基于COⅠ基因探讨北京及其周边地区跳钩虾种群遗传结构
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摘要
跳钩虾Platorchestia japonica栖息于湖泊、河流岸边,是重要的环境指示生物。本研究以线粒体COⅠ基因片段为分子标记,对北京及其周边地区22个采样点的128个样本进行种群遗传多样性和遗传结构研究。结果显示,623 bp的COⅠ基因序列中有567个保守位点、56个变异位点和38个简约信息位点。128个样本检测到43个单倍型,单倍型多样性为0.938,核苷酸多样性为0.011 72。最大似然法和贝叶斯法构建的系统发育树以及单倍型网络图表明,研究区域跳钩虾没有明显的地理种群结构,但所有单倍型形成2个遗传进化支。分子变异分析结果证实,跳钩虾2个进化支间的遗传变异显著高于进化支内的,进化支间固定系数为0.852 19,表明2个进化支遗传分化明显。本研究为进一步研究中国区域跳钩虾的遗传结构提供了有意义的基础数据。
Crustaceans of Platorchestia japonica have been investigated for their suitability to serve as indicators for the quality of water bodies, since they normally live along rivers and lakes. This study intends to explore the population genetics of P. japonica around Beijing and its adjacent regions. The mitochondrial COⅠ genes of 128 P. japonica individuals collected from 22 sampling sites were sequenced. Polymorphism analysis of P. japonica COⅠ gene showed that there were 567 conserved sites, 56 variable sites, and 38 parsimony informative sites. Genetic diversity analysis discovered 43 haplotypes, with haplotype diversity of 0.938 and nucleotide diversity of 0.011 72. Phylogenetic analyses using Maximum Likelihood, Bayesian methods and network analyses revealed that the haplotypes of P. japonica showed no apparent phylogeographic structure, but all haplotypes clustered into 2 clades. The results of molecular variance analyses approved that the genetic variation among the clades of P. japonica was significantly higher than that within clades, with a F_(st) value of 0.852 19. These findings provide a scientific basis for further studying the genetic structure of P. japonica in China.
Crustaceans of Platorchestia japonica have been investigated for their suitability to serve as indicators for the quality of water bodies, since they normally live along rivers and lakes. This study intends to explore the population genetics of P. japonica around Beijing and its adjacent regions. The mitochondrial COⅠ genes of 128 P. japonica individuals collected from 22 sampling sites were sequenced. Polymorphism analysis of P. japonica COⅠ gene showed that there were 567 conserved sites, 56 variable sites, and 38 parsimony informative sites. Genetic diversity analysis discovered 43 haplotypes, with haplotype diversity of 0.938 and nucleotide diversity of 0.011 72. Phylogenetic analyses using Maximum Likelihood, Bayesian methods and network analyses revealed that the haplotypes of P. japonica showed no apparent phylogeographic structure, but all haplotypes clustered into 2 clades. The results of molecular variance analyses approved that the genetic variation among the clades of P. japonica was significantly higher than that within clades, with a F_(st) value of 0.852 19. These findings provide a scientific basis for further studying the genetic structure of P. japonica in China.
引文
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Silvestro D,Michalak I.2012.raxmlGUI:a graphical front-end for RAxML[J].Organisms,Diversity & Evolution,12:335-337.
Yang L,Hou Z,Li S.2013.Marine incursion into east Asia:a forgotten driving force of biodiversity[J].Proceedings of the Royal Society B,280(1757):20122892.DOI:10.1098/rspb.2012.2892.
Wright S.1965.The interpretation of population structure by F-statistics with special regard to systems of mating[J].Evolution,19(3):395-420.
董梦书,杨琳,陈祥盛,等.2017.基于线粒体COⅠ基因部分序列的缅甸安小叶蝉地理种群遗传多样性研究[J].四川动物,36(3):277-283.
李大命,张彤晴,唐晟凯,等.2018.基于线粒体Cyt b基因和D-loop区序列的洪泽湖湖鲚遗传多样性分析[J].江苏农业科学,46(20):36-39.
杨璐,侯仲娥,李枢强.2013.海侵驱动的生物多样性增加[J].动物分类学报,38(4):901-903.
Cheng YT,Nakazono K,Lin YK,et al.2011.Cryptic diversity of the semi-terrestrial amphipod Platorchestia japonica (Tattersall,1922)(Amphipoda:Talitrida:Talitridae) in Japan and Taiwan with description of a new species[J].Zootaxa,2787:1-18.
Costa FO,de Waard JR,Boutillier J,et al.2007.Biological identifications through DNA barcodes:the case of the Crustacea[J].Canadian Journal of Fisheries and Aquatic Sciences,64(2):272-295.
Duan Y,Guttman SI,Oris JT,et al.2000.Genotype and toxicity relationships among Hyalella azteca:Ⅱ.Acute exposure to fluoranthene-contaminated sediment[J].Environmental Toxicology and Chemistry,19(5):1422-1426.
Excoffier L,Lischer HE.2010.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,10(3):564-567.
Folmer O,Black M,Hoeh W,et al.1994.DNA primers for amplification of mitochondrial cytochrome c oxidase subunit Ⅰ from diverse metazoan invertebrates[J].Molecular Marine Biology and Biotechnology,3(5):294-299.
Hou Z,Li S.2003.Terrestrial talitrid amphipods (Crustacea:Amphipoda) from China and Vietnam:studies on the collection of IZCAS[J].Journal of Natural History,37(20):2441-2460.
Kumar S,Stecher G,Tamura K.2016.MEGA 7:molecular evolutionary genetics analysis version 7.0 for bigger datasets[J].Molecular Biology and Evolution,33(7):1870-1874.
Leigh JW,Bryant D.2015.POPART:full-feature software for haplotype network construction[J].Methods in Ecology and Evolution,6(9):1110-1116.
Maddison DR,Maddison WP.2000.MacClade 4:analysis of phylogeny and character evolution[M].Sunderland,MA:Sinauer Associates.
Posada D.2008.jModelTest:phylogenetic model averaging[J].Molecular Biology Evolution,25:1253-1256.
Ronquist F,Teslenko M,van der Mark P,et al.2012.MrBayes 3.2:efficient Bayesian phylogenetic inference and model choice across a large model space[J].Systematic Biology,61:539-542.
Rozas J,Ferrer-Mata A,Sánchez-DelBarrio JC,et al.2017.DnaSP v6:DNA sequence polymorphism analysis of large datasets[J].Molecular Biology and Evolution,34:3299-3302.
Silvestro D,Michalak I.2012.raxmlGUI:a graphical front-end for RAxML[J].Organisms,Diversity & Evolution,12:335-337.
Yang L,Hou Z,Li S.2013.Marine incursion into east Asia:a forgotten driving force of biodiversity[J].Proceedings of the Royal Society B,280(1757):20122892.DOI:10.1098/rspb.2012.2892.
Wright S.1965.The interpretation of population structure by F-statistics with special regard to systems of mating[J].Evolution,19(3):395-420.