Developmental evidence for serial homology of the vertebrate jaw and gill arch skeleton

Paleo-evo-devo implications of a revised conceptualization of enameloids and enamels

Understanding the origin and evolution of the mineralized skeleton is crucial for unravelling vertebrate history. However, several limitations hamper our progress. The first obstacle is the lack of uniformity and clarity in the literature for the definition of the tissues of concern, especially of enameloid(s) and enamel(s), resulting in ambiguous terminology and inconsistencies among studies. Moreover, the identification criteria currently employed to characterize hypermineralized tissues in extinct taxa, such as the presence or absence of tubules for enameloids, may lead to unsupported conclusions. We suggest that comparative developmental studies may be key to unambiguous terminology, truly diagnostic identification criteria and developmentally informed evolutionary hypotheses. We exemplify this approach by: (i) introducing a new conceptual framework for enameloid(s) and enamel(s), with clear terminologies, definitions and interactions between concepts; (ii) suggesting more rigorous ways to identify tissues, based on the observation of defining or additional properties, as well as on the comparison of developmental scenarios when possible; (iii) constructing a clear phylogenetic framework to discuss their homologies and highlighting possible transitions between these tissues; and by (iv) proposing developmental models that explain both enamel and enameloid formation, and suggest possible transitions between them.

Paired fins in vertebrate evolution and ontogeny

The origin of paired appendages became one of the most important adaptations of vertebrates, allowing them to lead active lifestyles and explore a wide range of ecological niches. The basic form of paired appendages in evolution is the fins of fishes. The problem of paired appendages has attracted the attention of researchers for more than 150 years. During this time, a number of theories have been proposed, mainly based on morphological data, two of which, the Balfour-Thacher-Mivart lateral fold theory and Gegenbaur's gill arch theory, have not lost their relevance. So far, however, none of the proposed ideas has been supported by decisive evidence. The study of the evolutionary history of the appearance and development of paired appendages lies at the intersection of several disciplines and involves the synthesis of paleontological, morphological, embryological, and genetic data. In this review, we attempt to summarize and discuss the results accumulated in these fields and to analyze the theories put forward regarding the prerequisites and mechanisms that gave rise to paired fins and limbs in vertebrates.

DLX gene expression in the developing chick pharyngeal arches and relationship to endothelin signaling and avian jaw patterning

BACKGROUND

A hinged jaw that articulates with the skull base is a striking feature of the vertebrate head and has been greatly modified between, and within, vertebrate classes. Genes belonging to the DLX homeobox family are conserved mediators of local signaling pathways that distinguish the dorsal and ventral aspects of the first pharyngeal arch. Specifically, a subset of DLX genes are expressed in the cranial neural crest-derived mandibular ectomesenchyme in response to ventral endothelin signaling, an important step that confers the first arch with maxillary and mandibular identities. Downstream targets of DLX genes then execute the morphogenetic processes that lead to functional jaws. Identifying lineage-specific variations in DLX gene expression and the regulatory networks downstream of DLX action is necessary to understand how different kinds of jaws evolved.

RESULTS

Here, we describe and compare the expression of all six DLX genes in the chick pharyngeal arches, focusing on the period of active patterning in the first arch. Disruption of endothelin signaling results in the down-regulation of ventral-specific DLX genes and confirms their functional role in avian jaw patterning.

CONCLUSIONS

This expression resource will be important for comparative embryology and for identifying synexpression groups of DLX-regulated genes in the chick.

Protein-protein interaction network module changes associated with the vertebrate fin-to-limb transition

Evolutionary phenotypic transitions, such as the fin-to-limb transition in vertebrates, result from modifications in related proteins and their interactions, often in response to changing environment. Identifying these alterations in protein networks is crucial for a more comprehensive understanding of these transitions. However, previous research has not attempted to compare protein-protein interaction (PPI) networks associated with evolutionary transitions, and most experimental studies concentrate on a limited set of proteins. Therefore, the goal of this work was to develop a network-based platform for investigating the fin-to-limb transition using PPI networks. Quality-enhanced protein networks, constructed by integrating PPI networks with anatomy ontology data, were leveraged to compare protein modules for paired fins (pectoral fin and pelvic fin) of fishes (zebrafish) to those of the paired limbs (forelimb and hindlimb) of mammals (mouse). This also included prediction of novel protein candidates and their validation by enrichment and homology analyses. Hub proteins such as shh and bmp4, which are crucial for module stability, were identified, and their changing roles throughout the transition were examined. Proteins with preserved roles during the fin-to-limb transition were more likely to be hub proteins. This study also addressed hypotheses regarding the role of non-preserved proteins associated with the transition.

Rhythmic chew cycles with distinct fast and slow phases are ancestral to gnathostomes

Intra-oral food processing, including chewing, is important for safe swallowing and efficient nutrient assimilation across tetrapods. Gape cycles in tetrapod chewing consist of four phases (fast open and -close, and slow open and -close), with processing mainly occurring during slow close. Basal aquatic-feeding vertebrates also process food intraorally, but whether their chew cycles are partitioned into distinct phases, and how rhythmic their chewing is, remains unknown. Here, we show that chew cycles from sharks to salamanders are as rhythmic as those of mammals, and consist of at least three, and often four phases, with phase distinction occasionally lacking during jaw opening. In fishes and aquatic-feeding salamanders, fast open has the most variable duration, more closely resembling mammals than basal amniotes (lepidosaurs). Across ontogenetically or behaviourally mediated terrestrialization, salamanders show a distinct pattern of the second closing phase (near-contact) being faster than the first, with no clear pattern in partitioning of variability across phases. Our results suggest that distinct fast and slow chew cycle phases are ancestral for jawed vertebrates, followed by a complicated evolutionary history of cycle phase durations and jaw velocities across fishes, basal tetrapods and mammals. These results raise new questions about the mechanical and sensorimotor underpinnings of vertebrate food processing. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

The genetics-morphology-behavior trifecta: Unraveling the single greatest limitation affecting our understanding of chondrichthyan evolution

Sharks, rays, and chimaera form the clade Chondrichthyes, an ancient group of morphologically and ecologically diverse vertebrates that has played an important role in our understanding of gnathostome evolution. Increasingly, studies seek to investigate evolutionary processes operating within the chondrichthyan crown group, with the broad aim of understanding the driving forces behind the vast phenotypic diversity observed among its constituent taxa. Genetic, morphological, and behavioral studies have all contributed to our understanding of phenotypic evolution yet are typically considered in isolation in the context of Chondrichthyes. In this viewpoint, I discuss why such isolation is prevalent in the literature, how it constrains our understanding of evolution, and how it might be overcome. I argue that integrating these core fields of organismal biology is vital if we are to understand the evolutionary processes operating in contemporary chondrichthyan taxa and how such processes have contributed to past phenotypic evolution. Despite this, the necessary tools to overcome this major limitation already exist and have been applied to other taxa.

Vertebrate origins are informed by larval lampreys (ammocoetes): a response to Miyashita et al., 2021

This paper addresses a recent claim by Miyashita and co-authors that the filter-feeding larval lamprey is a new evolutionary addition to the lamprey life-cycle and does not provide information about early vertebrates, in contrast to the traditional view that this ammocoete stage resembles the first vertebrates. The evidence behind this revolutionary claim comes from fossil lampreys from 360–306 Mya that include young stages – even yolk-sac hatchlings – with adult (predacious) feeding structures. However, the traditional view is not so easily dismissed. The phylogeny on which the non-ammocoete theory is based was not tested in a statistically meaningful way. Additionally, the target article did not consider the known evidence for the traditional view, namely that the complex filter-feeding structures are highly similar in ammocoetes and the invertebrate chordates, amphioxus and tunicates. In further support of the traditional view, I show that ammocoetes are helpful for reconstructing the first vertebrates and the jawless, fossil stem gnathostomes called ostracoderms – their pharynx, oral cavity, mouth opening, lips and filter-feeding mode (but, ironically, not their mandibular/jaw region). From these considerations, I offer a scenario for the evolution of vertebrate life-cycles that fits the traditional, ammocoete-informed theory and puts filter feeding at centre stage.

First observation of the mating, egg-laying and hatching behaviour of a captive female Kong skate, Okamejei kenojei (Müller & Henle, 1841)

This study provides a novel record of the reproductive behaviour of the Kong skate (Okamejei kenojei) in captivity. These skates were found to mate and deposit eggs at a temperature of 16.5 ± 0.5°C. The results showed that 76.13% of the eggs possessed one yolk, 0.77% of the eggs possessed two yolks and 23.11% of the eggs had no yolk (N = 1043). The deposition of non-yolk and double-yolk eggs was random. A total of 100 eggs were collected. After nearly 92 ± 5 days of incubation, 28 eggs failed to hatch, and 72 skates were successfully hatched with a female-to-male ratio of 1:1 (P > 0.05). The results enrich our knowledge of the reproduction in cartilaginous fishes and can inform management and conservation strategies for this species.

“Arch”-etyping vertebrates

Cellular details of gill arches in Cambrian fossils reignite a centuries-old debate

The pseudobranch of jawed vertebrates is a mandibular arch-derived gill

The pseudobranch is a gill-like epithelial elaboration that sits behind the jaw of most fishes. This structure was classically regarded as a vestige of the ancestral gill arch-like condition of the gnathostome jaw. However, more recently, hypotheses of jaw evolution by transformation of a gill arch have been challenged, and the pseudobranch has alternatively been considered a specialised derivative of the second (hyoid) pharyngeal arch. Here, we demonstrate in the skate (Leucoraja erinacea) that the pseudobranch does, in fact, derive from the mandibular arch, and that it shares gene expression features and cell types with gills. We also show that the skate mandibular arch pseudobranch is supported by a spiracular cartilage that is patterned by a shh-expressing epithelial signalling centre. This closely parallels the condition seen in the gill arches, where cartilaginous appendages called branchial rays, which support the respiratory lamellae of the gills, are patterned by a shh-expressing gill arch epithelial ridge. Together with similar discoveries in zebrafish, our findings support serial homology of the pseudobranch and gills, and an ancestral origin of gill arch-like anatomical features from the gnathostome mandibular arch.

Summary: The skate pseudobranch is a gill serial homologue and reveals the ancestral gill arch-like nature of the jawed vertebrate mandibular arch.

Distinct proliferative and middle ear skeletal-patterning functions for SHH-expressing epithelia in the chick hyoid arch

During chick craniofacial development, the second (hyoid) pharyngeal arch expands to close the neck and gives rise to skeletal elements, including the columella of the middle ear (a homologue of the mammalian stapes). Sonic hedgehog (SHH) signalling has been implicated in hyoid arch expansion and columella formation, but spatial and temporal aspects of these signalling interactions within the hyoid arch remain poorly understood. Here, we show that SHH is initially expressed in the posterior endoderm of the hyoid arch, and that this domain subsequently splits into a distal domain at the site of arch expansion (the posterior epithelial margin, PEM), and a proximal domain that lines the foregut (the proximal hyoid epithelium, PHE). Pharmacological manipulations and heterotopic grafting experiments demonstrate that SHH signalling is required for hyoid arch expansion and skeletogenesis, and reveal distinct roles for the PEM and PHE in these processes. The PEM promotes mesenchymal cell proliferation during arch expansion but is not sufficient to repattern the columella. Conversely, the PHE promotes mesenchymal cell survival, and PHE grafts induce partial duplication of the columella. This work demonstrates crucial and distinct roles for endodermal SHH signalling in hyoid arch morphogenesis and patterning of the middle ear skeleton.

Big insight from the little skate: Leucoraja erinacea as a developmental model system

The vast majority of extant vertebrate diversity lies within the bony and cartilaginous fish lineages of jawed vertebrates. There is a long history of elegant experimental investigation of development in bony vertebrate model systems (e.g., mouse, chick, frog and zebrafish). However, studies on the development of cartilaginous fishes (sharks, skates and rays) have, until recently, been largely descriptive, owing to the challenges of embryonic manipulation and culture in this group. This, in turn, has hindered understanding of the evolution of developmental mechanisms within cartilaginous fishes and, more broadly, within jawed vertebrates. The little skate (Leucoraja erinacea) is an oviparous cartilaginous fish and has emerged as a powerful and experimentally tractable developmental model system. Here, we discuss the collection, husbandry and management of little skate brood stock and eggs, and we present an overview of key stages of skate embryonic development. We also discuss methods for the manipulation and culture of skate embryos and illustrate the range of tools and approaches available for studying this system. Finally, we summarize a selection of recent studies on skate development that highlight the utility of this system for inferring ancestral anatomical and developmental conditions for jawed vertebrates, as well as unique aspects of cartilaginous fish biology.

Pupil dilation and constriction in the skate Leucoraja erinacea in a simulated natural light field

The skate Leucoraja erinacea has an elaborately shaped pupil, whose characteristics and functions have received little attention. The goal of our study was to investigate the pupil response in relation to natural ambient light intensities. First, we took a recently developed sensory–ecological approach, which gave us a tool for creating a controlled light environment for behavioural work: during a field survey, we collected a series of calibrated natural habitat images from the perspective of the skates' eyes. From these images, we derived a vertical illumination profile using custom-written software for quantification of the environmental light field (ELF). After collecting and analysing these natural light field data, we created an illumination set-up in the laboratory, which closely simulated the natural vertical light gradient that skates experience in the wild and tested the light responsiveness – in particular the extent of dilation – of the skate pupil to controlled changes in this simulated light field. Additionally, we measured pupillary dilation and constriction speeds. Our results confirm that the skate pupil changes from nearly circular under low light to a series of small triangular apertures under bright light. A linear regression analysis showed a trend towards smaller skates having a smaller dynamic range of pupil area (dilation versus constriction ratio around 4-fold), and larger skates showing larger ranges (around 10- to 20-fold). Dilation took longer than constriction (between 30 and 45 min for dilation; less than 20 min for constriction), and there was considerable individual variation in dilation/constriction time. We discuss our findings in terms of the visual ecology of L. erinacea and consider the importance of accurately simulating natural light fields in the laboratory.

Shark and ray genomics for disentangling their morphological diversity and vertebrate evolution

Developmental studies of sharks and rays (elasmobranchs) have provided much insight into the process of morphological evolution of vertebrates. Although those studies are supposedly fueled by large-scale molecular sequencing information, whole-genome sequences of sharks and rays were made available only recently. One compelling difficulty of elasmobranch developmental biology is the low accessibility to embryonic study materials and their slow development. Another limiting factor is the relatively large size of their genomes. Moreover, their large body sizes restrict sustainable captive breeding, while their high body fluid osmolarity prevents reproducible cell culturing for in vitro experimentation, which has also limited our knowledge of their chromosomal organization for validation of genome sequencing products. This article focuses on egg-laying elasmobranch species used in developmental biology and provides an overview of the characteristics of the shark and ray genomes revealed to date. Developmental studies performed on a gene-by-gene basis are also reviewed from a whole-genome perspective. Among the popular regulatory genes studied in developmental biology, I scrutinize shark homologs of Wnt genes that highlight vanishing repertoires in many other vertebrate lineages, as well as Hox genes that underwent an unexpected modification unique to the elasmobranch lineage. These topics are discussed together with insights into the reconstruction of developmental programs in the common ancestor of vertebrates and its subsequent evolutionary trajectories that mark the features that are unique to, and those characterizing the diversity among, cartilaginous fishes.

Conserved and unique transcriptional features of pharyngeal arches in the skate (Leucoraja erinacea) and evolution of the jaw

The origin of the jaw is a long-standing problem in vertebrate evolutionary biology. Classical hypotheses of serial homology propose that the upper and lower jaw evolved through modifications of dorsal and ventral gill arch skeletal elements, respectively. If the jaw and gill arches are derived members of a primitive branchial series, we predict that they would share common developmental patterning mechanisms. Using candidate and RNAseq/differential gene expression analyses, we find broad conservation of dorsoventral (DV) patterning mechanisms within the developing mandibular, hyoid, and gill arches of a cartilaginous fish, the skate (Leucoraja erinacea). Shared features include expression of genes encoding members of the ventralizing BMP and endothelin signaling pathways and their effectors, the joint markers nkx3.2 and gdf5 and prochondrogenic transcription factor barx1, and the dorsal territory marker pou3f3. Additionally, we find that mesenchymal expression of eya1/six1 is an ancestral feature of the mandibular arch of jawed vertebrates, whereas differences in notch signaling distinguish the mandibular and gill arches in skate. Comparative transcriptomic analyses of mandibular and gill arch tissues reveal additional genes differentially expressed along the DV axis of the pharyngeal arches, including scamp5 as a novel marker of the dorsal mandibular arch, as well as distinct transcriptional features of mandibular and gill arch muscle progenitors and developing gill buds. Taken together, our findings reveal conserved patterning mechanisms in the pharyngeal arches of jawed vertebrates, consistent with serial homology of their skeletal derivatives, as well as unique transcriptional features that may underpin distinct jaw and gill arch morphologies.

Gene coexpression networks reveal molecular interactions underlying cichlid jaw modularity

Background

The oral and pharyngeal jaw of cichlid fishes are a classic example of evolutionary modularity as their functional decoupling boosted trophic diversification and contributed to the success of cichlid adaptive radiations. Most studies until now have focused on the functional, morphological, or genetic aspects of cichlid jaw modularity. Here we extend this concept to include transcriptional modularity by sequencing whole transcriptomes of the two jaws and comparing their gene coexpression networks.

Results

We show that transcriptional decoupling of gene expression underlies the functional decoupling of cichlid oral and pharyngeal jaw apparatus and the two units are evolving independently in recently diverged cichlid species from Lake Tanganyika. Oral and pharyngeal jaw coexpression networks reflect the common origin of the jaw regulatory program as there is high preservation of gene coexpression modules between the two sets of jaws. However, there is substantial rewiring of genetic architecture within those modules. We define a global jaw coexpression network and highlight jaw-specific and species-specific modules within it. Furthermore, we annotate a comprehensive in silico gene regulatory network linking the Wnt and AHR signalling pathways to jaw morphogenesis and response to environmental cues, respectively. Components of these pathways are significantly differentially expressed between the oral and pharyngeal jaw apparatus.

Conclusion

This study describes the concerted expression of many genes in cichlid oral and pharyngeal jaw apparatus at the onset of the independent life of cichlid fishes. Our findings suggest that – on the basis of an ancestral gill arch network—transcriptional rewiring may have driven the modular evolution of the oral and pharyngeal jaws, highlighting the evolutionary significance of gene network reuse. The gene coexpression and in silico regulatory networks presented here are intended as resource for future studies on the genetics of vertebrate jaw morphogenesis and trophic adaptation.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01787-9.

New Species Can Broaden Myelin Research: Suitability of Little Skate, Leucoraja erinacea

Although myelinated nervous systems are shared among 60,000 jawed vertebrates, studies aimed at understanding myelination have focused more and more on mice and zebrafish. To obtain a broader understanding of the myelination process, we examined the little skate, Leucoraja erinacea. The reasons behind initiating studies at this time include: the desire to study a species belonging to an out group of other jawed vertebrates; using a species with embryos accessible throughout development; the availability of genome sequences; and the likelihood that mammalian antibodies recognize homologs in the chosen species. We report that the morphological features of myelination in a skate hatchling, a stage that supports complex behavioral repertoires needed for survival, are highly similar in terms of: appearances of myelinating oligodendrocytes (CNS) and Schwann cells (PNS); the way their levels of myelination conform to axon caliber; and their identity in terms of nodal and paranodal specializations. These features provide a core for further studies to determine: axon-myelinating cell communication; the structures of the proteins and lipids upon which myelinated fibers are formed; the pathways used to transport these molecules to sites of myelin assembly and maintenance; and the gene regulatory networks that control their expressions.

Embryonic origin and serial homology of gill arches and paired fins in the skate, Leucoraja erinacea

Paired fins are a defining feature of the jawed vertebrate body plan, but their evolutionary origin remains unresolved. Gegenbaur proposed that paired fins evolved as gill arch serial homologues, but this hypothesis is now widely discounted, owing largely to the presumed distinct embryonic origins of these structures from mesoderm and neural crest, respectively. Here, we use cell lineage tracing to test the embryonic origin of the pharyngeal and paired fin skeleton in the skate (Leucoraja erinacea). We find that while the jaw and hyoid arch skeleton derive from neural crest, and the pectoral fin skeleton from mesoderm, the gill arches are of dual origin, receiving contributions from both germ layers. We propose that gill arches and paired fins are serially homologous as derivatives of a continuous, dual-origin mesenchyme with common skeletogenic competence, and that this serial homology accounts for their parallel anatomical organization and shared responses to axial patterning signals.

Evolution of vertebrate gill covers via shifts in an ancient Pou3f3 enhancer

Whereas the gill chambers of jawless vertebrates open directly into the environment, jawed vertebrates evolved skeletal appendages that drive oxygenated water unidirectionally over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single large gill cover in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here, we find that these divergent patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs. We identify a deeply conserved Pou3f3 arch enhancer present in humans through sharks but undetectable in jawless fish. Minor differences between the bony and cartilaginous fish enhancers account for their restricted versus pan-arch expression patterns. In zebrafish, mutation of Pou3f3 or the conserved enhancer disrupts gill cover formation, whereas ectopic pan-arch Pou3f3b expression generates ectopic skeletal elements resembling the multimeric covers of cartilaginous fishes. Emergence of this Pou3f3 arch enhancer >430 Mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution.

Development of the lamprey velum and implications for the evolution of the vertebrate jaw

BACKGROUND

The vertebrate jaw is thought to have evolved through developmental modification of the mandibular arch. An extant jawless vertebrate, the lamprey, possesses a structure called "velum"-a mandibular arch derivative-in addition to the oral apparatus. This leads us to assess the velum's possible contribution to the evolution of jaws.

RESULTS

The velar muscles develop from progenitor cells distinct from those from which the oral muscles develop. In addition, the oral and velar regions originate from the different sub-population of the trigeminal neural crest cells (NCCs): the former region receives NCCs from the midbrain, whereas the latter region receives NCCs from the anterior hindbrain. The expression of patterning genes (eg, DlxA and MsxA) is activated at a later developmental stage in the velum compared to the oral region, and more importantly, in different cells from those in the oral region.

CONCLUSION

The lamprey mandibular arch consists of two developmental units: the anterior oral unit and the posterior velar unit. Because structural elements of the lamprey velum may be homologous to the jaw, the evolution of vertebrate jaws may have occurred by the velum being released from its functional roles in feeding or respiration in jawless vertebrates.

nkx3.2 mutant zebrafish accommodate jaw joint loss through a phenocopy of the head shapes of Paleozoic jawless fish

The vertebrate jaw is a versatile feeding apparatus. To function, it requires a joint between the upper and lower jaws, so jaw joint defects are often highly disruptive and difficult to study. To describe the consequences of jaw joint dysfunction, we engineered two independent null alleles of a single jaw joint marker gene, nkx3.2, in zebrafish. These mutations caused zebrafish to become functionally jawless via fusion of the upper and lower jaw cartilages (ankylosis). Despite lacking jaw joints, nkx3.2 mutants survived to adulthood and accommodated this defect by: (a) having a remodeled skull with a fixed open gape, reduced snout and enlarged branchial region; and (b) performing ram feeding in the absence of jaw-generated suction. The late onset and broad extent of phenotypic changes in the mutants suggest that modifications to the skull are induced by functional agnathia, secondarily to nkx3.2 loss of function. Interestingly, nkx3.2 mutants superficially resemble ancient jawless vertebrates (anaspids and furcacaudiid thelodonts) in overall head shape. Because no homology exists in individual skull elements between these taxa, the adult nkx3.2 phenotype is not a reversal but rather a convergence due to similar functional requirements of feeding without moveable jaws. This remarkable analogy strongly suggests that jaw movements themselves dramatically influence the development of jawed vertebrate skulls. Thus, these mutants provide a unique model with which to: (a) investigate adaptive responses to perturbation in skeletal development; (b) re-evaluate evolutionarily inspired interpretations of phenocopies generated by gene knockdowns and knockouts; and (c) gain insight into feeding mechanics of the extinct agnathans.

A proposed extension to the elongated styloid process definition: A morphological study with high-resolution tomography computer

The objective of the present study was to evaluate the morphology and angulation of the styloid process (SP), analyzing results stratified by gender, side and age on asymptomatic patients. We retrospectively analyzed 99 high-resolution computed tomography study images from asymptomatic patients. The images were assessed intra-observatory by a head and neck expert radiologist. Data for length, morphology, and angulation in a coronal and sagittal plane were recorded and stratified by age and gender. Morphology was classified according to the Langlais modified by Guimares classification. The mean lengths were 31.67±0.97mm and 31.64±0.90mm for the right and left sides respectively. Using the Langlais modified by Guimares classification, the normal type was the most prevalent and without a statistically significant difference when comparing between genders. A total of 27.6% presented a morphologically elongated SP (>25mm of continuous process), 49.5% presented a radiologically elongated SP (>30mm), and a total of 9.59% had a longer length than the proposed≤45mm. The right transverse angle was greater in men than women, and a statistically significant difference was found (P=0.010). We show the morphological variability of the SP. Although our results are reported with the traditional definition, the high prevalence supports the need for a new definition of elongated SP and a normal angulation ranges.

Functional genetic analysis in a jawless vertebrate, the sea lamprey: insights into the developmental evolution of early vertebrates

Lampreys and hagfishes are the only surviving relicts of an ancient but ecologically dominant group of jawless fishes that evolved in the seas of the Cambrian era over half a billion years ago. Because of their phylogenetic position as the sister group to all other vertebrates (jawed vertebrates), comparisons of embryonic development between jawless and jawed vertebrates offers researchers in the field of evolutionary developmental biology the unique opportunity to address fundamental questions related to the nature of our earliest vertebrate ancestors. Here, we describe how genetic analysis of embryogenesis in the sea lamprey (Petromyzon marinus) has provided insight into the origin and evolution of developmental-genetic programs in vertebrates. We focus on recent work involving CRISPR/Cas9-mediated genome editing to study gene regulatory mechanisms involved in the development and evolution of neural crest cells and new cell types in the vertebrate nervous system, and transient transgenic assays that have been instrumental in dissecting the evolution of cis-regulatory control of gene expression in vertebrates. Finally, we discuss the broad potential for these functional genomic tools to address previously unanswerable questions related to the evolution of genomic regulatory mechanisms as well as issues related to invasive sea lamprey population control.

Evolution of the Chordate Telencephalon

The dramatic evolutionary expansion of the neocortex, together with a proliferation of specialized cortical areas, is believed to underlie the emergence of human cognitive abilities. In a broader phylogenetic context, however, neocortex evolution in mammals, including humans, is remarkably conservative, characterized largely by size variations on a shared six-layered neuronal architecture. By contrast, the telencephalon in non-mammalian vertebrates, including reptiles, amphibians, bony and cartilaginous fishes, and cyclostomes, features a great variety of very different tissue structures. Our understanding of the evolutionary relationships of these telencephalic structures, especially those of basally branching vertebrates and invertebrate chordates, remains fragmentary and is impeded by conceptual obstacles. To make sense of highly divergent anatomies requires a hierarchical view of biological organization, one that permits the recognition of homologies at multiple levels beyond neuroanatomical structure. Here we review the origin and diversification of the telencephalon with a focus on key evolutionary innovations shaping the neocortex at multiple levels of organization.

The pharynx of the stem-chondrichthyan Ptomacanthus and the early evolution of the gnathostome gill skeleton

The gill apparatus of gnathostomes (jawed vertebrates) is fundamental to feeding and ventilation and a focal point of classic hypotheses on the origin of jaws and paired appendages. The gill skeletons of chondrichthyans (sharks, batoids, chimaeras) have often been assumed to reflect ancestral states. However, only a handful of early chondrichthyan gill skeletons are known and palaeontological work is increasingly challenging other pre-supposed shark-like aspects of ancestral gnathostomes. Here we use computed tomography scanning to image the three-dimensionally preserved branchial apparatus in Ptomacanthus, a 415 million year old stem-chondrichthyan. Ptomacanthus had an osteichthyan-like compact pharynx with a bony operculum helping constrain the origin of an elongate elasmobranch-like pharynx to the chondrichthyan stem-group, rather than it representing an ancestral condition of the crown-group. A mixture of chondrichthyan-like and plesiomorphic pharyngeal patterning in Ptomacanthus challenges the idea that the ancestral gnathostome pharynx conformed to a morphologically complete ancestral type.

Our understanding of the origin of jaws is hampered by the poor fossil preservation of pharyngeal morphology. Here, Dearden et al. provide insight into the skull conditions of early jawed vertebrates through three-dimensional computed tomography imaging of a 415 million year old stem-chondrichthyan.

Diminution of pharyngeal segmentation and the evolution of the amniotes

BACKGROUND

The pharyngeal arches are a series of bulges found on the lateral surface of the head of vertebrate embryos, and it is within these segments that components of the later anatomy are laid down. In most vertebrates, the post-otic pharyngeal arches will form the branchial apparatus, while in amniotes these segments are believed to generate the larynx. It has been unclear how the development of these segments has been altered with the emergence of the amniotes.

RESULTS

In this study, we examined the development of pharyngeal arches in amniotes and show that the post-otic pharyngeal arches in this clade are greatly diminished. We find that the post-otic segments do not undergo myogenesis or skeletogenesis, but are remodelled before these processes occur. We also find that nested DLX expression, which is a feature of all the pharyngeal arches in anamniotes, is associated with the anterior segments but less so with the posterior arches in amniotes. We further show that the posterior arches of the mouse embryo fail to properly delineate, which demonstrates the lack of function of these posterior segments in later development.

CONCLUSION

In amniotes, there has been a loss of the ancestral "branchial" developmental programme that is a general feature of gnathostomes; myogenesis and skeletogenesis This is likely to have facilitated the emergence of the larynx as a new structure not constrained by the segmental organisation of the posterior pharyngeal region.

Rooting Phylogenies and the Tree of Life While Minimizing Ad Hoc and Auxiliary Assumptions

Phylogenetic methods unearth evolutionary history when supported by three starting points of reason: (1) the continuity axiom begs the existence of a "model" of evolutionary change, (2) the singularity axiom defines the historical ground plan (phylogeny) in which biological entities (taxa) evolve, and (3) the memory axiom demands identification of biological attributes (characters) with historical information. Axiom consequences are interlinked, making the retrodiction enterprise an endeavor of reciprocal fulfillment. In particular, establishing direction of evolutionary change (character polarization) roots phylogenies and enables testing the existence of historical memory (homology). Unfortunately, rooting phylogenies, especially the "tree of life," generally follow narratives instead of integrating empirical and theoretical knowledge of retrodictive exploration. This stems mostly from a focus on molecular sequence analysis and uncertainties about rooting methods. Here, we review available rooting criteria, highlighting the need to minimize both ad hoc and auxiliary assumptions, especially argumentative ad hocness. We show that while the outgroup comparison method has been widely adopted, the generality criterion of nesting and additive phylogenetic change embodied in Weston rule offers the most powerful rooting approach. We also propose a change of focus, from phylogenies that describe the evolution of biological systems to those that describe the evolution of parts of those systems. This weakens violation of character independence, helps formalize the generality criterion of rooting, and provides new ways to study the problem of evolution.

An ancestral role for Semaphorin3F-Neuropilin signaling in patterning neural crest within the new vertebrate head

The origin of the vertebrate head is one of the great unresolved issues in vertebrate evolutionary developmental biology. Although many of the novelties in the vertebrate head and pharynx derive from the neural crest, it is still unknown how early vertebrates patterned the neural crest within the ancestral body plan they inherited from invertebrate chordates. Here, using a basal vertebrate, the sea lamprey, we show that homologs of Semaphorin3F (Sema3F) ligand and its Neuropilin (Nrp) receptors show complementary and dynamic patterns of expression that correlate with key periods of neural crest development (migration and patterning of cranial neural crest-derived structures). Using CRISPR/Cas9-mediated mutagenesis, we demonstrate that lamprey Sema3F is essential for patterning of neural crest-derived melanocytes, cranial ganglia and the head skeleton, but is not required for neural crest migration or patterning of trunk neural crest derivatives. Based on comparisons with jawed vertebrates, our results suggest that the deployment of Nrp-Sema3F signaling, along with other intercellular guidance cues, was pivotal in allowing early vertebrates to organize and pattern cranial neural crest cells into many of the hallmark structures that define the vertebrate head.

Oldest known multituberculate stapes suggests an asymmetric bicrural pattern as ancestral for Multituberculata

Middle ear ossicles (malleus, incus, stapes) are known for few multituberculate taxa, and three different stapedial morphotypes have been suggested: (i) slender, columelliform and microperforate, (ii) robust and rod-like, and (iii) bicrural. Reinvestigation of Upper Jurassic (Kimmeridgian) mammalian petrosals from the Guimarota coal mine in central Portugal (Western Europe) revealed an asymmetric bicrural stapes (ABS) in the paulchoffatiid Pseudobolodon oreas The middle ear ossicles displaced inside the osseous vestibule were detected by a µCT analysis. The Kimmeridgian age of the Guimarota stapes exceeds the stapes from the Early Cretaceous (Barremian) of Asia (about 122-124 Ma) by approximately 30 Myr, and is only slightly younger than the stapes of the recently described Oxfordian euharamiyidan Arboroharamiya allinhopsoni The Guimarota stapes indicates that the stapes of Lambdopsalis, described as columelliform and microperforate (small stapedial foramen), does not represent a general condition for multituberculates. The stapes of Pseudobolodon is bicrural, the anterior crus sits centrally on the oval footplate, and the stapedial head is simple and smaller than the footplate. We hypothesize that the ABS evolved from the symmetric bicrural stapes (SBS) of non-mammaliaform cynodonts. The ABS appears to be the ancestral morphotype of the mammalian SBS, and the mammalian columelliform imperforate stapes.

Evolvability of the vertebrate craniofacial skeleton

The skull is a vertebrate novelty. Morphological adaptations of the skull are associated with major evolutionary transitions, including the shift to a predatory lifestyle and the ability to masticate while breathing. These adaptations include the chondrocranium, dermatocranium, articulated jaws, primary and secondary palates, internal choanae, the middle ear, and temporomandibular joint. The incredible adaptive diversity of the vertebrate skull indicates an underlying bauplan that promotes evolvability. Comparative studies in craniofacial development suggest that the craniofacial bauplan includes three secondary organizers, two that are bilaterally placed at the Hinge of the developing jaw, and one situated in the midline of the developing face (the FEZ). These organizers regulate tissue interactions between the cranial neural crest, the neuroepithelium, and facial and pharyngeal epithelia that regulate the development and evolvability of the craniofacial skeleton.

Specification of jaw identity by the Hand2 transcription factor

Acquisition of the lower jaw (mandible) was evolutionarily important for jawed vertebrates. In humans, syndromic craniofacial malformations often accompany jaw anomalies. The basic helix-loop-helix transcription factor Hand2, which is conserved among jawed vertebrates, is expressed in the neural crest in the mandibular process but not in the maxillary process of the first branchial arch. Here, we provide evidence that Hand2 is sufficient for upper jaw (maxilla)-to-mandible transformation by regulating the expression of homeobox transcription factors in mice. Altered Hand2 expression in the neural crest transformed the maxillae into mandibles with duplicated Meckel's cartilage, which resulted in an absence of the secondary palate. In Hand2-overexpressing mutants, non-Hox homeobox transcription factors were dysregulated. These results suggest that Hand2 regulates mandibular development through downstream genes of Hand2 and is therefore a major determinant of jaw identity. Hand2 may have influenced the evolutionary acquisition of the mandible and secondary palate.

An ancient dental gene set governs development and continuous regeneration of teeth in sharks

The evolution of oral teeth is considered a major contributor to the overall success of jawed vertebrates. This is especially apparent in cartilaginous fishes including sharks and rays, which develop elaborate arrays of highly specialized teeth, organized in rows and retain the capacity for life-long regeneration. Perpetual regeneration of oral teeth has been either lost or highly reduced in many other lineages including important developmental model species, so cartilaginous fishes are uniquely suited for deep comparative analyses of tooth development and regeneration. Additionally, sharks and rays can offer crucial insights into the characters of the dentition in the ancestor of all jawed vertebrates. Despite this, tooth development and regeneration in chondrichthyans is poorly understood and remains virtually uncharacterized from a developmental genetic standpoint. Using the emerging chondrichthyan model, the catshark (Scyliorhinus spp.), we characterized the expression of genes homologous to those known to be expressed during stages of early dental competence, tooth initiation, morphogenesis, and regeneration in bony vertebrates. We have found that expression patterns of several genes from Hh, Wnt/β-catenin, Bmp and Fgf signalling pathways indicate deep conservation over ~450 million years of tooth development and regeneration. We describe how these genes participate in the initial emergence of the shark dentition and how they are redeployed during regeneration of successive tooth generations. We suggest that at the dawn of the vertebrate lineage, teeth (i) were most likely continuously regenerative structures, and (ii) utilised a core set of genes from members of key developmental signalling pathways that were instrumental in creating a dental legacy redeployed throughout vertebrate evolution. These data lay the foundation for further experimental investigations utilizing the unique regenerative capacity of chondrichthyan models to answer evolutionary, developmental, and regenerative biological questions that are impossible to explore in classical models.

Distinct effects of Hoxa2 overexpression in cranial neural crest populations reveal that the mammalian hyomandibular-ceratohyal boundary maps within the styloid process

Most gnathostomata craniofacial structures derive from pharyngeal arches (PAs), which are colonized by cranial neural crest cells (CNCCs). The anteroposterior and dorsoventral identities of CNCCs are defined by the combinatorial expression of Hox and Dlx genes. The mechanisms associating characteristic Hox/Dlx expression patterns with the topology and morphology of PAs derivatives are only partially known; a better knowledge of these processes might lead to new concepts on the origin of taxon-specific craniofacial morphologies and of certain craniofacial malformations. Here we show that ectopic expression of Hoxa2 in Hox-negative CNCCs results in distinct phenotypes in different CNCC subpopulations. Namely, while ectopic Hoxa2 expression is sufficient for the morphological and molecular transformation of the first PA (PA1) CNCC derivatives into the second PA (PA2)-like structures, this same genetic alteration does not provoke the transformation of derivatives of other CNCC subpopulations, but severely impairs their development. Ectopic Hoxa2 expression results in the transformation of the proximal Meckel's cartilage and of the malleus, two ventral PA1 CNCCs derivatives, into a supernumerary styloid process (SP), a PA2-derived mammalian-specific skeletal structure. These results, together with experiments to inactivate and ectopically activate the Edn1-Dlx5/6 pathway, indicate a dorsoventral PA2 (hyomandibular/ceratohyal) boundary passing through the middle of the SP. The present findings suggest context-dependent function of Hoxa2 in CNCC regional specification and morphogenesis, and provide novel insights into the evolution of taxa-specific patterning of PA-derived structures.

Evolutionary and developmental origins of the cardiac neural crest: building a divided outflow tract

The cardiac neural crest cells (CNCCs) have played an important role in the evolution and development of the vertebrate cardiovascular system: from reinforcement of the developing aortic arch arteries early in vertebrate evolution, to later orchestration of aortic arch artery remodeling into the great arteries of the heart, and finally outflow tract septation in amniotes. A critical element necessary for the evolutionary advent of outflow tract septation was the co-evolution of the cardiac neural crest cells with the second heart field. This review highlights the major transitions in vertebrate circulatory evolution, explores the evolutionary developmental origins of the CNCCs from the third stream cranial neural crest, and explores candidate signaling pathways in CNCC and outflow tract evolution drawn from our knowledge of DiGeorge Syndrome.

Development and evolution of the pharyngeal apparatus

The oral or pharyngeal apparatus facilitates the dual functions of respiration and feeding. It develops during embryogenesis from transient structures called pharyngeal arches (PAs), which comprise a reiterated series of outgrowths on the lateral side of the head. The PAs and their segmental arrangement are highly conserved throughout evolution from invertebrate chordates such as amphioxus, through to vertebrate agnathans including avians, squamates, and mammals. The structural organization of the PAs is also highly conserved and involves contributions from each of the three primary endoderm, mesoderm, and ectoderm germ layers. The endoderm is particularly important for PA formation and segmentation and also plays a critical role in tissue-specific differentiation. The ectoderm gives rise to neural crest cells (NCC) which provide an additional layer of complexity to PA development and differentiation in vertebrates compared to invertebrate chordates that do not possess NCC. Collectively, the PAs give rise to much of the neurovasculature and musculoskeletal systems in the head and neck. The complexity of development renders the pharyngeal apparatus prone to perturbation and subsequently the pathogenesis of birth defects. Hence it is important to understand the signals and mechanisms that govern the development and evolution of the pharyngeal complex.

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes.  In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate.  SkateBase ( http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources.

Distinct populations within Isl1 lineages contribute to appendicular and facial skeletogenesis through the β-catenin pathway

Isl1 expression marks progenitor populations in developing embryos. In this study, we investigated the contribution of Isl1-expressing cells that utilize the β-catenin pathway to skeletal development. Inactivation of β-catenin in Isl1-expressing cells caused agenesis of the hindlimb skeleton and absence of the lower jaw (agnathia). In the hindlimb, Isl1-lineages broadly contributed to the mesenchyme; however, deletion of β-catenin in the Isl1-lineage caused cell death only in a discrete posterior domain of nascent hindlimb bud mesenchyme. We found that the loss of posterior mesenchyme, which gives rise to Shh-expressing posterior organizer tissue, caused loss of posterior gene expression and failure to expand chondrogenic precursor cells, leading to severe truncation of the hindlimb. In facial tissues, Isl1-expressing cells broadly contributed to facial epithelium. We found reduced nuclear β-catenin accumulation and loss of Fgf8 expression in mandibular epithelium of Isl1(-/-) embryos. Inactivating β-catenin in Isl1-expressing epithelium caused both loss of epithelial Fgf8 expression and death of mesenchymal cells in the mandibular arch without affecting epithelial proliferation and survival. These results suggest a Isl1→β-catenin→Fgf8 pathway that regulates mesenchymal survival and development of the lower jaw in the mandibular epithelium. By contrast, activating β-catenin signaling in Isl1-lineages caused activation of Fgf8 broadly in facial epithelium. Our results provide evidence that, despite its broad contribution to hindlimb mesenchyme and facial epithelium, the Isl1-β-catenin pathway regulates skeletal development of the hindlimb and lower jaw through discrete populations of cells that give rise to Shh-expressing posterior hindlimb mesenchyme and Fgf8-expressing mandibular epithelium.

Heterogeneous conservation of Dlx paralog co-expression in jawed vertebrates

Background

The Dlx gene family encodes transcription factors involved in the development of a wide variety of morphological innovations that first evolved at the origins of vertebrates or of the jawed vertebrates. This gene family expanded with the two rounds of genome duplications that occurred before jawed vertebrates diversified. It includes at least three bigene pairs sharing conserved regulatory sequences in tetrapods and teleost fish, but has been only partially characterized in chondrichthyans, the third major group of jawed vertebrates. Here we take advantage of developmental and molecular tools applied to the shark Scyliorhinus canicula to fill in the gap and provide an overview of the evolution of the Dlx family in the jawed vertebrates. These results are analyzed in the theoretical framework of the DDC (Duplication-Degeneration-Complementation) model.

Results

The genomic organisation of the catshark Dlx genes is similar to that previously described for tetrapods. Conserved non-coding elements identified in bony fish were also identified in catshark Dlx clusters and showed regulatory activity in transgenic zebrafish. Gene expression patterns in the catshark showed that there are some expression sites with high conservation of the expressed paralog(s) and other expression sites with events of paralog sub-functionalization during jawed vertebrate diversification, resulting in a wide variety of evolutionary scenarios within this gene family.

Conclusion

Dlx gene expression patterns in the catshark show that there has been little neo-functionalization in Dlx genes over gnathostome evolution. In most cases, one tandem duplication and two rounds of vertebrate genome duplication have led to at least six Dlx coding sequences with redundant expression patterns followed by some instances of paralog sub-functionalization. Regulatory constraints such as shared enhancers, and functional constraints including gene pleiotropy, may have contributed to the evolutionary inertia leading to high redundancy between gene expression patterns.