Data from: A basin-scale application of environmental DNA assessment for rare endemic species and closely related exotic species in rivers: a case study of giant salamanders in Japan

1. To prevent the invasion of exotic species causing a decline in an
endangered endemic species, it is important to determine the distribution
of both species at an early stage, when the density of the exotic species
is still low, and to manage the invasion immediately. However,
distinguishing between closely related species is difficult because they
share similar characteristics. 2. The identification of DNA fragments
sampled from a body of water (environmental DNA) has become a popular
technique for rapidly determining the distribution of a target species. In
this study, we analysed environmental DNA in water samples from 37 sites
across the Katsura River basin in Japan. We used TaqMan real-time PCR to
distinguish the Japanese giant salamander Andrias japonicus from the
closely related Chinese giant salamander Andrias davidianus, which is
known to invade Japanese rivers and hybridize with the Japanese species.
3. In environmental samples, we detected mtDNA of the endemic species at
25 sites and mtDNA of the exotic species at nine sites. The DNA detection
sites were concentrated in the upstream region. The exotic species DNA was
found beyond the limits of an earlier capturing survey. 4. Synthesis and
applications. Using environmental DNA to monitor the two salamander
species requires less time and effort than traditional surveys, so a
wide-ranging survey can be conducted rapidly. Our results showed that
performing three environmental DNA surveys for each site between autumn
and winter is desirable for giant salamanders. Further collection of
environmental DNA, in combination with conventional population surveys,
will provide valuable information that can help protect rare endemic
species in a variety of aquatic ecosystems and can help monitor the
invasion of exotic species.

1. 为防止外来物种入侵导致濒危特有物种种群数量下降，在外来物种密度仍处于低位的早期阶段，明确两类物种的分布并及时开展入侵治理工作至关重要。然而，由于近缘物种具有相似的生物学特征，对其进行准确区分往往存在较大难度。
2. 对从水体中采集的DNA片段开展鉴定的环境DNA（environmental DNA）技术，已成为快速确定目标物种分布的主流手段。本研究针对日本桂川流域的37个采样点的水体样本开展环境DNA分析，采用TaqMan实时荧光定量PCR技术，对日本大鲵（Andrias japonicus）与其近缘入侵物种中国大鲵（Andrias davidianus）进行区分——后者已被证实会入侵日本河流并与日本大鲵发生杂交。
3. 本次环境样本检测结果显示，25个采样点检出该特有物种的线粒体DNA（mtDNA），9个采样点检出外来物种的线粒体DNA。DNA阳性采样点集中分布于流域上游区域，且外来物种的DNA检出范围超出了早期捕获调查所划定的入侵边界。
4. 总结与应用。相较于传统种群调查方法，利用环境DNA监测这两种大鲵物种所需的时间与人力成本显著更低，因此可快速完成大范围的普查工作。研究结果表明，针对大鲵的环境DNA监测，建议在秋季至冬季期间对每个采样点开展3次采样。将环境DNA采样与常规种群调查相结合开展后续研究，可为多种水生生态系统中的珍稀特有物种保护提供宝贵参考，同时也有助于对外来物种的入侵情况进行动态监测。