Assessing the genetic diversity of the critically endangered Chinese sturgeon Acipenser sinensis using mitochondrial markers and genome-wide single-nucleotide polymorphisms from RAD-seq  

作　　者：Jian Liu Xinxin You Pao Xu Ping Zhuang Yueping Zheng Kai Zhang Min Wang Yunyun Lv Gangchun Xu Feng Zhao Jianhui Wu Houyong Fan Jianan Xu Zhiqiang Ruan Chao Bian Kai Liu Dongpo Xu Jinhui Chen Junmin Xu Qiong Shi 

机构地区：[1]Superintendency Department of Shanghai Yangtze Estuarine Nature Reserve for Chinese Sturgeon, [2]Shanghai 200092, China [2]Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals,BGI Marine,BGI,shenzhen 518083, China [3]Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences,Wuxi 214081, China [4]Key and Open Laboratory of Marine and Estuarine Fisheries Resources and Ecology, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences,Shanghai 200090, China [5]College of Fisheries and Life Sciences, Shanghai Ocean University,Shanghai 201306, China [6]BGI-Zhenjiang Institute of Hydrobiology,Zhenjiang 212000, China [7]College of Marine Sciences, Shanghai Ocean University,Shanghai 201306, China [8]BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences,Shenzhen 518083, China [9]Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University,Shenzhen 518060, China

出　　处：《Science China(Life Sciences)》2018年第9期1090-1098,共9页中国科学（生命科学英文版）

基　　金：supported by National Natural Science Foundation of China (31370047, U1301252);Shenzhen Scientific R & D Grant (GJHS20160331150703934);Shenzhen Dapeng Special Program for Industrial Development (KY20160102);Zhenjiang Leading Talent Program for Innovation and Entrepreneurship

摘　　要：As a living fossil, the endangered Chinese sturgeon(Acipenser sinensis) has been considered a national treasure in China. Here,the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes.The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths(10–35 cm) were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA(mtDNA) D-loop region and 1,481,620 SNPs(singlenucleotide polymorphisms) generated by restriction site-associated DNA sequencing(RAD-seq). For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.As a living fossil, the endangered Chinese sturgeon（Acipenser sinensis） has been considered a national treasure in China. Here,the famous Gezhouba Dam and Three Gorges Dam on the Yangtze River were built in 1988 and 2006, for economic purposes.The natural population of Chinese sturgeon has declined since then, as these dams block its migratory route to the original spawning grounds in the middle reaches of the Yangtze River. In 2013 and 2014, there was an absence of spawning where it typically happened near the Gezhouba Dam. Nevertheless, from April to June in 2015, over 1,000 larvae with different body lengths（10-35 cm） were detected along the Shanghai Yangtze Estuary; but only little is currently known about the population genetic structure of the Chinese sturgeon. Herein, we inferred population genetic parameters from 462 available Chinese sturgeon specimens based on a 421-bp fragment of the mitochondrial DNA（mtDNA） D-loop region and 1,481,620 SNPs（singlenucleotide polymorphisms） generated by restriction site-associated DNA sequencing（RAD-seq）. For the D-loop dataset, 15 haplotypes were determined. Randomly picked 23 individuals, representing the 15 D-loop haplotype groups, were subsequently used for further RAD-seq validation. The average nucleotide diversity calculated from the mtDNA and RAD datasets was 0.0086 and 0.000478, respectively. The overall effective female population size was calculated to be 1,255 to 2,607, and the long-term effective population size was estimated to range from 11,950 to 119,500. We observed that the genetic variability and the effective female population size of the current population in the Yangtze River are severely low, which are similar to the data reported over 10 years ago. The deduced relatively small effective population of female fish, limiting the genetic connectivity among Chinese sturgeon, should be considered a serious threat to this endangered species.

关 键 词：Acipenser sinensis genetic diversity effective female population size mtDNA RAD-seq 

分 类 号：S917.4[农业科学—水产科学]