Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation
Abstract Gnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stresse...
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| Format: | Article |
| Language: | English |
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Wiley
2023-09-01
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| Series: | Environmental DNA |
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| Online Access: | https://doi.org/10.1002/edn3.408 |
| _version_ | 1797449898632675328 |
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| author | Kei Wakimura Kimiko Uchii Takeshi Kikko |
| author_facet | Kei Wakimura Kimiko Uchii Takeshi Kikko |
| author_sort | Kei Wakimura |
| collection | DOAJ |
| description | Abstract Gnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition of G. caerulescens using environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of local G. caerulescens populations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that the G. caerulescens population had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity (h), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources. |
| first_indexed | 2024-03-09T14:32:40Z |
| format | Article |
| id | doaj.art-6c5703b0207041b78abb3c57b854d4ee |
| institution | Directory Open Access Journal |
| issn | 2637-4943 |
| language | English |
| last_indexed | 2024-03-09T14:32:40Z |
| publishDate | 2023-09-01 |
| publisher | Wiley |
| record_format | Article |
| series | Environmental DNA |
| spelling | doaj.art-6c5703b0207041b78abb3c57b854d4ee2023-11-27T21:20:53ZengWileyEnvironmental DNA2637-49432023-09-015597398610.1002/edn3.408Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservationKei Wakimura0Kimiko Uchii1Takeshi Kikko2Faculty of Pharmacy Osaka Ohtani University Tondabayashi JapanFaculty of Pharmacy Osaka Ohtani University Tondabayashi JapanFaculty of Agriculture Kindai University Nara JapanAbstract Gnathopogon caerulescens, an endemic fish of Lake Biwa, Japan, is one of the most important fishes for lake fisheries. It has been listed as an endangered species following its population decline in the 1990s and thus needs conservation. An increasing number of studies have recently stressed on the importance of incorporating genetic diversity for conservation purposes. In this study, we aimed to evaluate the mitochondrial DNA haplotype composition of G. caerulescens using environmental DNA (eDNA) to determine the genetic diversity of this species. We developed an eDNA‐based haplotyping approach using high‐throughput sequencing (HTS), which can accurately detect and eliminate erroneous HTS reads, even when the target sequences are differentiated by a single or a few mismatches. Field surveys using the developed method successfully revealed the genetic structure of local G. caerulescens populations. We found star‐shaped haplotype networks with two major haplotypes accompanied by several rare haplotypes for all local populations except one, which suggested that the G. caerulescens population had undergone a historical expansion, and its population size did not shrink to the extent that rare haplotypes were eliminated during the population decline in the 1990s. We also observed that the genetic diversity was lower in the northern populations in terms of haplotype number and haplotype diversity (h), suggesting that the decline in population was more severe in the north than in the south. We demonstrated the practical use of eDNA analysis in population genetics of endangered species. Continuous monitoring using this approach would facilitate the conservation and management of fish resources.https://doi.org/10.1002/edn3.408eDNAhaplotypehigh‐throughput sequencingintraspecific diversitypopulation genetics |
| spellingShingle | Kei Wakimura Kimiko Uchii Takeshi Kikko Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation Environmental DNA eDNA haplotype high‐throughput sequencing intraspecific diversity population genetics |
| title | Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation |
| title_full | Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation |
| title_fullStr | Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation |
| title_full_unstemmed | Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation |
| title_short | Evaluation of genetic diversity in an endangered fish Gnathopogon caerulescens using environmental DNA and its potential use in fish conservation |
| title_sort | evaluation of genetic diversity in an endangered fish gnathopogon caerulescens using environmental dna and its potential use in fish conservation |
| topic | eDNA haplotype high‐throughput sequencing intraspecific diversity population genetics |
| url | https://doi.org/10.1002/edn3.408 |
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