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

  • 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
Research Paper

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 genetic diversity effective female population size mtDNA RAD-seq 

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Notes

Acknowledgements

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

Supplementary material

11427_2017_9254_MOESM1_ESM.pdf (185 kb)
Table S1 Sample information for this study
11427_2017_9254_MOESM2_ESM.docx (13 kb)
Table S2 Estimates of genetic distance between sequences. COI-H1 and COI-H2 represent the 2 haplotypes of COI. Evolutionary analyses were conducted by MEGA6
11427_2017_9254_MOESM3_ESM.docx (35 kb)
Table S3 Variable nucleotide sites within the 421-bp amplified mtDNA D-loop (light strand) of Chinese sturgeon (A. sinensis)
11427_2017_9254_MOESM4_ESM.docx (14 kb)
Table S4 Collective information of the specimens (used for RAD analyses), sequence data, unique stacks, loci and SNPs

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Copyright information

© Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Jian Liu
    • 1
  • Xinxin You
    • 2
  • Pao Xu
    • 3
  • Ping Zhuang
    • 4
  • Yueping Zheng
    • 1
    • 4
    • 5
  • Kai Zhang
    • 2
  • Min Wang
    • 2
    • 6
  • Yunyun Lv
    • 2
  • Gangchun Xu
    • 3
  • Feng Zhao
    • 4
  • Jianhui Wu
    • 1
    • 7
  • Houyong Fan
    • 1
  • Jianan Xu
    • 1
  • Zhiqiang Ruan
    • 2
  • Chao Bian
    • 2
    • 6
  • Kai Liu
    • 3
  • Dongpo Xu
    • 3
  • Jinhui Chen
    • 1
  • Junmin Xu
    • 2
    • 6
    • 8
  • Qiong Shi
    • 2
    • 6
    • 8
    • 9
  1. 1.Superintendency Department of Shanghai Yangtze Estuarine Nature Reserve for Chinese SturgeonShanghaiChina
  2. 2.Shenzhen Key Lab of Marine GenomicsGuangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Marine, BGIShenzhenChina
  3. 3.Freshwater Fisheries Research CenterChinese Academy of Fishery SciencesWuxiChina
  4. 4.Key and Open Laboratory of Marine and Estuarine Fisheries Resources and Ecology, East China Sea Fisheries Research InstituteChinese Academy of Fishery SciencesShanghaiChina
  5. 5.College of Fisheries and Life SciencesShanghai Ocean UniversityShanghaiChina
  6. 6.BGI-Zhenjiang Institute of HydrobiologyZhenjiangChina
  7. 7.College of Marine SciencesShanghai Ocean UniversityShanghaiChina
  8. 8.BGI Research Center for Aquatic GenomicsChinese Academy of Fishery SciencesShenzhenChina
  9. 9.Laboratory of Aquatic Genomics, College of Life Sciences and OceanographyShenzhen UniversityShenzhenChina

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