基于线粒体COⅠ序列的南海北部栉江珧遗传多样性分析
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摘要
为了解南海栉江珧(Atrina pectinata)的群体遗传变异特征,研究利用线粒体DNA COⅠ(细胞色素氧化酶亚单位Ⅰ)基因部分序列对7个群体共191个栉江珧个体进行群体遗传多样性和遗传结构分析。结果显示:在600 bp长的序列中,共检测到113个核苷酸变异位点,定义了73个单倍型。南海北部栉江珧总体呈现较高的单倍型多样性(0.8996)和较高的核苷酸多样性(0.0257),但L1组内6个群体(汕头、阳江、湛江、海口、琼海、北海)呈现较高的单倍型多样性(0.8133—0.9286)和较低的核苷酸多样性(0.0033—0.0045)。单倍型系统发育树和网络支系图将7个群体划分为L1和L2(防城港群体)两大类群,但L1组单倍型并未表现出与地理位置相对应的谱系结构。F_(st)分析显示, L1组内6个群体间不存在明显的遗传分化(F_(st)=–0.0200—–0.0055, P>0.05),但L1组与L2组间存在极显著的遗传分化(F_(st)=0.8729—0.8821, P<0.01)。L1组的Tajima’s D检验(D=–2.3190, P=0)和Fu’s F_s检验(F_s=–26.8316, P=0)均为显著负值,核苷酸不配对分布呈明显的单峰分布; L2组的Tajima’s D检验(D=–1.4320, P=0.0565)为不显著负值, Fu’s F_s检验(F_s=4.9540, P=0.9620)为不显著正值。以上数据说明, L1组和L2组栉江珧可能已经分化为两个群体, L1组内6个群体具有频繁的基因交流,导致了较高的遗传同质性。
Atrina pectinata is a commercially important species in the Northern South China Sea. This study analzyed genetic diversity and genetic structure of A. pectinata in Northern South China Sea based on 191 individuals of 7 populations using Cytochrome Oxidase Ⅰ(COⅠ) sequence. A 600 bp segment of COⅠ genes were sequenced, from which113 polymorphic sites were tested and 73 haplotypes were defined. The total population in Northern South China Sea had high haplotype diversity(0.8996) and high nucleotide diversity(0.0257). However, 6 populations in L1 group(ST,YJ, ZJ, HK, QH, BH) had high haplotype diversity(0.8133—0.9286) and low nucleotide diversity(0.0033—0.0045).Based on neighbor-joining tree and haplotype network, 7 populations were classified into two groups, named L1 group and L2 group(FCG), and no clustering corresponding to sampling localities was found in L1 group haplotypes. Fst analysis showed no obvious genetic differentiation among 6 populations in L1 group(F_(st)= –0.0200— –0.0055, P>0.05)and significant genetic differentiation between L1 group and L2 group(F_(st)=0.8729—0.8821, P<0.01). Both Tajima's D(D= –2.3190, P=0) and Fu's Fs(F_s= –26.7990, P=0) of L1 group yielded significant negative values. Unimodal distribution was observed in L1 group. However, in L2 group, Tajima's D(D= –1.4320, P=0.0565) was insignificant negative value, and Fu's Fs(F_s=4.9540, P=0.9620) was insignificant positive value. These data implied L1 group and L2 group might have differentiated into two populations. The frequent gene exchange resulted in high genetic homogeneity among 6 populations in L1 group.
Atrina pectinata is a commercially important species in the Northern South China Sea. This study analzyed genetic diversity and genetic structure of A. pectinata in Northern South China Sea based on 191 individuals of 7 populations using Cytochrome Oxidase Ⅰ(COⅠ) sequence. A 600 bp segment of COⅠ genes were sequenced, from which113 polymorphic sites were tested and 73 haplotypes were defined. The total population in Northern South China Sea had high haplotype diversity(0.8996) and high nucleotide diversity(0.0257). However, 6 populations in L1 group(ST,YJ, ZJ, HK, QH, BH) had high haplotype diversity(0.8133—0.9286) and low nucleotide diversity(0.0033—0.0045).Based on neighbor-joining tree and haplotype network, 7 populations were classified into two groups, named L1 group and L2 group(FCG), and no clustering corresponding to sampling localities was found in L1 group haplotypes. Fst analysis showed no obvious genetic differentiation among 6 populations in L1 group(F_(st)= –0.0200— –0.0055, P>0.05)and significant genetic differentiation between L1 group and L2 group(F_(st)=0.8729—0.8821, P<0.01). Both Tajima's D(D= –2.3190, P=0) and Fu's Fs(F_s= –26.7990, P=0) of L1 group yielded significant negative values. Unimodal distribution was observed in L1 group. However, in L2 group, Tajima's D(D= –1.4320, P=0.0565) was insignificant negative value, and Fu's Fs(F_s=4.9540, P=0.9620) was insignificant positive value. These data implied L1 group and L2 group might have differentiated into two populations. The frequent gene exchange resulted in high genetic homogeneity among 6 populations in L1 group.
引文
[1]Li M S.Identification of microsatellite markers and analysis of genetic diversity of Atrina pectinata[D].Thesis for Master of Science.Nanjing Agricultural University,Nanjing.2008[李明爽.栉江珧微卫星标记的筛选及其遗传多样性的研究.硕士学位论文,南京农业大学,南京.2008]
[2]Wang R C,Wang Z P.Science of Marine Shellfish Culture[M].Qingdao:China Ocean University Press.2008,532-534[王如才,王昭萍.海水贝类养殖学.青岛:中国海洋大学出版社.2008,532-534]
[3]Zhen Y X,Yang A G,Wu B,et al.Studies on the spawning inducement and the conditions for the larval culture of Atrina pectinata[J].Progress in Fishery Sciences,2015,36(6):127-133[郑言鑫,杨爱国,吴彪,等.栉江珧(Atrina pectinata)催产方法及幼虫培养条件.渔业科学进展,2015,36(6):127-133]
[4]Yan J K,Yang A G,Zhou L Q,et al.The genetic diversity and phylogenetic studies of five populations of Atrina pectinata[J].Progress in Fishery Sciences,2013,34(2):29-35[严加坤,杨爱国,周丽青,等.我国不同地理群体栉江珧遗传多样性及系统发生分析.渔业科学进展,2013,34(2):29-35]
[5]LüJ,Wu S,Zhang Y,et al.Assessment of four DNAfragments(COI,16S rDNA,ITS2,12S rDNA)for species identification of the Ixodida(Acari:Ixodida)[J].Parasit Vectors,2014,7:93
[6]Xue D X,Wang H Y,Zhang T,et al.Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers[J].PLoS One,2014,9(4):e95436
[7]Thompson J D,Gibson T J,Plewniak F,et al.The Clustal_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4876-4882
[8]Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452
[9]Excoffier L,Lischer H E L.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10(3):564-567
[10]Tamura K,Stecher G,Peterson D,et al.MEGA6:molecular evolutionary genetics analysis version 6.0[J].Molecular Biology and Evolution,2013,30(12):2725-2729
[11]Niu S F,Su Y Q,Wang J,et al.Genetic polymorphism of mitochondrial control region and cyt b in Trachurus japonicus from Fujian coastal waters[J].Journal of Fishery Sciences of China,2011,18(1):66-74[牛素芳,苏永全,王军,等.福建近海竹荚鱼线粒体DNA控制区和细胞色素b遗传多态性.中国水产科学,2011,18(1):66-74]
[12]Deng J Y,Zhao C Y,Tang Q S,et al.Marine Fisheries Biology[M].Beijing:Agriculture Press.1991,485-518[邓景耀,赵传絪,唐启升,等.海洋渔业生物学.北京:农业出版社.1991,485-518]
[13]Chen X,Yang S Y,Pan C.Genetic polymorphism of mitochondrial control region in Chiloscyllium plagiosum from coastal waters of southern China[J].Acta Oceanologica Sinica,2008,30(6):115-121[陈骁,杨圣云,潘聪.我国南部海域条纹斑竹鲨线粒体DNA控制区遗传多态性研究.海洋学报,2008,30(6):115-121]
[14]Grant W S,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(5):415-426
[15]Zhu Y X,Cheng Q Q,Rogers S M.Genetic structure of Scomber japonicus(Perciformes:Scombridae)along the coast of China revealed by complete mitochondrial cytochrome b sequences[J].Mitochondrial DNA Part A,2016,27(6):3828-3836
[16]He L J,Mukai T,Chu K H,et al.Biogeographical role of the Kuroshio current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data[J].Scientific Reports,2015,5:15645
[17]Hewitt G M.Some genetic consequences of ice ages,and their role in divergence and speciation[J].Biological Journal of the Linnean Society,1996,58(3):247-276
[18]Selkoe K,Toonen RJ.Marine connectivity:a new look at pelagic larval duration and genetic metrics of dispersal[J].Marine Ecology Progress Seriesm,2011,436:291-305
[19]Song N,Wang H N,Liu S D,et al.Genetic study on Sphyrna lewini from Qingdao coastal waters[J].Acta Hydrobiologica Sinica,2017,41(3):603-608[宋娜,王航宁,刘淑德,等.青岛近海路氏双髻鲨群体遗传学分析.水生生物学报,2017,41(3):603-608]
[20]Wang M F,Yu X Y,Ye F L.The gonad development of Pinna(Atrina)pectinata in Beibu Gulf and adjoining coast[J].Guangxi Sciences,2000,7(2):140-143,157[王梅芳,余祥勇,叶富良.北部湾及附近海域栉江珧性腺发育研究.广西科学,2000,7(2):140-143,157]
[21]Ge Q.Paleoenvironmental and Paleoclimatic records from the South China Sea since the late last glacical[D].Thesis for Master of Science.China University of Geosciences,Wuhan.2010[葛倩.晚末次冰期以来南海古环境和古气候记录.硕士学位论文,中国地质大学,武汉.2010]
[22]Qiao F L(Eds.),Regional Oceanography of China SeasPhysical Oceanography[M].Beijing:Ocean Press.2012,310-350[乔方利主编.中国区域海洋学-物理海洋学.北京:海洋出版社.2012,310-350]
[23]Claremont M,Williams S T,Barraclough T G,et al.The geographic scale of speciation in a marine snail with high dispersal potential[J].Journal of Biogeography,2011,38(6):1016-1032
[24]Wang Z R.Fauna Sinica,Phylum Mollusca,Order Mytiloida[M].Beijing:Science Press.1997,362[王祯瑞.中国动物志:软体动物门双壳纲贻贝目.北京:科学出版社.1997,362]
[25]An H S,Kim B H,Lee J W,et al.Comparison between wild and hatchery populations of Korean Pen Shell(Atrina pectinata)using microsatellite DNA markers[J].International Journal of Molecular Sciences,2011,12(9):6024-6039
[26]Liu J,Li Q,Kong L,et al.Cryptic diversity in the pen shell Atrina pectinata(Bivalvia:Pinnidae):high divergence and hybridization revealed by molecular and morphological data[J].Molecular Ecology,2011,20(20):4332-4345
[27]Chen G,Hare M P.Cryptic ecological diversification of a planktonic estuarine copepod,Acartia tonsa[J].Molecular Ecology,2008,17(6):1451-1468
[28]Zhao K,Duan Z Y,Peng Z G,et al.The youngest split in sympatric schizothoracine fish(Cyprinidae)is shaped by ecological adaptations in a Tibetan Plateau glacier lake[J].Molecular Ecology,2009,18(17):3616-3628
[29]Laegdsgaard P,Johnson C.Why do juvenile fish utilize mangrove habitats[J]?Journal of Experimental Marine Biology and Ecology,2001,257(2):229-253
[30]Meng Z N,Zhuang Z M,Jin X S,et al.Variation analysis of RAPD and mitochondrial DNA 16S rRNA sequence of Trichiurus japonicus and Eupleurogrammus muticus from the Yellow Sea[J].Progress in Natural Science,2003,13(11):1170-1176[蒙子宁,庄志猛,金显仕,等.黄海带鱼、小带鱼RAPD和线粒体16S rRNA基因序列变异分析.自然科学进展,2003,13(11):1170-1176]
[2]Wang R C,Wang Z P.Science of Marine Shellfish Culture[M].Qingdao:China Ocean University Press.2008,532-534[王如才,王昭萍.海水贝类养殖学.青岛:中国海洋大学出版社.2008,532-534]
[3]Zhen Y X,Yang A G,Wu B,et al.Studies on the spawning inducement and the conditions for the larval culture of Atrina pectinata[J].Progress in Fishery Sciences,2015,36(6):127-133[郑言鑫,杨爱国,吴彪,等.栉江珧(Atrina pectinata)催产方法及幼虫培养条件.渔业科学进展,2015,36(6):127-133]
[4]Yan J K,Yang A G,Zhou L Q,et al.The genetic diversity and phylogenetic studies of five populations of Atrina pectinata[J].Progress in Fishery Sciences,2013,34(2):29-35[严加坤,杨爱国,周丽青,等.我国不同地理群体栉江珧遗传多样性及系统发生分析.渔业科学进展,2013,34(2):29-35]
[5]LüJ,Wu S,Zhang Y,et al.Assessment of four DNAfragments(COI,16S rDNA,ITS2,12S rDNA)for species identification of the Ixodida(Acari:Ixodida)[J].Parasit Vectors,2014,7:93
[6]Xue D X,Wang H Y,Zhang T,et al.Population genetic structure and demographic history of Atrina pectinata based on mitochondrial DNA and microsatellite markers[J].PLoS One,2014,9(4):e95436
[7]Thompson J D,Gibson T J,Plewniak F,et al.The Clustal_X windows interface:flexible strategies for multiple sequence alignment aided by quality analysis tools[J].Nucleic Acids Research,1997,25(24):4876-4882
[8]Librado P,Rozas J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452
[9]Excoffier L,Lischer H E L.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10(3):564-567
[10]Tamura K,Stecher G,Peterson D,et al.MEGA6:molecular evolutionary genetics analysis version 6.0[J].Molecular Biology and Evolution,2013,30(12):2725-2729
[11]Niu S F,Su Y Q,Wang J,et al.Genetic polymorphism of mitochondrial control region and cyt b in Trachurus japonicus from Fujian coastal waters[J].Journal of Fishery Sciences of China,2011,18(1):66-74[牛素芳,苏永全,王军,等.福建近海竹荚鱼线粒体DNA控制区和细胞色素b遗传多态性.中国水产科学,2011,18(1):66-74]
[12]Deng J Y,Zhao C Y,Tang Q S,et al.Marine Fisheries Biology[M].Beijing:Agriculture Press.1991,485-518[邓景耀,赵传絪,唐启升,等.海洋渔业生物学.北京:农业出版社.1991,485-518]
[13]Chen X,Yang S Y,Pan C.Genetic polymorphism of mitochondrial control region in Chiloscyllium plagiosum from coastal waters of southern China[J].Acta Oceanologica Sinica,2008,30(6):115-121[陈骁,杨圣云,潘聪.我国南部海域条纹斑竹鲨线粒体DNA控制区遗传多态性研究.海洋学报,2008,30(6):115-121]
[14]Grant W S,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(5):415-426
[15]Zhu Y X,Cheng Q Q,Rogers S M.Genetic structure of Scomber japonicus(Perciformes:Scombridae)along the coast of China revealed by complete mitochondrial cytochrome b sequences[J].Mitochondrial DNA Part A,2016,27(6):3828-3836
[16]He L J,Mukai T,Chu K H,et al.Biogeographical role of the Kuroshio current in the amphibious mudskipper Periophthalmus modestus indicated by mitochondrial DNA data[J].Scientific Reports,2015,5:15645
[17]Hewitt G M.Some genetic consequences of ice ages,and their role in divergence and speciation[J].Biological Journal of the Linnean Society,1996,58(3):247-276
[18]Selkoe K,Toonen RJ.Marine connectivity:a new look at pelagic larval duration and genetic metrics of dispersal[J].Marine Ecology Progress Seriesm,2011,436:291-305
[19]Song N,Wang H N,Liu S D,et al.Genetic study on Sphyrna lewini from Qingdao coastal waters[J].Acta Hydrobiologica Sinica,2017,41(3):603-608[宋娜,王航宁,刘淑德,等.青岛近海路氏双髻鲨群体遗传学分析.水生生物学报,2017,41(3):603-608]
[20]Wang M F,Yu X Y,Ye F L.The gonad development of Pinna(Atrina)pectinata in Beibu Gulf and adjoining coast[J].Guangxi Sciences,2000,7(2):140-143,157[王梅芳,余祥勇,叶富良.北部湾及附近海域栉江珧性腺发育研究.广西科学,2000,7(2):140-143,157]
[21]Ge Q.Paleoenvironmental and Paleoclimatic records from the South China Sea since the late last glacical[D].Thesis for Master of Science.China University of Geosciences,Wuhan.2010[葛倩.晚末次冰期以来南海古环境和古气候记录.硕士学位论文,中国地质大学,武汉.2010]
[22]Qiao F L(Eds.),Regional Oceanography of China SeasPhysical Oceanography[M].Beijing:Ocean Press.2012,310-350[乔方利主编.中国区域海洋学-物理海洋学.北京:海洋出版社.2012,310-350]
[23]Claremont M,Williams S T,Barraclough T G,et al.The geographic scale of speciation in a marine snail with high dispersal potential[J].Journal of Biogeography,2011,38(6):1016-1032
[24]Wang Z R.Fauna Sinica,Phylum Mollusca,Order Mytiloida[M].Beijing:Science Press.1997,362[王祯瑞.中国动物志:软体动物门双壳纲贻贝目.北京:科学出版社.1997,362]
[25]An H S,Kim B H,Lee J W,et al.Comparison between wild and hatchery populations of Korean Pen Shell(Atrina pectinata)using microsatellite DNA markers[J].International Journal of Molecular Sciences,2011,12(9):6024-6039
[26]Liu J,Li Q,Kong L,et al.Cryptic diversity in the pen shell Atrina pectinata(Bivalvia:Pinnidae):high divergence and hybridization revealed by molecular and morphological data[J].Molecular Ecology,2011,20(20):4332-4345
[27]Chen G,Hare M P.Cryptic ecological diversification of a planktonic estuarine copepod,Acartia tonsa[J].Molecular Ecology,2008,17(6):1451-1468
[28]Zhao K,Duan Z Y,Peng Z G,et al.The youngest split in sympatric schizothoracine fish(Cyprinidae)is shaped by ecological adaptations in a Tibetan Plateau glacier lake[J].Molecular Ecology,2009,18(17):3616-3628
[29]Laegdsgaard P,Johnson C.Why do juvenile fish utilize mangrove habitats[J]?Journal of Experimental Marine Biology and Ecology,2001,257(2):229-253
[30]Meng Z N,Zhuang Z M,Jin X S,et al.Variation analysis of RAPD and mitochondrial DNA 16S rRNA sequence of Trichiurus japonicus and Eupleurogrammus muticus from the Yellow Sea[J].Progress in Natural Science,2003,13(11):1170-1176[蒙子宁,庄志猛,金显仕,等.黄海带鱼、小带鱼RAPD和线粒体16S rRNA基因序列变异分析.自然科学进展,2003,13(11):1170-1176]