基于线粒体D-loop序列的长江口中华鲟幼鱼遗传多样性分析
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摘要
采用线粒体DNA控制区(D-loop)序列对2015年和2017年长江口中华鲟(Acipenser sinensis)幼鱼样本进行了遗传多样性分析。2015年的682个样本共检测出11个单倍型,2017年的158个样本共检测出8个单倍型。2015年和2017年长江口中华鲟幼鱼的平均单倍型多样性(h)为0. 857±0. 006,核苷酸多样性(π)为0. 010 2±0. 005 5,均低于截流前数据(h=0. 949±0. 010;π=0. 011±0. 006)。分子变异方差分析(AMOVA)显示,中华鲟幼鱼的遗传变异主要来自于群体内,但其年度样本之间出现了中等程度的遗传分化。
Chinese sturgeon Acipenser sinensis,a typically anadromous fish,is mainly distributed in the continent shelf of the Yellow and East China Seas,and the middle and lower reaches of the Yangtze River.Extensive studies have shown that the natural resources of wild Chinese sturgeon decreased rapidly since the closure of Gezhouba Dam. Chinese sturgeon is on the verge of extinction and was listed as a category Ⅰnationally protected species in China in 1988. And in 2010,this species was considered by the International Union for the Conservation of Nature( IUCN) as critically endangered. In 2013,2015 and 2017,natural propagation of Chinese sturgeon was not observed in the spawning ground,thus it faces survival crisis.Muscle and fin samples of juvenile Chinese sturgeon were collected from the Yangtze Estuary in 2015 and2017. A 462 bp mitochondrial D-loop sequence was amplified by PCR and then used for genetic analysis. We detected 11 haplotypes of 672 samples in 2015 and 8 haplotypes of 158 samples in 2017. The average haplotype diversity( h) of 2015 and 2017 was 0. 857 ± 0. 006,and the average nucleotide diversity( π) was0. 010 2 ± 0. 005 5. The genetic diversity was lower than that of the spawning population samples in 1995—2000( h = 0. 949 ± 0. 010; π = 0. 011 ± 0. 006). AMOVA analysis indicated that 91. 70% of the genetic variability occurred within each year's juvenile populations. The value of Fstshows a middle genetic diversity between annual samples.
Chinese sturgeon Acipenser sinensis,a typically anadromous fish,is mainly distributed in the continent shelf of the Yellow and East China Seas,and the middle and lower reaches of the Yangtze River.Extensive studies have shown that the natural resources of wild Chinese sturgeon decreased rapidly since the closure of Gezhouba Dam. Chinese sturgeon is on the verge of extinction and was listed as a category Ⅰnationally protected species in China in 1988. And in 2010,this species was considered by the International Union for the Conservation of Nature( IUCN) as critically endangered. In 2013,2015 and 2017,natural propagation of Chinese sturgeon was not observed in the spawning ground,thus it faces survival crisis.Muscle and fin samples of juvenile Chinese sturgeon were collected from the Yangtze Estuary in 2015 and2017. A 462 bp mitochondrial D-loop sequence was amplified by PCR and then used for genetic analysis. We detected 11 haplotypes of 672 samples in 2015 and 8 haplotypes of 158 samples in 2017. The average haplotype diversity( h) of 2015 and 2017 was 0. 857 ± 0. 006,and the average nucleotide diversity( π) was0. 010 2 ± 0. 005 5. The genetic diversity was lower than that of the spawning population samples in 1995—2000( h = 0. 949 ± 0. 010; π = 0. 011 ± 0. 006). AMOVA analysis indicated that 91. 70% of the genetic variability occurred within each year's juvenile populations. The value of Fstshows a middle genetic diversity between annual samples.
引文
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[4]刘鉴毅,危起伟,陈细华,等.葛洲坝下中华鲟繁殖生物学特性及其人工繁殖效果[J].应用生态学报,2007,18(6):1397-1402.LIU J Y,WEI Q W,CHEN X H,et al.Reproductive biology and artificial propagation of Acipenser sinensis below Gezhouba Dam[J].Chinese Journal of Applied Ecology,2007,18(6):1397-1402.
[5]ZHUANG P,ZHAO F,ZHANG T,et al.New evidence may support the persistence and adaptability of the near-extinct Chinese sturgeon[J].Biological Conservation,2016(193):66-69.
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[7]吴金明,王成友,张书环,等.从连续到偶发:中华鲟在葛洲坝下发生小规模自然繁殖[J].中国水产科学,2017,24(3):425-431.WU J M,WANG C Y,ZHANG S H,et al.From continuous to occasional:Small-scale natural reproduction of Chinese sturgeon occurred in the Gezhouba spawning found,Yichang,China[J].Journal of Fishery Sciences China,2017,24(3):425-431.
[8]WU J M,WANG C Y,ZHANG H,et al.Drastic decline in spawning activity of Chinese sturgeon,Acipenser sinensis Gray 1835,in the remaining spawning ground of the Yangtze River since the construction of hydrodams[J].Journal of Applied Ichthyology,2015,31(5):839-842.
[9]张四明,邓怀,危起伟,等.中华鲟天然群体蛋白质水平遗传多样性贫乏的初步证据[J].动物学研究,1999,20(2):95-98.ZHANG S M,DENG H,WEI Q W,et al.The preliminary evidence for low genetic diversity in Chinese sturgeon(Acipenser sinensis)revealed by protein electrophoresis[J].Zoological Research,1999,20(2):95-98.
[10]张四明,邓怀,晏勇,等.中华鲟随机扩增多态性DNA及遗传多样性研究[J].海洋与湖沼,2000,31(1):1-7.ZHANG S M,DENG H,YAN Y,et al.Random amplified polymorphic DNA(RAPD)and genetic diversity of Chinese sturgeon(Acipenser sinensis)[J].Oceanologia Et Limnologa Sinica,2000,31(1):1-7.
[11]赵娜.基于微卫星标记的中华鲟繁殖群体遗传学分析与人工繁殖对自然幼鲟群体的贡献评估[D].武汉:中国科学院研究生院(水生生物研究所),2006.ZHAO N.Genetic analyses of the spawning stock of Chinese sturgeon(Acipenser sinensis)and contribution assessment of artificial propagation on natural juvenile population based on microsatellite markers[D].Wuhan:Institute of Hydrobiology,Chinese Academy of Sciences,2006.
[12]曾勇,危起伟,汪登强.长江中华鲟遗传多样性变化[J].海洋科学,2007,31(10):67-69.ZENG Y,WEI Q W,WANG D Q.The variation of genetic diversity of Chinese sturgeon(Acipenser sinensis)in the Yangtze River[J].Marine Sciences,2007,31(10):67-69.
[13]长江三峡工程环境与环境监测公报[R].中华人民共和国生态环境部,2018.http://www.zhb.gov.cn/hjzl/shj/sxgb Bulletin on the ecological and environmental monitoring results of the Three Gorges Project[R].Ministry of Ecology and Environment of the People's Republic of China,2018.http://www.zhb.gov.cn/hjzl/shj/sxgb
[14]BROWN J R,BECKENBACH A T,SMITH M J.Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon[J].Molecular Biology&Evolution,1993,10(2):326-341.
[15]JEANMOUGIN F,THOMPSON J D,GOUY M,et al.Multiple sequence alignment with Clustal X[J].Trends in Biochemical Sciences,1998,23(10):403-405.
[16]LIBRADO P,ROZAS J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[17]TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods.[J].Molecular Biology&Evolution,2011,28(10):2731-2739.
[18]EXCOFFIER L,LAVAL G,SCHNEIDER S.Arlequin(version 3.0):An integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2005,1(4A):47-50.
[19]WEIR B S,COCKERHAM C C.Estimating F-statistics for the analysis of population structure[J].Evolution,1984,38(6):1358.
[20]刘云国.水产生物DNA分子标记技术[M].北京:科学出版社,2009.LIU Y G.Aquatic biology DNA molecular marker technology[M].Beijing:Science Press,2009.
[21]廖小林,朱滨,常剑波.中华鲟物种保护研究[J].人民长江,2017,48(11):16-20.LIAO X L,ZHU B,CHANG J B.Study on conservation of Chinese sturgeon[J].Yangtze River,2017,48(11):16-20.
[22]胡德高,柯福恩,张国良,等.葛洲坝下中华鲟产卵场的调查研究[J].淡水渔业,1992(5):6-11.HU D G,KE F E,ZHANG G L,et al.Research of the spawning ground of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1992(5):6-11.
[23]胡德高,柯福恩,张国良.葛洲坝下中华鲟产卵情况初步调查及探讨[J].淡水渔业,1983(3):15-18.HU D G,KE F E,ZHANG G L.Preliminary investigation and discussion of the spawning ground of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1983(3):15-18.
[24]胡德高,柯福恩,张国良,等.葛洲坝下中华鲟产卵场的第二次调查[J].淡水渔业,1985(3):22-24.HU D G,KE F E,ZHANG G L,et al.Second survey of the spawning ground of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1985(3):22-24.
[25]柯福恩,胡德高,张国良,等.葛洲坝下中华鲟产卵群体性腺退化的观察[J].淡水渔业,1985(4):18,38-41.HU D G,KE F,ZHANG G L,et al.Observation of gonadal degeneration in spawning population of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1985(4):18,38-41.
[26]柯福恩.论中华鲟的保护与开发[J].淡水渔业,1999,29(9):4-8.KE F E.The protection and development of Chinese sturgeon[J].Freshwater Fisheries,1999,29(9):4-8.
[27]陈锦辉,刘健,吴建辉,等.长江口中华鲟幼鲟补充量波动特征分析[J].上海海洋大学学报,2016,25(3):381-387.CHEN J H,LIU J,WU J H,et al.Analysis on the fluctuation features of recruitment for juvenile Chinese sturgeon,Acipenser sinensis in the Yangtze River estuary[J].Journal of Shanghai Ocean University,2016,25(3):381-387.
[28]ZHANG S M,WANG D Q,ZHANG Y P.Mitochondrial DNA variation,effective female population size and population history of the endangered Chinese sturgeon,Acipenser sinensis[J].Conservation Genetics,2003,4(6):673-683.
[29]陈细华.鲟形目鱼类生物学与资源现状[M].北京:海洋出版社,2007.CHEN X H.The status of biology and resources of Acipenseriformes fish[M].Beijing:China Ocean Press,2007.
[30]WRIGHT S.The interpretation of population structure by F-statistics with special regard to syserms of mating[J].Evolution,1965,19(3):395-420.
[31]张书环,杨焕超,辛苗苗,等.长江江苏溆浦段2015年发现中华鲟野生幼鱼的形态和分子鉴定[J].中国水产科学,2016,23(1):1-9.ZHANG S H,YANG H C,XIN M M,et al.External morphology and molecular identification of wild juvenile Acipenser sinensis newly found in the Jiangsu Xupu section of the Yangtze River[J].Journal of Fishery Sciences of China,2016,23(1):1-9
[2]庄平,刘健,王云龙,等.长江口中华鲟自然保护区科学考察与综合管理[M].北京:海洋出版社,2009.ZHUANG P,LIU J,WANG Y L,et al.The Yangtze Estuary nature research for Chinese sturgeon:Scientific studies and management[M].Beijing:China Ocean Press,2009.
[3]危起伟,陈细华,杨德国,等.葛洲坝截流24年来中华鲟产卵群体结构的变化[J].中国水产科学,2005,12(4):452-457.WEI Q W,CHEN X H,YANG D G,et al.Variations in spawning stock structure of Acipenser sinensis within 24 years since damming of Gezhouba Dam[J].Journal of Fishery Sciences of China,2005,12(4):452-457.
[4]刘鉴毅,危起伟,陈细华,等.葛洲坝下中华鲟繁殖生物学特性及其人工繁殖效果[J].应用生态学报,2007,18(6):1397-1402.LIU J Y,WEI Q W,CHEN X H,et al.Reproductive biology and artificial propagation of Acipenser sinensis below Gezhouba Dam[J].Chinese Journal of Applied Ecology,2007,18(6):1397-1402.
[5]ZHUANG P,ZHAO F,ZHANG T,et al.New evidence may support the persistence and adaptability of the near-extinct Chinese sturgeon[J].Biological Conservation,2016(193):66-69.
[6]黄真理,王鲁海,任家盈.葛洲坝截流前后长江中华鲟繁殖群体数量变动研究[J].中国科学:技术科学,2017,47(8):871-881.HUANG Z L,WANG L H,REN J Y.Study on the spawning population fluctuation of Chinese sturgeons around the closure of Gezhouba Dam[J].Scientia Sinica Technologica,2017,47(8):871-881.
[7]吴金明,王成友,张书环,等.从连续到偶发:中华鲟在葛洲坝下发生小规模自然繁殖[J].中国水产科学,2017,24(3):425-431.WU J M,WANG C Y,ZHANG S H,et al.From continuous to occasional:Small-scale natural reproduction of Chinese sturgeon occurred in the Gezhouba spawning found,Yichang,China[J].Journal of Fishery Sciences China,2017,24(3):425-431.
[8]WU J M,WANG C Y,ZHANG H,et al.Drastic decline in spawning activity of Chinese sturgeon,Acipenser sinensis Gray 1835,in the remaining spawning ground of the Yangtze River since the construction of hydrodams[J].Journal of Applied Ichthyology,2015,31(5):839-842.
[9]张四明,邓怀,危起伟,等.中华鲟天然群体蛋白质水平遗传多样性贫乏的初步证据[J].动物学研究,1999,20(2):95-98.ZHANG S M,DENG H,WEI Q W,et al.The preliminary evidence for low genetic diversity in Chinese sturgeon(Acipenser sinensis)revealed by protein electrophoresis[J].Zoological Research,1999,20(2):95-98.
[10]张四明,邓怀,晏勇,等.中华鲟随机扩增多态性DNA及遗传多样性研究[J].海洋与湖沼,2000,31(1):1-7.ZHANG S M,DENG H,YAN Y,et al.Random amplified polymorphic DNA(RAPD)and genetic diversity of Chinese sturgeon(Acipenser sinensis)[J].Oceanologia Et Limnologa Sinica,2000,31(1):1-7.
[11]赵娜.基于微卫星标记的中华鲟繁殖群体遗传学分析与人工繁殖对自然幼鲟群体的贡献评估[D].武汉:中国科学院研究生院(水生生物研究所),2006.ZHAO N.Genetic analyses of the spawning stock of Chinese sturgeon(Acipenser sinensis)and contribution assessment of artificial propagation on natural juvenile population based on microsatellite markers[D].Wuhan:Institute of Hydrobiology,Chinese Academy of Sciences,2006.
[12]曾勇,危起伟,汪登强.长江中华鲟遗传多样性变化[J].海洋科学,2007,31(10):67-69.ZENG Y,WEI Q W,WANG D Q.The variation of genetic diversity of Chinese sturgeon(Acipenser sinensis)in the Yangtze River[J].Marine Sciences,2007,31(10):67-69.
[13]长江三峡工程环境与环境监测公报[R].中华人民共和国生态环境部,2018.http://www.zhb.gov.cn/hjzl/shj/sxgb Bulletin on the ecological and environmental monitoring results of the Three Gorges Project[R].Ministry of Ecology and Environment of the People's Republic of China,2018.http://www.zhb.gov.cn/hjzl/shj/sxgb
[14]BROWN J R,BECKENBACH A T,SMITH M J.Intraspecific DNA sequence variation of the mitochondrial control region of white sturgeon[J].Molecular Biology&Evolution,1993,10(2):326-341.
[15]JEANMOUGIN F,THOMPSON J D,GOUY M,et al.Multiple sequence alignment with Clustal X[J].Trends in Biochemical Sciences,1998,23(10):403-405.
[16]LIBRADO P,ROZAS J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[17]TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:Molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods.[J].Molecular Biology&Evolution,2011,28(10):2731-2739.
[18]EXCOFFIER L,LAVAL G,SCHNEIDER S.Arlequin(version 3.0):An integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2005,1(4A):47-50.
[19]WEIR B S,COCKERHAM C C.Estimating F-statistics for the analysis of population structure[J].Evolution,1984,38(6):1358.
[20]刘云国.水产生物DNA分子标记技术[M].北京:科学出版社,2009.LIU Y G.Aquatic biology DNA molecular marker technology[M].Beijing:Science Press,2009.
[21]廖小林,朱滨,常剑波.中华鲟物种保护研究[J].人民长江,2017,48(11):16-20.LIAO X L,ZHU B,CHANG J B.Study on conservation of Chinese sturgeon[J].Yangtze River,2017,48(11):16-20.
[22]胡德高,柯福恩,张国良,等.葛洲坝下中华鲟产卵场的调查研究[J].淡水渔业,1992(5):6-11.HU D G,KE F E,ZHANG G L,et al.Research of the spawning ground of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1992(5):6-11.
[23]胡德高,柯福恩,张国良.葛洲坝下中华鲟产卵情况初步调查及探讨[J].淡水渔业,1983(3):15-18.HU D G,KE F E,ZHANG G L.Preliminary investigation and discussion of the spawning ground of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1983(3):15-18.
[24]胡德高,柯福恩,张国良,等.葛洲坝下中华鲟产卵场的第二次调查[J].淡水渔业,1985(3):22-24.HU D G,KE F E,ZHANG G L,et al.Second survey of the spawning ground of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1985(3):22-24.
[25]柯福恩,胡德高,张国良,等.葛洲坝下中华鲟产卵群体性腺退化的观察[J].淡水渔业,1985(4):18,38-41.HU D G,KE F,ZHANG G L,et al.Observation of gonadal degeneration in spawning population of Chinese sturgeon below the Gezhouba Dam[J].Freshwater Fisheries,1985(4):18,38-41.
[26]柯福恩.论中华鲟的保护与开发[J].淡水渔业,1999,29(9):4-8.KE F E.The protection and development of Chinese sturgeon[J].Freshwater Fisheries,1999,29(9):4-8.
[27]陈锦辉,刘健,吴建辉,等.长江口中华鲟幼鲟补充量波动特征分析[J].上海海洋大学学报,2016,25(3):381-387.CHEN J H,LIU J,WU J H,et al.Analysis on the fluctuation features of recruitment for juvenile Chinese sturgeon,Acipenser sinensis in the Yangtze River estuary[J].Journal of Shanghai Ocean University,2016,25(3):381-387.
[28]ZHANG S M,WANG D Q,ZHANG Y P.Mitochondrial DNA variation,effective female population size and population history of the endangered Chinese sturgeon,Acipenser sinensis[J].Conservation Genetics,2003,4(6):673-683.
[29]陈细华.鲟形目鱼类生物学与资源现状[M].北京:海洋出版社,2007.CHEN X H.The status of biology and resources of Acipenseriformes fish[M].Beijing:China Ocean Press,2007.
[30]WRIGHT S.The interpretation of population structure by F-statistics with special regard to syserms of mating[J].Evolution,1965,19(3):395-420.
[31]张书环,杨焕超,辛苗苗,等.长江江苏溆浦段2015年发现中华鲟野生幼鱼的形态和分子鉴定[J].中国水产科学,2016,23(1):1-9.ZHANG S H,YANG H C,XIN M M,et al.External morphology and molecular identification of wild juvenile Acipenser sinensis newly found in the Jiangsu Xupu section of the Yangtze River[J].Journal of Fishery Sciences of China,2016,23(1):1-9