Graduate School of Simulation Studies, University of Hyogo, Minatojima-minamimachi, Kobe, 650-0047, Japan.
National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan.
Sci Rep. 2019 Mar 5;9(1):3581. doi: 10.1038/s41598-019-40233-1.
Environmental DNA (eDNA) metabarcoding is a recently developed method to assess biodiversity based on a high-throughput parallel DNA sequencing applied to DNA present in the ecosystem. Although eDNA metabarcoding enables a rapid assessment of biodiversity, it is prone to species detection errors that may occur at sequential steps in field sampling, laboratory experiments, and bioinformatics. In this study, we illustrate how the error rates in the eDNA metabarcoding-based species detection can be accounted for by applying the multispecies occupancy modelling framework. We report a case study with the eDNA sample from an aquarium tank in which the detection probabilities of species in the two major steps of eDNA metabarcoding, filtration and PCR, across a range of PCR annealing temperatures, were examined. We also show that the results can be used to examine the efficiency of species detection under a given experimental design and setting, in terms of the efficiency of species detection, highlighting the usefulness of the multispecies site occupancy modelling framework to study the optimum conditions for molecular experiments.
环境 DNA(eDNA) 代谢组学是一种最近开发的方法，基于高通量平行 DNA 测序应用于生态系统中存在的 DNA，以评估生物多样性。虽然 eDNA 代谢组学能够快速评估生物多样性，但它容易发生物种检测错误，这些错误可能发生在野外采样、实验室实验和生物信息学的连续步骤中。在本研究中，我们通过应用多物种占有模型框架来说明如何解释基于 eDNA 代谢组学的物种检测中的错误率。我们报告了一个水族馆水箱的 eDNA 样本案例研究，其中检查了 eDNA 代谢组学的两个主要步骤——过滤和 PCR——在一系列 PCR 退火温度下的物种检测概率。我们还表明，这些结果可用于根据给定的实验设计和设置，以物种检测效率的方式，检查在给定实验设计和设置下的物种检测效率，突出了多物种位点占有模型框架在研究分子实验最佳条件方面的有用性。
