细条天竺鲷群体线粒体DNA控制区序列比较分析
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摘要
基于线粒体DNA控制区序列比较分析了细条天竺鲷乳山、胶南、上海和舟山4个群体的遗传多样性。结果显示:114个个体的线粒体DNA控制区序列定义了30个单倍型,并检测到变异位点25个。4个地理群体的单倍型多样度和核苷酸多样度均较低;基于控制区单倍型序列构建的邻接关系树显示4个群体个体相互混杂,没有明显的分支与之对应;两两群体间的Fst值在-0.015到0.067之间,表明群体间的遗传差异不显著;确切P检验结果显示不同群体间存在随机交配现象。Tajima’s D和Fu’Fs中性检验的结果暗示细条天竺鲷经历过近期的群体扩张事件,核苷酸不配对分布结果也呈单峰型。基于核苷酸不配对分布的峰值τ计算得到细条天竺鲷发生群体扩张事件的时间在62 450～12 490a前,属于更新世晚期。乳山到舟山海域间地理障碍的缺少以及洋流的扩散作用可能是导致不同群体间无明显遗传分化的主要原因。
Genetic diversity and population genetic structure of Apogon lineatus(Temminck & Schlegel,1842)collected from Yellow Sea and East China Sea were studied based on the mitochondrial DNA control region segments.The results of the present study showed that a total of 30 haplotypes were defined and 25 variable sites were found in 114 specimens.Low haplotype diversity nucleotide diversity were detected for 4 populations.The neighbor-joining(NJ)phylogenetic tree was constructed based on30 haplotypes,and there was no genealogy appearing in the haplotypes tree.The star burst structure of the haplotype network also suggested no population structure existed.Significant genealogical structure corresponding to sampling locations was found neither in neighbor-joining tree nor in minimum spanning trees.Results of pair-wise Fst(-0.015 to 0.067)revealed no significant genetic differentiation and structure among 4 populations.Both mismatch distribution analysis and neutrality tests indicated that Apogon lineatus had experienced a recent population expansion,and the expanding time might be nearly62 450～124 900 years ago in the late Pleistocene.Low genetic variation among different populations was mostly caused by lack of genealogical barriers and transport function of ocean currents in the coastal waters between Rushan and Zhoushan.
Genetic diversity and population genetic structure of Apogon lineatus(Temminck & Schlegel,1842)collected from Yellow Sea and East China Sea were studied based on the mitochondrial DNA control region segments.The results of the present study showed that a total of 30 haplotypes were defined and 25 variable sites were found in 114 specimens.Low haplotype diversity nucleotide diversity were detected for 4 populations.The neighbor-joining(NJ)phylogenetic tree was constructed based on30 haplotypes,and there was no genealogy appearing in the haplotypes tree.The star burst structure of the haplotype network also suggested no population structure existed.Significant genealogical structure corresponding to sampling locations was found neither in neighbor-joining tree nor in minimum spanning trees.Results of pair-wise Fst(-0.015 to 0.067)revealed no significant genetic differentiation and structure among 4 populations.Both mismatch distribution analysis and neutrality tests indicated that Apogon lineatus had experienced a recent population expansion,and the expanding time might be nearly62 450～124 900 years ago in the late Pleistocene.Low genetic variation among different populations was mostly caused by lack of genealogical barriers and transport function of ocean currents in the coastal waters between Rushan and Zhoushan.
引文
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[17]Shamblin B M,Bagley D A,Ehrhart L M,et al.Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences[J].Conservation Genetics,2015,16(3):673-685.
[18]Liu J X,Gao T X,Zhuang Z M,et al.Late Pleistocene divergence and subsequent population expansion of two closely related fish species,Japanese anchovy(Engraulis japonicus)and Australian anchovy(Engraulis australis)[J].Molecular Phylogenetics and Evolution,2006,40:712-723.
[19]宋娜,宋林,高天翔,等.斑尾复虾虎鱼群体遗传多样性比较分析[J].水产学报,2011,35(3):321-326.Song N,Song L,Gao T X X,et al.Comparative analysis of genetic diversity of Synechogobius ommaturus based on the mitochondrial DNA control region[J].Journal of Fisheries China,2011,35:321-325.
[20]Kwan Y S,Song H K,Lee H J,et al.Population genetic structure and evidence of demographic expansion of the Ayu(Plecoglossus altivelis)in East Asia[J].Animal Systematics,Evolution and Diversity,2012,4:279-290.
[21]Hewitt G.The genetic legacy of the quaternary ice ages[J].Nature,2000,405(6789):907-913.
[22]Dynesius M,Jansson R.Evolutionary consequences of changes in species'geographical distributions driven by Milankovitch climate oscillations[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97:9115.
[23]Song N,Ma G,Zhang X,Gao T X,et al.Genetic structure and historical demography of Collichthys lucidus inferred from mtD-NA sequence analysis[J].Environmental Biology of Fishes,2014,97(1):69-77.
[24]Excoffier L,Laval G,Schneider S.Arlequin ver.3.0:An integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics,2005,1:47-50.
[25]Excoffier L,Smouse P E,Quattro J M.Analysis of molecular variance inferred from metric distances among DNA haplotypes:Application to human mitochondrial DNA restriction data[J].Genetics,1992,131:479.
[26]Rice W R.Analyzing tables of statistical tests[J].Evolution:International Journal of Organic Evolution,1989,43(1):223-225.
[27]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123:585-595.
[28]Fu Y X.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J].Genetics,1997,147(2):915-925.
[29]Rogers A R,Harpending H.Population growth makes waves in the distribution of pairwise genetic differences[J].Molecular Biology and Evolution,1992,9(3):552-569.
[30]Huenneke L F,Falk D A,Holsinger K E.Ecological implications of genetic variation in plant populations[M].//Falk D A,Holsinger K E.Genetics and Conservation of Rare Plants.Oxfor:Oxford University Press:1992:31-44.
[31]Avise J C,Arnold J,Ball R M,et al.Intraspecific phylogeography:The mitochondrial DNA bridge between population genetics and systematics[J].Annual Review of Ecology and Systematics,1987,18(X):489-522.
[32]Waples R S.Separating the wheat from the chaff:patterns of genetic differentiation in high gene flow species[J].Journal of Heredity,1998,89(5):438-450.
[33]Xiao Y S,Gao T X,Zhang Y,et al.Demographic history and population structure of blackfin flounder(Glyptocephalus stelleri)in Japan revealed by mitochondrial control region sequences[J].Biochemical Genetics,2010,48(5-6):402-417.
[34]Rivera M A J,Kelley C D,Roderick G K.Subtle population genetic structure in the Hawaiian grouper,Epinephelus quernus(Serranidae)as revealed by mitochondrial DNA analyses[J].Biological Journal of the Linnean Society,2015,81(3):449-468.
[35]Read C I,Bellwood D R,Herwerden L V,et al.Ancient origins of Indo-Pacific coral reef fish biodiversity:A case study of the leopard wrasses(Labridae:Macropharyngodon)[J].Molecular Phylogenetics and Evolution,2006,38(3):808-819.
[36]龚金波,苏天凤,夏军红,等.中国近海黑鲷线粒体DNA控制区序列多态性分析[J].南方水产科学,2006,2(4):24-30.Gong J B,Su T F,Xia J H,et al.Polymorphism study of the mitochondrial DNA D-loop control region sequence from black porgy Acanthopagrus schlegeli in the costal waters of China[J].South China Fisheries Science,2006,2(4):24-30.
[37]李渊,张丽艳,王良明,等.台湾海峡斑鰶群体遗传学研究[J].应用海洋学学报,2016,35(4):522-528.Li Y,Zhang L Y,Wang L M,et al.Population genetics of Konosirus punctatus in Taiwan Strait[J].Journal of Applied Oceanography,2016,35(4):522-528.
[38]Lambeck K,Esat T M,Potter E K.Links between climate and sea levels for the past three million years[J].Nature,2002,419(6903):199.
[39]Mcmanus J W.Marine speciation,tectonics and sea-level changes in Southeast Asia[C].//5th International Coral Reef Symposium.Tahiti:[s.n.],1985.
[40]Seeger C.Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas[J].Ecography,2016,39(9):825-835.
[41]Excoffier L.Patterns of DNA sequence diversity and genetic structure after a range expansion:Lessons from the infinite-island model[J].Molecular Ecology,2004,13(4):853-864.
[2]朱元鼎.南海诸岛海域鱼类志[M].北京:科学出版社,1979:148-154.Zhu Y D,Zhang C L,Cheng Q T,et al.The Fishes of the Island in the South China Sea[M].Beijing:Science Press,1979:148-154.
[3]Nelson J S.Fishes of the World[M].4th ed.Hoboken:Wiley,2006:356.
[4]Mabuchi K,Fraser T H,Song H,et al.Revision of the systematics of the cardinalfishes(Percomorpha:Apogonidae)based on molecular analyses and comparative reevaluation of morphological characters[J].Zootaxa,2014,3846(2):151-203.
[5]金海卫,薛利建,朱增军,等.东海和黄海南部细条天竺鲷的摄食习性[J].海洋渔业,2012,34(4):361-370.Jin H W,Xue L J,Zhu Z J,et al.Feeding habits of Apogon lineatus in the East China Sea and southern Yellow Sea[J].Marine Fisheries,2012,34(4):361-370.
[6]林龙山,郑元甲,刘勇,等.东海区小型鱼类生态研究Ⅰ---小型鱼类的种类组成及季节变化[J].海洋科学,2006,30(8):58-63.Lin L S,Zhen Y J,Liu Y,et al.The ecological study of small sized fish in the East China SeaⅠ-the species composition and seasonal variation of small sized fish[J].Marine Science,2006,30(8):58-63.
[7]严利平,李建生,沈德刚,等.黄海南部、东海北部小黄鱼饵料组成和摄食强度的变化[J].海洋渔业,2006,28(2):117-123.Yan L P,Li J S,Shen D G,et al.Variations in diet composition and feeding intensity of small yellow croaker Larimichthys polyactis Bleeker in the southern Yellow Sea and northern East China Sea[J].Marine Fisheries,2006,28(2):117-123.
[8]张寒野,林龙山.东海带鱼和小型鱼类空间异质性及其空间关系[J].应用生态学报,2005,16(4):708-711.Zhang H Y,Lin L S.Spatial heterogeneity of Trichiurus japonicas and small-scale fish in East China Sea and their spatial relationships[J].Chinese Journal of Applied Ecology,2005,16(4):708-711.
[9]李忠义,林群,戴芳群,等.主成分分析对黄海6种主要饵料鱼类的质量分析评价[J].渔业科学进展,2009,30(5):64-68.Li Z Y,Lin Q,Dai F Q.Food quality analysis of some forge fish in Yellow Sea with principal component method[J].Progress in Fishery Science,2009,30(5):64-68.
[10]叶振江,张弛,王英俊,等.中国天竺鲷属鱼类的矢耳石形态特征[J].海洋学报,2010,32(5):87-92.Ye Z J,Zhang C,Wang Y J,et al.Morphologic characteristics of the sagittal otoliths of fishes of the genus Apogonin China’seas[J].Acta Oceanologica Sinica,2010,32(5):87-92.
[11]麻秋云,薛莹,徐宾铎,等.胶州湾12种饵料鱼类耳石大小与体长的关系[J].水生生物学报,2013,37(3):481-487.Ma Q Y,Xue Y,Xu B D,et al.Relationships between otolith size and fish size for twelve prey fish species from Jiaozhou Bay[J].Acta Hydrobiologica Sinica,2013,37(3):481-487.
[12]李显森,于振海,孙珊,等.长江口及其毗邻海域鱼类群落优势种的生态位宽度与重叠[J].应用生态学报,2013,24(8):2353-2359.Li X S,Yu Z H,Sun S,et al.Ecological niche breadth and niche overlap of dominant species of fish assemblage in Yangtze River estuary and its adjacent waters[J].Chinese Journal of Applied E-cology,2013,24(8):2353-2359.
[13]张亮,王尽文,任荣珠,等.海洲湾北部海域春季渔业资源的群落结构特征[J].渔业科学进展,2014,35(5):1-7.Zhang L,Wang J W,Ren R Z,et al.Fishery resources in northern Haizhou Bay in spring[J].Progress in Fishery Science,2014,35(5):1-7.
[14]Beck S V,Carvalho G R,Barlow A,et al.Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish,Aplocheilus panchax[J].Plos One,2017,12(7):e0179557.
[15]Avise,J C.Phylogeography:The History and Formation of Species[M].Boston:Harvard University Press,2000.
[16]Whitehead A,Anderson S L,Kuivila K M,et al.Genetic variation among interconnected populations of Catostomus occidentalis:Implications for distinguishing impacts of contaminants from biogeographical structuring[J].Molecular Ecology,2003,12(10):2817-2833.
[17]Shamblin B M,Bagley D A,Ehrhart L M,et al.Genetic structure of Florida green turtle rookeries as indicated by mitochondrial DNA control region sequences[J].Conservation Genetics,2015,16(3):673-685.
[18]Liu J X,Gao T X,Zhuang Z M,et al.Late Pleistocene divergence and subsequent population expansion of two closely related fish species,Japanese anchovy(Engraulis japonicus)and Australian anchovy(Engraulis australis)[J].Molecular Phylogenetics and Evolution,2006,40:712-723.
[19]宋娜,宋林,高天翔,等.斑尾复虾虎鱼群体遗传多样性比较分析[J].水产学报,2011,35(3):321-326.Song N,Song L,Gao T X X,et al.Comparative analysis of genetic diversity of Synechogobius ommaturus based on the mitochondrial DNA control region[J].Journal of Fisheries China,2011,35:321-325.
[20]Kwan Y S,Song H K,Lee H J,et al.Population genetic structure and evidence of demographic expansion of the Ayu(Plecoglossus altivelis)in East Asia[J].Animal Systematics,Evolution and Diversity,2012,4:279-290.
[21]Hewitt G.The genetic legacy of the quaternary ice ages[J].Nature,2000,405(6789):907-913.
[22]Dynesius M,Jansson R.Evolutionary consequences of changes in species'geographical distributions driven by Milankovitch climate oscillations[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97:9115.
[23]Song N,Ma G,Zhang X,Gao T X,et al.Genetic structure and historical demography of Collichthys lucidus inferred from mtD-NA sequence analysis[J].Environmental Biology of Fishes,2014,97(1):69-77.
[24]Excoffier L,Laval G,Schneider S.Arlequin ver.3.0:An integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics,2005,1:47-50.
[25]Excoffier L,Smouse P E,Quattro J M.Analysis of molecular variance inferred from metric distances among DNA haplotypes:Application to human mitochondrial DNA restriction data[J].Genetics,1992,131:479.
[26]Rice W R.Analyzing tables of statistical tests[J].Evolution:International Journal of Organic Evolution,1989,43(1):223-225.
[27]Tajima F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123:585-595.
[28]Fu Y X.Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J].Genetics,1997,147(2):915-925.
[29]Rogers A R,Harpending H.Population growth makes waves in the distribution of pairwise genetic differences[J].Molecular Biology and Evolution,1992,9(3):552-569.
[30]Huenneke L F,Falk D A,Holsinger K E.Ecological implications of genetic variation in plant populations[M].//Falk D A,Holsinger K E.Genetics and Conservation of Rare Plants.Oxfor:Oxford University Press:1992:31-44.
[31]Avise J C,Arnold J,Ball R M,et al.Intraspecific phylogeography:The mitochondrial DNA bridge between population genetics and systematics[J].Annual Review of Ecology and Systematics,1987,18(X):489-522.
[32]Waples R S.Separating the wheat from the chaff:patterns of genetic differentiation in high gene flow species[J].Journal of Heredity,1998,89(5):438-450.
[33]Xiao Y S,Gao T X,Zhang Y,et al.Demographic history and population structure of blackfin flounder(Glyptocephalus stelleri)in Japan revealed by mitochondrial control region sequences[J].Biochemical Genetics,2010,48(5-6):402-417.
[34]Rivera M A J,Kelley C D,Roderick G K.Subtle population genetic structure in the Hawaiian grouper,Epinephelus quernus(Serranidae)as revealed by mitochondrial DNA analyses[J].Biological Journal of the Linnean Society,2015,81(3):449-468.
[35]Read C I,Bellwood D R,Herwerden L V,et al.Ancient origins of Indo-Pacific coral reef fish biodiversity:A case study of the leopard wrasses(Labridae:Macropharyngodon)[J].Molecular Phylogenetics and Evolution,2006,38(3):808-819.
[36]龚金波,苏天凤,夏军红,等.中国近海黑鲷线粒体DNA控制区序列多态性分析[J].南方水产科学,2006,2(4):24-30.Gong J B,Su T F,Xia J H,et al.Polymorphism study of the mitochondrial DNA D-loop control region sequence from black porgy Acanthopagrus schlegeli in the costal waters of China[J].South China Fisheries Science,2006,2(4):24-30.
[37]李渊,张丽艳,王良明,等.台湾海峡斑鰶群体遗传学研究[J].应用海洋学学报,2016,35(4):522-528.Li Y,Zhang L Y,Wang L M,et al.Population genetics of Konosirus punctatus in Taiwan Strait[J].Journal of Applied Oceanography,2016,35(4):522-528.
[38]Lambeck K,Esat T M,Potter E K.Links between climate and sea levels for the past three million years[J].Nature,2002,419(6903):199.
[39]Mcmanus J W.Marine speciation,tectonics and sea-level changes in Southeast Asia[C].//5th International Coral Reef Symposium.Tahiti:[s.n.],1985.
[40]Seeger C.Historical and contemporary determinants of global phylogenetic structure in tropical reef fish faunas[J].Ecography,2016,39(9):825-835.
[41]Excoffier L.Patterns of DNA sequence diversity and genetic structure after a range expansion:Lessons from the infinite-island model[J].Molecular Ecology,2004,13(4):853-864.
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