Summary Environmental DNA (eDNA) analysis for detecting the presence of aquatic and terrestrial organisms is an established method, and the eDNA concentration of a species can reflect its abundance/biomass at a site. However, attempts to estimate the abundance/biomass of aquatic species using eDNA concentrations in large stream and river ecosystems have received little attention. We determined the eDNA concentration and abundance/biomass of a stream fish, Plecoglossus altivelis, by conducting a snorkelling survey in the Saba River, Japan. Furthermore, we evaluated the relationship between eDNA concentrations and the estimated abundance/biomass of P. altivelis, and determined its spatial distribution within the river. Across the three seasons from spring to autumn, we found significant correlations between the eDNA concentration of P. altivelis and its abundance/biomass at study sites within the river. We detected the eDNA at the sites where we found only feeding traces on stones (where P. altivelis was not directly observed), but not at sites without feeding traces. Additionally, we tested the optimal number of qPCR replicates needed for the eDNA evaluation of P. altivelis abundance and biomass; only a small number of replicates was required when the eDNA concentration was high. Our findings suggest that eDNA analysis is a useful tool to estimate fish abundance/biomass as well as their spatial distribution in rivers.

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1. For effective biodiversity conservation, verifying the correspondence of conservation sites among taxa and identifying the environmental characteristics of these sites are essential; however, only a few such studies have been performed in estuaries. The aim of the present study was to verify the surrogacy of estuarine gobies and crabs, to identify tidal rivers of high conservation priority, and to describe their environmental characteristics. 2. Distribution data for gobies and crabs were collected from 158 tidal rivers in the Kyushu region, Japan. Three conservation scenarios were analysed based on the distribution data of gobies alone, of crabs alone, and of both taxa, in order to assess the correspondence of the conservation candidates (i.e. tidal rivers) between taxa. 3. The degree of correspondence was poor for the candidates selected on the basis of the distribution data of gobies or crabs separately. More efficient candidates were selected based on the data for both taxa. The environmental characteristics of tidal rivers with high irreplaceability for conservation differed between the taxa. Tidal rivers forming and maintaining large tidal flats covered with fine sediment might have high irreplaceability for goby conservation, whereas rivers with saltmarshes connected to supratidal and intertidal zones might have high irreplaceability for crab conservation. 4. Tidal rivers with a high priority for conservation were identified by overlapping the candidates for three scenarios. These tidal rivers are not necessarily large, but have steep basins with river mouths that are less exposed to ocean waves. Moreover, the percentage of artificial areas in these rivers was low, suggesting that these rivers have not been exposed to excessive anthropogenic disturbance that leads to loss of estuarine habitat. 5. These results show that gobies and crabs are not surrogates for one another.

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