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Sci China Life Sci. 2018 Sep;61(9):1090-1098. doi: 10.1007/s11427-017-9254-6. Epub 2018 Mar 30.

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

Liu J1, You X2, Xu P3, Zhuang P4, Zheng Y1,4,5, Zhang K2, Wang M2,6, Lv Y2, Xu G3, Zhao F4, Wu J1,7, Fan H1, Xu J1, Ruan Z2, Bian C2,6, Liu K3, Xu D3, Chen J8, Xu J9,10,11, Shi Q12,13,14,15.

Author information

1
Superintendency Department of Shanghai Yangtze Estuarine Nature Reserve for Chinese Sturgeon, 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
Superintendency Department of Shanghai Yangtze Estuarine Nature Reserve for Chinese Sturgeon, Shanghai, 200092, China. 1114260882@qq.com.
9
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Marine, BGI, Shenzhen, 518083, China. xujunmin@genomics.cn.
10
BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China. xujunmin@genomics.cn.
11
BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, 518083, China. xujunmin@genomics.cn.
12
Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Marine, BGI, Shenzhen, 518083, China. shiqiong@genomics.cn.
13
BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, 212000, China. shiqiong@genomics.cn.
14
BGI Research Center for Aquatic Genomics, Chinese Academy of Fishery Sciences, Shenzhen, 518083, China. shiqiong@genomics.cn.
15
Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China. shiqiong@genomics.cn.

Abstract

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 (single-nucleotide 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.

KEYWORDS:

Acipenser sinensis; RAD-seq; effective female population size; genetic diversity; mtDNA

PMID:
29948902
DOI:
10.1007/s11427-017-9254-6
[Indexed for MEDLINE]

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