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Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens

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Gnathopogon caerulescens is an endangered but commercially important fish in Lake Biwa, Japan. The population size of G. caerulescens has drastically reduced in the past decades, and there is a strong need to develop effective resource management frameworks for the sustainable use of this species. In the management of endangered species, it is important to monitor and grasp their distribution and abundance. Although catch-based methods have generally been employed for this purpose, these methods require more labor and time and can damage the populations of endangered species. In this study, we aimed to develop a rapid and non-invasive monitoring tool for G. caerulescens using an environmental DNA-based approach. We developed a real-time PCR assay that specifically detects and quantifies G. caerulescens DNA and applied the developed assay to monitor the concentrations of G. caerulescens DNA in water in Lake Biwa. The dynamics of G. caerulescens DNA concentrations well reproduced the main characteristics of life history of G. caerulescens, suggesting the promising use of environmental DNA-based methods for monitoring the distribution and abundance of this species.

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The cytochrome b sequences of Gnathopogon caerulescens, G. elongatus, Biwia zezera, Pseudogobio esocinus and Abbottina rivularis obtained in this study were deposited in DDBJ (accession nos LC602486-LC602497, LC633197- LC633199).


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This study was supported by JSPS KAKENHI Grant Number 18K11733 to KU and by the Environment Research and Technology Development Fund (JPMEERF20204004) to KU, HY, TK and KT. We thank N. Oue (Shiga Prefectural Fisheries Experimental Station) who kindly offered valuable information on G. caerulescens, G. Ito (Ryukoku University) who provided us the tissue samples of A. rivularis and T. Iseki who helped with the field survey.

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Correspondence to Kimiko Uchii.

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Uchii, K., Wakimura, K., Kikko, T. et al. Environmental DNA monitoring method of the commercially important and endangered fish Gnathopogon caerulescens. Limnology 23, 49–56 (2022).

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