Co-occurrence patterns of endangered Sakhalin taimen and introduced rainbow trout in Hokkaido, Japan, inferred by environmental DNA metabarcoding

The distribution of endangered aquatic organisms is difficult to estimate, and so is species interaction in aquatic environments. In this study, an environmental DNA (eDNA) metabarcoding assay was developed to identify Salmoninae species and the co-occurrence of two salmonid species: Sakhalin taimen (Parahucho perryi, a critically endangered salmonid species) and invasive rainbow trout (Oncorhynchus mykiss) in Hokkaido, the second-largest main island of Japan.The newly developed eDNA metabarcoding assay was successful in identifying 16 different Salmoninae species in an aquarium test and to provide a semi-quantitative measure of eDNA concentration.The eDNA metabarcoding was then applied to 319 eDNA samples from 278 river systems in Hokkaido. The eDNA from Sakhalin taimen was identified in 17 river systems, of which nine also hosted rainbow trout according to the eDNA detections, suggesting a significantly disproportionate overlap of their distributions with Sakhalin taimen (P = 0.029). In addition, both species showed low eDNA concentrations (as a proxy of biomass) where they co-occur, presumably reflecting negative interactions between them.This study provides strong evidence that Sakhalin taimen is indeed endangered in Hokkaido. Rainbow trout have been widespread since their introduction to Hokkaido decades ago, and they are expected to spawn shortly after the spawning season of Sakhalin taimen. Therefore, the significant overlap of their distributions further increases the risk of extinction. The results encourage conservation efforts to limit the expansion of rainbow trout into rivers that currently support Sakhalin taimen.