Genetic characteristics of Neophocaena sunameri in Liaoning coastal waters based on whole genome resequencing

doi:10.16829/j.slxb.151080

Abstract

Abstract: In order to better understand the population structure and genetic differences of the East Asian finless porpoise (Neophocaena sunameri) distributed in Liaoning coastal waters, and to provide scientific basis for species conservation, this study collected muscle tissues from 47 individuals of the northern population of N. sunameri (NSN) from Liaoning coastal waters for whole genome resequencing, with a sequencing depth of 10×. Subsequently, the sequence data of finless porpoises from the southern population of N. sunameri (NSS) from the Yangtze River estuary, the population of N. asiaeorientalis (NA) from the Yangtze River basin, and the population of N. phocaenoides (NP) from the Fujian sea area were downloaded from the NCBI database. Genetic diversity analysis, genetic structure analysis, principal component analysis, phylogenetic tree construction, genetic differentiation index, gene flow, and genetic distance analysis were conducted using sequencing data from the four populations. The observed heterozygosity (Ho) and expected heterozygosity (He) of the population in Liaoning coastal waters were 0. 312 3 and 0. 321 0, respectively, indicating that the genetic diversity of the finless porpoise distributed in the Liaoning oastal waters is not low and represents a large and stable population. The results of phylogenetic tree analysis, principal component analysis, and genetic structure analysis were consistent, all of which can distinguish different populations. Overall, the four populations can be divided into three groups. Group I includes NP population, Group II represents NA population and Group III represents the East Asian finless porpoise population, including the MSN and NSS populations. The genetic differentiation index between NSN and NP was 0. 178 0, the genetic differentiation index between NSN and NA was 0. 047 8, the genetic differentiation index between NSN and NSS was 0. 023 1, the genetic distance was 0. 031 9, and the gene flow was 10. 554 5. In summary, East Asian finless porpoises distributed in the Liaoning coastal waters exhibit relatively high genetic diversity. They belong to the same species as NSS, with sufficient gene exchange and low genetic differentiation, and can be protected as a management unit.

Key words: Whole genome resequencing, Neophocaena sunameri, Population structure, Genetic differentiation, Liaoning coastal waters

摘要： 为更好地了解分布于辽宁海域的东亚江豚（Neophocaena sunameri）群体结构和遗传差异，为物种保护提供科学依据，本研究采集来源于辽宁海域的47头东亚江豚北方群体（NSN）的肌肉组织用于全基因组重测序，测序深度为10 ×。随后，从NCBI数据库下载来源于长江口临近海域的东亚江豚南方群体（NSS）、来源于长江流域的长江江豚（N.asiaeorientalis）群体（NA）及来源于福建等海域的印太江豚（N.phocaenoides）群体（NP）的江豚序列数据。使用上述4个群体的测序数据进行遗传多样性分析、遗传结构分析、主成分分析和系统进化树构建，以及遗传分化指数、基因流和遗传距离分析。结果显示，辽宁海域东亚江豚的观测杂合度（Ho）和期望杂合度（He）分别为0.312 3和0.321 0，是江豚4个群体中杂合度较高的群体，说明分布于我国辽宁海域的江豚遗传多样性不低，属于一个大而稳定的种群。系统发育树分析、主成分分析结果和遗传结构分析较一致，皆能区分不同群体，总体上4个群体可以分为3个类群：类群Ⅰ，印太江豚群体（NP）；类群Ⅱ，长江江豚群体（NA）；类群Ⅲ，东亚江豚群体，包括东亚江豚北方群体（NSN）与东亚江豚南方群体（NSS）。NSN与NP的遗传分化指数为0.178 0，与NA的遗传分化指数为0.047 8；NSN与NSS的遗传分化指数最小（0.023 1），遗传距离最小（0.031 9），基因流最大（10.554 5）。综上所述，分布于辽宁海域的东亚江豚遗传多样性较好，与长江口邻近海域的东亚江豚南方群体同属东亚江豚，基因交流充分，遗传分化较低，可以作为一个管理单位进行保护。

关键词: 全基因组重测序, 东亚江豚, 群体结构, 遗传差异, 辽宁海域

CLC Number:

Q346

GAO Xianggang, WANG Zhen, LU Zhichuang, DU Jing, XING Yankuo, HAN Jiabo, TIAN Jiashen. Genetic characteristics of Neophocaena sunameri in Liaoning coastal waters based on whole genome resequencing[J]. ACTA THERIOLOGICA SINICA, 2026, 46(4): 575-585.

高祥刚, 王震, 鹿志创, 杜静, 邢衍阔, 韩家波, 田甲申. 基于全基因组重测序的辽宁海域东亚江豚遗传特性研究[J]. 兽类学报, 2026, 46(4): 575-585.

Add to citation manager EndNote|Ris|BibTeX

URL: https://www.mammal.cn/EN/10.16829/j.slxb.151080

https://www.mammal.cn/EN/Y2026/V46/I4/575

References

Alexander D H, Novembre J, Lange K, 2009. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome Research,19 (9):1655-1664. DOI:10.1161/01. ATV. 0000137 190. 63214. c5.
Catchen J, Amores A, Hohenlohe P A, Cresko W, Postlethwait J H, 2011. Stacks:building and genotyping loci de novo from short-read sequences[J]. G3 Genesgenetics,1 (3):171-182.DOI:10.1534/g3. 111. 000240.
Catchen J,Hohenlohe P A,Bassham S,Amores A,Cresko W A, 2013. Stacks:an analysis tool set for population genomics[J]. Molecular Ecology, 22 (11):3124-3140. DOI:10.1111/mec. 12354.
Chen Bingyao,Yang Congwen,2024. The prediction of global suitable habitat distribution for East Asian finless porpoise[J]. Journal of Nanjing Normal University (Natural Science Edition), 47 (2):76-83. DOI:10.3969/j. issn. 1001-4616. 2024. 02. 009. (in Chinese with English abstract)
Chen L,Bruford M W,Xu S X,Zhou K Y,Yang G,2010. Microsatellite variation and significant population genetic structure of endangered finless porpoises (Neophocaena phocaenoides) in Chinese coastal waters and the Yangtze River[J]. Mar Biol,157(7):1453-1462. DOI:10.1007/s00227-010-1420-x.
Chen Yaxin,2016. Genetic diversity and genetic structure of the finless porpoise populations based on D-Loop and Cyt b gene[D]. Shanghai:Shanghai Ocean University, 31-40. DOI:CNKI:CDMD:2. 1016. 912380. (in Chinese with English abstract)
Chen Zhaolong,Li Yongtao,Zuo Tao,Niu Mingxiang,Wang Jun, 2024. Threats and conservation strategies of the East Asian finless porpoise in China[J]. Journal of Applied Oceanography,43(3):597-606. DOI:10.3969/J. ISSN. 2095-4972. 20230601002. (in Chinese with English abstract)
Dong Jinhai,Wang Guangjie,Xiao Zhizhong,1993. Migration and population difference of the finless porpoise in China[J]. Journal of Marine Science,5:42-45. (in Chinese with English abstract)
Gao Anli, Zhou Kaiya, 1995a. Geographical variations of postcranial skeleton among the populations of Neophocaena in Chinese waters[J]. Acta Theriologica Sinica,15 (4):246-253. DOI:10.16829/j. slxb. 1995. 04. 002. (in Chinese with English abstract)
Gao Anli, Zhou Kaiya, 1995b. Geographical variations of skull among thepopulations of Neophocaena in Chinese waters[J]. Acta Theriologica Sinica,15 (3):161-169. DOI:10.16829/j. slxb. 1995. 03. 001. (in Chinese with English abstract)
Gao Xianggang,Bao Xiangbo,Gao Meiling,2017. Analysis of genetic diversity of Chinese mitten crab (Eriocheir sinensis) with genotyping-by-sequencing gechnology[J]. Journal of Anhui Agricultural Sciences 45 (36):80-82. DOI:10.3969/j. issn. 0517-6611. 2017. 36. 025. (in Chinese with English abstract)
Jefferson T A,Wang J Y,2011. Revision of the taxonomy of finless porpoises (genus Neophocaena):the existence of two species[J]. Journal of Marine Animals and Their Ecology,4 (1):3-16.
Li Fugui, Sun Yiwen, Chen Kai, Yu Jinxiang, Wan Jiming, Kui Linli,Liang Ximei,Wang Yihua,Dai Yingen, 2024. Genetic diversity of Yangtze finless porpoises population in Poyang Lake Basin[J]. Acta Agriculturae Universitatis Jiangxiensis,46 (5):1298-1307. DOI:10.3724/aauj. 2024114. (in Chinese with English abstract)
Li L, Jiang J, Wang X, Jiang X, 2013. Nested clade phylogeographical analysis of the finless porpoise (Neophocaena phocaenoides) inhabiting Chinese and Japanese coasts[J]. Genet Mol Res, 12 (3):2528-2536. DOI:10.4238/2013. February. 28. 20.
Li X,Liu Y Y,Tzika A C,Zhu Q,Doninck K V,Milinkovitch M C, 2011. Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters[J]. Mar Biol, 158:1791-1804. DOI:10.1007/s00227-011-1692-9.
Liu F,Qu Y K,Geng C,Wang A M,Zhang J H,Li J F,Chen K J, Liu B,Tian H Y,Yang W P,Yu Y B,2020. Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers[J]. Electron J Biotechnol, 47:59-71. DOI:10.1016/j. ejbt. 2020. 06. 007.
Liu Zhenni, Li Jianjun, Lian Hai, Lei Xiaowen, Tan Donghai, Zeng Qingyuan, Cheng Di, Tian Yuling, Kong Zhiwei, Xie Hualiang, Zhong Yunping, 2024. Population evolution analysis of Ganzhou muscovy duck based on whole genome resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 55(11):4992-5002. DOI:10.11843/j. issn. 0366-6964. 2024. 11. 018. (in Chinese with English abstract)
Mcconnell S,Hamilton L,Morris D,Cook D,Paquet D,Bentzen P,Wright J,1995. Isolation of salmonid microsatellite loci and their application to the population genetics of Canadian east coast stocks of Atlantic salmon[J]. Aquaculture, 137 (4):19-30.DOI:10.1016/0044-8486 (95) 01111-0.
Nei M,1972. Genetic distance between populations[J]. The American Naturalist,106 (949):283-292. DOI:10.1086/282771.
Qiu Guoqiang, Li Rui, Shi Jian, Chen Yijie, Yuan Liying, Yang Yongchun,Ma Xiang,Li Houhui,Niu Dong,2025. Analysis of genetic diversity and genetic structure of Deqing Nipponia nippon population based on whole-genome resequencing[J]. Life Science Research,29 (2):123-130,155. DOI:10.16605/j.cnki. 1007-7847. 2024. 05. 0152. (in Chinese with English abstract)
Shafer A B A, Wolf J B W, 2013. Widespread evidence for incipient ecological speciation:a meta-analysis of isolation-by-ecology[J]. Ecology Letters,16:940-950. DOI:10.1111/ele. 12120.
Slatkin M, 1987. Gene flow and the geographic structure of natural populations[J]. Science, 236 (4803):787-792. DOI:10.1126/science. 3576198.
Sun Di, 2018. Genomics of finless porpoise population and adaptation mechanism of whale skeletal microstructure[D]. Nanjing:Nanjing Normal University, 30-55. DOI:CNKI:CDMD:1. 1018. 290338. (in Chinese with English abstract)
Tian Jiashen,2023. Research on feeding characteristics and bioaccumulation of typical environmental pollutants in the food chain of East Asian finless porpoises Neophocaena asiaeorientalis sunameri, with healthy risk assessment[D]. Shantou:Shantou University,13-14. (in Chinese with English abstract)
Wang Jun, Li Hongzhi, Zuo Tao, Li Yongtao, Cheng Zhaolong, Yuan Wei,Niu Mingxiang,2021. A review of studies concerning the marine finless porpoise[J]. Progress in Fishery Sciences, 42 (5):188-196. DOI:10.19663/j. issn2095-9869. 20200515001. (in Chinese with English abstract)
Wang Peilie, 1984. Distribution of whales in China 's coastal waters[J]. Chinese Journal of Zoology,(6):52-56. (in Chinese with English abstract)
Wang Renyong,Chen Minmin,Wan Xiaoling,Tang Bin,He Yujiang, Mei Zhigang, Fan Fei, Wang Kexiong, Wang Ding, Zheng Jinsong,2023. Microsatellite genetic diversity evaluation and development prediction of the Yangtze finless porpoise population in the Poyang Lake[J]. Acta Hydrobiologica Sinica, 47(10):1693-1700. DOI:10.7541/2023. 2022. 0345. (in Chinese with English abstract)
Wang Yaorong,Yang Wei,Ren Xilin,Jiang Dongneng,Deng Siping,Chen Huapu,Zhu Chunhua,Li Guangli,2020. Distribution patterns of microsatellites and development of polymorphic markers from Scatophagus argus genome[J]. Journal of Guangdong Ocean University, 40 (4):7-14. DOI:10.3969/j.issn. 1673-9159. 2020. 04. 002. (in Chinese with English abstract)
Wen M,Wang S,Zhu C,Zhang Y,Liu Z,Wu C,Wang S,Ren L,Tao M,2024. Identification of sex locus and a male-specific marker in blunt-snout bream (Megalobrama amblycephala) using a whole genome resequencing method[J]. Aquaculture, 582:740559. DOI:10.1016/j. aquaculture. 2024. 740559.
Wu Bin, He Gang, Wang Weiping, 2022. Research progress of Yangtze finless porpoise (Neophocaena phocaenoides) biology[J]. Chinese Agricultural Science Bulletin, 38 (24):158-164. DOI:10.11924/j. issn. 1000-6850. casb2021-0856.(in Chinese with English abstract)
Yang Guang,Zhou Kaiya,1997. Genetic variation of three populations of finless porpoise (Neophocaena phocaenoides) in Chinese waters[J]. Acta Zoologica Sinica, 4:411-419. (in Chinese with English abstract)
Yang G,Ren WH,Zhou K Y,Liu S,Ji G Q,Yan J,Wang L M, 2002. Population genetic structure of finless porpoises,Neophocaena phocaenoides, in Chinese waters, inferred from mitochondrial control region sequences[J]. Marine Mammal Science, 18:336-347. DOI:10.1111/j. 1748-7692. 2002. tb01041. x.
Yang G, Liu S, Ren W H, Zhou KY, Wei F, 2003. Mitochondrial control region variability of Baiji and the Yangtze finless porpoises, two sympatric small cetaceans in the Yangtze River[J]. Acta theriologica, 48 (4):469-483. DOI:10.1007/bf03192493.
Yang G,Guo L,Bruford M,Wei F W,Zhou K Y,2010. Mitochondrial phylogeography and population history of finless porpoises in Sino-Japanese waters[J]. Biol J Linn Soc, 95:193-204. DOI:10.1111/j. 1095-8312. 2008. 0932. x.
Yang Hualin, Li Wei, Ji Liqin, Zhu Xinping, Hong Xiaoyou, 2024. Analysis genetic diversity and structural analysis of three aquaculture populations of crocodile turtles based on whole genome resequencing[J]. Journal of Southern Agriculture, 55(11):3392-3403. DOI:10.3969/j. issn. 2095-1191. 2024. 11. 018. (in Chinese with English abstract)
Yang J,Lee S H,Goddard M E,Visscher P M,2011. GCTA:a tool for genome-wide complex trait analysis[J]. The American Journal of Human Genetics,88 (1):76-82. DOI:10.1016/j.ajhg. 2010. 11. 011.
Yin D H,Chen C H,Lin D Q,Zhang J L,Ying C P,Liu Y,Cao Z C,Zhao C X,Wang C H,Liang L P,Xu P,Jian J B,Liu K, 2022. Gapless genome assembly of East Asian finless porpoise[J]. Sci Data, 9:765. DOI:10.1038/s41597-022-01868-4.
Yin D H, Chen C H, Lin D Q, Hua Z, Ying C P, Zhang J L, Zhao C X,Liu Y,Cao Z C, Zhang H,Wang C H, Liang L P, Xu P, Jian J B, Liu K, 2024. Telomere-to-telomere gap-free genome assembly of the endangered Yangtze finless porpoise and East Asian finless porpoise[J]. GigaScience, 13:giae067. DOI:10.1093/gigascience/giae067.
Zhang Feng,Zhang Baowei,Tang Wenqiao,Liu Jian,Wu Jianhui, Tang Bin,2018. Analysis of genetic diversity and population dynamics of the narrow-ridged finless porpoise in the Yangtze River Estuary[J]. Journal of Shanghai Ocean University, 27 (5):656-665. DOI:10.12024/jsou. 20180302234. (in Chinese with English abstract)
Zhou X,Guang X,Sun D,Xu S,Li M,Seim I,Jie W,Yang L, Zhu Q, Xu J, Gao Q, Kaya A, Dou Q, Chen B, Ren W, Li S,Zhou K,Gladyshev V N,Nielsen R,Fang X,Yang G, 2018. Population genomics of finless porpoises reveal an incipient cetacean species adapted to freshwater[J]. Nature Communications,9 (1):1276. DOI:10.1038/s41467-018-03722-x.
Zhu P, He L, Li Y, Huang W, Feng X, Lin L, Zhi Q, Zhang W,Tang Y T,Geng C,2015. OTG-snpcaller:An optimized pipeline based on TMAP and GATK for SNP calling from Ion Torrent Data[J]. PLoS ONE,10 (9):e0138824. DOI:10.1371/journal. pone. 0097507.
王仁勇,陈敏敏,万晓玲,唐斌,郝玉江,梅志刚,范飞,王克雄,王丁,郑劲松,2023.鄱阳湖长江江豚的微卫星遗传多样性及发展预测[J].水生生物学报, 47 (10):1693-1700.DOI:10.7541/2023. 2022. 0345.
王丕烈, 1984.中国近海鲸类的分布[J].动物学杂志,(6):52-56.
王丕烈, 2011.中国海鲸类[M].北京:化学工业出版社, 363-378.
王俊,李洪志,左涛,李永涛,程兆龙,袁伟,牛明香,2021.海洋江豚的研究概述[J].渔业科学进展,42 (5):188-196.DOI:10.19663/j. issn2095-9869. 20200515001.
王耀嵘,杨尉,任席林,江东能,邓思平,陈华谱,朱春华,李广丽,2020.金钱鱼基因组微卫星分布特征分析及多态性标记开发[J].广东海洋大学学报,40 (4):7-14. DOI:10.3969/j. issn. 1673-9159. 2020. 04. 002.
孙迪, 2018.江豚种群基因组学及鲸类骨骼微结构适应机制研究[D].南京:南京师范大学, 30-55. DOI:CNKI:CDMD:1. 1018. 290338.
田甲申,2023.东亚江豚摄食特征及其食物链中典型环境污染物的生物累积研究与健康风险评估[D].汕头:汕头大学,13-14.
刘珍妮,李建军,连海,雷小文,谭东海,曾庆远,成笛,田玉玲,孔智伟,谢华亮,钟云平,2024.基于全基因组重测序对赣州番鸭的群体进化分析[J].畜牧兽医学报,55 (11):4992-5002. DOI:10.11843/j. issn. 0366-6964. 2024. 11. 018.
李福贵,孙艺文,陈凯,余进祥,阮记明,隗黎丽,梁惜梅,王义华,戴银根,2024.鄱阳湖流域长江江豚种群遗传差异分析[J].江西农业大学学报, 46 (5):1298-1307. DOI:10.3724/aauj. 2024114.
杨光,周开亚,1997.中国水域江豚种群遗传变异的研究[J].动物学报,4:411-419.
杨华琳,李伟,纪利芹,朱新平,洪孝友,2024.基于全基因组重测序的拟鳄龟遗传多样性及遗传结构分析[J].南方农业学报, 55 (11):3392-3403. DOI:10.3969/j. issn. 2095-1191. 2024. 11. 018.
张枫,张保卫,唐文乔,刘健,吴建辉,唐斌,2018.长江口江豚的遗传多样性现状及种群动态[J].上海海洋大学学报,27(5):656-665. DOI:10.12024/jsou. 20180302234.
陈炳耀,杨丛汶,2024.东亚江豚全球适宜栖息地分布预测[J].南京师大学报 (自然科学版), 47 (2):76-83. DOI:10.3969/j. issn. 1001-4616. 2024. 02. 009.
邱国强,李瑞,石坚,陈奕洁,袁李莹,杨永春,马翔,宋厚辉,牛冬,2025.全基因组重测序解析德清朱鹮群体遗传多样性及群体遗传结构[J].生命科学研究,29 (2):123-130,155.DOI:10.16605/j. cnki. 1007-7847. 2024. 05. 0152.
吴斌,贺刚,王伟萍,2022.长江江豚生物学研究进展[J].中国农学通报, 38 (24):158-164. DOI:10.11924/j. issn. 1000-6850. casb2021-0856.
高安利,周开亚,1995a.中国水域江豚颅后骨骼的地理变异[J].兽类学报, 15 (4):246-253. DOI:10.16829/j. slxb. 1995. 04. 002.
高安利,周开亚,1995b.中国水域江豚颅骨的地理变异[J].兽类学报, 15 (3):161-169. DOI:10.16829/j. slxb. 1995. 03. 001.
高祥刚,鲍相渤,高美玲,2017.基于 GBS技术的中华绒螯蟹的遗传特征分析[J].安徽农业科学,45 (36):80-82. DOI:10.3969/j. issn. 0517-6611. 2017. 36. 025.
程兆龙,李永涛,左涛,牛明香,王俊,2024.我国东亚江豚的研究现状、面临的威胁与保护建议[J].应用海洋学学报,43(3):597-606. DOI:10.3969/j. issn. 2095-4972. 20230601002.
程亚欣,2016.基于线粒体控制区和细胞色素 B基因的江豚种群遗传多样性和遗传结构分析[D].上海:上海海洋大学,31-40.DOI:CNKI:CDMD:2. 1016. 912380.
董金海,王广洁,肖志忠,1993.黄、渤海及东海江豚的洄游和种群差异[J].海洋科学,5:42-45.
魏辅文,2022.中国兽类分类与分布[M].北京:科学出版社, 458-460.

[1]	GAO Hui, QIAO Fujie, TENG Liwei, LI Junle, YU Mengqi, LIU Zhensheng. Genetic diversity and structure of the Alashan red deer (Cervus elaphus alashanicus) in Helan Mountains, China [J]. ACTA THERIOLOGICA SINICA, 2020, 40(5): 458-466.
[2]	ZHOU Le, YANG Shengmei, YU Zhiyong, YIN Baofa, HUAI Huyin, LI Shiping,WEI Wanhong. Genetic diversity and differentiation in four natural populations of plateau pika (Ochotona curzoniae) [J]. , 2007, 27(3): 221-228.