National Institute for Environmental Studies, Tsukuba, Japan.
The Institute of Statistical Mathematics, Tachikawa, Japan.
Mol Ecol. 2021 Jul;30(13):3057-3067. doi: 10.1111/mec.15530. Epub 2020 Jul 20.
Molecular analysis of DNA left in the environment, known as environmental DNA (eDNA), has proven to be a powerful and cost-effective approach to infer occurrence of species. Nonetheless, relating measurements of eDNA concentration to population abundance remains difficult because detailed knowledge on the processes that govern spatial and temporal distribution of eDNA should be integrated to reconstruct the underlying distribution and abundance of a target species. In this study, we propose a general framework of abundance estimation for aquatic systems on the basis of spatially replicated measurements of eDNA. The proposed method explicitly accounts for production, transport and degradation of eDNA by utilizing numerical hydrodynamic models that can simulate the distribution of eDNA concentrations within an aquatic area. It turns out that, under certain assumptions, population abundance can be estimated via a Bayesian inference of a generalized linear model. Application to a Japanese jack mackerel (Trachurus japonicus) population in Maizuru Bay revealed that the proposed method gives an estimate of population abundance comparable to that of a quantitative echo sounder method. Furthermore, the method successfully identified a source of exogenous input of eDNA (a fish market), which may render a quantitative application of eDNA difficult to interpret unless its effect is taken into account. These findings indicate the ability of eDNA to reliably reflect population abundance of aquatic macroorganisms; when the "ecology of eDNA" is adequately accounted for, population abundance can be quantified on the basis of measurements of eDNA concentration.
环境 DNA（eDNA）是指留在环境中的 DNA 分子，对其进行分子分析已被证明是一种强大且具有成本效益的推断物种存在的方法。然而，将 eDNA 浓度的测量值与种群丰度相关联仍然很困难，因为需要整合关于控制 eDNA 时空分布的过程的详细知识，以重建目标物种的基础分布和丰度。在这项研究中，我们提出了一种基于 eDNA 空间重复测量的水生系统丰度估计的一般框架。该方法通过利用可以模拟水生区域内 eDNA 浓度分布的数值水动力模型，明确考虑了 eDNA 的产生、运输和降解过程，从而对其进行了量化。结果表明，在某些假设下，可以通过广义线性模型的贝叶斯推断来估计种群丰度。该方法在对日本马鲛鱼（Trachurus japonicus）在舞鹤湾的种群进行应用后表明，该方法给出的种群丰度估计值与定量回声测深法相当。此外，该方法成功地识别了 eDNA 外源输入的来源（一个鱼市场），除非考虑其影响，否则其定量应用可能难以解释。这些发现表明，eDNA 能够可靠地反映水生大型生物的种群丰度；当充分考虑“eDNA 的生态学”时，可以根据 eDNA 浓度的测量值来量化种群丰度。
