Journal of Experimental Zoology Part B: Molecular and Developmental Evolution

Scyphozoan jellyfish have a complex life cycle that includes a characteristic transition known as strobilation. Retinoid signaling has been suggested to be involved in jellyfish metamorphosis and development. However, the genomic basis of signaling pathways associated with metamorphosis has not been sufficiently compared at the class level. Experimental studies have reported that indole compounds can induce metamorphosis in some jellyfish species. Indole- and tryptophan-derived metabolites are known to function as ligands for the aryl hydrocarbon receptor (AhR) in other organisms. However, the potential role of AhR signaling in jellyfish metamorphosis has not been previously explored. We compared the distribution of retinoid- and AhR-associated gene families across multiple scyphozoan genomes. This analysis aimed to characterize their distribution patterns in relation to signaling pathways associated with development and environmental responses. A standard gene prediction and annotation pipeline was applied to 20 species from 21 publicly available scyphozoan reference genome assemblies retrieved from the NCBI database. The distribution and copy number of these gene families were compared across species. Retinoid-associated gene families were detected across almost all Scyphozoa genomes, and core components of AhR signaling (AhR, ARNT) were identified in most species. These results suggest that scyphozoan genomes contain genetic components of retinoid- and AhR-related signals. This study presents the distribution of gene families related to developmental signaling across Scyphozoa using a comparative genomic approach. It does not imply direct functional involvement of retinoid or AhR signaling, but instead focuses on potential signaling pathways at the genome level. It also provides an overview of currently available scyphozoan genomic data. These findings provide a basis for future hypothesis generation and functional validation in jellyfish metamorphosis research.

High and low tides occur twice a day (every [~]12.4 hours), with the largest tidal ranges during spring tides around new and full moons (every [~]14.765 days). While these lunar cycles are known to influence many animal phenotypes, particularly the reproduction of coastal animals, the genetic basis of lunar-related rhythms remains unclear. Since phenotypic variation is a valuable resource for elucidating such mechanisms, we examined geographic variation in the lunar-regulated mass spawning of the grass puffer (Takifugu alboplumbeus) along the Japanese coast. We found that western populations spawn during the first half of the spring tides, whereas eastern populations spawn during the second half. Furthermore, although spawning typically occurs a few hours before high tide, this timing is restricted to a specific time window that is earlier in the western populations than in the eastern ones. Behavioral analysis of larvae also revealed a shorter free-running circadian period ({tau}) in the western population than in the eastern ones. As differences in {tau} affect individual variation in the timing of physiological functions and behaviors, we hypothesized that differences in {tau} could account for the different time windows and consequently the observed difference in spawning days. Population genomics analysis identified proline-rich transmembrane protein 1-like (prrt1l) as a candidate gene. Expression of prrt1l was observed in the circadian pacemaker suprachiasmatic nucleus, and triple CRISPR F0 knockout of prrt1l shortened the free-running period in larvae. These findings suggest a potential mechanism underlying the geographic variation in lunar-synchronized spawning behavior. HighlightsO_LIThe geographic variation exists in the lunar-regulated spawning of the grass puffer, with differences in spawning dates and times between western and eastern Japan. C_LIO_LIThe free-running period of western populations is shorter than that of eastern populations, which is consistent with their earlier spawning timing. C_LIO_LIPopulation genomics analysis identified prrt1l as a candidate gene harboring population-specific missense mutations, the knockout of which shortens the free-running period. C_LI

The evolution of body shape reflects the interplay between functional constraints and habitat structure. In fishes, cave environments are well known for promoting regressive traits such as eye and pigment loss, yet their influence on overall body form remains poorly understood. Here, we examine patterns of body shape variation in cave- and surface-dwelling trichomycterid catfishes from northeastern Colombia to assess whether consistent associations exist between habitat type and morphology. Using geometric morphometric analyses, we quantified differences in body shape among species inhabiting subterranean and surface environments. Our results reveal significant habitat-associated differentiation in body shape along the main axes of morphological variation. Cave-dwelling species exhibit more elongated and fusiform body shapes, whereas surface-dwelling species tend to show deeper and more robust morphologies. In a functional context, these contrasting body patterns suggest associations with differing locomotor demands imposed by subterranean versus surface habitats. Although we do not explicitly test convergence or performance, the recurrence of similar body shapes among species from different clades occupying comparable habitats is consistent with repeated morphological responses to shared ecological constraints. Research HighligthsO_LIMultivariate shape analyses reveal significant habitat-associated variation in trichomycterid fishes. Recurrent morphological patterns suggest repeated responses potentially mediated by habitat constraints. C_LIO_LIBody shape differs consistently between cave- and surface-dwelling trichomycterids. Cave species exhibit more elongated and fusiform forms, whereas surface species display deeper body configurations. C_LI

In many oviparous animals, egg yolk is the sole source of nutrition until feeding begins, and carbohydrates are present in only small amounts in the yolk. Glucose plays an important role in the developmental processes of various animals. In addition, gluconeogenesis has been reported to occur in the yolk syncytial layer (YSL) of cartilaginous fish and teleosts. In contrast, the role of gluconeogenesis in tetrapods remains unclear. In this study, we used Xenopus tropicalis, an anuran amphibian, which lacks YSL, and therefore provide an opportunity to examine the evolutionary conservation of gluconeogenic mechanisms among vertebrates. In X. tropicalis, liquid chromatography/mass spectrometry revealed that glucose levels increased before liver formation. Subsequent tracer experiments using 13C-labeled metabolic substrates detected gluconeogenesis activity from glycerol and lactate. Expression analyses showed that gluconeogenic genes are expressed in the epidermis and endoderm. Consistently, G0 knockout of fbp1, a key gluconeogenic gene, resulted in a significant reduction in glucose levels, affecting brain development. These findings first demonstrate that gluconeogenesis supports development of X. tropicalis. To the best of our knowledge, gluconeogenesis in developing epidermis has not been reported, highlighting previously unrecognized diversity in tissue-specific metabolism during vertebrate development. Comparative analyses across species will provide further insights into the evolution and functional significance of embryonic gluconeogenesis and nutrient metabolism.

We examined the overlap in the genes associated with daily rhythms and with behavioral plasticity in ants. We first investigated the daily rhythms of gene expression in the harvester ant, Pogonomyrmex barbatus, and how the rhythmic genes overlap with others previously shown to be associated with plasticity of foraging behavior. Then, to consider whether the overlap is conserved across ant species, we compared rhythms of gene expression in the diurnal, desert harvester ants with those previously reported for a distantly related nocturnal, subtropical carpenter ant, Camponotus floridanus. First, daily transcriptomes in P. barbatus showed that most genes were expressed in light-dark (LD) and constantly dark (DD) conditions at about the same levels; only 11 genes showed at least a two-fold change in expression. Network analysis identified eleven modules of P. barbatus genes under LD conditions. Of these 11 clusters, modules C1 and C2 seem to be central nodes of the gene expression network, because they are the most highly connected in LD, and show the strongest preservation in DD vs. LD, and contain core clock gene Period. Only one module, C2, showed significant overlap with P. barbatus genes that have 24h-rhythmic expression in both LD and DD. There was significant overlap between modules C1, C2, C10, C11, and P. barbatus genes found previously to be associated with plasticity in the regulation of foraging activity to manage water loss. A comparison of the daily transcriptome of P. barbatus with that of C. floridanus showed significant overlap of 24h-rhythmic genes in LD. Modules C1 and C2 of P. barbatus also overlap with C. floridanus genes previously shown to differ in expression rhythms in nurses and foragers. In combination, these results indicate that genes linking plasticity of the circadian clock and of behavior may be broadly conserved in ants.

Dental enamel, the hardest mineralised tissue in the human body, has proven to be an excellent source of ancient proteins, which have been found to survive within dental enamel for at least twenty million years. In archaeological and palaeontological contexts, the enamel proteome is generally considered to be rather small, consisting of about twelve proteins, most of which are unique to enamel. During amelogenesis these proteins undergo in vivo digestion by matrix metalloproteinase 20 (MMP20) and kallikrein 4 (KLK4) as well as serine phosphorylation by family with sequence similarity member 20-C (FAM20C) that alter their characteristics. Gaining knowledge of the previously understudied influence of amelogenesis on the archaeological human dental enamel proteome could benefit various palaeoproteomic analysis, especially in an human evolutionary context. Here we present archaeological dental enamel proteomes and explore protein cleavage patterns and sequence coverage to estimate the effects of in vivo digestion, as well as explore phosphorylation patterns. Additionally, we present a new marker based on phosphorylation to estimate genetic sex.

In tunicates, larvaceans represent a fascinating case of evolution, where the chordate body plan has been maintained despite a rapidly evolving genome characterized by strong In contrast to other tunicates, larvaceans keep the chordate body plan during their entire life. They have acquired a highly specialized epithelium in charge of producing the "house", a complex extracellular apparatus used for filter feeding in the plankton. To what extent the house and this epithelium represent true molecular innovations withing chordates is a question for which thorough transcriptomics can bring novel insights. We conducted a developmental profiling of gene expression at the single-cell level in the larvacean Oikopleura dioica. We provide detailed descriptions of cellular transcriptomes associated with the house-synthesizing organ, which permits to define the molecular specifics of epithelial cell territories. We followed their emergence during development, and we identified genes that represent key candidate molecules for regulating the morphogenesis of the house-producing organ. Dynamic changes in gene expression and cell identities during major developmental transitions of the lifecycle illustrate that our dataset effectively allows access to the diversity of O. dioicas cell types in embryos and in adults. The resources presented here constitute critical assets to investigate larvacean biology and evolution for mechanistic and comparative goals.

Sarita Lake, British Columbia houses a distinctive population of threespine stickleback (Gastrosteus aculeatus L.) with a phenotype characterized by unusually large individuals relative to nearby conspecifics. We tested the hypothesis that members of this population are not isometrically larger but rather exhibit variation in allometric trajectories that reflect changes in developmental timing impacting the developmental-genetic architecture of the phenotype. We used 3D geometric morphometrics to characterize the size and shape of skulls, pectoral girdles and pelvic girdles from a sample of individuals from nearby freshwater and marine populations and compare them to a sample from Sarita Lake. We showed that individuals from the Sarita Lake population are larger in each body region compared to most other populations examined. Further, these individuals have dorsally expanded skulls and relatively robust pelvic armour. We also showed that the relationship between size and shape is differently structured among body regions and is heavily influenced by non-uniform sexually-mediated variation across populations sampled. Our results reflect complex underlying developmental trajectories, and we suggest that the large phenotype observed may be driven by fecundity selection on female size in combination with a limnetic trophic niche and relatively increased predation pressure in Sarita Lake.

Harbour porpoises (Phocoena phocoena) in the North and Baltic Seas are increasingly impacted by anthropogenic pressures, including underwater noise, fisheries and pollution. These pressures correlate with declining population health, particularly affecting the respiratory system. Growing pathological lesions, partly resulting from high prevalence of parasitic infestations and subsequent diseases, can impair tissue function and oxygen supply to distant end-organs. In this study, we applied an integrative MultiOmics approach (proteomics, metabolomics, lipidomics) to analyse the lungs and muscles of 12 wild harbour porpoises with compromised respiratory health. Our aim was to identify dysregulated biological pathways across omics layers to advance insights into adaptive physiological responses and to define disease-associated molecular signatures that could assist health assessments. Our analysis revealed pronounced immune system and antioxidative responses in the lungs and muscles, indicated by enhanced immunoglobulins, plasmalogens and glutathione-related proteins. In the lungs, high cardiolipin levels and reduced collagen suggest impaired tissue structure and function, while tissue maintenance processes were elevated in the muscle. Both tissues exhibited metabolic alterations suggestive of energetic imbalance, including increased purine metabolism in the lung and decreased lipid metabolism in the muscle. Several dysregulated molecules were shared across tissues, pointing to pathophysiological effects. The proposed disease-associated molecular signatures included the protein SLC25A4, the metabolite O-phosphoethanolamine and the lipid TG O-16:0_16:0_20:4 for the lung, and the protein SPEG, the metabolite pipecolic acid, and the lipid BMP 18:1_22:6 in the muscle. Our findings elucidate the complexity of molecular mechanisms linking anthropogenic and environmental stressors with vulnerability and resilience in a marine sentinel species. Furthermore, this study highlights the potential of integrative omics to define disease-related marker panels, thereby supporting ongoing and future health monitoring and conservation efforts.

The cockroach Blattella germanica possesses panoistic ovaries, in which oocytes lack nurse cells and therefore need to rely on their own transcriptional activity to support embryogenesis. Ovarian development in this species involves the development of a single basal ovarian follicle (BOF) per gonadotropic cycle, a process strictly regulated by endocrine signals, primarily juvenile hormone and ecdysone, which act at both the transcriptional and translational levels. In addition, transcriptional activity in these ovaries is necessary for both regulating and genome protection, and at this level, PIWI-interacting RNAs (piRNAs) play an essential role. Although insect ovaries are known to be particularly rich in piRNAs, their function in ovary maturation is still not well defined. For this purpose, we characterize the piRNA expression dynamics across seven key developmental and reproductive stages, ranging from late nymphal instars to post-vitellogenic adults. piRNA expression in B. germanica shows coordinated fluctuations. Expression remains stable in previtellogenic ovaries, whereas vitellogenic ovaries show pronounced changes. Moreover, vitellogenic ovaries exhibit reduced piRNA diversity due to strong enrichment of a subset of highly expressed piRNAs. Our data show that although piRNAs predominantly map to transposable elements, particularly LINEs, there is a notable increase in gene-derived piRNAs toward the end of the cycle. Our results suggest regulatory roles of piRNAs in modulating both TEs and mRNAs during BOF maturation, likely related to changes in the follicular cell program.

Ancient human dental calculus is one of the richest archives of archaeological biomolecular information, providing direct evidence of diet, oral health, and the oral microbiome. Proteomic analyses of this biological matrix have so far focused mainly on oral microbes and dietary proteins, with milk proteins such as beta-lactoglobulin (BLG) providing the largest corpus of proteomic evidence. Despite the close relation between the various stages of dental calculus formation and mineralization with the dental enamel surface, proteins from the dental enamel matrix have not previously been reported outside of dental enamel tissue. Here we reanalysed 498 ancient dental calculus proteomes from 14 published studies (n=434 individuals) reporting the presence of BLG, spanning from the Neolithic to the Victorian Era and applying different protein extraction protocols (FASP, GASP, SP3 and in-solution digestion). Dental enamel matrix proteins were identified in ten studies (n=37 individuals), with amelogenin being the most frequently detected. Enamel peptides occurred more often in studies that applied SP3, although amelogenin was successfully identified through both SP3 and FASP. Structural proteins, including enamelin, ameloblastin, and MMP20, were also identified. The detection of AMELX and AMELY peptide sequences provided new insights into cases where the sex was previously undetermined. These findings establish dental enamel proteins as a new category of biomolecules detected in dental calculus, broadening its application beyond diet and microbiome studies to possible sex estimation. HighlightsO_LIDental calculus entraps oral microbes along with endogenous and exogenous particles during formation and mineralization C_LIO_LIWe conduct reanalysis of 14 published ancient dental calculus studies (n = 434 individuals) spanning the Neolithic to Victorian Era C_LIO_LIDental enamel proteins AMELX, AMELY, AMBN, COL17A1, ENAM and MMP20 are identified in ancient human dental calculus C_LIO_LIAmelogenin was the most frequently detected enamel protein C_LIO_LIWe expand dental calculus palaeoproteomics beyond diet and oral microbiome to potentially include sex estimation C_LI

Although cartilage in tetrapod skeletons is typically said to lack blood vessels, this is only true for adult cartilage. In young bird and mammal cartilage, a dense network of vasculature-containing tunnels --cartilage canals-- perforate the growing skeleton, helping nourish the cartilage and develop the ossification centers that will later form the skeletons epiphyseal bone. As the canals and their rich vascular network typically recede as animals age, the healthy cartilage of adult animals is typically known to be avascular. Here, however, we use a range of tissue characterization and visualization techniques --including light/electron microscopy and microCT-- to show that the skeletons of rays and sharks (elasmobranch fishes) not only possess cartilage canals, but that these structures persist in the adult skeleton. The morphology and tissue composition of elasmobranch cartilage canals argues homology with mammalian cartilage canals and an ancient invasion of the vascular system into cartilage. However, the anatomical location of canals --extending away from mineralized tissue not toward it-- and the lack of endochondral ossification in ray and shark cartilage suggest that cartilage canals developed early in vertebrates as a transport system for nutrients and mesenchymal cells into the growing skeleton. We describe distinctive features and variation in elasmobranch cartilage canals, discuss their possible roles and their potential for tissue mineralization, and the biomedical implications for their presence in a clade of animals with continuously growing cartilaginous skeletons.

The Meckels cartilage (MC) is a fundamental component of mandibular development across vertebrates. In mammals, MC is transient and functions primarily as an early template for mandibular ossification, whereas other vertebrates, including zebrafish, retain MC within the mandible throughout life. Despite its importance, the requirements for MC in sustaining mandibular growth and how signaling pathways implicated in MC development contribute to this process remain unclear. Here, we investigated the dosage-dependent roles of BMP antagonists during zebrafish MC development using mutant alleles of grem1a, nog2, and nog3. Compound mutant adults exhibited fully penetrant mandibular truncation. MC shortening emerged after early larval stages, indicating a requirement for BMP antagonism to sustain cartilage growth. Chondrocyte number remained unchanged as phenotypes developed, but mutants displayed disorganized cartilage morphology and increased chondrocyte volume. Molecular analyses revealed reduced col2a1a domains and expanded ihha and col10a1a expression, consistent with ectopic hypertrophic-like differentiation. Constitutive activation of BMP receptor signaling in chondrocytes recapitulated these phenotypes. Although osteogenesis appeared unaffected by 14 dpf, loss of a tnn skeletal mesenchyme population was observed. Together, these findings demonstrate that BMP antagonists sustain MC growth by regulating chondrocyte differentiation and cartilage organization to support mandibular growth in non-mammalian vertebrates. Summary StatementThis study leverages zebrafish to define the cellular and molecular mechanisms by which BMP antagonism sustains mandibular growth.

The presence of multiple discrete color patterns within a species has captivated evolutionary biologists for more than a century, especially when such polymorphism is confined to one sex. The brown anole Anolis sagrei exhibits a female-limited polymorphism in dorsal patterning, which is controlled by allelic variation at the autosomal gene CCDC170. Here, we present and test a threshold model that can explain why the polymorphism is female-limited. We hypothesize that allelic variation at the CCDC170 locus affects only female color pattern because this gene is co-expressed with its neighboring gene ESR1, highly expressed in female, but not male, embryos. By manipulating embryonic estradiol levels, we show that genetic males can be induced to express the polymorphism according to allelic variation at the CCDC170 locus, which is naturally masked by low expression levels of this gene. Inversely, treating genetic females with fadrozole, which depletes estradiol, leads to monomorphic patterns irrespective of genotype, as for natural males. Using RT-qPCR, we demonstrate that these effects are accompanied by a direct influence of estradiol and fadrozole on gene expression levels of CCDC170 and ESR1, thereby validating the threshold model. Our results suggest that the CCDC170-ESR1-locus is part of a mechanistic link between the morph-determining and the sex differentiation systems and provide a causal explanation for the developmental origin of a sex-limited color polymorphism.

At a mere 20 cells, the Caenorhabditis elegans intestine regulates metabolism, energy homeostasis, host defense, yolk production, and genetic aging, all while dynamically responding to its environment. How the intestine develops to carry out these disparate functions is unknown, and how cells differ along the length of the intestine is unclear. To address these questions, we performed single-cell RNA sequencing (scRNA-seq) on FACS-enriched intestinal cells from mixed-stage C. elegans embryos. The resulting single-cell transcriptomes of 974 cells organized into 13 clusters, suggesting a diversity of cell types and states. We used two post hoc approaches to ascribe identities to each cluster. First, genes with known developmental timing in early-, mid-, and late-stages were used to place clusters in time, and smiFISH microscopy was used to fine-tune the assignments. Second, the eight late-stage clusters were assessed for their region of origin. To assign these clusters to anatomical regions, we identified marker genes for each cluster and assessed their expression along the anterior-to-posterior length of the intestine using smiFISH microscopy. Genes associated with growth and cell division were expressed in early stages, whereas genes associated with immune responses and metabolism were expressed later. Genes associated with biotic responses and RNA metabolism were the most likely to vary across the intestines anterior-posterior axis. Finally, perturbation of anterior-localized intestinal transcripts more robustly affected intestinal function compared to central or posterior-localized genes. Overall, this research illustrates the intrinsic heterogeneity across the 20 cells of the embryonic intestine and sets the stage for future works aimed at understanding cell-specific intestinal responses to diet and the environment. ARTICLE SUMMARYWe investigate how the Caenorhabditis elegans intestine develops specialized functions on a spatiotemporal scale. We used single-cell RNA-sequencing to analyze embryonic intestinal cells and identify 13 distinct clusters. Combining gene expression analysis with microscopy, we assigned clusters to developmental stages and anatomical regions. Clusters associated with early intestine development express genes linked to growth and cell division, while later-stage clusters express genes involved in metabolism and immune responses. Genes varied across the intestines anterior-to-posterior axis, and disrupting anterior-specific genes produced stronger functional effects. These findings reveal previously unrecognized intestinal diversity and provide insight into how intestinal cells specialize during development.

The protein composition of sperm and seminal fluid are key to male fitness. However, we currently lack an understanding of the factors that shape seminal proteome composition. The common bedbug (Cimex lectularius) mates by traumatic insemination, subjecting the ejaculate to a unique selective environment as sperm traverse the female genital and paragenital system. We provide the first high-throughput proteomic characterisation of the sperm and seminal fluid proteome in a hemimetabolous insect and the first in-depth proteomic characterisation of the male bedbug reproductive system. Our analysis revealed conserved and unique features of the sperm and seminal fluid proteome with possible links to features of sperm behaviour linked to traumatic insemination. The sperm proteome showed elevated rates of molecular evolution, unlike most other studied species. Conversely, the sperm proteome also contained many conserved proteins. Notably, we found an expansion of Sperm-leucylaminopeptidases (S-Laps) in bedbugs and other hemimetabolous insects, suggesting the origin of S-Laps is perhaps even more ancient than previously thought. Using in silico protein-ligand binding predictions, we show that S-Laps have likely retained catalytic activity. Our results provide a list of candidate proteins involved in reproduction and a foundation for future studies of this expanding global pest.

Transgenerational epigenetic inheritance (TEI) allows organisms to express heritable responses to environmental stresses, and can potentially contribute to adaptive evolution. The microbivorous model organism Caenorhabditis elegans is perhaps the best example, as it can learn to avoid pathogenic Pseudomonas bacteria and transmit this learned avoidance to its offspring. However, the extent to which TEI is widespread in nature remains unclear, and therefore our understanding of the generality of this response is limited. To address this, we conducted the first comparative study of TEI across five Caenorhabditis nematode worm species (C. kamaaina, C. elegans, C. tropicalis, C. remanei and C. briggsae). These species differ in RNA interference competence and in the degree of sequence homology between Caenorhabditis worm genes and bacterial RNAs, two factors thought to influence epigenetic responses. We examined transgenerational avoidance of P. vranovensis, a pathogen that reduces fitness in all five species tested. In addition to C. elegans, we found that C. remanei also exhibited transgenerational avoidance of P. vranovensis, whereas neither learning nor inheritance was observed in the other three species. In addition, parental exposure to P. vranovensis also conferred a transgenerational survival benefit upon pathogen encounter in C. elegans, C. remanei and C. tropicalis. Our findings show that TEI of pathogen avoidance extends beyond C. elegans but is not a general response across Caenorhabditis species. This shows that TEI is a species-specific response and highlights the need to understand TEI alongside other responses to environmental variability.

Dauer larvae are a dormant developmental stage in nematodes that is induced by a range of environmental cues. The molecular mechanisms that transduce these cues to regulate dauer entry have been well characterized in Caenorhabditis elegans, whereas those in other nematode species remain unclear. The closest known sibling species of C. elegans, Caenorhabditis inopinata, occupies a distinct ecological niche and shows an extremely low frequency of dauer formation by starvation in laboratory conditions, suggesting that it could serve as a useful comparative model for analyzing dauer-inducing mechanisms. To support such analysis, we generated a fluorescent dauer reporter, Cin-col-183p::mCherry, in C. inopinata based on a previously reported dauer-specific reporter in C. elegans. This reporter showed fluorescence specifically in the pre-dauer and dauer stages, but not in other developmental stages, indicating that it functions as a dauer-specific marker in C. inopinata. Using these marker strains, we compared the responses to high temperature and RNAi-mediated knockdown of insulin/IGF-1 pathway genes (daf-2, age-1, and pdk-1), and found that dauer induction differs mechanistically between C. elegans and C. inopinata. This dauer-specific fluorescent strain will be a useful tool for investigating the diversity of dauer-inducing mechanisms across nematode species. Article SummaryDauer is a dormant developmental stage in nematodes induced by environmental stress. Although its regulation is well studied in Caenorhabditis elegans, the mechanisms in other species remain unclear. Here, we developed a fluorescent dauer reporter, Cin-col-183p::mCherry, in Caenorhabditis inopinata, a close relative of C. elegans. The reporter was specifically expressed in pre-dauer and dauer stages, confirming its usefulness as a dauer marker. Using this strain, we found that responses to high temperature and insulin/IGF-1 pathway gene knockdown differ between C. elegans and C. inopinata. This reporter will help reveal diversity in dauer-inducing mechanisms across nematode species.

The head of chelicerates, such as spiders, scorpions and mites, is composed of the ocular, chelicerae and pedipalp segments and is considered to be homologous to the procephalon of insects which comprises the ocular, antennal and intercalary segments. Head segmentation in the spider, Parasteatoda tepidariorum, is a dynamic process in which a single stripe of expression of the P. tepidariorum hedgehog (hh) gene splits twice to form three separate stripes, which help pattern the three spider head segments. This dynamic hh stripe splitting process is dependent on spider homologues of the transcription factors orthodenticle (otd) and odd-paired (opa). Here we investigate the conservation of this dynamic patterning mechanism in two insect models: the hemimetabolous pea aphid, Acyrthosiphon pisum, and the holometabolous red flour beetle, Tribolium castaneum.. We show that insect hh, otd and opa homologues are expressed in a highly conserved temporal and spatial pattern during procephalon development in these insects. Our data are consistent with an ancestral insect state in which a single hh stripe splitting event underpins patterning of the ocular and antennal segments, followed by de novo formation of the intercalary hh stripe. Using parental RNAi in T. castaneum, we show that hh, otd and opa homologues exhibit striking similarities in their regulatory interactions during spider and insect head/procephalon segmentation. Our data suggest that hh, otd and opa homologues contribute to an ancient and largely conserved gene network controlling head/procephalon patterning in arthropods. We discuss the implications of these data for our understanding of the origin and evolution of the arthropod head, and propose a new model for the evolution of anterior patterning in holometabolous insects.

Cellular metabolism and gene transcription are closely linked. The conserved transcriptional regulator SIN3 acts as a scaffold for histone deacetylase (HDAC)-containing complexes and is crucial for development, stress resistance, and overall organismal health. SIN3 regulates metabolic gene expression in Drosophila cultured cells, however, an understanding of the extent of its role in coordinating responses to metabolic stress in whole organisms is incomplete. In this study, we explored how SIN3 controls glycolytic gene expression across developmental stages and under genetic and dietary disruption of glycolysis in Drosophila melanogaster. Focusing on four key glycolytic enzymes: phosphofructokinase (Pfk), enolase (Eno), pyruvate kinase (Pyk), and pyruvate dehydrogenase beta (Pdhb), we found that reducing Sin3A levels increases their expression in both larvae and adults, indicating that SIN3 plays a consistent role in balancing metabolic gene transcription. Genetic interaction experiments indicate that Sin3A interacts with Pyk and Eno, regulating transcription in a gene-specific manner. Disrupting glycolysis via genetic or dietary means alters glycolytic gene expression, and SIN3 modulates this response. These findings indicate that SIN3 functions as a metabolic sensor, regulating transcription in response to cellular metabolic stress. Additionally, we demonstrate that reducing Sin3A levels shortens Drosophila lifespan on both low- and high-sucrose diets, emphasizing the importance of SIN3 in longevity. Overall, these results show that SIN3 is a context-dependent regulator of glycolytic gene expression and lifespan in Drosophila, integrating metabolic signals with chromatin-based transcriptional regulation. SummaryTo survive and thrive, organisms must adapt to distinct metabolic inputs. We investigated the response of the conserved transcriptional regulator SIN3 to metabolic stress and its control of glycolytic gene expression in Drosophila melanogaster. By measuring glycolytic gene expression, testing genetic interactions, and assessing lifespan under genetic and dietary perturbations, we found that Sin3A knockdown elevates glycolytic gene expression in a gene-specific manner and decreases longevity. SIN3 also modulates transcriptional responses to disrupted glycolysis and influences lifespan under sucrose stress. These findings identify SIN3 as a context-dependent transcription regulator that links gene expression with organismal metabolic adaptation.