Pub Date : 2024-07-06DOI: 10.1101/2024.07.03.601798
Pranav Garg, Cameron Frey, William E Browne, Steven S Plotkin
Ctenophores are an attractive lineage for studying animal evolution due to their early divergence from other metazoans. Among Ctenophora, Mnemiopsis leidyi is a model system for developmental, cellular, molecular genetic, and evolutionary studies. Until recently, many of these studies were conducted on wild-caught animals, limiting access to researchers on the coast. Here we present significant advancements towards culturing M. leidyi in laboratories without coastal access, enabling its wider use as an experimental and genetic model system. We detail updated feeding regimes that take advantage of co-culturing Brachionus rotifers with Apocyclops copepods, and quantify the reproductive output of our M. leidyi lab strain on this diet. Our updated feeding regime maintains reproductive fitness comparable to wild-caught individuals. Importantly, we have eliminated the logistical complexities and costs of regularly feeding live larval fish to M. leidyi. Our updated protocols make it feasible to maintain continuous ctenophore cultures independent of access to both coastal populations of wild M. leidyi and larval fish culturing facilities.
栉水母是研究动物进化的一个极具吸引力的类群，因为它们很早就与其他后生动物分化开来。在栉水母中，栉水母（Mnemiopsis leidyi）是发育、细胞、分子遗传和进化研究的模型系统。直到最近，许多此类研究都是在野生捕获的动物身上进行的，这限制了沿海地区研究人员的研究机会。在这里，我们介绍了在没有沿海通道的实验室中培养 M. leidyi 的重大进展，使其能更广泛地用作实验和遗传模型系统。我们详细介绍了利用 Brachionus 轮虫与 Apocyclops 桡足类共同培养的最新饲养方法，并量化了我们的 M. leidyi 实验室品系在这种食物下的繁殖能力。我们更新后的喂养方法可保持与野生个体相当的繁殖能力。重要的是，我们消除了定期给M. leidyi喂食活幼鱼的后勤复杂性和成本。我们更新的方案使我们能够不受沿海野生栉水母种群和幼鱼养殖设施的限制，持续保持栉水母的养殖。
{"title":"Reproductive success of inbred strain MV31 of the ctenophore Mnemiopsis leidyi in a self-sustaining inland laboratory culture system","authors":"Pranav Garg, Cameron Frey, William E Browne, Steven S Plotkin","doi":"10.1101/2024.07.03.601798","DOIUrl":"https://doi.org/10.1101/2024.07.03.601798","url":null,"abstract":"Ctenophores are an attractive lineage for studying animal evolution due to their early divergence from other metazoans. Among Ctenophora, <em>Mnemiopsis leidyi</em> is a model system for developmental, cellular, molecular genetic, and evolutionary studies. Until recently, many of these studies were conducted on wild-caught animals, limiting access to researchers on the coast. Here we present significant advancements towards culturing <em>M. leidyi</em> in laboratories without coastal access, enabling its wider use as an experimental and genetic model system. We detail updated feeding regimes that take advantage of co-culturing <em>Brachionus</em> rotifers with <em>Apocyclops</em> copepods, and quantify the reproductive output of our <em>M. leidyi</em> lab strain on this diet. Our updated feeding regime maintains reproductive fitness comparable to wild-caught individuals. Importantly, we have eliminated the logistical complexities and costs of regularly feeding live larval fish to <em>M. leidyi</em>. Our updated protocols make it feasible to maintain continuous ctenophore cultures independent of access to both coastal populations of wild <em>M. leidyi</em> and larval fish culturing facilities.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-05DOI: 10.1101/2024.07.03.601651
Simone Macri, Nicolas Di-Poi
Advancements in non-invasive surface and internal imaging techniques, along with computational methods, have revolutionized 3D visualization of organismal morphology. These breakthroughs not only enhance research and medical anatomical analysis, but also facilitate the preservation and digital archiving of scientific specimens. We introduce the SmARTR pipeline (Small Animal Realistic Three-dimensional Rendering), a comprehensive workflow integrating wet lab procedures, 3D data acquisition, and processing to produce photorealistic 3D scientific data through cinematic rendering. This versatile pipeline supports multi-scale visualizations, from tissue-level to whole-organism details across diverse living organisms and is adaptable to various imaging sources and platforms. Its modular design and customizable rendering scenarios, provided by detailed SmARTR networks in a free software environment, make it a powerful tool for 3D data analysis. Accessible to a broad audience, SmARTR serves as a valuable resource not only for multiple fields of research in life sciences but also for education, diagnosis, outreach, and artistic endeavors.
{"title":"The SmARTR pipeline: a modular workflow for the cinematic rendering of 3D scientific imaging data","authors":"Simone Macri, Nicolas Di-Poi","doi":"10.1101/2024.07.03.601651","DOIUrl":"https://doi.org/10.1101/2024.07.03.601651","url":null,"abstract":"Advancements in non-invasive surface and internal imaging techniques, along with computational methods, have revolutionized 3D visualization of organismal morphology. These breakthroughs not only enhance research and medical anatomical analysis, but also facilitate the preservation and digital archiving of scientific specimens. We introduce the SmARTR pipeline (Small Animal Realistic Three-dimensional Rendering), a comprehensive workflow integrating wet lab procedures, 3D data acquisition, and processing to produce photorealistic 3D scientific data through cinematic rendering. This versatile pipeline supports multi-scale visualizations, from tissue-level to whole-organism details across diverse living organisms and is adaptable to various imaging sources and platforms. Its modular design and customizable rendering scenarios, provided by detailed SmARTR networks in a free software environment, make it a powerful tool for 3D data analysis. Accessible to a broad audience, SmARTR serves as a valuable resource not only for multiple fields of research in life sciences but also for education, diagnosis, outreach, and artistic endeavors.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-03DOI: 10.1101/2024.07.02.601800
Anja Tamara Zai, Diana Isabel Rodrigues, Anna E Stepien, Iris Adam, Corinna Lorenz, Nicolas Giret, Richard H.R. Hahnloser
Despite the wide use of zebra finches as an animal model to study vocal learning and production, little is known about impacts on their welfare caused by routine experimental manipulations such as changing their social context. Here we conduct a post-hoc analysis of singing rate, an indicator of positive welfare, to gain insights into stress caused by social isolation, a common experimental manipulation. We find that isolation in an unfamiliar environment reduces singing rate for several days, indicating the presence of an acute stressor. However, we find no such decrease when social isolation is caused by either removal of a social companion or by transfer to a familiar environment. Furthermore, during repeated brief periods of isolation, singing rate remains high when isolation is induced by removal of social companions, but it fails to recover from a suppressed state when isolation is induced by recurrent transfer to an unknown environment. These findings suggest that stress from social isolation is negligible compared to stress caused by environmental changes and that frequent short visits of an unfamiliar environment are detrimental rather than beneficial. Together, these insights can serve to refine experimental studies and design paradigms maximizing the birds' wellbeing and vocal output.
{"title":"Familiarity of an environment prevents song suppression in isolated zebra finches","authors":"Anja Tamara Zai, Diana Isabel Rodrigues, Anna E Stepien, Iris Adam, Corinna Lorenz, Nicolas Giret, Richard H.R. Hahnloser","doi":"10.1101/2024.07.02.601800","DOIUrl":"https://doi.org/10.1101/2024.07.02.601800","url":null,"abstract":"Despite the wide use of zebra finches as an animal model to study vocal learning and production, little is known about impacts on their welfare caused by routine experimental manipulations such as changing their social context. Here we conduct a post-hoc analysis of singing rate, an indicator of positive welfare, to gain insights into stress caused by social isolation, a common experimental manipulation. We find that isolation in an unfamiliar environment reduces singing rate for several days, indicating the presence of an acute stressor. However, we find no such decrease when social isolation is caused by either removal of a social companion or by transfer to a familiar environment. Furthermore, during repeated brief periods of isolation, singing rate remains high when isolation is induced by removal of social companions, but it fails to recover from a suppressed state when isolation is induced by recurrent transfer to an unknown environment. These findings suggest that stress from social isolation is negligible compared to stress caused by environmental changes and that frequent short visits of an unfamiliar environment are detrimental rather than beneficial. Together, these insights can serve to refine experimental studies and design paradigms maximizing the birds' wellbeing and vocal output.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141550455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-07-02DOI: 10.1101/2024.06.30.601430
Rachel A Roston, Sophie M Whikehart, Sara M Rolfe, A. Murat Maga
In the past few decades, advances in 3D imaging have created new opportunities for reverse genetic screens. Rapidly growing datasets of 3D images of genetic knockouts require high-throughput, automated computational approaches for identifying and characterizing new phenotypes. However, exploratory, discovery-oriented image analysis pipelines used to discover these phenotypes can be difficult to validate because, by their nature, the expected outcome is not known a priori. Introducing known morphological variation through simulation can help distinguish between real phenotypic differences and random variation; elucidate the effects of sample size; and test the sensitivity and reproducibility of morphometric analyses. Here we present a novel approach for 3D morphological simulation that uses open-source, open-access tools available in 3D Slicer, SlicerMorph, and Advanced Normalization Tools in R (ANTsR). While we focus on diffusible-iodine contrast-enhanced micro-CT (diceCT) images, this approach can be used on any volumetric image. We then use our simulated datasets to test whether tensor-based morphometry (TBM) can recover our introduced differences; to test how effect size and sample size affect detectability; and to determine the reproducibility of our results. In our approach to morphological simulation, we first generate a simulated deformation based on a reference image and then propagate this deformation to subjects using inverse transforms obtained from the registration of subjects to the reference. This produces a new dataset with a shifted population mean while retaining individual variability because each sample deforms more or less based on how different or similar it is from the reference. TBM is a widely-used technique that statistically compares local volume differences associated with local deformations. Our results showed that TBM recovered our introduced morphological differences, but that detectability was dependent on the effect size, the sample size, and the region of interest (ROI) included in the analysis. Detectability of subtle phenotypes can be improved both by increasing the sample size and by limiting analyses to specific body regions. However, it is not always feasible to increase sample sizes in screens of essential genes. Therefore, methodical use of ROIs is a promising way to increase the power of TBM to detect subtle phenotypes. Generating known morphological variation through simulation has broad applicability in developmental, evolutionary, and biomedical morphometrics and is a useful way to distinguish between a failure to detect morphological difference and a true lack of morphological difference. Morphological simulation can also be applied to AI-based supervised learning to augment datasets and overcome dataset limitations.
过去几十年来，三维成像技术的进步为反向遗传筛选创造了新的机会。快速增长的基因敲除三维图像数据集需要高通量、自动化的计算方法来识别和描述新的表型。然而，用于发现这些表型的探索性、以发现为导向的图像分析管道可能难以验证，因为就其本质而言，预期结果并不是先验已知的。通过模拟引入已知的形态变异有助于区分真实的表型差异和随机变异；阐明样本大小的影响；测试形态计量分析的灵敏度和可重复性。在此，我们介绍一种新颖的三维形态模拟方法，该方法使用 3D Slicer、SlicerMorph 和 R 中的高级归一化工具（ANTsR）中的开源、开放式工具。我们将重点放在可扩散碘对比增强 micro-CT (diceCT) 图像上，但这种方法可用于任何容积图像。然后，我们使用模拟数据集来测试基于张量的形态计量学（TBM）是否能恢复我们引入的差异；测试效应大小和样本大小如何影响可探测性；以及确定我们结果的可重复性。在我们的形态学模拟方法中，我们首先根据参考图像生成模拟变形，然后使用从受试者与参考图像配准中获得的反变换将此变形传播给受试者。这就产生了一个新的数据集，该数据集具有移动的群体平均值，同时保留了个体的可变性，因为每个样本都会根据其与参考图像的不同或相似程度发生或多或少的变形。TBM 是一种广泛使用的技术，可对与局部变形相关的局部体积差异进行统计比较。我们的研究结果表明，TBM 恢复了我们引入的形态差异，但可检测性取决于效应大小、样本大小和分析中包含的感兴趣区（ROI）。通过增加样本量和限制对特定身体区域的分析，可以提高对微妙表型的可检测性。然而，在筛选重要基因时增加样本量并不总是可行的。因此，有条不紊地使用 ROI 是提高 TBM 检测微妙表型能力的一种可行方法。通过模拟产生已知的形态变异在发育、进化和生物医学形态计量学中具有广泛的适用性，是区分未能检测到形态差异和真正缺乏形态差异的有用方法。形态模拟还可应用于基于人工智能的监督学习，以增强数据集并克服数据集的局限性。
{"title":"Morphological simulation tests the limits on phenotype discovery in 3D image analysis","authors":"Rachel A Roston, Sophie M Whikehart, Sara M Rolfe, A. Murat Maga","doi":"10.1101/2024.06.30.601430","DOIUrl":"https://doi.org/10.1101/2024.06.30.601430","url":null,"abstract":"In the past few decades, advances in 3D imaging have created new opportunities for reverse genetic screens. Rapidly growing datasets of 3D images of genetic knockouts require high-throughput, automated computational approaches for identifying and characterizing new phenotypes. However, exploratory, discovery-oriented image analysis pipelines used to discover these phenotypes can be difficult to validate because, by their nature, the expected outcome is not known a priori. Introducing known morphological variation through simulation can help distinguish between real phenotypic differences and random variation; elucidate the effects of sample size; and test the sensitivity and reproducibility of morphometric analyses. Here we present a novel approach for 3D morphological simulation that uses open-source, open-access tools available in 3D Slicer, SlicerMorph, and Advanced Normalization Tools in R (ANTsR). While we focus on diffusible-iodine contrast-enhanced micro-CT (diceCT) images, this approach can be used on any volumetric image. We then use our simulated datasets to test whether tensor-based morphometry (TBM) can recover our introduced differences; to test how effect size and sample size affect detectability; and to determine the reproducibility of our results. In our approach to morphological simulation, we first generate a simulated deformation based on a reference image and then propagate this deformation to subjects using inverse transforms obtained from the registration of subjects to the reference. This produces a new dataset with a shifted population mean while retaining individual variability because each sample deforms more or less based on how different or similar it is from the reference. TBM is a widely-used technique that statistically compares local volume differences associated with local deformations. Our results showed that TBM recovered our introduced morphological differences, but that detectability was dependent on the effect size, the sample size, and the region of interest (ROI) included in the analysis. Detectability of subtle phenotypes can be improved both by increasing the sample size and by limiting analyses to specific body regions. However, it is not always feasible to increase sample sizes in screens of essential genes. Therefore, methodical use of ROIs is a promising way to increase the power of TBM to detect subtle phenotypes. Generating known morphological variation through simulation has broad applicability in developmental, evolutionary, and biomedical morphometrics and is a useful way to distinguish between a failure to detect morphological difference and a true lack of morphological difference. Morphological simulation can also be applied to AI-based supervised learning to augment datasets and overcome dataset limitations.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141517718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-30DOI: 10.1101/2024.06.26.600876
Aaron R Ashbrook, Melbert Schwarz, Coby Schal, Aram Mikaelyan
The Eastern subterranean termite, Reticulitermes flavipes (Kollar), is a significant pest, causing extensive damage to structures that amount to substantial economic losses. Traditional termite control methods have utilized boric acid, known for its broad-spectrum insecticidal properties, yet its impact on termite gut microbiomes and the implications of such effects remain understudied. Our study evaluates the dose-dependent mortality of R. flavipes upon being provided boric acid treated filter papers and investigates the resulting dysbiosis within the termite gut microbiome. Consistent with reports from other insects, mortality increased in a dose-dependent manner, with the highest boric acid concentration (203.7 ug/cm2 of filter paper) significantly reducing termite survival. 16S rRNA gene sequencing of the gut microbiome revealed notable shifts in composition, indicating boric acid-induced dysbiosis. Aside from an overall decrease in microbial diversity, the relative abundance of some symbionts essential for termite nutrition decreased in response to higher boric acid concentrations, while several putative pathogens increased. Our findings extend the understanding of boric acid's mode of action in termites, emphasizing its effect beyond direct toxicity to include significant microbiome modulation that can have dire effects on termite biology. Considering its potential to induce dysbiosis and potentially augment the effectiveness of entomopathogens, our study supports the continued use of boric acid and related compounds for termite-resistant treatments for wood.
{"title":"Lethal Disruption of the Symbiotic Gut Community in Eastern Subterranean Termite Caused by Boric Acid","authors":"Aaron R Ashbrook, Melbert Schwarz, Coby Schal, Aram Mikaelyan","doi":"10.1101/2024.06.26.600876","DOIUrl":"https://doi.org/10.1101/2024.06.26.600876","url":null,"abstract":"The Eastern subterranean termite, Reticulitermes flavipes (Kollar), is a significant pest, causing extensive damage to structures that amount to substantial economic losses. Traditional termite control methods have utilized boric acid, known for its broad-spectrum insecticidal properties, yet its impact on termite gut microbiomes and the implications of such effects remain understudied. Our study evaluates the dose-dependent mortality of R. flavipes upon being provided boric acid treated filter papers and investigates the resulting dysbiosis within the termite gut microbiome. Consistent with reports from other insects, mortality increased in a dose-dependent manner, with the highest boric acid concentration (203.7 ug/cm2 of filter paper) significantly reducing termite survival. 16S rRNA gene sequencing of the gut microbiome revealed notable shifts in composition, indicating boric acid-induced dysbiosis. Aside from an overall decrease in microbial diversity, the relative abundance of some symbionts essential for termite nutrition decreased in response to higher boric acid concentrations, while several putative pathogens increased. Our findings extend the understanding of boric acid's mode of action in termites, emphasizing its effect beyond direct toxicity to include significant microbiome modulation that can have dire effects on termite biology. Considering its potential to induce dysbiosis and potentially augment the effectiveness of entomopathogens, our study supports the continued use of boric acid and related compounds for termite-resistant treatments for wood.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-27DOI: 10.1101/2024.06.23.600287
Katherine Olivia Montana, Terrence M. Gosliner, Sarah C. Crews, Lynn J. Bonomo, James T. Carlton, Rebecca F. Johnson
In the aftermath of the 2011 east Japanese earthquake and tsunami, anthropogenic debris from the east coast of Japan floated across the Pacific Ocean to the west coast of North America. One such vessel from Iwate Prefecture arrived on the coast of Oregon, and the fouling community included specimens identified as the nudibranch Hermissenda crassicornis, which was previously thought to range from Japan to Baja California but has since been split into three species: H. crassicornis (Alaska to southern CA), H. opalescens (British Columbia to Baja California), and H. emurai (Japan, Korea, Russian Far East). Previous work suggested that all of the motile invertebrates found in the tsunami debris fouling community were either pelagic or Japanese in origin. Our study sought to determine whether the nudibranch specimens collected from the Iwate vessel were, according to the new classification system, only H. emurai or whether the Eastern Pacific Hermissenda were present as well. Results from DNA sequencing and morphological analysis suggest that specimens of H. crassicornis, as it is currently recognized, and H. opalescens were found on the vessel. This finding indicates either that these species settled after arrival to the west coast of North America or that H. crassicornis and H. opalescens is found in Japan, suggesting Hermissenda ranges need to be investigated further. Occurrence data shared on the iNaturalist platform were also used to assess current ranges. Our phylogenetic tree and haplotype network constructed from COI data from all Hermissenda species indicate that H. opalescens and H. emurai are most closely related with H. opalescens sister to the clade that contains H. opalescens and H. emurai. This study demonstrates the power of combining volunteer naturalist data with lab-collected data to understand evolutionary relationships, species ranges, and biogeography.
2011 年日本东部发生地震和海啸后，来自日本东海岸的人为碎片漂过太平洋，到达北美西海岸。其中一艘来自岩手县的船只抵达俄勒冈州海岸，污损群落中包括被确认为裸鳃动物 Hermissenda crassicornis 的标本：H.crassicornis（阿拉斯加至加利福尼亚南部）、H. opalescens（不列颠哥伦比亚至加利福尼亚下加利福尼亚）和 H. emurai（日本、韩国、俄罗斯远东地区）。以前的研究表明，在海啸残骸污损群落中发现的所有活动无脊椎动物都来自中上层或日本。我们的研究旨在确定，根据新的分类系统，从岩手县船只上采集的裸鳃标本是否仅为 H. emurai，或者是否也有东太平洋的 Hermissenda。DNA 测序和形态分析结果表明，在该船上发现了目前公认的 H. crassicornis 和 H. opalescens 的标本。这一发现要么表明这些物种在到达北美西海岸后定居下来，要么表明 H. crassicornis 和 H. opalescens 在日本被发现，这表明 Hermissenda 的分布范围需要进一步调查。在iNaturalist平台上共享的出现数据也被用来评估目前的分布范围。我们根据所有 Hermissenda 物种的 COI 数据构建的系统发生树和单倍型网络表明，H. opalescens 和 H. emurai 的亲缘关系最为密切，其中 H. opalescens 是包含 H. opalescens 和 H. emurai 的支系的姐妹支系。这项研究表明，将志愿博物学家的数据与实验室收集的数据相结合，对了解进化关系、物种范围和生物地理学很有帮助。
{"title":"Why didn’t the nudibranch cross the ocean? Understanding biogeographic and evolutionary relationships of Hermissenda (Nudibranchia: Myrrhinidae) Bergh, 1878","authors":"Katherine Olivia Montana, Terrence M. Gosliner, Sarah C. Crews, Lynn J. Bonomo, James T. Carlton, Rebecca F. Johnson","doi":"10.1101/2024.06.23.600287","DOIUrl":"https://doi.org/10.1101/2024.06.23.600287","url":null,"abstract":"In the aftermath of the 2011 east Japanese earthquake and tsunami, anthropogenic debris from the east coast of Japan floated across the Pacific Ocean to the west coast of North America. One such vessel from Iwate Prefecture arrived on the coast of Oregon, and the fouling community included specimens identified as the nudibranch Hermissenda crassicornis, which was previously thought to range from Japan to Baja California but has since been split into three species: H. crassicornis (Alaska to southern CA), H. opalescens (British Columbia to Baja California), and H. emurai (Japan, Korea, Russian Far East). Previous work suggested that all of the motile invertebrates found in the tsunami debris fouling community were either pelagic or Japanese in origin. Our study sought to determine whether the nudibranch specimens collected from the Iwate vessel were, according to the new classification system, only H. emurai or whether the Eastern Pacific Hermissenda were present as well. Results from DNA sequencing and morphological analysis suggest that specimens of H. crassicornis, as it is currently recognized, and H. opalescens were found on the vessel. This finding indicates either that these species settled after arrival to the west coast of North America or that H. crassicornis and H. opalescens is found in Japan, suggesting Hermissenda ranges need to be investigated further. Occurrence data shared on the iNaturalist platform were also used to assess current ranges. Our phylogenetic tree and haplotype network constructed from COI data from all Hermissenda species indicate that H. opalescens and H. emurai are most closely related with H. opalescens sister to the clade that contains H. opalescens and H. emurai. This study demonstrates the power of combining volunteer naturalist data with lab-collected data to understand evolutionary relationships, species ranges, and biogeography.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-20DOI: 10.1101/2024.06.17.599383
Emmanuel Odii, Nnaemeka Joe Okonkwo, Ibeabuchi Uko
Methanolic and hexane extract of black pepper Piper guineense Schum & Thonn was evaluated for its insecticidal against the larger grain borer Prostephanus truncatus in stored cassava chips. The extracts were applied at various concentrations (4000, 2000, 1000, 500, 250 μl/ml) with ordinary acetone as control. The experimental setup involved placing ten unsexed adults of each insect species into petri dishes treated with each of the extracts as applicable for residual treatment application. Also, cassava chips weighing twenty grams were treated with the different concentrations of the extracts and the control before being artificially infested with Prostephanus truncatus and left for a period of thirty-three days. All of the treatments significantly reduced emergence holes and grain damage compared with the control.
{"title":"Effect of Hexane and Methanol Extracts of Piper guineense (Schum and Thonn) Seeds against the Larger grain borer (Prostephanus truncatus) in Stored Cassava Chips","authors":"Emmanuel Odii, Nnaemeka Joe Okonkwo, Ibeabuchi Uko","doi":"10.1101/2024.06.17.599383","DOIUrl":"https://doi.org/10.1101/2024.06.17.599383","url":null,"abstract":"Methanolic and hexane extract of black pepper Piper guineense Schum & Thonn was evaluated for its insecticidal against the larger grain borer Prostephanus truncatus in stored cassava chips. The extracts were applied at various concentrations (4000, 2000, 1000, 500, 250 μl/ml) with ordinary acetone as control. The experimental setup involved placing ten unsexed adults of each insect species into petri dishes treated with each of the extracts as applicable for residual treatment application. Also, cassava chips weighing twenty grams were treated with the different concentrations of the extracts and the control before being artificially infested with Prostephanus truncatus and left for a period of thirty-three days. All of the treatments significantly reduced emergence holes and grain damage compared with the control.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-20DOI: 10.1101/2024.06.18.599476
Deepak Nain, Anjali Rana, Rhitoban Raychoudhury, Ruchira Sen
We report the morphology, biology and phylogeny of a new strepsipteran endoparasitic species: Xenos gadagkari, from the primitively eusocial wasp Polistes wattii from Punjab, India. We report a high abundance of the endoparasite in P. wattii population of our study area and provide the morphological description of adult males, male puparium and neotenic females. This species is sufficiently different from other Xenos sp reported from various social wasps and therefore, constitutes a new species, X. gadagkari Sen and Nain, sp. nov. Although there are a few reports of Strepsipteran parasites from India, this is the first confirmational report with a thorough description of a Xenos species from the Indian population of P. wattii and underscores the need for further investigation of the diversity and distribution of this group in India. Our findings contribute to the growing body of knowledge on Xenos and provide a foundation for future behavioural, microbial and molecular studies on this enigmatic group of insects.
我们报告了一种新的链格氏内寄生物种的形态学、生物学和系统发育：Xenos gadagkari。我们报告了该内寄生虫在我们研究地区的 P. wattii 群体中的高丰度，并提供了成年雄蜂、雄蜂蛹和新生雌蜂的形态描述。该物种与其他从各种社会性胡蜂中报告的 Xenos sp 有足够的不同，因此构成了一个新物种，即 X. gadagkari Sen 和 Nain，sp. nov。尽管有一些关于印度链格孢霉属寄生虫的报道，但这是第一份对来自印度瓦提氏黄蜂种群的 Xenos 物种进行详尽描述的确证报告，并强调了进一步调查该类寄生虫在印度的多样性和分布情况的必要性。我们的研究结果有助于加深对 Xenos 的了解，并为今后对这一神秘昆虫类群进行行为、微生物和分子研究奠定了基础。
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Stingless bees, prevalent in tropical and subtropical regions, are a tribe of eusocial bees that are crucial pollinators for economic crops and native plants, producing honey and pollen. However, colony expansion is limited by a shortage of queens for new colonies. Therefore, mass artificial rearing of virgin queens could address this in commercially managed meliponiculture. Furthermore, the in vitro rearing of queen stingless bees can improve meliponiculture management and conservation efforts. Herein, we explored the efficacy of in vitro queen rearing for Heterotrigona itama assessing the queen’s body size, reproductive organ size (ovary and spermatheca), acceptance rate into new, small colonies, and mating frequency. H. itama larvae developed into queens when fed with 120 µL–150 µL of larval food, resulting in in vitro queens having body sizes similar to those of naturally produced queens. Microscopic analysis revealed well-developed ovaries and spermathecae in in vitro-reared queens, unlike the smaller ovaries and the absence of spermathecae in the naturally produced workers. Acceptance of in vitro-reared queens was independent of worker age, and mating frequency was low but not significantly different from naturally produced queens. These findings could enhance stingless beekeeping practices and conservation efforts for the native stingless bee species.
无刺蜂盛行于热带和亚热带地区，是雄蜂的一个分支，是经济作物和本地植物的重要授粉者，生产蜂蜜和花粉。然而，蜂群的扩大受到新蜂群蜂王短缺的限制。因此，在商业化管理的蜜蜂养殖中，大量人工饲养处女蜂王可以解决这一问题。此外，体外饲养蜂王还能改善蜜蜂养殖管理和保护工作。在此，我们探讨了体外饲养无刺蜂王（Heterotrigona itama）的效果，评估了蜂王的体型、生殖器官大小（卵巢和精巢）、对新的小型蜂群的接受率以及交配频率。用 120 µL-150 µL 幼虫食物喂养 H. itama 幼虫后，幼虫发育成蜂王，体外蜂王的体型与自然生产的蜂王相似。显微镜分析显示，体外培育的蜂王卵巢和精巢发育良好，而自然生产的工蜂卵巢较小，也没有精巢。体外培育蜂王的接受程度与工蜂年龄无关，交配频率较低，但与自然生产的蜂王没有显著差异。这些研究结果可促进无刺蜂的饲养实践和本地无刺蜂物种的保护工作。
{"title":"External morphometric and microscopic analysis of the reproductive system in in- vitro reared stingless bee queens, Heterotrigona itama, and their mating frequency","authors":"Kanyanat Wongsa, Orawan Duangphakdee, Pisit Poolprasert, ATSALEK RATTANAWANNEE","doi":"10.1101/2024.06.12.598741","DOIUrl":"https://doi.org/10.1101/2024.06.12.598741","url":null,"abstract":"Stingless bees, prevalent in tropical and subtropical regions, are a tribe of eusocial bees that are crucial pollinators for economic crops and native plants, producing honey and pollen. However, colony expansion is limited by a shortage of queens for new colonies. Therefore, mass artificial rearing of virgin queens could address this in commercially managed meliponiculture. Furthermore, the in vitro rearing of queen stingless bees can improve meliponiculture management and conservation efforts. Herein, we explored the efficacy of in vitro queen rearing for Heterotrigona itama assessing the queen’s body size, reproductive organ size (ovary and spermatheca), acceptance rate into new, small colonies, and mating frequency. H. itama larvae developed into queens when fed with 120 µL–150 µL of larval food, resulting in in vitro queens having body sizes similar to those of naturally produced queens. Microscopic analysis revealed well-developed ovaries and spermathecae in in vitro-reared queens, unlike the smaller ovaries and the absence of spermathecae in the naturally produced workers. Acceptance of in vitro-reared queens was independent of worker age, and mating frequency was low but not significantly different from naturally produced queens. These findings could enhance stingless beekeeping practices and conservation efforts for the native stingless bee species.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The Sunda pangolin (Manis javanica) is a burrowing and nocturnal animal, and they have poor vision, thus, intraspecies communication relies on olfaction, such as mating, warning, and scent-marking. However, the intraspecies pheromone in pangolins remains unknown. In this study, all the odorant-binding proteins in Sunda pangolins were functionally expressed, and they were screened against a panel of 32 volatiles that were derived from the pangolin's urine, feces, and anal gland secretions. Reverse chemical ecology identified that M. javanica odorant-binding protein 3 (MjavOBP3) possesses the highest binding affinity to muscone. A subsequent behavior-tracking assay showed that only males can sense muscone; thus, we hypothesize that muscone is a male-specific scent-marking pheromone. Meanwhile, the structural study showed that Tyr117 contributes the most to muscone's binding, which was further validated by site-directed mutagenesis. The findings clarify the scent-marking mechanism in pangolins, and muscone could potentially be used to support the monitoring and conservation of this endangered animal.
{"title":"Muscone-specific olfactory protein reveals the putative scent-marking pheromone in the Sunda pangolin (Manis javanica)","authors":"Zhongbo Yu, Tao Meng, Luyao Yu, Yichen Zhou, Tengcheng Que, Meihong He, Haijing Wang, Yingjiao Li, Liling Liu, Wenjian Liu, Yinliang Wang, Bingzhong Ren","doi":"10.1101/2024.06.04.597258","DOIUrl":"https://doi.org/10.1101/2024.06.04.597258","url":null,"abstract":"The Sunda pangolin (Manis javanica) is a burrowing and nocturnal animal, and they have poor vision, thus, intraspecies communication relies on olfaction, such as mating, warning, and scent-marking. However, the intraspecies pheromone in pangolins remains unknown. In this study, all the odorant-binding proteins in Sunda pangolins were functionally expressed, and they were screened against a panel of 32 volatiles that were derived from the pangolin's urine, feces, and anal gland secretions. Reverse chemical ecology identified that M. javanica odorant-binding protein 3 (MjavOBP3) possesses the highest binding affinity to muscone. A subsequent behavior-tracking assay showed that only males can sense muscone; thus, we hypothesize that muscone is a male-specific scent-marking pheromone. Meanwhile, the structural study showed that Tyr117 contributes the most to muscone's binding, which was further validated by site-directed mutagenesis. The findings clarify the scent-marking mechanism in pangolins, and muscone could potentially be used to support the monitoring and conservation of this endangered animal.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141253185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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