基于线粒体COI基因的中国西南地区木领针蓟马地理种群的遗传分化分析
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摘要
【目的】木领针蓟马Helionothrips mube近年来成为芋头Colocasia esculenta上的一种常见害虫。本研究旨在探讨其中国西南地区地理种群间的遗传变异。【方法】通过Sanger法测定了21个地理种群132头木领针蓟马的线粒体COI基因序列,利用MEGA, DnaSP, Arlequin和Network等软件对木领针蓟马种群间的遗传多样性、遗传分化、分子变异等进行分析。【结果】获得的木领针蓟马132条线粒体COI序列(643 bp)中共发现34个变异位点、16种单倍型,其中单倍型H1出现频率最高、分布最广。木领针蓟马总群体的遗传多样性较高(Hd=0.712,Pi=0.00413,K=2.655),遗传分化程度极大(Fst=0.3443),基因交流水平不高(Nm=0.96)。分子方差分析(AMOVA)表明,木领针蓟马的遗传分化主要来自种群内部,Mantel检测出种群地理距离与遗传距离呈正相关。总群体中性检验Tajima’s D值显著负值,Fu’s Fs值不显著,错配分布曲线呈多峰。综合种群间遗传距离、单倍型系统发育树及中介网络图结果,表明四川成都(CHD)、云南昌宁(CHN)和贵州遵义(ZY)3个种群的遗传分化程度均高于其他种群。【结论】中国西南地区木领针蓟马总群体的遗传多样性较高,遗传分化明显,种群间的基因交流受到地理距离的影响,总群体在较近的历史时期内没有出现扩张现象。
【Aim】 Helionothrips mube has become a common pest on the taro(Colocasia esculenta) in recent years. This study aims to investigate the genetic differentiation among different geographic populations of H. mube in southwestern China. 【Methods】 The mitochondrial COI gene sequences of 132 individuals of H. mube from 21 geographic populations were obtained through Sanger sequencing, and the genetic diversity, genetic differentiation and molecular variance were analyzed by MEGA, DnaSP, Arlequin and Network software. 【Results】 Thirty-four variable sites were observed and 16 haplotypes were defined based on the 132 mitochondrial COI sequences(643 bp) from 21 geographic populations of H. mube, of which H1 had the highest frequency and the widest distribution. High levels of genetic diversity(Hd=0.712, Pi=0.00413, K=2.655) and genetic differentiation(Fst=0.3443), and low gene flow(Nm=0.96) were detected in the total population of H. mube. The analysis of molecular variance(AMOVA) indicated that the genetic differentiation of H. mube was mainly attributed to the intra-population. The Mantel test showed a positive correlation between the geographic distance and genetic distance. The neutral test showed that Tajima's D value was significantly negative, but Fu's Fs was not significant, and the mismatch distribution curve showed multiple peaks based on the whole datasets. The results of genetic distance among populations, haplotype phylogenetic tree and median-joining network all supported that the population genetic differentiation among the three populations of Chengdu, Sichuan(CHD), Changning, Yunnan(CHN) and Zunyi, Guizhou(ZY) were greater than that among other populations. 【Conclusion】 The H. mube populations in southwestern China are characterized by high genetic diversity and obvious genetic differentiation, the gene flow among populations might be affected by geographical distance, and the population of H. mube has not experienced recent expansion.
【Aim】 Helionothrips mube has become a common pest on the taro(Colocasia esculenta) in recent years. This study aims to investigate the genetic differentiation among different geographic populations of H. mube in southwestern China. 【Methods】 The mitochondrial COI gene sequences of 132 individuals of H. mube from 21 geographic populations were obtained through Sanger sequencing, and the genetic diversity, genetic differentiation and molecular variance were analyzed by MEGA, DnaSP, Arlequin and Network software. 【Results】 Thirty-four variable sites were observed and 16 haplotypes were defined based on the 132 mitochondrial COI sequences(643 bp) from 21 geographic populations of H. mube, of which H1 had the highest frequency and the widest distribution. High levels of genetic diversity(Hd=0.712, Pi=0.00413, K=2.655) and genetic differentiation(Fst=0.3443), and low gene flow(Nm=0.96) were detected in the total population of H. mube. The analysis of molecular variance(AMOVA) indicated that the genetic differentiation of H. mube was mainly attributed to the intra-population. The Mantel test showed a positive correlation between the geographic distance and genetic distance. The neutral test showed that Tajima's D value was significantly negative, but Fu's Fs was not significant, and the mismatch distribution curve showed multiple peaks based on the whole datasets. The results of genetic distance among populations, haplotype phylogenetic tree and median-joining network all supported that the population genetic differentiation among the three populations of Chengdu, Sichuan(CHD), Changning, Yunnan(CHN) and Zunyi, Guizhou(ZY) were greater than that among other populations. 【Conclusion】 The H. mube populations in southwestern China are characterized by high genetic diversity and obvious genetic differentiation, the gene flow among populations might be affected by geographical distance, and the population of H. mube has not experienced recent expansion.
引文
Bandelt HJ, Forster P, Rohl A, 1999. Median-joining networks for inferring intraspecific phylogenies. Mol. Biol. Evol., 16(1): 37-48.
Boivin T, Bouvier JC, Beslay D, Suphanor B, 2004. Variability in diapause propensity within populations of a temperate insect species: interactions between insecticide resistance genes and photoperiodism. Biol. J. Linn. Soc., 83(3): 341-351.
Buckman RS, Mound LA, Whiting MF, 2013. Phylogeny of thrips (Insecta: Thysanoptera) based on five molecular loci. Syst. Entomol., 38(1): 123-133.
Cao LJ, Wang ZH, Gong YJ, Zhu L, Hoffmann AA, Wei SJ, 2017. Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread. Evol. Appl., 10(4): 391-401.
Dickey AM, Kumar V, Hoddle MS, Funderburk JE, Morgan JK, Jara-Cavieres A, Shatters GJ, Osborne LS, Mckenzie CL, 2015. The Scirtothrips dorsalis species complex: endemism and invasion in a global pest. PLoS ONE, 10(4): e0123747.
Excoffier L, Lischer HEL, 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res., 10: 564-567.
Fang Y, Shi WQ, Zhang Y, 2017. Molecular phylogeny of Anopheles hyrcanus group members based on ITS2 rDNA. Parasit. Vectors, 10: 417.
Feng JN, Yang XN, Zhang GL, 2007. Taxonomic study of the genus Helionothrips from China (Thysanoptera, Thripidae). Acta Zool. Sin., 32(2): 451-454. [冯纪年, 杨晓娜, 张桂玲, 2007. 领针蓟马属的分类研究. 动物分类学报, 32(2): 451-454]
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol., 3(5): 294-299.
Fu YX, 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147: 915-925.
Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST, 1998. Genetic traces of ancient demography. Proc. Natl. Acad. Sci. USA, 95(4): 1961-1967.
Hebert PD, Cywinska A, Ball SL, 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B Biol. Sci., 270(1512): 313-321.
Hu L, Zhang Z, Wang H, Zhang T, 2018. Molecular phylogeography and population history of Crassostrea sikamea (Amemiya, 1928) based on mitochondrial DNA. J. Exp. Mar. Biol. Ecol., 503: 23-30.
Hudson RR, Slatkin M, Maddison WP, 1992. Estimation of levels of gene flow from DNA sequence data. Genetics, 132: 583-589.
Jermiin LS, Crozier RH, 1994. The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: sequence divergence in Hymenoptera may be associated with nucleotide content. J. Mol. Evol., 38(3): 282-294.
Kud? I, 1992. Panchaetothripinae in Japan (Thysanoptera, Thripidae) 2. Panchaetothripini, the genus Helionothrips. Jpn. J. Entomol., 60(2): 271-289.
Li QD, Yang YP, Li Y, Zhou QM, 2004. Studies on genetic diversity and taxology of taro in China. J. Hunan Agric. Univ. (Nat. Sci.), 30(5): 424-428. [李庆典, 杨永平, 李颖, 周清明, 2004. 中国芋种质资源的遗传多样性及分类研究. 湖南农业大学学报(自然科学版), 30(5): 424-428]
Librado P, Rozas J, 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(1): 1451-1452.
Lu W, Zhang HR, Li ZY, Lu XX, 2016. Recognition of Helionothrips and its damage to taro. J. South. Agric., 47(5): 667-671. [卢葳, 张宏瑞, 李正跃, 陆星星, 2016. 领针蓟马(Helionothrips)识别及其对芋头的危害. 南方农业学报, 47(5): 667-671]
Lyu Z, Zhi J, Zhou Y, Meng Z, Yue W, 2016. Genetic diversity and origin of Dendrothrips minowai (Thysanoptera: Thripidae) in Guizhou, China. J. Asia Pac. Entomol., 19(4): 1035-1042.
Mirab-Balou M, Wang Z, Tong X, 2017. Review of the Panchaetothripinae (Thysanoptera: Thripidae) of China, with two new species descriptions. Can. Entomol., 149(2): 141-158.
Negi RK, Joshi BD, Johnson JA, De R, Goyal SP, 2018. Phylogeography of freshwater fish Puntius sophore in India. Mitochondrial DNA Part A DNA Mapp. Seq. Anal., 29(2): 256-265.
Peakall R, Smouse PE, 2012. GENALEX 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28(19): 2537-2539.
Pu YD, Yang YP, Xu JC, Qian J, 1999. Germplasm resource and its utilization of taro in Yunnan. China Seeds, (1): 1-4. [普迎冬, 杨永平, 许建初, 钱洁, 1999. 云南芋头种质资源及利用. 作物品种资源, (1): 1-4]
Ramos-Onsins SE, Rozas J, 2002. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol., 19: 2092-2100.
Simon C, Frati F, Beckenbach AT, Crespi B, Liu H, Flook P, 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am., 87(6): 651-701.
Tajima F, 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3): 585-595.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S, 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol., 30(12): 2725-2729.
Tonione MA, Fisher RN, Zhu C, Moritz C, 2016. Deep divergence and structure in the Tropical Oceanic Pacific: a multilocus phylogeography of a widespread gekkonid lizard (Squamata: Gekkonidae: Gehyra oceanica). J. Biol., 43(2): 268-278.
Tuda M, Kagoshima K, Toquenaga Y, Arnqvist G, 2014. Global genetic differentiation in a cosmopolitan pest of stored beans: effects of geography, host-plant usage and anthropogenic factors. PLoS ONE, 9(9): e106268.
Tyagi K, Kumar V, Singha D, Chandra K, Laskar BA, Kundu S, Chakraborty R, Chatterjee S, 2017. DNA barcoding studies on thrips in India: cryptic species and species complexes. Sci. Rep., 7(1): 4898.
Wang E, Van Wijk RE, Braun MS, Wink M, 2017. Gene flow and genetic drift contribute to high genetic diversity with low phylogeographical structure in European hoopoes (Upupa epops). Mol. Phylogenet. Evol., 113: 113-125.
Wright S, 1978. Evolution and the Genetics of Populations, Vol. 4. University of Chicago Press, Chicago and London. 79-103.
Xun H, Li H, Li S, Wei S, Zhang L, Song F, Jiang P, Yang H, Han F, Cai W, 2016. Population genetic structure and post-LGM expansion of the plant bug Nesidiocoris tenuis (Hemiptera: Miridae) in China. Sci. Rep., 6: 26755.
Zhang HR, Okajima S, Mound LA, 2006. Collecting and slide preparation methods of thrips. Chin. Bull. Entomol., 43(5): 725-728. [张宏瑞, Okajima S, Mound LA, 2006. 蓟马采集和玻片标本的制作. 昆虫知识, 43(5): 725-728]
Zhang LJ, Shen DR, Zhang HR, Zhang HW, Li ZY, 2011. Method improvement for extraction genomic DNA from thrips. Chin. J. Appl. Entomol., 48(3): 775-781. [张利娟, 沈登荣, 张宏瑞, 张宏伟, 李正跃, 2011. 蓟马基因组DNA 提取方法的改进. 应用昆虫学报, 48(3): 775-781]
Zheng S, Li Y, Yang X, Chen J, Hua J, Gao Y, 2018. DNA barcoding identification of Pseudococcidae (Hemiptera: Coccoidea) using the mitochondrial COI gene. Mitochondrial DNA Part B, 3(1): 419-423.
Boivin T, Bouvier JC, Beslay D, Suphanor B, 2004. Variability in diapause propensity within populations of a temperate insect species: interactions between insecticide resistance genes and photoperiodism. Biol. J. Linn. Soc., 83(3): 341-351.
Buckman RS, Mound LA, Whiting MF, 2013. Phylogeny of thrips (Insecta: Thysanoptera) based on five molecular loci. Syst. Entomol., 38(1): 123-133.
Cao LJ, Wang ZH, Gong YJ, Zhu L, Hoffmann AA, Wei SJ, 2017. Low genetic diversity but strong population structure reflects multiple introductions of western flower thrips (Thysanoptera: Thripidae) into China followed by human-mediated spread. Evol. Appl., 10(4): 391-401.
Dickey AM, Kumar V, Hoddle MS, Funderburk JE, Morgan JK, Jara-Cavieres A, Shatters GJ, Osborne LS, Mckenzie CL, 2015. The Scirtothrips dorsalis species complex: endemism and invasion in a global pest. PLoS ONE, 10(4): e0123747.
Excoffier L, Lischer HEL, 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res., 10: 564-567.
Fang Y, Shi WQ, Zhang Y, 2017. Molecular phylogeny of Anopheles hyrcanus group members based on ITS2 rDNA. Parasit. Vectors, 10: 417.
Feng JN, Yang XN, Zhang GL, 2007. Taxonomic study of the genus Helionothrips from China (Thysanoptera, Thripidae). Acta Zool. Sin., 32(2): 451-454. [冯纪年, 杨晓娜, 张桂玲, 2007. 领针蓟马属的分类研究. 动物分类学报, 32(2): 451-454]
Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R, 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol. Mar. Biol. Biotechnol., 3(5): 294-299.
Fu YX, 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147: 915-925.
Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST, 1998. Genetic traces of ancient demography. Proc. Natl. Acad. Sci. USA, 95(4): 1961-1967.
Hebert PD, Cywinska A, Ball SL, 2003. Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B Biol. Sci., 270(1512): 313-321.
Hu L, Zhang Z, Wang H, Zhang T, 2018. Molecular phylogeography and population history of Crassostrea sikamea (Amemiya, 1928) based on mitochondrial DNA. J. Exp. Mar. Biol. Ecol., 503: 23-30.
Hudson RR, Slatkin M, Maddison WP, 1992. Estimation of levels of gene flow from DNA sequence data. Genetics, 132: 583-589.
Jermiin LS, Crozier RH, 1994. The cytochrome b region in the mitochondrial DNA of the ant Tetraponera rufoniger: sequence divergence in Hymenoptera may be associated with nucleotide content. J. Mol. Evol., 38(3): 282-294.
Kud? I, 1992. Panchaetothripinae in Japan (Thysanoptera, Thripidae) 2. Panchaetothripini, the genus Helionothrips. Jpn. J. Entomol., 60(2): 271-289.
Li QD, Yang YP, Li Y, Zhou QM, 2004. Studies on genetic diversity and taxology of taro in China. J. Hunan Agric. Univ. (Nat. Sci.), 30(5): 424-428. [李庆典, 杨永平, 李颖, 周清明, 2004. 中国芋种质资源的遗传多样性及分类研究. 湖南农业大学学报(自然科学版), 30(5): 424-428]
Librado P, Rozas J, 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25(1): 1451-1452.
Lu W, Zhang HR, Li ZY, Lu XX, 2016. Recognition of Helionothrips and its damage to taro. J. South. Agric., 47(5): 667-671. [卢葳, 张宏瑞, 李正跃, 陆星星, 2016. 领针蓟马(Helionothrips)识别及其对芋头的危害. 南方农业学报, 47(5): 667-671]
Lyu Z, Zhi J, Zhou Y, Meng Z, Yue W, 2016. Genetic diversity and origin of Dendrothrips minowai (Thysanoptera: Thripidae) in Guizhou, China. J. Asia Pac. Entomol., 19(4): 1035-1042.
Mirab-Balou M, Wang Z, Tong X, 2017. Review of the Panchaetothripinae (Thysanoptera: Thripidae) of China, with two new species descriptions. Can. Entomol., 149(2): 141-158.
Negi RK, Joshi BD, Johnson JA, De R, Goyal SP, 2018. Phylogeography of freshwater fish Puntius sophore in India. Mitochondrial DNA Part A DNA Mapp. Seq. Anal., 29(2): 256-265.
Peakall R, Smouse PE, 2012. GENALEX 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics, 28(19): 2537-2539.
Pu YD, Yang YP, Xu JC, Qian J, 1999. Germplasm resource and its utilization of taro in Yunnan. China Seeds, (1): 1-4. [普迎冬, 杨永平, 许建初, 钱洁, 1999. 云南芋头种质资源及利用. 作物品种资源, (1): 1-4]
Ramos-Onsins SE, Rozas J, 2002. Statistical properties of new neutrality tests against population growth. Mol. Biol. Evol., 19: 2092-2100.
Simon C, Frati F, Beckenbach AT, Crespi B, Liu H, Flook P, 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am., 87(6): 651-701.
Tajima F, 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3): 585-595.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S, 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol., 30(12): 2725-2729.
Tonione MA, Fisher RN, Zhu C, Moritz C, 2016. Deep divergence and structure in the Tropical Oceanic Pacific: a multilocus phylogeography of a widespread gekkonid lizard (Squamata: Gekkonidae: Gehyra oceanica). J. Biol., 43(2): 268-278.
Tuda M, Kagoshima K, Toquenaga Y, Arnqvist G, 2014. Global genetic differentiation in a cosmopolitan pest of stored beans: effects of geography, host-plant usage and anthropogenic factors. PLoS ONE, 9(9): e106268.
Tyagi K, Kumar V, Singha D, Chandra K, Laskar BA, Kundu S, Chakraborty R, Chatterjee S, 2017. DNA barcoding studies on thrips in India: cryptic species and species complexes. Sci. Rep., 7(1): 4898.
Wang E, Van Wijk RE, Braun MS, Wink M, 2017. Gene flow and genetic drift contribute to high genetic diversity with low phylogeographical structure in European hoopoes (Upupa epops). Mol. Phylogenet. Evol., 113: 113-125.
Wright S, 1978. Evolution and the Genetics of Populations, Vol. 4. University of Chicago Press, Chicago and London. 79-103.
Xun H, Li H, Li S, Wei S, Zhang L, Song F, Jiang P, Yang H, Han F, Cai W, 2016. Population genetic structure and post-LGM expansion of the plant bug Nesidiocoris tenuis (Hemiptera: Miridae) in China. Sci. Rep., 6: 26755.
Zhang HR, Okajima S, Mound LA, 2006. Collecting and slide preparation methods of thrips. Chin. Bull. Entomol., 43(5): 725-728. [张宏瑞, Okajima S, Mound LA, 2006. 蓟马采集和玻片标本的制作. 昆虫知识, 43(5): 725-728]
Zhang LJ, Shen DR, Zhang HR, Zhang HW, Li ZY, 2011. Method improvement for extraction genomic DNA from thrips. Chin. J. Appl. Entomol., 48(3): 775-781. [张利娟, 沈登荣, 张宏瑞, 张宏伟, 李正跃, 2011. 蓟马基因组DNA 提取方法的改进. 应用昆虫学报, 48(3): 775-781]
Zheng S, Li Y, Yang X, Chen J, Hua J, Gao Y, 2018. DNA barcoding identification of Pseudococcidae (Hemiptera: Coccoidea) using the mitochondrial COI gene. Mitochondrial DNA Part B, 3(1): 419-423.