基于线粒体控制区的中国近海棘头梅童鱼群体遗传结构研究
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摘要
为研究我国沿海棘头梅童鱼(Collichthys lucidus)的种群遗传结构,运用线粒体D-loop区全序列比较分析了中国连云港(LYG)、大丰(DF)、崇明(CM)、舟山(ZS)、温州(WZ)、宁德(ND)、厦门(XM)棘头梅童鱼7个野生群体的遗传结构特征。7个群体共208个样本的D-loop序列中,共检测到83种单倍型,66个变异位点,碱基组成符合AT碱基偏好性特点。7个群体的单倍型多样性为(0.55400±0.00998)～(0.95400±0.00067),核苷酸多样性为0.00183～0.00708,说明我国沿海棘头梅童鱼遗传多样性较高;根据海洋鱼类遗传多样性划分的分布模式,符合高h低π特点,说明其经历了快速扩张期。群体总的遗传分化系数Fst=0.86647 (P=0),两两群体间的遗传距离在0.004～0.039范围内,且明显的分为北方群体(LYG、DF、CM和ZS)和南方群体(WZ、ND和XM),DF和LYG、WZ和ND两两群体间存在显著的基因交流。AMOVA分析显示组间变异百分比为85.97%,符合南北分化特点。基于单倍型构建的单倍型邻接关系树和单倍型简约网络图等结果均表明,棘头梅童鱼以舟山为界,具有明显的南北地理遗传结构。中性检验(Tajima’s D、Fu’s Fs)和错配分析结果显示,棘头梅童鱼在3.87～12.9万年前(更新世冰期)经历了种群的规模性扩张或定向选择。本研究结果可为棘头梅童鱼资源的保护与利用提供基础数据。
Collichthys lucidus is an important economic species,widely distributed in the coastal waters of China,including the Yellow Sea,the East China Sea and the South China Sea. In order to evaluate the population structure of C. lucidus,we analyzed the genetic variation of mitochondrial DNA D-loop region among 7 wild populations(Lian Yungang,Dafeng,Chongming,Zhoushan,Ningde,Xiamen and Wenzhou)of C. lucidus. By using PCR amplification and sequencing,795 bp of D-loop sequences were obtained. A total of 83 haplotypes and 66 variable sites were detected in all 208 C. lucidus individuals,no shared haplotype was found and its overall base composition was in accordance with the structural characteristics of rich AT. The haplotype diversity and nucleotide diversity of the 7 populations ranged from(0.55400 ± 0.00998) to(0.95400 ± 0.00067) and 0.00183 to 0.00708,respectively,it showed that its genetic diversity was high. The Fstvalue of the total populations was 0.86647(P = 0),and genetic distance between every two populations ranged from 0.004 to 0.039. AMOVA showed that the percentage of variation is 85.97%. Fst,Nm,genetic distance,AMOVA,haplotype adjacency tree and haplotype network all showed that C. lucidus had obvious geographic genetic structure,was divided into north groups(Lian Yungang,Chongming,Dafeng,Zhoushan) and south(Wenzhou,Ningde and Xiamen group). The neutrality test(Tajima's D,Fu's Fs) and mismatch distribution analysis both showed that all 7 C. lucidus populations were not at equilibrium and were under an expansion phase. Our results could be beneficial to the conservation and use of C. lucidus resources.
Collichthys lucidus is an important economic species,widely distributed in the coastal waters of China,including the Yellow Sea,the East China Sea and the South China Sea. In order to evaluate the population structure of C. lucidus,we analyzed the genetic variation of mitochondrial DNA D-loop region among 7 wild populations(Lian Yungang,Dafeng,Chongming,Zhoushan,Ningde,Xiamen and Wenzhou)of C. lucidus. By using PCR amplification and sequencing,795 bp of D-loop sequences were obtained. A total of 83 haplotypes and 66 variable sites were detected in all 208 C. lucidus individuals,no shared haplotype was found and its overall base composition was in accordance with the structural characteristics of rich AT. The haplotype diversity and nucleotide diversity of the 7 populations ranged from(0.55400 ± 0.00998) to(0.95400 ± 0.00067) and 0.00183 to 0.00708,respectively,it showed that its genetic diversity was high. The Fstvalue of the total populations was 0.86647(P = 0),and genetic distance between every two populations ranged from 0.004 to 0.039. AMOVA showed that the percentage of variation is 85.97%. Fst,Nm,genetic distance,AMOVA,haplotype adjacency tree and haplotype network all showed that C. lucidus had obvious geographic genetic structure,was divided into north groups(Lian Yungang,Chongming,Dafeng,Zhoushan) and south(Wenzhou,Ningde and Xiamen group). The neutrality test(Tajima's D,Fu's Fs) and mismatch distribution analysis both showed that all 7 C. lucidus populations were not at equilibrium and were under an expansion phase. Our results could be beneficial to the conservation and use of C. lucidus resources.
引文
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[13]KUMAR S,DUDLEY J,NEI M,et al.MEGA:Abiologist-centric software for evolutionary analysis of DNA and protein sequences[J].Briefings in Bioinformatics,2008(9):299-306.
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[15]EXCOFFIER L,LAVALl G,SCHNEIDER S.Arlequin Ver.3.1:An integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2005(1):47-50.
[16]郑连明,林元烧,李少菁,等.台湾海峡多管水母属---新种及基于线粒体COI序列分析鉴定多管水母[J].海洋学报,2008,30(4):139-146.ZHENG L M,LIN Y S,LIi S J,et al.Morphological and molecular evidences of Aequorea taiwanensis sp.from Taiwan Strait,with mt COIsequence analysis for genus Aequorea[J].Acta Oceanologica Sinica,2008,30(4):139-146.
[17]邹方振,郝家胜,黄敦元,等.基于线粒体ND1和16S rRNA基因序列探讨中国蝴蝶12科的系统发育关系(鳞翅目:双孔次亚目:蝶类)[J].昆虫学报,2009,52(2):191-201.ZOU F Z,HE J S,HUANG D Y,et al.Molecular phylogeny of 12 families of the Chinese butterflies based on mitochondrial ND1 and 16S rRNA gene sequences(Lepidoptera:Ditrysia;Rhopalocera)[J].Acta Entomologica Sinica,2009,52(2):191-201.
[18]张红艳.中国鱚群体形态学及遗传学研究[D].上海:上海海洋大学,2013.ZHANG H Y.Study on morphology and genetic of Sillago sinica[D].Shanghai:Shanghai Ocean University,2013.
[19]彭婧煜.岛屿猕猴种群遗传结构和分子系统地理学研究[D].广州:华南师范大学,2010.PENG J Y.Population genetic structure and molecular phylogeography of Macaca mulatta[D].Guangzhou:South China Normal University,2010.
[20]BROWN G G,GADALTTA G,PEPE G,et al.Structural conservation and variation in the D-loopcontaining region of vertebrate mitochondrial DNA[J].Journal of Molecular Biology,1986,192(3):503-511.
[21]赵峰,庄平,章龙珍,等.基于线粒体Cytb基因的黄海南部和东海银鲳群体遗传结构分析[J].水生生物学报,2011,35(5):745-752.ZHAO F,ZHUANG P,ZHANG L Z,et al.Populations genetic structure of Pampus argenteus in the south Yellow sea and East China sea based on the mitochondrial Cytb sequence[J].Acta Hydrobiologica Sinica,2011,35(5):745-752.
[22]GRANT W,BOWEN B W.Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89:415-426.
[23]刘博,匡友谊,佟广香,等.微卫星分析9个哲罗鱼野生群体的遗传多样性[J].动物学研究,2011,32(6):597-604.LIU B,KUANG Y Y,TONG G X,et al.Analysis of genetic diversity on 9 wild stocks of Taimen(Hucho taimen)by microsatellite markers J].Zoological Research,2011,32(6):597-604.
[24]刘汝.三疣梭子蟹微卫星文库的构建及多态性位点筛选[D].上海:上海海洋大学,2010.LIU R.Microsatellite library construction and polymorphic loci screening for the swimming crab,Portunus trituberculatus[D].Shanghai:Shanghai Ocean University,2010.
[25]CHAKRABORTY R,DANKER-HOPFE H.Analysis of population structure:A comparative study of different estimators of wright’s fixation indices[J].Handbook of Statistics,1991(8):203-254.
[26]王长忠.长江中下游地区克氏原螯虾群体遗传多样性分析[D].武汉:华中农业大学,2009.WANG C Z.Assessment of 6 wild crayfish for evaluation of genetic diversity in the middle and lower reaches of the Yangtze River[D].Wuhan:Huazhong Agricultural University,2009.
[27]WRIGHT S.Evolution in mendelian populations[J].Genetics,1931(16):97-159.
[28]赵明,宋炜,马春艳,等.基于线粒体COI基因序列的棘头梅童鱼7个野生群体遗传结构分析[J].中国水产科学,2015,22(2):233-242.ZHAO M,SONG W,MA C Y,et al.Population genetic structure of Collichthys lucidus based on the mitochondrial cytochrome oxidase subunit 1 sequence[J].Journal of Fishery Sciences of China,2015,22(2):233-242.
[29]郑德锋,赵金良,周文玉,等.我国沿海棘头梅童鱼群体遗传结构的AFLP分析[J].海洋与湖沼,2011,42(3):443-447.ZHENG D F,ZHAO J L,ZHOU W Y,et al.Genetic structure of Collichthys lucidus populations from China coastal areas by AFLP analysis[J].Oceanologia et Limnologia Sinica,2011,42(3):443-447.
[30]梁述章,宋炜,赵明,等.黄海、东海近海七个棘头梅童鱼地理群体的形态差异分析[J].中国水产科学,2018,25(3):576-585.LIANG S Z,SONG W,ZHAO M,et al.Morphology of seven Collichthys lucidus populations near the coast of the Yellow Sea and East China Sea[J].Journal of Fishery Sciences of China,2018,25(3):576-585.
[31]MACHADO-S G,GARCIA-V E.Isolation and characterization of microsatellite loci in Merluccius australis and cross-species amplification[J].Molecular Ecology Resources,2009,9(2):585-587.
[32]谢起浪,单乐州,王铁杆,等.浙南飞云江口棘头梅童鱼的资源调查和研究[J].渔业现代化,2006(1):35-36.XIE Q L,SHAN L Z,WANG T G,et al.Resource survey and research of Collichthys lucidus of Feiyunjiang Estuary in north of Zhejiang[J].Fishery Modernization,2006(1):35-36.
[2]CHEN W,SONG W,CHEN F F,et al.Development and characterization of SNP derived from spinyhead croaker(Collichthys lucidus)by RNA-seq[J].Conservation Genetics Resources,2017,Suppl(1):1-5.
[3]朱元鼎,伍汉霖.东海鱼类志[M].北京:科学出版社,1963:286-293.ZHU Y D,WU H L.Fishes annals of East China Sea[M].Beijing:Science Press,1963:286-293.
[4]吴常文,王伟宏.浙江近海棘头梅童鱼的分布生物学与资源变动[J].海洋渔业,1991,13(1):6-10.WU C W,WANG W H.The biology distribution and resources changes of Collichthys lucidus in Zhejiang offshore[J].Marine Fishery,1991,13(1):6-10.
[5]宋炜,孟永永,蒋科技,等.棘头梅童鱼七个野生群体遗传多样性的微卫星分析[J].水产学报,2017,41(1):31-39.SONG W,MENG Y Y,JIANG K J,et al.Analysis of genetic diversity among seven wild Collichthys lucidus populations by using microsatellite marker[J].Journal of Fisheries of China,2017,41(1):31-39.
[6]BROWN W M,GEORGE M,WILSON A C.Rapid evolution of animal mitochondrial-DNA[J].Proceedings of the National Academy of Sciences of the United States of America,1979(76):1967-1971.
[7]吕金磊,章群,杨喜书,等.基于线粒体控制区的中国南海海域卵形鲳鯵遗传多样性[J].海洋渔业,2017,39(3):241-248.LV J L,ZHANG Q,YANG X S,et al.Genetic diversity of Trachinotus ovatus in the South China Sea inferred from Mitochondrial DNA control region sequences[J].Marine Fisheries,2017,39(3):241-248.
[8]LUO Y,YANG X,GAO Y.Mitochondrial DNAresponse to high altitude:A new perspective on highaltitude adaptation[J].Mitochondrial DNA,2013(24):313-319.
[9]肖武汉,张亚平.鱼类线粒体DNA的遗传与进化[J].水生生物学报,2000,24(4):384-391.XIAO W H,ZHANG Y P.Genetics and evolution of mitochondrial DNA in fish[J].Acta Hydrobiologica Sinica,2000,24(4):384-391.
[10]谢振宇,杜继曾,陈学群,等.线粒体控制区在鱼类种内遗传分化中的意义[J].遗传,2006,28(3):362-368.XIE Z Y,DU J Z,CHEN X Q,et al.The significance of mitochondria control region(D-Loop)in intraspecific genetic differentiation of Fish[J].Hereditas,2006,28(3):362-368.
[11]郑德峰,赵金良,周文玉.棘头梅童鱼线粒体控制区的序列变异与群体遗传结构[J].渔业科学进展,2011,32(3):34-40.ZHENG D F,ZHAO J L,ZHOU W Y.mt DNAcontrol region sequence variation and genetic structure of Collichthys lucidus populations[J].Progress in Fishery Sciences,2011,32(3):34-40.
[12]殷丽娜.棘头梅童鱼的遗传多样性与种群遗传结构研究[D].青岛:中国海洋大学,2013.YIN L N.studies on genetic diversity and population structure of Collichthys lucidus[D].Qingdao:Ocean University of China,2013.
[13]KUMAR S,DUDLEY J,NEI M,et al.MEGA:Abiologist-centric software for evolutionary analysis of DNA and protein sequences[J].Briefings in Bioinformatics,2008(9):299-306.
[14]ROZAS J,SANCHEZ-DELBARRIO J C,MESSENGUERX,et al.DNA polymorphism analysis by the coalescent and other methods[J].Bioinformatics,2003(19):2496-2497.
[15]EXCOFFIER L,LAVALl G,SCHNEIDER S.Arlequin Ver.3.1:An integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2005(1):47-50.
[16]郑连明,林元烧,李少菁,等.台湾海峡多管水母属---新种及基于线粒体COI序列分析鉴定多管水母[J].海洋学报,2008,30(4):139-146.ZHENG L M,LIN Y S,LIi S J,et al.Morphological and molecular evidences of Aequorea taiwanensis sp.from Taiwan Strait,with mt COIsequence analysis for genus Aequorea[J].Acta Oceanologica Sinica,2008,30(4):139-146.
[17]邹方振,郝家胜,黄敦元,等.基于线粒体ND1和16S rRNA基因序列探讨中国蝴蝶12科的系统发育关系(鳞翅目:双孔次亚目:蝶类)[J].昆虫学报,2009,52(2):191-201.ZOU F Z,HE J S,HUANG D Y,et al.Molecular phylogeny of 12 families of the Chinese butterflies based on mitochondrial ND1 and 16S rRNA gene sequences(Lepidoptera:Ditrysia;Rhopalocera)[J].Acta Entomologica Sinica,2009,52(2):191-201.
[18]张红艳.中国鱚群体形态学及遗传学研究[D].上海:上海海洋大学,2013.ZHANG H Y.Study on morphology and genetic of Sillago sinica[D].Shanghai:Shanghai Ocean University,2013.
[19]彭婧煜.岛屿猕猴种群遗传结构和分子系统地理学研究[D].广州:华南师范大学,2010.PENG J Y.Population genetic structure and molecular phylogeography of Macaca mulatta[D].Guangzhou:South China Normal University,2010.
[20]BROWN G G,GADALTTA G,PEPE G,et al.Structural conservation and variation in the D-loopcontaining region of vertebrate mitochondrial DNA[J].Journal of Molecular Biology,1986,192(3):503-511.
[21]赵峰,庄平,章龙珍,等.基于线粒体Cytb基因的黄海南部和东海银鲳群体遗传结构分析[J].水生生物学报,2011,35(5):745-752.ZHAO F,ZHUANG P,ZHANG L Z,et al.Populations genetic structure of Pampus argenteus in the south Yellow sea and East China sea based on the mitochondrial Cytb sequence[J].Acta Hydrobiologica Sinica,2011,35(5):745-752.
[22]GRANT W,BOWEN B W.Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation[J].Journal of Heredity,1998,89:415-426.
[23]刘博,匡友谊,佟广香,等.微卫星分析9个哲罗鱼野生群体的遗传多样性[J].动物学研究,2011,32(6):597-604.LIU B,KUANG Y Y,TONG G X,et al.Analysis of genetic diversity on 9 wild stocks of Taimen(Hucho taimen)by microsatellite markers J].Zoological Research,2011,32(6):597-604.
[24]刘汝.三疣梭子蟹微卫星文库的构建及多态性位点筛选[D].上海:上海海洋大学,2010.LIU R.Microsatellite library construction and polymorphic loci screening for the swimming crab,Portunus trituberculatus[D].Shanghai:Shanghai Ocean University,2010.
[25]CHAKRABORTY R,DANKER-HOPFE H.Analysis of population structure:A comparative study of different estimators of wright’s fixation indices[J].Handbook of Statistics,1991(8):203-254.
[26]王长忠.长江中下游地区克氏原螯虾群体遗传多样性分析[D].武汉:华中农业大学,2009.WANG C Z.Assessment of 6 wild crayfish for evaluation of genetic diversity in the middle and lower reaches of the Yangtze River[D].Wuhan:Huazhong Agricultural University,2009.
[27]WRIGHT S.Evolution in mendelian populations[J].Genetics,1931(16):97-159.
[28]赵明,宋炜,马春艳,等.基于线粒体COI基因序列的棘头梅童鱼7个野生群体遗传结构分析[J].中国水产科学,2015,22(2):233-242.ZHAO M,SONG W,MA C Y,et al.Population genetic structure of Collichthys lucidus based on the mitochondrial cytochrome oxidase subunit 1 sequence[J].Journal of Fishery Sciences of China,2015,22(2):233-242.
[29]郑德锋,赵金良,周文玉,等.我国沿海棘头梅童鱼群体遗传结构的AFLP分析[J].海洋与湖沼,2011,42(3):443-447.ZHENG D F,ZHAO J L,ZHOU W Y,et al.Genetic structure of Collichthys lucidus populations from China coastal areas by AFLP analysis[J].Oceanologia et Limnologia Sinica,2011,42(3):443-447.
[30]梁述章,宋炜,赵明,等.黄海、东海近海七个棘头梅童鱼地理群体的形态差异分析[J].中国水产科学,2018,25(3):576-585.LIANG S Z,SONG W,ZHAO M,et al.Morphology of seven Collichthys lucidus populations near the coast of the Yellow Sea and East China Sea[J].Journal of Fishery Sciences of China,2018,25(3):576-585.
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[32]谢起浪,单乐州,王铁杆,等.浙南飞云江口棘头梅童鱼的资源调查和研究[J].渔业现代化,2006(1):35-36.XIE Q L,SHAN L Z,WANG T G,et al.Resource survey and research of Collichthys lucidus of Feiyunjiang Estuary in north of Zhejiang[J].Fishery Modernization,2006(1):35-36.
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