DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

Yun-He Wu¹, Shao-Bing Hou^{1

2}, Zhi-Yong Yuan¹, Ke Jiang¹, Ru-Yi Huang³, Kai Wang¹, Qin Liu⁴, Zhong-Bin Yu¹, Hai-Peng Zhao⁵, Bao-Lin Zhang¹, Jin-Min Chen¹, Li-Jun Wang⁶, Bryan L Stuart⁷, E Anne Chambers⁸, Yu-Fan Wang⁹, Wei Gao¹, Da-Hu Zou^{1

10}, Fang Yan¹, Gui-Gang Zhao¹, Zhong-Xiong Fu¹¹, Shao-Neng Wang¹², Ming Jiang¹³, Liang Zhang¹⁴, Jin-Long Ren¹⁵, Ya-Yong Wu⁴, Lu-Yang Zhang¹⁶, Dian-Cheng Yang¹⁷, Jie-Qiong Jin¹, Ting-Ting Yin¹, Jia-Tang Li¹⁵, Wen-Ge Zhao¹⁸, Robert W Murphy^{1

19}, Song Huang¹⁷, Peng Guo⁴, Ya-Ping Zhang¹, Jing Che¹

Affiliations

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 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 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 Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada.

PMID: 36924341
DOI: 10.1111/1755-0998.13784

DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

Yun-He Wu et al. Mol Ecol Resour. 2023 Jul.

. 2023 Jul;23(5):1124-1141.

doi: 10.1111/1755-0998.13784. Epub 2023 Mar 26.

Authors

Affiliations

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 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 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 Reptilia Zoo and Education Centre, Vaughn, Ontario, L4K 2N6, Canada.

PMID: 36924341
DOI: 10.1111/1755-0998.13784

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: China; DNA barcoding; barcoding library; cryptic diversity; snakes.

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References

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DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

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DNA barcoding of Chinese snakes reveals hidden diversity and conservation needs

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