大鳞副泥鳅群体线粒体DNA D-loop序列遗传变异分析
|
摘要
为探明大鳞副泥鳅野生资源状况,利用线粒体DNA D-loop序列,对天津5个大鳞副泥鳅自然群体的遗传多样性、遗传结构及种群历史动态进行分析。5个群体72个个体的D-loop基因序列全长912~914bp,其中多态性位点30个,共检测到22个单倍型,平均单倍型多样性和核苷酸多样性分别为0.813和0.0015,呈现高单倍型多样性和低核苷酸多样性的模式。5个群体间的遗传分化指数为-0.0205~0.0795,总的遗传分化指数为0.0712,属中等程度的遗传分化。单倍型网络进化图和单倍型系统发育树均未显示出明显的地理分布格局,中性检验和核苷酸不配对分布分析均表明,大鳞副泥鳅经历过种群扩张,扩张事件发生在第四纪更新世晚期。研究结果表明,应加强5个湿地大鳞副泥鳅群体的保护,适时开展大鳞副泥鳅良种选育工作,减少对大鳞副泥鳅野生资源的破坏。
In order to understand the current situation of wild resources for large scale loach Paramisgur nusdabryanus,the genetic diversity,genetic structure and historical dynamics of five populations in Tianjin were analysed by sequencing the D-loop genes in the mitochondrial DNA.The full sequences of D-loop genes of 72 individual samples were 912—914 bp,of which 30 mutations of nucleotide acids and 22 haplotypes were identified,with haplotype diversity of 0.813 and mean nucleotide diversity of 0.0015.The analysis of D-loop genes from the five large scale loach populations showed a high haplotype diversity and low nucleotide diversity pattern.The fixation indices(Fst)among the five populations were varied from-0.0205 to 0.0795 and the total Fst value was 0.0712,showing a moderate level of genetic differentiation.Haplotype network and phylogenetic trees of the five large scale loach populations revealed that there was no clear geographic distribution pattern.Both neutrality tests and mismatch distribution analysis suggested a late Pleistocene population expansion for the five populations.The findings show that the protection of the five large scale loach populations should be strengthened,and that the breeding work should be carried out in time to reduce the destruction of the wild resources of the large scale loach.
In order to understand the current situation of wild resources for large scale loach Paramisgur nusdabryanus,the genetic diversity,genetic structure and historical dynamics of five populations in Tianjin were analysed by sequencing the D-loop genes in the mitochondrial DNA.The full sequences of D-loop genes of 72 individual samples were 912—914 bp,of which 30 mutations of nucleotide acids and 22 haplotypes were identified,with haplotype diversity of 0.813 and mean nucleotide diversity of 0.0015.The analysis of D-loop genes from the five large scale loach populations showed a high haplotype diversity and low nucleotide diversity pattern.The fixation indices(Fst)among the five populations were varied from-0.0205 to 0.0795 and the total Fst value was 0.0712,showing a moderate level of genetic differentiation.Haplotype network and phylogenetic trees of the five large scale loach populations revealed that there was no clear geographic distribution pattern.Both neutrality tests and mismatch distribution analysis suggested a late Pleistocene population expansion for the five populations.The findings show that the protection of the five large scale loach populations should be strengthened,and that the breeding work should be carried out in time to reduce the destruction of the wild resources of the large scale loach.
引文
[1]李明德.天津鱼类志[M].天津:天津科学技术出版社,2011:85.
[2]张征云,李莉,孙艳青,等.天津湿地存在的主要问题与保护对策建议[J].农业灾害研究,2014,4(12):58-60.
[3]刘东云,王琦,杜林芳,等.1999-2007年天津湿地景观格局及水鸟生境变化[J].湿地科学,2012,10(3):350-358.
[4]彭士涛,赵益栋,张光玉,等.七里海湿地生物多样性现状及其保护对策[J].水道港口,2009,30(2):135-138.
[5]陈四海,区又君,李加儿.鱼类线粒体DNA及其研究进展[J].生物技术通报,2011(3):13-20.
[6]赵旭.黄河流域大鳞副泥鳅遗传多样性分析[D].新乡:河南师范大学,2012.
[7]胡建华,祖国掌,荣朝振,等.大鳞副泥鳅mtDNACytb基因序列分析及分子系统发育研究[J].水产科学,2011,30(9):551-554.
[8]王亚楠,李秀启,王钦东.南四湖大鳞副泥鳅mtDNAD-loop区遗传多样性分析[J].水产学杂志,2011,24(4):54-58.
[9]Li Y H,Wang W M,Liu X L,et al.DNA extraction from crayfish exoskeleton[J].Indian Journal of Experimental Biology,2011,49(12):953-957.
[10]Hall T A.BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows95/98/NT[J].Nucleic Acids Symposium Series,1999(41):95-98.
[11]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.
[12]Rozas J,Anchez-DelBarrio J C,Esseguer X M,et al.DnaSP,DNA polymorphism analyses by the coalescent and other methods[J].Bioinformatics,2003,19(18):2496-2497.
[13]Clement M,Posada D,Crandall K A.TCS:a computer program to estimate gene genealogies[J].Molecular Ecology,2000,9(10):1657-1659.
[14]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 E-cology Resources,2010,10(3):564-567.
[15]施晓峰,苏永全,王文成,等.基于mtDNA控制区序列的3个黑棘鲷群体遗传结构特性研究[J].热带海洋学报,2015,34(1):56-63.
[16]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.
[17]荣朝振,祖国掌,胡建华,等.泥鳅线粒体DNA控制区结构分析及遗传多样性研究[J].南方水产科学,2011,7(5):55-62.
[18]杨子拓,孙际佳,李桂峰,等.基于线粒体D-loop基因的珠江翘嘴鲌遗传多样性与遗传分化研究[J].中山大学学报:自然科学版,2016,55(2):89-96.
[19]赵林林,毕潇潇,宋林,等.松江鲈线粒体DNA控制区结构和遗传多样性分析[J].水生生物学报,2016,40(1):35-41.
[20]钟立强,刘朋朋,潘建林,等.长江中下游5个湖泊黄颡鱼种群线粒体细胞色素b基因的遗传变异分析[J].湖泊科学,2013,25(2):302-308.
[21]李秀启,刘峰,冷春梅,等.基于线粒体DNA控制区的南四湖湖鲚(Coilia ectenes taihuensis)群体遗传结构和种群扩散[J].湖泊科学,2015,27(4):686-692.
[22]陈会娟,汪登强,段辛斌,等.长江中游鳊群体的遗传多样性[J].生态学杂志,2016,35(8):2175-2181.
[23]库喜英,周传江,何舜平.中国黄颡鱼的线粒体DNA多样性及其分子系统学[J].生物多样性,2010,18(3):262-274.
[24]Balloux F,Lugon-Moulin N.The estimation of population differentiation with microsatellite markers[J].Molecular Ecology,2002,11(2):155-165.
[25]刘朋朋,钟立强,潘建林,等.基于线粒体D-loop区分析黄颡鱼(Pelteobagrus fulvidraco)五个淡水湖泊群体的遗传多样性[J].海洋与湖沼,2013,44(3):728-733.
[26]Abbas K.Genetic diversity and population structure of Chinese Misgurnus anguillicaudatus and Elopichthys bambusain the Yangtze River basin as revealed by molecular markers[D].Wuhan:Huazhong Agricultural University,2009.
[27]秦磊.天津七里海古泻湖湿地环境演变研究[J].湿地科学,2012,10(2):181-186.
[2]张征云,李莉,孙艳青,等.天津湿地存在的主要问题与保护对策建议[J].农业灾害研究,2014,4(12):58-60.
[3]刘东云,王琦,杜林芳,等.1999-2007年天津湿地景观格局及水鸟生境变化[J].湿地科学,2012,10(3):350-358.
[4]彭士涛,赵益栋,张光玉,等.七里海湿地生物多样性现状及其保护对策[J].水道港口,2009,30(2):135-138.
[5]陈四海,区又君,李加儿.鱼类线粒体DNA及其研究进展[J].生物技术通报,2011(3):13-20.
[6]赵旭.黄河流域大鳞副泥鳅遗传多样性分析[D].新乡:河南师范大学,2012.
[7]胡建华,祖国掌,荣朝振,等.大鳞副泥鳅mtDNACytb基因序列分析及分子系统发育研究[J].水产科学,2011,30(9):551-554.
[8]王亚楠,李秀启,王钦东.南四湖大鳞副泥鳅mtDNAD-loop区遗传多样性分析[J].水产学杂志,2011,24(4):54-58.
[9]Li Y H,Wang W M,Liu X L,et al.DNA extraction from crayfish exoskeleton[J].Indian Journal of Experimental Biology,2011,49(12):953-957.
[10]Hall T A.BioEdit:a user-friendly biological sequence alignment editor and analysis program for Windows95/98/NT[J].Nucleic Acids Symposium Series,1999(41):95-98.
[11]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.
[12]Rozas J,Anchez-DelBarrio J C,Esseguer X M,et al.DnaSP,DNA polymorphism analyses by the coalescent and other methods[J].Bioinformatics,2003,19(18):2496-2497.
[13]Clement M,Posada D,Crandall K A.TCS:a computer program to estimate gene genealogies[J].Molecular Ecology,2000,9(10):1657-1659.
[14]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 E-cology Resources,2010,10(3):564-567.
[15]施晓峰,苏永全,王文成,等.基于mtDNA控制区序列的3个黑棘鲷群体遗传结构特性研究[J].热带海洋学报,2015,34(1):56-63.
[16]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.
[17]荣朝振,祖国掌,胡建华,等.泥鳅线粒体DNA控制区结构分析及遗传多样性研究[J].南方水产科学,2011,7(5):55-62.
[18]杨子拓,孙际佳,李桂峰,等.基于线粒体D-loop基因的珠江翘嘴鲌遗传多样性与遗传分化研究[J].中山大学学报:自然科学版,2016,55(2):89-96.
[19]赵林林,毕潇潇,宋林,等.松江鲈线粒体DNA控制区结构和遗传多样性分析[J].水生生物学报,2016,40(1):35-41.
[20]钟立强,刘朋朋,潘建林,等.长江中下游5个湖泊黄颡鱼种群线粒体细胞色素b基因的遗传变异分析[J].湖泊科学,2013,25(2):302-308.
[21]李秀启,刘峰,冷春梅,等.基于线粒体DNA控制区的南四湖湖鲚(Coilia ectenes taihuensis)群体遗传结构和种群扩散[J].湖泊科学,2015,27(4):686-692.
[22]陈会娟,汪登强,段辛斌,等.长江中游鳊群体的遗传多样性[J].生态学杂志,2016,35(8):2175-2181.
[23]库喜英,周传江,何舜平.中国黄颡鱼的线粒体DNA多样性及其分子系统学[J].生物多样性,2010,18(3):262-274.
[24]Balloux F,Lugon-Moulin N.The estimation of population differentiation with microsatellite markers[J].Molecular Ecology,2002,11(2):155-165.
[25]刘朋朋,钟立强,潘建林,等.基于线粒体D-loop区分析黄颡鱼(Pelteobagrus fulvidraco)五个淡水湖泊群体的遗传多样性[J].海洋与湖沼,2013,44(3):728-733.
[26]Abbas K.Genetic diversity and population structure of Chinese Misgurnus anguillicaudatus and Elopichthys bambusain the Yangtze River basin as revealed by molecular markers[D].Wuhan:Huazhong Agricultural University,2009.
[27]秦磊.天津七里海古泻湖湿地环境演变研究[J].湿地科学,2012,10(2):181-186.