中国特有森林树种华山松的群体进化历史研究
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摘要
利用现代分子群体遗传学的分析手段,对华山松27个自然群体129个个体的样本进行双亲遗传核基因AGP6片段的测序分析,检测该物种在第四纪冰期时的避难所和群体进化历史。结果表明:(1)华山松群体在AGP6基因座位上具有较高水平的核苷酸多态性,其沉默位点多样性值(πt=0.013 8,πsil=0.030 6)显著高于其他松属植物。(2)基于Bayesian聚类分析结果表明,华山松具有明显的群体遗传结构,地理分布区上能够分为中国中部和中国西南部两大区域族群,Network网络分析和系统发育分析均得到了相似的结果。(3)分子变异(AMO-VA)分析结果表明,遗传变异主要存在于群体内(65.65%)和族群间(30.18%),群体间存在较小的变异量(4.17%);物种水平和族群水平上的群体错配分析分布均呈多峰模式,说明华山松群体未经历过近期的扩张事件。(4)秦岭山脉和横断山区的群体存在较高水平的单倍型多样性和较多的特有稀有单倍型,进一步结合单倍型间的多样性关系,推测这些区域可能是华山松在第四纪冰期时期的避难所。研究认为,不同避难所地区间长期的地理隔离以及高大山脉、河流等异质性生境的形成可能促使了华山松在中国中部和西南部两大区域族群的异质性分化以及物种较高水平的核苷酸多态性。
In this study,we investigated the population genetic structure and evolutionary history of Pinus armandii and we aim to speculate the refugia of this species during Quaternary ice ages.The bipaternallyinherited nuclear gene AGP6 was utilized to study the genetic variations within and among 27 natural populations(129 individuals)of P.armandiiin China.The results showed that:(1)P.armandii have a higher level of nucleotide diversity(πt=0.013 8,πsil=0.030 6)than the other Pinus species.(2)Bayesian clustering divided the total samples into two groups:one was from the middle-eastern region and another was the southwestern group in China.Both the Network and phylogenetic analyses supported this conclusion.(3)Analysis of molecular variance(AMOVA)showed that the genetic variation mainly occurred within populations(65.65%)and among groups(30.18%),and only a little genetic variation occurred among populations(4.17%).A strongly multimodal mismatch distribution curve indicated that no recently population expansion took place for this endemic species.(4)Based on the geographic distributions and genetic diversity patterns of AGP6 haplotype,we speculated that P.armandii had several refugia in the Qinling Mountain and the Hengduan Mountain areas.The long-time geographic isolation between different refugium areas and heterogeneous habitats induced by large mountains and rivers may have resulted in the high level of population differentiation.In addition,the distinctly population genetic structure and evolutionary dynamics could be another contributing factor to the high level of nucleotide diversity of P.armandii.
In this study,we investigated the population genetic structure and evolutionary history of Pinus armandii and we aim to speculate the refugia of this species during Quaternary ice ages.The bipaternallyinherited nuclear gene AGP6 was utilized to study the genetic variations within and among 27 natural populations(129 individuals)of P.armandiiin China.The results showed that:(1)P.armandii have a higher level of nucleotide diversity(πt=0.013 8,πsil=0.030 6)than the other Pinus species.(2)Bayesian clustering divided the total samples into two groups:one was from the middle-eastern region and another was the southwestern group in China.Both the Network and phylogenetic analyses supported this conclusion.(3)Analysis of molecular variance(AMOVA)showed that the genetic variation mainly occurred within populations(65.65%)and among groups(30.18%),and only a little genetic variation occurred among populations(4.17%).A strongly multimodal mismatch distribution curve indicated that no recently population expansion took place for this endemic species.(4)Based on the geographic distributions and genetic diversity patterns of AGP6 haplotype,we speculated that P.armandii had several refugia in the Qinling Mountain and the Hengduan Mountain areas.The long-time geographic isolation between different refugium areas and heterogeneous habitats induced by large mountains and rivers may have resulted in the high level of population differentiation.In addition,the distinctly population genetic structure and evolutionary dynamics could be another contributing factor to the high level of nucleotide diversity of P.armandii.
引文
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[10]张明霞,王得祥,康冰,等.秦岭华山松天然次生林优势种群的种间联结性[J].林业科学,2015,51(1):12-21.ZHANG M X,WANG D X,KANG B,et al.Interspecific associations of dominant plant populations in secondary forest of Pinus armandii in Qinling Mountains[J].Scientia Silvae Sinicae,2015,51(1):12-21.
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[12]蒲晓娟,陈辉.华山松蓝变真菌(Leptographium qinlingensis)的生物学特性研究[J].西北农林科技大学学报(自然科学版),2008,36(5):129-134.PU X J,CHEN H.Biological characteristics of blue-stain fungus(Leptographium qinlingensis)in Pinus armandi[J].Journal of Northwest A&F University(Natural Science E-dition),2008,36(5):129-134.
[13]张蕾蕾,陈辉,陈霞.华山松大小蠹的入侵对华山松挥发物成分的影响[J].西北林学院学报,2011,26(2):114-118.ZHANG L L,CHEN H,CHEN X.Effect of Dendroctonus armandi infection on the volatile constituents of Pinus armandi in Qinling Mountains[J].Journal of Northwest Forestry University,2011,26(2):114-118.
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[16]TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2 731-2 739.
[17]LIBRADO P,ROZAS J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1 451-1 452.
[18]BURBAN C,PETIT R J,CARCREFF E,et al.Range wide variation of the maritime pine bast scale Matsucoccus feytaudi Duc.(Homoptera:Matsucoccidae)in relation to the genetic structure of its host[J].Molecular Ecology,1999,8(10):1 593-1 602.
[19]ROSENBERG N A,PRITCHARD J K,WEBER J L,et al.The genetic structure of human populations[J].Science,2002,298(5 602):2 381-2 385.
[20]DRUMMOND A J,SUCHARD M A,XIE D,et al.Bayesian phylogenetics with BEAUti and the BEAST 1.7[J].Molecular Biology and Evolution,2012,29(8):1 969-1 973.
[21]BANDELT H J,FORSTER P,RHL A.Median-joining networks for inferring intraspecific phylogenies[J].Molecular Biology and Evolution,1999,16(1):37-48.
[22]EXCOFFIER L,LAVAL G,SCHNEIDER S.Arlequin(version3.0):an integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2007,1:47-50
[23]TAJIMA F.The effect of change in population size on DNApolymorphism[J].Genetics,1989,123(3):597-601.
[24]FU Y X,LI W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693-709.
[25]LI Z H,ZOU J B,MAO K S,et al.Population genetic evidence for complex evolutionary histories of four high altitude juniper species in the Qinghai-Tibetan Plateau[J].Evolution,2012,66(3):831-845.
[26]刘芳.基于核基因序列的白皮松谱系地理学研究[D].西安:西北大学,2011.
[27]GLSOY A D,GLSOY A M,ENGEL B,et al.The evolutionary divergence of Pinus nigra subsp.pallasiana and its varieties based on noncoding trnregions of chloroplast genome[J].Turkish Journal of Botany,2014,38:627-636.
[28]AIZAWA M,YOSHIMARU H,TAKAHASHI M,et al.Genetic structure of Sakhalin spruce(Picea glehnii)in northern Japan and adjacent regions revealed by nuclear microsatellites and mitochondrial gene sequences[J].Journal of Plant Research,2015,128(1):91-102.
[29]LIU L,HAO Z Z,LIU Y Y,et al.Phylogeography of Pinus armandii and its relatives:heterogeneous contributions of geography and climate changes to the genetic differentiation and diversification of Chinese white pines[J].PLoS One,2014,9(1):e85920.
[30]文亚峰,韩文军,吴顺.植物遗传多样性及其影响因素[J].中南林业科技大学学报,2010,30(12):80-87.WEN Y F,HAN W J,WU S.Plant genetic diversity and its influencing factors[J].Journal of Central South University of Forestry&Technology,2010,30(12):80-87.
[31]AIZAWA M,KIM Z S,YOSHIMARU H.Phylogeography of the Korean pine(Pinus koraiensis)in northeast Asia:inferences from organelle gene sequences[J].Journal of Plant Research,2012,125(6):713-723.
[32]PETIT R J,DUMINIL J,FINESCHI S,et al.Comparative organization of chloroplast,mitochondrial and nuclear diversity in plant populations[J].Molecular Ecology,2005,14(3):689-701.
[33]WANG H W,GE S.Phylogeography of the endangered Cathaya argyrophylla(Pinaceae)inferred from sequence variation of mitochondrial and nuclear DNA[J].Molecular Ecology,2006,15(13):4 109-4 122.
[34]柏国清.金钱槭属植物谱系地理学研究[D].西安:西北大学,2010.
[35]于海彬,张镱锂.青藏高原及其周边地区高山植物谱系地理学研究进展[J].西北植物学报,2013,33(6):1 268-1 278.YU H B,ZHANG Y L.Advances in phylogeography of alpine plants in the Tibetan Plateau and adjacent regions[J].Acta Botanica Boreali-Occidentalia Sinica,2013,33(6):1 268-1 278.
[3]李林强,李建科,刘迎利.超声波处理提取华山松籽油的研究[J].西北农林科技大学学报(自然科学版),2003,31(5):115-117.LI L Q,LI J K,LIU Y L.Study on the extraction of seed kernel oil of Pinus armandi via ultrasonic treatment[J].Journal of Northwest A&F University(Natural Science Edition),2003,31(5):115-117.
[4]张桢,李春艳,郑永唐,等.华山松松塔体外抗HIV活性的研究[J].时珍国医国药,2014,25(1):25-26.ZHANG Z,LI C Y,ZHENG Y T,et al.In vitro anti-HIVactivities of extracts from Pinus armandii Franch[J].Lishizhen Medicine and Materia Medica Research,2014,25(1):25-26.
[5]陈涛,王小蓉,罗华,等.9个野生中国樱桃群体叶绿体DNAtrnQ-rps16序列变异及其遗传结构分析[J].遗传,2012,34(11):1 475-1 483.CHEN T,WANG X R,LUO H,et al.Chloroplast DNAtrnQ-rps16variation and genetic structure of nine wild Chinese cherry(Cerasus pseudocerasus Lindl.)populations[J].Hereditas,2012,34(11):1 475-1 483.
[6]张利锐,彭艳玲,任广朋,等.马尾松和黄山松两个核基因位点的群体遗传多样性和种间分化[J].植物生态学报,2011,35(5):531-538.ZHANG L R,PENG Y L,REN G P,et al.Population genetic diversity and species divergence of Pinus massoniana and P.hwangshanensis at two nucleotide loci[J].Chinese Journal of Plant Ecology,2011,35(5):531-538.
[7]丁小飞,杨桂芬,董梅,等.白皮松天然群体遗传多样性的等位酶分析[J].广东林业科技,2011,27(1):8-12.DING X F,YANG G F,DONG M,et al.Allozyme analysis of genetic diversity between natural populations of Pinus bungeana[J].Guangdong Forestry Science and Technology,2011,27(1):8-12.
[8]龚维.孑遗植物银杏的分子亲缘地理学研究[D].杭州:浙江大学,2007.
[9]SYRING J,WILLYARD A,CRONN R,et al.Evolutionary relationships among Pinus(Pinaceae)subsections inferred from multiple low-copy nuclear loci[J].American Journal of Botany,2005,92(12):2 086-2 100.
[10]张明霞,王得祥,康冰,等.秦岭华山松天然次生林优势种群的种间联结性[J].林业科学,2015,51(1):12-21.ZHANG M X,WANG D X,KANG B,et al.Interspecific associations of dominant plant populations in secondary forest of Pinus armandii in Qinling Mountains[J].Scientia Silvae Sinicae,2015,51(1):12-21.
[11]费世民,何亚平,陈秀明,等.秦岭水灾迹地油松和华山松更新种群数量特征[J].植物生态学报,2008,32(1):95-105.FEI S M,HE Y P,CHEN X M,et al.Quantitative features of populations of Pinus tabulaeformis and P.armandii regenerated following water damage at Qinling Mountain,China[J].Chinese Journal of Plant Ecology,2008,32(1):95-105.
[12]蒲晓娟,陈辉.华山松蓝变真菌(Leptographium qinlingensis)的生物学特性研究[J].西北农林科技大学学报(自然科学版),2008,36(5):129-134.PU X J,CHEN H.Biological characteristics of blue-stain fungus(Leptographium qinlingensis)in Pinus armandi[J].Journal of Northwest A&F University(Natural Science E-dition),2008,36(5):129-134.
[13]张蕾蕾,陈辉,陈霞.华山松大小蠹的入侵对华山松挥发物成分的影响[J].西北林学院学报,2011,26(2):114-118.ZHANG L L,CHEN H,CHEN X.Effect of Dendroctonus armandi infection on the volatile constituents of Pinus armandi in Qinling Mountains[J].Journal of Northwest Forestry University,2011,26(2):114-118.
[14]FARJON A.Pinus armandii.The IUCN Red List of Threatened Species
[15]DOYLE J J,DOYLE J L.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J].Phytochemical Bulletin,1987,19:11-15.
[16]TAMURA K,PETERSON D,PETERSON N,et al.MEGA5:molecular evolutionary genetics analysis using maximum likelihood,evolutionary distance,and maximum parsimony methods[J].Molecular Biology and Evolution,2011,28(10):2 731-2 739.
[17]LIBRADO P,ROZAS J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1 451-1 452.
[18]BURBAN C,PETIT R J,CARCREFF E,et al.Range wide variation of the maritime pine bast scale Matsucoccus feytaudi Duc.(Homoptera:Matsucoccidae)in relation to the genetic structure of its host[J].Molecular Ecology,1999,8(10):1 593-1 602.
[19]ROSENBERG N A,PRITCHARD J K,WEBER J L,et al.The genetic structure of human populations[J].Science,2002,298(5 602):2 381-2 385.
[20]DRUMMOND A J,SUCHARD M A,XIE D,et al.Bayesian phylogenetics with BEAUti and the BEAST 1.7[J].Molecular Biology and Evolution,2012,29(8):1 969-1 973.
[21]BANDELT H J,FORSTER P,RHL A.Median-joining networks for inferring intraspecific phylogenies[J].Molecular Biology and Evolution,1999,16(1):37-48.
[22]EXCOFFIER L,LAVAL G,SCHNEIDER S.Arlequin(version3.0):an integrated software package for population genetics data analysis[J].Evolutionary Bioinformatics Online,2007,1:47-50
[23]TAJIMA F.The effect of change in population size on DNApolymorphism[J].Genetics,1989,123(3):597-601.
[24]FU Y X,LI W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693-709.
[25]LI Z H,ZOU J B,MAO K S,et al.Population genetic evidence for complex evolutionary histories of four high altitude juniper species in the Qinghai-Tibetan Plateau[J].Evolution,2012,66(3):831-845.
[26]刘芳.基于核基因序列的白皮松谱系地理学研究[D].西安:西北大学,2011.
[27]GLSOY A D,GLSOY A M,ENGEL B,et al.The evolutionary divergence of Pinus nigra subsp.pallasiana and its varieties based on noncoding trnregions of chloroplast genome[J].Turkish Journal of Botany,2014,38:627-636.
[28]AIZAWA M,YOSHIMARU H,TAKAHASHI M,et al.Genetic structure of Sakhalin spruce(Picea glehnii)in northern Japan and adjacent regions revealed by nuclear microsatellites and mitochondrial gene sequences[J].Journal of Plant Research,2015,128(1):91-102.
[29]LIU L,HAO Z Z,LIU Y Y,et al.Phylogeography of Pinus armandii and its relatives:heterogeneous contributions of geography and climate changes to the genetic differentiation and diversification of Chinese white pines[J].PLoS One,2014,9(1):e85920.
[30]文亚峰,韩文军,吴顺.植物遗传多样性及其影响因素[J].中南林业科技大学学报,2010,30(12):80-87.WEN Y F,HAN W J,WU S.Plant genetic diversity and its influencing factors[J].Journal of Central South University of Forestry&Technology,2010,30(12):80-87.
[31]AIZAWA M,KIM Z S,YOSHIMARU H.Phylogeography of the Korean pine(Pinus koraiensis)in northeast Asia:inferences from organelle gene sequences[J].Journal of Plant Research,2012,125(6):713-723.
[32]PETIT R J,DUMINIL J,FINESCHI S,et al.Comparative organization of chloroplast,mitochondrial and nuclear diversity in plant populations[J].Molecular Ecology,2005,14(3):689-701.
[33]WANG H W,GE S.Phylogeography of the endangered Cathaya argyrophylla(Pinaceae)inferred from sequence variation of mitochondrial and nuclear DNA[J].Molecular Ecology,2006,15(13):4 109-4 122.
[34]柏国清.金钱槭属植物谱系地理学研究[D].西安:西北大学,2010.
[35]于海彬,张镱锂.青藏高原及其周边地区高山植物谱系地理学研究进展[J].西北植物学报,2013,33(6):1 268-1 278.YU H B,ZHANG Y L.Advances in phylogeography of alpine plants in the Tibetan Plateau and adjacent regions[J].Acta Botanica Boreali-Occidentalia Sinica,2013,33(6):1 268-1 278.