南沙群岛密斑马面鲀群体遗传多样性分析
|
摘要
密斑马面鲀Thamnaconustessellatus是在我国南海海域较为常见的一种马面鲀属鱼类。本研究基于线粒体DNA控制区序列对南沙群岛密斑马面鲀3个群体的遗传结构及其遗传多样性进行了分析。研究结果显示,密斑马面鲀的控制区序列变异程度较大,86尾个体序列的变异位点数为38个,共定义了28个单倍型;3个密斑马面鲀群体的单倍型多样度和核苷酸多样度均较高,且相差不大;密斑马面鲀群体间未检测到显著的群体遗传结构,分子方差分析表明,99.67%的遗传差异来自于群体内,群体间遗传差异仅为0.33%。贝叶斯树和最大似然树均显示出密斑马面鲀单倍型间松散的分布,未检测到显著的谱系结构。群体历史动态分析结果表明密斑马面鲀的群体经历了更新世的群体扩张事件。
Thamnaconus tessellatus is a common marine fish distributed in the South China Sea.To determine the genetic diversity of T.tessellatus,a control region segment of mitochondrial DNA was sequenced for three populations collected from the Nansha Islands.Thirty-eight polymorphic sites were detected among 86 individuals,showing a high genetic variation.These polymorphic sites defined 28 haplotypes.The three populations showed a similar high haplotype diversity and nucleotide diversity.No significant population genetic differentiation was detected among the three populations.The results show that the proportion of genetic variation was 99.67% within-populations and only 0.33% among-populations.The topology of the Bayesian inference tree and maximum likelihood tree were shallow,showing no significant genealogical branches or clusters corresponding to the sampling localities.Both mismatch distribution analysis and neutrality tests showed that T.tessellatus has experienced a recent population expansion.
Thamnaconus tessellatus is a common marine fish distributed in the South China Sea.To determine the genetic diversity of T.tessellatus,a control region segment of mitochondrial DNA was sequenced for three populations collected from the Nansha Islands.Thirty-eight polymorphic sites were detected among 86 individuals,showing a high genetic variation.These polymorphic sites defined 28 haplotypes.The three populations showed a similar high haplotype diversity and nucleotide diversity.No significant population genetic differentiation was detected among the three populations.The results show that the proportion of genetic variation was 99.67% within-populations and only 0.33% among-populations.The topology of the Bayesian inference tree and maximum likelihood tree were shallow,showing no significant genealogical branches or clusters corresponding to the sampling localities.Both mismatch distribution analysis and neutrality tests showed that T.tessellatus has experienced a recent population expansion.
引文
苏锦祥,李春生,2002.中国动物志硬骨鱼纲鲀形目海蛾鱼目喉盘鱼目鮟鮟目.北京:科学出版社
李玉芳,2014.南海黄鳍马面鲀(Thamnaconus hypargyreus)种群分析.上海:上海海洋大学硕士学位论文
陈大刚,张美昭,2015.中国海洋鱼类.青岛:中国海洋大学出版社
陈丕茂,詹秉义,2000.绿鳍马面鲀年龄生长与合理利用.中国水产科学,7(1):35-40
郑元甲,1997.东海区马面鲀资源变动及其原因的初步研究.中国水产科学,4(4):18-24
郑元甲,李圣法,宓崇道等,2001.东海与南海的黄鳍马面鲀种群研究.中国水产科学,8(1):46-52
郜星晨,2015.基于线粒体COI序列的中国沿海鲀形目鱼类DNA条形码研究.广州:暨南大学硕士学位论文
钱世勤,1998.东海黄鳍马面鲀生物学特性和资源利用状况.中国水产科学,5(3):25-29
高天翔,任桂静,刘进贤等,2009.海洋鱼类分子系统地理学研究进展.中国海洋大学学报,39(5):897-902
韩志强,2008.三种海洋鱼类分子系统地理学研究.青岛:中国海洋大学博士学位论文
Ahti P A,Coleman R R,DiBattista J D et al,2016.Phylogeography of Indo-Pacific reef fishes:sister wrasses Coris gaimard and C.cuvieri in the Red Sea,Indian Ocean and Pacific Ocean.Journal of Biogeography,43(6):1103-1115
An H,Lee J,Park J et al,2013.Genetic structure of the Korean black scraper Thamnaconus modestus inferred from microsatellite marker analysis.Molecular Biology Reports,40(5):3445-3456
Avise J C,2000.Phylogeography:the History and Formation of Species.Harvard:Harvard University Press
Cann R L,Brown W M,Wilson A C,1984.Polymorphic sites and the mechanism of evolution in human mitochondrial DNA.Genetics,106(3):479-499
Drummond A J,Rambaut A,2007.BEAST:Bayesian evolutionary analysis by sampling trees.BMC Evolutionary Biology,7(1):214
Excoffier L,Lischer H E L,2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,10(3):564-567
Kumar S,Stecher G,Tamura K,2016.MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets.Molecular Biology and Evolution,33(7):1870-1874
Laikre L,Palm S,Ryman N,2005.Genetic population structure of fishes:implications for coastal zone management.Ambio,34(2):111-119
Liu J X,Gao T X,Wu S F et al,2007.Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish,Chelon haematocheilus(Temminck&Schlegel,1845).Molecular Ecology,16(2):275-288
Liu J Y,2013.Status of marine biodiversity of the China Seas.PLoS One,8(1):e50719
Ni G,Li Q,Kong L F et al,2014.Comparative phylogeography in marginal seas of the northwestern Pacific.Molecular Ecology,23(3):534-548
Posada D,2008.jModelTest:phylogenetic model averaging.Molecular Biology and Evolution,25(7):1253-1256
Raymond M,Rousset F,1995.An exact test for population differentiation.Evolution,49(6):1280-1283
Song N,Jia N,Yanagimoto T et al,2013.Genetic differentiation of Trachurus japonicus from the Northwestern Pacific based on the mitochondrial DNA control region.Mitochondrial DNA,24(6):705-712
Wang P X,1999.Response of Western Pacific marginal seas to glacial cycles:paleoceanographic and sedimentological features.Marine Geology,156(1-4):5-39
Wang Z Y,Zhang Y,Zhao L L et al,2016.Shallow mitochondrial phylogeographical pattern and high levels of genetic connectivity of Thamnaconus hypargyreus in the South China Sea and the East China Sea.Biochemical Systematics and Ecology,67:110-118
Wu Y J,Hsieh C H,Chen H M et al,2008.Identification of six common species of processed filefish using cytochrome b gene sequence and PCR-RFLP analysis.The Raffles Bulletin of Zoology,19:151-158
李玉芳,2014.南海黄鳍马面鲀(Thamnaconus hypargyreus)种群分析.上海:上海海洋大学硕士学位论文
陈大刚,张美昭,2015.中国海洋鱼类.青岛:中国海洋大学出版社
陈丕茂,詹秉义,2000.绿鳍马面鲀年龄生长与合理利用.中国水产科学,7(1):35-40
郑元甲,1997.东海区马面鲀资源变动及其原因的初步研究.中国水产科学,4(4):18-24
郑元甲,李圣法,宓崇道等,2001.东海与南海的黄鳍马面鲀种群研究.中国水产科学,8(1):46-52
郜星晨,2015.基于线粒体COI序列的中国沿海鲀形目鱼类DNA条形码研究.广州:暨南大学硕士学位论文
钱世勤,1998.东海黄鳍马面鲀生物学特性和资源利用状况.中国水产科学,5(3):25-29
高天翔,任桂静,刘进贤等,2009.海洋鱼类分子系统地理学研究进展.中国海洋大学学报,39(5):897-902
韩志强,2008.三种海洋鱼类分子系统地理学研究.青岛:中国海洋大学博士学位论文
Ahti P A,Coleman R R,DiBattista J D et al,2016.Phylogeography of Indo-Pacific reef fishes:sister wrasses Coris gaimard and C.cuvieri in the Red Sea,Indian Ocean and Pacific Ocean.Journal of Biogeography,43(6):1103-1115
An H,Lee J,Park J et al,2013.Genetic structure of the Korean black scraper Thamnaconus modestus inferred from microsatellite marker analysis.Molecular Biology Reports,40(5):3445-3456
Avise J C,2000.Phylogeography:the History and Formation of Species.Harvard:Harvard University Press
Cann R L,Brown W M,Wilson A C,1984.Polymorphic sites and the mechanism of evolution in human mitochondrial DNA.Genetics,106(3):479-499
Drummond A J,Rambaut A,2007.BEAST:Bayesian evolutionary analysis by sampling trees.BMC Evolutionary Biology,7(1):214
Excoffier L,Lischer H E L,2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows.Molecular Ecology Resources,10(3):564-567
Kumar S,Stecher G,Tamura K,2016.MEGA7:molecular evolutionary genetics analysis version 7.0 for bigger datasets.Molecular Biology and Evolution,33(7):1870-1874
Laikre L,Palm S,Ryman N,2005.Genetic population structure of fishes:implications for coastal zone management.Ambio,34(2):111-119
Liu J X,Gao T X,Wu S F et al,2007.Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish,Chelon haematocheilus(Temminck&Schlegel,1845).Molecular Ecology,16(2):275-288
Liu J Y,2013.Status of marine biodiversity of the China Seas.PLoS One,8(1):e50719
Ni G,Li Q,Kong L F et al,2014.Comparative phylogeography in marginal seas of the northwestern Pacific.Molecular Ecology,23(3):534-548
Posada D,2008.jModelTest:phylogenetic model averaging.Molecular Biology and Evolution,25(7):1253-1256
Raymond M,Rousset F,1995.An exact test for population differentiation.Evolution,49(6):1280-1283
Song N,Jia N,Yanagimoto T et al,2013.Genetic differentiation of Trachurus japonicus from the Northwestern Pacific based on the mitochondrial DNA control region.Mitochondrial DNA,24(6):705-712
Wang P X,1999.Response of Western Pacific marginal seas to glacial cycles:paleoceanographic and sedimentological features.Marine Geology,156(1-4):5-39
Wang Z Y,Zhang Y,Zhao L L et al,2016.Shallow mitochondrial phylogeographical pattern and high levels of genetic connectivity of Thamnaconus hypargyreus in the South China Sea and the East China Sea.Biochemical Systematics and Ecology,67:110-118
Wu Y J,Hsieh C H,Chen H M et al,2008.Identification of six common species of processed filefish using cytochrome b gene sequence and PCR-RFLP analysis.The Raffles Bulletin of Zoology,19:151-158