长江上游异鳔鳅鮀线粒体控制区遗传多样性
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摘要
异鳔鳅鮀(Xenophysogobio boulengeri)是长江上游特有鱼类,目前主要分布在长江上游干流及岷江江段,近年来其资源量呈显著下降趋势。本研究采用线粒体DNA(mt DNA)控制区序列,分析江津、南溪、犍为和水富4个群体共178尾异鰾鳅鮀的遗传多样性。结果表明:异鳔鳅鮀线粒体控制区序列共检测出38个变异位点,定义41个单倍型;平均单倍型多样性(Hd)和平均核苷酸多样性(Pi)分别为0.817和0.002;分子方差分析(AMOVA)显示总群体间无显著遗传分化,绝大部分变异来自群体内部;但基因流(Nm)分析显示部分群体间基因交流受到阻碍,两两群体间的FST值支持部分群体间出现初步分化;错配分布及中性检验表明,异鳔鳅鮀在历史上曾发生过群体扩张事件,发生群体扩张的时间是0.0173 Ma;单倍型网络结构及NJ系统发育分析显示异鳔鳅鮀遗传结构比较单一。基于上述结论,应将异鳔鳅鮀作为一个整体进行就地保护。
Xenophysogobio boulengeri is an endemic fish in the upper reaches of the Yangtze River,which mainly distribute in the main river from Chongqing to Shuifu and Minjiang River,a tributary of the Yangtze River. The natural resource of this species declined in recent years. In this study,mt DNA control region sequences were used to analyze the population genetic structure of X. boulengeri. A total of 38 polymorphic sites were detected from data set of 839 bp,which defined 41 haplotypes from 178 individuals. The average haplotype diversity( Hd) and nucleotide diversity( Pi) were 0.817 and 0.002,respectively. Analysis of molecular variance( AMOVA)indicated that most of the genetic variation( 96.05%) existed within populations. However,pairwise AMOVA showed that FSTvalues among Jiangjin population and other populations,and among Shuifu population and other populations were greater than 7%,indicating moderate genetic divergence between these populations. The mismatch distribution and neutral test revealed that X.boulengeri population had experienced an expansion event in about 0. 0173 Ma. The haplotype network structure and NJ phylogenetic tree demonstrated single genetic population. Our results suggest that X. boulengeri should be wholly conserved in situ.
Xenophysogobio boulengeri is an endemic fish in the upper reaches of the Yangtze River,which mainly distribute in the main river from Chongqing to Shuifu and Minjiang River,a tributary of the Yangtze River. The natural resource of this species declined in recent years. In this study,mt DNA control region sequences were used to analyze the population genetic structure of X. boulengeri. A total of 38 polymorphic sites were detected from data set of 839 bp,which defined 41 haplotypes from 178 individuals. The average haplotype diversity( Hd) and nucleotide diversity( Pi) were 0.817 and 0.002,respectively. Analysis of molecular variance( AMOVA)indicated that most of the genetic variation( 96.05%) existed within populations. However,pairwise AMOVA showed that FSTvalues among Jiangjin population and other populations,and among Shuifu population and other populations were greater than 7%,indicating moderate genetic divergence between these populations. The mismatch distribution and neutral test revealed that X.boulengeri population had experienced an expansion event in about 0. 0173 Ma. The haplotype network structure and NJ phylogenetic tree demonstrated single genetic population. Our results suggest that X. boulengeri should be wholly conserved in situ.
引文
曹文宣,余志堂,许蕴歼,等.1987.三峡工程对长江鱼类资源影响的初步评价及资源增殖途径的研究.长江三峡工程对生态与环境影响及其对策研究论文集.北京:科学出版社.
曹文宣,张国华,马骏,等.1991.洪湖鱼类资源小型化现象的初步探讨.《洪湖水体生物生产力的综合开发及湖泊生态环境优化研究》.北京:海洋出版社.
曹玉琼.2003.异鳔鳅的年龄与生长、繁殖生物学研究(硕士学位论文).武汉:华中农业大学.
陈会娟,汪登强,段辛斌,等.2016.长江中游鳊群体的遗传多样性.生态学杂志,35(8):2175-2181.
陈宜瑜,曹文宣,伍献文,等.1977.中国鲤科鱼类志.上海:上海科技出版社.
陈宜瑜.1998.中国动物志,硬骨鱼鲤形目(中卷).北京:科学出版社.
程晓凤.2013.长江上游特有鱼长鳍吻鮈遗传结构分析(硕士学位论文).重庆:西南大学.
丁瑞华,邓其祥,叶妙荣,等.1994.四川鱼类志.成都:四川科学技术出版社.
郭立,李隽,王忠锁,等.2011.基于四个线粒体基因片段的银鱼科鱼类系统发育.水生生物学报,35(3):449-459.
何舜平.1998.鳅鮀鱼类系统发育和生物地理学分析.动物分类学报,23(增刊):41.
景才瑞,刘会平.1999.论中国第四纪冰期与间冰期.成都理工学院学报,26(1):97-100.
刘建康,曹文宣.1992.长江流域的鱼类资源及其保护对策.长江流域资源与环境,1(1):17-18.
彭士明,施兆鸿,侯俊利.2010.基于线粒体D-loop区与COI基因序列比较分析养殖与野生银鲳群体遗传多样性.水产学报,34(1):19-25.
邵爱华,朱江,史全良,等.2007.暗纹东方鲀线粒体DNA控制区结构和系统发育分析.中国水产科学,14(3):352-360.
申绍祎,田辉伍,刘绍平,等.2017a.长江上游小眼薄鳅线粒体DNA遗传多样性.生态学杂志,36(10):2824-2830.
申绍祎,田辉伍,汪登强,等.2017b.长江上游特有鱼类红唇薄鳅线粒体控制区遗传多样性研究.淡水渔业,47(4):83-90.
田辉伍.2013.长江上游保护区长薄鳅和红唇薄鳅种群生态及遗传结构比较研究(博士学位论文).重庆:西南大学.
王生,罗宏伟,田辉伍,等.2014.长江上游异鳔鳅鮀种群资源现状.淡水渔业,44(4):35-40.
王生,田辉伍,罗宏伟,等.2012.异鳔鳅年龄结构、生长特性与生活史类型.动物学杂志,47(3):1-8.
王伟,何舜平,陈宜瑜.2002.线粒体DNA D-loop序列变异与鳅蛇亚科鱼类系统发育.自然科学进展,12(1):33-36.
谢平,陈宜瑜.1996.我国内陆水体中的魔鬼四重奏-生物多样性的丧失与人类活动.水生生物学报,20(增刊):6-23.
袁希平,严莉,徐树英,等.2008.长江流域铜鱼和圆口铜鱼的遗传多样性.中国水产科学,15(3):377-385.
曾晓芸.2015.长江上游圆筒吻鮈遗传结构分析(硕士学位论文).重庆:西南大学.
Aljanabi SM,Martinez I.1997.Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.Nucleic Acids Research,25:4692-4693.
Bandelt H,Forster P,Rohl A.1999.Median joining networks for inferring intraspecific phylogenies.Molecular Biology and Evolution,16:37-48.
Cheng XF,Tian HW,Wang DQ,et al.2012.Characterization and cross-species amplification of 14 polymorphic microsatellite loci in Xenophysogobio boulengeri.Conservation Genetics Resources,4:1015-1017.
Donaldson KA,Wilson RR Jr.1999.Amphi-Panamic geminates of snook(Percoidei:Centropomidae)provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes.Molecular Phylogenetics and Evolution,13:208-213.
Excoffier L,Laval G,Schneider S.2005.Arlequin ver.3.0:An integrated software package for population genetics data analysis.Evolutionary Bioinformatics Online,1:47-50.
Librado P,Rozas J.2009.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25:1451-1452.
Liu ZJ,Cordes JF.2004.DNA marker technologies and their applications in aquaculture genetics.Aquaculture,238:1-37.
Rogers AR,Harpending H.1992.Population growth makes waves in the distribution of pairwise genetic differences.Molecular Biology and Evolution,9:552-569.
Tamura K,Stecher G,Peterson D,et al.2013.MEGA6:Molecular Evolutionary Genetics Analysis,Version 6.0.Molecular Biology and Evolution,30:2725-2729.
Thompson JD,Gibson TJ,Plewniak F,et al.1997.The CLUSTAL X windows interface:Flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acids Research,2:4876-4882.
Vrijenhoek RC.1994.Genetic Diversity and Fitness in Small Populations.Conservation Genetics,68:37-53.
Wright S.1978.Evolution and the Genetics of populations.Volume 4:Variability within and among Natural Populations.Chicago:University of Chicago Press.
曹文宣,张国华,马骏,等.1991.洪湖鱼类资源小型化现象的初步探讨.《洪湖水体生物生产力的综合开发及湖泊生态环境优化研究》.北京:海洋出版社.
曹玉琼.2003.异鳔鳅的年龄与生长、繁殖生物学研究(硕士学位论文).武汉:华中农业大学.
陈会娟,汪登强,段辛斌,等.2016.长江中游鳊群体的遗传多样性.生态学杂志,35(8):2175-2181.
陈宜瑜,曹文宣,伍献文,等.1977.中国鲤科鱼类志.上海:上海科技出版社.
陈宜瑜.1998.中国动物志,硬骨鱼鲤形目(中卷).北京:科学出版社.
程晓凤.2013.长江上游特有鱼长鳍吻鮈遗传结构分析(硕士学位论文).重庆:西南大学.
丁瑞华,邓其祥,叶妙荣,等.1994.四川鱼类志.成都:四川科学技术出版社.
郭立,李隽,王忠锁,等.2011.基于四个线粒体基因片段的银鱼科鱼类系统发育.水生生物学报,35(3):449-459.
何舜平.1998.鳅鮀鱼类系统发育和生物地理学分析.动物分类学报,23(增刊):41.
景才瑞,刘会平.1999.论中国第四纪冰期与间冰期.成都理工学院学报,26(1):97-100.
刘建康,曹文宣.1992.长江流域的鱼类资源及其保护对策.长江流域资源与环境,1(1):17-18.
彭士明,施兆鸿,侯俊利.2010.基于线粒体D-loop区与COI基因序列比较分析养殖与野生银鲳群体遗传多样性.水产学报,34(1):19-25.
邵爱华,朱江,史全良,等.2007.暗纹东方鲀线粒体DNA控制区结构和系统发育分析.中国水产科学,14(3):352-360.
申绍祎,田辉伍,刘绍平,等.2017a.长江上游小眼薄鳅线粒体DNA遗传多样性.生态学杂志,36(10):2824-2830.
申绍祎,田辉伍,汪登强,等.2017b.长江上游特有鱼类红唇薄鳅线粒体控制区遗传多样性研究.淡水渔业,47(4):83-90.
田辉伍.2013.长江上游保护区长薄鳅和红唇薄鳅种群生态及遗传结构比较研究(博士学位论文).重庆:西南大学.
王生,罗宏伟,田辉伍,等.2014.长江上游异鳔鳅鮀种群资源现状.淡水渔业,44(4):35-40.
王生,田辉伍,罗宏伟,等.2012.异鳔鳅年龄结构、生长特性与生活史类型.动物学杂志,47(3):1-8.
王伟,何舜平,陈宜瑜.2002.线粒体DNA D-loop序列变异与鳅蛇亚科鱼类系统发育.自然科学进展,12(1):33-36.
谢平,陈宜瑜.1996.我国内陆水体中的魔鬼四重奏-生物多样性的丧失与人类活动.水生生物学报,20(增刊):6-23.
袁希平,严莉,徐树英,等.2008.长江流域铜鱼和圆口铜鱼的遗传多样性.中国水产科学,15(3):377-385.
曾晓芸.2015.长江上游圆筒吻鮈遗传结构分析(硕士学位论文).重庆:西南大学.
Aljanabi SM,Martinez I.1997.Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques.Nucleic Acids Research,25:4692-4693.
Bandelt H,Forster P,Rohl A.1999.Median joining networks for inferring intraspecific phylogenies.Molecular Biology and Evolution,16:37-48.
Cheng XF,Tian HW,Wang DQ,et al.2012.Characterization and cross-species amplification of 14 polymorphic microsatellite loci in Xenophysogobio boulengeri.Conservation Genetics Resources,4:1015-1017.
Donaldson KA,Wilson RR Jr.1999.Amphi-Panamic geminates of snook(Percoidei:Centropomidae)provide a calibration of the divergence rate in the mitochondrial DNA control region of fishes.Molecular Phylogenetics and Evolution,13:208-213.
Excoffier L,Laval G,Schneider S.2005.Arlequin ver.3.0:An integrated software package for population genetics data analysis.Evolutionary Bioinformatics Online,1:47-50.
Librado P,Rozas J.2009.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25:1451-1452.
Liu ZJ,Cordes JF.2004.DNA marker technologies and their applications in aquaculture genetics.Aquaculture,238:1-37.
Rogers AR,Harpending H.1992.Population growth makes waves in the distribution of pairwise genetic differences.Molecular Biology and Evolution,9:552-569.
Tamura K,Stecher G,Peterson D,et al.2013.MEGA6:Molecular Evolutionary Genetics Analysis,Version 6.0.Molecular Biology and Evolution,30:2725-2729.
Thompson JD,Gibson TJ,Plewniak F,et al.1997.The CLUSTAL X windows interface:Flexible strategies for multiple sequence alignment aided by quality analysis tools.Nucleic Acids Research,2:4876-4882.
Vrijenhoek RC.1994.Genetic Diversity and Fitness in Small Populations.Conservation Genetics,68:37-53.
Wright S.1978.Evolution and the Genetics of populations.Volume 4:Variability within and among Natural Populations.Chicago:University of Chicago Press.