Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
Environmental DNA analysis shows high potential as a tool for estimating intraspecific genetic diversity in a wild fish population
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环境 DNA 分析显示出作为评估野生鱼类种内遗传多样性的工具的巨大潜力
DOI：
10.1111/1755-0998.13165
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发表时间：
2020
影响因子：
7.7
通讯作者：
H. Yamanaka
中科院分区：
文献类型：
--
作者：
S. Tsuji; A. Maruyama; M. Miya; M. Ushio; H. Sato; T. Minamoto; H. Yamanaka
环境DNA（eDNA）分析近年来已被用作一种新的评估种内多样性的工具。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查。在这里，我们测试了捕获调查中检测到的香鱼（Plecoglossus altivelis altivelis）的单倍型是否也可以从含有低浓度和外源物质的各种单倍型的现场获得的eDNA样品中检测到。对同一天采集的一条河流的水样和香鱼标本分别进行了eDNA分析和桑格测序。将10 L水样分成20个过滤器，每个过滤器进行15次PCR重复。在高通量测序后，使用两种最广泛使用的去噪包unoise3和dada2进行去噪。从96份标本的桑格测序中获得的42种单倍型中，eDNA分析检测到38种（unoise 3）和41种（dada 2）单倍型。当使用endada2时，除了一个单倍型之外，从所有的过滤重复中检测到至少两个标本所拥有的单倍型。因此，尽管需要注意的是，基于eDNA的方法具有一定的局限性和一定的假阳性和假阴性风险，但本研究表明，用于评估种内遗传多样性的eDNA分析提供了与基于大规模捕获的常规方法相当的结果。我们的研究结果表明，基于eDNA的方法可能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。
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,unoise3anddada2. Of the 42 haplotypes obtained from the Sanger sequencing of 96 specimens, 38 (unoise3) and 41 (dada2) haplotypes were detected by eDNA analysis. Whendada2was 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.
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