Embryonic development and cranial ossification of the Japanese Aodaisho, Elaphe climacophora (Serpentes: Colubridae): with special reference to the prootic bone and auditory evolution in snakes.

Snakes show remarkably deviated "body plan" from other squamate reptiles. In addition to limb loss, they have accomplished enormous anatomical specialization of the skull associated with the pit organs and the reduction of the tympanic membranes and auditory canals in the outer ears. Despite being the most diverse group of snakes, our knowledge of the embryonic staging for organogenesis and cranial ossification has been minimal for Colubridae. Therefore, in the present observation, we provide the first embryonic description of the Japanese rat snake Elaphe climacophora. We based our study on the Standard Event System (SES) for external anatomical characters and on a description of the cranial ossification during post-ovipositional development. We further estimated the relative ossification timing of each cranial bony element and compared it with that of selected other snakes, lizards, turtles, and crocodilians. The present study shows that the relative ossification timing of the palatine and pterygoid bones is relatively early in squamates when compared to other reptiles, implying the developmental integration as the palate-pterygoid complex in this clade and functional demands for the unique feeding adaptation to swallow large prey with the help of their large palatine and pterygoid teeth. Furthermore, unlike in species with pit organs, the prootic bone of Ela. climacophora is expanded to provide articulation with the supratemporal, thereby contributing to the hearing system by detecting substrate vibration. We also demonstrate that the relative timing of the prootic ossification is significantly accelerated in colubrids compared to snakes with pit organs. Our finding suggests that the temporal changes of the prootic ossification underpin the evolution of the perception of the ground-bourne sound signals among snakes.

On the evolutionary developmental biology of the cell.

Organisms are complex assemblages of cells, cells that produce light, shoot harpoons, and secrete glue. Therefore, identifying the mechanisms that generate novelty at the level of the individual cell is essential for understanding how multicellular life evolves. For decades, the field of evolutionary developmental biology (Evo-Devo) has been developing a framework for connecting genetic variation that arises during embryonic development to the emergence of diverse adult forms. With increasing access to new single cell 'omics technologies and an array of techniques for manipulating gene expression, we can now extend these inquiries inward to the level of the individual cell. In this opinion, I argue that applying an Evo-Devo framework to single cells makes it possible to explore the natural history of cells, where this was once only possible at the organismal level.

Dev-ResNet: automated developmental event detection using deep learning.

Delineating developmental events is central to experimental research using early life stages, permitting widespread identification of changes in event timing between species and environments. Yet, identifying developmental events is incredibly challenging, limiting the scale, reproducibility and throughput of using early life stages in experimental biology. We introduce Dev-ResNet, a small and efficient 3D convolutional neural network capable of detecting developmental events characterised by both spatial and temporal features, such as the onset of cardiac function and radula activity. We demonstrate the efficacy of Dev-ResNet using 10 diverse functional events throughout the embryonic development of the great pond snail, Lymnaea stagnalis. Dev-ResNet was highly effective in detecting the onset of all events, including the identification of thermally induced decoupling of event timings. Dev-ResNet has broad applicability given the ubiquity of bioimaging in developmental biology, and the transferability of deep learning, and so we provide comprehensive scripts and documentation for applying Dev-ResNet to different biological systems.

Embryology of the fat-tailed dunnart (Sminthopsis crassicaudata): A marsupial model for comparative mammalian developmental and evolutionary biology.

BACKGROUND: Marsupials are a diverse and unique group of mammals, but remain underutilized in developmental biology studies, hindering our understanding of mammalian diversity. This study focuses on establishing the fat-tailed dunnart (Sminthopsis crassicaudata) as an emerging laboratory model, providing reproductive monitoring methods and a detailed atlas of its embryonic development. RESULTS: We monitored the reproductive cycles of female dunnarts and established methods to confirm pregnancy and generate timed embryos. With this, we characterized dunnart embryo development from cleavage to birth, and provided detailed descriptions of its organogenesis and heterochronic growth patterns. Drawing stage-matched comparisons with other species, we highlight the dunnarts accelerated craniofacial and limb development, characteristic of marsupials. CONCLUSIONS: The fat-tailed dunnart is an exceptional marsupial model for developmental studies, where our detailed practices for reproductive monitoring and embryo collection enhance its accessibility in other laboratories. The accelerated developmental patterns observed in the Dunnart provide a valuable system for investigating molecular mechanisms underlying heterochrony. This study not only contributes to our understanding of marsupial development but also equips the scientific community with new resources for addressing biodiversity challenges and developing effective conservation strategies in marsupials.

Ontogeny of the autopodial skeleton of the gecko Tarentola (Squamata: Phyllodactylidae).

Squamates exhibit evident diversity in their limb morphology. Gekkotans are a particularly diverse group in this respect. The appearance of toepads in gekkotans usually cooccurs with the reduction or loss of claws. The gecko Tarentola (Phyllodactylidae) shows a unique combination of features among geckos, with toepads, hyperphalangy, and dimorphism of claw expression (claws are retained on digits III and IV, but lost (manus) or strongly reduced (pes) on the remaining digits). Despite being a candidate model for studying embryonic skeletal development of the autopodium, no studies have investigated the autopodial development of the gecko Tarentola in detail. Here, we aim to follow up the development of the autopodial skeleton in T. annularis and T. mauritanica using acid-free double staining. The results indicate that the terminal phalanges of claw-bearing digits III and IV ossify earlier than in the remaining digits. This confirms the differential ossification as a result of claw regression in Tarentola. The strongly reduced second phalanges of digits IV in both the fore- and hindlimbs are the last ossifying phalanges. Such late ossification may precede the evolutionary loss of this phalanx. If this is correct, the autopodia of Tarentola would be an interesting example of both the hyperphalangy in digit I and the process of phalanx loss in digit IV. Delay in ossification of the miniaturised phalanx probably represents an example of paedomorphosis.

BLMP-1 is a critical temporal regulator of dietary-restriction-induced response in Caenorhabditis elegans.

The extrinsic diet and the intrinsic developmental programs are intertwined. Although extensive research has been conducted on how nutrition regulates development, whether and how developmental programs control the timing of nutritional responses remain barely known. Here, we report that a developmental timing regulator, BLMP-1/BLIMP1, governs the temporal response to dietary restriction (DR). At the end of larval development, BLMP-1 is induced and interacts with DR-activated PHA-4/FOXA, a key transcription factor responding to the reduced nutrition. By integrating temporal and nutritional signaling, the DR response regulates many development-related genes, including gska-3/GSK3ß, through BLMP-1-PHA-4 at the onset of adulthood. Upon DR, a precocious activation of BLMP-1 in early larval stages impairs neuronal development through gska-3, whereas the increase of gska-3 by BLMP-1-PHA-4 at the last larval stage suppresses WNT signaling in adulthood for DR-induced longevity. Our findings reveal a temporal checkpoint of the DR response that protects larval development and promotes adult health.

Translating the Timing of Developmental Benchmarks in Short-Tailed Opossums (Monodelphisdomestica) to Facilitate Comparisons with Commonly Used Rodent Models.

INTRODUCTION: The gray short-tailed opossum, Monodelhis domestica (M. domestica), is a widely used marsupial model species that presents unique advantages for neurodevelopmental studies. Notably their extremely altricial birth allows manipulation of postnatal pups at timepoints equivalent to embryonic stages of placental mammals. A robust literature exists on the development of short-tailed opossums, but many researchers working in the more conventional model species of mice and rats may find it daunting to identify the appropriate age at which to conduct experiments. METHODS: Here, we present detailed staging diagrams taken from photographic observations of 40 individual pups, in 6 litters, over 25 timepoints across postnatal development. We also present a comparative neurodevelopmental timeline of short-tailed opossums (M. domestica), the house mouse (Mus musculus), and the laboratory rat (Rattus norvegicus) during embryonic as well as postnatal development, using timepoints taken from this study and a review of existing literature, and use this dataset to present statistical models comparing the opossum to the rat and mouse. RESULTS: One aim of this research was to aid in testing the generalizability of results found in rodents to other mammalian brains, such as the more distantly related metatherians. However, this broad dataset also allows the identification of potential heterochronies in opossum development compared to rats and mice. In contrast to previous work, we found broad similarity between the pace of opossum neural development with that of rats and mice. We also found that development of some systems was accelerated in the opossum, such as the forelimb motor plant, oral motor control, and some aspects of the olfactory system, while the development of the cortex, some aspects of the retina, and other aspects of the olfactory system are delayed compared to the rat and mouse. DISCUSSION: The pace of opossum development is broadly similar to that of mice and rats, which underscores the usefulness of this species as a compliment to the more commonly used rodents. Many features that differ the most between opossums and rats and mice were either clustered around the day of birth and were features that have functional importance for the pup immediately after or during birth, or were features that have reduced functional importance for the pup until later in postnatal development, given that it is initially attached to the mother.

The Birth and Death of Floral Organs in Cereal Crops.

Florets of cereal crops are the basic reproductive organs that produce grains for food or feed. The birth of a floret progresses through meristem initiation and floral organ identity specification and maintenance. During these processes, both endogenous and external cues can trigger a premature floral organ death, leading to reproductive failure. Recent advances in different cereal crops have identified both conserved and distinct regulators governing the birth of a floret. However, the molecular underpinnings of floral death are just beginning to be understood. In this review, we first provide a general overview of the current findings in the field of floral development in major cereals and outline different forms of floral deaths, particularly in the Triticeae crops. We then highlight the importance of vascular patterning and photosynthesis in floral development and reproductive success and argue for an expanded knowledge of floral birth-death balance in the context of agroecology.

Temporal regulation of vegetative phase change in plants.

During their vegetative growth, plants reiteratively produce leaves, buds, and internodes at the apical end of the shoot. The identity of these organs changes as the shoot develops. Some traits change gradually, but others change in a coordinated fashion, allowing shoot development to be divided into discrete juvenile and adult phases. The transition between these phases is called vegetative phase change. Historically, vegetative phase change has been studied because it is thought to be associated with an increase in reproductive competence. However, this is not true for all species; indeed, heterochronic variation in the timing of vegetative phase change and flowering has made important contributions to plant evolution. In this review, we describe the molecular mechanism of vegetative phase change, how the timing of this process is controlled by endogenous and environmental factors, and its ecological and evolutionary significance.

Developmental and environmental plasticity in opsin gene expression in Lake Victoria cichlid fish.

In many organisms, sensory abilities develop and evolve according to the changing demands of navigating, foraging, and communication across different environments and life stages. Teleost fish inhabit heterogeneous light environments and exhibit a large diversity in visual system properties among species. Cichlids are a classic example of this diversity; visual system variation is generated by different tuning mechanisms that involve both genetic factors and phenotypic plasticity. Here, we document the developmental progression of visual pigment gene expression in Lake Victoria cichlids and test if these patterns are influenced by variation in light conditions. We reared two sister species of Pundamilia to adulthood in two distinct visual conditions that resemble the light environments that they naturally inhabit in Lake Victoria. We also included interspecific first-generation hybrids. We focused on the four opsins that are expressed in Pundamilia adults (using real-time quantitative polymerase chain reaction (RT-qPCR)) (SWS2B, SWS2A, RH2A, and LWS) at 17 time points. We find that opsin expression profiles progress from shorter-wavelength sensitive opsins to longer-wavelength sensitive opsins with increasing age, in both species and their hybrids. The developmental trajectories of opsin expression also responded plastically to the visual conditions. Developmental and environmental plasticity in opsin expression may provide an important stepping stone in the evolution of cichlid visual system diversity.

Patterns of Carpel Structure, Development, and Evolution in Monocots.

The phenomenon of heterochrony, or shifts in the relative timing of ontogenetic events, is important for understanding many aspects of plant evolution, including applied issues such as crop yield. In this paper, we review heterochronic shifts in the evolution of an important floral organ, the carpel. The carpels, being ovule-bearing organs, facilitate fertilisation, seed, and fruit formation. It is the carpel that provides the key character of flowering plants, angiospermy. In many angiosperms, a carpel has two zones: proximal ascidiate and distal plicate. When carpels are free (apocarpous gynoecium), the plicate zone has a ventral slit where carpel margins meet and fuse during ontogeny; the ascidiate zone is sac-like from inception and has no ventral slit. When carpels are united in a syncarpous gynoecium, a synascidiate zone has as many locules as carpels, whereas a symplicate zone is unilocular, at least early in ontogeny. In ontogeny, either the (syn)ascidiate or (sym)plicate zone is first to initiate. The two developmental patterns are called early and late peltation, respectively. In extreme cases, either the (sym)plicate or (syn)ascidiate zone is completely lacking. Here, we discuss the diversity of carpel structure and development in a well-defined clade of angiosperms, the monocotyledons. We conclude that the common ancestor of monocots had carpels with both zones and late peltation. This result was found irrespective of the use of the plastid or nuclear phylogeny. Early peltation generally correlates with ovules belonging to the (syn)ascidiate zone, whereas late peltation is found mostly in monocots with a fertile (sym)plicate zone.

Comparative phenomics: a new approach to study heterochrony.

Understanding the links between development and evolution is one of the major challenges of biology. 'Heterochronies', evolutionary alterations in the timings of development are posited as a key mechanism of evolutionary change, but their quantification requires gross simplification of organismal development. Consequently, how changes in event timings influence development more broadly is poorly understood. Here, we measure organismal development as spectra of energy in pixel values of video, creating high-dimensional landscapes integrating development of all visible form and function. This approach we termed 'Energy proxy traits' (EPTs) is applied alongside previously identified heterochronies in three freshwater pulmonate molluscs (Lymnaea stagnalis, Radix balthica and Physella acuta). EPTs were calculated from time-lapse video of embryonic development to construct a continuous functional time series. High-dimensional transitions in phenotype aligned with major sequence heterochronies between species. Furthermore, differences in event timings between conspecifics were associated with changes in high-dimensional phenotypic space. We reveal EPTs as a powerful approach to considering the evolutionary importance of alterations to developmental event timings. Reimagining the phenotype as energy spectra enabled continuous quantification of developmental changes in high-dimensional phenotypic space, rather than measurement of timings of discrete events. This approach has the possibility to transform how we study heterochrony and development more generally.

Using salamanders as model taxa to understand vertebrate feeding constraints during the late Devonian water-to-land transition.

The vertebrate water-to-land transition and the rise of tetrapods brought about fundamental changes for the groups undergoing these evolutionary changes (i.e. stem and early tetrapods). These groups were forced to adapt to new conditions, including the distinct physical properties of water and air, requiring fundamental changes in anatomy. Nutrition (or feeding) was one of the prime physiological processes these vertebrates had to successfully adjust to change from aquatic to terrestrial life. The basal gnathostome feeding mode involves either jaw prehension or using water flows to aid in ingestion, transportation and food orientation. Meanwhile, processing was limited primarily to simple chewing bites. However, given their comparatively massive and relatively inflexible hyobranchial system (compared to the more muscular tongue of many tetrapods), it remains fraught with speculation how stem and early tetrapods managed to feed in both media. Here, we explore ontogenetic water-to-land transitions of salamanders as functional analogues to model potential changes in the feeding behaviour of stem and early tetrapods. Our data suggest two scenarios for terrestrial feeding in stem and early tetrapods as well as the presence of complex chewing behaviours, including excursions of the jaw in more than one dimension during early developmental stages. Our results demonstrate that terrestrial feeding may have been possible before flexible tongues evolved. This article is part of the theme issue 'Food processing and nutritional assimilation in animals'.

Sexual conflict, heterochrony and tissue specificity as evolutionary problems of adaptive plasticity in development.

Differential gene expression represents a fundamental cause and manifestation of phenotypic plasticity. Adaptive phenotypic plasticity in gene expression as a trait evolves when alleles that mediate gene regulation serve to increase organismal fitness by improving the alignment of variation in gene expression with variation in circumstances. Among the diverse circumstances that a gene encounters are distinct cell types, developmental stages and sexes, as well as an organism's extrinsic ecological environments. Consequently, adaptive phenotypic plasticity provides a common framework to consider diverse evolutionary problems by considering the shared implications of alleles that produce context-dependent gene expression. From this perspective, adaptive plasticity represents an evolutionary resolution to conflicts of interest that arise from any negatively pleiotropic effects of expression of a gene across ontogeny, among tissues, between the sexes, or across extrinsic environments. This view highlights shared properties within the general relation of fitness, trait expression and context that may nonetheless differ substantively in the grain of selection within and among generations to influence the likelihood of adaptive plasticity as an evolutionary response. Research programmes that historically have focused on these separate issues may use the insights from one another by recognizing their shared dependence on context-dependent gene regulatory evolution.

Growth dynamics and molecular bases of evolutionary novel jaw extensions in halfbeaks and needlefishes (Beloniformes).

Evolutionary novelties-derived traits without clear homology found in the ancestors of a lineage-may promote ecological specialization and facilitate adaptive radiations. Examples for such novelties include the wings of bats, pharyngeal jaws of cichlids and flowers of angiosperms. Belonoid fishes (flying fishes, halfbeaks and needlefishes) feature an astonishing diversity of extremely elongated jaw phenotypes with undetermined evolutionary origins. We investigate the development of elongated jaws in a halfbeak (Dermogenys pusilla) and a needlefish (Xenentodon cancila) using morphometrics, transcriptomics and in situ hybridization. We confirm that these fishes' elongated jaws are composed of distinct base and novel 'extension' portions. These extensions are morphologically unique to belonoids, and we describe the growth dynamics of both bases and extensions throughout early development in both studied species. From transcriptomic profiling, we deduce that jaw extension outgrowth is guided by populations of multipotent cells originating from the anterior tip of the dentary. These cells are shielded from differentiation, but proliferate and migrate anteriorly during the extension's allometric growth phase. Cells left behind at the tip leave the shielded zone and undergo differentiation into osteoblast-like cells, which deposit extracellular matrix with both bone and cartilage characteristics that mineralizes and thereby provides rigidity. Such bone has characteristics akin to histological observations on the elongated 'kype' process on lower jaws of male salmon, which may hint at common conserved regulatory underpinnings. Future studies will evaluate the molecular pathways that govern the anterior migration and proliferation of these multipotent cells underlying the belonoids' evolutionary novel jaw extensions.

Heterochronic development of pelvic fins in zebrafish: possible involvement of temporal regulation of pitx1 expression.

Anterior and posterior paired appendages of vertebrates are notable examples of heterochrony in the relative timing of their development. In teleosts, posterior paired appendages (pelvic fin buds) emerge much later than their anterior paired appendages (pectoral fin buds). Pelvic fin buds of zebrafish (Danio rerio) appear at 3 weeks post-fertilization (wpf) during the larva-to-juvenile transition (metamorphosis), whereas pectoral fin buds arise from the lateral plate mesoderm on the yolk surface at the embryonic stage. Here we explored the mechanism by which presumptive pelvic fin cells maintain their fate, which is determined at the embryonic stage, until the onset of metamorphosis. Expression analysis revealed that transcripts of pitx1, one of the key factors for the development of posterior paired appendages, became briefly detectable in the posterior lateral plate mesoderm at early embryonic stages. Further analysis indicated that the pelvic fin-specific pitx1 enhancer was in the poised state at the larval stage and is activated at the juvenile stage. We discuss the implications of these findings for the heterochronic development of pelvic fin buds.

Flower heterochrony and crop yield.

Crop improvement has focused on enhancing yield, nutrient content, harvestability, and stress resistance using a trait-centered reductionist approach. This has downplayed the fact that plants are developmentally integrated and respond coordinately and predictably to genetic and environmental variation, with potential consequences for food production. Crop yield, including both fruit/seed production and the possibility of generating hybrid crop varieties, is highly dependent on flower morphology and sex, which, in turn, can be profoundly affected by slight shifts in the timing and rate of flower organ development (i.e., flower heterochrony). We argue that understanding the genetic and environmental bases of flower heterochrony and their effect on flower morphology and sex in cultivated plants and in their wild relatives can facilitate crop improvement.

Plant morpho evo-devo.

Evo-devo is often thought of as being the study of which genes underlie which phenotypes. However, evo-devo is much more than this, especially in plant science. In leaf scars along stems, cell changes across wood growth rings, or flowers along inflorescences, plants trace a record of their own development. Plant morpho evo-devo provides data that genes could never furnish on themes such as heterochrony, the evolution of temporal phenotypes, modularity, and phenotype-first evolution. As plant science surges into increasingly -omic realms, it is essential to keep plant morpho evo-devo in full view as an honored member of the evo-devo canon, ensuring that plant scientists can, wherever they are, generate fundamental insights at the appropriate level of biological organization.

On time: developmental timing within and across species.

Organisms across species differ in the relative size and complexity of their tissues to serve the specific purposes of the host. Correct timing is a crucial ingredient in the development of tissues, as reaching the right size and complexity requires a careful balance between cellular proliferation and differentiation. Premature or delayed differentiation, for instance, can result in tissue imbalance, malformation or malfunction. Despite seemingly rigid constraints on development, however, there is flexibility in both the timing and differentiation trajectories within and between species. In this Spotlight, we discuss how time is measured and regulated in development, and question whether developmental timing is in fact different between species.

Modularity, homology, heterochrony: Gavin de Beer's legacy to the mammalian skull.

Modularity (segmentation), homology and heterochrony were essential concepts embraced by Gavin de Beer in his studies of the development and evolution of the vertebrate skull. While his pioneering contributions have stood the test of time, our understanding of the biological processes that underlie each concept has evolved. We assess de Beer's initial training as an experimental embryologist; his switch to comparative and descriptive studies of skulls, jaws and middle ear ossicles; and his later research on the mammalian skull, including his approach to head segmentation. The role of cells of neural crest and mesodermal origin in skull development, and developmental, palaeontological and molecular evidence for the origin of middle ear ossicles in the evolutionary transition from reptiles to mammals are used to illustrate our current understanding of modularity, homology and heterochrony. This article is part of the theme issue 'The mammalian skull: development, structure and function'.