DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang
Abstract The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I...
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Wiley
2024-10-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.70352 |
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| author | Ling‐Ling Zheng Dan Yu Ning Sun Cheng Wang Wen‐Jun Chen Zu‐Fa Ding Shun‐Ping He Lian‐Dong Yang |
| author_facet | Ling‐Ling Zheng Dan Yu Ning Sun Cheng Wang Wen‐Jun Chen Zu‐Fa Ding Shun‐Ping He Lian‐Dong Yang |
| author_sort | Ling‐Ling Zheng |
| collection | DOAJ |
| description | Abstract The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor‐Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources. |
| format | Article |
| id | doaj-art-50041ac4cdf44a359658a017cdce0b70 |
| institution | OA Journals |
| issn | 2045-7758 |
| language | English |
| publishDate | 2024-10-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-50041ac4cdf44a359658a017cdce0b702025-08-20T02:32:14ZengWileyEcology and Evolution2045-77582024-10-011410n/an/a10.1002/ece3.70352DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, XinjiangLing‐Ling Zheng0Dan Yu1Ning Sun2Cheng Wang3Wen‐Jun Chen4Zu‐Fa Ding5Shun‐Ping He6Lian‐Dong Yang7State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaState Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaSchool of Ecology and Environment Anhui Normal University Wuhu Anhui ChinaState Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaState Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaState Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaState Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaState Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology, Chinese Academy of Sciences Wuhan ChinaAbstract The Ili River Valley, located in the northwest of China, serves as a vital repository for fish genetic resources. Its extensive water network and diverse climate have given rise to a unique fish composition and endemic species. In this study, we collected the cytochrome c oxidase subunit I (COI) sequences from 660 fish specimens in the Ili River Valley. The effectiveness of DNA barcoding in identifying fish species in the area was assessed by examining genetic distances, constructing phylogenetic trees, and performing ABGD (Automatic Barcode Gap Discovery) analyses, among other methods. In total, 20 species were identified, including one unidentified species (Silurus sp.). Except for Silurus asotus and Hypophthalmichthys molitrix (only one sample), the maximum intraspecific genetic distance among the remaining species was smaller than the minimum interspecific distance, which proves that the species exhibit obvious barcode gaps. In the Neighbor‐Joining trees, 20 species formed separate monophyletic branches. According to ABGD analysis, 660 sequences were categorized into 19 Operational Taxonomic Units, with Silurus sp. and S. asotus grouped into a single OTU. The Silurus in this study exhibits shared haplotypes and significant genetic divergence, suggesting the potential presence of cryptic species. Furthermore, the nucleotide diversity across all species fell below the threshold level, indicating that the local fish population is gradually declining. In conclusion, this study has demonstrated the effectiveness of DNA barcoding in identifying fish species in the Ili River Valley, providing valuable data to support the conservation of local fish resources.https://doi.org/10.1002/ece3.70352cryptic speciescytochrome c oxidase subunit IDNA barcodingfish identificationgenetic diversity |
| spellingShingle | Ling‐Ling Zheng Dan Yu Ning Sun Cheng Wang Wen‐Jun Chen Zu‐Fa Ding Shun‐Ping He Lian‐Dong Yang DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang Ecology and Evolution cryptic species cytochrome c oxidase subunit I DNA barcoding fish identification genetic diversity |
| title | DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang |
| title_full | DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang |
| title_fullStr | DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang |
| title_full_unstemmed | DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang |
| title_short | DNA barcoding and cryptic diversity in fishes from the Ili River Valley in China, Xinjiang |
| title_sort | dna barcoding and cryptic diversity in fishes from the ili river valley in china xinjiang |
| topic | cryptic species cytochrome c oxidase subunit I DNA barcoding fish identification genetic diversity |
| url | https://doi.org/10.1002/ece3.70352 |
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