Assessing the cost‐efficiency of environmental DNA sampling
Assessing the cost‐efficiency of environmental DNA sampling
复制标题
DOI：
10.1111/2041-210x.12598
复制
发表时间：
2016-11
影响因子：
6.6
通讯作者：
Adam S. Smart;A. Weeks;Anthony R. Rooyen;Alana L. Moore;M. McCarthy;R. Tingley
中科院分区：
文献类型：
--
作者：
Adam S. Smart;A. Weeks;Anthony R. Rooyen;Alana L. Moore;M. McCarthy;R. Tingley
环境DNA （Environmental DNA, eDNA）取样是一种高灵敏度的水生分类群检测方法；然而，与传统方法相比，该技术的成本效率尚未得到严格评估。我们展示了解释不完美和随机检测的方法如何用于(i)确定固定预算下eDNA采样调查工作的最佳分配（即确定水样与实地考察的最佳组合），以及（ii）相对于传统调查技术评估eDNA采样的成本效率。我们通过比较最近在澳大利亚墨尔本发现的一种外来蝾螈（Lissotriton v. vulgaris）的eDNA取样和瓶捕法来说明这种方法。瓶捕集器的检出率比eDNA取样低得多，但两种方法的成本效率相似，因为瓶捕集器每个样品的成本更低。两种取样方法的相对成本-效率对可用的调查预算、eDNA引物/探针开发和样品处理的成本以及用于指定水样为蝾螈DNA阳性的定量PCR阳性检测（qpcr）的数量敏感。当引物/探针开发和样品处理成本较低时，环境DNA取样比瓶捕更具成本效益，并且使用1/4或2/4阳性qpcr标记水样为蝾螈eDNA阳性。然而，无论qPCR阈值或调查预算如何，当引物/探针开发和样品处理成本较高时，瓶捕集器通常比eDNA取样更具成本效益。与eDNA采样相比，传统采样方法的检测概率可能较低，但在某些情况下，总成本会使eDNA采样的效率低于传统技术。我们的方法提供了一个定量框架，用于确定需要多少水样和现场访问才能最大化eDNA采样的检测概率，并且可以计算任何采样方法的成本效率。
Environmental DNA (eDNA) sampling can be a highly sensitive method for detecting aquatic taxa; however, the cost‐efficiency of this technique relative to traditional methods has not been rigorously assessed. We show how methods that account for imperfect and stochastic detection can be used to (i) determine the optimal allocation of survey effort with eDNA sampling for a fixed budget (i.e. identify the optimal combination of water samples vs. site visits), and (ii) assess the cost‐efficiency of eDNA sampling relative to traditional survey techniques. We illustrate this approach by comparing eDNA sampling and bottle‐trapping for an exotic newt species (Lissotriton v. vulgaris) recently detected in Melbourne, Australia. Bottle traps produced much lower detection rates than eDNA sampling, but the cost‐efficiency of the two methods can be similar because bottle‐trapping is cheaper per sample. The relative cost‐efficiency of the two sampling methods was sensitive to the available survey budget, the costs of eDNA primer/probe development and sample processing and the number of positive quantitative PCR assays (qPCRs) used to designate a water sample as positive for newt DNA. Environmental DNA sampling was more cost‐efficient than bottle‐trapping for small to intermediate budgets when primer/probe development and sample processing costs were low, and 1/4 or 2/4 positive qPCRs were used to label a water sample as positive for newt eDNA. However, bottle traps were generally more cost‐efficient than eDNA sampling when primer/probe development and sample processing costs were high, regardless of qPCR threshold or survey budget. Traditional sampling methods may achieve lower detection probabilities compared to eDNA sampling, but the totality of costs can make eDNA sampling less efficient than traditional techniques in some circumstances. Our approach provides a quantitative framework for determining how many water samples and site visits are required to maximize detection probabilities with eDNA sampling, and can calculate the cost‐efficiency of any sampling method.