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

Abstract

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.

Environmental DNA unveils deep phylogeographic structure of a freshwater fish

“…River water samples for eDNA were collected in a total of 293 rivers in Hokkaido, Japan from October to November in 2017 and 2018. This sample set had been used in another research project (Kanbe et al., 2023). To mitigate sampling bias, all the sampling sites were selected around lower reaches of each river, up to approximately 1.0 km from the river mouth.…”

“…Details of parameters in the pipeline were the same as described in ref. (Kanbe et al, 2023). After the denoising process, ASVs were subjected to taxonomic assignments with an identity >98.5% with the reference sequence database (MiFish DB ver.…”

“…Through future studies on this species in Sakhalin and other Far East regions, we could understand the distribution expansion of B. toni and other species from the continent to the islands.Our findings highlight that B. toni, which has been overlooked as a common species, is a valuable source of biogeographic information on past geology and environments.6 | MATERIAL S AND ME THODS6.1 | eDNA collection and extractionRiver water samples for eDNA were collected in a total of 293 rivers in Hokkaido, Japan from October to November in 2017 and 2018. This sample set had been used in another research project(Kanbe et al, 2023). To mitigate sampling bias, all the sampling sites were selected around lower reaches of each river, up to approximately 1.0 km from the river mouth.…”

“…After the filtration, 2.0 mL of RNAlater (Thermo Fisher Scientific, Waltham, MA, USA) was added into the cartridge for DNA preservation.At each sampling point, two filter samples were collected as field replicates. Details of the procedures were described in ref Kanbe et al (2023)Yatsuyanagi and Araki (2020).…”