Journal of experimental zoology. Part B, Molecular and developmental evolution最新文献

{"title":"Fractal Dimension of Dental Crowns: An Innovative Method for Age Estimation in Toxodonts.","authors":"Donato Costamagna, Guillermo Cassini, Vanina Cabral, Gabriela I Schmidt, Brenda S Ferrero","doi":"10.1002/jez.b.23319","DOIUrl":"https://doi.org/10.1002/jez.b.23319","url":null,"abstract":"<p><p>Toxodonts constitute a group of extinct native South American ungulates that have been subject of extensive paleobiological research. Among the traits analyzed, enamel crest complexity (ECC; through fractal dimension) and occlusal surface tooth area (OTA) have recently been studied. However, they have not yet been applied to evaluate differences between ontogenetic stages, (e.g., juveniles, subadults, and adults). Here, we analyzed these traits in the p2-m3 of three species of Toxodontidae, Adinotherium ovinum (n = 8), Nesodon imbricatus (n = 11), and Toxodon platensis (n = 19), along ontogeny by standardized major axis regressions using OTA of m1 as an age proxy, and compared adult and young individuals (i.e., m3 not fully erupted) by Kruskal-Wallis test. Our results showed that ECC decreases with age in all teeth, and p2-m1 seems to share a common slope for Adinotherium and Nesodon. Kruskal-Wallis test showed significant differences between age and species in p3 and molars, with young individuals having higher ECC values than adults. There is a decreasing trend in ECC values from A. ovinum (highest), through N. imbricatus (intermediate), to T. platensis (lowest). These differences are more pronounced from m1 to m3. We conclude that both ECC and OTA can serve as effective tools for differentiating adult toxodonts from those that have not yet reached adulthood. The lower ECC in adult molars may be due to crown simplification during ontogeny, as teeth wear over time by abrasion from food particles during chewing. Conversely, OTA increases in adults as a mixed effect of wear and the larger size of their teeth compared to younger individuals.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144642724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recently Evolved, Stage-Specific Genes Are Enriched at Life-Stage Transitions in Flies.","authors":"Andreas Remmel, Karl K Käther, Peter F Stadler, Steffen Lemke","doi":"10.1002/jez.b.23317","DOIUrl":"https://doi.org/10.1002/jez.b.23317","url":null,"abstract":"<p><p>Understanding how genomic information is selectively utilized across different life stages is essential for deciphering the developmental and evolutionary strategies of metazoans. In holometabolous insects, the dynamic expression of genes enables distinct functional adaptations at embryonic, larval, pupal, and adult stages, likely contributing to their evolutionary success. While Drosophila melanogaster (D. melanogaster) has been extensively studied, less is known about the evolutionary dynamics that could govern stage-specific gene expression. To address this question, we compared the distribution of stage-specific genes, that is, genes expressed in temporally restricted developmental stages, across the development of D. melanogaster and Aedes aegypti (A. aegypti). Using tau-scoring, a computational method to determine gene expression specificity, we found that, on average, a large proportion of genes (20%-30% of all protein-coding genes) in both species exhibit restricted expression to specific developmental stages. Phylostratigraphy analysis, a method to date the age of genes, further revealed that stage-specific genes fall into two major categories: highly conserved and recently evolved. Notably, many of the recently evolved and stage-specific genes identified in A. aegypti and D. melanogaster are restricted to Diptera order (20%-35% of all stage-specific genes), highlighting ongoing evolutionary processes that continue to shape life-stage transitions. Overall, our findings underscore the complex interplay between gene evolutionary age, expression specificity, and morphological transformations in development. These results suggest that the attraction of genes to critical life-stage transitions is an ongoing process that may not be constant across evolutionary time or uniform between different lineages, offering new insights into the adaptability and diversification of dipteran genomes.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144637122","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Interplay of Ontogeny and Phylogeny at the Transcriptome Level of the Tetrapod Heart.","authors":"G A Cordero, A K Holloway, T Friedrich, J Eme, W Eckalbar, K Kusumi, F J Janzen, J W Hicks, F L Conlon, B G Bruneau, K S Pollard","doi":"10.1002/jez.b.23312","DOIUrl":"https://doi.org/10.1002/jez.b.23312","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In the Spotlight-Established Researcher.","authors":"Gregor Bucher","doi":"10.1002/jez.b.23310","DOIUrl":"https://doi.org/10.1002/jez.b.23310","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144553648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole-Mount Acetylcholinesterase Staining Reveals Unique Motor Innervation of the Lamprey Oral Region: With Special Reference to the Evolutionary Origin of the Vertebrate Jaw.","authors":"Motoki Tamura, Daichi G Suzuki","doi":"10.1002/jez.b.23316","DOIUrl":"https://doi.org/10.1002/jez.b.23316","url":null,"abstract":"<p><p>The evolutionary change of the trigeminal nerve-innervation pattern is essential to reveal the mechanism underlying jaw acquisition. However, the homology of the branches between gnathostomes (jawed vertebrates) and cyclostomes (living jawless vertebrates) remains unclear. In this study, we focused on a subbranch called the ramus subpharyngeus, which belongs to the second branch of the lamprey trigeminal nerve and projects to the lower lip, investigating whether it contains motor components. To visualize motor fibers, we performed acetylcholinesterase (AChE) staining, a histochemical method that visualizes intrinsic activities of the catabolic enzymes produced by motor neurons and muscle fibers. As a result, we found AChE staining signals that correspond to the innervation course of the ramus subpharyngeus. To confirm that these signals in this region do not mark the motoneuronal somata nor muscle fibers, we conducted gene expression analysis by in situ hybridization. The results support that the signals mark the motor fibers. Based on these results, we propose that the lamprey oral apparatus is chiefly controlled by the second (i.e., premandibular) branch of the trigeminal nerve and further suggest that a drastic reorganization of the anterior craniofacial region occurred during the acquisition of the vertebrate jaw.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144560265","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of Gene Expression in Aedes aegypti Suggests Changes in Early Genetic Control of Mosquito Development.","authors":"Renata Coutinho-Dos-Santos, Danielle Santos, Lupis Ribeiro, Jonathan J Mucherino-Muñoz, Marcelle Uhl, Carlos Logullo, A Mendonça-Amarante, M Fantappie, Rodrigo Nunes-da-Fonseca","doi":"10.1002/jez.b.23315","DOIUrl":"https://doi.org/10.1002/jez.b.23315","url":null,"abstract":"<p><p>Aedes aegypti, a critical vector for tropical diseases, poses significant challenges for studying its embryogenesis due to difficulties in removing its rigid chorion and achieving effective fixation for in situ hybridization. Here, we present novel methodologies for fixation, dechorionation, DAPI staining, and in situ hybridization, enabling the detailed analysis of gene expression throughout Ae. aegypti embryogenesis. By synchronizing eggs at various developmental stages (0-72 h), we localized the transcripts of the gap gene mille-pattes (mlpt), the dorsoventral gene cactus (cact), and the pioneer transcription factor (pTF) zelda (zld). In situ hybridization and RT-qPCR analyses revealed that mlpt and cact are maternally expressed, while zld expression begins zygotically during cellularization and later becomes prominent in neuroblasts. Analysis of previously published transcriptomes suggests that three other pTFs, CLAMP, grainyhead, and GAF, are also maternally expressed and may function as pioneer transcription factors during Ae. aegypti embryogenesis. These findings suggest that the transcription factors responsible for genome activation in mosquitoes differ from those in fruit flies, highlighting significant divergence in the genetic regulation of early Dipteran embryogenesis.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144540448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Vertebrate Morphology Research in Argentina: Methodological Advances and Challenges.","authors":"Adriana S Manzano, Fratani Jessica","doi":"10.1002/jez.b.23309","DOIUrl":"https://doi.org/10.1002/jez.b.23309","url":null,"abstract":"<p><p>The V Argentine Workshop on Vertebrate Morphology (Taller Argentino de Morfología de Vertebrados-TAMV) was held in the CICyTTP-CONICET, city of Diamante, Entre Ríos, Argentina, from September 4th to 6th, 2024. Over the course of 3 days, 32 Argentine morphologists congregated to share the progress of their research, discuss emerging trends in morphology, and particularly, to delve into the utilization of new methodologies as indispensable tools for advancing their work. The workshop was based on a dynamic format featuring the presentation of manuscripts or expanded abstracts, along with three hands-on workshops on current methodologies implemented in the participants' research lines.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144325925","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Land of Evo-Devo: The 2024 Latin American Developmental Biology Conference in Valparaíso, Chile.","authors":"Sayoni Chatterjee, Tetsuya Nakamura","doi":"10.1002/jez.b.23308","DOIUrl":"https://doi.org/10.1002/jez.b.23308","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144234250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ATAC-seq in Emerging Model Organisms: Challenges and Strategies.","authors":"Duğçar Ebrar Erdoğan, Shadi Karimifard, Mozhgan Khodadadi, Liucong Ling, Luisa Linke, Ana Catalán, Vincent Doublet, Amanda Glaser-Schmitt, Oliver Niehuis, Katja Nowick, Antonella Soro, Natascha Turetzek, Barbara Feldmeyer, Nico Posnien","doi":"10.1002/jez.b.23305","DOIUrl":"https://doi.org/10.1002/jez.b.23305","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144199296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Calpain Proteases and the Evolving Signaling Network in Insect Embryonic Patterning.","authors":"Alison Julio, Helena Araujo","doi":"10.1002/jez.b.23307","DOIUrl":"https://doi.org/10.1002/jez.b.23307","url":null,"abstract":"<p><p>Early embryogenesis relies on a series of maternal factors to coordinate cell division and axial patterning. In insects, maternal Toll receptor and Bone Morphogenetic Protein (BMP) pathway activities drive the spatial allocation of zygotic gene expression territories along the dorsal-ventral (DV) axis. The respective contribution of each pathway varies among insect orders and suggests that Toll was co-opted from an ancestral immune function for insect DV patterning. The Ca⁺² dependent modulatory Calpain proteases also influence insect DV patterning, in addition to their role in regulating mitosis. Calpains alter gene expression patterns in insect species that depend on either Toll or BMPs for the establishment of DV territories, raising the question of when calpains acquired this crucial role. Here we review the function of calpains in early embryogenesis within the context of an evolving insect DV patterning landscape. We discuss the essential components for the transition from BMP-driven to Toll-centered axial patterning and how insect Calpains may have adapted to this changing regulatory network.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.8,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144199297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}