Pub Date : 2024-04-22DOI: 10.1101/2024.04.18.590067
Shu D Dan, Danielle S Taylor, Jaime Yockey, Gavin J Svenson, Joshua P Martin
The form of an animal's limbs has to balance multiple functions: locomotion, grasping, climbing, and jumping, among others. For cryptic animals, especially those that resemble elements of their habitat like sticks or grasses, the limbs may also be modified to enhance the camouflage. The performance of a limb in one category may require a tradeoff, reducing performance in another category. Praying mantises provide a diverse group of insects who all use their forelegs for one function, capturing prey, while some species use them as part of their camouflage. Here we use a large database of images of mantis species to capture the variation in morphology across the order, and to calculate the largest prey that their forelegs can hold. We find that the length and thickness of the femur and the length of the tibia comprise most of the variability across species. The majority of species have similar foreleg morphology, with two large groups extending into areas of the morphospace with thicker or thinner forelegs. A geometric relationship between dimensions of the foreleg and the optimal prey diameter maps directly onto the variability across species determined by principal components analysis; legs with thinner femurs and shorter tibia can't hold large prey, and the distribution of the species across the morphospace follows the gradient of optimum prey size. These results suggest that some species trade ability to grasp larger prey for benefits including crypsis, and the praying mantises are an ideal system for studying morphological and functional variation in limbs.
{"title":"The geometry of prey capture in praying mantis forelegs","authors":"Shu D Dan, Danielle S Taylor, Jaime Yockey, Gavin J Svenson, Joshua P Martin","doi":"10.1101/2024.04.18.590067","DOIUrl":"https://doi.org/10.1101/2024.04.18.590067","url":null,"abstract":"The form of an animal's limbs has to balance multiple functions: locomotion, grasping, climbing, and jumping, among others. For cryptic animals, especially those that resemble elements of their habitat like sticks or grasses, the limbs may also be modified to enhance the camouflage. The performance of a limb in one category may require a tradeoff, reducing performance in another category. Praying mantises provide a diverse group of insects who all use their forelegs for one function, capturing prey, while some species use them as part of their camouflage. Here we use a large database of images of mantis species to capture the variation in morphology across the order, and to calculate the largest prey that their forelegs can hold. We find that the length and thickness of the femur and the length of the tibia comprise most of the variability across species. The majority of species have similar foreleg morphology, with two large groups extending into areas of the morphospace with thicker or thinner forelegs. A geometric relationship between dimensions of the foreleg and the optimal prey diameter maps directly onto the variability across species determined by principal components analysis; legs with thinner femurs and shorter tibia can't hold large prey, and the distribution of the species across the morphospace follows the gradient of optimum prey size. These results suggest that some species trade ability to grasp larger prey for benefits including crypsis, and the praying mantises are an ideal system for studying morphological and functional variation in limbs.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"141 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140637185","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 : 2024-04-22DOI: 10.1101/2024.04.18.590155
Alejandro Damian-Serrano, Kaiden A Walton, Anneliese Bishop-Perdue, Sophie Bagoye, Kevin T. Du Clos, Bradford J Gemmell, Sean P Colin, John H Costello, Kelly R Sutherland
Salps are marine pelagic tunicates with a complex life cycle including a solitary and colonial stage. Salp colonies are composed of asexually budded individuals that coordinate their swimming by multi-jet propulsion. Colonies develop into species-specific architectures with distinct zooid orientations. We hypothesize that colonial architecture drives differences in swimming performance between salps due to differences in how frontal drag scales with the number of propeller zooids in the colony. Moreover, we hypothesize that faster-swimming taxa are more energetically efficient in their locomotion since less energy would be devoted to overcoming drag forces. We (1) compare swimming speed across salp species and architectures, (2) evaluate how swimming speed scales with the number of zooids in the colony in architectures with constant and scaling frontal cross-sectional area, and (3) compare the metabolic cost of transport across different species and how it scales with swimming speed. To measure their swimming speeds, we recorded swimming salp colonies using in situ videography while SCUBA diving in the open ocean. To estimate the cost of transport, we measured the respiration rates of swimming and anesthetized salps collected in situ using jars equipped with non-invasive oxygen sensors. We found that linear colonies generally swim faster and with a lower cost of transport due to their differential advantage in frontal drag scaling with an increasing number of zooids. These findings underscore the importance of considering propeller arrangement to optimize speed and energy efficiency in bioinspired underwater vehicle design, leveraging lessons learned from the diverse natural laboratory provided by salp diversity.
{"title":"Colonial Architecture Modulates the Speed and Efficiency of Multi-Jet Swimming in Salp Colonies","authors":"Alejandro Damian-Serrano, Kaiden A Walton, Anneliese Bishop-Perdue, Sophie Bagoye, Kevin T. Du Clos, Bradford J Gemmell, Sean P Colin, John H Costello, Kelly R Sutherland","doi":"10.1101/2024.04.18.590155","DOIUrl":"https://doi.org/10.1101/2024.04.18.590155","url":null,"abstract":"Salps are marine pelagic tunicates with a complex life cycle including a solitary and colonial stage. Salp colonies are composed of asexually budded individuals that coordinate their swimming by multi-jet propulsion. Colonies develop into species-specific architectures with distinct zooid orientations. We hypothesize that colonial architecture drives differences in swimming performance between salps due to differences in how frontal drag scales with the number of propeller zooids in the colony. Moreover, we hypothesize that faster-swimming taxa are more energetically efficient in their locomotion since less energy would be devoted to overcoming drag forces. We (1) compare swimming speed across salp species and architectures, (2) evaluate how swimming speed scales with the number of zooids in the colony in architectures with constant and scaling frontal cross-sectional area, and (3) compare the metabolic cost of transport across different species and how it scales with swimming speed. To measure their swimming speeds, we recorded swimming salp colonies using in situ videography while SCUBA diving in the open ocean. To estimate the cost of transport, we measured the respiration rates of swimming and anesthetized salps collected in situ using jars equipped with non-invasive oxygen sensors. We found that linear colonies generally swim faster and with a lower cost of transport due to their differential advantage in frontal drag scaling with an increasing number of zooids. These findings underscore the importance of considering propeller arrangement to optimize speed and energy efficiency in bioinspired underwater vehicle design, leveraging lessons learned from the diverse natural laboratory provided by salp diversity.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140637075","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 : 2024-04-20DOI: 10.1101/2024.04.17.589896
Ben Jacob Novak, Pete Gober, Robyn Bortner, Della Garelle, Mary Wright, Justin Novak, Marlys L Houck, Oliver A Ryder, Dennis Milutinovich, Jill Benavidez, Kerry Ryan, Shawn Walker, Sanaz Sadeghieh Arenivas, Lauren Aston, Blake Russell, Paul Marinari, Adrienne Crosier, Kelly Helmick, Mary R Gibson, Daniel P Carlson, Bradley J Swanson, Samantha M Wisely, Zoe S White, Colleen Lynch, Ryan Phelan
An endangered black-footed ferret female that died in 1988 with no living descendants in the current population was successfully cloned from cryopreserved cells using cross-species somatic cell nuclear transfer, producing three healthy kits. Incorporating progeny from these clones would provide an 8th founder to the breeding program and increase genetic variation to the species' limited gene-pool. This marks the first time a native U.S. endangered species has been cloned.
{"title":"First endangered black-footed ferrets, Mustela nigripes, cloned for genetic rescue","authors":"Ben Jacob Novak, Pete Gober, Robyn Bortner, Della Garelle, Mary Wright, Justin Novak, Marlys L Houck, Oliver A Ryder, Dennis Milutinovich, Jill Benavidez, Kerry Ryan, Shawn Walker, Sanaz Sadeghieh Arenivas, Lauren Aston, Blake Russell, Paul Marinari, Adrienne Crosier, Kelly Helmick, Mary R Gibson, Daniel P Carlson, Bradley J Swanson, Samantha M Wisely, Zoe S White, Colleen Lynch, Ryan Phelan","doi":"10.1101/2024.04.17.589896","DOIUrl":"https://doi.org/10.1101/2024.04.17.589896","url":null,"abstract":"An endangered black-footed ferret female that died in 1988 with no living descendants in the current population was successfully cloned from cryopreserved cells using cross-species somatic cell nuclear transfer, producing three healthy kits. Incorporating progeny from these clones would provide an 8th founder to the breeding program and increase genetic variation to the species' limited gene-pool. This marks the first time a native U.S. endangered species has been cloned.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140628970","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 : 2024-04-20DOI: 10.1101/2024.04.17.589948
Jing Cai, Sergei Nikonov, Alison M Sweeney
Marine animals with polarization vision are able to effectively detect moving objects in shallow waters, which are illuminated by dynamic fluctuations of downwelling light known as caustics. While behavioral studies across different animal species have demonstrated the support of polarization vision in moving object detection within this noisy environment, little is known about how their retinal photoreceptors, absorbing polarized photons, respond to moving objects, or how each photoreceptor contributes to the collective retinal reaction to changes in polarization. In this study, we employed multi-electrode array recordings to examine the retinal neural response of squid to polarized light stimuli that were designed to simulate caustics environment. Extracellular retinal recordings not only exhibit neural activities selective to the direction of polarization but also demonstrate a significant enhancement in response to stimuli with changing polarization compared to constant polarization. This enhancement is robust in almost all recording channels, but absent in a random permutation of the recordings from different trial types. These results suggest that the retinal photoreceptors directly encode the change of polarization stimuli, thereby contributing to signal detections with polarization vision. Together, our research represents a novel neural exploration of cephalopod polarization vision in a caustic environment, and advances our understanding of how nature parses scenes with salient, dynamic polarization in animal vision.
{"title":"Enhancements in squid retinal responses to change of polarizations in a caustic shallow water","authors":"Jing Cai, Sergei Nikonov, Alison M Sweeney","doi":"10.1101/2024.04.17.589948","DOIUrl":"https://doi.org/10.1101/2024.04.17.589948","url":null,"abstract":"Marine animals with polarization vision are able to effectively detect moving objects in shallow waters, which are illuminated by dynamic fluctuations of downwelling light known as caustics. While behavioral studies across different animal species have demonstrated the support of polarization vision in moving object detection within this noisy environment, little is known about how their retinal photoreceptors, absorbing polarized photons, respond to moving objects, or how each photoreceptor contributes to the collective retinal reaction to changes in polarization. In this study, we employed multi-electrode array recordings to examine the retinal neural response of squid to polarized light stimuli that were designed to simulate caustics environment. Extracellular retinal recordings not only exhibit neural activities selective to the direction of polarization but also demonstrate a significant enhancement in response to stimuli with changing polarization compared to constant polarization. This enhancement is robust in almost all recording channels, but absent in a random permutation of the recordings from different trial types. These results suggest that the retinal photoreceptors directly encode the change of polarization stimuli, thereby contributing to signal detections with polarization vision. Together, our research represents a novel neural exploration of cephalopod polarization vision in a caustic environment, and advances our understanding of how nature parses scenes with salient, dynamic polarization in animal vision.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"221 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140629026","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 : 2024-04-20DOI: 10.1101/2024.04.16.589807
Abigail A Chapman, Alison McAfee, David R Tarpy, Julia Fine, Zoe Rempel, Kira Peters, Rob Currie, Leonard Foster
With their long lives and extreme reproductive output, social insect queens have escaped the classic trade-off between fecundity and lifespan but evidence for a trade-off between fecundity and immunity has been inconclusive. This is in part because pathogenic effects are seldom decoupled from effects of immune induction. We conducted parallel, blind virus infection experiments in the laboratory and in the field to interrogate the idea of a reproductive immunity trade-off and better understand how these ubiquitous honey bee stressors affect queen health. We found that queens injected with infectious virus had smaller ovaries and were less likely to recommence egg-laying than controls, while queens injected with UV-inactivated virus displayed an intermediate phenotype. In the field, heavily infected queens had smaller ovaries and infection was a meaningful predictor of whether supersedure cells were observed in the colony. Immune responses in queens receiving live virus were similar to queens receiving inactivated virus, and several of the same immune proteins were negatively associated with ovary mass in the field. This work solidifies the relationship between virus infection and symptoms associated with queen failure and suggests that a reproductive-immunity trade-off is partially, but not wholly responsible for these effects.
{"title":"Common viral infections inhibit egg laying in honey bee queens and are linked to premature supersedure","authors":"Abigail A Chapman, Alison McAfee, David R Tarpy, Julia Fine, Zoe Rempel, Kira Peters, Rob Currie, Leonard Foster","doi":"10.1101/2024.04.16.589807","DOIUrl":"https://doi.org/10.1101/2024.04.16.589807","url":null,"abstract":"With their long lives and extreme reproductive output, social insect queens have escaped the classic trade-off between fecundity and lifespan but evidence for a trade-off between fecundity and immunity has been inconclusive. This is in part because pathogenic effects are seldom decoupled from effects of immune induction. We conducted parallel, blind virus infection experiments in the laboratory and in the field to interrogate the idea of a reproductive immunity trade-off and better understand how these ubiquitous honey bee stressors affect queen health. We found that queens injected with infectious virus had smaller ovaries and were less likely to recommence egg-laying than controls, while queens injected with UV-inactivated virus displayed an intermediate phenotype. In the field, heavily infected queens had smaller ovaries and infection was a meaningful predictor of whether supersedure cells were observed in the colony. Immune responses in queens receiving live virus were similar to queens receiving inactivated virus, and several of the same immune proteins were negatively associated with ovary mass in the field. This work solidifies the relationship between virus infection and symptoms associated with queen failure and suggests that a reproductive-immunity trade-off is partially, but not wholly responsible for these effects.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140624915","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 : 2024-04-20DOI: 10.1101/2024.04.16.589736
Kiran Afshan, Yuchen Liu, Mark Viney
Strongyloides nematodes are parasites of livestock, and S. papillosus infects ruminant livestock that can cause disease. Recent genomic analysis of several Strongyloides species is now facilitating the population genomic analyses of natural Strongyloides infections, for example finding that S. ratti in wild UK rats exists as an assemblage of long-lived, asexual lineages. Here we have investigated the population genomics of S. papillosus in goats in Pakistan. We find that S. papillosus is common, with a prevalence of 28 %; that the population is genetically diverse and that individual goats commonly have mixed-genotype infections; and that there is evidence of only limited admixture. These results now provoke further questions about the host range of different S. papillosus genotypes that can in the future be investigated by further population genomic analyses.
Strongyloides 线虫是家畜的寄生虫，S. papillosus 感染反刍家畜会导致疾病。近来对一些斯特龙线虫物种的基因组分析有助于对自然斯特龙线虫感染进行种群基因组分析，例如发现英国野生大鼠中的 S. ratti 是一个长寿命、无性系的集合体。在这里，我们研究了巴基斯坦山羊中乳头疮囊菌的种群基因组学。我们发现乳头状瘤病毒很常见，发病率为 28%；该种群具有基因多样性，个别山羊通常会出现混合基因型感染；而且只有有限的混杂证据。这些结果引发了有关不同乳头状瘤病毒基因型宿主范围的更多问题，今后可通过进一步的群体基因组分析进行研究。
{"title":"The population genetics of Strongyloides papillosus in Pakistani goats revealed by whole genome sequencing","authors":"Kiran Afshan, Yuchen Liu, Mark Viney","doi":"10.1101/2024.04.16.589736","DOIUrl":"https://doi.org/10.1101/2024.04.16.589736","url":null,"abstract":"Strongyloides nematodes are parasites of livestock, and S. papillosus infects ruminant livestock that can cause disease. Recent genomic analysis of several Strongyloides species is now facilitating the population genomic analyses of natural Strongyloides infections, for example finding that S. ratti in wild UK rats exists as an assemblage of long-lived, asexual lineages. Here we have investigated the population genomics of S. papillosus in goats in Pakistan. We find that S. papillosus is common, with a prevalence of 28 %; that the population is genetically diverse and that individual goats commonly have mixed-genotype infections; and that there is evidence of only limited admixture. These results now provoke further questions about the host range of different S. papillosus genotypes that can in the future be investigated by further population genomic analyses.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"77 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140629036","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 : 2024-04-17DOI: 10.1101/2024.04.14.589444
Sydney K. Brannoch, Julian Katzke, Danielle S Taylor, Evan P Economo, Yuri Ogawa, Ajay Narendra, Gavin J Svenson, Joshua P Martin
Animals' sensory systems enable them to navigate and interact with their environments. Adaptive specializations of these systems can generate novel structures or organs that support highly unique niche adaptations. We report the discovery of a novel sensory organ in a group of praying mantises (Insecta, Mantodea, Nanomantoidea), which have an unusual leaf-planking ecomorphic life strategy, laying against the undersides of broadleaf vegetation. Histology, scanning electron microscopy, and x-ray computed tomography all support the novelty of this distinct morphology while electrophysiology reveals that the sensory organ, herein designated the gustifolium organ, detects plant volatiles. The location of the gustifolium organon the ventral thoracic surface of these mantises appears to facilitate the chemical detection of the leaves on which it resides. The gustifolium is a novel plant volatile-detecting sensory structure in an obligate predatory insect, directly linked to a newly-identified, highly-adapted life strategy.
动物的感官系统使它们能够导航并与环境互动。这些系统的适应性特化可以产生支持高度独特的生态位适应的新型结构或器官。我们报告了在一群螳螂（昆虫纲，螳螂目，南螳螂科）中发现的一种新型感觉器官，这种螳螂有一种不寻常的铺叶异形生活策略，即靠着阔叶植被的背面铺叶。组织学、扫描电子显微镜和 X 射线计算机断层扫描都证实了这种独特形态的新颖性，而电生理学则揭示了该感觉器官（在此命名为 gustifolium 器官）能够检测植物挥发物。腮腺器官位于这些螳螂的腹部胸部表面，这似乎有利于对其所在的叶片进行化学检测。腮腺器官是一种新型的植物挥发性检测感官结构，存在于一种必须捕食的昆虫体内，与一种新发现的高度适应的生活策略直接相关。
{"title":"A new leaf sensing organ in a predatory insect group, the praying mantises (Mantodea)","authors":"Sydney K. Brannoch, Julian Katzke, Danielle S Taylor, Evan P Economo, Yuri Ogawa, Ajay Narendra, Gavin J Svenson, Joshua P Martin","doi":"10.1101/2024.04.14.589444","DOIUrl":"https://doi.org/10.1101/2024.04.14.589444","url":null,"abstract":"Animals' sensory systems enable them to navigate and interact with their environments. Adaptive specializations of these systems can generate novel structures or organs that support highly unique niche adaptations. We report the discovery of a novel sensory organ in a group of praying mantises (Insecta, Mantodea, Nanomantoidea), which have an unusual leaf-planking ecomorphic life strategy, laying against the undersides of broadleaf vegetation. Histology, scanning electron microscopy, and x-ray computed tomography all support the novelty of this distinct morphology while electrophysiology reveals that the sensory organ, herein designated the gustifolium organ, detects plant volatiles. The location of the gustifolium organon the ventral thoracic surface of these mantises appears to facilitate the chemical detection of the leaves on which it resides. The gustifolium is a novel plant volatile-detecting sensory structure in an obligate predatory insect, directly linked to a newly-identified, highly-adapted life strategy.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140613811","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 : 2024-04-17DOI: 10.1101/2024.04.15.589466
Anubhab Khan, Yulianto Yulianto, Sabhrina Gita Aninta, Wirdateti Wirdateti
Big cats are of conservation concern throughout their range. Genetic tools are often employed to study them for various purposes. However, there are several difficulties in using genetic tools for big cat conservation which may be resolved by modern methods of DNA sequencing. Recent reports of discovery of Javan tigers in West Java, Indonesia highlights this. We reanalysed the data of the original reports and find that the results were unreliable. However, resequencing of the DNA extracts confirm that the sighting could have been that of a tiger, but the subspecies cannot be confirmed. The work highlights the urgency for development of high throughput sequencing infrastructure in the tropics and the need for reliable databases for studies of big cats.
大型猫科动物在整个分布区都受到保护。为了各种目的，人们经常使用基因工具来研究它们。然而，将基因工具用于大型猫科动物保护存在一些困难，而现代 DNA 测序方法可以解决这些问题。最近在印度尼西亚西爪哇发现爪哇虎的报道就突出了这一点。我们重新分析了原始报告的数据，发现结果并不可靠。然而，DNA提取物的重新测序证实，目击者可能是老虎，但亚种无法确认。这项工作凸显了在热带地区发展高通量测序基础设施的紧迫性，以及为大型猫科动物研究建立可靠数据库的必要性。
{"title":"Reanalysis of sequences of alleged Javan tiger highlights the difficulties in studying big cats and the need for high throughput sequencing.","authors":"Anubhab Khan, Yulianto Yulianto, Sabhrina Gita Aninta, Wirdateti Wirdateti","doi":"10.1101/2024.04.15.589466","DOIUrl":"https://doi.org/10.1101/2024.04.15.589466","url":null,"abstract":"Big cats are of conservation concern throughout their range. Genetic tools are often employed to study them for various purposes. However, there are several difficulties in using genetic tools for big cat conservation which may be resolved by modern methods of DNA sequencing. Recent reports of discovery of Javan tigers in West Java, Indonesia highlights this. We reanalysed the data of the original reports and find that the results were unreliable. However, resequencing of the DNA extracts confirm that the sighting could have been that of a tiger, but the subspecies cannot be confirmed. The work highlights the urgency for development of high throughput sequencing infrastructure in the tropics and the need for reliable databases for studies of big cats.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"18 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140613802","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 : 2024-04-14DOI: 10.1101/2024.04.10.588974
Stephanie May Bamford, Frank Seebacher
Performance measures are an important tool to assess the impact of environmental change on animals. In fish, performance is often measured as critical sustained swimming speed (Ucrit), which reflects individual physiological capacities. A drawback of Ucrit is that trials are relatively long (~30-75 min). Ucrit is therefore not suitable for repeated measurements because of the potential for training effects, long recovery periods, and low throughput. Here we test a shorter (~4-5 min) protocol, "Ucrit fast" (UCfast) in zebrafish (Danio rerio). We show that UCfast and Ucrit have similar, significant repeatabilities within individuals. Unlike Ucrit, repeated UCfast trials do not elicit a training effect. Both UCfast and Ucrit provide the same insights into thermal acclimation, and both provide similar estimates of individual acclimation capacity in doubly acclimated fish. We propose that UCfast is a valid substitute for Ucrit particularly when higher throughput and repeated measures are necessary.
{"title":"A fast fish swimming protocol that provides similar insights as critical sustained swimming speed","authors":"Stephanie May Bamford, Frank Seebacher","doi":"10.1101/2024.04.10.588974","DOIUrl":"https://doi.org/10.1101/2024.04.10.588974","url":null,"abstract":"Performance measures are an important tool to assess the impact of environmental change on animals. In fish, performance is often measured as critical sustained swimming speed (Ucrit), which reflects individual physiological capacities. A drawback of Ucrit is that trials are relatively long (~30-75 min). Ucrit is therefore not suitable for repeated measurements because of the potential for training effects, long recovery periods, and low throughput. Here we test a shorter (~4-5 min) protocol, \"Ucrit fast\" (UCfast) in zebrafish (Danio rerio). We show that UCfast and Ucrit have similar, significant repeatabilities within individuals. Unlike Ucrit, repeated UCfast trials do not elicit a training effect. Both UCfast and Ucrit provide the same insights into thermal acclimation, and both provide similar estimates of individual acclimation capacity in doubly acclimated fish. We propose that UCfast is a valid substitute for Ucrit particularly when higher throughput and repeated measures are necessary.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"16 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599886","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 : 2024-04-11DOI: 10.1101/2024.04.08.588384
Zheng-Yan Sui, Nobuyuki Yamaguchi, Yue-Chen Liu, Hao-Ran Xue, Xin Sun, Philip Nyhus, Shu-Jin Luo
A paper recently published in Oryx by Wirdateti et al. (2024) suggests that the extinct Javan tiger may still survive on the Island of Java, Indonesia, based on mtDNA analysis of a single hair collected from a claimed tiger encounter site. After carefully re-analyzing the data presented in Wirdateti et al. (2024), we conclude that there is little support for the authors’ statements. Importantly, the sequences of the putative tiger hair and museum Javan tiger specimens generated by the authors are not from tiger cytoplasmic mitochondrial DNA but more likely the nuclear copies of mitochondrial DNA. In addition, the high mismatches found between the two “Javan tiger” sequences generated by the authors is unusual for homologous sequences that are both from tigers and hence indicative of data unreliability. Yet, too few details regarding the quality control were provided in Wirdateti et al. (2024) to rule out the possibility of contamination introduced during the data production process. In conclusion, it is inappropriate to use these unreliable sequences presented in Wirdateti et al. (2024) to infer the existence of the Javan tiger.
{"title":"No Reliable Evidence Supports the Presence of Javan Tigers - Data Issues Related to the DNA Analysis of a Recent Hair Sample","authors":"Zheng-Yan Sui, Nobuyuki Yamaguchi, Yue-Chen Liu, Hao-Ran Xue, Xin Sun, Philip Nyhus, Shu-Jin Luo","doi":"10.1101/2024.04.08.588384","DOIUrl":"https://doi.org/10.1101/2024.04.08.588384","url":null,"abstract":"A paper recently published in <em>Oryx</em> by Wirdateti et al. (2024) suggests that the extinct Javan tiger may still survive on the Island of Java, Indonesia, based on mtDNA analysis of a single hair collected from a claimed tiger encounter site. After carefully re-analyzing the data presented in Wirdateti et al. (2024), we conclude that there is little support for the authors’ statements. Importantly, the sequences of the putative tiger hair and museum Javan tiger specimens generated by the authors are not from tiger cytoplasmic mitochondrial DNA but more likely the nuclear copies of mitochondrial DNA. In addition, the high mismatches found between the two “Javan tiger” sequences generated by the authors is unusual for homologous sequences that are both from tigers and hence indicative of data unreliability. Yet, too few details regarding the quality control were provided in Wirdateti et al. (2024) to rule out the possibility of contamination introduced during the data production process. In conclusion, it is inappropriate to use these unreliable sequences presented in Wirdateti et al. (2024) to infer the existence of the Javan tiger.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600033","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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