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Comparative study on nuclear and mitochondrial DNA of Ayu Plecoglossus altivelis for environmental DNA-based spawning evaluation

  • Special Feature: Original Paper
  • Environmental DNA as a Practical Tool for Aquatic Conservation and Restoration
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Abstract

Understandings of fish spawning are important for the effective riverine ecosystem and fisheries resources management. Application of environmental DNA (eDNA) analysis would allow fish spawning evaluation at a high temporal and spatial resolution due to its less-labor intensive property, compared to the conventional collection methods. However, the relative performance of the two eDNA-based methods used to evaluate fish spawning, pre and post comparisons of eDNA concentrations and nuclear DNA to mitochondrial DNA ratio, has not been compared in the field. We evaluated whether spawning events of Ayu Plecoglossus altivelis could be identified from day (pre-spawning) to night (post-spawning) changes in eDNA concentrations using nuclear DNA (RAG1, nuDNA) and nuDNA/mitochondrial DNA ratio in comparison to the conventional mitochondrial DNA (cyt b, mtDNA). In addition, the relative sensitivity of nuDNA concentrations in spawning evaluation was compared with mtDNA concentrations. Water samples were collected biweekly in the lower Takatsu River, western Japan, between early October and early December 2020, covering the spawning season of the fish species. Generalized linear mixed-effects models (GLMM) showed that Ayu spawning could be detected by nuDNA concentrations likewise by mtDNA concentrations, while nuDNA/mtDNA ratio could not detect spawning earlier in the spawning season. GLS models showed that the day-to-night increase in the eDNA concentrations was more profound for nuDNA than for mtDNA during the main spawning period of the fish. Our findings insist that the application of nuDNA concentrations better serves as a tool for evaluating Ayu spawning intensity in eDNA analysis.

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Acknowledgements

We thank M. Amimoto, T. Kodama, and K. Kobayashi, Yamaguchi University, for field or analytical assistance. We also thank A. Okino, H. Terakado, and Y. Taniguchi, Shimane Prefectural Fisheries Technology Center, and T. Hatama, Yamaguchi Prefectural Fisheries Research Center, for valuable information on the Ayu in the Takatsu River. Takatsu River Fisheries Cooperative Association provided us with permission to conduct this study and valuable information on the Ayu stock management in the Takatsu River. Thorough and constructive comments from two anonymous reviewers helped improve the manuscript. This work was partly supported and funded by the Hamada Office of River and National Highway, Ministry of Land, Infrastructure, Transport, and Tourism, as a part of the research project, “A study on the effects of the sediment replenishment on the environment in the Gonokawa River”.

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Authors and Affiliations

  1. Graduate School of Science and Technology for Innovation, Yamaguchi University, 2‒16‒1 Tokiwadai, Ube, Yamaguchi, 755‒8611, Japan

    Minoru Saito, Ryohei Nakao, Seiji Miyazono & Yoshihisa Akamatsu

  2. Fisheries Division, Japan International Research Center for Agricultural Sciences, 1‒1 Ohwashi, Tsukuba, Ibaraki, 305‒8686, Japan

    Minoru Saito

  3. Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, Kyoto, 606‒8502, Japan

    Satsuki Tsuji

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  1. Minoru Saito
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  2. Satsuki Tsuji
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Correspondence to Minoru Saito.

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Saito, M., Tsuji, S., Nakao, R. et al. Comparative study on nuclear and mitochondrial DNA of Ayu Plecoglossus altivelis for environmental DNA-based spawning evaluation. Landscape Ecol Eng 19, 55–67 (2023). https://doi.org/10.1007/s11355-022-00519-5

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