Lauren C. White, Jenny L. Nelson, Maria Cardoso, Carlo Pacioni
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The spot-tailed quoll (<i>Dasyurus maculatus</i>), a carnivorous marsupial found in eastern Australia, is a difficult species to detect as it is rare and has large home ranges, often in remote and difficult to access habitat.</p><strong> Aims</strong><p>In this study, we aimed to evaluate the feasibility of using eDNA soil analysis as a viable alternative or complement to traditional monitoring techniques for detecting spot-tailed quoll.</p><strong> Methods</strong><p>We developed a species-specific assay and validated it using synthetic oligos, tissue samples and soil collected from a captive quoll enclosure. We then assessed the assay on natural environment soil samples taken from the Snowy River region from communal quoll defecation sites (latrines) and from broader quoll habitat. We used amplification success data to model the concentration of quoll DNA in soil from different site types and calculate the sensitivity of our assay.</p><strong> Key results</strong><p>Sensitivity was highest at latrine sites, but decreased sharply when sampling just 1 m away. In non-latrine habitat, the positive amplification rate was too low to allow for meaningful statistical analyses, suggesting that a prohibitively large number of samples would need to be analysed for detection probabilities to be adequate for routine monitoring programs.</p><strong> Conclusions</strong><p>Overall, we found that low sensitivity was driven by the low concentration of spot-tailed quoll DNA at many of the surveyed sites.</p><strong> Implications</strong><p>Given that quoll latrines can usually be identified from the accumulation of scats, and scats themselves can be sampled for DNA, we suggest that eDNA analysis of soil is unlikely to offer improvements over current spot-tailed quoll monitoring methods.</p>","PeriodicalId":23971,"journal":{"name":"Wildlife Research","volume":"7 1","pages":""},"PeriodicalIF":1.6000,"publicationDate":"2024-01-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Environmental DNA detection of spot-tailed quoll from soil is unlikely to be useful for routine monitoring\",\"authors\":\"Lauren C. 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The spot-tailed quoll (<i>Dasyurus maculatus</i>), a carnivorous marsupial found in eastern Australia, is a difficult species to detect as it is rare and has large home ranges, often in remote and difficult to access habitat.</p><strong> Aims</strong><p>In this study, we aimed to evaluate the feasibility of using eDNA soil analysis as a viable alternative or complement to traditional monitoring techniques for detecting spot-tailed quoll.</p><strong> Methods</strong><p>We developed a species-specific assay and validated it using synthetic oligos, tissue samples and soil collected from a captive quoll enclosure. We then assessed the assay on natural environment soil samples taken from the Snowy River region from communal quoll defecation sites (latrines) and from broader quoll habitat. We used amplification success data to model the concentration of quoll DNA in soil from different site types and calculate the sensitivity of our assay.</p><strong> Key results</strong><p>Sensitivity was highest at latrine sites, but decreased sharply when sampling just 1 m away. In non-latrine habitat, the positive amplification rate was too low to allow for meaningful statistical analyses, suggesting that a prohibitively large number of samples would need to be analysed for detection probabilities to be adequate for routine monitoring programs.</p><strong> Conclusions</strong><p>Overall, we found that low sensitivity was driven by the low concentration of spot-tailed quoll DNA at many of the surveyed sites.</p><strong> Implications</strong><p>Given that quoll latrines can usually be identified from the accumulation of scats, and scats themselves can be sampled for DNA, we suggest that eDNA analysis of soil is unlikely to offer improvements over current spot-tailed quoll monitoring methods.</p>\",\"PeriodicalId\":23971,\"journal\":{\"name\":\"Wildlife Research\",\"volume\":\"7 1\",\"pages\":\"\"},\"PeriodicalIF\":1.6000,\"publicationDate\":\"2024-01-19\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Wildlife Research\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1071/wr23095\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"ECOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Wildlife Research","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1071/wr23095","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"ECOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
背景有关物种存在和分布的准确监测数据对于有效的保护管理至关重要。基于环境 DNA(eDNA)的技术可以从环境中发现的微量 DNA 中检测物种,是一种很有前途的工具,可以补充传统的监测方法并提高检测效率。然而,不完全检测是所有调查方法的一个特点,应该对其进行适当评估,以便确定在目标物种存在的地点检测到该物种 DNA 的概率(即该方法的灵敏度)。斑尾疣鼻猴(Dasyurus maculatus)是一种发现于澳大利亚东部的食肉有袋类动物,是一种难以检测的物种,因为它非常罕见,而且巢穴范围很大,通常位于偏远且难以进入的栖息地。目的在这项研究中,我们旨在评估使用 eDNA 土壤分析作为传统监测技术的替代或补充来检测斑尾丘的可行性。方法我们开发了一种物种特异性检测方法,并使用人工合成寡核苷酸、组织样本和从圈养的斑尾鸊围栏中采集的土壤对其进行了验证。然后,我们对从雪河地区的褐尾鸝公共排泄点(厕所)和更广阔的褐尾鸝栖息地采集的自然环境土壤样本进行了评估。我们利用扩增成功率数据来模拟不同地点类型土壤中的quoll DNA浓度,并计算出检测方法的灵敏度。主要结果灵敏度在厕所地点最高,但在距离厕所仅 1 米的地方取样时灵敏度急剧下降。在非厕所栖息地,阳性扩增率太低,无法进行有意义的统计分析,这表明需要对大量样本进行分析,检测概率才能满足常规监测计划的要求。结论总体而言,我们发现灵敏度低的原因是许多调查地点的斑尾鸊DNA浓度较低。启示鉴于通常可以通过粪便的堆积来识别quoll厕所,而且粪便本身也可以进行DNA采样,我们认为土壤的eDNA分析不太可能比目前的斑尾quoll监测方法有所改进。
Environmental DNA detection of spot-tailed quoll from soil is unlikely to be useful for routine monitoring
Context
Accurate monitoring data on species presence and distribution are crucial for effective conservation management. Environmental DNA (eDNA)-based techniques, in which species are detected from trace amounts of DNA found throughout the environment, are promising tools that may complement traditional monitoring methods and improve detection. However, imperfect detection is a feature of all survey methods that should be properly assessed so that the probability of detecting a target species’ DNA at a site where it is present (i.e. the sensitivity of the method) can be determined. The spot-tailed quoll (Dasyurus maculatus), a carnivorous marsupial found in eastern Australia, is a difficult species to detect as it is rare and has large home ranges, often in remote and difficult to access habitat.
Aims
In this study, we aimed to evaluate the feasibility of using eDNA soil analysis as a viable alternative or complement to traditional monitoring techniques for detecting spot-tailed quoll.
Methods
We developed a species-specific assay and validated it using synthetic oligos, tissue samples and soil collected from a captive quoll enclosure. We then assessed the assay on natural environment soil samples taken from the Snowy River region from communal quoll defecation sites (latrines) and from broader quoll habitat. We used amplification success data to model the concentration of quoll DNA in soil from different site types and calculate the sensitivity of our assay.
Key results
Sensitivity was highest at latrine sites, but decreased sharply when sampling just 1 m away. In non-latrine habitat, the positive amplification rate was too low to allow for meaningful statistical analyses, suggesting that a prohibitively large number of samples would need to be analysed for detection probabilities to be adequate for routine monitoring programs.
Conclusions
Overall, we found that low sensitivity was driven by the low concentration of spot-tailed quoll DNA at many of the surveyed sites.
Implications
Given that quoll latrines can usually be identified from the accumulation of scats, and scats themselves can be sampled for DNA, we suggest that eDNA analysis of soil is unlikely to offer improvements over current spot-tailed quoll monitoring methods.
期刊介绍:
Wildlife Research represents an international forum for the publication of research and debate on the ecology, management and conservation of wild animals in natural and modified habitats. The journal combines basic research in wildlife ecology with advances in science-based management practice. Subject areas include: applied ecology; conservation biology; ecosystem management; management of over-abundant, pest and invasive species; global change and wildlife management; diseases and their impacts on wildlife populations; human dimensions of management and conservation; assessing management outcomes; and the implications of wildlife research for policy development. Readers can expect a range of papers covering well-structured field studies, manipulative experiments, and analytical and modelling studies. All articles aim to improve the practice of wildlife management and contribute conceptual advances to our knowledge and understanding of wildlife ecology.
Wildlife Research is a vital resource for wildlife scientists, students and managers, applied ecologists, conservation biologists, environmental consultants and NGOs and government policy advisors.
Wildlife Research is published with the endorsement of the Commonwealth Scientific and Industrial Research Organisation (CSIRO) and the Australian Academy of Science.