Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii)
Combining population genetics with genomic data has transformed scientist’s ability and resolution of making ecological inferences, thus making it possible to detect previously unidentified structures and obtain more accurate estimates of demographic parameters in wild populations. Ark shell is an e...
| Main Authors: | , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-06-01
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| Series: | Aquaculture Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352513422000965 |
| _version_ | 1817977427191660544 |
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| author | Xiangfeng Liu Xi Xie Hongyue Liu Hongtao Nie Haitao Ma Dacheng Li Weiming Teng Hualin Li Zuoan Yu Yongxin Sun Yun Zhang Ming Zhang Qingzhi Wang |
| author_facet | Xiangfeng Liu Xi Xie Hongyue Liu Hongtao Nie Haitao Ma Dacheng Li Weiming Teng Hualin Li Zuoan Yu Yongxin Sun Yun Zhang Ming Zhang Qingzhi Wang |
| author_sort | Xiangfeng Liu |
| collection | DOAJ |
| description | Combining population genetics with genomic data has transformed scientist’s ability and resolution of making ecological inferences, thus making it possible to detect previously unidentified structures and obtain more accurate estimates of demographic parameters in wild populations. Ark shell is an economically and ecologically important marine species for fisheries industry in China, but its habitats have been severely damaged due to overexploitation of natural resources. Recently, protection of the ark shell as a natural resource has attracted extensive attention. Here, we identified 10,108 single-nucleotide polymorphisms using Restriction-site Associated DNA Sequencing (2b-RAD) to explore the structure of seven populations of S. broughtonii from the Asian Pacific Northwest region (four sites in China, two in Korea, and one in North Korea). A high level of genetic diversity was detected in all seven S. broughtonii populations. Pairwise FST estimates and neighbor-joining (NJ) tree topologies showed a clear division between the populations from China and Korea, and Chinese populations exhibited low levels of divergence from one another. This significant genetic divergence of the Chinese population implies that translocation of individuals for aquaculture should be properly managed for the preservation of genetic diversity and eventual local adaptation in natural populations. |
| first_indexed | 2024-04-13T22:16:16Z |
| format | Article |
| id | doaj.art-32ddcc5702da48efacbb625173e631ca |
| institution | Directory Open Access Journal |
| issn | 2352-5134 |
| language | English |
| last_indexed | 2024-04-13T22:16:16Z |
| publishDate | 2022-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj.art-32ddcc5702da48efacbb625173e631ca2022-12-22T02:27:29ZengElsevierAquaculture Reports2352-51342022-06-0124101100Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii)Xiangfeng Liu0Xi Xie1Hongyue Liu2Hongtao Nie3Haitao Ma4Dacheng Li5Weiming Teng6Hualin Li7Zuoan Yu8Yongxin Sun9Yun Zhang10Ming Zhang11Qingzhi Wang12Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaCollege of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, ChinaSouth China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, ChinaLiaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, China; Corresponding authors.Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian 116023, China; Corresponding authors.Combining population genetics with genomic data has transformed scientist’s ability and resolution of making ecological inferences, thus making it possible to detect previously unidentified structures and obtain more accurate estimates of demographic parameters in wild populations. Ark shell is an economically and ecologically important marine species for fisheries industry in China, but its habitats have been severely damaged due to overexploitation of natural resources. Recently, protection of the ark shell as a natural resource has attracted extensive attention. Here, we identified 10,108 single-nucleotide polymorphisms using Restriction-site Associated DNA Sequencing (2b-RAD) to explore the structure of seven populations of S. broughtonii from the Asian Pacific Northwest region (four sites in China, two in Korea, and one in North Korea). A high level of genetic diversity was detected in all seven S. broughtonii populations. Pairwise FST estimates and neighbor-joining (NJ) tree topologies showed a clear division between the populations from China and Korea, and Chinese populations exhibited low levels of divergence from one another. This significant genetic divergence of the Chinese population implies that translocation of individuals for aquaculture should be properly managed for the preservation of genetic diversity and eventual local adaptation in natural populations.http://www.sciencedirect.com/science/article/pii/S2352513422000965Scapharca broughtoniiPopulation genomics2b-RADPopulation structure |
| spellingShingle | Xiangfeng Liu Xi Xie Hongyue Liu Hongtao Nie Haitao Ma Dacheng Li Weiming Teng Hualin Li Zuoan Yu Yongxin Sun Yun Zhang Ming Zhang Qingzhi Wang Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii) Aquaculture Reports Scapharca broughtonii Population genomics 2b-RAD Population structure |
| title | Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii) |
| title_full | Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii) |
| title_fullStr | Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii) |
| title_full_unstemmed | Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii) |
| title_short | Population genomic evidence for genetic divergence in the Northwest Pacific Ark shell (Scapharca broughtonii) |
| title_sort | population genomic evidence for genetic divergence in the northwest pacific ark shell scapharca broughtonii |
| topic | Scapharca broughtonii Population genomics 2b-RAD Population structure |
| url | http://www.sciencedirect.com/science/article/pii/S2352513422000965 |
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