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

{"title":"“Only Insects (and Angels) Were Able to Acquire Wings Without Sacrificing a Limb”: Remembering the Evodevo Legacy of Insect Paleontologist Jarmila Kukalová-Peck","authors":"Markus Friedrich","doi":"10.1002/jez.b.23314","DOIUrl":"https://doi.org/10.1002/jez.b.23314","url":null,"abstract":"<div>\u0000 \u0000 <p>On August 13, 2024, comparative biology lost paleontologist Jarmila Kukalová-Peck, a consummate integrative biologist and the pioneer of an innovative model of insect wing evolution, which, partly informed by developmental genetics, remains a key reference in molecular evodevo studies of insect flight appendage evolution. An effort is made to retrace key steps toward this achievement in the scientific trajectory of a unique and exemplary scientist.</p>\u0000 </div>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 8","pages":"477-481"},"PeriodicalIF":1.7,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145537908","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":"10.1002/jez.b.23310","url":null,"abstract":"&lt;p&gt;&lt;/p&gt;&lt;p&gt;Gregor Bucher was awarded the Heisenberg Professorship of the German Science Foundation (DFG) in 2013 and since 2017 has been Full Professor at the University of Göttingen. He has been interested in the genetic basis of the development and evolution of the insect head and brain and has contributed to using RNAi in pest control. Further, his lab has been pioneering transgenic tools for the emerging model organism &lt;i&gt;Tribolium Castaneum&lt;/i&gt;, the red flour beetle. He initiated and led the first genome-wide RNAi screen in an insect outside &lt;i&gt;Drosophila&lt;/i&gt; (DFG research unit FOR1234 “&lt;i&gt;iBeetle&lt;/i&gt;”) and has been part of the steering committee of the DFG priority program &lt;i&gt;SPP2349 GEvol&lt;/i&gt;.&lt;/p&gt;&lt;p&gt;Gregor Bucher is a Guest Coeditor of this special issue on the &lt;i&gt;Genomic Basis of Evolutionary Innovations in Insect&lt;/i&gt;s.&lt;/p&gt;&lt;p&gt;Google Scholar page: https://scholar.google.com/citations?user=rRpyk9sAAAAJ&lt;/p&gt;&lt;p&gt;I did my studies in genetics, zoology, and medical physiology at the Ludwig-Maximilians-University (LMU) in Munich. I especially enjoyed the lectures and courses on developmental biology and still build on the concepts so clearly presented by Harry MacWilliams. The course, which I most vividly remember was on hydra regeneration by Charles David and Thomas Bosch: Even after dissociating these little creatures into single cells and pelleting those cells via centrifugation, they would eventually start growing out little heads.&lt;/p&gt;&lt;p&gt;Understanding how things actually function has always been interesting to me—starting from the mechanics of my cassette recorder to the formation of thunderstorm clouds. But understanding life has always been most fascinating to me; so I had contemplated several closely related study programs: chemistry (with a focus on biochemistry) or medicine (with a focus on biomedical research) ending up with biology.&lt;/p&gt;&lt;p&gt;Funded by DAAD, I went to study in Concepción, Chile for 1 year. There I took classes on evolution, where we read Darwin's &lt;i&gt;On the Origin of Species&lt;/i&gt; and at the same time, we observed early development in marine animals in a developmental biology course. This combination made me think that you need to understand the divergence of developmental processes to understand the emergence of morphological diversity. Back in Munich, I looked for research groups in that area and was very, very lucky: At LMU, Diethard Tautz had pioneered the beetle &lt;i&gt;Tribolium castaneum&lt;/i&gt; as an insect model for EvoDevo research and Martin Klingler had started a mutagenesis screen in this species because, at the time, this tedious genetic procedure had been the only way to gain information on gene function (no RNAi, no genome editing, no transgenesis). So I joined Martin Klingler's lab to follow that approach. One year into my PhD, RNAi was discovered and made this approach (and 1 year of my PhD) obsolete.&lt;/p&gt;&lt;p&gt;For a long time, EvoDevo research relied on the candidate gene approach—testing the function of orthologs of genes","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 7","pages":"377-378"},"PeriodicalIF":1.7,"publicationDate":"2025-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23310","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":"OA","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"346 3","pages":"195-199"},"PeriodicalIF":1.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148082496","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":"","authors":"","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"346 3","pages":"188-194"},"PeriodicalIF":1.7,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148066797","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,&nbsp;Shadi Karimifard,&nbsp;Mozhgan Khodadadi,&nbsp;Liucong Ling,&nbsp;Luisa Linke,&nbsp;Ana Catalán,&nbsp;Vincent Doublet,&nbsp;Amanda Glaser-Schmitt,&nbsp;Oliver Niehuis,&nbsp;Katja Nowick,&nbsp;Antonella Soro,&nbsp;Natascha Turetzek,&nbsp;Barbara Feldmeyer,&nbsp;Nico Posnien","doi":"10.1002/jez.b.23305","DOIUrl":"10.1002/jez.b.23305","url":null,"abstract":"<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":"344 7","pages":"394-414"},"PeriodicalIF":1.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23305","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":"OA","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}

{"title":"In the Spotlight-Established Researcher.","authors":"Rodrigo Nunes-da-Fonseca","doi":"10.1002/jez.b.23306","DOIUrl":"10.1002/jez.b.23306","url":null,"abstract":"","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":" ","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144150579","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":"Gene and Genome Duplication in Spiders","authors":"Chetan Munegowda,&nbsp;Matthias Pechmann,&nbsp;Nikola-Michael Prpic-Schäper,&nbsp;Natascha Turetzek","doi":"10.1002/jez.b.23304","DOIUrl":"10.1002/jez.b.23304","url":null,"abstract":"<p>Gene and genome duplications are widely observed across various organisms, including plants, yeasts, and animals. Numerous studies link gene duplications to the emergence of novel phenotypes, supporting the hypothesis that duplication events are advantageous for adaptive evolution. Whole-genome duplications (WGD) are especially prevalent in plants and have also occurred ancestrally in vertebrates. However, large-scale duplication events in other animal groups remain understudied, partly due to limited genomic resources. Arthropods, particularly insects, represent one of the most diverse animal clades in terms of both species and phenotypic diversity. With increasing availability of chromosome-level genomes, large-scale duplications appear to be rare in insects but are more frequent in chelicerates (e.g. spiders, scorpions, and horseshoe crabs). This makes chelicerates an intriguing group for comparing the mechanisms, fates, and evolutionary impacts of large-scale duplications with those seen in plants and vertebrates. In this review, we synthesize and discuss current research on WGD in spiders and discuss different scenarios for genes following gene duplication events (conservation, nonfunctionalization, subfunctionalization, specialization, drift, neofunctionalization) in the context of experimental studies. We hypothesize if there might be common trajectories after duplication and how these could be tested.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 7","pages":"379-393"},"PeriodicalIF":1.7,"publicationDate":"2025-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23304","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144142241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"De Novo Whole Genome Assemblies of Unusual Case-Making Caddisflies (Trichoptera) Highlight Genomic Convergence in the Composition of the Major Silk Gene (h-fibroin)","authors":"Xiling Deng,&nbsp;Steffen U. Pauls,&nbsp;Ryoichi B. Kuranishi,&nbsp;Paul B. Frandsen,&nbsp;Jacqueline Heckenhauer","doi":"10.1002/jez.b.23301","DOIUrl":"10.1002/jez.b.23301","url":null,"abstract":"<p>Trichoptera (caddisflies) is one of the most species-rich orders of aquatic insects. Species of caddisflies cover a broad ecological diversity as exemplified by various uses of underwater silk secretions. Diversity of silk use generally aligns with the evolution of major caddisfly lineages, specifically at the subordinal level: Annulipalpia (retreat makers) and Integripalpia (cocoon and tube-case makers). However, silk use within suborders differs for a few exceptional species in these clades. In this study, we provide the first whole genome assemblies and annotations for two unusual Integripalpia species: <i>Limnocentropus insolitus</i>, whose hard tube-case is anchored to boulders by a rigid, elongated silken stalk, and <i>Phryganopsyche brunnea</i> which builds a “floppy” cylindrical case that lacks the typical robustness of tube-cases. Its texture rather resembles that of the flexible retreats built by Annulipalpia. Using the two high-quality genome assemblies, we identified and annotated the major silk gene, <i>h-fibroin</i>, and compared its amino acid composition across various groups, including retreat, cocoon, and tube-case makers. Our phylogenetic analysis confirmed the phylogenetic position of the two species in the tube-case-making clade. The major silk gene of <i>L. insolitus</i> shows a similar amino acid composition to other tube-case-making species. In contrast, the amino acid composition of <i>P. brunnea</i> resembles that of retreat-making species, in particular with regard to the high content of proline. This is consistent with the hypothesis that proline could be linked to enhanced extensibility of silk fibers. Taken together, our results underscore the role of silk genes in shaping the evolutionary ecology of retreat- and tube-case-making in caddisflies.</p>","PeriodicalId":15682,"journal":{"name":"Journal of experimental zoology. Part B, Molecular and developmental evolution","volume":"344 7","pages":"442-453"},"PeriodicalIF":1.7,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/jez.b.23301","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144093634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}