唐古特虎耳草谱系地理学研究
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摘要
利用叶绿体基因(trnL-trnF和rpl16)对青藏高原地区的18个唐古特虎耳草(Saxifraga tangutica Engl.)居群(209个个体)进行谱系地理学研究,以揭示唐古特虎耳草的现有遗传结构及其历史演化过程。结果表明:(1)从209个个体中共检测到74个单倍型,且只有单倍型H5在居群中广泛分布,71.62%的单倍型为居群特有单倍型。(2)分子变异分析(AMOVA)显示,91.85%的遗传变异来源于居群内,居群间遗传分化不明显(F_(ST)=0.081);遗传分化系数N_(ST)(0.109)大于G_(ST)(0.097,P>0.05)但不显著,表明唐古特虎耳草在其整个分布范围内没有明显的谱系地理结构。(3)中性检验表明,Tajima’s D(-2.045 07,P<0.05)和Fu&Li’D*值(-3.629 27,P<0.05)均为显著的负值,结合单峰的错配分布曲线,表明该物种经历过近期扩张。研究推测,唐古特虎耳草在第四纪冰期时可能存在多个微型避难所,由于第四纪冰期气候的反复波动,使得原来连续的居群片段化,避难所内的居群单独进化,从而形成了大量特有单倍型;唐古特虎耳草居群对第四纪冰期气候波动的反应可能更多的表现为垂直海拔高度的迁移,而非大规模的水平迁移。
Two chloroplast DNA intergenic spacers,trnL-trnF and rpl16,were employed to study phylogeography of Saxifraga tangutica,which aimed to explore genetic structure and phylogeographical history of this species.The result showed that:(1)based on range-wide sampling(18 populations and 209 individuals),we detected 74 haplotypes.Only one haplotype(H5)was widespread,while 71.62% were private haplotypes,i.e.,observed in single populations.(2)Analysis of molecular variance showed that within-population variation was described as 91.85% of the total variation,while among-population variation was not distinct(F_(ST)= 0.081).An estimation of non-significantly larger N_(ST)(0.109)than G_(ST)(0.097,P >0.05)value across all populations suggested an absence of phylogeographical structure across the whole distribution range.(3)Neutrality tests of Tajima's D(-2.045 07,P < 0.05)and Fu & Li'D*(-3.629 27,P < 0.05)showed significantly negative values,in combination with unimodal of mis-match distribution analysis,suggested a recent demographic expansion of S.tangutica.Based on results given above,we speculated that there might be multi microrefugia for S.tanguticaon the Qinghai-Tibetan Plateau platform during Quaternary glaciations.Climatic oscillations during Quaternary glaciations fragmented the distribution range of S.tanguticainto isolated populations,subsequent allopatric divergence resulted in the formation of numerous private haplotypes across its distribution range.Populations of S.tanguticapossibly experienced in situ altitudinal migrations to respond glacial and interglacial intervals,instead of extensively horizontal migration.
Two chloroplast DNA intergenic spacers,trnL-trnF and rpl16,were employed to study phylogeography of Saxifraga tangutica,which aimed to explore genetic structure and phylogeographical history of this species.The result showed that:(1)based on range-wide sampling(18 populations and 209 individuals),we detected 74 haplotypes.Only one haplotype(H5)was widespread,while 71.62% were private haplotypes,i.e.,observed in single populations.(2)Analysis of molecular variance showed that within-population variation was described as 91.85% of the total variation,while among-population variation was not distinct(F_(ST)= 0.081).An estimation of non-significantly larger N_(ST)(0.109)than G_(ST)(0.097,P >0.05)value across all populations suggested an absence of phylogeographical structure across the whole distribution range.(3)Neutrality tests of Tajima's D(-2.045 07,P < 0.05)and Fu & Li'D*(-3.629 27,P < 0.05)showed significantly negative values,in combination with unimodal of mis-match distribution analysis,suggested a recent demographic expansion of S.tangutica.Based on results given above,we speculated that there might be multi microrefugia for S.tanguticaon the Qinghai-Tibetan Plateau platform during Quaternary glaciations.Climatic oscillations during Quaternary glaciations fragmented the distribution range of S.tanguticainto isolated populations,subsequent allopatric divergence resulted in the formation of numerous private haplotypes across its distribution range.Populations of S.tanguticapossibly experienced in situ altitudinal migrations to respond glacial and interglacial intervals,instead of extensively horizontal migration.
引文
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[3]HUGHES C E.The tropical Andean plant diversity powerhouse[J].New Phytologist,2016,210(4):1 152-1 154.
[4]FAVRE A,PACKERT M,PAULS S U,et al.The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan biotas[J].Biological Reviews,2015,90(1):236-253.
[5]WEN J,ZHANG J-Q,NIE Z-L,et al.Evolutionary diversifications of plants on the Qinghai-Tibetan Plateau[J].Frontiers in Genetics,2014,5:4.
[6]XING Y,REE R H.Uplift-driven diversification in the Hengduan Mountains,a temperate biodiversity hotspot[J].Proceedings of the National Academy of Sciences of the United States of America,2017,114(17):E3444-E3451.
[7]EATON D A R,FENSTER C B,HEREFORD J,et al.Floral diversity and community structure in Pedicularis(Orobanchaceae)[J].Ecology,2012,93(8):S182-S194.
[8]ZHANG J Q,MENG S Y,WEN J,et al.Phylogenetic relationships and character evolution of Rhodiola(Crassulaceae)based on nuclear ribosomal ITS and plastid trnL-F and psbAtrnH sequences[J].Systematic Botany,2014,39(2):441-451.
[9]WANG Y J,SUSANNA A,VON RAAB-STRAUBE E,et al.Island-like radiation of Saussurea(Asteraceae:Cardueae)trigged by uplifts of the Qinghai-Tibetan Plateau[J].Botanical Journal of the Linnean Society,2009,97(4):893-903.
[10]GAO Q B,LI Y H,GORNALL R J,et al.Phylogeny and speciation in Saxifragasect.Ciliatae(Saxifragaceae):evidence frompsbA-trnH,trnL-Fand ITS sequences[J].Taxon,2015,64(4):703-713.
[11]EBERSBACH J,MUELLNER-RIEHL A N,MICHALAK I,et al.In and out of the Qinghai-Tibet Plateau:divergence time estimation and historical biogeography of the large arctic-alpine genus Saxifraga L[J].Journal of Biogeography,2017,44(4):900-910.
[12]LIU J Q,WANG Y J,WANG A L,et al.Radiation and diversification within the Ligularia-Cremanthodium-Parasenecio complex(Asteraceae)trigged by uplift of the Qinghai-Tibetan Plateau[J].Molecular Phylogenetics and Evolution,2006,38(1):31-49.
[13]ZHENG B,XU Q,SHEN Y.The relationship between climate change and Quaternary glacial cycles on the Qinghai-Tibetan Plateau:review and speculation[J].Quaternary International,2002,97-98(1):93-101.
[14]OWEN L A,BENN D I.Equilibrium-line altitudes of the Last Glacial Maximum for the Himalaya and Tibet:an assessment and evaluation of results[J].Quaternary International,2005,138-139(3):55-78.
[15]LEHMKUHL F,OWEN L A.Late Quaternary glaciation of Tibet and the bordering mountains:a review[J].Boreas,2005,34(2):87-100.
[16]HEWITT G M.Post-glacial re-colonization of European biota[J].Biological Journal of the Linnean Society,1999,68(1/2):87-112.
[17]HEWITT G M.Speciation,hybrid zones and phylogeography-or seeing genes in space and time[J].Molecular Ecology,2001,10(3):537-549.
[18]ZHANG D,FENGQUAN L,JIANMIN B.Eco-environmental effects of the Qinghai-Tibet Plateau uplift during the Quaternary in China[J].Environmental Geology,2000,39(12):1 352-1 358.
[19]HEWITT G M.Genetic consequences of climatic oscillations in the Quaternary[J].Philosophical Transactions of the Royal Society of London B:Biological Sciences,2004,359(1 442):183-195.
[20]ZHANG Q,CHIANG T Y,GEORGE M,et al.Phylogeography of the Qinghai-Tibetan Plateau endemic Juniperus przewalskii(Cupressaceae)inferred from chloroplast DNA sequence variation[J].Molecular Ecology,2005,14(11):3 513-3 524.
[21]MENG L,YANG R,ABBOTT R J,et al.Mitochondrial and chloroplast phylogeography of Picea crassifolia Kom.(Pinaceae)in the Qinghai-Tibetan Plateau and adjacent highlands[J].Molecular Ecology,2007,16(19):4 128-4 137.
[22]WANG L Y,IKEDA H,LIU T L,et al.Repeated range expansion and glacial endurance of Potentilla glabra(Rosaceae)in the Qinghai-Tibetan Plateau[J].Journal of Integrative Plant Biology,2009,51(7):698-706.
[23]WANG L,ABBOTT R J,ZHENG W,et al.History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau:Aconitum gymnandrum(Ranunculaceae)[J].Molecular Ecology,2009,18(4):709-721.
[24]GAO Q,ZHANG D,DUAN Y,et al.Intraspecific divergences of Rhodiola alsia(Crassulaceae)based on plastid DNA and internal transcribed spacer fragments[J].Botanical Journal of the Linnean Society,2012,168(2):204-215.
[25]OPGENOORTH L,VENDRAMIN G G,MAO K,et al.Tree endurance on the Tibetan Plateau marks the world’s highest known tree line of the Last Glacial Maximum[J].New Phytologist,2010,185(1):332-342.
[26]WANG H,QIONG L,SUN K,et al.Phylogeographic structure of Hippophae tibetana(Elaeagnaceae)highlights the highest microrefugia and the rapid uplift of the QinghaiTibetan Plateau[J].Molecular Ecology,2010,19(14):2 964-2 979.
[27]GAO Q B,ZHANG F Q,XING R,et al.Phylogeographic study revealed microrefugia for an endemic species on the Qinghai-Tibetan Plateau:Rhodiola chrysanthemifolia(Crassulaceae)[J].Plant Systematics and Evolution,2016,302(9):1 179-1 193.
[28]WU C Y,RAVEN P H.Flora of China[M].Beijing:Science Press;St.Louis:Missouri Botanical Garden Press,2001,8:208-344.
[29]ABBOTT R J,COMES H P.Evolution in the Arctic:aphylogeographic analysis of the circumarctic plant,Saxifraga oppositifolia(Purple saxifrage)[J].New Phytologist,2003,161(1):211-224.
[30]DECHAINE E G,ANDERSON S A,MCNEW J M,et al.On the evolutionary and biogeographic history of Saxifraga sect.Trachyphyllum(Gaud.)Koch(Saxifragaceae Juss.)[J].PLoS One,2013,8(7):e69814.
[31]EBERSBACH J,SCHNITZLER J,FAVRE A,et al.Evolutionary radiations in the species-rich mountain genus Saxifraga L[J].BMC Evolutionary Biology,2017,17(1):119.
[32]GAO Q B,LI Y,GENGJI Z M,et al.Population genetic differentiation and taxonomy of three closely related species of Saxifraga(Saxifragaceae)from southern Tibet and the Hengduan Mountains[J].Frontiers in Plant Science,2017,8:1 325.
[33]DOYLE J J,DOYLE J L.A rapid DNA isolation procedure for small quantities of fresh leaf material[J].Phytochemical Bulletin,Botanical Society of America,1987,19(1):11-15.
[34]TABERLET P,GIELLY L,PAUTOU G,et al.Universal primers for amplification of three non-coding regions of chloroplast[J].Plant Molecular Biology,1991,17(5):1 105-1 109.
[35]SCARCELLI N,BARNAUD A,EISERHARDT W,et al.A set of 100chloroplast DNA primer pairs to study population genetics and phylogeny in Monocotyledons[J].PLoS One,2011,6(5):e19954.
[36]KUMAR S,STECHER G,TAMURA K.MEGA 7:Molecular evolutionary genetics analysis version 7.0for bigger datasets[J].Molecular Biology and Evolution,2016,33(7):1 870-1 874.
[37]LIBRADO P,ROZAS J.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1 451-1 452.
[38]PONS O,PETIT R J.Measuring and testing genetic differentiation with ordered versus unordered alleles[J].Genetics,1996,144(3):1 237-1 245.
[39]EXCOFFIER L,LISCHER H E L.Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under Linux and Windows[J].Molecular Ecology Resources,2010,10(3):564-567.
[40]WEIR B S,COCKERHAM C C.Estimating F-Statistics for the analysis of population structure[J].Evolution,1984,38(6):1 358-1 370.
[41]TAJIMA F.Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J].Genetics,1989,123(3):585-595.
[42]FU Y X,LI W H.Statistical tests of neutrality of mutations[J].Genetics,1993,133(3):693-709.
[43]BANDELT H J,FORSTER P,ROHL A.Median-joining networks for inferring intraspecific phylogenies[J].Molecular Biology and Evolution,1999,16(1):37-48.
[44]POLZIN T,DANESHMAND S V.On Steiner trees and minimum spanning trees in hypergrahs[J].Operations Research Letters,2003,31(1):12-20.
[45]GOLDING G B.The detection of deleterious selection using ancestors inferred from a phylogenetic history[J].Genetics Research,1987,49(1):71-82.
[46]CRANDALL K A,TEMPLETON A R.Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction[J].Genetics,1993,134(3):959-969.
[47]WANG F Y,GONG X,HU C M,et al.Phylogeography of an alpine species Primula secundiflora inferred from the chloroplast DNA sequence variation[J].Journal of Systematics and Evolution,2008,46(1):13-22.
[48]王晓雄,乐霁培,孙航,等.青藏高原高山流石滩特有植物绵参的谱系地理学研究[J].植物分类与资源学报,2011,33(6):605-614.WANG X X,YUE J P,SUN H,et al.Phylogeographical study on Eriophyton wallichii(Labiatae)from Alpine scree of Qinghai-Tibetan Plateau[J].Plant Diversity&Resources,2011,33(6):605-614.
[49]DYNESIUS M,JANSSON R.Evolutionary consequences of changes in species'geographical distributions driven by Milankovitch climate oscillations[J].Proceedings of the National Academy of Sciences of the United States of America,2000,97(16):9 115-9 120.
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