Sensitive and efficient surveillance of Japanese giant salamander (Andrias japonicus) distribution in Western Japan using multi-copy nuclear DNA marker

Abstract

Japanese giant salamander (Andrias japonicus) is one of the largest amphibian species in the world and an iconic species in Japan. However, as its distribution has recently declined across the country, rapid and extensive monitoring of its distribution is urgently required for its efficient conservation. Here, we used environmental DNA (eDNA) analysis to assess the distribution of Japanese giant salamanders in Western Japan; 410 water samples were collected from 12 rivers. We then developed a new eDNA assay for multi-copy nuclear DNA (nuDNA) of the giant salamander and compared the eDNA detectability of the nuDNA marker with that of the mitochondrial DNA (mtDNA) marker. Throughout the survey, we detected the target eDNA from 162 water samples using either of the markers, which generally corresponded to the known natural distribution range of the species. Additionally, the use of a nuDNA marker allowed for higher detectability and site-level occupancy probability of the target eDNA than the mtDNA marker. Moreover, the detectability of target eDNA decreased substantially in water samples with higher conductivity and partly in those with higher pH, indicating its negative impact on the salamander’s ecology. The results demonstrated that eDNA analysis with a multi-copy nuDNA marker is highly useful for efficient and sensitive surveillance of the distribution of Japanese giant salamander. Our study provides fundamental resources and methodology for monitoring their distribution using eDNA analysis and facilitating their conservation.