喜马拉雅—横断山区优越虎耳草谱系地理学研究
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摘要
利用叶绿体DNA非基因编码区rpl20-rps12和trn L-trn F作为分子标记,对喜马拉雅—横断山区优越虎耳草13个居群151个个体进行谱系地理学研究,旨在揭示优越虎耳草现有的遗传结构及其演化历程。共检测到19个单倍型,其中63%的单倍型为居群特有单倍型。研究还发现,优越虎耳草居群总的遗传多样性较高(H_t=0. 868),居群内平均遗传多样性较低(H_s=0. 466)。分子变异分析(AMOVA)表明,优越虎耳草居群57. 37%的遗传变异来自居群内,居群间遗传变异为42. 63%。居群遗传分化系数N_(st)大于G_(st)(N_(st)=0. 463,G_(st)=0. 438,P>0. 05),但不显著,表明优越虎耳草在其整个分布范围内没有明显的谱系地理结构。中性检验结果表明,Tajima’s D为负值(-1. 348 32,P> 0. 05)而Fu’s F_s*为正值(18. 915 72,P> 0. 05),但均不显著,结合歧点分布分析发现该物种在整个分布范围内未经历过居群扩张。此外,在本研究中优越虎耳草遗传多样性和核苷酸多样性较高的居群及大量特有单倍型在整个分布范围内随机分布,符合"微型避难所"假说。优越虎耳草居群在冰期可能随气候波动而发生分布范围的不断变化,最终在相互隔离的"高山岛屿"中发生异域分化,导致大量特有单倍型产生。因此,推测优越虎耳草与其生境中的乔木和灌木可能具有相似的谱系地理历史,它们可为优越虎耳草提供微型避难所而使之在冰期时保留下来。
The experiment was conducted to studygenetic structure and phylogeographic history of Saxifraga egregia,by using two chloroplast DNA sequences,rpl20-rps12 and trn L-trn F,and a sampling strategy of 151 individuals from 13 populations in the Himalaya-Hengduan Mountains. Nineteen haplotypes( H1-H19) were detected based on the concatenated sequences of rpl20-rps12 and trn L-trn F. Haplotype H2 was wide-spread across the distribution range of S. egregia,while 63% were private haplotypes. Genetic structure analysis detected a high level of total gene diversity( H_t= 0. 868),however,average within-population diversity was relatively low( H_s= 0. 466). By analysis of molecular variance,57. 37% of the total variation was described aswithin-population variation,while among-population variation was represented as 42. 63%. An estimation of non-significantly larger N_(st)( 0. 463) than G_(st)( 0. 438,P > 0. 05) value suggested an absence of phylogeographic structure across the whole distribution range of S. egregia. Recent range expansion or demographic expansion at the level of total gene pool of S. egregia were rejected according to neutrality tests and mismatch distribution analysis. Genetic signal of a stochastic distribution of private haplotypes,as well as populations with high gene diversity and nucleotide diversity,suggesting the existence of multi-microrefugia of S. egregia during Quaternary glaciations. Repeated expansion and contraction of distribution range of S. egregia during Quaternary glaciations could have finally fragmented its distribution range into isolated "alpine islands",and have facilitated allopatric divergence,resulting in the formation of high proportion of private haplotypes across the distribution range of S.egregia. It has been reported that some trees and shrubs inhabited by S. egregia showed multi microrefugiain the Qinghai-Tibetan Plateau during Quaternary glaciations,which may have provided suitable micro-environment for the in situ survival of S. egregia during glacials.
The experiment was conducted to studygenetic structure and phylogeographic history of Saxifraga egregia,by using two chloroplast DNA sequences,rpl20-rps12 and trn L-trn F,and a sampling strategy of 151 individuals from 13 populations in the Himalaya-Hengduan Mountains. Nineteen haplotypes( H1-H19) were detected based on the concatenated sequences of rpl20-rps12 and trn L-trn F. Haplotype H2 was wide-spread across the distribution range of S. egregia,while 63% were private haplotypes. Genetic structure analysis detected a high level of total gene diversity( H_t= 0. 868),however,average within-population diversity was relatively low( H_s= 0. 466). By analysis of molecular variance,57. 37% of the total variation was described aswithin-population variation,while among-population variation was represented as 42. 63%. An estimation of non-significantly larger N_(st)( 0. 463) than G_(st)( 0. 438,P > 0. 05) value suggested an absence of phylogeographic structure across the whole distribution range of S. egregia. Recent range expansion or demographic expansion at the level of total gene pool of S. egregia were rejected according to neutrality tests and mismatch distribution analysis. Genetic signal of a stochastic distribution of private haplotypes,as well as populations with high gene diversity and nucleotide diversity,suggesting the existence of multi-microrefugia of S. egregia during Quaternary glaciations. Repeated expansion and contraction of distribution range of S. egregia during Quaternary glaciations could have finally fragmented its distribution range into isolated "alpine islands",and have facilitated allopatric divergence,resulting in the formation of high proportion of private haplotypes across the distribution range of S.egregia. It has been reported that some trees and shrubs inhabited by S. egregia showed multi microrefugiain the Qinghai-Tibetan Plateau during Quaternary glaciations,which may have provided suitable micro-environment for the in situ survival of S. egregia during glacials.
引文
1. Avise J C,Arnold J,Ball R M,et al. Intraspecific phylogeography:the mitochondrial DNA bridge between population genetics and systematics[J]. Annual Review of Ecology and Systematics,1987,18:489-522.
2. Liu J Q,Sun Y S,Ge X J,et al. Phylogeographic studies of plants in China:Advances in the past and directions in the future[J]. Journal of Systematics and Evolution,2012,50(4):267-275.
3. Avise J C. Phylogeography:the history and formation of species[M]. Cambridge,MA,USA:Harvard University Press,2000.
4. Hewitt G M. Speciation,hybrid zones and phylogeographyor seeing genes in space and time[J]. Molecular Ecology,2001,10(3):537-549.
5. Myers N,Mittermeier R A,Mittermeier C G,et al. Biodiversity hotspots for conservation priorities[J]. Nature,2000,403(6772):853-858.
6. 武素功,杨永平,费勇.青藏高原高寒地区种子植物区系的研究[J].云南植物研究,1995,17(3):233-250.Wu S G,Yang Y P,Fei Y. On the flora of the alpine region in the Qinghai-Xizang(Tibet)Plateau[J]. Acta Botanica Yunnanica,1995,17(3):233-250.
7. 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.
8. Eaton D A R,Fensterc B,Hereford J,et al. Floral diversity and community structure in Pedicularis(Orobanchaceae)[J]. Ecology,2012,93(sp8):S182-S194.
9. Wang Y J,Susanna A,Von Raab-Straube E,et al. Islandlike radiation of Saussurea(Asteraceae:Cardueae)triggered by uplifts of the Qinghai-Tibetan Plateau[J]. Biological Journal of the Linnean Society,2009,97(4):893-903.
10. 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 trn L-F and psb A-trn H sequences[J]. Systematic Botany,2014,39(2):441-451.
11. Hewitt G M. Genetic consequences of climatic oscillations in the Quaternary[J]. Philosophical Transactions of the Royal Society B:Biological Sciences,2004,359(1442):183-195.
12. 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):3513-3524.
13. Meng L H,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):4128-4137.
14. Yang F S,Li Y F,Ding X,et al. Extensive population expansion of Pedicularis longiflora(Orobanchaceae)on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change[J]. Molecular Ecology,2008,17(23):5135-5145.
15. Duan Y Z,Gao Q B,Zhang F Q,et al. Phylogeographic analysis of the endemic species Sibiraea angustata reveals a marginal refugium in the Qinghai-Tibet Plateau[J]. Nordic Journal of Botany,2011,29(5):615-624.
16. Gao Q B,Zhang F Q,Xing R,et al. Phylogeographic study revealed microrefugia foran endemic species on the Qinghai-Tibetan Plateau:Rhodiola chrysanthemifolia(Crassulaceae)[J]. Plant Systematics and Evolution,2016,302(9):1179-1193.
17. 更吉卓玛,李彦,贾留坤,等.唐古特虎耳草谱系地理学研究[J].西北植物学报,2018,38(2):370-380.Gengji Z M,Li Y,Jia L K,et al. Phylogeography of Saxifraga tangutica Engl.(Saxifragaceae)[J]. Acta Botanica Boreali-Occidentalia Sinica,2018,38(2):370-380.
18. Wang H,Qiong L,Sun K,et al. Phylogeographic structure of Hippophae tibetana(Elaeagnaceae)highlights the highest microrefugia and the rapid uplift of the Qinghai-Tibetan Plateau[J]. Molecular Ecology,2010,19(14):2964-2979.
19. 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.
20. Pan J T,Richard G,Hideaki O. Flora of China[M]. Beijing:Science Press,2001.
21. 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.
22. 中国科学院中国植物志委员会.中国植物志:第34卷第2分册[M].北京:科学出版社,1992.Chinese Academy of Sciences. Reipubliacepopularissinice[M]. Beijing:Science Press,1992.
23. Doyle J J,Doyle J L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochemical Bulletin,1987,19(1):11-15.
24. Hamilton M B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation[J]. Molecular Ecology,1999,8(3):521-523.
25. Taberlet P,Gielly L,Pautou G,et al. Universal primers for amplification of three non-coding regions of chloroplast DNA[J]. Plant Molecular Biology,1991,17(5):1105-1109.
26. Tamura K,Stecher G,Peterson D,et al. MEGA6:Molecular evolutionary genetics analysis version 6. 0[J]. Molecular Biology and Evolution,2013,30(12):2725-2729.
27. Librado P,Rozas J. Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics,2009,25(11):1451-1452.
28. Pons O,Petit R J. Measuring and testing genetic differentiation with ordered versus unordered alleles[J]. Genetics,1996,144(3):1237-1245.
29. 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.
30. Weir B S,Cockerham C C. Estimating F-statistics for the analysis of population structure[J]. Evolution,1984,38(6):1358-1370.
31. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics,1989,123(3):585-595.
32. Fu Y X. Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J]. Genetics,1997,147(2):915-925.
33. Bandelt H J,Forster P,R9hl A. Median-joining networks for inferring intraspecific phylogenies.[J]. Molecular Biology and Evolution,1999,16(1):37-48.
34. Golding G B. The detection of deleterious selection using ancestors inferred from a phylogenetic history[J]. Genetical Research,1987,49(1):71-82.
35. Wang L Y,Abbott R J,Zheng W,et al. History and evolution of alpine plants endemicto the Qinghai-Tibetan Plateau:Aconitum gymnandrum(Ranunculaceae)[J]. Molecular Ecology,2009,18(4):709-721.
36. Gao Q B,Zhang D J,Duan Y Z,et al. Intraspecific divergences of Rhodiolaalsia(Crassulaceae)based on plastid DNA and internal transcribed spacer fragments[J]. Botanical Journal of the Linnean Society,2012,168(2):204-215.
37. 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.
38. Opgenoorth L,Vendramin G G,Mao K S,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.
39. Zhang Y H,Volis S,Sun H. Chloroplast phylogeny and phylogeography of Stellera chamaejasme on the Qinghai-Tibet Plateau and in adjacent regions[J]. Molecular Phylogeneticsand Evolution,2010,57(3):1162-1172.
40. 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):1268-1278.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):1268-1278.
41. Chen S Y,Wu G L,Zhang D J,et al. Potential refugium on the Qinghai-Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata(Gentianaceae)[J]. Botanical Journal of the Linnean Society,2008,157(1):125-140.
2. Liu J Q,Sun Y S,Ge X J,et al. Phylogeographic studies of plants in China:Advances in the past and directions in the future[J]. Journal of Systematics and Evolution,2012,50(4):267-275.
3. Avise J C. Phylogeography:the history and formation of species[M]. Cambridge,MA,USA:Harvard University Press,2000.
4. Hewitt G M. Speciation,hybrid zones and phylogeographyor seeing genes in space and time[J]. Molecular Ecology,2001,10(3):537-549.
5. Myers N,Mittermeier R A,Mittermeier C G,et al. Biodiversity hotspots for conservation priorities[J]. Nature,2000,403(6772):853-858.
6. 武素功,杨永平,费勇.青藏高原高寒地区种子植物区系的研究[J].云南植物研究,1995,17(3):233-250.Wu S G,Yang Y P,Fei Y. On the flora of the alpine region in the Qinghai-Xizang(Tibet)Plateau[J]. Acta Botanica Yunnanica,1995,17(3):233-250.
7. 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.
8. Eaton D A R,Fensterc B,Hereford J,et al. Floral diversity and community structure in Pedicularis(Orobanchaceae)[J]. Ecology,2012,93(sp8):S182-S194.
9. Wang Y J,Susanna A,Von Raab-Straube E,et al. Islandlike radiation of Saussurea(Asteraceae:Cardueae)triggered by uplifts of the Qinghai-Tibetan Plateau[J]. Biological Journal of the Linnean Society,2009,97(4):893-903.
10. 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 trn L-F and psb A-trn H sequences[J]. Systematic Botany,2014,39(2):441-451.
11. Hewitt G M. Genetic consequences of climatic oscillations in the Quaternary[J]. Philosophical Transactions of the Royal Society B:Biological Sciences,2004,359(1442):183-195.
12. 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):3513-3524.
13. Meng L H,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):4128-4137.
14. Yang F S,Li Y F,Ding X,et al. Extensive population expansion of Pedicularis longiflora(Orobanchaceae)on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change[J]. Molecular Ecology,2008,17(23):5135-5145.
15. Duan Y Z,Gao Q B,Zhang F Q,et al. Phylogeographic analysis of the endemic species Sibiraea angustata reveals a marginal refugium in the Qinghai-Tibet Plateau[J]. Nordic Journal of Botany,2011,29(5):615-624.
16. Gao Q B,Zhang F Q,Xing R,et al. Phylogeographic study revealed microrefugia foran endemic species on the Qinghai-Tibetan Plateau:Rhodiola chrysanthemifolia(Crassulaceae)[J]. Plant Systematics and Evolution,2016,302(9):1179-1193.
17. 更吉卓玛,李彦,贾留坤,等.唐古特虎耳草谱系地理学研究[J].西北植物学报,2018,38(2):370-380.Gengji Z M,Li Y,Jia L K,et al. Phylogeography of Saxifraga tangutica Engl.(Saxifragaceae)[J]. Acta Botanica Boreali-Occidentalia Sinica,2018,38(2):370-380.
18. Wang H,Qiong L,Sun K,et al. Phylogeographic structure of Hippophae tibetana(Elaeagnaceae)highlights the highest microrefugia and the rapid uplift of the Qinghai-Tibetan Plateau[J]. Molecular Ecology,2010,19(14):2964-2979.
19. 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.
20. Pan J T,Richard G,Hideaki O. Flora of China[M]. Beijing:Science Press,2001.
21. 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.
22. 中国科学院中国植物志委员会.中国植物志:第34卷第2分册[M].北京:科学出版社,1992.Chinese Academy of Sciences. Reipubliacepopularissinice[M]. Beijing:Science Press,1992.
23. Doyle J J,Doyle J L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J]. Phytochemical Bulletin,1987,19(1):11-15.
24. Hamilton M B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation[J]. Molecular Ecology,1999,8(3):521-523.
25. Taberlet P,Gielly L,Pautou G,et al. Universal primers for amplification of three non-coding regions of chloroplast DNA[J]. Plant Molecular Biology,1991,17(5):1105-1109.
26. Tamura K,Stecher G,Peterson D,et al. MEGA6:Molecular evolutionary genetics analysis version 6. 0[J]. Molecular Biology and Evolution,2013,30(12):2725-2729.
27. Librado P,Rozas J. Dna SP v5:a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics,2009,25(11):1451-1452.
28. Pons O,Petit R J. Measuring and testing genetic differentiation with ordered versus unordered alleles[J]. Genetics,1996,144(3):1237-1245.
29. 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.
30. Weir B S,Cockerham C C. Estimating F-statistics for the analysis of population structure[J]. Evolution,1984,38(6):1358-1370.
31. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics,1989,123(3):585-595.
32. Fu Y X. Statistical tests of neutrality of mutations against population growth,hitchhiking and background selection[J]. Genetics,1997,147(2):915-925.
33. Bandelt H J,Forster P,R9hl A. Median-joining networks for inferring intraspecific phylogenies.[J]. Molecular Biology and Evolution,1999,16(1):37-48.
34. Golding G B. The detection of deleterious selection using ancestors inferred from a phylogenetic history[J]. Genetical Research,1987,49(1):71-82.
35. Wang L Y,Abbott R J,Zheng W,et al. History and evolution of alpine plants endemicto the Qinghai-Tibetan Plateau:Aconitum gymnandrum(Ranunculaceae)[J]. Molecular Ecology,2009,18(4):709-721.
36. Gao Q B,Zhang D J,Duan Y Z,et al. Intraspecific divergences of Rhodiolaalsia(Crassulaceae)based on plastid DNA and internal transcribed spacer fragments[J]. Botanical Journal of the Linnean Society,2012,168(2):204-215.
37. 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.
38. Opgenoorth L,Vendramin G G,Mao K S,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.
39. Zhang Y H,Volis S,Sun H. Chloroplast phylogeny and phylogeography of Stellera chamaejasme on the Qinghai-Tibet Plateau and in adjacent regions[J]. Molecular Phylogeneticsand Evolution,2010,57(3):1162-1172.
40. 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):1268-1278.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):1268-1278.
41. Chen S Y,Wu G L,Zhang D J,et al. Potential refugium on the Qinghai-Tibet Plateau revealed by the chloroplast DNA phylogeography of the alpine species Metagentiana striata(Gentianaceae)[J]. Botanical Journal of the Linnean Society,2008,157(1):125-140.