Skip to main content

Advertisement

SpringerLink
Log in

Genetic variation of the small yellow croaker (Larimichthys polyactis) inferred from mitochondrial DNA provides novel insight into the fluctuation of resources

  • Published:
Acta Oceanologica Sinica Aims and scope Submit manuscript

Abstract

The small yellow croaker (Larimichthys polyactis) belongs to the family Sciaenidae, which is an offshore warm fish species and widely distributed in the western Pacific. In this study, the variation of genetic diversity and genetic differentiation among L. polyactis populations was analyzed by mitochondrial DNA control region. A total of 110 polymorphic sites were checked, which defined 134 haplotypes. High level of haplotype diversity (h=0.993±0.002) was detected in the examined range. Population genetic structure analyse (analysis of molecular variance, Fst) showed there were high gene flow among L. polyactis populations. The result showed that there were relatively high genetic diversity and low genetic differentiation among the Yellow Sea and the East China Sea populations, which can be attributed to diverse habitats, wide distribution range and high mutation rate of control region. Using phylogenetic methods, coalescent analyses (neutrality tests, mismatch distribution analysis, Bayesian skyline analyses) and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we inferred that the genetic make-up of extant populations of L. polyactis was shaped by Pleistocene environmental impacts on the historical demography of this species. Besides, relatively constant genetic diversity and larger effective population size were detected in recent L. polyactis population. The result showed that the fishing policy certainly, such as the summer closed fishing, played a role in protecting resources of L. polyactis. This study can offer a wealth of biological novelties which indicates genetic structure of L. polyactis population and provides the foundation for resources protection and policy setting.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bouckaert R, Heled J, Kühnert D, et al. 2014. BEAST 2: A software platform for Bayesian evolutionary analysis. PLoS Computational Biology, 10(4): e1003537, doi: https://doi.org/10.1371/journal.pcbi.1003537

    Article  Google Scholar 

  • Chen Yongjun, Mao Jun, Senanan W, et al. 2020. Identification of a large dataset of SNPs in Larimichthys polyactis using high-throughput 2b-RAD sequencing. Animal Genetics, 51(6): 964–967, doi: https://doi.org/10.1111/age.13000

    Article  Google Scholar 

  • Chen Zuozhi, Xu Shannan, Qiu Yongsong, et al. 2009. Modeling the effects of fishery management and marine protected areas on the Beibu Gulf using spatial ecosystem simulation. Fisheries Research, 100(3): 222–229, doi: https://doi.org/10.1016/j.fishres.2009.08.001

    Article  Google Scholar 

  • Cheng Jiahua, Lin Longshan, Ling Jianzhong, et al. 2004. Effects of summer close season and rational utilization on redlip croaker (Larimichthys polyactis Bleeker) resource in the East China Sea Region. Journal of Fishery Sciences of China, 11(6): 554–560

    Google Scholar 

  • Dann T H, Habicht C, Baker T T, et al. 2013. Exploiting genetic diversity to balance conservation and harvest of migratory salmon. Canadian Journal of Fisheries and Aquatic Sciences, 70(5): 785–793, doi: https://doi.org/10.1139/cjfas-2012-0449

    Article  Google Scholar 

  • Excoffier L, Laval G, Schneider S. 2007. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47–50

    Google Scholar 

  • Excoffier L, Smouse P E, Quattro J M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics, 131(2): 479–491, doi: https://doi.org/10.1093/genetics/131.2.479

    Article  Google Scholar 

  • Felsenstein J, Kuhner M K, Yamato J, et al. 1999. Likelihoods on coalescents: a Monte Carlo sampling approach to inferring parameters from population samples of molecular data. Lecture Notes-Monograph Series, 33: 163–185

    Article  Google Scholar 

  • Fu Yunxin. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147(2): 915–925, doi: https://doi.org/10.1093/genetics/147.2.915

    Article  Google Scholar 

  • Gao Tianxiang, Ying Yiping, Yang Qiaoli, et al. 2020. The mitochondrial markers provide new insights into the population demographic history of Coilia nasus with two ecotypes (anadromous and freshwater). Frontiers in Marine Science, 7: 576161, doi: https://doi.org/10.3389/fmars.2020.576161

    Article  Google Scholar 

  • Giovannoni S J, Britschgi T B, Moyer C L, et al. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature, 345(6270): 60–63, doi: https://doi.org/10.1038/345060a0

    Article  Google Scholar 

  • Glenn T C, Stephan W, Braun M J. 1999. Effects of a population bottleneck on whooping crane mitochondrial DNA variation. Conservation Biology, 13(5): 1097–1107, doi: https://doi.org/10.1046/J.1523-1739.1999.97527.x

    Article  Google Scholar 

  • Han Zhiqiang, Lin Longshan, Shui Bonian, et al. 2009. Genetic diversity of small yellow croaker Larimichthys polyactis revealed by AFLP markers. African Journal of Agricultural Research, 4(7): 605–610

    Google Scholar 

  • Han Qingpeng, Shan Xiujuan, Wan Rong, et al. 2019. Spatiotemporal distribution and the estimated abundance indices of Larimichthys polyactis in winter in the Yellow Sea based on geostatistical delta-generalized linear mixed models. Journal of Fisheries of China, 43(7): 1603–1614

    Google Scholar 

  • Herbert T D, Schuffert J D, Andreasen D, et al. 2001. Collapse of the California current during glacial maxima linked to climate change on land. Science, 293(5527): 71–76, doi: https://doi.org/10.1126/science.1059209

    Article  Google Scholar 

  • Huang Hao. 2011. Morphological variation and genetic diversity of five populations of small yellow croaker (Larimichthys polyactis)(in Chinese)[dissertation]. Wuxi: Nanjing Agricultural University

    Google Scholar 

  • Ikeda I. 1964. Studies on the fisheries biology of the yellow croaker in the East China and the Yellow Seas. Seikai Reg Fish Resource Library, 31: 1–81

    Google Scholar 

  • Ishikawa S, Aoyama J, Tsukamoto K, et al. 2001. Population structure of the Japanese eel Anguilla japonica as examined by mitochondrial DNA sequencing. Fisheries Science, 67(2): 246–253, doi: https://doi.org/10.1046/j.1444-2906.2001.00227.x

    Article  Google Scholar 

  • Kim J K, Kim Y H, Kim M J, et al. 2010. Genetic diversity, relationships and demographic history of the small yellow croaker, Larimichthys polyactis (Pisces: Sciaenidae) from Korea and China inferred from mitochondrial control region sequence data. Animal Cells & Systems, 14(1): 45–51

    Article  Google Scholar 

  • Kim Y H, Lee S K, Lee J B, et al. 2006. Age and growth of small yellow croaker, Larimichthys polyactis in the South Sea of Korea. Korean Journal of Ichthyology, 18(1): 45–54

    Google Scholar 

  • Kim J K, Min G S, Yoon M, et al. 2012. Genetic structure of Larimichthys polyactis (Pisces: Sciaenidae) in the Yellow and East China Seas inferred from microsatellite and mitochondrial DNA analyses. Animal Cells and Systems, 16(4): 313–320, doi: https://doi.org/10.1080/19768354.2011.652668

    Article  Google Scholar 

  • Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16(2): 111–120, doi: https://doi.org/10.1007/BF01731581

    Article  Google Scholar 

  • Kuhner M K. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics, 22(6): 768–770, doi: https://doi.org/10.1093/bioinformatics/btk051

    Article  Google Scholar 

  • Li Yuan, Han Zhiqiang, Song Na, et al. 2013. New evidence to genetic analysis of small yellow croaker (Larimichthys polyactis) with continuous distribution in China. Biochemical Systematics and Ecology, 50: 331–338, doi: https://doi.org/10.1016/j.bse.2013.05.003

    Article  Google Scholar 

  • Librado P, Rozas J. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(11): 1451–1452, doi: https://doi.org/10.1093/bioinformatics/btp187

    Article  Google Scholar 

  • Lin Longshan, Cheng Jiaye. 2004. An analysis of the current situation of fishery biology of small yellow croaker in the East China Sea. Periodical of Ocean University of China, 34(4): 565–570

    Google Scholar 

  • Lin Longshan, Cheng Jiaye, Jiang Yazhou, et al. 2008. Spatial distribution and environmental characteristics of the spawning grounds of small yellow croaker in the southern Yellow Sea and the East China Sea. Acta Ecologica Sinica, 28(8): 3485–3494

    Google Scholar 

  • Lin Longshan, Jiang Yazhou, Liu Zunlei, et al. 2010. Analysis of the distribution difference of small yellow croaker between the southern Yellow Sea and the East China Sea. Periodical of Ocean University of China, 40(3): 1–6

    Google Scholar 

  • Lin Longshan, Jiang Yazhou, Yan Liping, et al. 2009. Study on the distribution characteristics and fecundity of spawning stock of Larimichthys polyactis in the southern Yellow Sea and the East China Sea. Journal of Shanghai Ocean University, 18(4): 453–459

    Google Scholar 

  • Lin Longshan, Liu Zunlei, Jiang Yazhou. 2011. Current status of small yellow croaker resources in the southern Yellow Sea and the East China Sea. Chinese Journal of Oceanology and Limnology, 29(3): 547–555, doi: https://doi.org/10.1007/s00343-011-0182-8

    Article  Google Scholar 

  • Meng Zining, Zhuang Zhimeng, Jin Xianshi, et al. 2003. Genetic diversity in small yellow croaker (Pseudosciaena polyactis) by RAPD analysis. Biodiversity Science, 11(3): 197–203, doi: https://doi.org/10.17520/biods.2003026

    Article  Google Scholar 

  • Moritz C, Dowling T E, Brown W M. 1987. Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annual Review of Ecology and Systematics, 18: 269–292, doi: https://doi.org/10.1146/annurev.es.18.110187.001413

    Article  Google Scholar 

  • Nei M. 1987. Molecular Evolutionary Genetics. New York: Columbia University Press

    Book  Google Scholar 

  • Palumbi S R. 1994. Genetic divergence, reproductive isolation, and marine speciation. Annual Review of Ecology and Systematics, 25(1): 547–572, doi: https://doi.org/10.1146/annurev.es.25.110194.002555

    Article  Google Scholar 

  • Rambaut A, Drummond A J, Xie Dong, et al. 2018. Posterior summarization in Bayesian phylogenetics using tracer 1.7. Systematic Biology, 67(5): 901–904, doi: https://doi.org/10.1093/sysbio/syy032

    Article  Google Scholar 

  • Rogers A R, Harpending H. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9(3): 552–569

    Google Scholar 

  • Sambrook J, Fritsch E F, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press

    Google Scholar 

  • Shan Binbin, Liu Yan, Song Na, et al. 2020. Genetic diversity and population structure of black sea bream (Acanthopagrus schlegelii) based on mitochondrial control region sequences: the genetic effect of stock enhancement. Regional Studies in Marine Science, 35: 101188, doi: https://doi.org/10.1016/j.rsma.2020.101188

    Article  Google Scholar 

  • Simons A M, Wood R M, Heath L S, et al. 2001. Phylogenetics of Scaphirhynchus based on mitochondrial DNA sequences. Transactions of the American Fisheries Society, 130(3): 359–366, doi: https://doi.org/10.1577/1548-8659(2001)130<0359:POSBOM>2.0.CO;2

    Article  Google Scholar 

  • Slatkin M, Hudson R R. 1991. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129(2): 555–562, doi: https://doi.org/10.1093/genetics/129.2.555

    Article  Google Scholar 

  • Song Na, Ma Guoqiang, Zhang Xiumei, et al. 2014. Genetic structure and historical demography of Collichthys lucidus inferred from mtDNA sequence analysis. Environmental Biology of Fishes, 97(1): 69–77, doi: https://doi.org/10.1007/s10641-013-0124-8

    Article  Google Scholar 

  • Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3): 585–595, doi: https://doi.org/10.1093/genetics/123.3.585

    Article  Google Scholar 

  • Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731–2739, doi: https://doi.org/10.1093/molbev/msr121

    Article  Google Scholar 

  • Tang Jianhua, Zhou Jin. 1999. Resource and management of the small yellow croaker in the East China Sea. Marine Fisheries, 21(4): 173–174, 180

    Google Scholar 

  • Teacher A G, André C, Jonsson P R, et al. 2013. Oceanographic connectivity and environmental correlates of genetic structuring in Atlantic herring in the Baltic Sea. Evolutionary Applications, 6(3): 549–567, doi: https://doi.org/10.1111/eva.12042

    Article  Google Scholar 

  • Tokuyama T, Shy J Y, Lin Huichen, et al. 2020. Genetic population structure of the fiddler crab Austruca lactea (De Haan, 1835) based on mitochondrial DNA control region sequences. Crustacean Research, 49: 141–153, doi: https://doi.org/10.18353/crustacea.49.0_141

    Article  Google Scholar 

  • Wang Yali, Hu Cuilin, Li Zhenhua, et al. 2021. Population structure and resource change of Larimichthys polyactis in spring in Zhoushan fishery spawning ground protection area, China. Chinese Journal of Applied Ecology, 32(9): 3349–3356

    Google Scholar 

  • Weir B S, Cockerham C C. 1984. Estimating F-statistics for the analysis of population structure. Evolution, 38(6): 1358–1370

    Google Scholar 

  • Wirgin I, Waldman J R, Rosko J, et al. 2000. Genetic structure of Atlantic sturgeon populations based on mitochondrial DNA control region sequences. Transactions of the American Fisheries Society, 129(2): 476–486, doi: https://doi.org/10.1577/1548-8659(2000)129<0476:GSOASP>2.0.CO;2

    Article  Google Scholar 

  • Wu Renxie, Liu Shufang, Zhuang Zhimeng, et al. 2012. Population genetic structure and demographic history of small yellow croaker, Larimichthys polyactis (Bleeker, 1877), from coastal waters of China. African Journal of Biotechnology, 11(61): 12500–12509

    Google Scholar 

  • Xiao Yongshuang, Song Na, Li Jun, et al. 2015. Significant population genetic structure detected in the small yellow croaker Larimichthys polyactis inferred from mitochondrial control region. Mitochondrial DNA, 26(3): 409–419, doi: https://doi.org/10.3109/19401736.2013.843076

    Article  Google Scholar 

  • Xiao Yongshuang, Zhang Xiumei, Gao Tianxiang, et al. 2009. Genetic diversity in the mtDNA control region and population structure in the small yellow croaker Larimichthys polyactis. Environmental Biology of Fishes, 85(4): 303–314, doi: https://doi.org/10.1007/s10641-009-9497-0

    Article  Google Scholar 

  • Xu Zhaoli, Cheng Jiajie. 2009. Analysis on migratory routine of Larimichthy polyactis. Journal of Fishery Sciences of China, 16(6): 931–940

    Google Scholar 

  • Yan Liping, Liu Zunlei, Jin Yan, et al. 2019. Effects of prolonging the trawl net summer fishing moratorium period in the East China Sea on the conservation of fishery resources. Journal of Fishery Sciences of China, 26(1): 118–123, doi: https://doi.org/10.3724/SP.J.1118.2019.18243

    Article  Google Scholar 

  • Zhang Hanye, Cheng Jiahua. 2005. Geostatistical analysis on spatial patterns of small yellow croaker (Larimichthys polyactis) in the East China Sea. Journal of Fishery Sciences of China, 12(4): 419–423

    Google Scholar 

  • Zhang Jian, Jin Yufeng, Peng Yongzhang. 2014. On construction improvement in net mouth of traditional stow net. Marine Fisheries, 36(1): 63–67

    Google Scholar 

  • Zhang Baidong, Xue Dongxiu, Wang Juan, et al. 2016. Development and preliminary evaluation of a genomewide single nucleotide polymorphisms resource generated by RAD-seq for the small yellow croaker (Larimichthys polyactis). Molecular Ecology Resources, 16(3): 755–768, doi: https://doi.org/10.1111/1755-0998.12476

    Article  Google Scholar 

  • Zheng Xuebin, Du Chen, Wang Jingqian, et al. 2020. Physiological characteristics and cryopreservation effect of Larimichthys polyactis sperm. Oceanologia et Limnologia Sinica, 51(1): 193–205

    Google Scholar 

  • Zheng Wenjuan, Lai Yuhong, You Xinyu, et al. 2012. Genetic diversity of Pseudosciaena polyactis in Zhoushan based on mitochondrial DNA D-loop region sequences. Zoological Research, 33(3): 329–336

    Article  Google Scholar 

Download references

Acknowledgements

We thank Pengfei Li, Zhicheng Sun, Yehui Wang and Xiang Zhao for collecting the samples.

Funding

The National Key Research and Development Program of China under contract No. 2018YFD0900905.

Author information

Authors and Affiliations

  1. Key Laboratory of Mariculture of Ministry of Education, Ocean University of China, Qingdao, 266003, China

    Jian Zheng & Na Song

  2. Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China

    Tianxiang Gao

  3. College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China

    Yunrong Yan

Authors
  1. Jian Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tianxiang Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yunrong Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Na Song
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Na Song.

Electronic Supplementary Material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Zheng, J., Gao, T., Yan, Y. et al. Genetic variation of the small yellow croaker (Larimichthys polyactis) inferred from mitochondrial DNA provides novel insight into the fluctuation of resources. Acta Oceanol. Sin. 41, 88–95 (2022). https://doi.org/10.1007/s13131-022-2039-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s13131-022-2039-8

Key words

Search

Navigation