Population decline of an endangered unionid, Pronodularia japanensis, in streams is revealed by eDNA and conventional monitoring approaches

Abstract

Environmental DNA (eDNA) is useful to detect the presence of aquatic organisms from water samples, especially for rare and cryptic species. Two freshwater unionid mussels¸ Pronodularia japanensis and Nodularia douglasiae, have rapidly declined over the last three decades and are now threatened with extinction on the Matsuyama Plain, south-western Japan. We designed a species-specific eDNA marker targeting the COI region of P. japanensis. The distribution of this species in the Kunichi River system on the Matsuyama Plain was investigated using both quantitative PCR with this eDNA marker and conventional surveying. We show that the distribution area of P. japanensis did not change between 2013–2014 and 2020–2021, but its density decreased by 99%. eDNA of P. japanensis was detected, with 100% success, from sites where this species was collected by hand. Furthermore, eDNA was detected at nine sites where P. japanensis was not collected but was expected to occur. This study has established a species-specific eDNA marker targeting the COI region of P. japanensis, and this eDNA marker has been validated as effective for surveying the distribution of this species. Using this eDNA marker, extensive investigation of remaining populations and the monitoring of them should improve conservation practices.