杨属分子系统发育及三个山杨物种的生物地理学研究
|
摘要
植物物种的系统发育关系和物种形成过程一直以来都是植物进化生物学研究中最基本的问题。系统发育关系的重建能够很好的解决各个物种间的关系，而物种形成研究是理解自然界物种多样性产生和变化的基础。准确估算各植物类群的出现时间对于推断其生物地理学具有非常重要的意义。在过去二十多年中，生物技术和理论方法的进步极大地推动了进化生物学的发展，促进了人们对一些重要植物类群系统发育关系、物种形成及生物地理学的认识，如拟南芥、玉米或水稻等。在木本植物中，利用核苷酸序列的变异式样对不同类群的系统发育关系、物种形成模式及生物地理学的研究已经非常成熟。但是对于模式植物杨属（Populus）来说，上述研究还鲜有报道。本文中，通过多基因位点序列的使用探讨了杨属分子系统发育关系及白杨派（section Populus）内中国山杨（P.davidiana）、欧洲山杨（P. tremula）和美洲山杨（P. tremuloides）的生物地理学。主要研究结果如下：
1）使用生物信息学的方法，利用毛果杨（P. trichocarpa）和钻天柳（Salix arbutifolia）全基因组数据，筛选了24个在杨柳科内通用的单拷贝核基因位点作为遗传标记，并分别使用中国山杨和旱柳（S. matsudana）20个个体及杨属各派及柳属代表物种对其中15个位点的核苷酸多样性进行了计算。结果表明所有位点均含有丰富的系统发育信息并且均符合中性进化假设，满足了本文后续分析的需要。
2）由于杨属种间杂交渐渗比较严重及种内形态变异比较大，杨属种间系统发育关系一直没有得到较好的解决。基于24个单拷贝核基因位点和12个叶绿体位点，对杨属各派及派内物种间系统发育关系做了深入研究。结果表明杨属是一个单系类群。在叶绿体系统发育树中，所有杨属物种形成两个分枝，一枝包括白杨派、大叶杨派及黑杨派和青杨派个别物种，另一枝包括胡杨派及黑杨派、青杨派的物种，这种拓扑结构表明杨属的母系祖先类群在形成初期即产生了分化。在核基因系统发育树中，胡杨派作为其他各派的基部类群，大叶杨派和白杨派次之，而青杨派和黑杨派占据系统发育树的末端位置。胡杨派与白杨派为单系类群而黑杨派和青杨派为复系类群。白杨派、黑杨派和青杨派很可能都是杂交起源的。对比分析核基因和叶绿体系统发育树可以发现，杨属中很多物种都是杂交起源的，如毛白杨、欧洲黑杨等。理解了这些物种的杂交起源方式有助于深刻剖析杨属中广泛存在的网状进化事件。在杨属的进化历史中，网状进化起到了非常关键的作用，同时也推动了杨属物种在不同分布区内的快速适应辐射。
3）中国山杨、欧洲山杨和美洲山杨的外部形态非常相似并且亲缘关系非常近，这导致国内外学者对于三种山杨的分类学界定产生了矛盾，同时对于三种山杨的物种形成模式和生物地理学也缺少研究。本文中，通过大规模多居群多样本的采集，使用6个单拷贝核基因位点和3个叶绿体位点对上述问题进行了研究。结果表明，三种山杨都表现出非常高的核苷酸多样性，某些位点的多样性甚至与一年生植物相当。三种山杨之间产生了非常显著的遗传分化，Structure分析结果表明K=3为最佳聚类模型，并且三种山杨没有共享的叶绿体单倍型。上述结果表明将中国山杨划分为欧洲山杨的一个亚种或者将三种山杨合并为一个物种的分类学处理都是不合适的，三种山杨应该各自划分为独立的物种。叶绿体单倍型系统发育树和核基因位点物种树结果都表明美洲山杨是三个物种中最原始的类群。Beast宽松分子钟计算结果表明三个物种的分化处于第四纪初期。三个物种的祖先类群通过白令陆桥从北美大陆扩散至欧亚大陆并在较短时间内在欧亚大陆广泛分布。白令海峡的形成和青藏高原北部及邻近地区在第四纪的持续隆升将三个物种的分布区隔离开来。三个物种自共同祖先分化后种群经历了扩张-缩减的过程，并且彼此间并无显著的基因流，三个物种的物种形成模式为地理隔离形成导致的异域物种形成。
Inferring phylogeny and speciation process of plant species is one of the mostfundamental problems in plant evolution biology. Reconstruction of phylogeny will dissectrelationships among species and understanding speciation process is a prerequisite to explainorigin and variation of species diversity. It is of great helpful to infer the divergence and originof species accurately in detecting the biogeography history. In the past decades, advance onboth biological techniques and theoretical methodologies have remarkably reshaped ourunderstanding of phylogeny, speciation and biogeography history among model organisms,such as Arabidopsis, maize and rice. In tree species, researches on the phylogeny, speciationand biogeography history of different lineages using the variance pattern of nucleotidesequence have accumulated, however, rareness has been reported in model tree species,Populus. In this study, using multiple nucleotide loci, the molecular phylogeny of Populus andthe speciation model and biogeography of three aspens in section Populus, P. davidiana, P.tremula and P. tremuloides were explored. The main results are as follows:
1)24single-copy nuclear markers were developed through bioinformatics methods basedon whole genomic sequences of P. trichocarpa and Salix arbutifolia. Twenty individuals of P.davidiana and S. matsudana were used to evaluate the basic application of15loci with respectto marker length and diversity indices, respectively. Results indicated that all the15locicontained abundant high phylogenetic information and fitted the null hypothesis of neutralevolution well. The utility of single-copy nuclear markers will facilitate subsequent studies onphylogeny, population genetics and biogeography, as well as the evolutionary dynamics ofSalicaceae.
2) The complex reticulate evolution (hybridization, introgression) and highly variableintraspecific morphological traits have posed difficulties in resolving the phylogeny of Populus.Based on a large data set of nuclear and chloroplast DNA sequences, we reconstructed robustphylogeny of Populus using maximum parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter-andintra-sectional level than previous studies. The results revealed monophyly of Populus.CpDNA based phylogenetic tree resulted in two main clades, one consisted section Populus,Leucoides and species of section Aigeiros and Tacamahaca, the other comprised of sectionTuranga and the remaining species of section Aigeiros and Tacamahaca. This topologysuggested an early divergence of the maternal progenitors of Populus. In the nuclear DNAbased phylogenetic tree, section Turanga occupied the basal position following sectionPopulus and Leucoides, section Aigeiros and Tacamahaca took the terminal position. SectionPopulus and Turanga were monophyly and section Aigeiros and Tacamahaca were polyphyly.The three advanced sections, Populus, Aigeiros and Tacamahaca may be hybridized origin.Comparative analysis of the cpDNA and nuclear DNA based phylogeny elucidated that somespecies were hybrid origin, such as P. tomentosa, P. nigra and P. deltoides. Realizing the hybridorigin of species in Populus will conspicuously promote our understanding the reticulateevolution in Populus, which may have played a significant role in the evolution history ofPopulus by facilitating rapid adaptive radiations into different environments.
3) Morphological traits and relationships among P. davidiana, P. tremula and P.tremuloides were close, which caused huge controversy on the taxonomical delimitation of thethree aspens. Furthermore, speciation model and biogeography of these three aspens havenever been reported before. In this study, these questions were addressed using multilocusnucleotide sequences and multiple samples. All the three aspens showed high nucleotidediversity, which was comparable with that of annual plant species in some loci. Significantgenetic differentiation was detected among the three aspens and Structure results showed thebest clustering model when K=3. Furthermore, no shared cpDNA haplotype was probed. Basedon these findings, we proposed that previous taxonomic classification which classified P.davidiana as a subspecies of P. tremula or classified these three aspens as one species wasinappropriate. The three aspens should be delimitated as three single species. Phylogenetic treebased on cpDNA haplotypes and BEST species tree based on6nuclear loci showed that P.tremuloides was the more ancestral lineage in the three species. Divergence of the three species inferred from Beast relaxed molecular clock occurred in early Quaternary. The ancestrallineage dispersed from North America to Eurasia through Beringia land bridge (BLB) followedby fast expansion throughout Eurasia. The formation of Bering strait and the uplift of thenorthern Qinghai-Tibetan Plateau (QTP) and adjacent area in Quaternary isolated thedistribution of the three species, which have undergone a process of populationexpansion-contraction dynamics since divergence from the common ancestor. No obvious geneflow was detected which suggested that the present patterns of nucleotide variation was notshaped by migration among these species and that introgression was not pervasive in the groupof species. The speciation model of the three species was allopatric speciation caused byvicariance.
1）使用生物信息学的方法，利用毛果杨（P. trichocarpa）和钻天柳（Salix arbutifolia）全基因组数据，筛选了24个在杨柳科内通用的单拷贝核基因位点作为遗传标记，并分别使用中国山杨和旱柳（S. matsudana）20个个体及杨属各派及柳属代表物种对其中15个位点的核苷酸多样性进行了计算。结果表明所有位点均含有丰富的系统发育信息并且均符合中性进化假设，满足了本文后续分析的需要。
2）由于杨属种间杂交渐渗比较严重及种内形态变异比较大，杨属种间系统发育关系一直没有得到较好的解决。基于24个单拷贝核基因位点和12个叶绿体位点，对杨属各派及派内物种间系统发育关系做了深入研究。结果表明杨属是一个单系类群。在叶绿体系统发育树中，所有杨属物种形成两个分枝，一枝包括白杨派、大叶杨派及黑杨派和青杨派个别物种，另一枝包括胡杨派及黑杨派、青杨派的物种，这种拓扑结构表明杨属的母系祖先类群在形成初期即产生了分化。在核基因系统发育树中，胡杨派作为其他各派的基部类群，大叶杨派和白杨派次之，而青杨派和黑杨派占据系统发育树的末端位置。胡杨派与白杨派为单系类群而黑杨派和青杨派为复系类群。白杨派、黑杨派和青杨派很可能都是杂交起源的。对比分析核基因和叶绿体系统发育树可以发现，杨属中很多物种都是杂交起源的，如毛白杨、欧洲黑杨等。理解了这些物种的杂交起源方式有助于深刻剖析杨属中广泛存在的网状进化事件。在杨属的进化历史中，网状进化起到了非常关键的作用，同时也推动了杨属物种在不同分布区内的快速适应辐射。
3）中国山杨、欧洲山杨和美洲山杨的外部形态非常相似并且亲缘关系非常近，这导致国内外学者对于三种山杨的分类学界定产生了矛盾，同时对于三种山杨的物种形成模式和生物地理学也缺少研究。本文中，通过大规模多居群多样本的采集，使用6个单拷贝核基因位点和3个叶绿体位点对上述问题进行了研究。结果表明，三种山杨都表现出非常高的核苷酸多样性，某些位点的多样性甚至与一年生植物相当。三种山杨之间产生了非常显著的遗传分化，Structure分析结果表明K=3为最佳聚类模型，并且三种山杨没有共享的叶绿体单倍型。上述结果表明将中国山杨划分为欧洲山杨的一个亚种或者将三种山杨合并为一个物种的分类学处理都是不合适的，三种山杨应该各自划分为独立的物种。叶绿体单倍型系统发育树和核基因位点物种树结果都表明美洲山杨是三个物种中最原始的类群。Beast宽松分子钟计算结果表明三个物种的分化处于第四纪初期。三个物种的祖先类群通过白令陆桥从北美大陆扩散至欧亚大陆并在较短时间内在欧亚大陆广泛分布。白令海峡的形成和青藏高原北部及邻近地区在第四纪的持续隆升将三个物种的分布区隔离开来。三个物种自共同祖先分化后种群经历了扩张-缩减的过程，并且彼此间并无显著的基因流，三个物种的物种形成模式为地理隔离形成导致的异域物种形成。
Inferring phylogeny and speciation process of plant species is one of the mostfundamental problems in plant evolution biology. Reconstruction of phylogeny will dissectrelationships among species and understanding speciation process is a prerequisite to explainorigin and variation of species diversity. It is of great helpful to infer the divergence and originof species accurately in detecting the biogeography history. In the past decades, advance onboth biological techniques and theoretical methodologies have remarkably reshaped ourunderstanding of phylogeny, speciation and biogeography history among model organisms,such as Arabidopsis, maize and rice. In tree species, researches on the phylogeny, speciationand biogeography history of different lineages using the variance pattern of nucleotidesequence have accumulated, however, rareness has been reported in model tree species,Populus. In this study, using multiple nucleotide loci, the molecular phylogeny of Populus andthe speciation model and biogeography of three aspens in section Populus, P. davidiana, P.tremula and P. tremuloides were explored. The main results are as follows:
1)24single-copy nuclear markers were developed through bioinformatics methods basedon whole genomic sequences of P. trichocarpa and Salix arbutifolia. Twenty individuals of P.davidiana and S. matsudana were used to evaluate the basic application of15loci with respectto marker length and diversity indices, respectively. Results indicated that all the15locicontained abundant high phylogenetic information and fitted the null hypothesis of neutralevolution well. The utility of single-copy nuclear markers will facilitate subsequent studies onphylogeny, population genetics and biogeography, as well as the evolutionary dynamics ofSalicaceae.
2) The complex reticulate evolution (hybridization, introgression) and highly variableintraspecific morphological traits have posed difficulties in resolving the phylogeny of Populus.Based on a large data set of nuclear and chloroplast DNA sequences, we reconstructed robustphylogeny of Populus using maximum parsimony, maximum likelihood and Bayesian inference methods. The resulting phylogenetic trees showed better resolution at both inter-andintra-sectional level than previous studies. The results revealed monophyly of Populus.CpDNA based phylogenetic tree resulted in two main clades, one consisted section Populus,Leucoides and species of section Aigeiros and Tacamahaca, the other comprised of sectionTuranga and the remaining species of section Aigeiros and Tacamahaca. This topologysuggested an early divergence of the maternal progenitors of Populus. In the nuclear DNAbased phylogenetic tree, section Turanga occupied the basal position following sectionPopulus and Leucoides, section Aigeiros and Tacamahaca took the terminal position. SectionPopulus and Turanga were monophyly and section Aigeiros and Tacamahaca were polyphyly.The three advanced sections, Populus, Aigeiros and Tacamahaca may be hybridized origin.Comparative analysis of the cpDNA and nuclear DNA based phylogeny elucidated that somespecies were hybrid origin, such as P. tomentosa, P. nigra and P. deltoides. Realizing the hybridorigin of species in Populus will conspicuously promote our understanding the reticulateevolution in Populus, which may have played a significant role in the evolution history ofPopulus by facilitating rapid adaptive radiations into different environments.
3) Morphological traits and relationships among P. davidiana, P. tremula and P.tremuloides were close, which caused huge controversy on the taxonomical delimitation of thethree aspens. Furthermore, speciation model and biogeography of these three aspens havenever been reported before. In this study, these questions were addressed using multilocusnucleotide sequences and multiple samples. All the three aspens showed high nucleotidediversity, which was comparable with that of annual plant species in some loci. Significantgenetic differentiation was detected among the three aspens and Structure results showed thebest clustering model when K=3. Furthermore, no shared cpDNA haplotype was probed. Basedon these findings, we proposed that previous taxonomic classification which classified P.davidiana as a subspecies of P. tremula or classified these three aspens as one species wasinappropriate. The three aspens should be delimitated as three single species. Phylogenetic treebased on cpDNA haplotypes and BEST species tree based on6nuclear loci showed that P.tremuloides was the more ancestral lineage in the three species. Divergence of the three species inferred from Beast relaxed molecular clock occurred in early Quaternary. The ancestrallineage dispersed from North America to Eurasia through Beringia land bridge (BLB) followedby fast expansion throughout Eurasia. The formation of Bering strait and the uplift of thenorthern Qinghai-Tibetan Plateau (QTP) and adjacent area in Quaternary isolated thedistribution of the three species, which have undergone a process of populationexpansion-contraction dynamics since divergence from the common ancestor. No obvious geneflow was detected which suggested that the present patterns of nucleotide variation was notshaped by migration among these species and that introgression was not pervasive in the groupof species. The speciation model of the three species was allopatric speciation caused byvicariance.
引文
Akaike, H.1973. Information theory and an extension of the maximum likelihood principle. In: Secondinternational symposium on information theory, pp.267-281.
Altschul, S.F., Madden, T.L., Sch ffer, A.A., et al.1997, Gapped BLAST and PSI-BLAST: a new generationof protein database search programs. Nucleic acids research,25(17):3389-3402.
Antonelli, A., Nylander, J.A., Persson, C., et al.2009, Tracing the impact of the Andean uplift on Neotropicalplant evolution. Proceedings of the National Academy of Sciences,106(24):9749-9754.
Arunyawat, U., Stephan, W., St dler, T.2007, Using multilocus sequence data to assess population structure,natural selection, and linkage disequilibrium in wild tomatoes. Molecular Biology and Evolution,24(10):2310-2322.
Augustin, L., Barbante, C., Barnes, P.R., et al.2004, Eight glacial cycles from an Antarctic ice core. Nature,429(6992):623-628.
Bailey, J.K., Deckert, R., Schweitzer, J.A., et al.2005, Host plant genetics affect hidden ecological players:links among Populus, condensed tannins, and fungal endophyte infection. Canadian Journal of Botany,83(4):356-361.
Barbier, P.1989, Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon,1:Population differentiation in life-history traits and isozymic loci. Japanese Journal of Genetics (Japan).
Barker, N.P., Weston, P.H., Rutschmann, F., et al.2007, Molecular dating of the ‘Gondwanan’plant familyProteaceae is only partially congruent with the timing of the break‐up of Gondwana. Journal ofBiogeography,34(12):2012-2027.
Barluenga, M., St lting, K.N., Salzburger, W., et al.2006, Sympatric speciation in Nicaraguan crater lakecichlid fish. Nature,439(7077):719-723.
Barnes, B.V.1967, Indications of possible mid-Cenozoic hybridization in the aspens of the Columbia Plateau.Rhodora,69(777).
Barnes, B.V.1975, Phenotypic variation of trembling aspen in western North America. Forest Science,21(3):319-328.
Barraclough, T.G., Nee, S.2001, Phylogenetics and speciation. Trends in ecology&evolution,16(7):391-399.
Batalha-Filho, H., Cabanne, G.S., Miyaki, C.Y.2012, Phylogeography of an Atlantic forest passerine revealsdemographic stability through the last glacial maximum. Molecular Phylogenetics and Evolution,65(3):892-902.
Baudet, á.B.1999, Notes on the taxonomy of Aeonium urbicum and A. appendiculatum sp. nova(Crassulaceae). Willdenowia-Annals of the Botanic Garden and Botanical Museum Berlin-Dahlem,29(1-2):1-2.
]Bennett, K.1990, Milankovitch cycles and their effects on species in ecological and evolutionary time.Paleobiology11-21.
Bennett, K.2004, Continuing the debate on the role of Quaternary environmental change for macroevolution.Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences,359(1442):295-303.
Bobowski, B., Hole, D., Wolf, P., et al.1999, Identification of roots of woody species using polymerasechain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. MolecularEcology,8(3):485-491.
Bott, M.H.P.,1983, Structure and development of the Greenland-Scotland Ridge: new methods and concepts,Vol1981. Plenum Pub Corp.
Braatne, J., Hinckley, T., Stettler, R.1992, Influence of soil water on the physiological and morphologicalcomponents of plant water balance in Populus trichocarpa, Populus deltoides and their F1hybrids. TreePhysiology,11(4):325-339.
Bradshaw, H., Ceulemans, R., Davis, J., et al.2000, Emerging model systems in plant biology: poplar(Populus) as a model forest tree. Journal of Plant Growth Regulation,19(3):306-313.
Breen, A.L., Glenn, E., Yeager, A., et al.2009, Nucleotide diversity among natural populations of a NorthAmerican poplar (Populus balsamifera, Salicaceae). New Phytologist,182(3):763-773.
Bremer, B., Bremer, K., Chase, M., et al.2009, An update of the Angiosperm Phylogeny Group classificationfor the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society.
Brower, A.V.1996, A new mimetic species of Heliconius (Lepidoptera: Nymphalidae), from southeasternColombia, revealed by cladistic analysis of mitochondrial DNA sequences. Zoological Journal of theLinnean Society,116(3):317-332.
Burgess, R., Yang, Z.2008, Estimation of hominoid ancestral population sizes under Bayesian coalescentmodels incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution,25(9):1979-1994.
Busby, P.E., Catherine Aime, M., Newcombe, G.2012, Foliar pathogens of Populus angustifolia areconsistent with a hypothesis of Beringian migration into North America. Fungal Biology,116(7):792-801.
Campana, M., Hunt, H., Jones, H., et al.2011, CorrSieve: software for summarizing and evaluating Structureoutput. Molecular ecology resources,11(2):349-352.
Campbell, J.S., Mahoney, J.M., Rood, S.B.1993, A lack of heterosis in natural poplar hybrids from southernAlberta. Canadian Journal of Botany,71(1):37-42.
Cervera, M., Storme, V., Soto, A., et al.2005, Intraspecific and interspecific genetic and phylogeneticrelationships in the genus Populus based on AFLP markers. TAG Theoretical and Applied Genetics,111(7):1440-1456.
Charlesworth, D.2003, Effects of inbreeding on the genetic diversity of populations. PhilosophicalTransactions of the Royal Society of London. Series B: Biological Sciences,358(1434):1051-1070.
Chase, M.W., Zmarzty, S., Lledó, M.D., et al.2002, When in doubt, put it in Flacourtiaceae: a molecularphylogenetic analysis based on plastid rbcL DNA sequences. Kew Bulletin,57(1):141-181.
Chaw, S.-M., Parkinson, C.L., Cheng, Y., et al.2000, Seed plant phylogeny inferred from all three plantgenomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proceedings of theNational Academy of Sciences,97(8):4086-4091.
Chaw, S.-M., Zharkikh, A., Sung, H.-M., et al.1997, Molecular phylogeny of extant gymnosperms and seedplant evolution: analysis of nuclear18S rRNA sequences. Molecular Biology and Evolution,14(1):56-68.
Chu, Y., Su, X., Huang, Q., et al.2009, Patterns of DNA sequence variation at candidate gene loci in blackpoplar (Populus nigra L.) as revealed by single nucleotide polymorphisms. Genetica,137(2):141-150.
Clayton, J.W., Soltis, P.S., Soltis, D.E.2009, Recent long-distance dispersal overshadows ancientbiogeographical patterns in a pantropical angiosperm family (Simaroubaceae, Sapindales). SystematicBiology,58(4):395-410.
Cockram, J., White, J., Leigh, F.J., et al.2008, Association mapping of partitioning loci in barley. BMCgenetics,9(1):16.
Cole, C.T.2005, Allelic and population variation of microsatellite loci in aspen (Populus tremuloides). NewPhytologist,167(1):155-164.
Cox, C.B., Moore, P.D.,2010, Biogeography: an ecological and evolutionary approach. John Wiley&Sons.
Coyne, J.A., Orr, H.A.,2004, Speciation, Vol37. Sinauer Associates Sunderland, MA.
Crisci, J., Katinas, L., Posadas, P., et al.2009, Historical biogeography: an introduction. Harvard UniversityPress.
Cronk, Q.2005, Plant eco‐devo: the potential of poplar as a model organism. New Phytologist,166(1):39-48.
D’horta, F., Cabanne, G.S., Meyer, D., et al.2011, The genetic effects of Late Quaternary climatic changesover a tropical latitudinal gradient: diversification of an Atlantic Forest passerine. Molecular Ecology,20(9):1923-1935.
Davis, C.C., Bell, C.D., Mathews, S., et al.2002a, Laurasian migration explains Gondwanan disjunctions:evidence from Malpighiaceae. Proceedings of the National Academy of Sciences,99(10):6833-6837.
Davis, C.C., Fritsch, P.W., Li, J., et al.2002b, Phylogeny and biogeography of Cercis (Fabaceae): evidencefrom nuclear ribosomal ITS and chloroplast ndhF sequence data. Systematic Botany,27(2):289-302.
de Queiroz, A., Gatesy, J.2007, The supermatrix approach to systematics. Trends in ecology&evolution,22(1):34-41.
Delsuc, F., Brinkmann, H., Philippe, H.2005, Phylogenomics and the reconstruction of the tree of life.Nature Reviews Genetics,6(5):361-375.
Demesure, B., Sodzi, N., Petit, R.1995, A set of universal primers for amplification of polymorphic non‐coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology,4(1):129-134.
DiFazio, S., Slavov, G., Joshi, C.2011, Populus: A Premier Pionner System for Plant Genomics. Joshi CD, S.&Kole, C.(ed) Genetics, Genomics and Breeding of poplar. Science Publishers1-28.
Dillen, S.Y., Marron, N., Bastien, C., et al.2007, Effects of environment and progeny on biomassestimations of five hybrid poplar families grown at three contrasting sites across Europe. ForestEcology and Management,252(1):12-23.
Donoghue, M.J., Bell, C.D., Li, J.2001, Phylogenetic patterns in Northern Hemisphere plant geography.International Journal of Plant Sciences,162(S6): S41-S52.
Donoghue, M.J., Moore, B.R.2003, Toward an integrative historical biogeography. Integrative andComparative Biology,43(2):261-270.
Doyle, J.A.1978, Origin of angiosperms. Annual Review of Ecology and Systematics,9(1):365-392.
Doyle, J.A.1998, Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales.Molecular Phylogenetics and Evolution,9(3):448-462.
Doyle, J.J.1987, A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull,1911-15.
Drew, B.T., Ruhfel, B.R., Smith, S.A., et al.2014, Another Look at the Root of the Angiosperms Reveals aFamiliar Tale. Systematic Biologysyt108.
Drummond, A.J., Rambaut, A.2007, BEAST: Bayesian evolutionary analysis by sampling trees. BMCEvolutionary Biology,7(1):214.
Duarte, J.M., Wall, P.K., Edger, P.P., et al.2010, Identification of shared single copy nuclear genes inArabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels.BMC Evolutionary Biology,10(1):61.
Eckenwalder, J.E.,1977. Systematics of Populus L.(Salicaceae) in southwestern North America with specialreference to sect. Aigeiros Duby. University of California, Berkeley,
Eckenwalder, J.E.1984, Natural intersectional hybridization between North American species of Populus(Salicaceae) in sections Aigeiros and Tacamahaca. II. Taxonomy. Canadian Journal of Botany,62(2):325-335.
Eckenwalder, J.E.1996, Systematics and evolution of Populus. Biology of Populus and its implications formanagement and conservation,732.
Edwards, S.V.2009, Is a new and general theory of molecular systematics emerging? Evolution,63(1):1-19.
Edwards, S.V., Liu, L., Pearl, D.K.2007, High-resolution species trees without concatenation. Proceedingsof the National Academy of Sciences,104(14):5936-5941.
EL Little, J.1971, Atlas of United States trees. Volume1. Conifers and important hardwoods. MiscellaneousPublications. United States Department of Agriculture(1146.).
Eldredge, N., Thompson, J.N., Brakefield, P.M., et al.2005, The dynamics of evolutionary stasis.Paleobiology,31(sp5):133-145.
Evanno, G., Regnaut, S., Goudet, J.2005, Detecting the number of clusters of individuals using the softwareSTRUCTURE: a simulation study. Molecular ecology,14(8):2611-2620.
Ewen, K.R., Bahlo, M., Treloar, S.A., et al.2000, Identification and analysis of error types inhigh-throughput genotyping. The American Journal of Human Genetics,67(3):727-736.
Excoffier, L., Laval, G., Schneider, S.2005, Arlequin (version3.0): an integrated software package forpopulation genetics data analysis. Evolutionary bioinformatics online,147.
Excoffier, L., Smouse, P.E., Quattro, J.M.1992, Analysis of molecular variance inferred from metricdistances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics,131(2):479-491.
Felsenstein, J.1981, Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal ofmolecular evolution,17(6):368-376.
Felsenstein, J.1988, Phylogenies from molecular sequences: inference and reliability. Annual review ofgenetics,22(1):521-565.
Felsenstein, J., Felenstein, J.,2004, Inferring phylogenies, Vol2. Sinauer Associates Sunderland.
Fitch, W.M.1971, Toward defining the course of evolution: minimum change for a specific tree topology.Systematic Biology,20(4):406-416.
Floate, K.D.2004, Extent and patterns of hybridization among the three species of Populus that constitutethe riparian forest of southern Alberta, Canada. Canadian Journal of Botany,82(2):253-264.
Fu, Y.-X., Li, W.-H.1993, Statistical tests of neutrality of mutations. Genetics,133(3):693-709.
Fussi, B., Lexer, C., Heinze, B.2010, Phylogeography of Populus alba (L.) and Populus tremula (L.) inCentral Europe: secondary contact and hybridisation during recolonisation from disconnected refugia.Tree Genetics&Genomes,6(3):439-450.
Futuyma, D.J.2010, Evolutionary constraint and ecological consequences. Evolution,64(7):1865-1884.
Gilchrist, E.J., Haughn, G.W., Ying, C.C., et al.2006, Use of Ecotilling as an efficient SNP discovery tool tosurvey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology,15(5):1367-1378.
Givnish, T.J.1998, Adaptive plant evolution on islands: classical patterns, molecular data, new insights.Evolution on islands,281304.
Givnish, T.J., Barfuss, M.H., Van Ee, B., et al.2011, Phylogeny, adaptive radiation, and historicalbiogeography in Bromeliaceae: insights from an eight-locus plastid phylogeny. American journal ofbotany,98(5):872-895.
Goldman, N.1993, Statistical tests of models of DNA substitution. Journal of molecular evolution,36(2):182-198.
Gompert, Z., Fordyce, J.A., Forister, M.L., et al.2006, Homoploid hybrid speciation in an extreme habitat.Science,314(5807):1923-1925.
González‐Martínez, S.C., Krutovsky, K.V., Neale, D.B.2006, Forest‐tree population genomics andadaptive evolution. New Phytologist,170(2):227-238.
Goremykin, V.V., Nikiforova, S.V., Biggs, P.J., et al.2013, The evolutionary root of flowering plants.Systematic Biology,62(1):50-61.
Grant, M., Mitton, J.2010a, Case study: the glorious, golden, and gigantic quaking aspen. Nature EducationKnowledge,3(10):40.
Grant, V.,1971, Plant speciation, Vol183. Columbia University Press New York.
Grant, V.,1981, Plant speciation. New York: Columbia University Press xii,563p.-illus., maps, chrom. nos..En2nd edition. Maps, Chromosome numbers. General (KR,198300748).
Gray, R.D., Drummond, A.J., Greenhill, S.J.2009, Language phylogenies reveal expansion pulses andpauses in Pacific settlement. Science,323(5913):479-483.
Hall, T.A.,1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program forWindows95/98/NT. In: Nucleic acids symposium series, pp.95-98.
Hamrick, J., Godt, M.1996, Effects of life history traits on genetic diversity in plant species. PhilosophicalTransactions of the Royal Society of London. Series B: Biological Sciences,351(1345):1291-1298.
Hamrick, J.L., Godt, M.J.W., Sherman-Broyles, S.L.,1992, Factors influencing levels of genetic diversity inwoody plant species, In: Population genetics of forest trees. Springer, pp.95-124.
Hamzeh, M., Dayanandan, S.2004, Phylogeny of Populus (Salicaceae) based on nucleotide sequences ofchloroplast trnT-trnF region and nuclear rDNA. American journal of botany,91(9):1398-1408.
Hamzeh, M., Périnet, P., Dayanandan, S.2006, Genetic Relationships among species of Populus (Salicaceae)based on nuclear genomic data1. The Journal of the Torrey Botanical Society,133(4):519-527.
Hamzeh, M.H.M., Sawchyn, C.S.C., Périnet, P.P.P., et al.2007, Asymmetrical natural hybridization betweenPopulus deltoides and P. balsamifera (Salicaceae) This note is one of a selection of papers published inthe Special Issue on Poplar Research in Canada. Botany,85(12):1227-1232.
Harrison, R.G.1991, Molecular changes at speciation. Annual Review of Ecology and Systematics,22281-308.
Harrison, T.M., Copeland, P., Kidd, W., et al.1992, Raising tibet. Science,255(5052):1663-1670.
Hartigan, J.A.1973, Minimum mutation fits to a given tree. Biometrics53-65.
Hastings, W.K.1970, Monte Carlo sampling methods using Markov chains and their applications.Biometrika,57(1):97-109.
Hedrick, P.W.,2011, Genetics of populations. Jones&Bartlett Publishers.
Heuertz, M., De Paoli, E., K llman, T., et al.2006, Multilocus patterns of nucleotide diversity, linkagedisequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics,174(4):2095-2105.
Hewitt, G.2000, The genetic legacy of the Quaternary ice ages. Nature,405(6789):907-913.
Hewitt, G.M.1996, Some genetic consequences of ice ages, and their role in divergence and speciation.Biological Journal of the Linnean Society,58(3):247-276.
Hewitt, G.M.2004, Genetic consequences of climatic oscillations in the Quaternary. PhilosophicalTransactions Of The Royal Society Of London Series B-Biological Sciences,359(1442):183-195.
Hey, J.2010a, The divergence of chimpanzee species and subspecies as revealed in multipopulationisolation-with-migration analyses. Molecular Biology and Evolution,27(4):921-933.
Hey, J.2010b, Isolation with migration models for more than two populations. Molecular Biology andEvolution,27(4):905-920.
Hey, J., Nielsen, R.2004, Multilocus methods for estimating population sizes, migration rates anddivergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.Genetics,167(2):747-760.
Hey, J., Nielsen, R.2007, Integration within the Felsenstein equation for improved Markov chain MonteCarlo methods in population genetics. Proceedings of the National Academy of Sciences,104(8):2785.
Hickerson, M., Carstens, B., Cavender-Bares, J., et al.2010, Phylogeography’s past, present, and future:10years after. Molecular Phylogenetics and Evolution,54(1):291-301.
Hipp, A.L., Hall, J.C., Sytsma, K.J.2004, Congruence versus phylogenetic accuracy: revisiting theincongruence length difference test. Systematic Biology,53(1):81-89.
Huang, S.S., Hwang, S.Y., Lin, T.P.2002, Spatial pattern of chloroplast DNA variation of Cyclobalanopsisglauca in Taiwan and East Asia. Molecular Ecology,11(11):2349-2358.
Hubisz, M.J., Falush, D., Stephens, M., et al.2009, Inferring weak population structure with the assistance ofsample group information. Molecular ecology resources,9(5):1322-1332.
Hudson, R.R., Kaplan, N.L.1985, Statistical properties of the number of recombination events in the historyof a sample of DNA sequences. Genetics,111(1):147-164.
Hudson, R.R., Kreitman, M., Aguadé, M.1987, A test of neutral molecular evolution based on nucleotidedata. Genetics,116(1):153-159.
Huelsenbeck, J.P., Ronquist, F.2001, MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics,17(8):754-755.
Ingvarsson, P.K.2005a, Molecular population genetics of herbivore-induced protease inhibitor genes inEuropean aspen (Populus tremula L., Salicaceae). Molecular Biology and Evolution,22(9):1802-1812.
Ingvarsson, P.K.2005b, Nucleotide polymorphism and linkage disequilibrium within and among naturalpopulations of European aspen (Populus tremula L., Salicaceae). Genetics,169(2):945-953.
Ingvarsson, P.K.2008, Multilocus patterns of nucleotide polymorphism and the demographic history ofPopulus tremula. Genetics,180(1):329-340.
Ingvarsson, P.K., García, M.V., Hall, D., et al.2006, Clinal variation in phyB2, a candidate gene forday-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen(Populus tremula). Genetics,172(3):1845-1853.
Ismail, M., Soolanayakanahally, R.Y., Ingvarsson, P.K., et al.2012, Comparative Nucleotide DiversityAcross North American and European Populus Species. Journal of molecular evolution1-16.
Jakobsson, M., Rosenberg, N.A.2007, CLUMPP: a cluster matching and permutation program for dealingwith label switching and multimodality in analysis of population structure. Bioinformatics,23(14):1801-1806.
Jelinski, D.E., Cheliak, W.1992, Genetic diversity and spatial subdivision of Populus tremuloides(Salicaceae) in a heterogeneous landscape. American journal of botany728-736.
Jennings, W.B., Edwards, S.V.2005, Speciational history of Australian Grass Finches (Poephila) inferredfrom thirty gene trees. Evolution,59(9):2033-2047.
Jia, D.R., Abbott, R.J., Liu, T.L., et al.2012, Out of the Qinghai–Tibet Plateau: Evidence for the origin anddispersal of Eurasian temperate plants from a phylogeographic study of Hippopha rhamnoides(Elaeagnaceae). New Phytologist.
Joly, S., McLenachan, P.A., Lockhart, P.J.2009, A statistical approach for distinguishing hybridization andincomplete lineage sorting. The American Naturalist,174(2): E54-E70.
Kanaga, M.K., Ryel, R.J., Mock, K.E., et al.2008, Quantitative-genetic variation in morphological andphysiological traits within a quaking aspen (Populus tremuloides) population. Canadian Journal ofForest Research,38(6):1690-1694.
Keim, P., Paige, K., Whitham, T., et al.1989, Genetic analysis of an interspecific hybrid swarm of Populus:occurrence of unidirectional introgression. Genetics,123(3):557-565.
Keller, S.R., Olson, M.S., Silim, S., et al.2010, Genomic diversity, population structure, and migrationfollowing rapid range expansion in the Balsam Poplar, Populus balsamifera. Molecular Ecology,19(6):1212-1226.
Kingman, J.F.C.1982, The coalescent. Stochastic processes and their applications,13(3):235-248.
Kliman, R.M., Andolfatto, P., Coyne, J.A., et al.2000, The population genetics of the origin and divergenceof the Drosophila simulans complex species. Genetics,156(4):1913-1931.
Kliman, R.M., Hey, J.1993, DNA sequence variation at the period locus within and among species of theDrosophila melanogaster complex. Genetics,133(2):375-387.
Knowles, L.L., Carstens, B.C., Keat, M.L.2007, Coupling genetic and ecological-niche models to examinehow past population distributions contribute to divergence. Current biology,17(11):940-946.
Kramer, B., Van der Bank, H., Flint, N., et al.2003, Evidence for parapatric speciation in the Mormyrid fish,Pollimyrus castelnaui (Boulenger,1911), from the Okavango–Upper Zambezi River Systems: P.marianne sp. nov., defined by electric organ discharges, morphology and genetics. EnvironmentalBiology of Fishes,67(1):47-70.
Kuanyu, L., Minren, H., Huixin, P., et al.1996. Study on origin of Populus tomentosa Carr. In:International Poplar Commission. Sess.20, Budapest (Hungary),1-4Oct1996.
Kumar, S., Nei, M., Dudley, J., Tamura, K.2008, MEGA: a biologist-centric software for evolutionaryanalysis of DNA and protein sequences. Briefings in bioinformatics,9(4):299-306.
Langley, C.H., Fitch, W.M.1974, An examination of the constancy of the rate of molecular evolution.Journal of molecular evolution,3(3):161-177.
Leskinen, E., Alstr m-Rapaport, C.1999, Molecular phylogeny of Salicaceae and closely relatedFlacourtiaceae: Evidence from5.8S, ITS1and ITS2of the rDNA. Plant Systematics and Evolution,215(1):209-227.
Levsen, N.D., Tiffin, P., Olson, M.S.2012, Pleistocene speciation in the genus Populus (Salicaceae).Systematic Biology.
Lexer, C., Fay, M., Joseph, J., et al.2005, Barrier to gene flow between two ecologically divergent Populusspecies, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history ingene introgression. Molecular Ecology,14(4):1045-1057.
Lexer, C., van Loo, M.2006, Contact zones: natural labs for studying evolutionary transitions. Currentbiology,16(11): R407-R409.
Liao, C., Downie, S.R., Li, Q., et al.2013, New Insights into the Phylogeny of Angelica and its Allies(Apiaceae) with Emphasis on East Asian Species, Inferred from nrDNA, cpDNA, and MorphologicalEvidence. Systematic Botany,38(1):266-281.
Librado, P., Rozas, J.2009, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25(11):1451-1452.
Liu, L.2008, BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics,24(21):2542-2543.
Liu, L., Pearl, D.K.2007, Species trees from gene trees: reconstructing Bayesian posterior distributions of aspecies phylogeny using estimated gene tree distributions. Systematic Biology,56(3):504-514.
Liu, Z., Furnier, G.1993, Comparison of allozyme, RFLP, and RAPD markers for revealing genetic variationwithin and between trembling aspen and bigtooth aspen. Theoretical and Applied Genetics,87(1-2):97-105.
Llopart, A., Herrig, D., Brud, E., et al.2014, Sequential adaptive introgression of the mitochondrial genomein Drosophila yakuba and D. santomea. Molecular Ecology.
Llopart, A., Lachaise, D., Coyne, J.A.2005, Multilocus analysis of introgression between two sympatricsister species of Drosophila: Drosophila yakuba and D. santomea. Genetics,171(1):197-210.
Love, A., Love, D.1975, Nomenclatural notes on arctic plants. Bot. Notiser,128(4):497-523.
Lowry, D.B., Rockwood, R.C., Willis, J.H.2008, Ecological reproductive isolation of coast and inland racesof Mimulus guttatus. Evolution,62(9):2196-2214.
Müller, A., Leuschner, C., Horna, V., et al.2012, Photosynthetic characteristics and growth performance ofclosely related aspen taxa: On the systematic relatedness of the Eurasian Populus tremula and the NorthAmerican P. tremuloides. Flora-Morphology, Distribution, Functional Ecology of Plants,207(2):87-95.
M ser, P., Thomine, S., Schroeder, J.I., et al.2001, Phylogenetic relationships within cation transporterfamilies of Arabidopsis. Plant Physiology,126(4):1646-1667.
Ma, J.2011, Reconstructing the history of large-scale genomic changes: biological questions andcomputational challenges. Journal of Computational Biology,18(7):879-893.
MacGinitie, H.D.,1969, The Eocene Green River flora of northwestern Colorado and northeastern Utah.University of California Press.
Machado, C.A., Kliman, R.M., Markert, J.A., et al.2002, Inferring the history of speciation from multilocusDNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology andEvolution,19(4):472-488.
Madritch, M.D., Greene, S.L., Lindroth, R.L.2009, Genetic mosaics of ecosystem functioning acrossaspen-dominated landscapes. Oecologia,160(1):119-127.
Maliouchenko, O., Palmé, A.E., Buonamici, A., et al.2007, Comparative phylogeography and populationstructure of European Betula species, with particular focus on B. pendula and B. pubescens. Journal ofBiogeography,34(9):1601-1610.
Mallet, J.2007, Hybrid speciation. Nature,446(7133):279-283.
Manchester, S.R., Dilcher, D.L., Tidwell, W.D.1986, Interconnected reproductive and vegetative remains ofPopulus (Salicaceae) from the middle Eocene Green River Formation, northeastern Utah. Americanjournal of botany156-160.
Manchester, S.R., Judd, W.S., Handley, B.2006, Foliage and fruits of early poplars (Salicaceae: Populus)from the Eocene of Utah, Colorado, and Wyoming. International Journal of Plant Sciences,167(4):897-908.
Mao, K., Milne, R.I., Zhang, L., et al.2012, Distribution of living Cupressaceae reflects the breakup ofPangea. Proceedings of the National Academy of Sciences.
Marincovich, L., Gladenkov, A.Y.1999, Evidence for an early opening of the Bering Strait. Nature,397(6715):149-151.
Marra, M.A., Jones, S.J., Astell, C.R., et al.2003, The genome sequence of the SARS-associated coronavirus.Science,300(5624):1399-1404.
Martinsen, G.D., Whitham, T.G., Turek, R.J., et al.2001, Hybrid populations selectively filter geneintrogression between species. Evolution,55(7):1325-1335.
Mayr, E.,1970, Populations, species, and evolution: an abridgment of animal species and evolution. HarvardUniversity Press.
Mayr, E.,1982, The growth of biological thought: Diversity, evolution, and inheritance. Harvard UniversityPress.
Mes, T., Hart, H.1996, The evolution of growth‐forms in the Macaronesian genus Aeonium (Crassulaceae)inferred from chloroplast DNA RFLPs and morphology. Molecular Ecology,5(3):351-363.
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., et al.2004, Equation of state calculations by fastcomputing machines. The journal of chemical physics,21(6):1087-1092.
Milne, R.I., Abbott, R.J.2002, The origin and evolution of Tertiary relict floras. Advances in BotanicalResearch,38281-314.
Milne, R.I.A.N.2006, Northern Hemisphere plant disjunctions: a window on tertiary land bridges andclimate change? Annals of Botany,98(3):465-472.
Mitton, J.B., Grant, M.C.1996, Genetic variation and the natural history of quaking aspen. Bioscience,46(1):25-31.
Mock, K.E., Rowe, C., Hooten, M.B., et al.2008, Clonal dynamics in western North American aspen(Populus tremuloides). Molecular Ecology,17(22):4827-4844.
Moeller, D.A., Tenaillon, M.I., Tiffin, P.2007, Population structure and its effects on patterns of nucleotidepolymorphism in teosinte (Zea mays ssp. parviglumis). Genetics,176(3):1799-1809.
Monod, L., Prendini, L.2014, Evidence for Eurogondwana: the roles of dispersal, extinction and vicariancein the evolution and biogeography of Indo‐Pacific Hormuridae (Scorpiones: Scorpionoidea).Cladistics.
Morin, N.R.,2000, Flora of North America. Flora of North America Association.
Morrell, P.L., Lundy, K.E., Clegg, M.T.2003, Distinct geographic patterns of genetic diversity aremaintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proceedings of theNational Academy of Sciences,100(19):10812-10817.
Namroud, M.C., Park, A., Tremblay, F., et al.2005, Clonal and spatial genetic structures of aspen (Populustremuloides Michx.). Molecular Ecology,14(10):2969-2980.
Nei, M.1973, Analysis of gene diversity in subdivided populations. Proceedings of the National Academy ofSciences,70(12):3321-3323.
Nei, M.,1987, Molecular evolutionary genetics. Columbia University Press.
Nei, M., Kumar, S.,2000, Molecular evolution and phylogenetics. Oxford University Press.
Nei, M., Li, W.-H.1979, Mathematical model for studying genetic variation in terms of restrictionendonucleases. Proceedings of the National Academy of Sciences,76(10):5269-5273.
Nie, Z.-L., Funk, V., Sun, H., et al.2013, Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) withbiogeographic implications in the Northern Hemisphere. Journal of plant research,126(1):17-32.
Nielsen, R., Wakeley, J.2001, Distinguishing migration from isolation: a Markov chain Monte Carloapproach. Genetics,158(2):885-896.
Nystedt, B., Street, N.R., Wetterbom, A., et al.2013, The Norway spruce genome sequence and conifergenome evolution. Nature.
Okumura, S., Sawada, M., Park, Y.W., et al.2006, Transformation of poplar (Populus alba) plastids andexpression of foreign proteins in tree chloroplasts. Transgenic research,15(5):637-646.
Olson, M.S., Robertson, A.L., Takebayashi, N., et al.2010, Nucleotide diversity and linkage disequilibriumin balsam poplar (Populus balsamifera). New Phytologist,186(2):526-536.
Ostrowski, M., David, J., Santoni, S., et al.2006, Evidence for a large‐scale population structure amongaccessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkagedisequilibrium. Molecular Ecology,15(6):1507-1517.
Page, R.D.2000, Extracting species trees from complex gene trees: reconciled trees and vertebratephylogeny. Molecular Phylogenetics and Evolution,14(1):89-106.
Pakull, B., Groppe, K., Meyer, M., et al.2009, Genetic linkage mapping in aspen (Populus tremula L. andPopulus tremuloides Michx.). Tree Genetics&Genomes,5(3):505-515.
Palmé, A., Semerikov, V., Lascoux, M.2003, Absence of geographical structure of chloroplast DNAvariation in sallow, Salix caprea L. Heredity,91(5):465-474.
Palmer, J.D., Jansen, R.K., Michaels, H.J., et al.1988, Chloroplast DNA variation and plant phylogeny.Annals of the Missouri Botanical Garden (USA).
Paten, B., Herrero, J., Fitzgerald, S., et al.2008, Genome-wide nucleotide-level mammalian ancestorreconstruction. Genome Research,18(11):1829-1843.
Pellis, A., Laureysens, I., Ceulemans, R.2008, Genetic variation of the bud and leaf phenology of seventeenpoplar clones in a short rotation coppice culture. Plant Biology,6(1):38-46.
Peng, D., Wang, X.Q.2008, Reticulate evolution in Thuja inferred from multiple gene sequences:Implications for the study of biogeographical disjunction between eastern Asia and North America.Molecular Phylogenetics and Evolution,47(3):1190-1202.
Petit, R.J., Aguinagalde, I., de Beaulieu, J.L., et al.2003, Glacial refugia: hotspots but not melting pots ofgenetic diversity. Science,300(5625):1563.
Planet, P.J.2006, Tree disagreement: measuring and testing incongruence in phylogenies. Journal ofbiomedical informatics,39(1):86-102.
Pons, O., Petit, R.1996, Measwring and Testing Genetic Differentiation With Ordered Versus UnorderedAlleles. Genetics,144(3):1237-1245.
Posada, D.2003, Using Modeltest and PAUP*to select a model of nucleotide substitution. Current protocolsin bioinformatics6.5.1-6.5.14.
Posada, D., Crandall, K.A.2001, Intraspecific gene genealogies: trees grafting into networks. Trends inecology&evolution,16(1):37-45.
Pritchard, J.K., Stephens, M., Donnelly, P.2000, Inference of population structure using multilocus genotypedata. Genetics,155(2):945-959.
Pyh j rvi, T., García-Gil, M.R., Knürr, T., et al.2007, Demographic history has influenced nucleotidediversity in European Pinus sylvestris populations. Genetics,177(3):1713-1724.
Qiu, Y.L., Li, L., Wang, B., et al.2007, A nonflowering land plant phylogeny inferred from nucleotidesequences of seven chloroplast, mitochondrial, and nuclear genes. International Journal of PlantSciences,168(5):691-708.
Qiu, Y.X., Fu, C.X., Comes, H.P.2011, Plant molecular phylogeography in China and adjacent regions:Tracing the genetic imprints of Quaternary climate and environmental change in the world's mostdiverse temperate flora. Molecular Phylogenetics and Evolution.
Qiu, Y.X., Sun, Y., Zhang, X.P., et al.2009, Molecular phylogeography of East Asian Kirengeshoma(Hydrangeaceae) in relation to Quaternary climate change and landbridge configurations. NewPhytologist,183(2):480-495.
Queiroz, A.2005, The resurrection of oceanic dispersal in historical biogeography. Trends in ecology&evolution,20(2):68-73.
Quicke, D.L., Jones, O.R., Epstein, D.R.2007, Correcting the problem of false incongruence due to noiseimbalance in the incongruence length difference (ILD) test. Systematic Biology,56(3):496-503.
Rabosky, D.L., Adams, D.C.2012, Rates of morphological evolution are correlated with species richness insalamanders. Evolution,66(6):1807-1818.
Rajora, O., Dancik, B.1992, Chloroplast DNA inheritance in Populus. TAG Theoretical and AppliedGenetics,84(3):280-285.
Rajora, O., Dancik, B.1995, Chloroplast DNA variation in Populus. II. Interspecific restriction fragmentpolymorphisms and genetic relationships among Populus deltoides, P. nigra, P. maximowiczii, and P. xcanadensis. Theoretical and Applied Genetics,90(3-4):324-330.
Rajora, O.P., Zsuffa, L.1990, Allozyme divergence and evolutionary relationships among Populus deltoides,P. nigra, and P. maximowiczii. Genome,33(1):44-49.
Rambaut, A.2008, FigTree v1.1.1. Published by the author.
Rambaut, A., Drummond, A.2007, Tracer v1.5. htt p. tree. bio. ed. ac. uk/software/tracer.
Ramos-Onsins, S.E., Rozas, J.2002, Statistical properties of new neutrality tests against population growth.Molecular Biology and Evolution,19(12):2092-2100.
Ramos-Onsins, S.E., Stranger, B.E., Mitchell-Olds, T., et al.2004, Multilocus analysis of variation andspeciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics,166(1):373-388.
Ramos‐Onsins, S., Puerma, E., BALA á‐ALCAIDE, D., et al.2008, Multilocus analysis of variationusing a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana. Molecularecology,17(5):1211-1223.
Rannala, B., Yang, Z.1996, Probability distribution of molecular evolutionary trees: a new method ofphylogenetic inference. Journal of molecular evolution,43(3):304-311.
Rannala, B., Yang, Z.2003, Bayes estimation of species divergence times and ancestral population sizesusing DNA sequences from multiple loci. Genetics,164(4):1645-1656.
Ree, R.H., Smith, S.A.2008, Maximum likelihood inference of geographic range evolution by dispersal,local extinction, and cladogenesis. Systematic Biology,57(1):4-14.
Remington, D., Robichaux, R.2007, Influences of gene flow on adaptive speciation in the Dubautiaarborea–D. ciliolata complex. Molecular ecology,16(19):4014-4027.
Renner, S.S.2005, Relaxed molecular clocks for dating historical plant dispersal events. Trends in plantscience,10(11):550-558.
Reyes-Prieto, A., Bhattacharya, D.2007, Phylogeny of Calvin cycle enzymes supports Plantae monophyly.Molecular Phylogenetics and Evolution,45(1):384-391.
Richards, C.L., Carstens, B.C., Lacey Knowles, L.2007, Distribution modelling and statisticalphylogeography: an integrative framework for generating and testing alternative biogeographicalhypotheses. Journal of Biogeography,34(11):1833-1845.
Richardson, J.E., Pennington, R.T., Pennington, T.D., et al.2001, Rapid diversification of a species-richgenus of neotropical rain forest trees. Science,293(5538):2242-2245.
Rokas, A., Carroll, S.B.2006, Bushes in the tree of life. PLoS Biology,4(11): e352.
Ronquist, F.1997, Dispersal-vicariance analysis: a new approach to the quantification of historicalbiogeography. Systematic Biology,46(1):195-203.
Ronquist, F., Huelsenbeck, J.P.2003, MrBayes3: Bayesian phylogenetic inference under mixed models.Bioinformatics,19(12):1572-1574.
Rood, S.B., Campbell, J.S., Despins, T.1986, Natural poplar hybrids from southern Alberta. I. Continuousvariation for foliar characteristics. Canadian Journal of Botany,64(7):1382-1388.
Rosenberg, N.A.2004, DISTRUCT: a program for the graphical display of population structure. MolecularEcology Notes,4(1):137-138.
Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., et al.2014, From algae to angiosperms-inferring thephylogeny of green plants (Viridiplantae) from360plastid genomes. BMC Evolutionary Biology,14(1):23.
Saitou, N., Nei, M.1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution,4(4):406-425.
Salipante, S.J., Horwitz, M.S.2006, Phylogenetic fate mapping. Proceedings of the National Academy ofSciences,103(14):5448-5453.
San Mauro, D., Vences, M., Alcobendas, M., et al.2005, Initial diversification of living amphibians predatedthe breakup of Pangaea. The American Naturalist,165(5):590-599.
Sanders, K.L., Rasmussen, A.R., Guinea, M.L.2014, High rates of hybridisation reveal fragile reproductivebarriers between endangered Australian sea snakes. Biological Conservation,171200-208.
Sanderson, M.J.1997, A nonparametric approach to estimating divergence times in the absence of rateconstancy. Molecular Biology and Evolution,14(12):1218-1231.
Sanderson, M.J.2002, Estimating absolute rates of molecular evolution and divergence times: a penalizedlikelihood approach. Molecular Biology and Evolution,19(1):101-109.
Sang, T.2002, Utility of low-copy nuclear gene sequences in plant phylogenetics. Critical Reviews inBiochemistry and Molecular Biology,37(3):121-147.
Sang, T., Ge, S.2007, The puzzle of rice domestication. Journal of Integrative Plant Biology,49(6):760-768.
Sanmartín, I., Van Der Mark, P., Ronquist, F.2008, Inferring dispersal: a Bayesian approach to phylogeny‐based island biogeography, with special reference to the Canary Islands. Journal of Biogeography,35(3):428-449.
Sanmartin, I., Enghoff, H., Ronquist, F.2001, Patterns of animal dispersal, vicariance and diversification inthe Holarctic. Biological Journal of the Linnean Society,73(4):345-390.
Sanmartin, I., Ronquist, F.2004, Southern Hemisphere biogeography inferred by event-based models: plantversus animal patterns. Systematic Biology,53(2):216-243.
Savolainen, O., Pyh j rvi, T.2007, Genomic diversity in forest trees. Current opinion in plant biology,10(2):162-167.
Savolainen, V., Anstett, M.-C., Lexer, C., et al.2006, Sympatric speciation in palms on an oceanic island.Nature,441(7090):210-213.
Schaal, B., Hayworth, D., Olsen, K., et al.1998, Phylogeographic studies in plants: problems and prospects.Molecular Ecology,7(4):465-474.
Schliewen, U.K., Tautz, D., P bo, S.1994, Sympatric speciation suggested by monophyly of crater lakecichlids. Nature,368(6472):629-632.
Schmid, K.J., Ramos-Onsins, S., Ringys-Beckstein, H., et al.2005, A multilocus sequence survey inArabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequencepolymorphism. Genetics,169(3):1601-1615.
Schweitzer, J.A., Bailey, J.K., Hart, S.C., et al.2005, The interaction of plant genotype and herbivorydecelerate leaf litter decomposition and alter nutrient dynamics. Oikos,110(1):133-145.
Seifert, B.2010, Intranidal mating, gyne polymorphism, polygyny, and supercoloniality as factors forsympatric and parapatric speciation in ants. Ecological entomology,35(s1):33-40.
Shaw, J., Lickey, E.B., Beck, J.T., et al.2005, The tortoise and the hare II: relative utility of21noncodingchloroplast DNA sequences for phylogenetic analysis. American journal of botany,92(1):142-166.
Shaw, J., Lickey, E.B., Schilling, E.E., et al.2007, Comparison of whole chloroplast genome sequences tochoose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III.American journal of botany,94(3):275-288.
Shi, Y.,1998, Uplift and environmental changes of Qinghai-Xizang (Tibetan) Plateau in the late Cenozoic.Guangdong Scirence&Technology Press.
Slavov, G., DiFazio, S., Strauss, S.H., et al.2004. Gene flow in forest trees: gene migration patterns andlandscape modelling of transgene dispersal in hybrid poplar. In: Introgression from geneticallymodified plants into wild relatives. Proceedings of a conference organized by the University ofAmsterdam (Netherlands) and the Robert Koch Institute (Germany), in January2003., pp.89-106.
Slavov, G.T., Zhelev, P.,2010, Salient biological features, systematics, and genetic variation of Populus, In:Genetics and Genomics of Populus. Springer, pp.15-38.
Small, R.L., Cronn, R.C., Wendel, J.F.2004, LAS Johnson Review No.2. Use of nuclear genes forphylogeny reconstruction in plants. Australian Systematic Botany,17(2):145-170.
Smith, R.L., Sytsma, K.J.1990, Evolution of Populus nigra (sect. Aigeiros): introgressive hybridization andthe chloroplast contribution of Populus alba (sect. Populus). American journal of botany1176-1187.
Sobel, J.M., Chen, G.F., Watt, L.R., et al.2010, The biology of speciation. Evolution,64(2):295-315.
Soltis, D.E., Tago-Nakazawa, M., Xiang, Q.-Y., et al.2001, Phylogenetic relationships and evolution inChrysosplenium (Saxifragaceae) based on matK sequence data. American journal of botany,88(5):883-893.
Stebbins, G.L.1963, Perspective. American Scientist362-370.
Stettler, R.F.,1996, Biology of Populus and its implications for management and conservation. CanadianGovernment Publishing.
Strasburg, J.L., Rieseberg, L.H.2010, How robust are “Isolation with Migration” analyses to violations ofthe IM model? A simulation study. Molecular Biology and Evolution,27(2):297-310.
Strasburg, J.L., Rieseberg, L.H.2011, Interpreting the estimated timing of migration events betweenhybridizing species. Molecular ecology,20(11):2353-2366.
Swofford, D.L.2003,{PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version4.}.
Taberlet, P., Gielly, L., Pautou, G., et al.1991, Universal primers for amplification of three non-codingregions of chloroplast DNA. Plant molecular biology,17(5):1105-1109.
Tajima, F.1989, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.Genetics,123(3):585-595.
Takahata, N.1986, An attempt to estimate the effective size of the ancestral species common to two extantspecies from which homologous genes are sequenced. Genetical research,48(03):187-190.
Takahata, N., Satta, Y.1997, Evolution of the primate lineage leading to modern humans: phylogenetic anddemographic inferences from DNA sequences. Proceedings of the National Academy of Sciences,94(9):4811-4815.
Takahata, N., Satta, Y., Klein, J.1995, Divergence time and population size in the lineage leading to modernhumans. Theoretical population biology,48(2):198-221.
Talbot, P., Thompson, S.L., Schroeder, W., et al.2011, An efficient single nucleotide polymorphism assay todiagnose the genomic identity of poplar species and hybrids on the Canadian prairies. Canadian Journalof Forest Research,41(5):1102-1111.
Tang, L., Zou, X., Achoundong, G., et al.2010, Phylogeny and biogeography of the rice tribe (Oryzeae):evidence from combined analysis of20chloroplast fragments. Molecular Phylogenetics and Evolution,54(1):266-277.
Taylor, G.2002, Populus: Arabidopsis for forestry. Do we need a model tree? Annals of Botany,90(6):681-689.
Thompson, J.D., Gibson, T.J., Plewniak, F., et al.1997, The CLUSTAL_X windows interface: flexiblestrategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research,25(24):4876-4882.
Thompson, S.L., Lamothe, M., Meirmans, P.G., et al.2010, Repeated unidirectional introgression towardsPopulus balsamifera in contact zones of exotic and native poplars. Molecular Ecology,19(1):132-145.
Thorne, J.L., Kishino, H.2002, Divergence time and evolutionary rate estimation with multilocus data.Systematic Biology,51(5):689-702.
Tiffney, B.H.1985a, The Eocene North Atlantic land bridge: its importance in Tertiary and modernphytogeography of the Northern Hemisphere. J. Arnold Arbor,66(2):243-273.
Tiffney, B.H.1985b, Perspectives on the origin of the floristic similarity between eastern Asia and easternNorth America. Journal of the Arnold Arboretum,66.
Tiffney, B.H., Manchester, S.R.2001, The use of geological and paleontological evidence in evaluating plantphylogeographic hypotheses in the Northern Hemisphere Tertiary. International Journal of PlantSciences,162(S6): S3-S17.
Tuskan, G.A., Difazio, S., Jansson, S., et al.2006, The genome of black cottonwood, Populus trichocarpa(Torr.&Gray). Science,313(5793):1596-1604.
Vuli, M., Dionisio, F., Taddei, F., et al.1997, Molecular keys to speciation: DNA polymorphism and thecontrol of genetic exchange in enterobacteria. Proceedings of the National Academy of Sciences,94(18):9763-9767.
Wakeley, J., Hey, J.1997, Estimating ancestral population parameters. Genetics,145(3):847-855.
Wan, Y., Schwaninger, H.R., Baldo, A.M., et al.2013, A phylogenetic analysis of the grape genus (Vitis L.)reveals broad reticulation and concurrent diversification during neogene and quaternary climate change.BMC Evolutionary Biology,13(1):141.
Wang, Q., Abbott, R.J., Yu, Q.S., et al.2013, Pleistocene climate change and the origin of two desert plantspecies, Pugionium cornutum and Pugionium dolabratum (Brassicaceae), in northwest China. NewPhytologist.
Wang, X.-Q., Ran, J.-H.2014, Evolution and biogeography of gymnosperms. Molecular Phylogenetics andEvolution.
Watterson, G.1975, On the number of segregating sites in genetical models without recombination.Theoretical population biology,7(2):256-276.
Wayne, M.L., Simonsen, K.L.1998, Statistical tests of neutrality in the age of weak selection. Trends inecology&evolution,13(6):236-240.
Wei, X.-X., Yang, Z.-Y., Li, Y., et al.2010, Molecular phylogeny and biogeography of Pseudotsuga(Pinaceae): Insights into the floristic relationship between Taiwan and its adjacent areas. MolecularPhylogenetics and Evolution,55(3):776-785.
Wen, J.1999, Evolution of eastern Asian and eastern North American disjunct distributions in floweringplants. Annual Review of Ecology and Systematics421-455.
Wendel, J.F., Doyle, J.J.,1998, Phylogenetic incongruence: window into genome history and molecularevolution, In: Molecular systematics of plants II. Springer, pp.265-296.
Whelan, S., Liò, P., Goldman, N.2001, Molecular phylogenetics: state-of-the-art methods for looking intothe past. TRENDS in Genetics,17(5):262-272.
Whitham, T.G., Bailey, J.K., Schweitzer, J.A., et al.2006, A framework for community and ecosystemgenetics: from genes to ecosystems. Nature Reviews Genetics,7(7):510-523.
Whitham, T.G., DiFazio, S.P., Schweitzer, J.A., et al.2008, Extending genomics to natural communities andecosystems. Science,320(5875):492-495.
Willing, R., Pryor, L.1976, Interspecific hybridisation in poplar. Theoretical and Applied Genetics,47(3):141-151.
Willis, K.J., Niklas, K.J.2004, The role of Quaternary environmental change in plant macroevolution: theexception or the rule? Philosophical Transactions of the Royal Society of London. Series B: BiologicalSciences,359(1442):159-172.
Wimp, G.M., Martinsen, G.D., Floate, K.D., et al.2005, Plant genetic determinants of arthropod communitystructure and diversity. Evolution,59(1):61-69.
Winter, K.-U., Becker, A., Münster, T., et al.1999, MADS-box genes reveal that gnetophytes are moreclosely related to conifers than to flowering plants. Proceedings of the National Academy of Sciences,96(13):7342-7347.
Woerner, A.E., Cox, M.P., Hammer, M.F.2007, Recombination-filtered genomic datasets by informationmaximization. Bioinformatics,23(14):1851-1853.
Wolfe, J.A.1978, A Paleobotanical Interpretation of Tertiary Climates in the Northern Hemisphere: Datafrom fossil plants make it possible to reconstruct Tertiary climatic changes, which may be correlatedwith changes in the inclination of the earth's rotational axis.
Won, Y.-J., Hey, J.2005, Divergence population genetics of chimpanzees. Molecular Biology and Evolution,22(2):297-307.
Wood, T.E., Takebayashi, N., Barker, M.S., et al.2009, The frequency of polyploid speciation in vascularplants. Proceedings of the National Academy of Sciences,106(33):13875-13879.
Wright, S.,1984, Evolution and the genetics of populations, volume3: experimental results and evolutionarydeductions, Vol3. University of Chicago press.
Wright, S.I., Bi, I.V., Schroeder, S.G., et al.2005, The effects of artificial selection on the maize genome.Science,308(5726):1310-1314.
Wright, S.I., Gaut, B.S.2005, Molecular population genetics and the search for adaptive evolution in plants.Molecular Biology and Evolution,22(3):506-519.
Wu, C.-I., Ting, C.-T.2004, Genes and speciation. Nature Reviews Genetics,5(2):114-122.
Wu, Z.,1999, Flora of China. Science Press.
Xiang, Q.-Y., Soltis, D.E., Soltis, P.S.1998, The eastern Asian and eastern and western North Americanfloristic disjunction: congruent phylogenetic patterns in seven diverse genera. Molecular Phylogeneticsand Evolution,10(2):178-190.
Xiang, Q.Y.J., Manchester, S.R., Thomas, D.T., et al.2005, Phylogeny, biogeography, and molecular datingof cornelian cherries (Cornus, Cornaceae): tracking Tertiary plant migration. Evolution,59(8):1685-1700.
Yang, Z.2002, Likelihood and Bayes estimation of ancestral population sizes in hominoids using data frommultiple loci. Genetics,162(4):1811-1823.
Yang, Z.2010, A likelihood ratio test of speciation with gene flow using genomic sequence data. Genomebiology and evolution,2200.
Yang, Z., Rannala, B.1997, Bayesian phylogenetic inference using DNA sequences: a Markov chain MonteCarlo method. Molecular Biology and Evolution,14(7):717-724.
Yang, Z., Rannala, B.2006, Bayesian estimation of species divergence times under a molecular clock usingmultiple fossil calibrations with soft bounds. Molecular Biology and Evolution,23(1):212-226.
Yang, Z., Rannala, B.2010, Bayesian species delimitation using multilocus sequence data. Proceedings ofthe National Academy of Sciences,107(20):9264.
Yang, Z., Rannala, B.2012, Molecular phylogenetics: principles and practice. Nature Reviews Genetics,13(5):303-314.
Yang, Z.Y., Ran, J.H., Wang, X.Q.2012, Three Genome-based Phylogeny of Cupressaceae sl: FurtherEvidence for the Evolution of Gymnosperms and Southern Hemisphere Biogeography. MolecularPhylogenetics and Evolution.
Yeh, F., Chong, D., Yang, R.C.1995, RAPD variation within and among natural populations of tremblingaspen (Populus tremuloides Michx.) from Alberta. Journal of Heredity,86(6):454-460.
Zhang, D., Zhang, Z., Yang, K., et al.2004, Genetic mapping in (Populus tomentosa×Populus bolleana) andP. tomentosa Carr. using AFLP markers. Theoretical and Applied Genetics,108(4):657-662.
Zhang, JB., Li, RQ., Xiang, XG., et al.2013, Integrated Fossil and Molecular Data Reveal the BiogeographicDiversification of the Eastern Asian-Eastern North American Disjunct Hickory Genus (Carya Nutt.).PloS one,8(7): e70449.
Zhang, LB., Ge S.2007, Multilocus analysis of nucleotide variation and speciation in Oryza officinalis andits close relatives. Molecular Biology and Evolution,24(3):769-783.
Zhang, X., Zang, R., Li, C.2004, Population differences in physiological and morphological adaptations ofPopulus davidiana seedlings in response to progressive drought stress. Plant Science,166(3):791-797.
Zheng, H., Powell, C.M., An, Z., et al.2000, Pliocene uplift of the northern Tibetan Plateau. Geology,28(8):715-718.
Zheng, X., Ge, S.2010, Ecological divergence in the presence of gene flow in two closely related Oryzaspecies (Oryza rufipogon and O. nivara). Molecular Ecology,19(12):2439-2454.
Zhu, Q., Zheng, X., Luo, J., et al.2007, Multilocus analysis of nucleotide variation of Oryza sativa and itswild relatives: severe bottleneck during domestication of rice. Molecular Biology and Evolution,24(3):875-888.
Zou, X.H., Yang, Z., Doyle, J.J., et al.2013, Multilocus estimation of divergence times and ancestraleffective population sizes of Oryza species and implications for the rapid diversification of the genus.New Phytologist,198(4):1155-1164.
Zou, X.H., Zhang, F.M., Zhang, J.G., et al.2008, Analysis of142genes resolves the rapid diversification ofthe rice genus. Genome Biol,9(3): R49.
Zsuffa, L.,1975. A summary review of interspecific breeding in the genus Populus L. In: Proceedings14thmeeting of the Canadian Tree Improvement Association, part, pp.107-123.
Zuckerkandl, E., Pauling, L.1965, Evolutionary divergence and convergence in proteins. Evolving genesand proteins,9797-166.
戴玉成,沈瑞祥,周仲铭.1989,杨树栅锈菌Melampsora spp.的数量分类研究.林业科学,25(1):86-92.
韩联生,刘培林,袁显磊等.2006,小兴安岭山杨杂交新品系山地造林研究.林业科技,31(4):12-15.
李吉均,文世宣,张青松等.1979, A Discussion on the period, amplitude and type of the uplift of theQinghaiI-Xizang Plateau.中国科学,11:15-30.
李开隆,周光达,杨传平等.2004,中国山杨与美洲山杨杂交育种的研究.植物研究,24(2):215-219.
李善文,张有慧,张志毅等.2007,杨属部分种及杂种的AFLP分析.林业科学,43(1):35-41.
毛康珊.2010.广义柏科的生物地理学研究.兰州大学博士学位论文.
史全良,诸葛强,黄敏仁等.2001,用ITS序列研究杨属各组之间的系统发育关系.植物学报,43(3):323-325.
王丽娜,姜小龙,雷耘等.2012,北温带水青冈属的间断分布及其泛生物地理学解释.植物生态学报,36(5):393-402.
王源秀,徐立安,黄敏仁等.2007,林木比较基因组学研究进展. HEREDITAS (Beijing),101199-1206.
卫尊征,郭丽琴,张金凤等.2010,利用trnL—F序列分析杨属树种的系统发育关系.北京林业大学学报(2):27-33.
邢亚娟.2005.中国山杨与美洲山杨杂交种新品系选育研究.东北林业大学博士学位论文。
张德强,杨凯.2000,杨树分子标记研究进展.北京林业大学学报,22(006):79-84.
张奠湘.2003,历史生物地理学的进展.热带亚热带植物学报,11(3):283-289.
张金然,尚洁,王秋玉.2006,山杨杂种无性系的SSR分子标记遗传多样性.植物研究,26(4).
张守攻,齐力旺,陈成彬等.2003,中国杨属(Populus)植物染色体数目报道.中国细胞生物学学会第八届会员代表大会暨学术大会论文摘要集,12.
Altschul, S.F., Madden, T.L., Sch ffer, A.A., et al.1997, Gapped BLAST and PSI-BLAST: a new generationof protein database search programs. Nucleic acids research,25(17):3389-3402.
Antonelli, A., Nylander, J.A., Persson, C., et al.2009, Tracing the impact of the Andean uplift on Neotropicalplant evolution. Proceedings of the National Academy of Sciences,106(24):9749-9754.
Arunyawat, U., Stephan, W., St dler, T.2007, Using multilocus sequence data to assess population structure,natural selection, and linkage disequilibrium in wild tomatoes. Molecular Biology and Evolution,24(10):2310-2322.
Augustin, L., Barbante, C., Barnes, P.R., et al.2004, Eight glacial cycles from an Antarctic ice core. Nature,429(6992):623-628.
Bailey, J.K., Deckert, R., Schweitzer, J.A., et al.2005, Host plant genetics affect hidden ecological players:links among Populus, condensed tannins, and fungal endophyte infection. Canadian Journal of Botany,83(4):356-361.
Barbier, P.1989, Genetic variation and ecotypic differentiation in the wild rice species Oryza rufipogon,1:Population differentiation in life-history traits and isozymic loci. Japanese Journal of Genetics (Japan).
Barker, N.P., Weston, P.H., Rutschmann, F., et al.2007, Molecular dating of the ‘Gondwanan’plant familyProteaceae is only partially congruent with the timing of the break‐up of Gondwana. Journal ofBiogeography,34(12):2012-2027.
Barluenga, M., St lting, K.N., Salzburger, W., et al.2006, Sympatric speciation in Nicaraguan crater lakecichlid fish. Nature,439(7077):719-723.
Barnes, B.V.1967, Indications of possible mid-Cenozoic hybridization in the aspens of the Columbia Plateau.Rhodora,69(777).
Barnes, B.V.1975, Phenotypic variation of trembling aspen in western North America. Forest Science,21(3):319-328.
Barraclough, T.G., Nee, S.2001, Phylogenetics and speciation. Trends in ecology&evolution,16(7):391-399.
Batalha-Filho, H., Cabanne, G.S., Miyaki, C.Y.2012, Phylogeography of an Atlantic forest passerine revealsdemographic stability through the last glacial maximum. Molecular Phylogenetics and Evolution,65(3):892-902.
Baudet, á.B.1999, Notes on the taxonomy of Aeonium urbicum and A. appendiculatum sp. nova(Crassulaceae). Willdenowia-Annals of the Botanic Garden and Botanical Museum Berlin-Dahlem,29(1-2):1-2.
]Bennett, K.1990, Milankovitch cycles and their effects on species in ecological and evolutionary time.Paleobiology11-21.
Bennett, K.2004, Continuing the debate on the role of Quaternary environmental change for macroevolution.Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences,359(1442):295-303.
Bobowski, B., Hole, D., Wolf, P., et al.1999, Identification of roots of woody species using polymerasechain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. MolecularEcology,8(3):485-491.
Bott, M.H.P.,1983, Structure and development of the Greenland-Scotland Ridge: new methods and concepts,Vol1981. Plenum Pub Corp.
Braatne, J., Hinckley, T., Stettler, R.1992, Influence of soil water on the physiological and morphologicalcomponents of plant water balance in Populus trichocarpa, Populus deltoides and their F1hybrids. TreePhysiology,11(4):325-339.
Bradshaw, H., Ceulemans, R., Davis, J., et al.2000, Emerging model systems in plant biology: poplar(Populus) as a model forest tree. Journal of Plant Growth Regulation,19(3):306-313.
Breen, A.L., Glenn, E., Yeager, A., et al.2009, Nucleotide diversity among natural populations of a NorthAmerican poplar (Populus balsamifera, Salicaceae). New Phytologist,182(3):763-773.
Bremer, B., Bremer, K., Chase, M., et al.2009, An update of the Angiosperm Phylogeny Group classificationfor the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society.
Brower, A.V.1996, A new mimetic species of Heliconius (Lepidoptera: Nymphalidae), from southeasternColombia, revealed by cladistic analysis of mitochondrial DNA sequences. Zoological Journal of theLinnean Society,116(3):317-332.
Burgess, R., Yang, Z.2008, Estimation of hominoid ancestral population sizes under Bayesian coalescentmodels incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution,25(9):1979-1994.
Busby, P.E., Catherine Aime, M., Newcombe, G.2012, Foliar pathogens of Populus angustifolia areconsistent with a hypothesis of Beringian migration into North America. Fungal Biology,116(7):792-801.
Campana, M., Hunt, H., Jones, H., et al.2011, CorrSieve: software for summarizing and evaluating Structureoutput. Molecular ecology resources,11(2):349-352.
Campbell, J.S., Mahoney, J.M., Rood, S.B.1993, A lack of heterosis in natural poplar hybrids from southernAlberta. Canadian Journal of Botany,71(1):37-42.
Cervera, M., Storme, V., Soto, A., et al.2005, Intraspecific and interspecific genetic and phylogeneticrelationships in the genus Populus based on AFLP markers. TAG Theoretical and Applied Genetics,111(7):1440-1456.
Charlesworth, D.2003, Effects of inbreeding on the genetic diversity of populations. PhilosophicalTransactions of the Royal Society of London. Series B: Biological Sciences,358(1434):1051-1070.
Chase, M.W., Zmarzty, S., Lledó, M.D., et al.2002, When in doubt, put it in Flacourtiaceae: a molecularphylogenetic analysis based on plastid rbcL DNA sequences. Kew Bulletin,57(1):141-181.
Chaw, S.-M., Parkinson, C.L., Cheng, Y., et al.2000, Seed plant phylogeny inferred from all three plantgenomes: monophyly of extant gymnosperms and origin of Gnetales from conifers. Proceedings of theNational Academy of Sciences,97(8):4086-4091.
Chaw, S.-M., Zharkikh, A., Sung, H.-M., et al.1997, Molecular phylogeny of extant gymnosperms and seedplant evolution: analysis of nuclear18S rRNA sequences. Molecular Biology and Evolution,14(1):56-68.
Chu, Y., Su, X., Huang, Q., et al.2009, Patterns of DNA sequence variation at candidate gene loci in blackpoplar (Populus nigra L.) as revealed by single nucleotide polymorphisms. Genetica,137(2):141-150.
Clayton, J.W., Soltis, P.S., Soltis, D.E.2009, Recent long-distance dispersal overshadows ancientbiogeographical patterns in a pantropical angiosperm family (Simaroubaceae, Sapindales). SystematicBiology,58(4):395-410.
Cockram, J., White, J., Leigh, F.J., et al.2008, Association mapping of partitioning loci in barley. BMCgenetics,9(1):16.
Cole, C.T.2005, Allelic and population variation of microsatellite loci in aspen (Populus tremuloides). NewPhytologist,167(1):155-164.
Cox, C.B., Moore, P.D.,2010, Biogeography: an ecological and evolutionary approach. John Wiley&Sons.
Coyne, J.A., Orr, H.A.,2004, Speciation, Vol37. Sinauer Associates Sunderland, MA.
Crisci, J., Katinas, L., Posadas, P., et al.2009, Historical biogeography: an introduction. Harvard UniversityPress.
Cronk, Q.2005, Plant eco‐devo: the potential of poplar as a model organism. New Phytologist,166(1):39-48.
D’horta, F., Cabanne, G.S., Meyer, D., et al.2011, The genetic effects of Late Quaternary climatic changesover a tropical latitudinal gradient: diversification of an Atlantic Forest passerine. Molecular Ecology,20(9):1923-1935.
Davis, C.C., Bell, C.D., Mathews, S., et al.2002a, Laurasian migration explains Gondwanan disjunctions:evidence from Malpighiaceae. Proceedings of the National Academy of Sciences,99(10):6833-6837.
Davis, C.C., Fritsch, P.W., Li, J., et al.2002b, Phylogeny and biogeography of Cercis (Fabaceae): evidencefrom nuclear ribosomal ITS and chloroplast ndhF sequence data. Systematic Botany,27(2):289-302.
de Queiroz, A., Gatesy, J.2007, The supermatrix approach to systematics. Trends in ecology&evolution,22(1):34-41.
Delsuc, F., Brinkmann, H., Philippe, H.2005, Phylogenomics and the reconstruction of the tree of life.Nature Reviews Genetics,6(5):361-375.
Demesure, B., Sodzi, N., Petit, R.1995, A set of universal primers for amplification of polymorphic non‐coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology,4(1):129-134.
DiFazio, S., Slavov, G., Joshi, C.2011, Populus: A Premier Pionner System for Plant Genomics. Joshi CD, S.&Kole, C.(ed) Genetics, Genomics and Breeding of poplar. Science Publishers1-28.
Dillen, S.Y., Marron, N., Bastien, C., et al.2007, Effects of environment and progeny on biomassestimations of five hybrid poplar families grown at three contrasting sites across Europe. ForestEcology and Management,252(1):12-23.
Donoghue, M.J., Bell, C.D., Li, J.2001, Phylogenetic patterns in Northern Hemisphere plant geography.International Journal of Plant Sciences,162(S6): S41-S52.
Donoghue, M.J., Moore, B.R.2003, Toward an integrative historical biogeography. Integrative andComparative Biology,43(2):261-270.
Doyle, J.A.1978, Origin of angiosperms. Annual Review of Ecology and Systematics,9(1):365-392.
Doyle, J.A.1998, Molecules, morphology, fossils, and the relationship of angiosperms and Gnetales.Molecular Phylogenetics and Evolution,9(3):448-462.
Doyle, J.J.1987, A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull,1911-15.
Drew, B.T., Ruhfel, B.R., Smith, S.A., et al.2014, Another Look at the Root of the Angiosperms Reveals aFamiliar Tale. Systematic Biologysyt108.
Drummond, A.J., Rambaut, A.2007, BEAST: Bayesian evolutionary analysis by sampling trees. BMCEvolutionary Biology,7(1):214.
Duarte, J.M., Wall, P.K., Edger, P.P., et al.2010, Identification of shared single copy nuclear genes inArabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels.BMC Evolutionary Biology,10(1):61.
Eckenwalder, J.E.,1977. Systematics of Populus L.(Salicaceae) in southwestern North America with specialreference to sect. Aigeiros Duby. University of California, Berkeley,
Eckenwalder, J.E.1984, Natural intersectional hybridization between North American species of Populus(Salicaceae) in sections Aigeiros and Tacamahaca. II. Taxonomy. Canadian Journal of Botany,62(2):325-335.
Eckenwalder, J.E.1996, Systematics and evolution of Populus. Biology of Populus and its implications formanagement and conservation,732.
Edwards, S.V.2009, Is a new and general theory of molecular systematics emerging? Evolution,63(1):1-19.
Edwards, S.V., Liu, L., Pearl, D.K.2007, High-resolution species trees without concatenation. Proceedingsof the National Academy of Sciences,104(14):5936-5941.
EL Little, J.1971, Atlas of United States trees. Volume1. Conifers and important hardwoods. MiscellaneousPublications. United States Department of Agriculture(1146.).
Eldredge, N., Thompson, J.N., Brakefield, P.M., et al.2005, The dynamics of evolutionary stasis.Paleobiology,31(sp5):133-145.
Evanno, G., Regnaut, S., Goudet, J.2005, Detecting the number of clusters of individuals using the softwareSTRUCTURE: a simulation study. Molecular ecology,14(8):2611-2620.
Ewen, K.R., Bahlo, M., Treloar, S.A., et al.2000, Identification and analysis of error types inhigh-throughput genotyping. The American Journal of Human Genetics,67(3):727-736.
Excoffier, L., Laval, G., Schneider, S.2005, Arlequin (version3.0): an integrated software package forpopulation genetics data analysis. Evolutionary bioinformatics online,147.
Excoffier, L., Smouse, P.E., Quattro, J.M.1992, Analysis of molecular variance inferred from metricdistances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics,131(2):479-491.
Felsenstein, J.1981, Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal ofmolecular evolution,17(6):368-376.
Felsenstein, J.1988, Phylogenies from molecular sequences: inference and reliability. Annual review ofgenetics,22(1):521-565.
Felsenstein, J., Felenstein, J.,2004, Inferring phylogenies, Vol2. Sinauer Associates Sunderland.
Fitch, W.M.1971, Toward defining the course of evolution: minimum change for a specific tree topology.Systematic Biology,20(4):406-416.
Floate, K.D.2004, Extent and patterns of hybridization among the three species of Populus that constitutethe riparian forest of southern Alberta, Canada. Canadian Journal of Botany,82(2):253-264.
Fu, Y.-X., Li, W.-H.1993, Statistical tests of neutrality of mutations. Genetics,133(3):693-709.
Fussi, B., Lexer, C., Heinze, B.2010, Phylogeography of Populus alba (L.) and Populus tremula (L.) inCentral Europe: secondary contact and hybridisation during recolonisation from disconnected refugia.Tree Genetics&Genomes,6(3):439-450.
Futuyma, D.J.2010, Evolutionary constraint and ecological consequences. Evolution,64(7):1865-1884.
Gilchrist, E.J., Haughn, G.W., Ying, C.C., et al.2006, Use of Ecotilling as an efficient SNP discovery tool tosurvey genetic variation in wild populations of Populus trichocarpa. Molecular Ecology,15(5):1367-1378.
Givnish, T.J.1998, Adaptive plant evolution on islands: classical patterns, molecular data, new insights.Evolution on islands,281304.
Givnish, T.J., Barfuss, M.H., Van Ee, B., et al.2011, Phylogeny, adaptive radiation, and historicalbiogeography in Bromeliaceae: insights from an eight-locus plastid phylogeny. American journal ofbotany,98(5):872-895.
Goldman, N.1993, Statistical tests of models of DNA substitution. Journal of molecular evolution,36(2):182-198.
Gompert, Z., Fordyce, J.A., Forister, M.L., et al.2006, Homoploid hybrid speciation in an extreme habitat.Science,314(5807):1923-1925.
González‐Martínez, S.C., Krutovsky, K.V., Neale, D.B.2006, Forest‐tree population genomics andadaptive evolution. New Phytologist,170(2):227-238.
Goremykin, V.V., Nikiforova, S.V., Biggs, P.J., et al.2013, The evolutionary root of flowering plants.Systematic Biology,62(1):50-61.
Grant, M., Mitton, J.2010a, Case study: the glorious, golden, and gigantic quaking aspen. Nature EducationKnowledge,3(10):40.
Grant, V.,1971, Plant speciation, Vol183. Columbia University Press New York.
Grant, V.,1981, Plant speciation. New York: Columbia University Press xii,563p.-illus., maps, chrom. nos..En2nd edition. Maps, Chromosome numbers. General (KR,198300748).
Gray, R.D., Drummond, A.J., Greenhill, S.J.2009, Language phylogenies reveal expansion pulses andpauses in Pacific settlement. Science,323(5913):479-483.
Hall, T.A.,1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program forWindows95/98/NT. In: Nucleic acids symposium series, pp.95-98.
Hamrick, J., Godt, M.1996, Effects of life history traits on genetic diversity in plant species. PhilosophicalTransactions of the Royal Society of London. Series B: Biological Sciences,351(1345):1291-1298.
Hamrick, J.L., Godt, M.J.W., Sherman-Broyles, S.L.,1992, Factors influencing levels of genetic diversity inwoody plant species, In: Population genetics of forest trees. Springer, pp.95-124.
Hamzeh, M., Dayanandan, S.2004, Phylogeny of Populus (Salicaceae) based on nucleotide sequences ofchloroplast trnT-trnF region and nuclear rDNA. American journal of botany,91(9):1398-1408.
Hamzeh, M., Périnet, P., Dayanandan, S.2006, Genetic Relationships among species of Populus (Salicaceae)based on nuclear genomic data1. The Journal of the Torrey Botanical Society,133(4):519-527.
Hamzeh, M.H.M., Sawchyn, C.S.C., Périnet, P.P.P., et al.2007, Asymmetrical natural hybridization betweenPopulus deltoides and P. balsamifera (Salicaceae) This note is one of a selection of papers published inthe Special Issue on Poplar Research in Canada. Botany,85(12):1227-1232.
Harrison, R.G.1991, Molecular changes at speciation. Annual Review of Ecology and Systematics,22281-308.
Harrison, T.M., Copeland, P., Kidd, W., et al.1992, Raising tibet. Science,255(5052):1663-1670.
Hartigan, J.A.1973, Minimum mutation fits to a given tree. Biometrics53-65.
Hastings, W.K.1970, Monte Carlo sampling methods using Markov chains and their applications.Biometrika,57(1):97-109.
Hedrick, P.W.,2011, Genetics of populations. Jones&Bartlett Publishers.
Heuertz, M., De Paoli, E., K llman, T., et al.2006, Multilocus patterns of nucleotide diversity, linkagedisequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]. Genetics,174(4):2095-2105.
Hewitt, G.2000, The genetic legacy of the Quaternary ice ages. Nature,405(6789):907-913.
Hewitt, G.M.1996, Some genetic consequences of ice ages, and their role in divergence and speciation.Biological Journal of the Linnean Society,58(3):247-276.
Hewitt, G.M.2004, Genetic consequences of climatic oscillations in the Quaternary. PhilosophicalTransactions Of The Royal Society Of London Series B-Biological Sciences,359(1442):183-195.
Hey, J.2010a, The divergence of chimpanzee species and subspecies as revealed in multipopulationisolation-with-migration analyses. Molecular Biology and Evolution,27(4):921-933.
Hey, J.2010b, Isolation with migration models for more than two populations. Molecular Biology andEvolution,27(4):905-920.
Hey, J., Nielsen, R.2004, Multilocus methods for estimating population sizes, migration rates anddivergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis.Genetics,167(2):747-760.
Hey, J., Nielsen, R.2007, Integration within the Felsenstein equation for improved Markov chain MonteCarlo methods in population genetics. Proceedings of the National Academy of Sciences,104(8):2785.
Hickerson, M., Carstens, B., Cavender-Bares, J., et al.2010, Phylogeography’s past, present, and future:10years after. Molecular Phylogenetics and Evolution,54(1):291-301.
Hipp, A.L., Hall, J.C., Sytsma, K.J.2004, Congruence versus phylogenetic accuracy: revisiting theincongruence length difference test. Systematic Biology,53(1):81-89.
Huang, S.S., Hwang, S.Y., Lin, T.P.2002, Spatial pattern of chloroplast DNA variation of Cyclobalanopsisglauca in Taiwan and East Asia. Molecular Ecology,11(11):2349-2358.
Hubisz, M.J., Falush, D., Stephens, M., et al.2009, Inferring weak population structure with the assistance ofsample group information. Molecular ecology resources,9(5):1322-1332.
Hudson, R.R., Kaplan, N.L.1985, Statistical properties of the number of recombination events in the historyof a sample of DNA sequences. Genetics,111(1):147-164.
Hudson, R.R., Kreitman, M., Aguadé, M.1987, A test of neutral molecular evolution based on nucleotidedata. Genetics,116(1):153-159.
Huelsenbeck, J.P., Ronquist, F.2001, MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics,17(8):754-755.
Ingvarsson, P.K.2005a, Molecular population genetics of herbivore-induced protease inhibitor genes inEuropean aspen (Populus tremula L., Salicaceae). Molecular Biology and Evolution,22(9):1802-1812.
Ingvarsson, P.K.2005b, Nucleotide polymorphism and linkage disequilibrium within and among naturalpopulations of European aspen (Populus tremula L., Salicaceae). Genetics,169(2):945-953.
Ingvarsson, P.K.2008, Multilocus patterns of nucleotide polymorphism and the demographic history ofPopulus tremula. Genetics,180(1):329-340.
Ingvarsson, P.K., García, M.V., Hall, D., et al.2006, Clinal variation in phyB2, a candidate gene forday-length-induced growth cessation and bud set, across a latitudinal gradient in European aspen(Populus tremula). Genetics,172(3):1845-1853.
Ismail, M., Soolanayakanahally, R.Y., Ingvarsson, P.K., et al.2012, Comparative Nucleotide DiversityAcross North American and European Populus Species. Journal of molecular evolution1-16.
Jakobsson, M., Rosenberg, N.A.2007, CLUMPP: a cluster matching and permutation program for dealingwith label switching and multimodality in analysis of population structure. Bioinformatics,23(14):1801-1806.
Jelinski, D.E., Cheliak, W.1992, Genetic diversity and spatial subdivision of Populus tremuloides(Salicaceae) in a heterogeneous landscape. American journal of botany728-736.
Jennings, W.B., Edwards, S.V.2005, Speciational history of Australian Grass Finches (Poephila) inferredfrom thirty gene trees. Evolution,59(9):2033-2047.
Jia, D.R., Abbott, R.J., Liu, T.L., et al.2012, Out of the Qinghai–Tibet Plateau: Evidence for the origin anddispersal of Eurasian temperate plants from a phylogeographic study of Hippopha rhamnoides(Elaeagnaceae). New Phytologist.
Joly, S., McLenachan, P.A., Lockhart, P.J.2009, A statistical approach for distinguishing hybridization andincomplete lineage sorting. The American Naturalist,174(2): E54-E70.
Kanaga, M.K., Ryel, R.J., Mock, K.E., et al.2008, Quantitative-genetic variation in morphological andphysiological traits within a quaking aspen (Populus tremuloides) population. Canadian Journal ofForest Research,38(6):1690-1694.
Keim, P., Paige, K., Whitham, T., et al.1989, Genetic analysis of an interspecific hybrid swarm of Populus:occurrence of unidirectional introgression. Genetics,123(3):557-565.
Keller, S.R., Olson, M.S., Silim, S., et al.2010, Genomic diversity, population structure, and migrationfollowing rapid range expansion in the Balsam Poplar, Populus balsamifera. Molecular Ecology,19(6):1212-1226.
Kingman, J.F.C.1982, The coalescent. Stochastic processes and their applications,13(3):235-248.
Kliman, R.M., Andolfatto, P., Coyne, J.A., et al.2000, The population genetics of the origin and divergenceof the Drosophila simulans complex species. Genetics,156(4):1913-1931.
Kliman, R.M., Hey, J.1993, DNA sequence variation at the period locus within and among species of theDrosophila melanogaster complex. Genetics,133(2):375-387.
Knowles, L.L., Carstens, B.C., Keat, M.L.2007, Coupling genetic and ecological-niche models to examinehow past population distributions contribute to divergence. Current biology,17(11):940-946.
Kramer, B., Van der Bank, H., Flint, N., et al.2003, Evidence for parapatric speciation in the Mormyrid fish,Pollimyrus castelnaui (Boulenger,1911), from the Okavango–Upper Zambezi River Systems: P.marianne sp. nov., defined by electric organ discharges, morphology and genetics. EnvironmentalBiology of Fishes,67(1):47-70.
Kuanyu, L., Minren, H., Huixin, P., et al.1996. Study on origin of Populus tomentosa Carr. In:International Poplar Commission. Sess.20, Budapest (Hungary),1-4Oct1996.
Kumar, S., Nei, M., Dudley, J., Tamura, K.2008, MEGA: a biologist-centric software for evolutionaryanalysis of DNA and protein sequences. Briefings in bioinformatics,9(4):299-306.
Langley, C.H., Fitch, W.M.1974, An examination of the constancy of the rate of molecular evolution.Journal of molecular evolution,3(3):161-177.
Leskinen, E., Alstr m-Rapaport, C.1999, Molecular phylogeny of Salicaceae and closely relatedFlacourtiaceae: Evidence from5.8S, ITS1and ITS2of the rDNA. Plant Systematics and Evolution,215(1):209-227.
Levsen, N.D., Tiffin, P., Olson, M.S.2012, Pleistocene speciation in the genus Populus (Salicaceae).Systematic Biology.
Lexer, C., Fay, M., Joseph, J., et al.2005, Barrier to gene flow between two ecologically divergent Populusspecies, P. alba (white poplar) and P. tremula (European aspen): the role of ecology and life history ingene introgression. Molecular Ecology,14(4):1045-1057.
Lexer, C., van Loo, M.2006, Contact zones: natural labs for studying evolutionary transitions. Currentbiology,16(11): R407-R409.
Liao, C., Downie, S.R., Li, Q., et al.2013, New Insights into the Phylogeny of Angelica and its Allies(Apiaceae) with Emphasis on East Asian Species, Inferred from nrDNA, cpDNA, and MorphologicalEvidence. Systematic Botany,38(1):266-281.
Librado, P., Rozas, J.2009, DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25(11):1451-1452.
Liu, L.2008, BEST: Bayesian estimation of species trees under the coalescent model. Bioinformatics,24(21):2542-2543.
Liu, L., Pearl, D.K.2007, Species trees from gene trees: reconstructing Bayesian posterior distributions of aspecies phylogeny using estimated gene tree distributions. Systematic Biology,56(3):504-514.
Liu, Z., Furnier, G.1993, Comparison of allozyme, RFLP, and RAPD markers for revealing genetic variationwithin and between trembling aspen and bigtooth aspen. Theoretical and Applied Genetics,87(1-2):97-105.
Llopart, A., Herrig, D., Brud, E., et al.2014, Sequential adaptive introgression of the mitochondrial genomein Drosophila yakuba and D. santomea. Molecular Ecology.
Llopart, A., Lachaise, D., Coyne, J.A.2005, Multilocus analysis of introgression between two sympatricsister species of Drosophila: Drosophila yakuba and D. santomea. Genetics,171(1):197-210.
Love, A., Love, D.1975, Nomenclatural notes on arctic plants. Bot. Notiser,128(4):497-523.
Lowry, D.B., Rockwood, R.C., Willis, J.H.2008, Ecological reproductive isolation of coast and inland racesof Mimulus guttatus. Evolution,62(9):2196-2214.
Müller, A., Leuschner, C., Horna, V., et al.2012, Photosynthetic characteristics and growth performance ofclosely related aspen taxa: On the systematic relatedness of the Eurasian Populus tremula and the NorthAmerican P. tremuloides. Flora-Morphology, Distribution, Functional Ecology of Plants,207(2):87-95.
M ser, P., Thomine, S., Schroeder, J.I., et al.2001, Phylogenetic relationships within cation transporterfamilies of Arabidopsis. Plant Physiology,126(4):1646-1667.
Ma, J.2011, Reconstructing the history of large-scale genomic changes: biological questions andcomputational challenges. Journal of Computational Biology,18(7):879-893.
MacGinitie, H.D.,1969, The Eocene Green River flora of northwestern Colorado and northeastern Utah.University of California Press.
Machado, C.A., Kliman, R.M., Markert, J.A., et al.2002, Inferring the history of speciation from multilocusDNA sequence data: the case of Drosophila pseudoobscura and close relatives. Molecular Biology andEvolution,19(4):472-488.
Madritch, M.D., Greene, S.L., Lindroth, R.L.2009, Genetic mosaics of ecosystem functioning acrossaspen-dominated landscapes. Oecologia,160(1):119-127.
Maliouchenko, O., Palmé, A.E., Buonamici, A., et al.2007, Comparative phylogeography and populationstructure of European Betula species, with particular focus on B. pendula and B. pubescens. Journal ofBiogeography,34(9):1601-1610.
Mallet, J.2007, Hybrid speciation. Nature,446(7133):279-283.
Manchester, S.R., Dilcher, D.L., Tidwell, W.D.1986, Interconnected reproductive and vegetative remains ofPopulus (Salicaceae) from the middle Eocene Green River Formation, northeastern Utah. Americanjournal of botany156-160.
Manchester, S.R., Judd, W.S., Handley, B.2006, Foliage and fruits of early poplars (Salicaceae: Populus)from the Eocene of Utah, Colorado, and Wyoming. International Journal of Plant Sciences,167(4):897-908.
Mao, K., Milne, R.I., Zhang, L., et al.2012, Distribution of living Cupressaceae reflects the breakup ofPangea. Proceedings of the National Academy of Sciences.
Marincovich, L., Gladenkov, A.Y.1999, Evidence for an early opening of the Bering Strait. Nature,397(6715):149-151.
Marra, M.A., Jones, S.J., Astell, C.R., et al.2003, The genome sequence of the SARS-associated coronavirus.Science,300(5624):1399-1404.
Martinsen, G.D., Whitham, T.G., Turek, R.J., et al.2001, Hybrid populations selectively filter geneintrogression between species. Evolution,55(7):1325-1335.
Mayr, E.,1970, Populations, species, and evolution: an abridgment of animal species and evolution. HarvardUniversity Press.
Mayr, E.,1982, The growth of biological thought: Diversity, evolution, and inheritance. Harvard UniversityPress.
Mes, T., Hart, H.1996, The evolution of growth‐forms in the Macaronesian genus Aeonium (Crassulaceae)inferred from chloroplast DNA RFLPs and morphology. Molecular Ecology,5(3):351-363.
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., et al.2004, Equation of state calculations by fastcomputing machines. The journal of chemical physics,21(6):1087-1092.
Milne, R.I., Abbott, R.J.2002, The origin and evolution of Tertiary relict floras. Advances in BotanicalResearch,38281-314.
Milne, R.I.A.N.2006, Northern Hemisphere plant disjunctions: a window on tertiary land bridges andclimate change? Annals of Botany,98(3):465-472.
Mitton, J.B., Grant, M.C.1996, Genetic variation and the natural history of quaking aspen. Bioscience,46(1):25-31.
Mock, K.E., Rowe, C., Hooten, M.B., et al.2008, Clonal dynamics in western North American aspen(Populus tremuloides). Molecular Ecology,17(22):4827-4844.
Moeller, D.A., Tenaillon, M.I., Tiffin, P.2007, Population structure and its effects on patterns of nucleotidepolymorphism in teosinte (Zea mays ssp. parviglumis). Genetics,176(3):1799-1809.
Monod, L., Prendini, L.2014, Evidence for Eurogondwana: the roles of dispersal, extinction and vicariancein the evolution and biogeography of Indo‐Pacific Hormuridae (Scorpiones: Scorpionoidea).Cladistics.
Morin, N.R.,2000, Flora of North America. Flora of North America Association.
Morrell, P.L., Lundy, K.E., Clegg, M.T.2003, Distinct geographic patterns of genetic diversity aremaintained in wild barley (Hordeum vulgare ssp. spontaneum) despite migration. Proceedings of theNational Academy of Sciences,100(19):10812-10817.
Namroud, M.C., Park, A., Tremblay, F., et al.2005, Clonal and spatial genetic structures of aspen (Populustremuloides Michx.). Molecular Ecology,14(10):2969-2980.
Nei, M.1973, Analysis of gene diversity in subdivided populations. Proceedings of the National Academy ofSciences,70(12):3321-3323.
Nei, M.,1987, Molecular evolutionary genetics. Columbia University Press.
Nei, M., Kumar, S.,2000, Molecular evolution and phylogenetics. Oxford University Press.
Nei, M., Li, W.-H.1979, Mathematical model for studying genetic variation in terms of restrictionendonucleases. Proceedings of the National Academy of Sciences,76(10):5269-5273.
Nie, Z.-L., Funk, V., Sun, H., et al.2013, Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) withbiogeographic implications in the Northern Hemisphere. Journal of plant research,126(1):17-32.
Nielsen, R., Wakeley, J.2001, Distinguishing migration from isolation: a Markov chain Monte Carloapproach. Genetics,158(2):885-896.
Nystedt, B., Street, N.R., Wetterbom, A., et al.2013, The Norway spruce genome sequence and conifergenome evolution. Nature.
Okumura, S., Sawada, M., Park, Y.W., et al.2006, Transformation of poplar (Populus alba) plastids andexpression of foreign proteins in tree chloroplasts. Transgenic research,15(5):637-646.
Olson, M.S., Robertson, A.L., Takebayashi, N., et al.2010, Nucleotide diversity and linkage disequilibriumin balsam poplar (Populus balsamifera). New Phytologist,186(2):526-536.
Ostrowski, M., David, J., Santoni, S., et al.2006, Evidence for a large‐scale population structure amongaccessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkagedisequilibrium. Molecular Ecology,15(6):1507-1517.
Page, R.D.2000, Extracting species trees from complex gene trees: reconciled trees and vertebratephylogeny. Molecular Phylogenetics and Evolution,14(1):89-106.
Pakull, B., Groppe, K., Meyer, M., et al.2009, Genetic linkage mapping in aspen (Populus tremula L. andPopulus tremuloides Michx.). Tree Genetics&Genomes,5(3):505-515.
Palmé, A., Semerikov, V., Lascoux, M.2003, Absence of geographical structure of chloroplast DNAvariation in sallow, Salix caprea L. Heredity,91(5):465-474.
Palmer, J.D., Jansen, R.K., Michaels, H.J., et al.1988, Chloroplast DNA variation and plant phylogeny.Annals of the Missouri Botanical Garden (USA).
Paten, B., Herrero, J., Fitzgerald, S., et al.2008, Genome-wide nucleotide-level mammalian ancestorreconstruction. Genome Research,18(11):1829-1843.
Pellis, A., Laureysens, I., Ceulemans, R.2008, Genetic variation of the bud and leaf phenology of seventeenpoplar clones in a short rotation coppice culture. Plant Biology,6(1):38-46.
Peng, D., Wang, X.Q.2008, Reticulate evolution in Thuja inferred from multiple gene sequences:Implications for the study of biogeographical disjunction between eastern Asia and North America.Molecular Phylogenetics and Evolution,47(3):1190-1202.
Petit, R.J., Aguinagalde, I., de Beaulieu, J.L., et al.2003, Glacial refugia: hotspots but not melting pots ofgenetic diversity. Science,300(5625):1563.
Planet, P.J.2006, Tree disagreement: measuring and testing incongruence in phylogenies. Journal ofbiomedical informatics,39(1):86-102.
Pons, O., Petit, R.1996, Measwring and Testing Genetic Differentiation With Ordered Versus UnorderedAlleles. Genetics,144(3):1237-1245.
Posada, D.2003, Using Modeltest and PAUP*to select a model of nucleotide substitution. Current protocolsin bioinformatics6.5.1-6.5.14.
Posada, D., Crandall, K.A.2001, Intraspecific gene genealogies: trees grafting into networks. Trends inecology&evolution,16(1):37-45.
Pritchard, J.K., Stephens, M., Donnelly, P.2000, Inference of population structure using multilocus genotypedata. Genetics,155(2):945-959.
Pyh j rvi, T., García-Gil, M.R., Knürr, T., et al.2007, Demographic history has influenced nucleotidediversity in European Pinus sylvestris populations. Genetics,177(3):1713-1724.
Qiu, Y.L., Li, L., Wang, B., et al.2007, A nonflowering land plant phylogeny inferred from nucleotidesequences of seven chloroplast, mitochondrial, and nuclear genes. International Journal of PlantSciences,168(5):691-708.
Qiu, Y.X., Fu, C.X., Comes, H.P.2011, Plant molecular phylogeography in China and adjacent regions:Tracing the genetic imprints of Quaternary climate and environmental change in the world's mostdiverse temperate flora. Molecular Phylogenetics and Evolution.
Qiu, Y.X., Sun, Y., Zhang, X.P., et al.2009, Molecular phylogeography of East Asian Kirengeshoma(Hydrangeaceae) in relation to Quaternary climate change and landbridge configurations. NewPhytologist,183(2):480-495.
Queiroz, A.2005, The resurrection of oceanic dispersal in historical biogeography. Trends in ecology&evolution,20(2):68-73.
Quicke, D.L., Jones, O.R., Epstein, D.R.2007, Correcting the problem of false incongruence due to noiseimbalance in the incongruence length difference (ILD) test. Systematic Biology,56(3):496-503.
Rabosky, D.L., Adams, D.C.2012, Rates of morphological evolution are correlated with species richness insalamanders. Evolution,66(6):1807-1818.
Rajora, O., Dancik, B.1992, Chloroplast DNA inheritance in Populus. TAG Theoretical and AppliedGenetics,84(3):280-285.
Rajora, O., Dancik, B.1995, Chloroplast DNA variation in Populus. II. Interspecific restriction fragmentpolymorphisms and genetic relationships among Populus deltoides, P. nigra, P. maximowiczii, and P. xcanadensis. Theoretical and Applied Genetics,90(3-4):324-330.
Rajora, O.P., Zsuffa, L.1990, Allozyme divergence and evolutionary relationships among Populus deltoides,P. nigra, and P. maximowiczii. Genome,33(1):44-49.
Rambaut, A.2008, FigTree v1.1.1. Published by the author.
Rambaut, A., Drummond, A.2007, Tracer v1.5. htt p. tree. bio. ed. ac. uk/software/tracer.
Ramos-Onsins, S.E., Rozas, J.2002, Statistical properties of new neutrality tests against population growth.Molecular Biology and Evolution,19(12):2092-2100.
Ramos-Onsins, S.E., Stranger, B.E., Mitchell-Olds, T., et al.2004, Multilocus analysis of variation andspeciation in the closely related species Arabidopsis halleri and A. lyrata. Genetics,166(1):373-388.
Ramos‐Onsins, S., Puerma, E., BALA á‐ALCAIDE, D., et al.2008, Multilocus analysis of variationusing a large empirical data set: phenylpropanoid pathway genes in Arabidopsis thaliana. Molecularecology,17(5):1211-1223.
Rannala, B., Yang, Z.1996, Probability distribution of molecular evolutionary trees: a new method ofphylogenetic inference. Journal of molecular evolution,43(3):304-311.
Rannala, B., Yang, Z.2003, Bayes estimation of species divergence times and ancestral population sizesusing DNA sequences from multiple loci. Genetics,164(4):1645-1656.
Ree, R.H., Smith, S.A.2008, Maximum likelihood inference of geographic range evolution by dispersal,local extinction, and cladogenesis. Systematic Biology,57(1):4-14.
Remington, D., Robichaux, R.2007, Influences of gene flow on adaptive speciation in the Dubautiaarborea–D. ciliolata complex. Molecular ecology,16(19):4014-4027.
Renner, S.S.2005, Relaxed molecular clocks for dating historical plant dispersal events. Trends in plantscience,10(11):550-558.
Reyes-Prieto, A., Bhattacharya, D.2007, Phylogeny of Calvin cycle enzymes supports Plantae monophyly.Molecular Phylogenetics and Evolution,45(1):384-391.
Richards, C.L., Carstens, B.C., Lacey Knowles, L.2007, Distribution modelling and statisticalphylogeography: an integrative framework for generating and testing alternative biogeographicalhypotheses. Journal of Biogeography,34(11):1833-1845.
Richardson, J.E., Pennington, R.T., Pennington, T.D., et al.2001, Rapid diversification of a species-richgenus of neotropical rain forest trees. Science,293(5538):2242-2245.
Rokas, A., Carroll, S.B.2006, Bushes in the tree of life. PLoS Biology,4(11): e352.
Ronquist, F.1997, Dispersal-vicariance analysis: a new approach to the quantification of historicalbiogeography. Systematic Biology,46(1):195-203.
Ronquist, F., Huelsenbeck, J.P.2003, MrBayes3: Bayesian phylogenetic inference under mixed models.Bioinformatics,19(12):1572-1574.
Rood, S.B., Campbell, J.S., Despins, T.1986, Natural poplar hybrids from southern Alberta. I. Continuousvariation for foliar characteristics. Canadian Journal of Botany,64(7):1382-1388.
Rosenberg, N.A.2004, DISTRUCT: a program for the graphical display of population structure. MolecularEcology Notes,4(1):137-138.
Ruhfel, B.R., Gitzendanner, M.A., Soltis, P.S., et al.2014, From algae to angiosperms-inferring thephylogeny of green plants (Viridiplantae) from360plastid genomes. BMC Evolutionary Biology,14(1):23.
Saitou, N., Nei, M.1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees.Molecular Biology and Evolution,4(4):406-425.
Salipante, S.J., Horwitz, M.S.2006, Phylogenetic fate mapping. Proceedings of the National Academy ofSciences,103(14):5448-5453.
San Mauro, D., Vences, M., Alcobendas, M., et al.2005, Initial diversification of living amphibians predatedthe breakup of Pangaea. The American Naturalist,165(5):590-599.
Sanders, K.L., Rasmussen, A.R., Guinea, M.L.2014, High rates of hybridisation reveal fragile reproductivebarriers between endangered Australian sea snakes. Biological Conservation,171200-208.
Sanderson, M.J.1997, A nonparametric approach to estimating divergence times in the absence of rateconstancy. Molecular Biology and Evolution,14(12):1218-1231.
Sanderson, M.J.2002, Estimating absolute rates of molecular evolution and divergence times: a penalizedlikelihood approach. Molecular Biology and Evolution,19(1):101-109.
Sang, T.2002, Utility of low-copy nuclear gene sequences in plant phylogenetics. Critical Reviews inBiochemistry and Molecular Biology,37(3):121-147.
Sang, T., Ge, S.2007, The puzzle of rice domestication. Journal of Integrative Plant Biology,49(6):760-768.
Sanmartín, I., Van Der Mark, P., Ronquist, F.2008, Inferring dispersal: a Bayesian approach to phylogeny‐based island biogeography, with special reference to the Canary Islands. Journal of Biogeography,35(3):428-449.
Sanmartin, I., Enghoff, H., Ronquist, F.2001, Patterns of animal dispersal, vicariance and diversification inthe Holarctic. Biological Journal of the Linnean Society,73(4):345-390.
Sanmartin, I., Ronquist, F.2004, Southern Hemisphere biogeography inferred by event-based models: plantversus animal patterns. Systematic Biology,53(2):216-243.
Savolainen, O., Pyh j rvi, T.2007, Genomic diversity in forest trees. Current opinion in plant biology,10(2):162-167.
Savolainen, V., Anstett, M.-C., Lexer, C., et al.2006, Sympatric speciation in palms on an oceanic island.Nature,441(7090):210-213.
Schaal, B., Hayworth, D., Olsen, K., et al.1998, Phylogeographic studies in plants: problems and prospects.Molecular Ecology,7(4):465-474.
Schliewen, U.K., Tautz, D., P bo, S.1994, Sympatric speciation suggested by monophyly of crater lakecichlids. Nature,368(6472):629-632.
Schmid, K.J., Ramos-Onsins, S., Ringys-Beckstein, H., et al.2005, A multilocus sequence survey inArabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequencepolymorphism. Genetics,169(3):1601-1615.
Schweitzer, J.A., Bailey, J.K., Hart, S.C., et al.2005, The interaction of plant genotype and herbivorydecelerate leaf litter decomposition and alter nutrient dynamics. Oikos,110(1):133-145.
Seifert, B.2010, Intranidal mating, gyne polymorphism, polygyny, and supercoloniality as factors forsympatric and parapatric speciation in ants. Ecological entomology,35(s1):33-40.
Shaw, J., Lickey, E.B., Beck, J.T., et al.2005, The tortoise and the hare II: relative utility of21noncodingchloroplast DNA sequences for phylogenetic analysis. American journal of botany,92(1):142-166.
Shaw, J., Lickey, E.B., Schilling, E.E., et al.2007, Comparison of whole chloroplast genome sequences tochoose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III.American journal of botany,94(3):275-288.
Shi, Y.,1998, Uplift and environmental changes of Qinghai-Xizang (Tibetan) Plateau in the late Cenozoic.Guangdong Scirence&Technology Press.
Slavov, G., DiFazio, S., Strauss, S.H., et al.2004. Gene flow in forest trees: gene migration patterns andlandscape modelling of transgene dispersal in hybrid poplar. In: Introgression from geneticallymodified plants into wild relatives. Proceedings of a conference organized by the University ofAmsterdam (Netherlands) and the Robert Koch Institute (Germany), in January2003., pp.89-106.
Slavov, G.T., Zhelev, P.,2010, Salient biological features, systematics, and genetic variation of Populus, In:Genetics and Genomics of Populus. Springer, pp.15-38.
Small, R.L., Cronn, R.C., Wendel, J.F.2004, LAS Johnson Review No.2. Use of nuclear genes forphylogeny reconstruction in plants. Australian Systematic Botany,17(2):145-170.
Smith, R.L., Sytsma, K.J.1990, Evolution of Populus nigra (sect. Aigeiros): introgressive hybridization andthe chloroplast contribution of Populus alba (sect. Populus). American journal of botany1176-1187.
Sobel, J.M., Chen, G.F., Watt, L.R., et al.2010, The biology of speciation. Evolution,64(2):295-315.
Soltis, D.E., Tago-Nakazawa, M., Xiang, Q.-Y., et al.2001, Phylogenetic relationships and evolution inChrysosplenium (Saxifragaceae) based on matK sequence data. American journal of botany,88(5):883-893.
Stebbins, G.L.1963, Perspective. American Scientist362-370.
Stettler, R.F.,1996, Biology of Populus and its implications for management and conservation. CanadianGovernment Publishing.
Strasburg, J.L., Rieseberg, L.H.2010, How robust are “Isolation with Migration” analyses to violations ofthe IM model? A simulation study. Molecular Biology and Evolution,27(2):297-310.
Strasburg, J.L., Rieseberg, L.H.2011, Interpreting the estimated timing of migration events betweenhybridizing species. Molecular ecology,20(11):2353-2366.
Swofford, D.L.2003,{PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version4.}.
Taberlet, P., Gielly, L., Pautou, G., et al.1991, Universal primers for amplification of three non-codingregions of chloroplast DNA. Plant molecular biology,17(5):1105-1109.
Tajima, F.1989, Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.Genetics,123(3):585-595.
Takahata, N.1986, An attempt to estimate the effective size of the ancestral species common to two extantspecies from which homologous genes are sequenced. Genetical research,48(03):187-190.
Takahata, N., Satta, Y.1997, Evolution of the primate lineage leading to modern humans: phylogenetic anddemographic inferences from DNA sequences. Proceedings of the National Academy of Sciences,94(9):4811-4815.
Takahata, N., Satta, Y., Klein, J.1995, Divergence time and population size in the lineage leading to modernhumans. Theoretical population biology,48(2):198-221.
Talbot, P., Thompson, S.L., Schroeder, W., et al.2011, An efficient single nucleotide polymorphism assay todiagnose the genomic identity of poplar species and hybrids on the Canadian prairies. Canadian Journalof Forest Research,41(5):1102-1111.
Tang, L., Zou, X., Achoundong, G., et al.2010, Phylogeny and biogeography of the rice tribe (Oryzeae):evidence from combined analysis of20chloroplast fragments. Molecular Phylogenetics and Evolution,54(1):266-277.
Taylor, G.2002, Populus: Arabidopsis for forestry. Do we need a model tree? Annals of Botany,90(6):681-689.
Thompson, J.D., Gibson, T.J., Plewniak, F., et al.1997, The CLUSTAL_X windows interface: flexiblestrategies for multiple sequence alignment aided by quality analysis tools. Nucleic acids research,25(24):4876-4882.
Thompson, S.L., Lamothe, M., Meirmans, P.G., et al.2010, Repeated unidirectional introgression towardsPopulus balsamifera in contact zones of exotic and native poplars. Molecular Ecology,19(1):132-145.
Thorne, J.L., Kishino, H.2002, Divergence time and evolutionary rate estimation with multilocus data.Systematic Biology,51(5):689-702.
Tiffney, B.H.1985a, The Eocene North Atlantic land bridge: its importance in Tertiary and modernphytogeography of the Northern Hemisphere. J. Arnold Arbor,66(2):243-273.
Tiffney, B.H.1985b, Perspectives on the origin of the floristic similarity between eastern Asia and easternNorth America. Journal of the Arnold Arboretum,66.
Tiffney, B.H., Manchester, S.R.2001, The use of geological and paleontological evidence in evaluating plantphylogeographic hypotheses in the Northern Hemisphere Tertiary. International Journal of PlantSciences,162(S6): S3-S17.
Tuskan, G.A., Difazio, S., Jansson, S., et al.2006, The genome of black cottonwood, Populus trichocarpa(Torr.&Gray). Science,313(5793):1596-1604.
Vuli, M., Dionisio, F., Taddei, F., et al.1997, Molecular keys to speciation: DNA polymorphism and thecontrol of genetic exchange in enterobacteria. Proceedings of the National Academy of Sciences,94(18):9763-9767.
Wakeley, J., Hey, J.1997, Estimating ancestral population parameters. Genetics,145(3):847-855.
Wan, Y., Schwaninger, H.R., Baldo, A.M., et al.2013, A phylogenetic analysis of the grape genus (Vitis L.)reveals broad reticulation and concurrent diversification during neogene and quaternary climate change.BMC Evolutionary Biology,13(1):141.
Wang, Q., Abbott, R.J., Yu, Q.S., et al.2013, Pleistocene climate change and the origin of two desert plantspecies, Pugionium cornutum and Pugionium dolabratum (Brassicaceae), in northwest China. NewPhytologist.
Wang, X.-Q., Ran, J.-H.2014, Evolution and biogeography of gymnosperms. Molecular Phylogenetics andEvolution.
Watterson, G.1975, On the number of segregating sites in genetical models without recombination.Theoretical population biology,7(2):256-276.
Wayne, M.L., Simonsen, K.L.1998, Statistical tests of neutrality in the age of weak selection. Trends inecology&evolution,13(6):236-240.
Wei, X.-X., Yang, Z.-Y., Li, Y., et al.2010, Molecular phylogeny and biogeography of Pseudotsuga(Pinaceae): Insights into the floristic relationship between Taiwan and its adjacent areas. MolecularPhylogenetics and Evolution,55(3):776-785.
Wen, J.1999, Evolution of eastern Asian and eastern North American disjunct distributions in floweringplants. Annual Review of Ecology and Systematics421-455.
Wendel, J.F., Doyle, J.J.,1998, Phylogenetic incongruence: window into genome history and molecularevolution, In: Molecular systematics of plants II. Springer, pp.265-296.
Whelan, S., Liò, P., Goldman, N.2001, Molecular phylogenetics: state-of-the-art methods for looking intothe past. TRENDS in Genetics,17(5):262-272.
Whitham, T.G., Bailey, J.K., Schweitzer, J.A., et al.2006, A framework for community and ecosystemgenetics: from genes to ecosystems. Nature Reviews Genetics,7(7):510-523.
Whitham, T.G., DiFazio, S.P., Schweitzer, J.A., et al.2008, Extending genomics to natural communities andecosystems. Science,320(5875):492-495.
Willing, R., Pryor, L.1976, Interspecific hybridisation in poplar. Theoretical and Applied Genetics,47(3):141-151.
Willis, K.J., Niklas, K.J.2004, The role of Quaternary environmental change in plant macroevolution: theexception or the rule? Philosophical Transactions of the Royal Society of London. Series B: BiologicalSciences,359(1442):159-172.
Wimp, G.M., Martinsen, G.D., Floate, K.D., et al.2005, Plant genetic determinants of arthropod communitystructure and diversity. Evolution,59(1):61-69.
Winter, K.-U., Becker, A., Münster, T., et al.1999, MADS-box genes reveal that gnetophytes are moreclosely related to conifers than to flowering plants. Proceedings of the National Academy of Sciences,96(13):7342-7347.
Woerner, A.E., Cox, M.P., Hammer, M.F.2007, Recombination-filtered genomic datasets by informationmaximization. Bioinformatics,23(14):1851-1853.
Wolfe, J.A.1978, A Paleobotanical Interpretation of Tertiary Climates in the Northern Hemisphere: Datafrom fossil plants make it possible to reconstruct Tertiary climatic changes, which may be correlatedwith changes in the inclination of the earth's rotational axis.
Won, Y.-J., Hey, J.2005, Divergence population genetics of chimpanzees. Molecular Biology and Evolution,22(2):297-307.
Wood, T.E., Takebayashi, N., Barker, M.S., et al.2009, The frequency of polyploid speciation in vascularplants. Proceedings of the National Academy of Sciences,106(33):13875-13879.
Wright, S.,1984, Evolution and the genetics of populations, volume3: experimental results and evolutionarydeductions, Vol3. University of Chicago press.
Wright, S.I., Bi, I.V., Schroeder, S.G., et al.2005, The effects of artificial selection on the maize genome.Science,308(5726):1310-1314.
Wright, S.I., Gaut, B.S.2005, Molecular population genetics and the search for adaptive evolution in plants.Molecular Biology and Evolution,22(3):506-519.
Wu, C.-I., Ting, C.-T.2004, Genes and speciation. Nature Reviews Genetics,5(2):114-122.
Wu, Z.,1999, Flora of China. Science Press.
Xiang, Q.-Y., Soltis, D.E., Soltis, P.S.1998, The eastern Asian and eastern and western North Americanfloristic disjunction: congruent phylogenetic patterns in seven diverse genera. Molecular Phylogeneticsand Evolution,10(2):178-190.
Xiang, Q.Y.J., Manchester, S.R., Thomas, D.T., et al.2005, Phylogeny, biogeography, and molecular datingof cornelian cherries (Cornus, Cornaceae): tracking Tertiary plant migration. Evolution,59(8):1685-1700.
Yang, Z.2002, Likelihood and Bayes estimation of ancestral population sizes in hominoids using data frommultiple loci. Genetics,162(4):1811-1823.
Yang, Z.2010, A likelihood ratio test of speciation with gene flow using genomic sequence data. Genomebiology and evolution,2200.
Yang, Z., Rannala, B.1997, Bayesian phylogenetic inference using DNA sequences: a Markov chain MonteCarlo method. Molecular Biology and Evolution,14(7):717-724.
Yang, Z., Rannala, B.2006, Bayesian estimation of species divergence times under a molecular clock usingmultiple fossil calibrations with soft bounds. Molecular Biology and Evolution,23(1):212-226.
Yang, Z., Rannala, B.2010, Bayesian species delimitation using multilocus sequence data. Proceedings ofthe National Academy of Sciences,107(20):9264.
Yang, Z., Rannala, B.2012, Molecular phylogenetics: principles and practice. Nature Reviews Genetics,13(5):303-314.
Yang, Z.Y., Ran, J.H., Wang, X.Q.2012, Three Genome-based Phylogeny of Cupressaceae sl: FurtherEvidence for the Evolution of Gymnosperms and Southern Hemisphere Biogeography. MolecularPhylogenetics and Evolution.
Yeh, F., Chong, D., Yang, R.C.1995, RAPD variation within and among natural populations of tremblingaspen (Populus tremuloides Michx.) from Alberta. Journal of Heredity,86(6):454-460.
Zhang, D., Zhang, Z., Yang, K., et al.2004, Genetic mapping in (Populus tomentosa×Populus bolleana) andP. tomentosa Carr. using AFLP markers. Theoretical and Applied Genetics,108(4):657-662.
Zhang, JB., Li, RQ., Xiang, XG., et al.2013, Integrated Fossil and Molecular Data Reveal the BiogeographicDiversification of the Eastern Asian-Eastern North American Disjunct Hickory Genus (Carya Nutt.).PloS one,8(7): e70449.
Zhang, LB., Ge S.2007, Multilocus analysis of nucleotide variation and speciation in Oryza officinalis andits close relatives. Molecular Biology and Evolution,24(3):769-783.
Zhang, X., Zang, R., Li, C.2004, Population differences in physiological and morphological adaptations ofPopulus davidiana seedlings in response to progressive drought stress. Plant Science,166(3):791-797.
Zheng, H., Powell, C.M., An, Z., et al.2000, Pliocene uplift of the northern Tibetan Plateau. Geology,28(8):715-718.
Zheng, X., Ge, S.2010, Ecological divergence in the presence of gene flow in two closely related Oryzaspecies (Oryza rufipogon and O. nivara). Molecular Ecology,19(12):2439-2454.
Zhu, Q., Zheng, X., Luo, J., et al.2007, Multilocus analysis of nucleotide variation of Oryza sativa and itswild relatives: severe bottleneck during domestication of rice. Molecular Biology and Evolution,24(3):875-888.
Zou, X.H., Yang, Z., Doyle, J.J., et al.2013, Multilocus estimation of divergence times and ancestraleffective population sizes of Oryza species and implications for the rapid diversification of the genus.New Phytologist,198(4):1155-1164.
Zou, X.H., Zhang, F.M., Zhang, J.G., et al.2008, Analysis of142genes resolves the rapid diversification ofthe rice genus. Genome Biol,9(3): R49.
Zsuffa, L.,1975. A summary review of interspecific breeding in the genus Populus L. In: Proceedings14thmeeting of the Canadian Tree Improvement Association, part, pp.107-123.
Zuckerkandl, E., Pauling, L.1965, Evolutionary divergence and convergence in proteins. Evolving genesand proteins,9797-166.
戴玉成,沈瑞祥,周仲铭.1989,杨树栅锈菌Melampsora spp.的数量分类研究.林业科学,25(1):86-92.
韩联生,刘培林,袁显磊等.2006,小兴安岭山杨杂交新品系山地造林研究.林业科技,31(4):12-15.
李吉均,文世宣,张青松等.1979, A Discussion on the period, amplitude and type of the uplift of theQinghaiI-Xizang Plateau.中国科学,11:15-30.
李开隆,周光达,杨传平等.2004,中国山杨与美洲山杨杂交育种的研究.植物研究,24(2):215-219.
李善文,张有慧,张志毅等.2007,杨属部分种及杂种的AFLP分析.林业科学,43(1):35-41.
毛康珊.2010.广义柏科的生物地理学研究.兰州大学博士学位论文.
史全良,诸葛强,黄敏仁等.2001,用ITS序列研究杨属各组之间的系统发育关系.植物学报,43(3):323-325.
王丽娜,姜小龙,雷耘等.2012,北温带水青冈属的间断分布及其泛生物地理学解释.植物生态学报,36(5):393-402.
王源秀,徐立安,黄敏仁等.2007,林木比较基因组学研究进展. HEREDITAS (Beijing),101199-1206.
卫尊征,郭丽琴,张金凤等.2010,利用trnL—F序列分析杨属树种的系统发育关系.北京林业大学学报(2):27-33.
邢亚娟.2005.中国山杨与美洲山杨杂交种新品系选育研究.东北林业大学博士学位论文。
张德强,杨凯.2000,杨树分子标记研究进展.北京林业大学学报,22(006):79-84.
张奠湘.2003,历史生物地理学的进展.热带亚热带植物学报,11(3):283-289.
张金然,尚洁,王秋玉.2006,山杨杂种无性系的SSR分子标记遗传多样性.植物研究,26(4).
张守攻,齐力旺,陈成彬等.2003,中国杨属(Populus)植物染色体数目报道.中国细胞生物学学会第八届会员代表大会暨学术大会论文摘要集,12.