avian embryos (Figure 5A; Evans and Noden, 2006 119], subsequently confirmed these previous results by labeling mesoderm through retroviral
infection). Furthermore, these current and previous findings coincide perfectly if
we admit misidentification of the boundary between the frontal and parietal regions
in mammals and avians: the supraoccipital region is the dorsal portion of a mesodermal
element serially homologous with the vertebrae, and the interparietal region may not
be present in avians (for the homology and evolution of the interparietal region,
see 129] and references therein).

One consistent aspect in this conundrum is that every argument has been based on the
firm assumption that evolutionarily conserved bony elements should arise from fixed
(homologous) cell lineages in development. This assumption is, of course, profoundly
linked to the cell-autonomous and precommitted potency of the neural crest cells in
morphological skeletal patterning (see 118],130]-133]), which is not per se completely correct 128],134]. Accordingly, the comparative morphological understanding cannot easily be formulated
into a simple developmental scheme 8]; in particular, developmental understanding of the neural crest–mesodermal boundaries
in the dermatocranial roof is conspicuously unsure compared with that for the cranial
base. Several evolutionary scenarios, not always mutually exclusive, may explain the
situation regarding the origins of the dermatocranial roof:

1. Morphological homologies of bony elements and the cell lineages that give rise
to these elements are regulated at different, decoupled levels, and the bony elements
can be conserved through evolution independent from the cell lineages, which are apt
to change more rapidly.

2. The ancestral developmental pattern and cell-lineage origins of the dermatocranial
elements were established in various fossil taxa, which are reflected in some modern
taxa, and are secondarily modified in others, possibly because of the loss or fusion
of ancestral elements or the addition of new elements.

3. The dermatocranium (excluding the supraoccipital region) primarily was derived
from the cranial neural crest ancestrally, and new mesodermal elements intercalated
secondarily to accommodate adaptation to the expansion of the cranial vault in different
ways in each animal lineage, obliterating homologies between some bones (as suggested
in Figure 7, the parietal bone represents a newly inserted mesodermal element).

4. The dermatocranium (excluding the supraoccipital bone) was primarily derived from
the mesoderm ancestrally, and new crest-derived elements were intercalated secondarily
to accommodate adaptation to the expansion of the cranial vault in different ways
in each animal lineage, thus obliterating homologies of bones.

5. The pattern of dermal elements belongs to most variable parts of the vertebrate
body, and developmental constraints assure homologies of dermal elements only within
limited levels of taxa (orders, superfamilies, etc.; see 135]-137]; reviewed by 113]).

6. Mesodermal dermal elements were associated primarily with various lateral lines
in ancestral forms, and other elements were all derived from the neural crest (Figure 5D and F).

7. The lateral line-induced dermal elements in ancestors have been lost, and the tetrapod
dermatocranium, predominantly derived from the neural crest, has been newly reorganized
in each animal lineage in its unique way.

None of the above scenarios has been assessed experimentally to date, nor have discrepancies
among experimental embryologic data been reconciled. According to the third scenario,
the parietal would have to be regarded as a synapomorphy in crown gnathostomes, which
however, may be refuted by the fact that the majority of placoderms possess this bone
59].

The situation may be even more confusing than that presented. If the apparent inconsistency
in the mesoderm–neural crest boundary could be explained, it may turn out to be attributable
to a misnaming of bony elements; this could be resolved by morphological and developmental
reexamination of homologous relationships 111]. Unfortunately, however, this confusion may be destined to be insurmountable. Transgenic
and chimeric approaches have revealed that the cranium of the frog violates generally
accepted rules of development—that is, the developmental origins of the visceral arch
and craniofacial skeletons are not found in a canonical set of crest cell streams
that are divided into mandibular, hyoid, and branchial arch streams; instead, morphologically
homologous dermal elements are derived from inconsistent cell lineages in frog embryos
(Figure 6D-F) 111],138]. Therefore, the skeletal development of the frog demonstrates the decoupling of embryonic
patterns, cell lineages, and adult morphology in a very radical manner. It is conceivable
that, especially in animals that go through metamorphosis, insertion of larval stages
causes topographical shifts of the neural crest-derived chondrogenic cells that go
on to form adult skeletons (although this does not explain the hyoid crest-origin
of the prechordal cranium in amphibians as reported by Olsson and Hanken (1996) 110]). The same may be the case in the development of the dermal skull roof; the morphological
patterns and homologies may reside in the local environment of the embryos, such that
they become specified during a later phase of development. This potential influence
of the local environment recalls the study of Schneider (1999) 139], in which cranial neural crest from the quail embryo was ectopically grafted within
mesenchymal populations destined to form the skull wall in the chicken embryo. In
resulting chimeras, these grafted cells gave rise to a skeletal element, which in
birds is normally derived from the mesoderm. There are many more examples that demonstrate
the importance of local tissue interaction in the specification of bony elements 128],140] (also see a review by 92]) by showing potential shifts of cell lineages and populations to generate morphologically
conserved skeletal patterns during evolution.

A similar situation is seen in the apparent discrepancy of the neural crest contributions
to the pectoral girdle bones between amniotes 30],141] and anamniotes 73],142]. It is generally accepted that, within the mesodermal cell population, the developmental
basis providing the skeletal identities of the digits shifted between non-homologous
primordia in the evolution from dinosaurs to birds (frame-shift hypothesis) 143]-145]. No accounts contradict the possibility that skeletal identities similarly shift
between neural crest and mesodermal cell populations.

Perspectives—beyond the complexity

The vertebrate skull initially attracted the attention of zoologists because of its
complex and elegant morphology, but its complexity clearly exceeds all expectations.
Theories regarding skeletogenesis and skeletal anatomy and its evolution have been—and
still are—fraught with confusion, which never seems to be resolved easily. This situation
cannot be ascribed only to the misuse of terminology in non-comparable contexts of
discussion; it also reflects the complexity of the developmental and evolutionary
diversity of the vertebrate skeletal system per se. Nor is the current developmental
understanding of skeletogenesis formulated in an orderly way into the pattern of embryos
and cell lineages.

The dilemma described here is tightly linked to the confusion regarding the concept
of homology. As noted earlier, morphological homology was in the past reduced to its
developmental origins in cell lineages and germ layers, as seen in von Baer’s germ
layer theory (reviewed by 6]). This theory was refuted as being based on inaccurate concepts of histogenesis,
including the concept that skeletogenic differentiation can take place equally in
mesodermal and ectodermal (neural crest) cell lineages. Still, the neural crest –
mesoderm distinction, as well as endochondral–membranous ossifications, was expected
to coincide with specific morphological components of the skull—a belief that could
be viewed as a modified version of the germ layer theory. Alternatively, a similar
reductionist argument was once widespread with a vague expectation in the dawn of
evolutionary developmental biology; namely, that morphologically homologous structures
should be patterned through certain unchanged infrastructures, like function of evolutionarily
conserved sets of regulatory genes or gene regulatory networks.

Expectations such as these often come true, as typically exemplified by the isomorphic
shifts of vertebral formula and Hox code 146] (also see 147]). In this context, the positional identities of vertebrae along the anteroposterior
axis of the vertebral column (such as occipital, cervical, thoracic, lumbar, and sacral
in mammals) coincide precisely with the expression domains of Hox genes in the prevertebral
anlagen, and under this Hox-code-mediated specification the number of segments can
vary during evolution (for variable numbers of vertebrae, see 147]). In this case, morphological homology is reduced to the regulation of homologous
Hox genes. Similar situations, in which the homology between structure and gene expression
is tightly conserved, include the expression of homeobox genes and primordial segments
in the developing vertebrate brain, differentiation of somite-derivatives, and dorsoventral
specification of the neural tube (reviewed by 148]). In an extreme reductionist argument that is focused on genes, cell-type identities,
which are classified by transcript repertoire (that is, molecular fingerprinting of
cell types), are comparable among phyla, even between the vertebrate- and annelid
body plans, for example, at the level of single neurons 149].

Unfortunately, relationships among homologies at different hierarchal levels—namely
at the levels of morphology, histogenesis, cell lineage and genes—remain murky, as
homologous skeletal elements can arise from different or shifted cell lineages throughout
evolution by means of different mechanisms of development, thus challenging the criteria
for morphological homology (e.g., 5],150],151]; reviewed by 152]). Inconsistency of this type occurs in various phenomena of organogenesis, in which
homologous structures are patterned by the actions of non-homologous regulatory genes
in each animal lineage 153],154]. In the evolutionary context, there are at least two significant effects worth considering.

One effect is evolutionary novelty and simultaneous loss of homology: the shift in
developmental interactions in time and place result in novel regulation of skeletogenic
genes, leading to a skeletal pattern incomparable to that in the ancestor. The other
effect is developmental drift: the developmental process and mechanisms would shift
without changing the readout of the shifted developmental process, thus maintaining
the ancestral morphological pattern in the adult. De Beer (1958) 61] noted the heterochronic factor behind similar phenomena, for example, in the creation
of the larval stage in development. One of the most conspicuous examples is found
in the columella auris (that is, hyomandibular bone) of certain frogs. In Xenopus, the anlage of the columella never appears during the larval stage, but arises during
metamorphosis 155],156]. In the mouse, the stapes (the homologue of this cartilage bone) is patterned during
embryogenesis in the dorsal part of the second pharyngeal arch and is specified through
the upregulation of Hoxa2131] in the ectomesenchyme. In Xenopus, homology of this skeletal element appears to be maintained—albeit decoupled from
the Hox code— and its differentiation is even suggestive of new involvement of the
thyroid hormone in the rewired regulatory network. We have already seen, in frog development,
how morphologically homologous cranial elements arise from cell populations or pharyngeal
arches not identical to those in other vertebrate groups.

It is true that the morphological homology of skeletal elements cannot be reduced
directly to the developmental program, or homology of genes, involved in the generation
of homologous structures. However, insofar as the criteria for homology largely rest
on the relative positions of organs (reviewed by 6]), developmental patterns may, to some extent, explain the impetus behind the manifestation
of the homologous patterns. This explanation is especially plausible given that the
relative positions suggest evolutionarily maintained topography of cell populations
and tissues, which act as the bases for embryonic interactions to establish the identities
of the skeletal anlagen, especially through the upregulation of specific sets of transcription
factor-encoding genes. Here we recall the experiment of Schneider (1999) 139] to show that neural crest-derived ectomesenchyme and cephalic mesoderm can be exchanged
to generate morphologically normal chondrocranium. This experiment indicates that
the developmental factor(s) for the morphological homology resides in the “position”
in the embryo, not in the embryonic cell lineages. Consistently, a same set of gene
expressions has been detected in endochondral ossifications of mesenchymal condensations
both derived from neural crest and mesodermal cells 157]. This implication stands in conspicuous contrast to the fact that species-specific
shape appears to evolve in the developmental program associated with specific cell
lineages 130],133].

To understand the mechanistic background for the burden of development, we have to
understand how selective pressure—especially stabilizing selection—at the phenotypic
level (adaptation) acts on the developmental program exerted from the genome. In other
words, we must identify parts or elements of the developmental program (for example,
gene regulatory networks, modules, sets of regulatory genes and their regulatory elements)
that can or cannot change when certain fixed phenotypic patterns are favored. These
efforts will uncover the aspects of the developmental program that are resistant to
change and those that are apt to change during evolution. In evolution, adaptation
and constraint cannot be discriminated a priori 158],159]. The key to discriminating between these two causal relationships behind evolution
is provided abductively through historical and experimental analyses of the correlation
between phenotype and the developmental program behind it (for example, skeletal elements
can be considered as a phenotype of a skeletal system). The patterns that allow minimal
shifts have been recognized to result from developmental constraint. The concept of
developmental constraint has not yet been explained thoroughly, but taxon-specific
conserved patterns of embryogenesis have been recognized as the so-called “phylotype,”
which tends to appear in the organogenetic stage of development (“phylotypic stage”
160]).

In transcendental morphology, the phylotype (pharyngula in vertebrates) has been viewed
as an embodiment of the conceptual archetype, a shared morphology of the embryos of
animals belonging to the vertebrates, from which various types of adult morphologies
can be derived 63]. This “derivation,” however, does not necessarily refer to the phylogenetic evolutionary
process, but rather to observers’ perceptions of homologous patterns and their developmental
changes. Morphologically, it is true that the pharyngula-stage embryo in vertebrates
is the stage at which the basic body plan, or a set of homologous anlagen, of this
animal group becomes established. In the evo-devo context, the phylotypic stage of
vertebrate development is recognized as the stage at which so-called tool-kit genes
(typically the Hox code) are expressed most conspicuously during development, thus
providing the mechanistic bases to explain the significance of this conserved embryonic
pattern 160]. Recent transcriptome analyses have shown that the most similar gene expression profiles
coincide with the phylotypic stage 161]. Importantly, as indicated by genomic analyses of turtles, the evolutionarily novel
patterns of the skeletal system in vertebrates appear to arise through spatiotemporal
developmental shifts after the establishment of the above-noted phylotype 162]. Taking into consideration the shifts in morphological homologies—specifically the
developmental patterns and processes involved in patterning of the evolutionarily
fixed patterns of craniofacial elements—it seems likely that the cranial pattern is
specified late relative to the specification of the phylotype. This delay suggests
the presence of another developmental constraint, which is more or less uncoupled
from those needed to maintain the phylotype. The search for such taxon-specific constraints,
as well as their mechanistic importance, is an intriguing focus for future evo-devo
studies. The results likely would further our understanding of the synapomorphies
used in the reconstruction of evolutionary history.