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DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs |
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| Authors: | Yun-He Wu Shao-Bing Hou Zhi-Yong Yuan Ke Jiang Ru-Yi Huang Kai Wang Qin Liu Zhong-Bin Yu Hai-Peng Zhao Bao-Lin Zhang Jin-Min Chen Li-Jun Wang Bryan L Stuart E Anne Chambers Yu-Fan Wang Wei Gao Da-Hu Zou Fang Yan Gui-Gang Zhao Zhong-Xiong Fu Shao-Neng Wang Ming Jiang Liang Zhang Jin-Long Ren Ya-Yong Wu Lu-Yang Zhang Dian-Cheng Yang Jie-Qiong Jin Ting-Ting Yin Jia-Tang Li Wen-Ge Zhao Robert W Murphy Song Huang Peng Guo Ya-Ping Zhang Jing Che |
| Institution: | 1. State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223 China;2. State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223 China
Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan, 650204 China;3. Shanghai Collaborative Innovation for Aquatic Animal Genetics and Breeding, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306 China;4. Faculty of Agriculture, Forest and Food Engineering, Yibin University, Yibin, Sichuan, 644007 China;5. School of Life Science, Henan University, Kaifeng, Henan, 475001 China;6. School of Life Sciences, Hainan Normal University, Haikou, Hainan, 571158 China;7. Section of Research & Collections, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, 27601 USA;8. Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, 94720 USA;9. Zhejiang Forest Resource Monitoring Center, Hangzhou, Zhejiang, 310020 China;10. State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223 China College of Science, Tibet University, Lhasa, Tibet, 850000 China;11. Yunnan Senye Biotechnology Co., Ltd, Xishuangbanna, Yunnan, 666100 China;12. Bureau of Guangxi Mao'er Mountain Nature Reserve, Guilin, Guangxi, 541316 China;13. Gongshan Bureau of Gaoligongshan National Nature Reserve, Gongshan, Yunnan, 650224 China;14. Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510260 China;15. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, 610041 China;16. Beijing Mountains & Seas Eco Technology Co. Ltd, Beijing, 101100 China;17. Anhui Province Key Laboratory of the Conservation and Exploitation of Biological Resource, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, 241000 China;18. College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, 150025 China;19. State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Conservation of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650223 China Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6 Canada |
| Abstract: | DNA barcoding has greatly facilitated studies of taxonomy, biodiversity, biological conservation, and ecology. Here, we establish a reliable DNA barcoding library for Chinese snakes, unveiling hidden diversity with implications for taxonomy, and provide a standardized tool for conservation management. Our comprehensive study includes 1638 cytochrome c oxidase subunit I (COI) sequences from Chinese snakes that correspond to 17 families, 65 genera, 228 named species (80.6% of named species) and 36 candidate species. A barcode gap analysis reveals gaps, where all nearest neighbour distances exceed maximum intraspecific distances, in 217 named species and all candidate species. Three species-delimitation methods (ABGD, sGMYC, and sPTP) recover 320 operational taxonomic units (OTUs), of which 192 OTUs correspond to named and candidate species. Twenty-eight other named species share OTUs, such as Azemiops feae and A. kharini, Gloydius halys, G. shedaoensis, and G. intermedius, and Bungarus multicinctus and B. candidus, representing inconsistencies most probably caused by imperfect taxonomy, recent and rapid speciation, weak taxonomic signal, introgressive hybridization, and/or inadequate phylogenetic signal. In contrast, 43 species and candidate species assign to two or more OTUs due to having large intraspecific distances. If most OTUs detected in this study reflect valid species, including the 36 candidate species, then 30% more species would exist than are currently recognized. Several OTU divergences associate with known biogeographic barriers, such as the Taiwan Strait. In addition to facilitating future studies, this reliable and relatively comprehensive reference database will play an important role in the future monitoring, conservation, and management of Chinese snakes. |
| Keywords: | barcoding library China cryptic diversity DNA barcoding snakes |