基于mtDNA控制区序列的3个黑棘鲷群体遗传结构特性研究
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摘要
本研究通过控制区序列片段,分析来源于浙江东极(DJ)、广东澳头(AT)及海南万宁(WN)海域3个黑棘鲷Acanthopagrus schlegelii野生群体间的遗传多样性、遗传结构及群体历史动态。D-loop基因序列测定结果表明,3个群体88个个体长序列长度范围为715~716bp,共定义了59个单倍型,单倍型多样性0.949~0.985,核苷酸多样性0.0068~0.00901,表明选取的3个野生群体都具有较高的遗传多样性水平;由AMOVA分析结果可以看出,东极与澳头2个群体的遗传分化较为明显,其余群体间则无明显的遗传分化;构建的单倍型邻接关系树显示出3个群体未有明显的谱系结构,从而支持了可将黑棘鲷南方群体归为同一个管理单元的观点;中性检验及核苷酸不配对分布表明黑棘鲷经历过更新世晚期的群体扩张事件。地理历史事件、海流及人工增殖放流的影响可能是黑棘鲷各群体现有的遗传多样性和遗传结构的主要原因。
In order to elucidate background information on the genetic diversity and population history of Acanthopagrus schlegelii, the genetic diversity, population genetic structure and demographic history of Dongji stock, Aotou stock and Wanning stock of the black porgy were analyzed based on the control region fragment of mitochondrial DNA in this study. The results showed that the sequences of 88 individuals of the three stocks were 715~716 bp in length and that there were 59 haplotypes. The value of haplotype diversity ranged from 0.949 to 0.985 and the nucleotide diversity, from 0.0068 to 0.00901. These results indicated that the three wild stocks presented a high level of genetic diversity. Significant population differentiation was detected for the two populations of Dongji stock and Aotou stock, while there was no significant genetic differentiation between Dongji stock and Wanning stock as well as between Aotou stock and Wanning stock. In addition, no obvious lineages and geographic clusters were found in the neighbor-joining tree, which supported the notion that unique management unit(MU) was recognized on the basis of the southern populations. Both neutrality tests and mismatch distribution analysis suggested a late Pleistocene population expansion for the three stocks. The genetic diversity and population genetic structure revealed were attributed to the absence of geographic barrier, influence of sea currents and human activities.
In order to elucidate background information on the genetic diversity and population history of Acanthopagrus schlegelii, the genetic diversity, population genetic structure and demographic history of Dongji stock, Aotou stock and Wanning stock of the black porgy were analyzed based on the control region fragment of mitochondrial DNA in this study. The results showed that the sequences of 88 individuals of the three stocks were 715~716 bp in length and that there were 59 haplotypes. The value of haplotype diversity ranged from 0.949 to 0.985 and the nucleotide diversity, from 0.0068 to 0.00901. These results indicated that the three wild stocks presented a high level of genetic diversity. Significant population differentiation was detected for the two populations of Dongji stock and Aotou stock, while there was no significant genetic differentiation between Dongji stock and Wanning stock as well as between Aotou stock and Wanning stock. In addition, no obvious lineages and geographic clusters were found in the neighbor-joining tree, which supported the notion that unique management unit(MU) was recognized on the basis of the southern populations. Both neutrality tests and mismatch distribution analysis suggested a late Pleistocene population expansion for the three stocks. The genetic diversity and population genetic structure revealed were attributed to the absence of geographic barrier, influence of sea currents and human activities.
引文
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萨姆布鲁克,拉塞尔.2002.分子克隆实验指南[M].北京:科学出版社:463–470.
史洁蔷.2008.长江流域两种新银鱼分子生态学初步研究[D].北京:首都师范大学:71.
孙冬芳,董丽娜,李永振,等.2010.南海北部海域多齿蛇鲻的种群分析[J].水产学报,9(34):1387–1394.
吴常文,许逸天,吕振明,等.2009.基于D-LOOP基因的中国沿海鳓鱼(Ilisha elongata)种群遗传结构研究[J].海洋与湖沼,40(3):330–337.
吴惠仙,徐雪娜,薛俊增,等.2009.中国沿海三疣梭子蟹的遗传结构和亲缘关系分析[J].海洋学研究,27(3):48–53.
吴仁协,刘静,樊冀蓉,等.2011.黑棘鲷的命名和分类地位探究[J].海洋科学,35(5):117–119.
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杨慧荣,江世贵,周发林,等.2004.3个不同地理群体黑鲷遗传变异的RAPD分析[J].中国水产科学,11(3):185–189.
姚玉鹏,刘羽.2010.第四纪作为地质年代和地层单位的国际争议与最终确立[J].地球科学进展,25(7):775–781.
郑德锋,赵金良,周文玉.2011.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,32(2):34–40.
仲雷.2007.海水池塘养殖黑鲷技术简介[J].齐鲁渔业,24(11):12.
朱爱意,谢佳彦,章韶兵.2007.黑鲷耗氧率昼夜变化及与体重、水温的关系研究[J].南方水产,3(6):63–66.
朱叶,章群,李贵生,等.2012.中国近海角木叶鲽(Pleuronichthyscornutus)种群遗传多样性研究[J].海洋通报,31(5):552–556.
朱元鼎.1985.福建鱼类志[M].福州:福建科学技术出版社:1023–1025.
庄平,王幼槐,李圣法.2006.长江口鱼类[M].上海:上海科学技术出版社:217–218.
赵爽,章群,乐小亮,等.2010.中国近海5个黑鲷地理群体的遗传变异[J].海洋科学,34(2):75–79.
EXCOFFIER L,LAVAL G,SCHNEIDER S.2005.Arlequin(version 3.0):An integrated software package for populationgenetics data analysis[J].Evol Bio OL,1:47–50.
FU YUNXIN.1997.Statistical tests of neutrality of mutationsagainst population growth,hitchhiking and backgroundselection[J].Genetics,147(2):915–925.
GRANT W S,BOWEN B W.1998.Shallow population histories indeep evolutionary lineages of marine fishes:insights fromsardines and anchovies and lessons for conservation[J].JHered,89(5):415–426.
HEWITT G M.1996.Some genetic consequences of ice ages,andtheir role in divergence and speciation[J].Biol J Linn Soc,58(3):247–276.
HWANG J S,WONG C K.2005.The China Coastal Current as adriving force for transporting Calanus sinicus(Copepoda:Calanoida)from its population centers to waters off Taiwanand Hong Kong during the winter northeast monsoonperiod[J].J Plankton Res,27(2):205–210.
JEAN CHUENTAN,LEE SINCHE,CHEN CHETSUNG,et al.1998.Variation in mitochondrial DNA sequences of blackporgy,Acanthopagrus schlegeli,in the Coastal Waters ofTaiwan[J].Zool Stud,37(1):22–30.
KUMAR S,NEI M,DUDLEY J,et al.2008.MEGA:abiologist-centric software for evolutionary analysis of DNAand protein sequences[J].Brief Bioinform,9(4):299–306.
LECOMTE F,GRANT W S,DODSON J J,et al.2004.Livingwith uncertainty:genetic imprints of climate shifts in EastPacific anchovy(Engraulis mordax)and sardine(Sardinopssagax)[J].Mol Ecol,13(8):2169–2182.
LEE W J,CONROY J,HOWELL W H,et al.1995.Structure andevolution of teleost mitochondrial control regions[J].J MolEvol,41(1):54–66.
PENG SHI-MING,SHI ZHAO-HONG,HOU JUN-LI,et al.2009.Genetic diversity of silver pomfret(Pampus argenteus)populations from the China Sea based on mitochondrial DNAcontrol region sequences[J].Biochem Syst Ecol,37(5):626–632.
ROZAS J,SáNCHEZ-DELBARRIO J C,MESSEGUER X,et al.2003.DnaS P,DNA polymorphism analyses by the coalescentand other methods[J].Bioinformatics,19(18):2496–2497.
SIMON C,BUCKLEY T R,FRATI F,et al.2006.Incorporatingmolecular evolution into phylogenetic analysis,and a newcompilation of conserved polymerase chain reaction primersfor animal mitochondrial DNA[J].Annu Rev Ecol Evol Syst,37:545–579.
TAJIMA F.1989.Statistical method for testing the neutralmutation hypothesis by DNA polymorphism[J].Genetics,123(3):585–595.
THOMPSON J D,GIBSON T J,PLEWNIAK F,et al.1997.TheCLUSTAL_X windows interface:flexible strategies formultiple sequence alignment aided by quality analysis tools[J]Nucleic Acids Res,25(24):4876–4882.
ZENG LIYAN,CHENG QIQUN,CHEN XIAOYONG.2012.Microsatellite analysis reveals the population structure andmigration patterns of Scomber japonicas(Scombridae)withcontinuous distribution in the East and South China Seas[J].Biochem Syst Ecol,42:83–93.
龚金波,苏天凤,夏军红,等.2006.中国近海黑鲷线粒体DNA控制区序列多态性分析[J].南方水产,2(4):24–30.
蒋宏雷,吴雄飞,石刚德,等.2007.真鲷与黑鲷杂交子一代的胚胎发育[J].河北渔业,14(2):40–42.
乐小亮,章群,赵爽,等.2010.中国近海真鲷遗传变异的线粒体控制区序列分析[J].广东农业科学,31(2):136–139.
李乃胜,赵松龄,瓦西里耶夫.2000.西北太平洋边缘海地质[M].哈尔滨:黑龙江教育出版社:435–446.
李成俊,骆振福,邓群,等.2010.地学时间单位Ma和Myr及其派生单位用法的探讨[J].煤田地质与勘探,38(2):79–80.
梁君,王伟定,林桂装,等.2010.浙江舟山人工生境水域日本黄姑鱼和黑鲷的增殖放流效果及评估[J].中国水产科学,17(5):1075–1084.
牛素芳,苏永全,王军,等.2012a.福建近海蓝圆鲹群体遗传结构分析[J].厦门大学学报:自然科学版,51(4):759–766.
牛素芳,苏永全,钟声平,等.2012b.福建近海2个鮐鱼群体遗传结构与遗传多样性分析[J].台湾海峡,31(4):509–516.
萨姆布鲁克,拉塞尔.2002.分子克隆实验指南[M].北京:科学出版社:463–470.
史洁蔷.2008.长江流域两种新银鱼分子生态学初步研究[D].北京:首都师范大学:71.
孙冬芳,董丽娜,李永振,等.2010.南海北部海域多齿蛇鲻的种群分析[J].水产学报,9(34):1387–1394.
吴常文,许逸天,吕振明,等.2009.基于D-LOOP基因的中国沿海鳓鱼(Ilisha elongata)种群遗传结构研究[J].海洋与湖沼,40(3):330–337.
吴惠仙,徐雪娜,薛俊增,等.2009.中国沿海三疣梭子蟹的遗传结构和亲缘关系分析[J].海洋学研究,27(3):48–53.
吴仁协,刘静,樊冀蓉,等.2011.黑棘鲷的命名和分类地位探究[J].海洋科学,35(5):117–119.
许思思.2011.人为影响下渤海渔业资源的衰退机制[D].青岛:中国科学院研究生院(海洋研究所):149.
杨慧荣,江世贵,周发林,等.2004.3个不同地理群体黑鲷遗传变异的RAPD分析[J].中国水产科学,11(3):185–189.
姚玉鹏,刘羽.2010.第四纪作为地质年代和地层单位的国际争议与最终确立[J].地球科学进展,25(7):775–781.
郑德锋,赵金良,周文玉.2011.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,32(2):34–40.
仲雷.2007.海水池塘养殖黑鲷技术简介[J].齐鲁渔业,24(11):12.
朱爱意,谢佳彦,章韶兵.2007.黑鲷耗氧率昼夜变化及与体重、水温的关系研究[J].南方水产,3(6):63–66.
朱叶,章群,李贵生,等.2012.中国近海角木叶鲽(Pleuronichthyscornutus)种群遗传多样性研究[J].海洋通报,31(5):552–556.
朱元鼎.1985.福建鱼类志[M].福州:福建科学技术出版社:1023–1025.
庄平,王幼槐,李圣法.2006.长江口鱼类[M].上海:上海科学技术出版社:217–218.
赵爽,章群,乐小亮,等.2010.中国近海5个黑鲷地理群体的遗传变异[J].海洋科学,34(2):75–79.
EXCOFFIER L,LAVAL G,SCHNEIDER S.2005.Arlequin(version 3.0):An integrated software package for populationgenetics data analysis[J].Evol Bio OL,1:47–50.
FU YUNXIN.1997.Statistical tests of neutrality of mutationsagainst population growth,hitchhiking and backgroundselection[J].Genetics,147(2):915–925.
GRANT W S,BOWEN B W.1998.Shallow population histories indeep evolutionary lineages of marine fishes:insights fromsardines and anchovies and lessons for conservation[J].JHered,89(5):415–426.
HEWITT G M.1996.Some genetic consequences of ice ages,andtheir role in divergence and speciation[J].Biol J Linn Soc,58(3):247–276.
HWANG J S,WONG C K.2005.The China Coastal Current as adriving force for transporting Calanus sinicus(Copepoda:Calanoida)from its population centers to waters off Taiwanand Hong Kong during the winter northeast monsoonperiod[J].J Plankton Res,27(2):205–210.
JEAN CHUENTAN,LEE SINCHE,CHEN CHETSUNG,et al.1998.Variation in mitochondrial DNA sequences of blackporgy,Acanthopagrus schlegeli,in the Coastal Waters ofTaiwan[J].Zool Stud,37(1):22–30.
KUMAR S,NEI M,DUDLEY J,et al.2008.MEGA:abiologist-centric software for evolutionary analysis of DNAand protein sequences[J].Brief Bioinform,9(4):299–306.
LECOMTE F,GRANT W S,DODSON J J,et al.2004.Livingwith uncertainty:genetic imprints of climate shifts in EastPacific anchovy(Engraulis mordax)and sardine(Sardinopssagax)[J].Mol Ecol,13(8):2169–2182.
LEE W J,CONROY J,HOWELL W H,et al.1995.Structure andevolution of teleost mitochondrial control regions[J].J MolEvol,41(1):54–66.
PENG SHI-MING,SHI ZHAO-HONG,HOU JUN-LI,et al.2009.Genetic diversity of silver pomfret(Pampus argenteus)populations from the China Sea based on mitochondrial DNAcontrol region sequences[J].Biochem Syst Ecol,37(5):626–632.
ROZAS J,SáNCHEZ-DELBARRIO J C,MESSEGUER X,et al.2003.DnaS P,DNA polymorphism analyses by the coalescentand other methods[J].Bioinformatics,19(18):2496–2497.
SIMON C,BUCKLEY T R,FRATI F,et al.2006.Incorporatingmolecular evolution into phylogenetic analysis,and a newcompilation of conserved polymerase chain reaction primersfor animal mitochondrial DNA[J].Annu Rev Ecol Evol Syst,37:545–579.
TAJIMA F.1989.Statistical method for testing the neutralmutation hypothesis by DNA polymorphism[J].Genetics,123(3):585–595.
THOMPSON J D,GIBSON T J,PLEWNIAK F,et al.1997.TheCLUSTAL_X windows interface:flexible strategies formultiple sequence alignment aided by quality analysis tools[J]Nucleic Acids Res,25(24):4876–4882.
ZENG LIYAN,CHENG QIQUN,CHEN XIAOYONG.2012.Microsatellite analysis reveals the population structure andmigration patterns of Scomber japonicas(Scombridae)withcontinuous distribution in the East and South China Seas[J].Biochem Syst Ecol,42:83–93.
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