Environmental DNA (eDNA) analysis has recently been used as a new tool for estimating intraspecific diversity. However, whether known haplotypes contained in a sample can be detected correctly using eDNA‐based methods has been examined only by an aquarium experiment. Here, we tested whether the haplotypes of Ayu fish (Plecoglossus altivelis altivelis) detected in a capture survey could also be detected from an eDNA sample derived from the field that contained various haplotypes with low concentrations and foreign substances. A water sample and Ayu specimens collected from a river on the same day were analysed by eDNA analysis and Sanger sequencing, respectively. The 10 L water sample was divided into 20 filters for each of which 15 PCR replications were performed. After high‐throughput sequencing, denoising was performed using two of the most widely used denoising packages, unoise3 and dada2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3) and 41 (dada2) haplotypes were detected by eDNA analysis. When dada2 was used, except for one haplotype, haplotypes owned by at least two specimens were detected from all the filter replications. Accordingly, although it is important to note that eDNA‐based method has some limitations and some risk of false positive and false negative, this study showed that the eDNA analysis for evaluating intraspecific genetic diversity provides comparable results for large‐scale capture‐based conventional methods. Our results suggest that eDNA‐based methods could become a more efficient survey method for investigating intraspecific genetic diversity in the field.

中文翻译：

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环境 DNA 分析显示出作为估计野生鱼类种群种内遗传多样性的工具的巨大潜力。

环境 DNA (eDNA) 分析最近被用作估计种内多样性的新工具。然而，是否可以使用基于 eDNA 的方法正确检测样本中包含的已知单倍型，仅通过水族馆实验进行了检验。在这里，我们测试了香鱼（Plecoglossus altivelis altivelis) 在捕获调查中检测到的也可以从来自现场的 eDNA 样本中检测到，该样本包含各种低浓度和外来物质的单倍型。同一天从河流中采集的水样和香鱼标本分别通过eDNA分析和Sanger测序进行分析。将 10 L 水样分成 20 个过滤器，每个过滤器进行 15 次 PCR 复制。在高通量测序后，使用两个最广泛使用的去噪包unoise3和dada2 进行去噪。在从 96 个样本的 Sanger 测序中获得的 42 个单倍型中，通过 eDNA 分析检测到38 个（unoise3）和 41 个（dada2）单倍型。当dada2被使用，除了一种单倍型，从所有过滤器复制中检测到至少两个样本拥有的单倍型。因此，尽管重要的是要注意基于 eDNA 的方法有一些局限性和一些假阳性和假阴性的风险，但本研究表明，用于评估种内遗传多样性的 eDNA 分析为基于大规模捕获的常规方法提供了可比的结果. 我们的结果表明，基于 eDNA 的方法可以成为一种更有效的调查方法，用于调查该领域的种内遗传多样性。