Pub Date : 2024-09-10DOI: 10.1186/s12983-024-00542-2
Yara Silberstein, Janina Büntge, Felix Felmy, Marina Scheumann
Drumming is a non-vocal auditory display producing airborne as well as seismic vibrations by tapping body extremities on a surface. It is mostly described as an alarm signal but is also discussed to signal dominance or mating quality. To clarify the function of drumming in Mongolian gerbils (Meriones unguiculatus), we compared the occurrence of drumming during predator, opposite-sex and same-sex encounters. We tested 48 captive Mongolian gerbils (Meriones unguiculatus) in three experiments. In predator experiments, subjects were exposed alone or with their cagemate to aerial and terrestrial predator dummies. In social encounter experiments, familiar and unfamiliar male–female dyads and same-sex dyads were confronted. For the same-sex encounters, a dominance index was calculated for each subject based on the number of won and lost conflicts. Drumming and drumming-call combinations were counted, and a multi-parametric sound analysis was performed. In all experiments drumming and drumming-call combinations occurred. In predator experiments, more subjects drummed when confronted with the predator stimulus than in the habituation phase. In social encounter experiments, more subjects drummed when facing an unfamiliar than a familiar conspecific. In addition, the accompanying call type and body posture of the sender differed between experiments. Thus, we suggest that whereas drumming signals an increased arousal state of the sender, the accompanying call type and the body posture signal context specific information.
{"title":"Context or arousal? Function of drumming in Mongolian gerbils (Meriones unguiculatus)","authors":"Yara Silberstein, Janina Büntge, Felix Felmy, Marina Scheumann","doi":"10.1186/s12983-024-00542-2","DOIUrl":"https://doi.org/10.1186/s12983-024-00542-2","url":null,"abstract":"Drumming is a non-vocal auditory display producing airborne as well as seismic vibrations by tapping body extremities on a surface. It is mostly described as an alarm signal but is also discussed to signal dominance or mating quality. To clarify the function of drumming in Mongolian gerbils (Meriones unguiculatus), we compared the occurrence of drumming during predator, opposite-sex and same-sex encounters. We tested 48 captive Mongolian gerbils (Meriones unguiculatus) in three experiments. In predator experiments, subjects were exposed alone or with their cagemate to aerial and terrestrial predator dummies. In social encounter experiments, familiar and unfamiliar male–female dyads and same-sex dyads were confronted. For the same-sex encounters, a dominance index was calculated for each subject based on the number of won and lost conflicts. Drumming and drumming-call combinations were counted, and a multi-parametric sound analysis was performed. In all experiments drumming and drumming-call combinations occurred. In predator experiments, more subjects drummed when confronted with the predator stimulus than in the habituation phase. In social encounter experiments, more subjects drummed when facing an unfamiliar than a familiar conspecific. In addition, the accompanying call type and body posture of the sender differed between experiments. Thus, we suggest that whereas drumming signals an increased arousal state of the sender, the accompanying call type and the body posture signal context specific information.","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"48 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-23DOI: 10.1186/s12983-024-00543-1
Simon Züger, Wencke Krings, Stanislav N. Gorb, Thies H. Büscher, Andy Sombke
Centipedes are terrestrial and predatory arthropods that possess an evolutionary transformed pair of appendages used for venom injection—the forcipules. Many arthropods incorporate reinforcing elements into the cuticle of their piercing or biting structures to enhance hardness, elasticity or resistance to wear and structural failure. Given their frequent exposure to high mechanical stress, we hypothesise that the cuticle of the centipede forcipule might be mechanically reinforced. With a combination of imaging, analytical techniques and mechanical testing, we explore the centipede forcipule in detail to shed light on its morphology and performance. Additionally, we compare these data to characteristics of the locomotory leg to infer evolutionary processes. We examined sclerotization patterns using confocal laser-scanning microscopy based on autofluorescence properties of the cuticle (forcipule and leg) and elemental composition by energy-dispersive X-ray spectroscopy in representative species from all five centipede lineages. These experiments revealed gradually increasing sclerotization towards the forcipular tarsungulum and a stronger sclerotization of joints in taxa with condensed podomeres. Depending on the species, calcium, zinc or chlorine are present with a higher concentration towards the distal tarsungulum. Interestingly, these characteristics are more or less mirrored in the locomotory leg’s pretarsal claw in Epimorpha. To understand how incorporated elements affect mechanical properties, we tested resistance to structural failure, hardness (H) and Young’s modulus (E) in two representative species, one with high zinc and one with high calcium content. Both species, however, exhibit similar properties and no differences in mechanical stress the forcipule can withstand. Our study reveals similarities in the material composition and properties of the forcipules in centipedes. The forcipules transformed from an elongated leg-like appearance into rigid piercing structures. Our data supports their serial homology to the locomotory leg and that the forcipule’s tarsungulum is a fusion of tarsus and pretarsal claw. Calcium or zinc incorporation leads to comparable mechanical properties like in piercing structures of chelicerates and insects, but the elemental incorporation does not increase H and E in centipedes, suggesting that centipedes followed their own pathways in the evolutionary transformation of piercing tools.
蜈蚣是陆生和掠食性节肢动物，拥有一对用于注射毒液的附肢--蟾蜍甲（forcipules）。许多节肢动物在其穿刺或咬合结构的表皮中加入强化元素，以增强硬度、弹性或抗磨损和结构失效的能力。鉴于蜈蚣经常暴露在高机械应力下，我们推测蜈蚣瓣膜的角质层可能被机械加固了。我们结合成像、分析技术和机械测试，详细研究了蜈蚣穹窿的形态和性能。此外，我们还将这些数据与运动腿的特征进行比较，以推断其进化过程。我们使用激光扫描共聚焦显微镜，根据蜈蚣所有五个品系的角质层（蹄甲和腿）的自发荧光特性和能量色散 X 射线光谱的元素组成，研究了蜈蚣的硬壳化模式。这些实验表明，硬质化程度向趾甲跗节逐渐增加，在荚膜凝聚的类群中，关节的硬质化程度更强。根据物种的不同，钙、锌或氯在跗关节远端含量较高。有趣的是，这些特征或多或少地反映在 Epimorpha 的运动腿前跗爪上。为了了解所含元素如何影响机械性能，我们测试了两个具有代表性的物种的抗结构破坏能力、硬度（H）和杨氏模量（E），一个含锌量高，一个含钙量高。然而，这两个物种都表现出相似的特性，并且在小穹窿所能承受的机械应力方面没有差异。我们的研究揭示了蜈蚣穹窿的材料成分和特性的相似性。穹窿从细长的腿状外观转变为坚硬的穿刺结构。我们的数据支持它们与运动腿的序列同源性，并支持穹窿跗节是跗节和前跗节爪的融合体。钙或锌的加入使蜈蚣具有与螯足类和昆虫的穿刺结构相似的机械特性，但元素的加入并没有增加蜈蚣的H和E，这表明蜈蚣在穿刺工具的进化转变过程中遵循了自己的路径。
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Pub Date : 2024-08-12DOI: 10.1186/s12983-024-00541-3
István Kiss, Gergő Erdélyi, Borbála Szabó
The conservation of aquatic and semiaquatic turtles requires knowledge of the area and vegetation structure of habitat used for nesting, and nesting migration route. We aimed to survey the effects of habitat features to the nest site selection, nesting success, and test the possibility of nest site fidelity. Our study was carried out at 10 different nesting areas, with special emphasis on data from returning females in a pond system in Hungary between 2014 and 2017. Most nesting attempts were found in closed sand steppes, uncharacteristic dry and semi-dry grasslands habitat patches. The principal component analysis (PCA) showed that increased sandy soil cover, sunlight and slope were important variables in nest site choice. The increasing PCA first axis score significantly increased the chance of an emergence. The degradation of open steppe vegetation, occurrence of weeds, invasive and disturbance tolerant species have a negative effect on the selection of nest sites. We observed that 96.55% of nests were located within 20 m south of a pine forest at preferred nest site at pond 5, which provided the right incubation temperature through partial shading. The returning females nested significantly closer to the northern pine forest than the single clutch females. Most probably the returning females already has the necessary experience to select the right nesting site. The individually marked females did not choose new nesting areas during the monitored years which suggests nesting area fidelity, but we did not find nest site fidelity. The maintenance of mosaic habitat structure, slowing down the succession process at the nesting area should be basic priorities in European pond turtle conservation programs. We suggested a spatial and temporal scheduling of land management and agricultural work to the local farmers. If the actual nest site is in an agricultural area, all work should be avoided throughout the year. Agricultural machinery should avoid the migration routes of adult turtles and emerged hatchlings during the concerned period. Under strong predation pressure, predator control should be carried out, and use nest protection.
{"title":"Nest site selection and fidelity of European pond turtle (Emys orbicularis) population of Babat Valley (Gödöllő, Hungary)","authors":"István Kiss, Gergő Erdélyi, Borbála Szabó","doi":"10.1186/s12983-024-00541-3","DOIUrl":"https://doi.org/10.1186/s12983-024-00541-3","url":null,"abstract":"The conservation of aquatic and semiaquatic turtles requires knowledge of the area and vegetation structure of habitat used for nesting, and nesting migration route. We aimed to survey the effects of habitat features to the nest site selection, nesting success, and test the possibility of nest site fidelity. Our study was carried out at 10 different nesting areas, with special emphasis on data from returning females in a pond system in Hungary between 2014 and 2017. Most nesting attempts were found in closed sand steppes, uncharacteristic dry and semi-dry grasslands habitat patches. The principal component analysis (PCA) showed that increased sandy soil cover, sunlight and slope were important variables in nest site choice. The increasing PCA first axis score significantly increased the chance of an emergence. The degradation of open steppe vegetation, occurrence of weeds, invasive and disturbance tolerant species have a negative effect on the selection of nest sites. We observed that 96.55% of nests were located within 20 m south of a pine forest at preferred nest site at pond 5, which provided the right incubation temperature through partial shading. The returning females nested significantly closer to the northern pine forest than the single clutch females. Most probably the returning females already has the necessary experience to select the right nesting site. The individually marked females did not choose new nesting areas during the monitored years which suggests nesting area fidelity, but we did not find nest site fidelity. The maintenance of mosaic habitat structure, slowing down the succession process at the nesting area should be basic priorities in European pond turtle conservation programs. We suggested a spatial and temporal scheduling of land management and agricultural work to the local farmers. If the actual nest site is in an agricultural area, all work should be avoided throughout the year. Agricultural machinery should avoid the migration routes of adult turtles and emerged hatchlings during the concerned period. Under strong predation pressure, predator control should be carried out, and use nest protection.","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"44 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918831","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-15DOI: 10.1186/s12983-024-00540-4
J. Levenets, S. Panteleeva, Zh. Reznikova, A. Gureeva, V. Kupriyanov, N. Feoktistova, A. Surov
Research into the hunting behavior in members of the Cricetidae family offers an opportunity to reveal what changes in the predatory behavioral sequences occur when a rodent species shifts from an omnivorous to a predatory lifestyle. The study tests the following hypotheses: are there phylogenetic differences in the divergence of species’ predatory lifestyles in hamsters or do ecological factors lead to shaping their hunting behavior? We applied the data compression approach for performing comparative analysis of hunting patterns as biological “texts.” The study presents a comparative analysis of hunting behaviors in five Cricetinae species, focusing on the new data obtained for the desert hamster Phodopus roborovskii whose behavior has never been studied before. The hunting behavior of P. roborovskii appeared to be the most variable one. In contrast, behavioral sequences in P. campbelli and Allocricetulus curtatus display more significant order and predictability of behavior during hunting. Optional hunting behavior in the most ancient species P. roborovskii displayed similarities with obligate patterns in “young” Allocricetulus species. It thus turned out to be the most advanced hunter among members of the Phodopus genus. Differences in hunting sequences among Phodopus representatives suggest that the hunting behavior of these species, despite its optional mode, was subject to selection during species splitting within the genus. These results did not reveal the role played by phylogenetic differences in the divergence of species’ predatory lifestyles. They suggested that ecological conditions are the main factors in speciation of the hunting behavior in hamsters.
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Pub Date : 2024-06-25DOI: 10.1186/s12983-024-00539-x
David Romero, Raúl Maneyro, José Carlos Guerrero, Raimundo Real
<p><b>Correction</b><b>: </b><b>Front Zool 20, 38 (2023)</b></p><p><b>https://doi.org/10.1186/s12983-023-00515-x</b></p><br/><p>Following publication of the original article [1], the authors reported that the link to the data repository is missing in section Availability of data and materials.</p><p>The original content of Availability of data and materials was:</p><p>The dataset supporting the conclusions of this article will be made available through a data repository.</p><p>The correction content should read:</p><p>The dataset supporting the conclusions of this article is available at https://doi.org/10.5061/dryad.0k6djhb6g.</p><p>The original article [1] has been updated.</p><ol data-track-component="outbound reference" data-track-context="references section"><li data-counter="1."><p>Romero D, Maneyro R, Guerrero JC, et al. Using fuzzy logic to compare species distribution models developed on the basis of expert knowledge and sampling records. Front Zool. 2023;20:38. https://doi.org/10.1186/s12983-023-00515-x.</p><p>Article PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden="true" focusable="false" height="16" role="img" width="16"><use xlink:href="#icon-eds-i-download-medium" xmlns:xlink="http://www.w3.org/1999/xlink"></use></svg></p><h3>Authors and Affiliations</h3><ol><li><p>Biogeography, Diversity, and Conservation Research Team, Department of Animal Biology, Faculty of Sciences, Universidad de Málaga, Málaga, Spain</p><p>David Romero & Raimundo Real</p></li><li><p>Laboratory of Systematics and Natural History of Vertebrates, Faculty of Sciences, Universidad de La República, Montevideo, Uruguay</p><p>Raúl Maneyro</p></li><li><p>Laboratory for Sustainable Development and Environmental Management, Faculty of Sciences, Universidad de La República, Montevideo, Uruguay</p><p>José Carlos Guerrero</p></li></ol><span>Authors</span><ol><li><span>David Romero</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Raúl Maneyro</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>José Carlos Guerrero</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Raimundo Real</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li></ol><h3>Corresponding author</h3><p>Correspondence to David Romero.</p><p><b>Open Access</b> This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party mat
更正：Front Zool 20, 38 (2023)https://doi.org/10.1186/s12983-023-00515-xFollowing 原文[1]发表后，作者报告说在数据和材料的可获得性一节中缺少指向数据存储库的链接。数据和材料的可获得性的原文内容为：支持本文结论的数据集将通过数据存储库提供。更正后的内容应为：支持本文结论的数据集可在 https://doi.org/10.5061/dryad.0 网站上获得。k6djhb6g.The original article [1] has been updated.Romero D, Maneyro R, Guerrero JC, et al. Using fuzzy logic to compare species distribution models developed on the basis of expert knowledge and sampling records.Front Zool.2023;20:38. https://doi.org/10.1186/s12983-023-00515-x.Article PubMed PubMed Central Google Scholar Download references作者及工作单位西班牙马拉加马拉加大学科学学院动物生物学系生物地理学、多样性和保护研究小组David Romero &；Raimundo Real 乌拉圭蒙得维的亚共和国大学科学系脊椎动物系统学与自然史实验室 Raúl Maneyro 蒙得维的亚共和国大学科学系可持续发展与环境管理实验室、乌拉圭José Carlos Guerrero作者：David Romero查看作者发表的文章您也可以在PubMed Google Scholar中搜索该作者劳尔-马内罗查看作者发表的文章您也可以在PubMed Google Scholar中搜索该作者José Carlos Guerrero查看作者发表的文章您也可以在PubMed Google Scholar中搜索该作者雷蒙多-雷亚尔查看作者发表的文章您也可以在PubMed Google Scholar中搜索该作者通讯作者：David Romero。开放存取 本文采用知识共享署名 4.0 国际许可协议进行许可，该协议允许以任何媒介或格式使用、共享、改编、分发和复制本文，但须注明原作者和出处，提供知识共享许可协议链接，并说明是否进行了修改。本文中的图片或其他第三方材料均包含在文章的知识共享许可协议中，除非在材料的署名栏中另有说明。如果材料未包含在文章的知识共享许可协议中，且您打算使用的材料不符合法律规定或超出许可使用范围，您需要直接从版权所有者处获得许可。要查看该许可的副本，请访问 http://creativecommons.org/licenses/by/4.0/。除非在数据的信用行中另有说明，否则创作共用公共领域专用免责声明（http://creativecommons.org/publicdomain/zero/1.0/）适用于本文提供的数据。转载与许可引用本文Romero, D., Maneyro, R., Guerrero, J.C. et al. Correction：使用模糊逻辑比较基于专家知识和采样记录建立的物种分布模型。Front Zool 21, 18 (2024). https://doi.org/10.1186/s12983-024-00539-xDownload citationPublished: 25 June 2024DOI: https://doi.org/10.1186/s12983-024-00539-xShare this articleAnyone you share the following link with will be able to read this content:Get shareable linkSorry, a shareable link is not currently available for this article.Copy to clipboard Provided by the Springer Nature SharedIt content-sharing initiative
{"title":"Correction: Using fuzzy logic to compare species distribution models developed on the basis of expert knowledge and sampling records","authors":"David Romero, Raúl Maneyro, José Carlos Guerrero, Raimundo Real","doi":"10.1186/s12983-024-00539-x","DOIUrl":"https://doi.org/10.1186/s12983-024-00539-x","url":null,"abstract":"<p><b>Correction</b><b>: </b><b>Front Zool 20, 38 (2023)</b></p><p><b>https://doi.org/10.1186/s12983-023-00515-x</b></p><br/><p>Following publication of the original article [1], the authors reported that the link to the data repository is missing in section Availability of data and materials.</p><p>The original content of Availability of data and materials was:</p><p>The dataset supporting the conclusions of this article will be made available through a data repository.</p><p>The correction content should read:</p><p>The dataset supporting the conclusions of this article is available at https://doi.org/10.5061/dryad.0k6djhb6g.</p><p>The original article [1] has been updated.</p><ol data-track-component=\"outbound reference\" data-track-context=\"references section\"><li data-counter=\"1.\"><p>Romero D, Maneyro R, Guerrero JC, et al. Using fuzzy logic to compare species distribution models developed on the basis of expert knowledge and sampling records. Front Zool. 2023;20:38. https://doi.org/10.1186/s12983-023-00515-x.</p><p>Article PubMed PubMed Central Google Scholar </p></li></ol><p>Download references<svg aria-hidden=\"true\" focusable=\"false\" height=\"16\" role=\"img\" width=\"16\"><use xlink:href=\"#icon-eds-i-download-medium\" xmlns:xlink=\"http://www.w3.org/1999/xlink\"></use></svg></p><h3>Authors and Affiliations</h3><ol><li><p>Biogeography, Diversity, and Conservation Research Team, Department of Animal Biology, Faculty of Sciences, Universidad de Málaga, Málaga, Spain</p><p>David Romero & Raimundo Real</p></li><li><p>Laboratory of Systematics and Natural History of Vertebrates, Faculty of Sciences, Universidad de La República, Montevideo, Uruguay</p><p>Raúl Maneyro</p></li><li><p>Laboratory for Sustainable Development and Environmental Management, Faculty of Sciences, Universidad de La República, Montevideo, Uruguay</p><p>José Carlos Guerrero</p></li></ol><span>Authors</span><ol><li><span>David Romero</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Raúl Maneyro</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>José Carlos Guerrero</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li><li><span>Raimundo Real</span>View author publications<p>You can also search for this author in <span>PubMed<span> </span>Google Scholar</span></p></li></ol><h3>Corresponding author</h3><p>Correspondence to David Romero.</p><p><b>Open Access</b> This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party mat","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"1 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141448281","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-20DOI: 10.1186/s12983-024-00538-y
Daniel J. Jackson, Nicolas Cerveau, Nico Posnien
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the ‘scientific status’ of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.
{"title":"De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide","authors":"Daniel J. Jackson, Nicolas Cerveau, Nico Posnien","doi":"10.1186/s12983-024-00538-y","DOIUrl":"https://doi.org/10.1186/s12983-024-00538-y","url":null,"abstract":"Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the ‘scientific status’ of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes.","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"44 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141430573","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Parental care benefits offspring but comes with costs. To optimize the trade-off of costs and benefits, parents should adjust care based on intrinsic and/or extrinsic conditions. The harm to offspring hypothesis suggests that parents should invest more in younger offspring than older offspring because younger offspring are more vulnerable. However, this hypothesis has rarely been comprehensively tested, as many studies only reveal an inverse correlation between parental care and offspring age, without directly testing the effects of offspring age on their vulnerability. To test this hypothesis, we studied Kurixalus eiffingeri, an arboreal treefrog with paternal care. We first performed a field survey by monitoring paternal care during embryonic development. Subsequently, we conducted a field experiment to assess the prevalence of egg predators (a semi-slug, Parmarion martensi) and the plasticity of male care. Finally, we conducted a laboratory experiment to assess how embryo age affects predation by P. martensi. Our results showed that (1) male attendance and brooding frequency affected embryo survival, and (2) males attended and brooded eggs more frequently in the early stage than in the late stage. The experimental results showed that (3) males increased attendance frequency when the predators were present, and (4) the embryonic predation by the semi-slug during the early was significantly higher than in the late stage. Our findings highlight the importance of paternal care to embryo survival, and the care behavior is plastic. Moreover, our results provide evidence consistent with the predictions of the harm to offspring hypothesis, as males tend to care more for younger offspring which are more vulnerable.
{"title":"Paternal care plasticity: males care more for early- than late-developing embryos in an arboreal breeding treefrog","authors":"Yuan-Cheng Cheng, Cai-Han Xie, Yu-Chen Chen, Nien-Tse Fuh, Ming-Feng Chuang, Yeong-Choy Kam","doi":"10.1186/s12983-024-00537-z","DOIUrl":"https://doi.org/10.1186/s12983-024-00537-z","url":null,"abstract":"Parental care benefits offspring but comes with costs. To optimize the trade-off of costs and benefits, parents should adjust care based on intrinsic and/or extrinsic conditions. The harm to offspring hypothesis suggests that parents should invest more in younger offspring than older offspring because younger offspring are more vulnerable. However, this hypothesis has rarely been comprehensively tested, as many studies only reveal an inverse correlation between parental care and offspring age, without directly testing the effects of offspring age on their vulnerability. To test this hypothesis, we studied Kurixalus eiffingeri, an arboreal treefrog with paternal care. We first performed a field survey by monitoring paternal care during embryonic development. Subsequently, we conducted a field experiment to assess the prevalence of egg predators (a semi-slug, Parmarion martensi) and the plasticity of male care. Finally, we conducted a laboratory experiment to assess how embryo age affects predation by P. martensi. Our results showed that (1) male attendance and brooding frequency affected embryo survival, and (2) males attended and brooded eggs more frequently in the early stage than in the late stage. The experimental results showed that (3) males increased attendance frequency when the predators were present, and (4) the embryonic predation by the semi-slug during the early was significantly higher than in the late stage. Our findings highlight the importance of paternal care to embryo survival, and the care behavior is plastic. Moreover, our results provide evidence consistent with the predictions of the harm to offspring hypothesis, as males tend to care more for younger offspring which are more vulnerable.","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"79 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141425424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-11DOI: 10.1186/s12983-024-00536-0
Zhi Huang, Dandan Wang, Jinrui Zhou, Hong He, Cong Wei
The most extraordinary systems of symbiosis in insects are found in the suborder Auchenorrhyncha of Hemiptera, which provide unique perspectives for uncovering complicated insect-microbe symbiosis. We investigated symbionts associated with bacteriomes and fat bodies in six cicada species, and compared transmitted cell number ratio of related symbionts in ovaries among species. We reveal that Sulcia and Hodgkinia or a yeast-like fungal symbiont (YLS) are segregated from other host tissues by the bacteriomes in the nymphal stage, then some of them may migrate to other organs (i.e., fat bodies and ovaries) during host development. Particularly, YLS resides together with Sulcia in the “symbiont ball” of each egg and the bacteriomes of young-instar nymphs, but finally migrates to the fat bodies of adults in the majority of Hodgkinia-free cicadas, whereas it resides in both bacteriome sheath and fat bodies of adults in a few other species. The transmitted Sulcia/YLS or Sulcia/Hodgkinia cell number ratio in ovaries varies significantly among species, which could be related to the distribution and/or lineage splitting of symbiont(s). Rickettsia localizes to the nuclei of bacteriomes and fat bodies in some species, but it was not observed to be transmitted to the ovaries, indicating that this symbiont may be acquired from environments or from father to offspring. The considerable difference in the transovarial transmission process of symbionts suggests that cellular mechanisms underlying the symbiont transmission are complex. Our results may provide novel insights into insect-microbe symbiosis.
{"title":"Segregation of endosymbionts in complex symbiotic system of cicadas providing novel insights into microbial symbioses and evolutionary dynamics of symbiotic organs in sap-feeding insects","authors":"Zhi Huang, Dandan Wang, Jinrui Zhou, Hong He, Cong Wei","doi":"10.1186/s12983-024-00536-0","DOIUrl":"https://doi.org/10.1186/s12983-024-00536-0","url":null,"abstract":"The most extraordinary systems of symbiosis in insects are found in the suborder Auchenorrhyncha of Hemiptera, which provide unique perspectives for uncovering complicated insect-microbe symbiosis. We investigated symbionts associated with bacteriomes and fat bodies in six cicada species, and compared transmitted cell number ratio of related symbionts in ovaries among species. We reveal that Sulcia and Hodgkinia or a yeast-like fungal symbiont (YLS) are segregated from other host tissues by the bacteriomes in the nymphal stage, then some of them may migrate to other organs (i.e., fat bodies and ovaries) during host development. Particularly, YLS resides together with Sulcia in the “symbiont ball” of each egg and the bacteriomes of young-instar nymphs, but finally migrates to the fat bodies of adults in the majority of Hodgkinia-free cicadas, whereas it resides in both bacteriome sheath and fat bodies of adults in a few other species. The transmitted Sulcia/YLS or Sulcia/Hodgkinia cell number ratio in ovaries varies significantly among species, which could be related to the distribution and/or lineage splitting of symbiont(s). Rickettsia localizes to the nuclei of bacteriomes and fat bodies in some species, but it was not observed to be transmitted to the ovaries, indicating that this symbiont may be acquired from environments or from father to offspring. The considerable difference in the transovarial transmission process of symbionts suggests that cellular mechanisms underlying the symbiont transmission are complex. Our results may provide novel insights into insect-microbe symbiosis.","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"51 1","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141304360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-29DOI: 10.1186/s12983-024-00535-1
Agnieszka Murawska, Paweł Migdał, Moritz Mating, Paweł Bieńkowski, Ewelina Berbeć, Ralf Einspanier
The investigation of the effects of artificial 50 Hz electric field (E-field) frequency on Apis mellifera is a relatively new field of research. Since the current literature focuses mainly on short-term effects, it is unknown whether E-fields have permanent effects on bees or whether their effects can be neutralized. In this study we assessed gene expression immediately after exposure to the E-field, as well as 7 days after exposure. The aim of this work was to identify potentially dysregulated gene transcripts in honey bees that correlate with exposure time and duration to E-fields.Newly emerged bees were marked daily with a permanent marker (one color for each group). Then bees were exposed to the 50 Hz E-field with an intensity of 5.0 kV/m or 10.0 kV/m for 1-3 h. After exposure, half of the bees were analyzed for gene expression changes. The other half were transferred to a colony kept in a mini-hive. After 7 days, marked bees were collected from the mini-hive for further analysis. Six regulated transcripts were selected of transcripts involved in oxidative phosphorylation (COX5a) and transcripts involved in endocrine functions (HBG-3, ILP-1), mitochondrial inner membrane transport (TIM10), and aging (mRPL18, mRPS30).Our study showed that in Apis mellifera the expression of selected genes is altered in different ways after exposure to 50 Hz electric fields -. Most of those expression changes in Cox5a, mRPL18, mRPS30, and HGB3, were measurable 7 days after a 1-3 h exposure. These results indicate that some E-field effects may be long-term effects on honey bees due to E-field exposure, and they can be observed 7 days after exposure.
{"title":"Metabolism gene expression in worker honey bees after exposure to 50Hz electric field - semi-field analysis.","authors":"Agnieszka Murawska, Paweł Migdał, Moritz Mating, Paweł Bieńkowski, Ewelina Berbeć, Ralf Einspanier","doi":"10.1186/s12983-024-00535-1","DOIUrl":"10.1186/s12983-024-00535-1","url":null,"abstract":"<p><p>The investigation of the effects of artificial 50 Hz electric field (E-field) frequency on Apis mellifera is a relatively new field of research. Since the current literature focuses mainly on short-term effects, it is unknown whether E-fields have permanent effects on bees or whether their effects can be neutralized. In this study we assessed gene expression immediately after exposure to the E-field, as well as 7 days after exposure. The aim of this work was to identify potentially dysregulated gene transcripts in honey bees that correlate with exposure time and duration to E-fields.Newly emerged bees were marked daily with a permanent marker (one color for each group). Then bees were exposed to the 50 Hz E-field with an intensity of 5.0 kV/m or 10.0 kV/m for 1-3 h. After exposure, half of the bees were analyzed for gene expression changes. The other half were transferred to a colony kept in a mini-hive. After 7 days, marked bees were collected from the mini-hive for further analysis. Six regulated transcripts were selected of transcripts involved in oxidative phosphorylation (COX5a) and transcripts involved in endocrine functions (HBG-3, ILP-1), mitochondrial inner membrane transport (TIM10), and aging (mRPL18, mRPS30).Our study showed that in Apis mellifera the expression of selected genes is altered in different ways after exposure to 50 Hz electric fields -. Most of those expression changes in Cox5a, mRPL18, mRPS30, and HGB3, were measurable 7 days after a 1-3 h exposure. These results indicate that some E-field effects may be long-term effects on honey bees due to E-field exposure, and they can be observed 7 days after exposure.</p>","PeriodicalId":55142,"journal":{"name":"Frontiers in Zoology","volume":"21 1","pages":"14"},"PeriodicalIF":2.8,"publicationDate":"2024-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11134740/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141163022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-06DOI: 10.1186/s12983-024-00533-3
Natsumi Hookabe, Rei Ueshima, Toru Miura
Various morphological adaptations are associated with symbiotic relationships between organisms. One such adaptation is seen in the nemertean genus Malacobdella. All species in the genus are commensals of molluscan hosts, attaching to the surface of host mantles with a terminal sucker. Malacobdella possesses several unique characteristics within the order Monostilifera, exhibiting the terminal sucker and the absence of eyes and apical/cerebral organs, which are related to their adaptation to a commensal lifestyle. Nevertheless, the developmental processes that give rise to these morphological characteristics during their transition from free-living larvae to commensal adults remain uncertain. In the present study, therefore, we visualized the developmental processes of the internal morphologies during postembryonic larval stages using fluorescent molecular markers. We demonstrated the developmental processes, including the formation of the sucker primordium and the functional sucker. Furthermore, our data revealed that sensory organs, including apical/cerebral organs, formed in embryonic and early postembryonic stages but degenerated in the late postembryonic stage prior to settlement within their host using a terminal sucker. This study reveals the formation of the terminal sucker through tissue invagination, shedding light on its adhesion mechanism. Sucker muscle development likely originates from body wall muscles. Notably, M. japonica exhibits negative phototaxis despite lacking larval ocelli. This observation suggests a potential role for other sensory mechanisms, such as the apical and cerebral organs identified in the larvae, in facilitating settlement and adhesive behaviors. The loss of sensory organs during larval development might reflect a transition from planktonic feeding to a stable, host-associated lifestyle. This study also emphasizes the need for further studies to explore the phylogenetic relationships within the infraorder Amphiporiina and investigate the postembryonic development of neuromuscular systems in closely related taxa to gain a more comprehensive understanding of ecological adaptations in Nemertea.
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