Environmental DNA (eDNA) method has recently been developed to estimate the distribution (i.e., presence and absence) of species by detecting their eDNA in the water sample with PCR. However, the eDNA applications for species were still limited. Here, our target species are a rare salamander, Onychodactylus japonicus, in headwater streams and few fish species in the ponds. We performed the eDNA analysis using real-time PCR for estimating the species distributions in headwater streams and ponds. We compared the eDNA detections of the target species to the distributions of the species, which were evaluated by traditional methods, such as the observation and capturing of the species.
In headwater streams, we found that the distribution of dsalamander was well evaluated by eDNA method rather than the capturing survey. Also, we found the eDNA was more detectable in surface water than in the bottom water under the stones, where we observed the salamanders. From the results, eDNA can be useful to evaluate the distribution of the rare salamander, even if inhabiting in the headwater streams.
In the ponds, we found that the distributions of fish species, including carp, bluegill and largemouth bass, were well fitted with the capturing survey. Also, we found the variations of the eDNA detections in several sampling points of the ponds, and it indicates that such multiple points are needed for the eDNA sampling.