Environmental DNA monitoring for short‐term reproductive migration of endemic anadromous species, Shishamo smelt (Spirinchus lanceolatus)

Abstract

Monitoring reproductive migration is essential for the conservation of anadromous species. Shishamo smelt (Spirinchus lanceolatus) is endemic to Hokkaido, the northernmost large island in Japan. S. lanceolatus is an anadromous species that is known to migrate into rivers for a very short period in early winter. While this species has a special value for local fisheries, the catch amount has drastically declined in the last few decades. Information about S. lanceolatus reproductive migration dynamics is limited, which prevents them from being efficiently managed as a resource. In this study, we used environmental DNA (eDNA) methods as a noninvasive molecular tool for estimating presence/absence and abundance/biomass of S. lanceolatus during their migration into rivers. We developed a species‐specific qPCR system for S. lanceolatus, examining (a) temporal variation in S. lanceolatus eDNA concentrations compared with catch data gathered by traditional methods and (b) variability of migratory patterns among river systems. In a core river for their spawning migration, we consistently detected S. lanceolatus eDNA throughout the spawning season, and the temporal distribution of eDNA concentration was consistent with that of the number of migrating S. lanceolatus estimated by catch survey data. In addition, we were able to detect S. lanceolatus eDNA even from rivers without any official record of their migration. Among rivers with eDNA detection, the relative eDNA concentrations varied, indicating that the population biomass differs largely among the river populations. Our study suggests that eDNA detection systems are useful for tracking reproductive migration of S. lanceolatus at fine spatio‐temporal scales.

Understanding seasonal migration of Shishamo smelt in coastal regions using environmental DNA

“…Therefore, continuous evaluation of the interaction between population dynamics of S. lanceolatus and environmental and community changes will be required for long-term management of this species and the surrounding ecosystems. Together with our previous eDNA study on the freshwater migration of S. lanceolatus [8], this study illustrates the usefulness of eDNA techniques for understanding the whole life history of this valuable endemic species.…”

“…Seven locations along the western Pacific coast of Hokkaido were selected as eDNA sampling sites (Nishikioka, Yufutsu, Mukawa, Saru, Atsuga, Niikappu, and Harutachi from the west to east; S1 Table, Fig 1). Within the study region, several spawning rivers for S. lanceolatus were identified according to previous records [7,8]. Sampling for eDNA was conducted from March to August in 2019, 14 times in total.…”

“…DNA extraction from the Sterivex TM -HV filter cartridge was performed largely following Yatsuyanagi et al [8] with a slight modification of the vacuuming step. Firstly, RNAlater put into the filter cartridge was vacuumed from the outlet port using a QIAvac 24 Plus manifold (Qiagen, Inc., Hilden, Germany) and circulating aspirator (ADVANTEC, Inc., Tokyo, Japan).…”

“…DNA quantification was performed using a species-specific qPCR assay established in Yatsuyanagi et al [8]. Details for PCR components, thermal cycling conditions, and standard curve preparation can also be found in Yatsuyanagi et al [8].…”

“…In this study, we conducted an eDNA survey from March to August along the Pacific coast of Hokkaido to gain an understanding of the seasonal habitat changes of S. lanceolatus at sea. Firstly, we investigated spatial and temporal eDNA concentrations at fixed sampling points nearshore using the species-specific eDNA detection system established in our previous study [8]. Next, we evaluated the relationships between eDNA concentrations and environmental factors.…”