An ancient Turing-like patterning mechanism regulates skin denticle development in sharks

Micropattern Fabricated by Acropetal Migration Controlled through Sequential Photo and Thermal Polymerization

Bottom-up patterning technology plays a significant role in both nature and synthetic materials, owing to its inherent advantages such as ease of implementation, spontaneity, and noncontact attributes, etc. However, constrained by the uncontrollability of molecular movement, energy interaction, and stress, obtained micropatterns tend to exhibit an inevitable arched outline, resulting in the limitation of applicability. Herein, inspired by auxin's action mode in apical dominance, a versatile strategy is proposed for fabricating precision self-organizing micropatterns with impressive height based on polymerization-induced acropetal migration. The copolymer containing fluorocarbon chains (low surface energy) and tertiary amine (coinitiator) is designed to self-assemble on the surface of the photo-curing system. The selective exposure under a photomask establishes a photocuring boundary and the radicals would be generated on the surface, which is pivotal in generating a vertical concentration difference of monomer. Subsequent heating treatment activates the material continuously transfers from the unexposed area to the exposed area and is accompanied by the obviously vertical upward mass transfer, resulting in the manufacture of a rectilinear profile micropattern. This strategy significantly broadens the applicability of self-organizing patterns, offering the potential to mitigate the complexity and time-consuming limitations associated with top-down methods.

Anatomy, development and regeneration of zebrafish elasmoid scales

Vertebrate skin appendages - particularly avian feathers and mammalian hairs, glands and teeth - are perennially useful systems for investigating fundamental mechanisms of development. The most common type of skin appendage in teleost fishes is the elasmoid scale, yet this structure has received much less attention than the skin appendages of tetrapods. Elasmoid scales are thin, overlapping plates of partially mineralized extracellular matrices, deposited in the skin in a hexagonal pattern by a specialized population of dermal cells in cooperation with the overlying epidermis. Recent years have seen rapid progress in our understanding of elasmoid scale development and regeneration, driven by the deployment of developmental genetics, live imaging and transcriptomics in larval and adult zebrafish. These findings are reviewed together with histological and ultrastructural approaches to understanding scale development and regeneration.

Husbandry conditions of spotted ratfish (Hydrolagus colliei, Chimaeriformes) in aquaria for successful embryonic development and long-term survival of juveniles

The spotted ratfish Hydrolagus colliei is the most common holocephalan species exhibited in aquaria worldwide for introducing deep-sea environments and raising awareness of their conservation. However, little is known about the biology of H. colliei. Current practices in aquaria allow long-term survival of sexually mature H. colliei specimens; however, this species struggles to complete a reproductive cycle in captivity mostly because embryos do not reach the hatchling stage. The aquarists of Planet Ocean Montpellier (POM, France) have bred H. colliei for 15 years and recorded parameters suitable for this species' successful embryonic and post-embryonic development. POM aquarists now regularly record egg-laying events of H. colliei and use four tanks to incubate eggs and raise neonates, late hatchlings, early and intermediate juveniles, subadults, and sexually mature specimens. In this work we provide the first long-term biometric data on H. colliei from the hatchling to the subadult stage. We also report the biotic and abiotic parameters sufficient to breed H. colliei in aquaria. We finally describe the methods used to facilitate individual monitoring of specimens along the ontogeny and several pathologies identified in this species, their putative causes, and the corresponding treatments. This work highlights the importance of ex situ research and points to the valuable outcomes of collaborative efforts between aquaria and academia in deciphering the biology of species whose study in the wild remains challenging.

Embryonic development in the bonnethead (Sphyrna tiburo), a viviparous hammerhead shark

BACKGROUND

The hammerhead sharks (family Sphyrnidae) are an immediately recognizable group of sharks due to their unique head shape. Though there has long been an interest in hammerhead development, there are currently no explicit staging tables published for any members of the group. The bonnethead Sphyrna tiburo is the smallest member of Sphyrnidae and is abundant in estuarine and nearshore waters in the Gulf of Mexico and Western North Atlantic Ocean. Due to their relative abundance, close proximity to shore, and brief gestation period, it has been possible to collect and document multiple embryonic specimens at progressive stages of development.

RESULTS

We present the first comprehensive embryonic staging series for the Bonnethead, a viviparous hammerhead shark. Our stage series covers a period of development from stages that match the vertebrate phylotypic period, from Stage 23, through stages of morphological divergence to complete development at birth-Stage 35). Notably, we use a variety of techniques to document crucial stages that lead to their extreme craniofacial diversity, resulting in the formation of one of the most distinctive characters of any shark species, the cephalofoil or hammer-like head.

CONCLUSION

Documenting the development of hard-to-access vertebrates, like this viviparous shark species, offers important information about how new and diverse morphologies arise that otherwise may remain poorly studied. This work will serve as a platform for future comparative developmental research both within sharks and across the phylogeny of vertebrates, underpinning the extreme potential of craniofacial development and morphological diversity in vertebrate animals.

Periodic pattern formation during embryonic development

During embryonic development many organs and structures require the formation of series of repeating elements known as periodic patterns. Ranging from the digits of the limb to the feathers of the avian skin, the correct formation of these embryonic patterns is essential for the future form and function of these tissues. However, the mechanisms that produce these patterns are not fully understood due to the existence of several modes of pattern generation which often differ between organs and species. Here, we review the current state of the field and provide a perspective on future approaches to studying this fundamental process of embryonic development.

Relationships in Shark Skin: Mechanical and Morphological Properties Vary between Sexes and among Species

Shark skin is a composite of mineralized dermal denticles embedded in an internal collagen fiber network and is sexually dimorphic. Female shark skin is thicker, has greater denticle density and denticle overlap compared to male shark skin, and denticle morphology differs between sexes. The skin behaves with mechanical anisotropy, extending farther when tested along the longitudinal (anteroposterior) axis but increasing in stiffness along the hoop (dorsoventral or circumferential) axis. As a result, shark skin has been hypothesized to function as an exotendon. This study aims to quantify sex differences in the mechanical properties and morphology of shark skin. We tested skin from two immature male and two immature female sharks from three species (bonnethead shark, Sphyrna tiburo; bull shark, Carcharhinus leucas; silky shark, Carcharhinus falciformis) along two orientations (longitudinal and hoop) in uniaxial tension with an Instron E1000 at a 2 mm s-1 strain rate. We found that male shark skin was significantly tougher than female skin, although females had significantly greater skin thickness compared to males. We found skin in the hoop direction was significantly stiffer than the longitudinal direction across sexes and species, while skin in the longitudinal direction was significantly more extensible than in the hoop direction. We found that shark skin mechanical behavior was impacted by sex, species, and direction, and related to morphological features of the skin.

Development shapes the evolutionary diversification of rodent stripe patterns

Vertebrate groups have evolved strikingly diverse color patterns. However, it remains unknown to what extent the diversification of such patterns has been shaped by the proximate, developmental mechanisms that regulate their formation. While these developmental mechanisms have long been inaccessible empirically, here we take advantage of recent insights into rodent pattern formation to investigate the role of development in shaping pattern diversification across rodents. Based on a broad survey of museum specimens, we first establish that various rodents have independently evolved diverse patterns consisting of longitudinal stripes, varying across species in number, color, and relative positioning. We then interrogate this diversity using a simple model that incorporates recent molecular and developmental insights into stripe formation in African striped mice. Our results suggest that, on the one hand, development has facilitated pattern diversification: The diversity of patterns seen across species can be generated by a single developmental process, and small changes in this process suffice to recapitulate observed evolutionary changes in pattern organization. On the other hand, development has constrained diversification: Constraints on stripe positioning limit the scope of evolvable patterns, and although pattern organization appears at first glance phylogenetically unconstrained, development turns out to impose a cryptic constraint. Altogether, this work reveals that pattern diversification in rodents can in part be explained by the underlying development and illustrates how pattern formation models can be leveraged to interpret pattern evolution.

Transient agonism of the sonic hedgehog pathway triggers a permanent transition of skin appendage fate in the chicken embryo

Vertebrate skin appendage early development is mediated by conserved molecular signaling composing a dynamical reaction-diffusion-like system. Variations to such systems contribute to the remarkable diversity of skin appendage forms within and among species. Here, we demonstrate that stage-specific transient agonism of sonic hedgehog (Shh) pathway signaling in chicken triggers a complete and permanent transition from reticulate scales to feathers on the ventral surfaces of the foot and digits. Resulting ectopic feathers are developmentally comparable to feathers adorning the body, with down-type feathers transitioning into regenerative, bilaterally symmetric contour feathers in adult chickens. Crucially, this spectacular transition of skin appendage fate (from nodular reticulate scales to bona fide adult feathers) does not require sustained treatment. Our RNA sequencing analyses confirm that smoothened agonist treatment specifically promotes the expression of key Shh pathway-associated genes. These results indicate that variations in Shh pathway signaling likely contribute to the natural diversity and regionalization of avian integumentary appendages.

Gap junctions in Turing-type periodic feather pattern formation

Periodic patterning requires coordinated cell-cell interactions at the tissue level. Turing showed, using mathematical modeling, how spatial patterns could arise from the reactions of a diffusive activator-inhibitor pair in an initially homogenous two-dimensional field. Most activators and inhibitors studied in biological systems are proteins, and the roles of cell-cell interaction, ions, bioelectricity, etc. are only now being identified. Gap junctions (GJs) mediate direct exchanges of ions or small molecules between cells, enabling rapid long-distance communications in a cell collective. They are therefore good candidates for propagating non-protein-based patterning signals that may act according to the Turing principles. Here, we explore the possible roles of GJs in Turing-type patterning using feather pattern formation as a model. We found seven of the twelve investigated GJ isoforms are highly dynamically expressed in the developing chicken skin. In ovo functional perturbations of the GJ isoform, connexin 30, by siRNA and the dominant-negative mutant applied before placode development led to disrupted primary feather bud formation, including patches of smooth skin and buds of irregular sizes. Later, after the primary feather arrays were laid out, inhibition of gap junctional intercellular communication in the ex vivo skin explant culture allowed the emergence of new feather buds in temporal waves at specific spatial locations relative to the existing primary buds. The results suggest that gap junctional communication may facilitate the propagation of long-distance inhibitory signals. Thus, the removal of GJ activity would enable the emergence of new feather buds if the local environment is competent and the threshold to form buds is reached. We propose Turing-based computational simulations that can predict the appearance of these ectopic bud waves. Our models demonstrate how a Turing activator-inhibitor system can continue to generate patterns in the competent morphogenetic field when the level of intercellular communication at the tissue scale is modulated.

A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions

Developmental complexity stemming from the dynamic interplay between genetic and biomechanic factors canalizes the ways genotypes and phenotypes can change in evolution. As a paradigmatic system, we explore how changes in developmental factors generate typical tooth shape transitions. Since tooth development has mainly been researched in mammals, we contribute to a more general understanding by studying the development of tooth diversity in sharks. To this end, we build a general, but realistic, mathematical model of odontogenesis. We show that it reproduces key shark-specific features of tooth development as well as real tooth shape variation in small-spotted catsharks Scyliorhinus canicula. We validate our model by comparison with experiments in vivo. Strikingly, we observe that developmental transitions between tooth shapes tend to be highly degenerate, even for complex phenotypes. We also discover that the sets of developmental parameters involved in tooth shape transitions tend to depend asymmetrically on the direction of that transition. Together, our findings provide a valuable base for furthering our understanding of how developmental changes can lead to both adaptive phenotypic change and trait convergence in complex, phenotypically highly diverse, structures.

Extensive embryonic patterning without cellular differentiation primes the plant epidermis for efficient post-embryonic stomatal activities

Plant leaves feature epidermal stomata that are organized in stereotyped patterns. How does the pattern originate? We provide transcriptomic, imaging, and genetic evidence that Arabidopsis embryos engage known stomatal fate and patterning factors to create regularly spaced stomatal precursor cells. Analysis of embryos from 36 plant species indicates that this trait is widespread among angiosperms. Embryonic stomatal patterning in Arabidopsis is established in three stages: first, broad SPEECHLESS (SPCH) expression; second, coalescence of SPCH and its targets into discrete domains; and third, one round of asymmetric division to create stomatal precursors. Lineage progression is then halted until after germination. We show that the embryonic stomatal pattern enables fast stomatal differentiation and photosynthetic activity upon germination, but it also guides the formation of additional stomata as the leaf expands. In addition, key stomatal regulators are prevented from driving the fate transitions they can induce after germination, identifying stage-specific layers of regulation that control lineage progression during embryogenesis.

Teeth outside the mouth: The evolution and development of shark denticles

Vertebrate skin appendages are incredibly diverse. This diversity, which includes structures such as scales, feathers, and hair, likely evolved from a shared anatomical placode, suggesting broad conservation of the early development of these organs. Some of the earliest known skin appendages are dentine and enamel-rich tooth-like structures, collectively known as odontodes. These appendages evolved over 450 million years ago. Elasmobranchs (sharks, skates, and rays) have retained these ancient skin appendages in the form of both dermal denticles (scales) and oral teeth. Despite our knowledge of denticle function in adult sharks, our understanding of their development and morphogenesis is less advanced. Even though denticles in sharks appear structurally similar to oral teeth, there has been limited data directly comparing the molecular development of these distinct elements. Here, we chart the development of denticles in the embryonic small-spotted catshark (Scyliorhinus canicula) and characterize the expression of conserved genes known to mediate dental development. We find that shark denticle development shares a vast gene expression signature with developing teeth. However, denticles have restricted regenerative potential, as they lack a sox2+ stem cell niche associated with the maintenance of a dental lamina, an essential requirement for continuous tooth replacement. We compare developing denticles to other skin appendages, including both sensory skin appendages and avian feathers. This reveals that denticles are not only tooth-like in structure, but that they also share an ancient developmental gene set that is likely common to all epidermal appendages.

Turing's turtles all the way down: A conserved role of EDAR in the carapacial ridge suggests a deep homology of prepatterns across ectodermal appendages

The scutes of the turtle shell are epidermal shields that begin their formation during the early stages of shell development. Like other skin appendages, turtle scutes are hypothesized to be patterned by reaction-diffusion systems. We have previously established ex vivo and in silico systems to study these mechanisms experimentally and have further shown that mathematical models can explain the dynamics of the induction of turtle scute primordia and the generation of final scute architecture. Using these foundations, we expand our current knowledge and test the roles of ectodysplasin and activin signaling in the development of turtle scutes. We find that these molecules play important roles in the prepatterning of scute primordia along the carapacial ridge and show that blocking Edar signaling may lead to a complete loss of marginal scute primordia. We show that it is possible to reproduce these observations using simple mathematical modeling, thereby suggesting a stabilizing role for ectodysplasin within the reaction-diffusion mechanisms. Finally, we argue that our findings further entrench turtle scutes within a class of developmental systems composed of hierarchically nested reaction-diffusion mechanisms, which is conserved across ectodermal organs.

Turing patterns by supramolecular self-assembly of a single salphen building block

In the 1950s, Alan Turing showed that concerted reactions and diffusion of activating and inhibiting chemical species can autonomously generate patterns without previous positional information, thus providing a chemical basis for morphogenesis in Nature. However, access to these patterns from only one molecular component that contained all the necessary information to execute agonistic and antagonistic signaling is so far an elusive goal, since two or more participants with different diffusivities are a must. Here, we report on a single-molecule system that generates Turing patterns arrested in the solid state, where supramolecular interactions are used instead of chemical reactions, whereas diffusional differences arise from heterogeneously populated self-assembled products. We employ a family of hydroxylated organic salphen building blocks based on a bis-Schiff-base scaffold with portions responsible for either activation or inhibition of assemblies at different hierarchies through purely supramolecular reactions, only depending upon the solvent dielectric constant and evaporation as fuel.

Leafy and weedy seadragon genomes connect genic and repetitive DNA features to the extravagant biology of syngnathid fishes

Seadragons are widely recognized for their derived traits, which include leaf-like appendages and extreme spinal curvature. Efforts to understand the genetic basis of these unique traits and conserve these species and their relatives have been limited by genomic resource gaps. In this paper we present full, annotated genomes of leafy and weedy seadragons, which we use to uncover surprising features of gene family and genome architecture evolution that likely relate to the extravagant phenotypic traits of seadragons and their pipefish and seahorse relatives. These genomes and their analyses are important advances for the study of elaborate vertebrate traits, leveraging this diverse, morphologically exceptional group of fishes.

Seadragons are a remarkable lineage of teleost fishes in the family Syngnathidae, renowned for having evolved male pregnancy. Comprising three known species, seadragons are widely recognized and admired for their fantastical body forms and coloration, and their specific habitat requirements have made them flagship representatives for marine conservation and natural history interests. Until recently, a gap has been the lack of significant genomic resources for seadragons. We have produced gene-annotated, chromosome-scale genome models for the leafy and weedy seadragon to advance investigations of evolutionary innovation and elaboration of morphological traits in seadragons as well as their pipefish and seahorse relatives. We identified several interesting features specific to seadragon genomes, including divergent noncoding regions near a developmental gene important for integumentary outgrowth, a high genome-wide density of repetitive DNA, and recent expansions of transposable elements and a vesicular trafficking gene family. Surprisingly, comparative analyses leveraging the seadragon genomes and additional syngnathid and outgroup genomes revealed striking, syngnathid-specific losses in the family of fibroblast growth factors (FGFs), which likely involve reorganization of highly conserved gene regulatory networks in ways that have not previously been documented in natural populations. The resources presented here serve as important tools for future evolutionary studies of developmental processes in syngnathids and hold value for conservation of the extravagant seadragons and their relatives.

An epithelial signalling centre in sharks supports homology of tooth morphogenesis in vertebrates

Development of tooth shape is regulated by the enamel knot signalling centre, at least in mammals. Fgf signalling regulates differential proliferation between the enamel knot and adjacent dental epithelia during tooth development, leading to formation of the dental cusp. The presence of an enamel knot in non-mammalian vertebrates is debated given differences in signalling. Here, we show the conservation and restriction of fgf3, fgf10, and shh to the sites of future dental cusps in the shark (Scyliorhinus canicula), whilst also highlighting striking differences between the shark and mouse. We reveal shifts in tooth size, shape, and cusp number following small molecule perturbations of canonical Wnt signalling. Resulting tooth phenotypes mirror observed effects in mammals, where canonical Wnt has been implicated as an upstream regulator of enamel knot signalling. In silico modelling of shark dental morphogenesis demonstrates how subtle changes in activatory and inhibitory signals can alter tooth shape, resembling developmental phenotypes and cusp shapes observed following experimental Wnt perturbation. Our results support the functional conservation of an enamel knot-like signalling centre throughout vertebrates and suggest that varied tooth types from sharks to mammals follow a similar developmental bauplan. Lineage-specific differences in signalling are not sufficient in refuting homology of this signalling centre, which is likely older than teeth themselves.

Redeployment of odontode gene regulatory network underlies dermal denticle formation and evolution in suckermouth armored catfish

Odontodes, i.e., teeth and tooth-like structures, consist of a pulp cavity and dentin covered by a mineralized cap. These structures first appeared on the outer surface of vertebrate ancestors and were repeatedly lost and gained across vertebrate clades; yet, the underlying genetic mechanisms and trajectories of this recurrent evolution remain long-standing mysteries. Here, we established suckermouth armored catfish (Ancistrus sp.; Loricariidae), which have reacquired dermal odontodes (dermal denticles) all over most of their body surface, as an experimental model animal amenable to genetic manipulation for studying odontode development. Our histological analysis showed that suckermouth armored catfish develop dermal denticles through the previously defined odontode developmental stages. De novo transcriptomic profiling identified the conserved odontode genetic regulatory network (oGRN) as well as expression of paired like homeodomain 2 (pitx2), previously known as an early regulator of oGRN in teeth but not in other dermal odontodes, in developing dermal denticles. The early onset of pitx2 expression in cranial dermal denticle placodes implies its function as one of the inducing factors of the cranial dermal denticles. By comprehensively identifying the genetic program for dermal odontode development in suckermouth armored catfish, this work illuminates how dermal odontodes might have evolved and diverged in distinct teleost lineages via redeployment of oGRN.

Irregular spots on body surfaces of vertebrates induced by supercritical pitchfork bifurcations

The classical Turing mechanism containing a long-range inhibition and a short-range self-enhancement provides a type of explanation for the formation of patterns on body surfaces of some vertebrates, e.g., zebras, giraffes, and cheetahs. For other type of patterns (irregular spots) on body surfaces of some vertebrates, e.g., loaches, finless eels, and dalmatian dogs, the classical Turing mechanism no longer applies. Here, we propose a mechanism, i.e., the supercritical pitchfork bifurcation, which may explain the formation of this type of irregular spots, and present a method to quantify the similarity of such patterns. We assume that, under certain conditions, the only stable state of "morphogen" loses its stability and transitions to two newly generated stable states with the influence of external noise, thus producing such ruleless piebald patterns in space. The difference between the competitiveness of these two states may affect the resulting pattern. Moreover, we propose a mathematical model based on this conjecture and obtain this type of irregular patterns by numerical simulation. Furthermore, we also study the influence of parameters in the model on pattern structures and obtain the corresponding pattern structures of some vertebrates in nature, which verifies our conjecture.

Evolved Bmp6 enhancer alleles drive spatial shifts in gene expression during tooth development in sticklebacks

Mutations in enhancers have been shown to often underlie natural variation but the evolved differences in enhancer activity can be difficult to identify in vivo. Threespine sticklebacks (Gasterosteus aculeatus) are a robust system for studying enhancer evolution due to abundant natural genetic variation, a diversity of evolved phenotypes between ancestral marine and derived freshwater forms, and the tractability of transgenic techniques. Previous work identified a series of polymorphisms within an intronic enhancer of the Bone morphogenetic protein 6 (Bmp6) gene that are associated with evolved tooth gain, a derived increase in freshwater tooth number that arises late in development. Here, we use a bicistronic reporter construct containing a genetic insulator and a pair of reciprocal two-color transgenic reporter lines to compare enhancer activity of marine and freshwater alleles of this enhancer. In older fish, the two alleles drive partially overlapping expression in both mesenchyme and epithelium of developing teeth, but the freshwater enhancer drives a reduced mesenchymal domain and a larger epithelial domain relative to the marine enhancer. In younger fish, these spatial shifts in enhancer activity are less pronounced. Comparing Bmp6 expression by in situ hybridization in developing teeth of marine and freshwater fish reveals similar evolved spatial shifts in gene expression. Together, these data support a model in which the polymorphisms within this enhancer underlie evolved tooth gain by shifting the spatial expression of Bmp6 during tooth development, and provide a general strategy to identify spatial differences in enhancer activity in vivo.

Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)

Background

Microbial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as many evolutionarily important clades remain unexamined. There is currently no data on the microbiota associated with any Chondrichthyan species during embryonic development, despite the global distribution, ecological importance, and phylogenetic position of this clade. In this study, we take the first steps towards filling this gap by investigating the microbiota associated with embryonic development in the little skate, Leucoraja erinacea, a common North Atlantic species and popular system for chondrichthyan biology.

Methods

To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, at six points during ontogeny. Community composition was analyzed using the QIIME2 pipeline and microbial continuity between stages was tracked using FEAST.

Results

We identify site-specific and stage-specific microbiota dominated by the bacterial phyla Proteobacteria and Bacteroidetes. This composition is similar to, but distinct from, that of previously published data on the adult microbiota of other chondrichthyan species. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop.

Conclusions

Our study is the first exploration of the chondrichthyan microbiota throughout ontogeny and provides the first evidence of vertical transmission in this group.

Supplementary Information

The online version contains supplementary material available at 10.1186/s42523-021-00136-x.

Edge-Enriched Large-Area Hexagonal BN Ultrathin Films with Enhanced Optical Second Harmonic Generation

The optical second harmonic generation (SHG) efficiency of hexagonal boron nitride (h-BN) layered materials is profoundly influenced by the symmetry properties, which has severely limited the usefulness of their SHG for nonlinear optical applications. Herein, we report on the controlled growth of large-area and continuous ultrathin h-BN films with a high density of exposed edges that show strongly enhanced SHG, owing to the breaking of inversion symmetry occurring naturally at edge sites. The large-area growth of edge-enriched BN films was accomplished through the introduction of Turing instability into a growth process that involves the liquid-gas interface self-limiting reaction between molten boron oxide (B₂O₃) with gaseous ammonia (NH₃) at elevated temperature. Remarkably, the edge-enriched BN films give rise to a SHG response up to nearly 3 orders of magnitude higher than that of the smooth BN films prepared through the same growth approach but with different growth parameters.

Capturing and analyzing pattern diversity: an example using the melanistic spotted patterns of leopard geckos

Animal color patterns are widely studied in ecology, evolution, and through mathematical modeling. Patterns may vary among distinct body parts such as the head, trunk or tail. As large amounts of photographic data is becoming more easily available, there is a growing need for general quantitative methods for capturing and analyzing the full complexity and details of pattern variation. Detailed information on variation in color pattern elements is necessary to understand how patterns are produced and established during development, and which evolutionary forces may constrain such a variation. Here, we develop an approach to capture and analyze variation in melanistic color pattern elements in leopard geckos. We use this data to study the variation among different body parts of leopard geckos and to draw inferences about their development. We compare patterns using 14 different indices such as the ratio of melanistic versus total area, the ellipticity of spots, and the size of spots and use these to define a composite distance between two patterns. Pattern presence/absence among the different body parts indicates a clear pathway of pattern establishment from the head to the back legs. Together with weak within-individual correlation between leg patterns and main body patterns, this suggests that pattern establishment in the head and tail may be independent from the rest of the body. We found that patterns vary greatest in size and density of the spots among body parts and individuals, but little in their average shapes. We also found a correlation between the melanistic patterns of the two front legs, as well as the two back legs, and also between the head, tail and trunk, especially for the density and size of the spots, but not their shape or inter-spot distance. Our data collection and analysis approach can be applied to other organisms to study variation in color patterns between body parts and to address questions on pattern formation and establishment in animals.

Conserved Mechanisms, Novel Anatomies: The Developmental Basis of Fin Evolution and the Origin of Limbs

The transformation of paired fins into tetrapod limbs is one of the most intensively scrutinized events in animal evolution. Early anatomical and embryological datasets identified distinctive morphological regions within the appendage and posed hypotheses about how the loss, gain, and transformation of these regions could explain the observed patterns of both extant and fossil appendage diversity. These hypotheses have been put to the test by our growing understanding of patterning mechanisms that regulate formation of the appendage axes, comparisons of gene expression data from an array of phylogenetically informative taxa, and increasingly sophisticated and elegant experiments leveraging the latest molecular approaches. Together, these data demonstrate the remarkable conservation of developmental mechanisms, even across phylogenetically and morphologically disparate taxa, as well as raising new questions about the way we view homology, evolutionary novelty, and the often non-linear connection between morphology and gene expression. In this review, we present historical hypotheses regarding paired fin evolution and limb origins, summarize key aspects of central appendage patterning mechanisms in model and non-model species, address how modern comparative developmental data interface with our understanding of appendage anatomy, and highlight new approaches that promise to provide new insight into these well-traveled questions.

The Dental Lamina: An Essential Structure for Perpetual Tooth Regeneration in Sharks

In recent years, nonclassical models have emerged as mainstays for studies of evolutionary, developmental, and regenerative biology. Genomic advances have promoted the use of alternative taxa for the study of developmental biology, and the shark is one such emerging model vertebrate. Our research utilizes the embryonic shark (Scyliorhinus canicula) to characterize key developmental and regenerative processes that have been overlooked or not possible to study with more classic developmental models. Tooth development is a major event in the construction of the vertebrate body plan, linked in part with the emergence of jaws. Early development of the teeth and morphogenesis is well known from the murine model, but the process of tooth redevelopment and regeneration is less well known. Here we explore the role of the dental lamina in the development of a highly regenerative dentition in sharks. The shark represents a polyphyodont vertebrate with continuously repeated whole tooth regeneration. This is presented as a major developmental shift from the more derived renewal process that the murine model offers, where incisors exhibit continuous renewal and growth of the same tooth. Not only does the shark offer a study system for whole unit dental regeneration, it also represents an important model for understanding the evolutionary context of vertebrate tooth regeneration.

Thyroid hormone regulates abrupt skin morphogenesis during zebrafish postembryonic development

Thyroid hormone is a key regulator of post-embryonic vertebrate development. Skin is a biomedically important thyroid hormone target organ, but the cellular and molecular mechanisms underlying skin pathologies associated with thyroid dysfunction remain obscure. The transparent skin of zebrafish is an accessible model system for studying vertebrate skin development. During post-embryonic development of the zebrafish, scales emerge in the skin from a hexagonally patterned array of dermal papillae, like other vertebrate skin appendages such as feathers and hair follicles. We show here that thyroid hormone regulates the rate of post-embryonic dermal development through interaction with nuclear hormone receptors. This couples skin development with body growth to generate a well ordered array of correctly proportioned scales. This work extends our knowledge of thyroid hormone actions on skin by providing in-vivo evidence that thyroid hormone regulates multiple aspects of dermal development.

The emergence of a complex pore-canal system in the dermal skeleton of Tremataspis (Osteostraci)

Thyestiids are a group of osteostracans (sister-group to jawed vertebrates) ranging in time from the early Silurian to Middle Devonian. Tremataspis is unique among thyestiids in having a continuous mesodentine and enameloid cover on its dermal elements, and an embedded pore-canal system divided into lower and upper parts by a perforated septum. The origin of this upper mesh canal system and its potential homology to similar canal systems of other osteostracans has remained a matter of debate. To investigate this, we use synchrotron radiation microtomography data of four species of Tremataspis and three other thyestiid genera. Procephalaspis oeselensis lacks an upper mesh canal system entirely, but Aestiaspis viitaensis has partially enclosed upper canals formed between slightly modified tubercles that generally only cover separate pore fields. Further modification of tubercles in Dartmuthia gemmifera forms a more extensive, semi-enclosed upper mesh canal system that overlies an extensive perforated septum, similar to that found in Tremataspis. Lower mesh canals in P. oeselensis are radially arranged and buried tubercles indicate a continuous growth and addition of dermal hard tissues. These features are lacking to varying degrees in the other investigated thyestiids, and Tremataspis probably had a determinate growth accompanied by a single mineralization phase of its dermal hard tissues. The previously proposed homology between the semi-enclosed upper canal system in Dartmuthia to the pore-canal system in Tremataspis is supported in this study, but the suggested homologies between these canals and other parts of the thyestiid vasculature to those in non-thyestiid osteostracans remain unclear. This study shows that three-dimensional modeling of high-resolution data can provide histological and structural details that can help clarify homology issues and elucidate the evolution of dermal hard tissues in osteostracans. In extension, this can give insights into how these tissues relate to those found among jawed vertebrates.

Tooth Removal in the Leopard Gecko and the de novo Formation of Replacement Teeth

Many reptiles are able to continuously replace their teeth through life, an ability attributed to the existence of epithelial stem cells. Tooth replacement occurs in a spatially and temporally regulated manner, suggesting the involvement of diffusible factors, potentially over long distances. Here, we locally disrupted tooth replacement in the leopard gecko (Eublepharis macularius) and followed the recovery of the dentition. We looked at the effects on local patterning and functionally tested whether putative epithelial stem cells can give rise to multiple cell types in the enamel organs of new teeth. Second generation teeth with enamel and dentine were removed from adult geckos. The dental lamina was either left intact or disrupted in order to interfere with local patterning cues. The dentition began to reform by 1 month and was nearly recovered by 2-3 months as shown in μCT scans and eruption of teeth labeled with fluorescent markers. Microscopic analysis showed that the dental lamina was fully healed by 1 month. The deepest parts of the dental lamina retained odontogenic identity as shown by PITX2 staining. A pulse-chase was carried out to label cells that were stimulated to enter the cell cycle and then would carry BrdU forward into subsequent tooth generations. Initially we labeled 70-78% of PCNA cells with BrdU. After a 1-month chase, the percentage of BrdU + PCNA labeled cells in the dental lamina had dropped to 10%, consistent with the dilution of the label. There was also a population of single, BrdU-labeled cells present up to 2 months post surgery. These BrdU-labeled cells were almost entirely located in the dental lamina and were the likely progenitor/stem cells because they had not entered the cell cycle. In contrast fragmented BrdU was seen in the PCNA-positive, proliferating enamel organs. Homeostasis and recovery of the gecko dentition was therefore mediated by a stable population of epithelial stem cells in the dental lamina.

Evolutionary developmental genetics of teeth and odontodes in jawed vertebrates: a perspective from the study of elasmobranchs

Most extant vertebrates display a high variety of tooth and tooth-like organs (odontodes) that vary in shape, position over the body and nature of composing tissues. The development of these structures is known to involve similar genetic cascades and teeth and odontodes are believed to share a common evolutionary history. Gene expression patterns have previously been compared between mammalian and teleost tooth development but we highlight how the comparative framework was not always properly defined to deal with different tooth types or tooth developmental stages. Larger-scale comparative analyses also included cartilaginous fishes: sharks display oral teeth and dermal scales for which the gene expression during development started to be investigated in the small-spotted catshark Scyliorhinus canicula during the past decade. We report several descriptive approaches to analyse the embryonic tooth and caudal scale gene expressions in S. canicula. We compare these expressions wih the ones reported in mouse molars and teleost oral and pharyngeal teeth and highlight contributions and biases that arise from these interspecific comparisons. We finally discuss the evolutionary processes that can explain the observed intra and interspecific similarities and divergences in the genetic cascades involved in tooth and odontode development in jawed vertebrates.

Oral and Palatal Dentition of Axolotl Arises From a Common Tooth-Competent Zone Along the Ecto-Endodermal Boundary

Vertebrate dentitions arise at various places within the oropharyngeal cavity including the jaws, the palate, or the pharynx. These dentitions develop in a highly organized way, where new tooth germs are progressively added adjacent to the initiator center, the first tooth. At the same time, the places where dentitions develop house the contact zones between the outer ectoderm and the inner endoderm, and this colocalization has instigated various suggestions on the roles of germ layers for tooth initiation and development. Here, we study development of the axolotl dentition, which is a complex of five pairs of tooth fields arranged into the typically tetrapod outer and inner dental arcades. By tracking the expression patterns of odontogenic genes, we reason that teeth of both dental arcades originate from common tooth-competent zones, one present on the mouth roof and one on the mouth floor. Progressive compartmentalization of these zones and a simultaneous addition of new tooth germs distinct for each prospective tooth field subsequently control the final shape and composition of the axolotl dentition. Interestingly, by following the fate of the GFP-labeled oral ectoderm, we further show that, in three out of five tooth field pairs, the first tooth develops right at the ecto-endodermal boundary. Our results thus indicate that a single tooth-competent zone gives rise to both dental arcades of a complex tetrapod dentition. Further, we propose that the ecto-endodermal boundary running through this zone should be accounted for as a potential source of instruction factors instigating the onset of the odontogenic program.

The developmental relationship between teeth and dermal odontodes in the most primitive bony fish Lophosteus

The ontogenetic trajectory of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically most basal stem osteichthyan, visualized by synchrotron microtomography, reveals a developmental relationship between teeth and dermal odontodes that is not evident from the adult morphology. The earliest odontodes are two longitudinal founder ridges formed at the ossification center. Subsequent odontodes that are added lingually to the ridges turn into conical teeth and undergo cyclic replacement, while those added labially achieve a stellate appearance. Stellate odontodes deposited directly on the bony plate are aligned with the alternate files of teeth, whereas new tooth positions are inserted into the files of sequential addition when a gap appears. Successive teeth and overgrowing odontodes show hybrid morphologies around the oral-dermal boundary, suggesting signal cross-communication. We propose that teeth and dermal odontodes are modifications of a single system, regulated and differentiated by the oral and dermal epithelia.

Influence of the Turing instability on the motion of domain boundaries

Turing's theory of pattern formation has provided crucial insights into the behavior of various biological, geographical, and chemical systems over the last few decades. Existing studies have focused on moving-boundary Turing systems for which the motion of the boundary is prescribed by an external agent. In this paper, we present an extension of this theory to a class of systems in which the front motion is governed by the physical processes that occur within the domain. Biological systems exhibiting apically dominant growth and corrosion of metals and alloys highlight some of the noteworthy examples of such systems. In this study, we characterize the nature of interaction between the moving front and the Turing-instability for both an activator-inhibitor and an activator-substrate model. Behavioral regimes of periodic, as well as nonperiodic (nonconstant), growth rates are obtained. Furthermore, the trends in the first show striking similarities with the cyclic-boundary-kinetics observed in experimental systems. In general, a stationary, periodic structure is also left behind the moving front. If the periodicity of the boundary kinetics agrees with the allowed range of the stable-periodic solutions, the pattern formed tends to persist. Otherwise, it evolves to a nearby energy-minimum either by peak-splitting, peak-decay, or by settling down to a spatially homogeneous state.

Development and regeneration of the crushing dentition in skates (Rajidae)

Sharks and rays (elasmobranchs) have the remarkable capacity to continuously regenerate their teeth. The polyphyodont system is considered the ancestral condition of the gnathostome dentition. Despite this shared regenerative ability, sharks and rays exhibit dramatic interspecific variation in their tooth morphology. Ray (batoidea) teeth typically constitute crushing pads of flattened teeth, whereas shark teeth are pointed, multi-cuspid units. Although recent research has addressed the molecular development of the shark dentition, little is known about that of the ray. Furthermore, how dental diversity within the elasmobranch lineage is achieved remains unknown. Here, we examine dental development and regeneration in two Batoid species: the thornback skate (Raja clavata) and the little skate (Leucoraja erinacea). Using in situ hybridization and immunohistochemistry, we examine the expression of a core gnathostome dental gene set during early development of the skate dentition and compare it to development in the shark. Elasmobranch tooth development is highly conserved, with sox2 likely playing an important role in the initiation and regeneration of teeth. Alterations to conserved genes expressed in an enamel knot-like signalling centre may explain the morphological diversity of elasmobranch teeth, thereby enabling sharks and rays to occupy diverse dietary and ecological niches.

Quantitative gene expression dynamics of key placode signalling factors in the embryonic chicken scleral ossicle system

Development of the scleral ossicles, a ring of bony elements within the sclera, is directed by a series of papillae that arise from placodes in the conjunctival epithelium over a 1.5-day induction period in the chicken embryo. The regular spacing of the papillae around the corneal-scleral limbus suggests that their induction may be regulated by a reaction-diffusion mechanism, similar to other epithelial appendages. Some key placode signalling molecules, including β-catenin, are known to be expressed throughout the induction period. However, others have been studied only at certain stages or have not been successfully detected. Here we use qPCR to study the gene expression patterns of the wingless integration (WNT)/β-catenin, bone morphogenetic protein (BMP), ectodysplasin (EDA), fibroblast growth factor (FGF) and hedgehog (HH) signalling families in discrete regions of the eye throughout the complete conjunctival placode and papillae induction period. This comprehensive analysis revealed a variable level of gene expression within specific eye regions, with some genes exhibiting high, moderate or low changes. Most genes exhibited an initial increase in gene expression, followed by a decrease or plateau as development proceeded, suggesting that some genes are important for a brief initial period whilst the sustained elevated expression level of other genes is needed for developmental progression. The timing or magnitude of these changes, and/or the overall gene expression trend differed in the temporal, nasal and/or dorsal eye regions for some, but not all genes, demonstrating that gene expression may vary across different eye regions. Temporal and nasal EDA receptor (EDAR) had the greatest number of strong correlations (r > 0.700) with other genes and β-catenin had the greatest number of moderate correlations (r = 0.400-0.700), while EDA had the greatest range in correlation strengths. Among the strongly correlated genes, two distinct signalling modules were identified, connected by some intermediate genes. The dynamic gene expression patterns of the five signalling pathways studied here from conjunctival placode formation through to papillae development is consistent with other epithelial appendages and confirms the presence of a conserved induction and patterning signalling network. Two unique gene expression patterns and corresponding gene interaction modules suggest functionally distinct roles throughout placode development. Furthermore, spatial differences in gene expression patterns among the temporal, nasal and dorsal regions of the eye may indicate that the expression of certain genes is influenced by mechanical forces exerted throughout development. Therefore, this study identifies key placode signalling factors and their interactions, as well as some potential region-specific features of gene expression in the scleral ossicle system and provides a basis for further exploration of the spatial expression of these genes and the patterning mechanism(s) active throughout conjunctival placode and papillae formation.

The Morphogenesis of Speech Gestures: From Local Computations to Global Patterns

A subtle property of speech gestures is the fact that they are spatially and temporally extended, meaning that phonological contrasts are expressed using spatially extended constrictions, and have a finite duration. This paper shows how this spatiotemporal particulation of the vocal tract, for the purpose of linguistic signaling, comes about. It is argued that local uniform computations among topographically organized microscopic units that either constrict or relax individual points of the vocal tract yield the global spatiotemporal macroscopic structures we call constrictions, the locus of phonological contrast. The dynamical process is a morphogenetic one, based on the Turing and Hopf patterns of mathematical physics and biology. It is shown that reaction-diffusion equations, which are introduced in a tutorial mathematical style, with simultaneous Turing and Hopf patterns predict the spatiotemporal particulation, as well as concrete properties of speech gestures, namely the pivoting of constrictions, as well as the intermediate value of proportional time to peak velocity, which is well-studied and observed. The goal of the paper is to contribute to Bernstein's program of understanding motor processes as the emergence of low degree of freedom descriptions from high degree of freedom systems by actually pointing to specific, predictive, dynamics that yield speech gestures from a reaction-diffusion morphogenetic process.

Symmetry breaking in the embryonic skin triggers directional and sequential plumage patterning

The development of an organism involves the formation of patterns from initially homogeneous surfaces in a reproducible manner. Simulations of various theoretical models recapitulate final states of natural patterns, yet drawing testable hypotheses from those often remains difficult. Consequently, little is known about pattern-forming events. Here, we surveyed plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins, together representing the three major taxa of the avian phylogeny, and built a unified model that not only reproduces final patterns but also intrinsically generates shared and varying directionality, sequence, and duration of patterning. We used in vivo and ex vivo experiments to test its parameter-based predictions. We showed that directional and sequential pattern progression depends on a species-specific prepattern: an initial break in surface symmetry launches a travelling front of sharply defined, oriented domains with self-organising capacity. This front propagates through the timely transfer of increased cell density mediated by cell proliferation, which controls overall patterning duration. These results show that universal mechanisms combining prepatterning and self-organisation govern the timely emergence of the plumage pattern in birds.

A survey of plumage patterns and their emergence in Galliformes, ratites, passerines, and penguins shows that their formation depends on a species-specific prepattern in the embryo and demonstrates that universal mechanisms govern the timely emergence of natural patterns in birds.

Conserved gene signalling and a derived patterning mechanism underlie the development of avian footpad scales

Background

Vertebrates possess a diverse range of integumentary epithelial appendages, including scales, feathers and hair. These structures share extensive early developmental homology, as they mostly originate from a conserved anatomical placode. In the context of avian epithelial appendages, feathers and scutate scales are known to develop from an anatomical placode. However, our understanding of avian reticulate (footpad) scale development remains unclear.

Results

Here, we demonstrate that reticulate scales develop from restricted circular domains of thickened epithelium, with localised conserved gene expression in both the epithelium and underlying mesenchyme. These domains constitute either anatomical placodes, or circular initiatory fields (comparable to the avian feather tract). Subsequent patterning of reticulate scales is consistent with reaction–diffusion (RD) simulation, whereby this primary domain subdivides into smaller secondary units, which produce individual scales. In contrast, the footpad scales of a squamate model (the bearded dragon, Pogona vitticeps) develop synchronously across the ventral footpad surface.

Conclusions

Widely conserved gene signalling underlies the initial development of avian reticulate scales. However, their subsequent patterning is distinct from the footpad scale patterning of a squamate model, and the feather and scutate scale patterning of birds. Therefore, we suggest reticulate scales are a comparatively derived epithelial appendage, patterned through a modified RD system.

Electronic supplementary material

The online version of this article (10.1186/s13227-019-0130-9) contains supplementary material, which is available to authorized users.

Evolution and Developmental Diversity of Skin Spines in Pufferfishes

Teleost fishes develop remarkable varieties of skin ornaments. The developmental basis of these structures is poorly understood. The order Tetraodontiformes includes diverse fishes such as the ocean sunfishes, triggerfishes, and pufferfishes, which exhibit a vast assortment of scale derivatives. Pufferfishes possess some of the most extreme scale derivatives, dermal spines, erected during their characteristic puffing behavior. We demonstrate that pufferfish scale-less spines develop through conserved gene interactions that underlie general vertebrate skin appendage formation, including feathers and hair. Spine development retains conservation of the EDA (ectodysplasin) signaling pathway, important for the development of diverse vertebrate skin appendages, including these modified scale-less spines of pufferfish. Further modification of genetic signaling from both CRISPR-Cas9 and small molecule inhibition leads to loss or reduction of spine coverage, providing a mechanism for skin appendage diversification observed throughout the pufferfishes. Pufferfish spines have evolved broad variations in body coverage, enabling adaptation to diverse ecological niches.