基于线粒体ND2基因序列的少鳞鱚遗传多样性研究
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摘要
以莱州、胶南、舟山、厦门、汕头和北海6个群体119尾少鳞鱚(Sillago japonica)为研究对象,采用PCR扩增测序获得长度为450 bp的线粒体DNA NADH脱氢酶亚基2 (ND2)基因片段,共检测到77个变异位点,其中简约信息位点30个,单变异位点28个,无碱基缺失。119条序列定义了61个单倍型,平均单倍型多样性(H_d)和核苷酸多样性(π)分别为0.945 3±0.015 5和0.009 718±0.005 445。6个群体间的平均遗传距离为0.008 3,遗传分化指数F_(ST)均小于0.05,各群体间无显著遗传分化。AMOVA分析得出少鳞鱚的遗传变异主要来自于种群内个体间(99.96%)。中性检验的Tajima's D和Fu's Fs统计值均为负值且显著偏离中性,核苷酸不配对分布图呈现明显的单峰分布,表明少鳞鱚历史上经历了群体扩张事件,估算扩张时间大约在(0.12～0.29)百万年前的第四纪更新世晚期。
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(H_d)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 F_(ST) 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.
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(H_d)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 F_(ST) 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.
引文
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[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.
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[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
[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.
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