Real‐time polymerase chain reaction assays for environmental DNA detection of three salmonid fish in Hokkaido, Japan: Application to winter surveys

Abstract

AbstractDolly Varden (Salvelinus malma) and Whitespotted Char (Salvelinus leucomaenis) are representative native fish of the family Salmonidae that inhabit the upper reaches of rivers on Hokkaido Island, Japan. They are threatened by the invasive Rainbow Trout (Oncorhynchus mykiss). In this study, environmental DNA (eDNA) real‐time polymerase chain reaction (PCR) assays to detect these three salmonids were developed and used to clarify the distribution pattern of these fish. A specificity test for each assay was conducted using DNA extracted from both target and closely related fish, and the specificity of each assay was confirmed. Then, we carried out eDNA surveys in two mountainous rivers around Mt. Daisetsu in winter, when snow depth was maximized. In the winter surveys, eDNA of all three species were successfully detected from river water samples, including under‐ice water samples. The results of eDNA detection corresponded with the results of an earlier distribution survey performed with Japanese‐style fly‐fishing and lure‐fishing. These results suggested that the eDNA assays developed in this study are applicable for inter‐seasonal surveys for these species.