Qu Chanjuan, Stewart Kathryn A
State Key Laboratory for Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, People's Republic of China.
Institute for Biodiversity and Ecosystem Dynamics, Department of Evolutionary and Population Biology, University of Amsterdam, Amsterdam, Netherlands.
Naturwissenschaften. 2019 Feb 18;106(3-4):9. doi: 10.1007/s00114-019-1605-1.
While conservation management has made tremendous strides to date, deciding where, when and how to invest limited monitoring budgets is a central concern for impactful decision-making. New analytical tools, such as environmental DNA (eDNA), are now facilitating broader biodiversity monitoring at unprecedented scales, in part, due to time, and presumably cost, of methodological efficiency. Genetic approaches vary from conventional PCR (cPCR; species presence), to metabarcoding (community structure), and qPCR (relative DNA abundance, detection sensitivity). Knowing when to employ these techniques over traditional protocols could enable practitioners to make more informed choices concerning data collection. Using 12 species-specific primers designed for cPCR, eDNA analysis of the Yangtze finless porpoise (YFP; Neophocaena asiaeorientalis asiaeorientalis), a critically endangered aquatic mammal within the Yangtze River, we validated and optimized these primers for use in qPCR. We tested repeatability and sensitivity to detect YFP eDNA and subsequently compared the cost of traditional (visual and capture) sampling to eDNA tools. Our results suggest cPCR as the least expensive sampling option but the lack of PCR sensitivity suggests it may not be the most robust method for this taxon, predominately useful as a supplementary tool or with large expected populations. Alternatively, qPCR remained less expensive than traditional surveys, representing a highly repeatable and sensitive method for this behaviorally elusive species. Cost comparisons of surveying practices have scarcely been discussed; however, given budgetary constraints particularly for developing countries with limited local oversight but high endemism, we encourage managers to carefully consider the trade-offs among accuracy, cost, coverage, and speed for biodiversity monitoring.
尽管迄今为止保护管理已取得巨大进展，但决定在何处、何时以及如何投入有限的监测预算是做出有效决策的核心关注点。新的分析工具，如环境DNA（eDNA），目前正在促进以前所未有的规模进行更广泛的生物多样性监测，部分原因在于方法效率所需的时间以及推测的成本。遗传方法从传统的聚合酶链式反应（cPCR；物种存在情况）到宏条形码分析（群落结构）以及定量聚合酶链式反应（qPCR；相对DNA丰度、检测灵敏度）各不相同。了解何时采用这些技术而非传统方案能够使从业者在数据收集方面做出更明智的选择。我们使用为cPCR设计的12种物种特异性引物，对长江江豚（YFP；Neophocaena asiaeorientalis asiaeorientalis）——长江内一种极度濒危的水生哺乳动物——进行eDNA分析，验证并优化了这些引物以用于qPCR。我们测试了检测YFP eDNA的可重复性和灵敏度，随后将传统（视觉和捕获）采样的成本与eDNA工具的成本进行了比较。我们的结果表明cPCR是成本最低的采样选项，但缺乏PCR灵敏度表明它可能不是针对该分类群的最可靠方法，主要用作补充工具或针对预期数量较大的种群。相比之下，qPCR仍然比传统调查成本更低，是针对这种行为难以捉摸的物种的一种高度可重复且灵敏的方法。几乎没有人讨论过调查方法的成本比较；然而，鉴于预算限制，特别是对于当地监督有限但特有物种丰富的发展中国家，我们鼓励管理人员在生物多样性监测的准确性、成本、覆盖范围和速度之间仔细权衡。
