ZHENG Deyu, GUO Yijia, YANG Tianyan, GAO Tianxiang, ZHENG Yao, YUAN Donghao, SI Shujin. Genetic diversity analysis of Sillago japonica based on mitochondrial DNA ND2 gene[J]. South China Fisheries Science, 2019, 15(5): 84-91. DOI: 10.12131/20190042
Citation: ZHENG Deyu, GUO Yijia, YANG Tianyan, GAO Tianxiang, ZHENG Yao, YUAN Donghao, SI Shujin. Genetic diversity analysis of Sillago japonica based on mitochondrial DNA ND2 gene[J]. South China Fisheries Science, 2019, 15(5): 84-91. DOI: 10.12131/20190042

Genetic diversity analysis of Sillago japonica based on mitochondrial DNA ND2 gene

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  • Received Date: February 24, 2019
  • Revised Date: April 23, 2019
  • Available Online: May 30, 2019
  • A total of 119 individuals of Sillago japonica were collected from six sampling sites (Laizhou, Jiaonan, Zhoushan, Xiamen, Shantou and Beihai). The length of 450 bp NADH dehydrogenase subunit 2 (ND2) gene fragment was amplified and sequenced. No base insertion or deletion mutations occurred and 77 mutation sites were detected, including 30 parsimony informative sites and 28 singleton polymorphic sites. Sixty-one haplotypes were defined in 119 sequences. The average haplotype diversity (Hd) and nucleotide diversity (π) were 0.945 3±0.015 5 and 0.009 718±0.005 445, respectively. The average genetic distance among the six populations was 0.008 3, and the genetic differentiation index FST value was less than 0.05, indicating no significant genetic differentiation among the populations. Analysis of molecular variance (AMOVA) shows that genetic variation of S. japonica mainly resided among individuals within populations (99.96%). The neutral tests (Tajima's D and Fu's Fs) were both negative and deviated from the neutral significantly. Besides, the nucleotide mismatches distribution showed a unimodal distribution, indicating that S. japonica had experienced population expansion in history. The estimated expansion time was about 0.12−0.29 million years ago in late Pleistocene.
  • [1]
    NELSON J S. Fishes of the world[M]. New Jersey: John Wiley & Sons, 2016: 503.
    [2]
    MCKAY R J. An annotated and illustrated catalogue of the sillago, smelt or Indo-Pacific whiting species known to date[R]. Rome: FAO, 1992: 1-83.
    [3]
    SANO J. Fisheries management by spawning per recruit analysis and yield per recruit analysis for Sillago japonica around the coastal waters of Itoshima [Japan] area[R]. Bulletin of Fukuoka Fisheries & Marine Technology Research Center, Fukuoka, 2004: 46-47.
    [4]
    SHIMASAKI Y, OSHIMA Y, INOUE S, et al. Effect of tributyltin on reproduction in Japanese whiting, Sillago japonica[J]. Mar Environ Res, 2006, 62(S): S245-S248.
    [5]
    OOZEKI Y, HWANG P P, HIRANO R. Larval development of the Japanese whiting, Sillago japonica[J]. Jpn J Ichthyol, 1992, 39(1): 59-66.
    [6]
    KASHIWAGI M, KONDO S, YOSHIDA W, et al. Effects of temperature and salinity on hatching success of Japanese whiting Sillago japonica eggs[J]. Suisan Zoshoku, 2000, 48(4): 637-642.
    [7]
    SULISTIONO S, WATANABE S, YOKOTA M. Reproduction of the Japanese whiting, Sillago japonica, in Tateyama Bay[J]. Aquacult Sci, 1999, 47(2): 209-214.
    [8]
    RAHMAN S M, MAJHI S K, SUZUKI T A, et al. Suitability of cryoprotectants and impregnation protocols for embryos of Japanese whiting Sillago japonica[J]. Cryobiology, 2008, 57(2): 170-174. doi: 10.1016/j.cryobiol.2008.08.002
    [9]
    RAHMAN S M, STRUESSMANN C A, SUZUKI T, et al. Electroporation enhances permeation of cryoprotectant (dimethyl sulfoxide) into Japanese whiting (Sillago japonica) embryos[J]. Theriogenology, 2013, 79(5): 853-858. doi: 10.1016/j.theriogenology.2013.01.002
    [10]
    SULISTIONO S, YOKOTA M, KITADA S, et al. Age and growth of Japanese whiting Sillago japonica in Tateyama Bay[J]. Fish Sci, 1999, 65(1): 117-122.
    [11]
    ARAYAMA K, IMAI H, KOHNO H, et al. Early life story of Japanese whiting Sillago japonica occurring in the surf zone of sandy beaches Tateyama Bay, central Japan[J]. Nippon Suisan Gakkaishi, 2003, 69(3): 359-367. doi: 10.2331/suisan.69.359
    [12]
    杨亚峰, 宋娜, 肖家光, 等. 莱州湾少鳞的形态特征描述[J]. 齐鲁渔业, 2016, 33(10): 8-10.
    [13]
    潘晓哲, 高天翔. 基于耳石形态的属鱼类鉴别[J]. 动物分类学报, 2010, 35(4): 799-805.
    [14]
    薛泰强, 杜宁, 高天翔. 基于线粒体COI及Cytb基因的4种科鱼类系统发育研究[J]. 中国海洋大学学报(自然科学版), 2010, 40(S1): 91-98.
    [15]
    肖家光. 基于线粒体基因组全序列的属鱼类系统发育研究[D]. 青岛: 中国海洋大学, 2015: 44-53.
    [16]
    GAO T X, YANG T Y, YANAGIMOTO T, et al. Levels and patterns of genetic variation in Japanese whiting (Sillago japonica) based on mitochondrial DNA control region[J]. Mitochondrial DNA Pt A, 2019, 30(1): 172-183. doi: 10.1080/24701394.2018.1467411
    [17]
    王林燕. 基于微卫星标记的中国和少鳞群体遗传学研究[D]. 青岛: 中国海洋大学, 2014: 36-64.
    [18]
    VELLEND M, GEBER M A. Connections between species diversity and genetic diversity[J]. Ecol Lett, 2005, 8(7): 767-781. doi: 10.1111/ele.2005.8.issue-7
    [19]
    JUAN Y, ZHONG Z Q, FEN L. Mitochondrial DNA and its application to the molecular population genetics of fish[J]. Ecol Sci, 2008, 27(4): 272-276.
    [20]
    WILSON A C, CANN R L, CARR S M, et al. Mitochondrial DNA and two perspectives on evolutionary genetics[J]. Biol J Linn Soc, 2010, 26(4): 375-400.
    [21]
    杨喜书, 章群, 余帆洋, 等. 华南6水系与澜沧江-湄公河攀鲈线粒体ND2基因的遗传多样性分析[J]. 南方水产科学, 2017, 13(3): 43-50. doi: 10.3969/j.issn.2095-0780.2017.03.006
    [22]
    阮燕如. 基于线粒体ND2基因序列的华南地区斑鳢遗传多样性研究[D]. 广州: 暨南大学, 2014: 52-53.
    [23]
    伊西庆. 中国东部6个大型湖泊翘嘴鲌(Culter alburnus)遗传多样性的线粒体ND2基因序列分析[D]. 广州: 暨南大学, 2009: 31-35.
    [24]
    GEORGE A L, CALDIERARO J B, CHARTRAND K M. Population genetics of the blue shiner, Cyprinella caerulea[J]. Southeast Nat, 2008, 7(4): 637-650. doi: 10.1656/1528-7092-7.4.637
    [25]
    VERISSIMO A, MCDOWELL J R, GRAVES J E. Genetic population structure and connectivity in a commercially exploited and wide-ranging deepwater shark, the leafscale gulper (Centrophorus squamosus)[J]. Mar Freshw Res, 2012, 63(6): 505-512. doi: 10.1071/MF11237
    [26]
    SAMBROOK J, FRITSCH E F, MANIATIS T. Molecular cloning: a laboratory manual[M]. New York: Cold Spring Harbor Laboratory Press, 1982: 76-82.
    [27]
    CLEWLEY J P. Macintosh sequence analysis software. DNAStar's LaserGene[J]. Mol Biotechnol, 1995, 3(3): 221-224. doi: 10.1007/BF02789332
    [28]
    ROZAS J, FERRERMATA A, SÁNCHEZDELBARRIO J C, et al. DnaSP 6: DNA sequence polymorphism analysis of large datasets[J]. Mol Biol Evol, 2017, 34(12): 3299-3302. doi: 10.1093/molbev/msx248
    [29]
    EXCOFFIER L, LISCHER H E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows[J]. Mol Ecol Resour, 2010, 10(3): 564-567. doi: 10.1111/men.2010.10.issue-3
    [30]
    KUMAR S, STECHER G, TAMURA K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets[J]. Mol Biol Evol, 2016, 33(7): 1870-1874. doi: 10.1093/molbev/msw054
    [31]
    ROGERS A R, HARPENDING H. Population growth makes waves in the distribution of pairwise genetic differences[J]. Mol Biol Evol, 1992, 9(3): 552-569.
    [32]
    BERMINGHAM E S, MCCAFFERTY A. Molecular systematics of fishes[M]. New York: Academic Press, 1997: 113-126.
    [33]
    FERGUSON J H. On the use of genetic divergence for identifying species[J]. Biol J Linn Soc, 2015, 75(4): 509-516.
    [34]
    SKIBINSKI D F. DNA tests of neutral theory: applications in marine genetics[M]. Berlin: Springer Netherlands, 2000: 137-152.
    [35]
    FU Y X. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection[J]. Genetics, 1997, 147(2): 915-925.
    [36]
    BONIN A, NICOLE F, POMPANON F, et al. Population adaptive index: a new method to help measure intraspecific genetic diversity and prioritize populations for conservation[J]. Conserv Biol, 2007, 21(3): 697-708. doi: 10.1111/cbi.2007.21.issue-3
    [37]
    NEI M. Molecular evolutionary genetics[M]. New York: Columbia University Press,1987: 92-145.
    [38]
    王秀亮. 玉筋鱼群体遗传多样性及其适应进化研究[D]. 舟山: 浙江海洋大学, 2017: 24-25.
    [39]
    XU S Y, SUN D R, SONG N, et al. Local adaptation shapes pattern of mitochondrial population structure in Sebastiscus marmoratus[J]. Environ Biol Fish, 2017, 100(7): 763-774. doi: 10.1007/s10641-017-0602-5
    [40]
    WRIGHT S. Evolution and the genetics of populations[M]. Chicago: University of Chicago Press, 1968: 76-79.
    [41]
    HEWITT G M. Genetic consequences of climatic oscillations in the quaternary[J]. Philos T R Soc B, 2004, 359(1442): 183-195. doi: 10.1098/rstb.2003.1388
    [42]
    刘海松. 地貌学及第四纪地质学[M]. 北京: 地质出版社, 2013: 10-11.
    [43]
    沈浪, 陈小勇, 李媛媛. 生物冰期避难所与冰期后的重新扩散[J]. 生态学报, 2002, 22(11): 1983-1990. doi: 10.3321/j.issn:1000-0933.2002.11.026
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