搜索结果：Journal of experimental zoology. Part B, Molecular and developmental evolution

The 2024 Latin American Developmental Biology Conference, held in Valparaíso, Chile, brought together a dynamic and diverse community of researchers to discuss current advances and prospectives in embryology. With participants from across the Americas and beyond, this extraordinary meeting highlighted the region's growing role in the field. A central theme throughout was the growing need for integrative approaches that connect multiple layers of biological phenomena to explain how form and function emerge during development: in Latin America, applications of genomics, imaging, genetics, and computational modelling to unique biological resource are transforming our understanding of developmental systems. The conference also fostered a highly inclusive and interactive environment with enthusiastic participation from trainees and early-career scientists. Poster sessions, lightning talks, and workshops offered platforms for critical reflection on issues such as challenges in funding, inclusion, and research ethics. Despite political and institutional challenges in the region, the conference showcased the creativity, resilience, and momentum of Latin American scientists, affirming their critical role in directing developmental biology towards the new horizon.

Biomineralization, the formation of mineralized tissues like skeletons and shells, is an essential developmental process in diverged phyla. Vertebrates' biomineralization involves the secretion of specialized extracellular matrix (ECM) proteins and the formation of Integrin-based focal adhesions, yet less is known about the role of such factors in invertebrates. A recent study has shown that focal adhesions form around the calcite spicule of the sea urchin larva, however, the skeletogenic expression and role of adhesion related proteins in this system are understudied. Here, we identified a set of ECM and adhesion genes that show enriched expression in the sea urchin skeletogenic cells and studied the role of the ECM protein, Npnt, in Paracentrotus lividus. The integrin alpha proteins, Pl-Ahi, Pl-Aji, Pl-Api, and the Pl-Talin protein are highly conserved between sea urchin and humans and the expression of these genes is enriched in the skeletogenic cells during early skeletogenesis. Pl-npnt is expressed specifically in skeletogenic cells throughout skeletogenesis and requires Vascular Endothelial Growth Factor (VEGF) signaling for its maintenance. Genetic perturbations of Pl-npnt result in skeletal defects, including reduced length of skeletal rods, ectopic spicule formation and branching, while skeletogenic cell migration remained unaffected. The activation of focal adhesion kinase (FAK) around the spicules is independent of Pl-Npnt activity in agreement with the loss of Integrin binding site in the sea urchin Npnt protein. Our findings set the stage for further analyses of ECM and adhesion-mediated mechanisms that drive sea urchin biomineralization, and most likely participate in skeletal development across metazoans.

The present review summarizes studies on the morphology and cell biology of the developing epidermis in the alligator as an example of archosaurian reptile. From an initial, two-layered epidermis, numerous suprabasal keratinocytes are produced at late stages of embryonic development, some days before hatching. The soft embryonic epidermis contains mucous granules, cysteine-poor IF-keratins and trichohyalin-like proteins produced from genes located in different chromosomal loci, including the EDC (Epidermal Differentiation Complex). These proteins contribute to the mild keratinization of the embryonic epidermis, resembling that of amphibians. The embryonic epidermis is composed from 3 to 4 layers of epidermal layers that are shed before hatching. The 3rd or 4th layer of the embryonic epidermis begins to accumulate Corneous Beta Proteins (CBPs), marking the transition into the definitive corneous epidermis with the production of spindle-shaped beta-cells. The latter accumulate large amount of CBPs, some lipids droplets and, in some areas also melanosomes, giving rise to a relatively hard and impermeable stratum corneous with a patterned pigmentation. The presence of Sox-oxidase in differentiating and maturing beta-cells, catalyzes the formation of numerous disulphide bonds, likely binding IFKs and CBPs in addition to their electrostatic interactions. Intra- and inter-molecular bonds contribute to hardening the corneous material, forming the definitive corneous layer. The latter, with the incorporated lipids allows to post-hatching, juveniles and adult alligators to withstand the freshwater contact and also the dry conditions of the terrestrial environment where they live. The evolution of numerous EDC proteins and CBPs mixed with lipids confers specific adaptive characteristics to the skin in this reptile.

The Assay for Transposase-Accessible Chromatin with sequencing (ATAC-seq) is a versatile and widely utilized method for identifying potential regulatory regions, such as promoters and enhancers, within a genome. ATAC-seq has been successfully applied to a wide range of established and emerging model organisms. However, implementing this method in emerging model systems, such as arthropods, can be challenging due to several factors that influence data quality. These factors include the availability of a sufficient amount and quality of tissue or cells, the need for species- and tissue-specific protocol optimization, the completeness and accuracy of the reference genome, and the quality of the genome annotation. In this article, we emphasize the key steps in the ATAC-seq protocol that, based on our experience, have the greatest impact on data quality when adapting this method for emerging model organisms. Specifically, we discuss the importance of nuclei isolation, the incubation conditions of the Tn5 transposase, and PCR amplification of the library. Furthermore, we outline essential quality checkpoints during the bioinformatic analysis of ATAC-seq data to assist in assessing data integrity and consistency. Given that many emerging model organisms may not be readily available in laboratory cultures, we also emphasize the importance of evaluating how different preservation methods affect ATAC-seq data quality. Based on examples in one spider and one ant species, we demonstrate that replication and thorough quality controls at all steps of the protocol and data analysis are essential to assess the usability of ATAC-seq data. Our data highlights the importance of isolating the right number of intact nuclei, as well as ensuring optimal amplification conditions during library preparation to obtain good-quality sequence data for downstream analyses. We recommend using fresh tissue samples if possible because we show that direct cryopreservation of the tissue may affect chromatin integrity. This effect could be avoided or reduced by preserving the homogenate in cell culture medium. Overall, we explain the ATAC-seq protocol and downstream analyses in detail and give step-by-step advice to researchers who are new to the field and want to implement this method. With careful planning and validation, ATAC-seq can reveal the regulatory landscape of a genome and aid in identifying elements that govern gene expression.

The mechanical loads from muscle contraction and gravity affect the biomechanical properties of long-bone limbs, varying according to the functional demands of each limb. In anurans, both limbs are used for locomotion, but the hindlimbs generate higher energy for jumping or swimming, and the forelimbs serve additional purposes (e.g., landing, amplexus, feeding, etc). This study examines the bone architecture of the forelimb bones (humerus and radioulna) and the hindlimb bones (femur, tibiafibula, tibiale, and fibulare) of 24 anuran species with different habitat uses within a phylogenetic context. Also, because of functional divergence among limbs, we investigate possible divergence in morphological integration among long bones depending on habitat use. Across all species, forelimb bones show significantly higher bone biomechanical properties values than hindlimbs, with aquatic and semiaquatic species exhibiting the most resistant bones to bending and fracture. The femur and tibiafibula of aquatic, semiaquatic, and terrestrial species showed similar and higher values, while arboreal species had the lowest values. The tibiale and fibulare bones show a unique stratified pattern across habitats, and in most species, these bones have higher values than the femur and tibiafibula. Although morphological integration varies across habitats-with terrestrial species showing the highest and aquatic and arboreal species the lowest, reflecting differences in limb specialization-the tibiale and fibulare uniquely exhibit significant covariation across all species. While phylogenetic factors may contribute to the observed variability, ecological factors play a crucial role in shaping bone geometry, highlighting the evolutionary adaptations of long bone resistance across ecological niches.

Behavioral stress responses allow animals to quickly adapt to local environments and are critical for survival. Stress responses provide an ideal model for investigating the evolution of complex behaviors due to their conservation across species, critical role in survival, and integration of behavioral and physiological components. The Mexican cavefish (Astyanax mexicanus) has evolved dramatically different stress responses compared to river-dwelling surface fish morphs, providing a model to investigate the neural and evolutionary basis of stress-like responses. Surface morphs inhabit predator-rich environments, whereas cave-dwelling morphs occupy predator-free habitats. While these key ecological variables may underlie differences in stress responses, the complexity of the behavioral differences has not been thoroughly examined. By leveraging automated pose-tracking and machine learning tools, we quantified a range of behaviors associated with stress, including freezing, bottom-dwelling, and hyperactivity, during a novel tank assay. Surface fish exhibited heightened stress responses characterized by prolonged bottom-dwelling and frequent freezing, while cavefish demonstrated reduced stress behaviors, marked by greater exploration and minimal freezing. Analysis of F2 hybrids revealed that a subset of behaviors, freezing and bottom-dwelling, co-segregated, suggesting shared genetic or physiological underpinnings. Our findings illustrate the power of computational tools for high-throughput behavioral phenotyping, enabling precise quantification of complex traits and revealing the genetic and ecological factors driving their evolution. This study provides a framework for understanding how integrated behavioral and physiological traits evolve, offering broader insights into the mechanisms underlying the diversification of animal behavior in natural systems.

Taxonomically restricted genes are increasingly understood to play major roles in evolution. However, a significant body of work has taken issue with the notion of widespread "novel" genes and argued that such genes have homologs in distant clades that can be found with either sufficiently powerful alignment techniques or by using synteny to find their ancestral sequences. Here, we argue that such work is misguided. Moreover, we argue that the whole notion of genetic assignment of function (and annotation) based on historical origin violates the levels of analysis distinction between origin and current utility. The evolutionary history of a gene is so often not reflective of its current utility that naming genes based on the function of their homologs is bad practice. This is nowhere more apparent than in the case of genes that have changed so radically from their ancestors that they bear no similarity to them at the sequence or protein folding levels. We coin the term, overwriting, for this process in which selection creates novel genes by completely changing the coding sequence of a gene in a manner that does not conserve function , and argue for the general importance of this mechanism.

In this article I am tracing the intellectual trajectory and historical context of Rupert Riedl's contributions to evolutionary theory, the book Order in Living Organisms (1978) and the accompanying article in the Quarterly Review of Biology (1977). These publications appeared at about the same time as Steven J. Gould's Ontogeny and Phylogeny as well as the "Spandrels" paper by Gould and Lewontin which initiated a major re-orientation of evolutionary biology. Riedl's work anticipated two major developments, the notion of developmental constraints in evolutionary developmental biology and the idea of evolvability. The factors that likely have limited the bibliometric impact of Riedl's work are also discussed.

Cell proliferation is a key driver of morphogenesis and body plan transformation in multicellular animals, yet its spatial organization remains poorly understood in many non-segmented spiralians. In this study, we examine the dynamics of cell division during larval growth and metamorphosis in the larvae and early juveniles of the phoronid Phoronopsis harmeri, using EdU incorporation, anti-phospho-histone H3 immunostaining, confocal laser scanning microscopy, and electron microscopy. Early larval proliferation is partly regionalized from the outset and becomes progressively more localized toward metamorphosis. We identify a tripartite organization of proliferative activity: (1) posterior ring-shaped domains in the telotroch that persist through metamorphosis and support elongation and anal chamber formation; (2) regional proliferative zones at tentacle bases, preoral and postoral regions; and (3) scattered proliferation driving the expansion of the trunk epidermis. This coexistence of posterior, regional, and scattered patterns underscores the developmental plasticity of phoronids and the diversity of growth strategies within Spiralia. Posterior proliferative domains in phoronids contribute important context to homology-convergence debates on posterior growth across spiralians, but are not decisive by themselves; viewed with the distributed epithelial proliferation, they underscore the coexistence of multiple proliferative programs within a single life cycle. In addition, we identify atypical mitotic characteristics in this species, including unconventional metaphase organization and signs of interkinetic nuclear migration in larval epithelia. Our results suggest that phoronids provide a valuable model for exploring how diverse architectures of cell proliferation contribute to larval growth, body elongation, and morphogenetic compartmentalization in Lophotrochozoa.

Nemertea is a phylum of predominantly marine worms that exhibit various larval forms, including the iconic pilidium. Pelagic lecithotrophic pilidia are considered more derived than pelagic planktotrophic pilidia, but data on the structure of lecithotrophic larvae are limited to the light-optical level. Here, we study the lecithotrophic reversed Iwata's larvae of an undescribed heteronemertean, Nipponomicrura sp. Using transmission electron microscopy and confocal laser scanning microscopy with F-actin, acetylated α-tubulin, and serotonin (5-hydroxytryptamine) labeling, the provisional structures of the larva are described. The larval envelope of Nipponomicrura sp. consists of three layers: the epidermis, the circular musculature, and the epithelium of the amnion. The larval epidermis contains a considerable amount of yolk, only half of which is consumed by the end of metamorphosis. The apical plate consists of 5-hydroxytryptamine-negative cells, each bearing a cilium surrounded by a collar of eight to nine microvilli. Four monociliated 5-hydroxytryptamine-like-immunoreactivity sensory apical neurons are associated with the apical plate. For the first time, a pair of longitudinal muscles running along the body of the juvenile and joining the anterior and posterior parts of the provisional epithelium has been identified in nemertean larvae. These muscles serve as retractors of the apical plate and fix the position of the juvenile within the larva. The obtained data indicate a similar morphology of the apical organ in Pilidiophora larvae; however, in the Nipponomicrura sp. larva, there are more layers under the apical plate, and the muscle-retractor is derived from two longitudinal muscle cords that pass through the juvenile's body, and in posterior pole, attach at the base of the larval envelope.

Synaptonemal complex protein 3 (Scp3), a structural component of the synaptonemal complex, serves as a key molecular marker for studying meiosis and germ cell development in teleosts. To elucidate the molecular mechanisms of germ cell meiosis and identify critical windows for sex differentiation in turbot (Scophthalmus maximus), a flatfish of considerable economic value in global aquaculture, this study cloned the full-length cDNA sequence of the scp3 gene. The obtained sequence is 1094&#x2009;bp in length, containing an open reading frame of 717&#x2009;bp that encodes a polypeptide of 238 amino acids, with bioinformatic analyses revealing characteristic coiled-coil domains. Tissue distribution analysis demonstrated that scp3 expression was predominantly restricted to the gonads. Quantitative PCR in an all-female lineage revealed that transcripts were initially detectable at 25 days post-hatching (dph), remained low until 55 dph, and increased significantly thereafter, peaking after 80 dph (p&#x2009;<&#x2009;0.05). In situ hybridization localized scp3 mRNA to the cytoplasm of early primary oocytes. The expression window, initiating at 25 dph and intensifying from 60 dph, aligns with the initiation of meiotic prophase I and precedes morphological sex differentiation. These results indicate that scp3 functions as a reliable noninvasive molecular marker for the onset of meiosis in female turbot and may play a specific role in oocyte proliferation. This study provides a crucial theoretical foundation and key temporal information for further elucidating the molecular mechanism of sex differentiation and advancing all-female population cultivation in turbot.

Ecomorphology examines how species' morphology adapt to their environments, providing insights into biodiversity and evolution. This field relies on three main components: a morphological matrix, an ecological matrix, and phylogeny. A major challenge in contemporary anuran ecomorphology is constructing the ecological matrix, as categorizing species' ecological roles lacks a standardized methodology, leading to inconsistencies across studies and complicating comparisons. In this study, we discuss the challenges of systematizing criteria for constructing the ecological matrix in anurans. To this end, we conducted a literature search, focusing on studies that consider microhabitats as ecological categories and locomotor abilities, using relevant keywords to the topic. A total of 31 studies from the last 46 years were selected for analysis, and information was extracted on the following aspects: analyzed species; microhabitat and locomotor mode categories; and whether or not own criteria for assigning ecological categories (i.e., microhabitat and locomotor modes) were specified. The analyzed studies reveal a high degree of consistency in the assignment of ecological categories for microhabitat classification but not for locomotor modes designation. The main discrepancies occur in the burrowing and/or fossorial categories, as well as climbing. Interestingly, these categories appear both as microhabitats and as locomotor modes. Key criteria include direct field observations and assignments based on primary literature sources. The variability in category assignments and data collection criteria underscores the need to develop more standardized protocols for ecological categorization to improve the accuracy and reproducibility of ecomorphological studies.

Asymmetry in a bilateral organism refers to the difference in the expression of a trait between right and left sides, which may result from genetic or environmental disturbances. Using geometric morphometrics and a phylogenetic approach, we studied asymmetry in dorsal and ventral views of the skulls of anuran species, representing 22 families, 16 of which belong to the Hyloidea clade. The cranial regions with the most pronounced shape asymmetry were identified. To discern species with elevated levels of asymmetry and to hypothesize its evolutionary trends across phylogeny we implemented the asymmetry index. Significant asymmetric skull shape variation was found between right and left sides, associated with the upper area of the mandibular joint and the anterior area of the nasals in dorsal view. In ventral view, the greatest variation was in the vomers and the ala of the parasphenoid. The degree of size-related asymmetry varied among species. Character mapping results indicate that cranial asymmetry is a conserved and widespread trait in the Hyloidea clade, representing an ancestral condition across both dorsal and ventral regions of the skull. The observed asymmetries were found in traits that develop later in their ontogeny, which would imply that as they establish fewer developmental dependencies with other traits and, consequently, are less phylogenetically constrained. The asymmetries we found belong to this category and would be more prone to change during evolution.

The ParaHox homeobox genes Gsx, Xlox, and Cdx are evolutionarily related to Hox genes and form part of the ANTP-class homeobox gene repertoire. Comparative genomic data indicate that ParaHox genes were already present before the cnidarian-bilaterian split. Across metazoans, ParaHox genes often show conserved associations with the anteroposterior body axis and have been implicated in both gut patterning and neural development, although gene complements and genomic organization vary substantially among lineages. To investigate ParaHox gene deployment in Gnathifera, we identified orthologs of Gsx and Cdx across gnathiferan lineages, including Chaetognatha, Monogononta, Bdelloidea, Seisonidea, and Acanthocephala, but found no evidence of Xlox, indicating a reduced ParaHox gene complement. We analyzed the genomic organization and embryonic expression of Gsx and Cdx in the monogonont rotifer Brachionus manjavacas (Bm). Genomic mapping revealed a dispersed ParaHox configuration, with Bm-Gsx and Bm-Cdx separated by 4.4&#x2009;Mb. Using whole-mount in situ hybridization, we detected Bm-Gsx expression in neurons of the foot region, as well as in a small number of cells with neuronal characteristics and probable involvement in stomatogastric system development. Bm-Cdx was expressed in FMRFamide-positive cells associated with the bladder, consistent with a neuroepithelial identity. Together, these data indicate that in rotifers, ParaHox gene expression is predominantly associated with neural structures. We propose that this pattern represents a derived condition reflecting the compact body plan and reduced gut organization characteristic of rotifers, highlighting the evolutionary flexibility of ParaHox gene deployment under lineage-specific developmental constraints.

Pigmentation has long served as a powerful system for exploring gene-trait relationships, yet much of the field has focused on a relatively narrow group of well-established genes involved in melanin production and pigment cell differentiation. Recent advances, however, have allowed pigmentation to be studied through a more comprehensive framework. By combining artificial intelligence (AI)-driven phenotyping with genomic mapping approaches such as genome-wide association studies, QTL mapping, and structural variant analysis, a broader range of pigmentation regulators has been identified across diverse animal taxa. This review highlights studies where AI methods, including deep learning, self-supervised modeling, and pattern recognition, have been used to quantify complex pigmentation traits in animals. These approaches have enabled the discovery of non-classical pigmentation genes involved in membrane trafficking, intracellular signaling, structural organization, and non-coding regulation. Rather than displacing the classical pigmentation paradigm, these findings extend it, revealing a wider set of genetic contributors to coloration and pattern diversity. We introduce the term AI-pigmentomics to describe the integration of AI-driven phenotyping with genomic mapping, as part of the broader emergence of AI-omics. Together, AI and genomic mapping are reshaping our understanding of pigmentation by uncovering unexpected biological mechanisms and providing a framework for investigating pigmentation in both model and non-model species.

In vertebrates, the provision of nutrients to developing embryos varies widely, ranging from yolk-dependent strategies to highly specialized forms of placental nourishment. Vitellogenins (VTGs) are essential proteins for egg yolk formation in oviparous and lecithotrophic species. In contrast, in eutherian mammals, the loss of VTGs is associated with the evolution of matrotrophy (placentotrophy and lactation), where maternal nutrition via the placenta replaces the need for large yolk reserves during embryonic development. Marisora sp., a placentotrophic viviparous lizard with the most complex placenta known in reptiles, exhibits truncated vitellogenesis, resulting in the production of microlecithal eggs. This study investigated the presence of VTGs in Marisora sp. using RNA-seq from the liver and ovary at previtellogenesis and vitellogenesis stages. No corresponding annotations for VTGs were found. This absence may be associated with the placentotrophic nutrition of the embryo, suggesting modifications in lipid production and transport to the ovarian follicles. Apolipoprotein B (ApoB) and microsomal triglyceride transfer proteins (MTP) were identified, which are closely related to VTGs and could fulfill their function, especially ApoB, which is involved in yolk formation in lecithotrophic species in which VTGs are absent. The absence of VTGs in the Marisora sp. transcriptome represents a key discovery in the evolution of obligate placentotrophic viviparity in reptiles, highlighting convergent traits with mammals. Genomic studies are required to determine if changes in VTG genes prevent or modify their expression, and proteomic studies are needed to fully understand the role of other lipid transport proteins in the preovulatory ovarian follicles of these lizards.

The tetrapod heart is characterized by three chambers in amphibians and non-avian reptiles, as opposed to four in birds, crocodilians and mammals. We explored this diversity via the most phylogenetically comprehensive comparison of heart transcriptomes undertaken to date. Transcriptomes representing the ontogeny of heart compartmentalization (septation) in alligator, chicken, frog, mouse, lizard and turtle embryos exhibited a clear species-specific signal, which was driven by genes involved in heart contraction. During the stage dominated by septation-related tissue transformations, the most highly expressed genes shared by species originated before the tetrapods diversified and were related to septum morphogenesis, ventricular development, and chamber formation. The expression of septation-related genes did not adhere to phylogeny or heart chamber number, and genes differentially expressed across developmental stages within species varied in their evolutionary ages and predicted functions. We discuss how the acquisition of novel structures in some lineages, convergent evolution of four heart chambers, embryonic metabolism, microstructural variation, and ontogenetic shifts (heterochronies), collectively, provide insight into evolved and conserved patterns of transcriptome-level variation. These data serve as a resource to further stimulate evo-devo research on complex organ systems, such as the heart.

The present study reveals the immunolocalization of the MARCKS-like protein in two urodeles and an anuran during the initial stages of appendage regeneration. This acidic protein of 22-32&#x2009;kDa interacts with the dynamic cytoskeleton of activated keratinocytes and blastema cells and is believed to be among the initial signaling factors stimulating limb regeneration in the axolotl. Bioinformatics controls indicate presence of homologous MARCKS-like proteins also in other amphibian species. The present study aims to generalize the presence of this protein during the first 2-8 days of appendage regeneration in amphibians. In the wound epidermis of the axolotl, the protein is prevalently localized in pale Leydig cells, a mucous cell type described in amphibian epidermis, many of which are present in the regenerating epidermis. A lower immunolabeling is found in the newt wound epidermis but is high in regenerating nerves. In the regenerating tail of frog tadpoles MARCKS-like immunolabeling is present in the wound epidermis, regenerating spinal cord, ganglia and nerves but also with lower intensity in myotubes and in the external layer of notochord. Low to absent MARCKS-like immunoreactivity is instead observed in the normal epidermis and in the wound epidermis of the non-regenerating tadpole limb. Although mainly cytoplasmic, also some nuclear labeling is detected in immunoreactive cells of different tissues, especially in the spinal cord, suggesting the activation of nuclear transcriptional process. The protein is present in tissues with high proliferative activity, but is low to absent in most blastema cells and connective tissues during regeneration. The study indicates that the presence of MARCKS-like protein is a general reaction that favors regeneration in amphibians and possibly also in other vertebrates.

The impact of land-to-water transition on chemosensory genes has been explored in marine tetrapod vertebrates, with scarce data on aquatic insect lineages. Diving beetles (Dytiscidae) are predaceous freshwater insects with strictly aquatic larvae and amphibious adults. Using RNA-seq, we compared the expression of odorant receptors (ORs), gustatory receptors (GRs), ionotropic receptors (IRs), and odorant-binding proteins (OBPs) in the cephalic appendages of larval and adult Cybister lateralimarginalis. Overall, larvae expressed fewer chemosensory genes than adults but larva-specific genes displayed a unique expression pattern, not previously observed in any other holometabolous insect, with five larva-specific ORs all having a close paralogue which is adult-specific, 14 larva-specific IRs all belonging to a single gene expansion in the IR tree, and no larva-specific GR. Expression profiles across appendage types mirrored those in aerial insects, with ORs mainly in antennae, GRs in labial palps, "Antennal class" IRs in antennae, and "Divergent class" IRs in palps. This suggests that the land-to-freshwater transition in this lineage did not involve major changes in deployment of the major families of chemosensory genes among cephalic appendages. Notably, the expression of a substantial repertoire of ORs specifically in the antennae of the larva suggests that hydrophobic chemical cues are important for long-range chemodetection in freshwater, contrary to prevailing views about constraints for chemosensation within a water medium.