基于线粒体Cytb序列的伯氏肩孔南极鱼群体遗传结构初步分析
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摘要
选择线粒体Cytb序列为遗传标记分析了伯氏肩孔南极鱼(Trematomus bernacchii)在5个采样点(凯西站、罗斯海、长城站、戴维斯站和中山站)的种群多样性、遗传结构与种群演化历史。从5个采样点98个样本的线粒体Cytb序列中共检测到27种单倍型。与其它分布于南大洋的鱼类相比,伯氏肩孔南极鱼有着相似的遗传多样性特征,即较高的单倍型多样性(haplotype diversity,h=0. 685 90±0. 002 36)和较低的核苷酸多样性(nucleotide diversity,Pi=0. 002 59±0. 013 43)。伯氏肩孔南极鱼种群间的平均遗传距离为0. 39%,分子变异分析(AMOVA)结果显示,组群间的变异为4. 42%(P <0. 05),群体内的为95. 58%(P <0. 05),基于单倍型构建的进化树的结果均表明伯氏肩孔南极鱼群体不具有明显的地理谱系结构。中性进化分析表明伯氏肩孔南极鱼群体在10万年前(大约中更新世时期)经历过快速扩张时期。分子方差分析和Fst表明伯氏肩孔南极鱼的遗传变异主要来自种群内的个体之间,极少数遗传变异来自于群体之间。研究结果显示南极地区的伯氏肩孔南极鱼5个采样点之间具有一定的基因交流,是一个随机交配的群体。
The general PCR technology was used for the amplification of mitochdrial Cytb gene of five groups of Trematomus bernacchii( Great Wall Station,Ross Sea,Casey Station,Davies station,Zhongshan Station) to analyze the population diversity,genetic structure,and population evolution history. A total of 98 specimens from five sampling sites were collected and analyzed to find 27 different haplotypes. In most cases,the haplotype diversity( h = 0. 685 9 ± 0. 002 36) level was high,while the nucleotide diversity was relatively low( Pi= 0. 002 59 ± 0. 0134 3). The base content of A + T( 53%) was higher than that of G + C( 47%). The average intra-specific genetic distance was 0. 39%. The distance between each sampling sites ranged0. 173 3% ～ 0. 714%. The results of AMOVA analysis showed that the variation among the groups was4. 42%( P < 0. 05) and 95. 58%( P < 0. 05) in the group. Cluster analysis method was used to build phylogenetic trees and determine the evolutionary relationship between the sequences. Neutral evolutionary analysis showed that the groups of Trematomus bernacchii experienced a period of rapid expansion about one hundred thousand years ago( about the Middle Pleistocene). Both molecular variance analysis and Fstanalysis showed that the genetic variation of Trematomus bernacchii mainly came from individuals in the specimens,and few came from the populations. The results show that there are certain genetic exchanges among five sampling points in the Antarctic,which is a random mating group.
The general PCR technology was used for the amplification of mitochdrial Cytb gene of five groups of Trematomus bernacchii( Great Wall Station,Ross Sea,Casey Station,Davies station,Zhongshan Station) to analyze the population diversity,genetic structure,and population evolution history. A total of 98 specimens from five sampling sites were collected and analyzed to find 27 different haplotypes. In most cases,the haplotype diversity( h = 0. 685 9 ± 0. 002 36) level was high,while the nucleotide diversity was relatively low( Pi= 0. 002 59 ± 0. 0134 3). The base content of A + T( 53%) was higher than that of G + C( 47%). The average intra-specific genetic distance was 0. 39%. The distance between each sampling sites ranged0. 173 3% ～ 0. 714%. The results of AMOVA analysis showed that the variation among the groups was4. 42%( P < 0. 05) and 95. 58%( P < 0. 05) in the group. Cluster analysis method was used to build phylogenetic trees and determine the evolutionary relationship between the sequences. Neutral evolutionary analysis showed that the groups of Trematomus bernacchii experienced a period of rapid expansion about one hundred thousand years ago( about the Middle Pleistocene). Both molecular variance analysis and Fstanalysis showed that the genetic variation of Trematomus bernacchii mainly came from individuals in the specimens,and few came from the populations. The results show that there are certain genetic exchanges among five sampling points in the Antarctic,which is a random mating group.
引文
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[2]SCHER H D,MARTIN E E.Timing and climatic consequences of the opening of the Drake Passage[J].Science,2006,312(5772):428-430.
[3]CLARKE A,CRAME J A.The origin of the Southern Ocean marine fauna[M].Geological Society,London,Special Publications,1989,47(1):253-268.
[4]FRANCIS J E,POOLE I.Cretaceous and early tertiary climates of Antarctica:Evidence from fossil wood[J].Palaeo-geography Palaeoclimatology Palaeoecology,2002,182(1):47-64.
[5]EASTMAN J T.Antarctic fish biology:Evolution in a unique environment[J].Copeia,1994(1):255.
[6]EASTMAN J T.The nature of the diversity of Antarctic fishes[J].Polar Biology,2005,28(2):93-107.
[7]SONG W,LI L Z,HUANG H L,et al.The complete mitochondrial genome sequence and gene organization of Trematomus bernacchii(Perciformes:Nototheniidae)with phylogenetic consideration[J].Mitochondrial DNA Part B:Resources,2016,11(1):50-51.
[8]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.
[9]LIBRA P,ROZAS J.Dna SP v5:A software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1451-1452.
[10]TAMURA K,PETERSON D,PETERSON N,et al.MEGA 5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance and maximum parsimony methods[J].Molecular Biology Evolution,2011,28(10):2731-2739.
[11]XIAO W H,ZHANG Y P,LIU H Z.Molecular systematics of xenocyprinae(Teleostei:Cyprinidae):Taxonomy,biogeography and coevolution of a special group restricted in East Asia[J].Molecular Phylogenetics and Evolution,2001,18(2):163-173.
[12]EXCOFFIER L,LAVAL G,SCHNEIDER S.Arlequin(version 3.0):an integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics,2005(1):47-50.
[13]EXCOFFIER L,SMOUSE P E,QUATTRO J M.Analysis of molecular variance inferred form metric distances among DNA haplotypes:Application to human mitochondrial DNA restriction data[J].Genetics,1992,16(1):37-48.
[14]RAYMOND M,ROUSSET F.An exact test for population differentiation[J].Evolution,1995,49(6):1280-1283.
[15]朱玉侠.中国沿海日本鲭的遗传多样性及演化历史研究[D].上海:上海海洋大学,2013.ZHU Y X.Study on genetic diversity and population history of Scomber japonicus along the coast of China[D].Shanghai:Shanghai Ocean University,2013.
[16]GON O,HEEMSTRA P C.Fishes of the southern ocean[M].Institute of Archaeology,the Hebrew University,1997:113-128.
[17]BERMINGHAM E,MCCAFFERTY S S,MARTIN AP.Fish biogeography and molecular clocks:Perspectives from the Panamanian Isthmus[J].Molecular Systematics of Fishes,1997.
[18]秦崇凯.新疆3个绵羊群体生产性状的遗传效应分析[D].新疆:新疆农业大学,2012.QIN C K.Genetic effect analysis on production traits of three sheep populations in Xinjiang[D].Xinjiang:Xinjiang Agricultural University,2012.
[19]GRANT W,BOWEN B.Shallow population histories in deep evolutionary lineages of marine fishes:Insights from sardines and anchovies and lessons for conservation[J].The Journal of Heredity,1998,89(5):415-426.
[20]彭士明,施兆鸿,侯俊利,等.银鲳3个野生群体线粒体COI基因的序列差异分析[J].上海海洋大学学报,2009,18(4):398-402.PENG S M,SHI Z H,HOU J L,et al.Genetic diversity of three wild silver pomfret(Pampus argenteus)populations based on COI gene sequences[J].Journal of Shanghai Ocean University,2009,18(4):398-402.
[21]高天翔,毕潇潇,赵林林,等.基于线粒体Cytb基因全序列的松江鲈鱼群体遗传结构分析[J].水生生物学报,2013,37(2):199-207.GAO T X,BI X X,ZHAO L L,et al.Population gnentic structure of roughskin sculpin Trachidermus fasciatus based on the mitochondrial Cytb sequence[J].Acta Hydrobiologica Sinica,2013,37(2):199-207.
[22]吴仁协,柳淑芳,庄志猛,等.基于线粒体Cytb基因的黄海、东海小黄鱼(Larimicthys polyactis)群体遗传结构[J].自然科学进展,2009,19(9):924-930.WU R X,LIU S F,ZHUANG Z M,et al.Population gnentic structure of Yellow Sea and East China Sea Larimicthys polyactis based on the mitochondrial Cytb sequence[J].Progress in Natural Science,2009,19(9):924-930.
[23]卢丽峰,章群,杨喜书,等.基于线粒体控制区的中国近海绿鳍鱼遗传多样性分析[J].海洋渔业,2018,40(30):257-264LU L F,ZHANG Q,YANG X S,et al.Genetic variation of Chelidonichthys kuma in the coastal waters of China based on mt DNA control region sequences[J].Marine Fisheries,2018,40(3):257-264.
[24]PESTER T A,WARD S M,FENWICK A L,et al.Genetic diversity of jointed goatgrass(Aegilops cylindrica)determined with RAPD and AFLPmarkers[J].Weed Science,2003,51(3):287-293.
[25]AVISE J C.The history and purview of phylogeography:a personal reflection[J].Molecular Ecology,1998,7(4):371-379.
[26]代应贵,韩雪,张晓杰.小口白甲鱼都柳江种群mt DNA D环的序列变异及遗传多样性[J].动物学杂志,2010,45(2):115-120.DAI Y G,HAN X,ZHANG X J.Genetic diversity and sequence variation of mt DNA D-loop in the population of vulnerable species onychostoma lini from the Duliu River[J].Chinese Journal of Zoology,2010,45(2):115-120.
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