• Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, et al. The genomic basis of adaptive evolution in threespine sticklebacks. Nature. 2012;484(7392):55–61.


    Google Scholar     

  • Kjærner-Semb E, Ayllon F, Furmanek T, Wennevik V, Dahle G, Niemelä E, et al. Atlantic salmon populations reveal adaptive divergence of immune related genes-a duplicated genome under selection. BMC Genomics. 2016;17(1):610.


    Google Scholar     

  • Zhang B, Xue D, Li Y, Liu J. RAD genotyping reveals fine-scale population structure and provides evidence for adaptive divergence in a commercially important fish from the Northwestern Pacific Ocean. PeerJ. 2019;7:e7242.


    Google Scholar     

  • Jian J, Yang L, Gan X, Wu B, Gao L, Zeng H, et al. Whole genome sequencing of silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis) provide novel insights into their evolution and speciation. Mol Ecol Resour. 2021;21(3):912–23.


    Google Scholar     

  • Li B, Chen L, Yan M, Zou X, Bai Y, Xue Y, et al. Intercross population study reveals that co-mutation of Mitfa genes in two subgenomes induces red skin color in common carp (Cyprinus carpio wuyuanensis). Zool Res. 2023;44(2):276.


    Google Scholar     

  • Richardson J. Report on the ichthyology of the seas of China and Japan. R. and JE Taylor; (M). .London, R. and J.E. Taylor. 18461787-1865. https://doi.org/10.5962/bhl.title.59530.

  • Zhang Q, Hong W, Yang S, Liu M. Discussion on the division of geographic populations for the large yellow croaker (Larimichthys crocea) (in Chinese). Fish Inform Strategy. 2011;26(2):3–8.


    Google Scholar     

  • Zhang K, Zhou Y, Song W, Jiang L, Yan X. Genome-wide Radseq reveals genetic differentiation of wild and cultured populations of large yellow croaker. Genes. 2023;14(7):1508.


    Google Scholar     

  • Hong Y, Geng J, Qiao S, Zhang Y, Ding L, Wang X, et al. Phosphorus fractions and matrix-bound phosphine in coastal surface sediments of the Southwest Yellow Sea. J Hazard Mater. 2010;181(1–3):556–64.


    Google Scholar     

  • Yang W, Zhou D. Research on the agglomeration level of china’s large yellow croaker industry (in Chinese). Mar Dev Manage. 2022;39(10):26–33.


    Google Scholar     

  • Hu Y. Historical evolution and current status analysis of the genetic resources of large yellow croaker (Larimichthys crocea) in the East China sea region (in Chinese). J Shaoxing University: Nat Sci Ed. 2006;26(1):49–53.


    Google Scholar     

  • Xu P, Ke Q, Su Y, Liu J, Zheng W. Current status and suggestions for the conservation and utilization of genetic resources of large yellow croaker (Larimichthys crocea) (in Chinese). J Fish China. 2022;46(04):674–82.


    Google Scholar     

  • Ministry of Agriculture and Rural Affairs. National Fishery Technology Extension Centre,China Society of Fisheries. China fishery statistical yearbook 2023.

  • Wang L, Shi X, Su Y, Meng Z, Lin H. Loss of genetic diversity in the cultured stocks of the large yellow croaker, Larimichthys crocea, revealed by microsatellites. Int J Mol Sci. 2012;13(5):5584–97.


    Google Scholar     

  • Li Z, Fang X, Chen J, Chang J, Lei G, Zhang G, Zhao B, Wang Z. Loss of the genetic diversity in cultivated populations of Pseudosciaena Crocea by AFLP. Oceanol Limnol Sin. 2009;40(4):446–50.


    Google Scholar     

  • Wang D, Wang J, Ding S, Su Y. Comparative studies on some genetic characteristics among four large yellow croaker (Pseudosciaena crocea) populations. Acta Oceanol Sin. 2007;1(4):148–55.


    Google Scholar     

  • Lei F, Chen M, Meng Y, Niu S, Wu R, Pan Y. Analysis of COI sequence variation in the wild and cultured populations of Larimichthys Crocea (in Chinese). Guangxi Sci. 2023;30(04):794–803.


    Google Scholar     

  • Zhou Z, Han K, Wu Y, Bai H, Ke Q, Pu F, et al. Genome-wide association study of growth and body-shape-related traits in large yellow croaker (Larimichthys crocea) using DdRAD sequencing. Mar Biotechnol. 2019;21(5):655–70.


    Google Scholar     

  • Chen S. Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. Imeta. 2023;2(2):e107.


    Google Scholar     

  • Browning BL, Tian X, Zhou Y, Browning SR. Fast two-stage phasing of large-scale sequence data. Am J Hum Genet. 2021;108(10):1880–90.


    Google Scholar     

  • Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. fly. 2012;6(2):80–92.


    Google Scholar     

  • Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and vcftools. Bioinformatics. 2011;27(15):2156–8.


    Google Scholar     

  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81(3):559–75.


    Google Scholar     

  • Peakall R, Smouse PE. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes. 2006;6(1):288–95.


    Google Scholar     

  • Pickrell J, Pritchard J. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet. 2012;8(11): e1002967. https://doi.org/10.1371/journal.pgen.1002967.


    Google Scholar     

  • Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat Genet. 2017;49(2):303–9.


    Google Scholar     

  • Hijmans RJ, Williams E, Vennes C, Hijmans MRJ. Package ‘geosphere’. Spherical Trigonometry. 2017;1(7):1–45.


    Google Scholar     

  • Goudet J, Jombart T, Kamvar Z, Archer E, Hardy O. Hierfstat: Estimation and tests of hierarchical F-statistics (0.5-7)[Package ‘hierfstat’]. Molecular Ecology Notes. 2020;27(1):1–10

  • Rousset F. Genetic differentiation and Estimation of gene flow from F-statistics under isolation by distance. Genetics. 1997;145(4):1219–28.


    Google Scholar     

  • Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, McGlinn D, Minchin P, O’hara R, Simpson G, Solymos P. vegan: Community Ecology Package. R package version 2.5-7. 2020. Preprint at. 2022:3.1–152.

  • Liu M, De Mitcheson YS. Profile of a fishery collapse: why mariculture failed to save the large yellow croaker. Fish Fish. 2008;9(3):219–42.


    Google Scholar     

  • Nishioka K, Daidoji T, Nakaya T. Downregulation of calcium-regulated heat stable protein 1 expression by low-temperature stimulation causes reduction of interferon-β expression and sensitivity to influenza viral infection. Virus Res. 2022;309:198659.


    Google Scholar     

  • Han Z, Guo X, Liu Q, Liu S, Zhang Z, Xiao S, et al. Whole-genome resequencing of Japanese whiting (Sillago japonica) provide insights into local adaptations. Zool Res. 2021;42(5):548.


    Google Scholar     

  • Boonanuntanasarn S, Jangprai A, Na-Nakorn U. Transcriptomic analysis of female and male gonads in juvenile snakeskin gourami (Trichopodus pectoralis). Sci Rep. 2020;10(1):5240.


    Google Scholar     

  • Chen T, Lin T, Li H, Lu T, Li J, Huang W, et al. Heat shock protein 40 (HSP40) in Pacific white shrimp (Litopenaeus vannamei): molecular cloning, tissue distribution and ontogeny, response to temperature, acidity/alkalinity and salinity stresses, and potential role in ovarian development. Front Physiol. 2018;9:1784.


    Google Scholar     

  • Xu Z, Jiang J, Chen Y. Study on low lethal temperature of different strains of Pseudosciaena Crocea (in Chinese). Journal of Ningbo University(Natural Sci Eng Edition). 2006;(04):462–4.

  • Cossins AR, Crawford DL. Fish as models for environmental genomics. Nat Rev Genet. 2005;6(4):324–33.


    Google Scholar     

  • Zhang Z, Lin W, He D, Wu Q, Cai C, Chen H, et al. Aquaculture environment changes fish behavioral adaptability directly or indirectly through personality traits: a case study. Rev Fish Biol Fish. 2023;33(4):1423–41.


    Google Scholar     

  • Sexton JP, Hangartner SB, Hoffmann AA. Genetic isolation by environment or distance: which pattern of gene flow is most common? Evolution. 2014;68(1):1–15.


    Google Scholar     

  • Chen B, Bai Y, Wang J, Ke Q, Zhou Z, Zhou T, et al. Population structure and genome-wide evolutionary signatures reveal putative climate-driven habitat change and local adaptation in the large yellow croaker. Mar Life Sci Technol. 2023;5(2):141–54.


    Google Scholar     

  • Liu B. Study on population genetic structure and local adaptation of small yellow croaker and Japanese eel (in Chinese) D). University of Chinese Academy of Sciences; 2017:35–61.

  • Sun C, Wei H, Chen X, Zhao Z, Du H, Song W, et al. ERBB3-rs2292239 as primary type 1 diabetes association locus among non-HLA genes in Chinese. Meta Gene. 2016;9:120–3.


    Google Scholar     

  • Wang H, Jin Y, Linga Reddy MP, Podolsky R, Liu S, Yang P, Bode B, Chip Reed J, Steed RD, Anderson SW. Genetically dependent ERBB3 expression modulates antigen presenting cell function and type 1 diabetes risk. PLoS. ONE. 2010;5(7):e11789.


    Google Scholar     

  • Murr R, Vaissiere T, Sawan C, Shukla V, Herceg Z. Orchestration of chromatin-based processes: mind the TRRAP. Oncogene. 2007;26(37):5358–72.


    Google Scholar     

  • Suzuki T, Hirai Y, Uehara T, Ohga R, Kosaki K, Kawahara A. Involvement of the zebrafish trrap gene in craniofacial development. Sci Rep. 2021;11(1):24166.


    Google Scholar     

  • Mandic M, Todgham AE, Richards JG. Mechanisms and evolution of hypoxia tolerance in fish. Proc R Soc Lond B Biol Sci. 2009;276(1657):735–44.


    Google Scholar     

  • Zhang X, Wang Y. Studies on oxygen consumption rate and suffocation point of Pseudosciaena crocea fry. J Econ Anim. 2007;11(3):148–52.


    Google Scholar     

  • Semenza GL. HIF-1: mediator of physiological and pathophysiological responses to hypoxia. J Appl Physiol. 2000;88(4):1474–80.


    Google Scholar     

  • Liu X, Cai X, Hu B, Mei Z, Zhang D, Ouyang G, et al. Forkhead transcription factor 3a (FOXO3a) modulates hypoxia signaling via up-regulation of the von Hippel-Lindau gene (VHL). J Biol Chem. 2016;291(49):25692–705.


    Google Scholar     

  • Rahman MS, Thomas P. Molecular cloning and characterization of two ARNT (ARNT-1 and ARNT‐2) genes in Atlantic croaker and their expression during coexposure to hypoxia and PCB77. Environ Toxicol. 2019;34(2):160–71.


    Google Scholar     

  • Seo K, Park J, Heo J, Jing K, Han J, Min K, et al. SIRT2 regulates tumour hypoxia response by promoting HIF-1α hydroxylation. Oncogene. 2015;34(11):1354–62.


    Google Scholar     

  • Casazza A, Laoui D, Wenes M, Rizzolio S, Bassani N, Mambretti M, et al. Impeding macrophage entry into hypoxic tumor areas by Sema3A/Nrp1 signaling blockade inhibits angiogenesis and restores antitumor immunity. Cancer Cell. 2013;24(6):695–709.


    Google Scholar     

  • Bensellam M, Maxwell EL, Chan JY, Luzuriaga J, West PK, Jonas J-C, et al. Hypoxia reduces ER-to-Golgi protein trafficking and increases cell death by inhibiting the adaptive unfolded protein response in mouse beta cells. Diabetologia. 2016;59(7):1492–502.


    Google Scholar