Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring
Navigating the trade‐offs between environmental DNA and conventional field surveys for improved amphibian monitoring
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权衡环境 DNA 和传统实地调查以改善两栖动物监测
DOI：
10.1002/ecs2.3941
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发表时间：
2022
期刊：
影响因子：
2.7
通讯作者：
Johnson, Pieter T.
中科院分区：
文献类型：
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作者：
Moss, Wynne E.;Harper, Lynsey R.;Davis, Mark A.;Goldberg, Caren S.;Smith, Matthew M.;Johnson, Pieter T.
对高效、准确的生物多样性监测的需求正在增长，特别是对全球濒危的分类群，如两栖动物。环境DNA （eDNA）分析在加强监测程序方面具有巨大的潜力，但随着这种工具越来越多地被采用，用户必须了解其潜在的优点和缺点。我们进行了一项比较研究，以评估两种eDNA方法（定量(q)PCR和元条形码）和传统的现场采样方法（围网、浸渍和视觉接触调查）在一个包含6种不同两栖动物物种的20个池塘系统中的有效性。使用占用模型框架，我们估计了不同方法检测灵敏度的差异，重点是如何进一步优化eDNA调查设计。总体而言，元条形码和qPCR都可以与传统方法竞争或改进。具体来说，qPCR（物种特异性方法）是检测两种稀有物种加利福尼亚虎蝾螈（Ambystoma californiense）和加利福尼亚红腿蛙（Rana draytonii）最有效的技术，每次调查的检测概率为>.80。元条形码（群落法）估算两栖动物多样性的平均比率与野外技术相当，并检测到41个额外的脊椎动物分类群。然而，对于两个丰富的物种（西部蟾蜍，Anaxyrus boreas和太平洋合唱蛙，Pseudacris regilla），野外技术优于元条形码，特别是在个体变形时。我们的研究结果表明，当eDNA方法与视觉接触调查相结合时，将最有效地检测陆地生命阶段，并且需要更多的优化，特别是引物的选择和验证。通过比较不同池塘和物种的方法，我们为将eDNA方法整合到两栖动物监测中的未来研究提供指导。
The need for efficient, accurate biodiversity monitoring is growing, especially for globally imperiled taxa, such as amphibians. Environmental DNA (eDNA) analysis holds enormous potential for enhancing monitoring programs, but as this tool is increasingly adopted, it is imperative for users to understand its potential benefits and shortcomings. We conducted a comparative study to evaluate the efficacy of two eDNA methodologies (quantitative (q)PCR and metabarcoding) and conventional field sampling approaches (seining, dipnetting, and visual encounter surveys) in a system of 20 ponds containing six different amphibian species. Using an occupancy modeling framework, we estimated differences in detection sensitivity across methods, with a focus on how eDNA survey design could be further optimized. Overall, both metabarcoding and qPCR were competitive with or improved upon conventional methods. Specifically, qPCR (species‐specific approach) was the most effective technique for detecting two rare species, the California tiger salamander (Ambystoma californiense) and California red‐legged frog (Rana draytonii), with a detection probability of >0.80 per survey. Metabarcoding (community approach) estimated amphibian diversity with comparable rates to field techniques on average, and detected an additional 41 vertebrate taxa. However, for two abundant species (western toads,Anaxyrus boreas, and Pacific chorus frogs,Pseudacris regilla), field techniques outperformed metabarcoding, especially as individuals metamorphosed. Our results indicate that eDNA approaches would be most effective when paired with visual encounter surveys to detect terrestrial life stages, and that more optimization, specifically primer choice and validation, is needed. By comparing methods across a diverse set of ponds and species, we provide guidance for future studies integrating eDNA approaches into amphibian monitoring.