东亚岛屿特有濒危植物舟山新木姜子（Neoltisea sericea）的亲缘地理学研究
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摘要
舟山新木姜子[Neolitsea sericea (Bl.) Koidz.]为樟科(Lauraceae)新木姜子属(Neolitsea)暖温带常绿阔叶乔木。该物种是一个东亚地区间断分布的残遗种,主要分布于我国的舟山群岛、台湾兰屿岛,日本的琉球、四国、九州、本州以及朝鲜半岛的沿海岛屿。因此,选择该东亚特有间断分布的舟山新木姜子作为研究对象进行亲缘地理学的研究,不仅可以检测舟山新木姜子的遗传多样性和群体遗传结构,而且可以揭示更新世时期气候与地质结构变化对该物种现有地理分布格局的影响,并最终阐明舟山新木姜子群体间断分布模式的成因、群体历史动态及其进化动力。
本研究利用10对多态性的微卫星(nSSR)引物和1对叶绿体(cpDNA)基因间隔区片段(psbA-trnH)引物对涵盖舟山新木姜子群体现有分布范围的31个群体进行遗传多样性、群体遗传结构及花粉流／种子流(r)的研究。基于nSSR和cpDNA的联合数据,应用Isolation-with-migration(IM)模型对舟山新木姜子群体进行分析,计算遗传谱系分化时间和群体动态参数。
研究结果表明,nSSR标记和cpDNA序列数据均显示舟山新木姜子群体分化为两个独特的遗传谱系(南部谱系和北部谱系)。两遗传谱系分别位于Tokara Gap的南北两侧,具有显著的地理分布格局。基于IM分析,两遗传谱系的分化时间约为0.07 Ma (90% HPD:0.02-0.38 Ma);并且两谱系分化后几乎没有基因交流。南北两遗传谱系的花粉流／种子流的比值(r)极低(接近于零),反映了舟山新木姜子群体的近期分化。
舟山新木姜子两遗传谱系的分化时间支持Kimura的"Shallow-time sea-barrier"假说,也就是基于地质证据而提出的晚更新世冰期Tokara Gap地区存在陆桥连接；而与Ota提出的Tokara Gap自上新世形成以来不存在陆桥连接的"Ancient sea-barrier"假说不一致。舟山新木姜子遗传谱系的分化与维持还与环境因子的梯度变化以及该地区岛屿地理结构有一定的关系。
Neolitsea sericea (B1.) Koitz. (Lauraceae) is an element in the dioecious, warm-temperate evergreen forests, which is distributed from Taiwan (Orchid Island), through the Ryukyus to southern Japan, but also occurs disjunctively in off-shore islands of both East China (Zhoushan Archipelago) and South Korea (Jeju Island). A phylogeographic study of Neolitsea sericea was conducted:(i) to assess the population genetic structure and demographic divergence history of a bird-dispersed tree, Neolitsea sericea, endemic to East Asian land-bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc.
We applied ten nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker (psbA-trnH intergenic spacer) to 31 populations from throughout the species'range to infer current patterns of genetic diversity and structure, and pollen-to-seed migration ratios (r). A coalescent-based isolation-with-migration (IM) model was fitted to the combined nSSR/cpDNA data set to estimate lineage divergence time and population demographic parameters.
The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the 'Tokara Gap', a narrow (c.37 km wide) but deep (> 1000 m) sea-strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages to c.0.07 Ma (90% highest posterior density interval:0.02-0.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post-divergence gene flow between them.
The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an'ancient sea-barrier hypothesis'for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence of N. sericea, including not only land-bridge submergence, but also island configuration, and/ or constraints on adaptation along a latitudinal temperature gradient.
本研究利用10对多态性的微卫星(nSSR)引物和1对叶绿体(cpDNA)基因间隔区片段(psbA-trnH)引物对涵盖舟山新木姜子群体现有分布范围的31个群体进行遗传多样性、群体遗传结构及花粉流／种子流(r)的研究。基于nSSR和cpDNA的联合数据,应用Isolation-with-migration(IM)模型对舟山新木姜子群体进行分析,计算遗传谱系分化时间和群体动态参数。
研究结果表明,nSSR标记和cpDNA序列数据均显示舟山新木姜子群体分化为两个独特的遗传谱系(南部谱系和北部谱系)。两遗传谱系分别位于Tokara Gap的南北两侧,具有显著的地理分布格局。基于IM分析,两遗传谱系的分化时间约为0.07 Ma (90% HPD:0.02-0.38 Ma);并且两谱系分化后几乎没有基因交流。南北两遗传谱系的花粉流／种子流的比值(r)极低(接近于零),反映了舟山新木姜子群体的近期分化。
舟山新木姜子两遗传谱系的分化时间支持Kimura的"Shallow-time sea-barrier"假说,也就是基于地质证据而提出的晚更新世冰期Tokara Gap地区存在陆桥连接；而与Ota提出的Tokara Gap自上新世形成以来不存在陆桥连接的"Ancient sea-barrier"假说不一致。舟山新木姜子遗传谱系的分化与维持还与环境因子的梯度变化以及该地区岛屿地理结构有一定的关系。
Neolitsea sericea (B1.) Koitz. (Lauraceae) is an element in the dioecious, warm-temperate evergreen forests, which is distributed from Taiwan (Orchid Island), through the Ryukyus to southern Japan, but also occurs disjunctively in off-shore islands of both East China (Zhoushan Archipelago) and South Korea (Jeju Island). A phylogeographic study of Neolitsea sericea was conducted:(i) to assess the population genetic structure and demographic divergence history of a bird-dispersed tree, Neolitsea sericea, endemic to East Asian land-bridge islands; and (2) to interpret the results in the light of controversies over the dating and configurations of land bridges through the Japanese Ryukyu Island Arc.
We applied ten nuclear microsatellites (nSSRs) and one chloroplast (cp) DNA sequence marker (psbA-trnH intergenic spacer) to 31 populations from throughout the species'range to infer current patterns of genetic diversity and structure, and pollen-to-seed migration ratios (r). A coalescent-based isolation-with-migration (IM) model was fitted to the combined nSSR/cpDNA data set to estimate lineage divergence time and population demographic parameters.
The geographic structure of nSSRs and the distribution of most cpDNA haplotypes revealed two distinct lineages located in areas north and south of the 'Tokara Gap', a narrow (c.37 km wide) but deep (> 1000 m) sea-strait between the northern and central Ryukyus. Based on the IM analyses, we (1) dated the divergence of these northern and southern lineages to c.0.07 Ma (90% highest posterior density interval:0.02-0.38 Ma); (2) estimated a slightly smaller effective population size for the northern compared to the southern lineage; and (3) recovered only trivial signals of post-divergence gene flow between them.
The estimated divergence time for northern and southern lineages is consistent with geological evidence for the existence of land connections in the Tokara region during cold stages of the latest Pleistocene; it is thus incompatible with an'ancient sea-barrier hypothesis'for the Ryukyu Arc, where we would have expected much older divergences related to the initial formation of the Tokara and Kerama tectonic straits during the Pliocene. Multiple factors are likely to have had a role in the divergence of N. sericea, including not only land-bridge submergence, but also island configuration, and/ or constraints on adaptation along a latitudinal temperature gradient.
引文
Adams K L, Palmer J D. Evolution of mitochondrial gene contenet:gene loss and transfer to the nucleus. Molecular Phylogenetics and Evolution,2003,29: 380-395.
Adsersen H.1995. Research on islands:Classic, recent and prospective approaches (eds. by P. M. Vitousek, L. L. Loope and H. Adsersen). Islands:Biological Diversity and Ecosystem Function. Springer-Verlag, Berlin.
Aoki K, Suzuki T, Hsu T W, Murakami N. Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation. Journal of Plant Research,2004,117:77-94.
Arai N, Kamitani T. Erratum:Seed rain and seedling establishment of the dioecious tree Neolitsea sericea (Lauraceae):effects of tree sex and density on invasion into a conifer plantation in central Japan. Canadian Journal of Botany,2005,83:1364.
Avise J C.2000. Phylogeography:the history and formation of species. Harvard University Press, Cambridge.
Avise J C. The history and purview of phylogeography:a personal reflection. Molecular Ecology,1998,7:371-379.
Avise J C, Arnold J, Ball R M, Bermingham E, Lamb T, Neigel E, Reeb C A, Saunders N C. Intraspecific phylogeography:the mitochondrial DNA bridge between population genetics and systematics. Annual Review Ecology system, 1987,18:489-522.
Avise J C, Hamrick J L.1996. Conservation genetics case histories from nature. Chapman & Hall, New York.
Baker W J, Hedderson T A, Dransfield J. Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Molecular Phylogenetic and Evolution,2000,14:195-217.
Bentham G.1880. Laurineae (eds. by G. Bentham and J. D. Hooker), pp.146-168. Genera Plantarum, Vol.3. London, L. Reeve.
Bittkau C, Comes H P. Evolutionary processes in a continental island system: molecular phylogeography of the Aegean Nigella arvensis alliance (Ranunculaceae) inferred from chloroplast DNA. Molecular Ecology,2005,14: 4065-4083.
Bousquet J, Strauss S H, Doerksen A H, Price R A. Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proceedings of the National Academy of Sciences, USA,1992,89:7844-7848.
Brown A H D, Burdon J J, Jarosz A M.1989. Isozyme analysis of plant mating system (eds. by A. D. Falk and K. E. Holsinger), pp.73-86. Genetics and conservation of rare plants. Oxford University Press, Oxford.
Broyles S B, Wyatt R. Allozyme diversity and genetic structure in southern Appalachian populations of poke milkweed, Asclepias exaliata. Systematic Botany,1993,18:18-30.
Caicedo A L, Schaal B A. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Evolution,2004,13: 1871-1882.
Carstens B C, Brunsfeld S J, Demboski J R, Good J M, Sullivan J. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem:hypothesis testing within a comparative phylogenetic framework. Evolution,2005,59: 1639-1652.
Carstens B C, Knowles L L. Shifting distributions and speciation:species divergence during rapid climate change. Molecular Ecology,2007,16:619-627.
Catasus L, Machin P, Matias-Guiu X, Part J. Microsatellite instability in endometrial carcinomas:clinicopatholoigic correlations in a series of 42 cases. Human Pathology,1998,29:1160-1164.
Cheng Y P, Hwang S Y, Lin T P. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Molecular Ecology,2005,14:2075-2085.
Chiang T Y, Schaal B A. Phylogeography of plants in Taiwan and the Ryukyu Archipelago. Taxon,2006,51:31-41.
Chung M G., Chung M Y, Oh G S, Epperson B K. Spatial genetic structure in a Neolitsea sericea population (Lauraceae). Heredity,2000,85:490-497.
Ciofi C, Beaumont M A, Swingland I R, Bruford M W. Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis. Proceedings of the Royal Society Biological sciences,1999,266:2269-2274.
Clarke K R, Gorley R N.2001. Primer v5:User manual/tutorial. Primer-E, Plymouth, United Kingdom.
Clegg M T, Gaut B S, Learn G H, Morton B R. Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences, USA,1994,91: 6795-6801.
Clement M, Posada D, Crandall K A. TCS:a computer program to estimate gene genealogies. Molecular Ecology,2000,9:1657-1659.
Comes H P, Tribsch A, Bittkau C. Plant speciation in continental island floras as exemplified by Nigella in the Aegean Archipelago. Philosophical Transactions of the Royal Society Biological sciences,2008,363:3083-3096.
Cornuet J M, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics,1996,144: 2001-2014.
Crawford D J, Stuessy T F.1997. Plant speciation on oceanic islands (eds. by K. Iwatsuki, and P. H. Raven). Evolution and Diversification in Land Plants. Springer-Verlag, Tokyo.
Dainou K, Bizoux J P, Doucet J L, Mahy G, Hardy O J, Heuertz M. Forest refugia revisited:nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Molecular Ecology,2010,19:4462-4477.
Demesure B, Sodzi N, Petit R J. A set of universal primers for amplification of non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology,1995,4:129-131
Ding F M, Zhang C B. Investigation report on Neolitsea sericea resources in Zhoushan. Journal of Zhejiang Forestry Science and Technology,2001,21:52-54. [In Chinese]
Dirienzo A, Petrson A C, Garza J C, Valdes A M, Slatkin M, Freimer N B. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA,1994,91:3166-3170.
Donnelly P, Tavare S. The ages of alleles and a coalescent. Advances in applied Probability,1986,18:1-19.
Donnelly P, Tavare S. Coalescents and genealogical structure under neutrality. Annual Review of Genetics,1995,29:401-421.
Doyle J.1991. DNA protocols for plants-CTAB total DNA isolation. Molecular techniques in taxonomy (eds. by G.M. Hewitt and A. Johnston), pp.283-293. Springer, Berlin.
Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Heled J.2010. Geneious v 5.0.4..
Dumolin-lapegue S, Pemonge M H, Petit R J. An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology,1997,6:393-397.
Ennos R A. Estimating the relative rates of pollen and seed migration among plant populations. Heredity,1994,72:250-259.
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study. Molecular Ecology,2005,14: 2611-2620.
Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distance among DNA haplotypes:application to human mitochondrial DNA restriction data. Genetics,1992,131:479-491.
Felsenstein J. Evolutionary trees from DNA sequences:a maximum likelihood approach. Journal of Molecular Evolution,1981,17:368-376.
Fu Y X, Li W H. Statistical tests of neutrality of mutations. Genetics,1993,133: 693-709.
Garcia-Verdugo C, Forrest A D, Fay M F, Vargas P. The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp. guanchica. Evolution,2010,64:3525-3536.
Garrick R C, Nason J D, Meadows C A, Dyer R J. Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Molecular Ecology,2009,18:1916-1931.
Gaut B S, Muse S V, Clark W D, Clegg M T. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. Journal of Molecular Evolution, 1992,35:292-303.
Ge X J, Liu M H, Wang W K, Schaal B A, Chiang T Y. Population structure of wild bananas, Musa balbisiana, in China determined by SSR fingerprinting and cpDNA PCR-RFLP. Molecular Ecology,2005,14:933-944.
Goudet J.2001. FSTAT, version 2.9.3.2. A program to estimate and test gene diversities and fixation indices. Available at: http://www2.unil.ch/popgen/siftwares/fstat.htm.
Griffiths R C, Tavare S. Simulating probability distributions in the coalescent. Theoretical Population Biology,1994,46:131-159.
Gugerli F, Senn J, Anzidei M, Madaghiele A, Bu|¨chler U, Sperisen C, Vdendramin G G. Chloroplast microsatellites and mitochondrial nadl intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila). Molecular Ecology,2001,10:1489-1497.
Hamilton M B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology Notes,1999,8:513-525.
Hamrick J L, Murawski D A, Nason J D. The influence of seed dispersal mechanisms on the genetic structure of tropical tree populations. Vegetatio,1993,107-108: 281-297.
Hamrick J L, Godt M J W.1990. Allozyme diversity in plant species (eds. by A. H. D. Brown, M. T. Clegg, A. L. Kahler and B. S. Weir), pp.43-63. Plant Population Genetics, Breeding and Genetic Resources. Sinauer Associates, Sunderland M A.
Haq B U, Hardenbol J, Vail P R. Chronology of fluctuating sea levels since the Triassic. Science,1987,235:1156-1167.
Hara H.1959. An outline of phytogeography of Japan. Distribution maps of flowering plants in Japan (eds. by H. Hara), pp.1-96. Inoue Book Co., Tokyo.
Hare M P. Prospects for nuclear gene phylogeography. Trends in Ecology & Evolution,2001,16:700-706.
Harrison S P, Yu G., Takahara H, Prentice I C. Palaeovegetation (communications arising):diversity of temperate plants in East Asia. Nature,2001,413:129-130.
Hewitt G M. The genetic legacy of the Quaternary ice ages. Nature,2000,405: 907-913.
Hey J, Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, USA,2007,104:2785-2790.
Hijimans R J, Graham C H. The ability of climate envelope models to predict the effect of climate change on species distributions. Global Change Biology,2006, 12:2272-228.
Hodgins K A, Barrett S C H. Population structure and genetic diversity in tristylous Narcissus triandrus:insights from microsatellite and chloroplast DNA variation. Molecular Ecology,2007,16:2317-2332.
Holder K, Montgomerie R, Friesen V L. A test of the glacial refugium hyphthesis using patterns of mitochondrial and nuclear DNA sequence variation in rock ptarmign (Lagopus mutus). Evolution,1999,53:1936-1950.
Huang S, Chiang Y C, Schaal B A, Chou C H, Chiang T Y. Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Molecular Ecology,2001,10:266-2681.
Hudson R R.1990. Gene genealogies and the coalescent process (eds. by D. Futuyma and J. Antonovics), pp.1-44. Oxford Surveys in Evolutionary Biology. Oxford University Press, Oxford.
Huelsenbeck J P, Rannala B. Phylogeny methods come of age:testing hypotheses in an evolutionary context. Science,2003,276:227-232.
Hubel E. Die sommergrunen Walder Japans und Westeurasiens, ein floristisch-klimatographischer Vergleich. Veroffentlichungen des Geobotanischen Instituts, ETH, Stiftung Rubel, Zurich,1988,98:225-298.
Hurlbert S H. The nonconcept of species diversity:a critique and alternative parameters. Ecology,1971,52:577-586.
Husband B C, Barrett S C H. A metapopulation perspective in plant population biology. Journal of Ecology,1996,84:461-469.
Hyland B P M. A revision of Lauraceae in Australia (excluding Cassytha). AustraliaJournal of Botany,1989,2:135-367.
Ikeda H, Fujii N, Setoguchi H. Application of the isolation with migration model demonstrates the Pleistocene origin of geographic differentiation in Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. Molecular Biology and Evolution,2009,26:2207-2216.
Innes J B, Zong Y Q, Chen Z Y, Chen C, Wang Z H, Wang H. Environmental history, palaeoecology and human activity at the early Neolithic forager/cultivator site at Kuahuqiao, Hangzhou, eastern China. Quaternary Science Reviews,2009,28: 2277-2294.
Kamei T. Fauna and flora of the Japanese islands in the last glacial time. Quaternary Resource (Daiyonki-Kenkyu),1981,20:191-205.
Kimura M. Paleography of the Ryukyu Islands. Tropics,2000,10:5-24.
King G M, Ferris C R A. Chloroplast DNA phylogeography of Alnus glutinosa L Gaertn. Molecular Ecology,1998,7:1151-1161.
King M G, Roalson E H. Discordance between phylogenetics and coalescent-based divergence modelling:exploring phylogeographic patterns of speciation in the Carex macrocephala species complex. Molecular Ecology,2009,18:468-482.
Kingman J F C. On the genealogy of large populations. Journal of Applied Probability, 1982,19:27-43.
Kostermans A J G H. Lauraceae. Pengumuman Balai Besar Penjelidikan Kehutanan Indonesia,1957,57:1-64.
Krauss R H, Kuddus N N, Dvorchik I. DNA polymorphism in the living fossil Ginkgo biloba from the eastern United States. Genome,2002,45:8-12.
Kropf M, Comes H P, Kadereit J W. Long-distance dispersal vs vicariance:the origin and genetic diversity of alpine plants in the Spanish Sierra Nevada. New Phytologist,2006,172:169-184.
Kuroda Y, Kaga A, Tomooka N, Vaughan D A. Population genetic structure of Japanese wild soybean(Glycine soja) based on microsatellite variation. Molecular Ecology,2006,15:959-974.
Lambeck K, Chappell J. Sea level change through the last glacial cycle. Science,2001, 292:679-686.
Lander E S. The new genomics:global views of biology. Science,1996,274: 536-539.
Liao P C, Havanond S, Huang S. Phylogeography of Ceriops tagal (Rhizophoraceae) in Southeast Asia:the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea. Conservation Genetics,2007,8:89-98.
Li L, Li J, Conran J G., Li X W, Li H W. Phylogeny of Neolitsea (Lauraceae) inferred from Bayesian analysis of nrDNA ITS and ETS sequences. Plant Systematics and Evolution,2007,269:203-221.
Li L, Wei S G., Huang Z L, Ye W H, Cao H L, Wang Z G, Lian J Y, Sun Y F, Ma K P, He F L. Spatial distributions of tree species in a subtropical forest of China. Oikos,2009,118:495-502.
Li J, Christophel D C, Conran J G, Li His-Wen. Phylogeneticrelationships within the 'core'Laureae (Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITSregions. Plant Systematics and Evolution,2004,26:19-36.
Lin Y H, McLenachan P A, Gore A R, Phillips M J, Ota R, Hendy M D, Penny D. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology and Evolution, 2002,19:2060-2070.
Li Z M, Li J, Li X W. Polyphyly of the genus Actinodaphne (Lauraceae) inferred from the analyses of nrDNA ITS and ETS sequences. Acta Phytotaxonomica Sinica, 2006,44:272-285.
Londo J P, Chiang Y C, Hung K H, Chiang T Y, Schaal B A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences, USA,2006,103:9578-9483.
Luikart G, Allendorf F W, Cornuet J M, Sherwin W B. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity, 1998,89:238-247.
Luikart G, Cornuet J M. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology,1998, 12:228-237a.
Luikart G, Sherwin W B, Steele B M, Allendorf F W. Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Molecular Ecology,1998,7:963-974b.
Mantel N A. The detection of disease clustering and a generalized regression approach. Cancer Research,1967,27:209-220.
Marshall T C, Slate J, Kruuk L E B. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology,1998,7:639-655.
Maruyamat, Fuerst P A. Population bottlenecks and nonequilibrium models in population geneties. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics,1985,111:675-689.
Merrill E D.1906. Neolitsea (Benth.) Merr. Philippine Journal of Science 1, (Suppl.):56-57.
Millien-Parra V, Jaeger J J. Island biogeography of the Japanese terrestrial mammal assemblage:an example of a relict fauna. Journal of Biogeography,1999,26: 959-972.
Mitton J B, Kvreiser B R, Latta R G. Glacial refugia of limber pine(Pinus flexilis James) inferred from the population structure of mitochondrial DNA. Molecular Ecology,2000,9:91-97.
Nakamura K, Denda T, Kokubugata G, Suwa R, Yang T Y A, Peng C I, Yokota M. Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands, the Ryukyu Archipelago, Japan. Journal of Biogeography,2010,37:1907-1918.
Nakamura K, Suwa R, Denda T, Yokota M. Geohistorical and current environmental influences on floristic differentiation in the Ryukyu Archipelago, Japan. Journal of Biogeography,2009,36:919-928.
Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution,1983,19:153-170.
Nekola J C, White P S. The distance decay of similarity in biogeography and ecology. Journal of Biogeography,1999,26:867-878.
Nielsen R, Wakeley J. Distinguishing migration from isolation:a Markov chain Monte Carlo approach. Genetics,2001,158:885-896.
Nybom H. Comparison of different nuclear DNA markers for estimating intraspecific genetic dversity in plants. Molecular Ecology,2004,13:1143-1155.
Nybom N, Bartish I. On the genealogy of large populations. Perspect Plant Ecology, 2002,3:93-114.
Oddou-Muratorio S, Petit R J, Le Guerroue B, Guesnet D, Demesure B. Pollen-versus seed-mediated gene flow in a scattered forest tree species. Evolution,2001,55: 1123-1135.
Oliver C, Hollingsworth P M, Gornall R J. Chloroplast DNA phylogeography of the arctic-montane species Saxifraga hirculus (Saxifragaceae). Heredity,2006,96: 222-231.
Ota H. Geographic patterns of endemism and speciation in amphibians and reptiles of the Ryukyu Archipelago, Japan, with special reference to their paleogeographical implications. Researches on Population Ecology,1998,40:189-204.
Ota T.1993. DISPAN version 1.1. Genetic Distance and Phylogenetic Analysis. Available at:http://homes.bio.psu.edu./people/faculty/nei/software.htm.
Palmer A E, Vendramin G G. Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana. Molecular Ecology,2002,11: 1769-1779.
Palmer J D.1992. Mitochondrial DNA in systematics:applications and limitations (eds. by P. S. Solits, D. E. Soltis and J. J. Doyle), pp.36-49. Molecular Systematics of Plants. Champman and Hall, New York.
Park Y C, Kitade O, Schwarz M, Kim J P, Kim W. Intraspecific molecular phylogeny, genetic variation and phylogeography of Reticulitermes speratus (Isoptera: Rhinotermitidae). Molecules and Cells,2006,21:89-103.
Peakall R, Smouse P E. GENALEX 6:genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes,2006,6:288-295. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2005.01155.x
Petit R J, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin G G. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology,2005,14:689-701.
Petit R J, Pineau E, Demesure B, Bacilieri P, Ducousso A, Kremer A. Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences,1997,94:9996-10001.
Pfeiffer W, Stamatakis A. Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. Parallel & Distributed Processing,2010,1-8.
Pons O, Petit R J. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics,1996,144:1237-1245.
Posada D, Crandall K A. MODELTEST:testing the model of DNA substitution, version 3.7. Bioinformatics,1998,14:817-818.
Pritchard J K, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics,2000,155:954-959.
Pritchard J K, Wen X, Falush D.2007. Documentation for STRUCTURE software: version 2.2. Available at:http://pritch.bsd.uchicago.edu/software.
Qian H, Ricklefs R E. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature,2000,407:180-182.
Qin J G.2006. Palynological study of Ningshao Plain and paleoenvironmental significance since late Pleistocene. PhD Thesis, Tongji University, Shanghai, China. [In Chinese]
Qiu Y X, Fu C X, Comes H P. Plant molecular phylogeography in China and adjacent regions:Tracing the genetic imprints of Quaternary climate environmental change in the world's most diverse temperate flora. Molecular Phylogenetics and Evolution,2011,59:225-244.
Qiu Y X, Guan B C, Fu C X, Comes H P. Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Molecular Phylogenetics and Evolution,2009,51:281-293.
Rambaut A, Drummond A J.2004. Tracer vl.3http://evolve.zoo. ox. ac.uk/software.html
Rannala B, Yang Z. Probability distribution of molecular evolutionary trees:a new method of phylogenetic inference. Journal of Molecular Ecology,1996,43: 304-311.
Rodriguez-Sanchez F, Guzman B, Valido A, Vargas P, Arroyo J. Late Neogene history of the laurel tree(Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations. Journal of Biogeography,2009,36: 1270-1281.
Rogers A R. Genetic evidence for a Pleistocene population explosion. Evolution,1995, 49:608-615.
Rogers A R, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution,1992,9:552-569.
Rohlf FJ.1997. NTSYS-pc:Numerical Taxonomy and Multivariate Analysis System Version 2.1. Exeter Software, Setauket, New York.
Rohwer J G.1993. Lauraceae (eds. by K. Kubizki, J. G. Rohwer and V. Bittrich), pp. 366-391. The Families and Genera of Vascular Plants. Springer-Verlag, Berlin.
Rohwer J G. Toward a phylogenetic classification of the Lauraceae:evidence from matK sequences. Systematic Botany,2000,25:60-71.
Rousset F. GenePop'007:A complete re-implementation of the GenePop software for Windows and Linux. Molecular Ecology Resources,2008,8:103-106.
Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. DnaSP:DNA polymorphism analyses by coalescent and other methods. Bioinformatics,2003, 19:2496-2497.
Sanjur O I, Piperno D R, Andres T C, Wessel-Beaver L. Phylogenetic relationship among domesticated and wild speices of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene:implications for crop plant evolution and areas of origin. Proceedings of the National Academy of Sciences, USA,2002,99:535-540.
Schaal B A. Phylogeography studies in plants:problems and prospects. Molecular Ecology,1998,7:465-474.
Schneider S, Roesslli D, Excoffier L.2000. Arlequin ver.3.0:a software for population genetics data analysis. Genetics and Biometrey Laboratory, University of Geneva, Switzerland.
Schoener T W.1988. Ecological interactions, (eds. by A. Myers and P. Giller), pp. 255-300. In Anolyticul Biogeography. An Integrated Approach to the Study of Animal and Plant Distributions Chapman and Hall, London.
Schwind M.1967. Das Japanische Inselreich. Eine Landeskunde nach Studien und Reisen in 3 Banden; Band 1:Die Naturlandschaft. Walter de Gruyter & Co., Berlin.
Slatkin M, Hudson R R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics,1991,129:555-562.
Soltis D E, Morris A, McLachlan J, Manos P S, Soltis P S. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology,2006, 15:4261-4293.
Solits P S, Solits D E. Genetic variation in endemic and widespread plant species: examples from Saxifragaceae and Polystichum (Dryopteridaceae). Aliso,1991,3: 215-223.
Sommer R, Benecke N. Late-and Post-Glacial history of the Mustelidae in Europe. Mammal Review,2004,34:249-284.
Sommer R, Nadachowski A. Glacial refugia of mammals in Europe:evidence from fossil records. Mammal Review,2006,36:251-265.
Spence C C, Neigel J E, Leberg P L. Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Molecular Ecology, 2000,9:1517-1528.
Stussy T F, Ono M.1998. Evolution and speciation of island plants. Cambridge University Press, Cambridge.
Sun X J, Du N Q, Chen M H. The vegetation and climate in the Humudu period. Acta Botanica Sinica,1981,23:146-151.
Swofford D L.1998. PAUP* 4.0:Phylogenetic analysis using parsimony (and other methods) beta vers.4.0. Sinauer Associates, Sunderland, Massa chusetts.
Takanose Y, Kamitani T. Fruiting of fleshy-fruited plants and abundance of frugivorous birds:phenological correspondence in a temperate forest in central Japan. Ornithological Science,2003,2:25-32.
Thuillet A C, Bru D, David J, Roumet P, Santoni S, Sourdille P, Bataillon T. Direct estimation of mutation rate for 10 microsatellite loci in durum wheat, Triticum turgidum (L.) Thell. ssp. durum desf. Molecular Biology and Evolution,2002,19: 122-125.
Tsukada M.1988. Vegetation history (eds. by B. Huntley and III. T. Webb), pp. 459-518. Kluwer Academic Publishers, Dordrecht.
van der Werff H. An annotated key to the genera of Lauraceae in the flora Malesiana region. Annals of the Missouri Botanical Garden,2001,46:125-140.
van der Werff H, Richter H G. Toward an improved classification of Lauraceae. Annals of the Missouri Botanical Garden,1996,78:377-387.
Vigoroux Y, Jacueth J S, Matsuoka Y, Smith O S, Beavis W D, Smith J S C, Doebley J. Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution,2002,19:1251-1260.
Wang H S. Floristic geography. Beijing, China:Science Press. [In Chinese]
Wang Z S, An S Q, Liu H, Leng X, Zheng J W, Liu Y H. Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan Archipelago using RAPD markers. Annals of Botany,2005,95:305-313.
Whittaker R J, Fernandez-Palacios J M.2007. Island Biogeography:Ecology, Evolution, and Conservation. Oxford University Press, Oxford.
Williams J G K, Kubelik A R, Livak K J, Rafalski J A, Tingey S V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research,1990,18:6531-6535.
Willis K J, Whittaker R J. The refugial debate. Science,2000,287:1406-1407.
Wolfe K H, Li W H, Sharp P M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, USA,1987,84:9054-9058.
Wright S.1978. Evolution and the genetics of populations. University of Chicago Press, Chicago.
Wright S. The genetical structure of population. Annals of Eugenics,1951,15: 323-354.
Xie GW.1997. On phytogeographical affinities of the forest floras between East China and Japan. Chinese Geography Science,1992,7:236-242.
Yamane K, Yano K, Kawahara T. Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Research, 2006,13:197-204.
Yang F S, Li Y F, Ding X, Wang X Q. Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Molecular Ecology,2008,17:5153-5145.
Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences:A Markov chain Monte Carlo method. Molecular Biology and Evolution,1997,14: 717-724.
Yiming L, Niemela J, Dianmo L. Nested distribution of amphibians in the Zhoushan archipelago, China:can selective extinction cause nested subsets of species? Oecologia,1998,113:557-564.
Yu G., Chen X, Ni J, Cheddadi R, Guiot J, Han H, Harrison S P, Huang C, Ke M, Kong Z, Li S, Li W, Liew P, Liu G, Liu J, Liu Q, Liu K B, Prentice IC, Qui W, Ren G., Song C, Sugita S, Sun X, Tang L, Van Campo E, Xia Y, Xu Q, Yan S, Yang X, Zhao J, Zheng Z. Palaeovegetation of China:a pollen data-based synthesis for the mid-Holocene and last glacial maximum. Journal of Biogeography,2000,27:635-664.
Yumoto T. Pollination systems of a warm temperature evergreen broad-leaved forest in Yakushima Islands. Ecological Research,1987,2:133-145.
Zhou W J, An S, Head D J. Stratigraphic division of Holocene loess in China. Radiocarbon,1994,36:37-46.
陈善元,张亚平.家养动物起源研究的遗传学方法及其应用科学通报,2006,51：2469-2475.
葛颂.1998.植物群体遗传结构研究的回顾和展望.李承森(主编),植物科学进展(第一卷).北京：高等教育出版社.
王慰,黄胜利,丁国剑,黄有军,黄坚钦,郑炳松.盐胁迫下舟山新木姜子1年生苗形态变化及生理反应.浙江林学院学报,2007,24：168-172.
王中生,安树青,冷欣,丁方明,郑建伟,陈琳.岛屿植物舟山新木姜子居群遗传多样性的RAPD分析.生态学报,2004,24：414-422.
刘占林,赵桂仿.居群遗传学原理及其在珍稀濒危植物保护中的应用.生物多样性,1999,7：340-346.
廖日京.1988.台湾樟科植物之学名订正.
邹喻苹,葛颂,王晓东.2001.系统与进化植物学中的分子标记.北京：科学出版社.
傅立国等.1992.中国植物红皮书第一册.北京.科学出版社.
葛颂.1994.同工酶和植物进化生物学研究.陈家宽,杨继(编著),植物进化生物学.武汉：武汉大学出版社.
沈浪,陈小勇,李媛媛.生物冰期避难所与冰期后的重新扩散.生态学报,2002,22：1984-1990.
田欣,李德铢.DNA序列在植物系统学研究中的应用.云南植物研究,2002,24：170-184.
汪松,解焱.2004.中国物种红色名录.北京：高等教育出版社.
Adsersen H.1995. Research on islands:Classic, recent and prospective approaches (eds. by P. M. Vitousek, L. L. Loope and H. Adsersen). Islands:Biological Diversity and Ecosystem Function. Springer-Verlag, Berlin.
Aoki K, Suzuki T, Hsu T W, Murakami N. Phylogeography of the component species of broad-leaved evergreen forests in Japan, based on chloroplast DNA variation. Journal of Plant Research,2004,117:77-94.
Arai N, Kamitani T. Erratum:Seed rain and seedling establishment of the dioecious tree Neolitsea sericea (Lauraceae):effects of tree sex and density on invasion into a conifer plantation in central Japan. Canadian Journal of Botany,2005,83:1364.
Avise J C.2000. Phylogeography:the history and formation of species. Harvard University Press, Cambridge.
Avise J C. The history and purview of phylogeography:a personal reflection. Molecular Ecology,1998,7:371-379.
Avise J C, Arnold J, Ball R M, Bermingham E, Lamb T, Neigel E, Reeb C A, Saunders N C. Intraspecific phylogeography:the mitochondrial DNA bridge between population genetics and systematics. Annual Review Ecology system, 1987,18:489-522.
Avise J C, Hamrick J L.1996. Conservation genetics case histories from nature. Chapman & Hall, New York.
Baker W J, Hedderson T A, Dransfield J. Molecular phylogenetics of subfamily Calamoideae (Palmae) based on nrDNA ITS and cpDNA rps16 intron sequence data. Molecular Phylogenetic and Evolution,2000,14:195-217.
Bentham G.1880. Laurineae (eds. by G. Bentham and J. D. Hooker), pp.146-168. Genera Plantarum, Vol.3. London, L. Reeve.
Bittkau C, Comes H P. Evolutionary processes in a continental island system: molecular phylogeography of the Aegean Nigella arvensis alliance (Ranunculaceae) inferred from chloroplast DNA. Molecular Ecology,2005,14: 4065-4083.
Bousquet J, Strauss S H, Doerksen A H, Price R A. Extensive variation in evolutionary rate of rbcL gene sequences among seed plants. Proceedings of the National Academy of Sciences, USA,1992,89:7844-7848.
Brown A H D, Burdon J J, Jarosz A M.1989. Isozyme analysis of plant mating system (eds. by A. D. Falk and K. E. Holsinger), pp.73-86. Genetics and conservation of rare plants. Oxford University Press, Oxford.
Broyles S B, Wyatt R. Allozyme diversity and genetic structure in southern Appalachian populations of poke milkweed, Asclepias exaliata. Systematic Botany,1993,18:18-30.
Caicedo A L, Schaal B A. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Evolution,2004,13: 1871-1882.
Carstens B C, Brunsfeld S J, Demboski J R, Good J M, Sullivan J. Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem:hypothesis testing within a comparative phylogenetic framework. Evolution,2005,59: 1639-1652.
Carstens B C, Knowles L L. Shifting distributions and speciation:species divergence during rapid climate change. Molecular Ecology,2007,16:619-627.
Catasus L, Machin P, Matias-Guiu X, Part J. Microsatellite instability in endometrial carcinomas:clinicopatholoigic correlations in a series of 42 cases. Human Pathology,1998,29:1160-1164.
Cheng Y P, Hwang S Y, Lin T P. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae). Molecular Ecology,2005,14:2075-2085.
Chiang T Y, Schaal B A. Phylogeography of plants in Taiwan and the Ryukyu Archipelago. Taxon,2006,51:31-41.
Chung M G., Chung M Y, Oh G S, Epperson B K. Spatial genetic structure in a Neolitsea sericea population (Lauraceae). Heredity,2000,85:490-497.
Ciofi C, Beaumont M A, Swingland I R, Bruford M W. Genetic divergence and units for conservation in the Komodo dragon Varanus komodoensis. Proceedings of the Royal Society Biological sciences,1999,266:2269-2274.
Clarke K R, Gorley R N.2001. Primer v5:User manual/tutorial. Primer-E, Plymouth, United Kingdom.
Clegg M T, Gaut B S, Learn G H, Morton B R. Rates and patterns of chloroplast DNA evolution. Proceedings of the National Academy of Sciences, USA,1994,91: 6795-6801.
Clement M, Posada D, Crandall K A. TCS:a computer program to estimate gene genealogies. Molecular Ecology,2000,9:1657-1659.
Comes H P, Tribsch A, Bittkau C. Plant speciation in continental island floras as exemplified by Nigella in the Aegean Archipelago. Philosophical Transactions of the Royal Society Biological sciences,2008,363:3083-3096.
Cornuet J M, Luikart G. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics,1996,144: 2001-2014.
Crawford D J, Stuessy T F.1997. Plant speciation on oceanic islands (eds. by K. Iwatsuki, and P. H. Raven). Evolution and Diversification in Land Plants. Springer-Verlag, Tokyo.
Dainou K, Bizoux J P, Doucet J L, Mahy G, Hardy O J, Heuertz M. Forest refugia revisited:nSSRs and cpDNA sequences support historical isolation in a wide-spread African tree with high colonization capacity, Milicia excelsa (Moraceae). Molecular Ecology,2010,19:4462-4477.
Demesure B, Sodzi N, Petit R J. A set of universal primers for amplification of non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology,1995,4:129-131
Ding F M, Zhang C B. Investigation report on Neolitsea sericea resources in Zhoushan. Journal of Zhejiang Forestry Science and Technology,2001,21:52-54. [In Chinese]
Dirienzo A, Petrson A C, Garza J C, Valdes A M, Slatkin M, Freimer N B. Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences, USA,1994,91:3166-3170.
Donnelly P, Tavare S. The ages of alleles and a coalescent. Advances in applied Probability,1986,18:1-19.
Donnelly P, Tavare S. Coalescents and genealogical structure under neutrality. Annual Review of Genetics,1995,29:401-421.
Doyle J.1991. DNA protocols for plants-CTAB total DNA isolation. Molecular techniques in taxonomy (eds. by G.M. Hewitt and A. Johnston), pp.283-293. Springer, Berlin.
Drummond A, Ashton B, Buxton S, Cheung M, Cooper A, Heled J.2010. Geneious v 5.0.4.
Dumolin-lapegue S, Pemonge M H, Petit R J. An enlarged set of consensus primers for the study of organelle DNA in plants. Molecular Ecology,1997,6:393-397.
Ennos R A. Estimating the relative rates of pollen and seed migration among plant populations. Heredity,1994,72:250-259.
Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE:a simulation study. Molecular Ecology,2005,14: 2611-2620.
Excoffier L, Smouse P E, Quattro J M. Analysis of molecular variance inferred from metric distance among DNA haplotypes:application to human mitochondrial DNA restriction data. Genetics,1992,131:479-491.
Felsenstein J. Evolutionary trees from DNA sequences:a maximum likelihood approach. Journal of Molecular Evolution,1981,17:368-376.
Fu Y X, Li W H. Statistical tests of neutrality of mutations. Genetics,1993,133: 693-709.
Garcia-Verdugo C, Forrest A D, Fay M F, Vargas P. The relevance of gene flow in metapopulation dynamics of an oceanic island endemic, Olea europaea subsp. guanchica. Evolution,2010,64:3525-3536.
Garrick R C, Nason J D, Meadows C A, Dyer R J. Not just vicariance: phylogeography of a Sonoran Desert euphorb indicates a major role of range expansion along the Baja peninsula. Molecular Ecology,2009,18:1916-1931.
Gaut B S, Muse S V, Clark W D, Clegg M T. Relative rates of nucleotide substitution at the rbcL locus of monocotyledonous plants. Journal of Molecular Evolution, 1992,35:292-303.
Ge X J, Liu M H, Wang W K, Schaal B A, Chiang T Y. Population structure of wild bananas, Musa balbisiana, in China determined by SSR fingerprinting and cpDNA PCR-RFLP. Molecular Ecology,2005,14:933-944.
Goudet J.2001. FSTAT, version 2.9.3.2. A program to estimate and test gene diversities and fixation indices. Available at: http://www2.unil.ch/popgen/siftwares/fstat.htm.
Griffiths R C, Tavare S. Simulating probability distributions in the coalescent. Theoretical Population Biology,1994,46:131-159.
Gugerli F, Senn J, Anzidei M, Madaghiele A, Bu|¨chler U, Sperisen C, Vdendramin G G. Chloroplast microsatellites and mitochondrial nadl intron 2 sequences indicate congruent phylogenetic relationships among Swiss stone pine (Pinus cembra), Siberian stone pine (Pinus sibirica), and Siberian dwarf pine (Pinus pumila). Molecular Ecology,2001,10:1489-1497.
Hamilton M B. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Molecular Ecology Notes,1999,8:513-525.
Hamrick J L, Murawski D A, Nason J D. The influence of seed dispersal mechanisms on the genetic structure of tropical tree populations. Vegetatio,1993,107-108: 281-297.
Hamrick J L, Godt M J W.1990. Allozyme diversity in plant species (eds. by A. H. D. Brown, M. T. Clegg, A. L. Kahler and B. S. Weir), pp.43-63. Plant Population Genetics, Breeding and Genetic Resources. Sinauer Associates, Sunderland M A.
Haq B U, Hardenbol J, Vail P R. Chronology of fluctuating sea levels since the Triassic. Science,1987,235:1156-1167.
Hara H.1959. An outline of phytogeography of Japan. Distribution maps of flowering plants in Japan (eds. by H. Hara), pp.1-96. Inoue Book Co., Tokyo.
Hare M P. Prospects for nuclear gene phylogeography. Trends in Ecology & Evolution,2001,16:700-706.
Harrison S P, Yu G., Takahara H, Prentice I C. Palaeovegetation (communications arising):diversity of temperate plants in East Asia. Nature,2001,413:129-130.
Hewitt G M. The genetic legacy of the Quaternary ice ages. Nature,2000,405: 907-913.
Hey J, Nielsen R. Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proceedings of the National Academy of Sciences, USA,2007,104:2785-2790.
Hijimans R J, Graham C H. The ability of climate envelope models to predict the effect of climate change on species distributions. Global Change Biology,2006, 12:2272-228.
Hodgins K A, Barrett S C H. Population structure and genetic diversity in tristylous Narcissus triandrus:insights from microsatellite and chloroplast DNA variation. Molecular Ecology,2007,16:2317-2332.
Holder K, Montgomerie R, Friesen V L. A test of the glacial refugium hyphthesis using patterns of mitochondrial and nuclear DNA sequence variation in rock ptarmign (Lagopus mutus). Evolution,1999,53:1936-1950.
Huang S, Chiang Y C, Schaal B A, Chou C H, Chiang T Y. Organelle DNA phylogeography of Cycas taitungensis, a relict species in Taiwan. Molecular Ecology,2001,10:266-2681.
Hudson R R.1990. Gene genealogies and the coalescent process (eds. by D. Futuyma and J. Antonovics), pp.1-44. Oxford Surveys in Evolutionary Biology. Oxford University Press, Oxford.
Huelsenbeck J P, Rannala B. Phylogeny methods come of age:testing hypotheses in an evolutionary context. Science,2003,276:227-232.
Hubel E. Die sommergrunen Walder Japans und Westeurasiens, ein floristisch-klimatographischer Vergleich. Veroffentlichungen des Geobotanischen Instituts, ETH, Stiftung Rubel, Zurich,1988,98:225-298.
Hurlbert S H. The nonconcept of species diversity:a critique and alternative parameters. Ecology,1971,52:577-586.
Husband B C, Barrett S C H. A metapopulation perspective in plant population biology. Journal of Ecology,1996,84:461-469.
Hyland B P M. A revision of Lauraceae in Australia (excluding Cassytha). AustraliaJournal of Botany,1989,2:135-367.
Ikeda H, Fujii N, Setoguchi H. Application of the isolation with migration model demonstrates the Pleistocene origin of geographic differentiation in Cardamine nipponica (Brassicaceae), an endemic Japanese alpine plant. Molecular Biology and Evolution,2009,26:2207-2216.
Innes J B, Zong Y Q, Chen Z Y, Chen C, Wang Z H, Wang H. Environmental history, palaeoecology and human activity at the early Neolithic forager/cultivator site at Kuahuqiao, Hangzhou, eastern China. Quaternary Science Reviews,2009,28: 2277-2294.
Kamei T. Fauna and flora of the Japanese islands in the last glacial time. Quaternary Resource (Daiyonki-Kenkyu),1981,20:191-205.
Kimura M. Paleography of the Ryukyu Islands. Tropics,2000,10:5-24.
King G M, Ferris C R A. Chloroplast DNA phylogeography of Alnus glutinosa L Gaertn. Molecular Ecology,1998,7:1151-1161.
King M G, Roalson E H. Discordance between phylogenetics and coalescent-based divergence modelling:exploring phylogeographic patterns of speciation in the Carex macrocephala species complex. Molecular Ecology,2009,18:468-482.
Kingman J F C. On the genealogy of large populations. Journal of Applied Probability, 1982,19:27-43.
Kostermans A J G H. Lauraceae. Pengumuman Balai Besar Penjelidikan Kehutanan Indonesia,1957,57:1-64.
Krauss R H, Kuddus N N, Dvorchik I. DNA polymorphism in the living fossil Ginkgo biloba from the eastern United States. Genome,2002,45:8-12.
Kropf M, Comes H P, Kadereit J W. Long-distance dispersal vs vicariance:the origin and genetic diversity of alpine plants in the Spanish Sierra Nevada. New Phytologist,2006,172:169-184.
Kuroda Y, Kaga A, Tomooka N, Vaughan D A. Population genetic structure of Japanese wild soybean(Glycine soja) based on microsatellite variation. Molecular Ecology,2006,15:959-974.
Lambeck K, Chappell J. Sea level change through the last glacial cycle. Science,2001, 292:679-686.
Lander E S. The new genomics:global views of biology. Science,1996,274: 536-539.
Liao P C, Havanond S, Huang S. Phylogeography of Ceriops tagal (Rhizophoraceae) in Southeast Asia:the land barrier of the Malay Peninsula has caused population differentiation between the Indian Ocean and South China Sea. Conservation Genetics,2007,8:89-98.
Li L, Li J, Conran J G., Li X W, Li H W. Phylogeny of Neolitsea (Lauraceae) inferred from Bayesian analysis of nrDNA ITS and ETS sequences. Plant Systematics and Evolution,2007,269:203-221.
Li L, Wei S G., Huang Z L, Ye W H, Cao H L, Wang Z G, Lian J Y, Sun Y F, Ma K P, He F L. Spatial distributions of tree species in a subtropical forest of China. Oikos,2009,118:495-502.
Li J, Christophel D C, Conran J G, Li His-Wen. Phylogeneticrelationships within the 'core'Laureae (Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITSregions. Plant Systematics and Evolution,2004,26:19-36.
Lin Y H, McLenachan P A, Gore A R, Phillips M J, Ota R, Hendy M D, Penny D. Four new mitochondrial genomes and the increased stability of evolutionary trees of mammals from improved taxon sampling. Molecular Biology and Evolution, 2002,19:2060-2070.
Li Z M, Li J, Li X W. Polyphyly of the genus Actinodaphne (Lauraceae) inferred from the analyses of nrDNA ITS and ETS sequences. Acta Phytotaxonomica Sinica, 2006,44:272-285.
Londo J P, Chiang Y C, Hung K H, Chiang T Y, Schaal B A. Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa. Proceedings of the National Academy of Sciences, USA,2006,103:9578-9483.
Luikart G, Allendorf F W, Cornuet J M, Sherwin W B. Distortion of allele frequency distributions provides a test for recent population bottlenecks. Journal of Heredity, 1998,89:238-247.
Luikart G, Cornuet J M. Empirical evaluation of a test for identifying recently bottlenecked populations from allele frequency data. Conservation Biology,1998, 12:228-237a.
Luikart G, Sherwin W B, Steele B M, Allendorf F W. Usefulness of molecular markers for detecting population bottlenecks via monitoring genetic change. Molecular Ecology,1998,7:963-974b.
Mantel N A. The detection of disease clustering and a generalized regression approach. Cancer Research,1967,27:209-220.
Marshall T C, Slate J, Kruuk L E B. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology,1998,7:639-655.
Maruyamat, Fuerst P A. Population bottlenecks and nonequilibrium models in population geneties. II. Number of alleles in a small population that was formed by a recent bottleneck. Genetics,1985,111:675-689.
Merrill E D.1906. Neolitsea (Benth.) Merr. Philippine Journal of Science 1, (Suppl.):56-57.
Millien-Parra V, Jaeger J J. Island biogeography of the Japanese terrestrial mammal assemblage:an example of a relict fauna. Journal of Biogeography,1999,26: 959-972.
Mitton J B, Kvreiser B R, Latta R G. Glacial refugia of limber pine(Pinus flexilis James) inferred from the population structure of mitochondrial DNA. Molecular Ecology,2000,9:91-97.
Nakamura K, Denda T, Kokubugata G, Suwa R, Yang T Y A, Peng C I, Yokota M. Phylogeography of Ophiorrhiza japonica (Rubiaceae) in continental islands, the Ryukyu Archipelago, Japan. Journal of Biogeography,2010,37:1907-1918.
Nakamura K, Suwa R, Denda T, Yokota M. Geohistorical and current environmental influences on floristic differentiation in the Ryukyu Archipelago, Japan. Journal of Biogeography,2009,36:919-928.
Nei M, Tajima F, Tateno Y. Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution,1983,19:153-170.
Nekola J C, White P S. The distance decay of similarity in biogeography and ecology. Journal of Biogeography,1999,26:867-878.
Nielsen R, Wakeley J. Distinguishing migration from isolation:a Markov chain Monte Carlo approach. Genetics,2001,158:885-896.
Nybom H. Comparison of different nuclear DNA markers for estimating intraspecific genetic dversity in plants. Molecular Ecology,2004,13:1143-1155.
Nybom N, Bartish I. On the genealogy of large populations. Perspect Plant Ecology, 2002,3:93-114.
Oddou-Muratorio S, Petit R J, Le Guerroue B, Guesnet D, Demesure B. Pollen-versus seed-mediated gene flow in a scattered forest tree species. Evolution,2001,55: 1123-1135.
Oliver C, Hollingsworth P M, Gornall R J. Chloroplast DNA phylogeography of the arctic-montane species Saxifraga hirculus (Saxifragaceae). Heredity,2006,96: 222-231.
Ota H. Geographic patterns of endemism and speciation in amphibians and reptiles of the Ryukyu Archipelago, Japan, with special reference to their paleogeographical implications. Researches on Population Ecology,1998,40:189-204.
Ota T.1993. DISPAN version 1.1. Genetic Distance and Phylogenetic Analysis. Available at:http://homes.bio.psu.edu./people/faculty/nei/software.htm.
Palmer A E, Vendramin G G. Chloroplast DNA variation, postglacial recolonization and hybridization in hazel, Corylus avellana. Molecular Ecology,2002,11: 1769-1779.
Palmer J D.1992. Mitochondrial DNA in systematics:applications and limitations (eds. by P. S. Solits, D. E. Soltis and J. J. Doyle), pp.36-49. Molecular Systematics of Plants. Champman and Hall, New York.
Park Y C, Kitade O, Schwarz M, Kim J P, Kim W. Intraspecific molecular phylogeny, genetic variation and phylogeography of Reticulitermes speratus (Isoptera: Rhinotermitidae). Molecules and Cells,2006,21:89-103.
Peakall R, Smouse P E. GENALEX 6:genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes,2006,6:288-295. http://www.blackwell-synergy.com/doi/abs/10.1111/j.1471-8286.2005.01155.x
Petit R J, Duminil J, Fineschi S, Hampe A, Salvini D, Vendramin G G. Comparative organization of chloroplast, mitochondrial and nuclear diversity in plant populations. Molecular Ecology,2005,14:689-701.
Petit R J, Pineau E, Demesure B, Bacilieri P, Ducousso A, Kremer A. Chloroplast DNA footprints of postglacial recolonization by oaks. Proceedings of the National Academy of Sciences,1997,94:9996-10001.
Pfeiffer W, Stamatakis A. Hybrid MPI/Pthreads parallelization of the RAxML phylogenetics code. Parallel & Distributed Processing,2010,1-8.
Pons O, Petit R J. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics,1996,144:1237-1245.
Posada D, Crandall K A. MODELTEST:testing the model of DNA substitution, version 3.7. Bioinformatics,1998,14:817-818.
Pritchard J K, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics,2000,155:954-959.
Pritchard J K, Wen X, Falush D.2007. Documentation for STRUCTURE software: version 2.2. Available at:http://pritch.bsd.uchicago.edu/software.
Qian H, Ricklefs R E. Large-scale processes and the Asian bias in species diversity of temperate plants. Nature,2000,407:180-182.
Qin J G.2006. Palynological study of Ningshao Plain and paleoenvironmental significance since late Pleistocene. PhD Thesis, Tongji University, Shanghai, China. [In Chinese]
Qiu Y X, Fu C X, Comes H P. Plant molecular phylogeography in China and adjacent regions:Tracing the genetic imprints of Quaternary climate environmental change in the world's most diverse temperate flora. Molecular Phylogenetics and Evolution,2011,59:225-244.
Qiu Y X, Guan B C, Fu C X, Comes H P. Did glacials and/or interglacials promote allopatric incipient speciation in East Asian temperate plants? Phylogeographic and coalescent analyses on refugial isolation and divergence in Dysosma versipellis. Molecular Phylogenetics and Evolution,2009,51:281-293.
Rambaut A, Drummond A J.2004. Tracer vl.3http://evolve.zoo. ox. ac.uk/software.html
Rannala B, Yang Z. Probability distribution of molecular evolutionary trees:a new method of phylogenetic inference. Journal of Molecular Ecology,1996,43: 304-311.
Rodriguez-Sanchez F, Guzman B, Valido A, Vargas P, Arroyo J. Late Neogene history of the laurel tree(Laurus L., Lauraceae) based on phylogeographical analyses of Mediterranean and Macaronesian populations. Journal of Biogeography,2009,36: 1270-1281.
Rogers A R. Genetic evidence for a Pleistocene population explosion. Evolution,1995, 49:608-615.
Rogers A R, Harpending H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution,1992,9:552-569.
Rohlf FJ.1997. NTSYS-pc:Numerical Taxonomy and Multivariate Analysis System Version 2.1. Exeter Software, Setauket, New York.
Rohwer J G.1993. Lauraceae (eds. by K. Kubizki, J. G. Rohwer and V. Bittrich), pp. 366-391. The Families and Genera of Vascular Plants. Springer-Verlag, Berlin.
Rohwer J G. Toward a phylogenetic classification of the Lauraceae:evidence from matK sequences. Systematic Botany,2000,25:60-71.
Rousset F. GenePop'007:A complete re-implementation of the GenePop software for Windows and Linux. Molecular Ecology Resources,2008,8:103-106.
Rozas J, Sanchez-DelBarrio J C, Messeguer X, Rozas R. DnaSP:DNA polymorphism analyses by coalescent and other methods. Bioinformatics,2003, 19:2496-2497.
Sanjur O I, Piperno D R, Andres T C, Wessel-Beaver L. Phylogenetic relationship among domesticated and wild speices of Cucurbita (Cucurbitaceae) inferred from a mitochondrial gene:implications for crop plant evolution and areas of origin. Proceedings of the National Academy of Sciences, USA,2002,99:535-540.
Schaal B A. Phylogeography studies in plants:problems and prospects. Molecular Ecology,1998,7:465-474.
Schneider S, Roesslli D, Excoffier L.2000. Arlequin ver.3.0:a software for population genetics data analysis. Genetics and Biometrey Laboratory, University of Geneva, Switzerland.
Schoener T W.1988. Ecological interactions, (eds. by A. Myers and P. Giller), pp. 255-300. In Anolyticul Biogeography. An Integrated Approach to the Study of Animal and Plant Distributions Chapman and Hall, London.
Schwind M.1967. Das Japanische Inselreich. Eine Landeskunde nach Studien und Reisen in 3 Banden; Band 1:Die Naturlandschaft. Walter de Gruyter & Co., Berlin.
Slatkin M, Hudson R R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics,1991,129:555-562.
Soltis D E, Morris A, McLachlan J, Manos P S, Soltis P S. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology,2006, 15:4261-4293.
Solits P S, Solits D E. Genetic variation in endemic and widespread plant species: examples from Saxifragaceae and Polystichum (Dryopteridaceae). Aliso,1991,3: 215-223.
Sommer R, Benecke N. Late-and Post-Glacial history of the Mustelidae in Europe. Mammal Review,2004,34:249-284.
Sommer R, Nadachowski A. Glacial refugia of mammals in Europe:evidence from fossil records. Mammal Review,2006,36:251-265.
Spence C C, Neigel J E, Leberg P L. Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Molecular Ecology, 2000,9:1517-1528.
Stussy T F, Ono M.1998. Evolution and speciation of island plants. Cambridge University Press, Cambridge.
Sun X J, Du N Q, Chen M H. The vegetation and climate in the Humudu period. Acta Botanica Sinica,1981,23:146-151.
Swofford D L.1998. PAUP* 4.0:Phylogenetic analysis using parsimony (and other methods) beta vers.4.0. Sinauer Associates, Sunderland, Massa chusetts.
Takanose Y, Kamitani T. Fruiting of fleshy-fruited plants and abundance of frugivorous birds:phenological correspondence in a temperate forest in central Japan. Ornithological Science,2003,2:25-32.
Thuillet A C, Bru D, David J, Roumet P, Santoni S, Sourdille P, Bataillon T. Direct estimation of mutation rate for 10 microsatellite loci in durum wheat, Triticum turgidum (L.) Thell. ssp. durum desf. Molecular Biology and Evolution,2002,19: 122-125.
Tsukada M.1988. Vegetation history (eds. by B. Huntley and III. T. Webb), pp. 459-518. Kluwer Academic Publishers, Dordrecht.
van der Werff H. An annotated key to the genera of Lauraceae in the flora Malesiana region. Annals of the Missouri Botanical Garden,2001,46:125-140.
van der Werff H, Richter H G. Toward an improved classification of Lauraceae. Annals of the Missouri Botanical Garden,1996,78:377-387.
Vigoroux Y, Jacueth J S, Matsuoka Y, Smith O S, Beavis W D, Smith J S C, Doebley J. Rate and pattern of mutation at microsatellite loci in maize. Molecular Biology and Evolution,2002,19:1251-1260.
Wang H S. Floristic geography. Beijing, China:Science Press. [In Chinese]
Wang Z S, An S Q, Liu H, Leng X, Zheng J W, Liu Y H. Genetic structure of the endangered plant Neolitsea sericea (Lauraceae) from the Zhoushan Archipelago using RAPD markers. Annals of Botany,2005,95:305-313.
Whittaker R J, Fernandez-Palacios J M.2007. Island Biogeography:Ecology, Evolution, and Conservation. Oxford University Press, Oxford.
Williams J G K, Kubelik A R, Livak K J, Rafalski J A, Tingey S V. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research,1990,18:6531-6535.
Willis K J, Whittaker R J. The refugial debate. Science,2000,287:1406-1407.
Wolfe K H, Li W H, Sharp P M. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences, USA,1987,84:9054-9058.
Wright S.1978. Evolution and the genetics of populations. University of Chicago Press, Chicago.
Wright S. The genetical structure of population. Annals of Eugenics,1951,15: 323-354.
Xie GW.1997. On phytogeographical affinities of the forest floras between East China and Japan. Chinese Geography Science,1992,7:236-242.
Yamane K, Yano K, Kawahara T. Pattern and rate of indel evolution inferred from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Research, 2006,13:197-204.
Yang F S, Li Y F, Ding X, Wang X Q. Extensive population expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the Quaternary climate change. Molecular Ecology,2008,17:5153-5145.
Yang Z, Rannala B. Bayesian phylogenetic inference using DNA sequences:A Markov chain Monte Carlo method. Molecular Biology and Evolution,1997,14: 717-724.
Yiming L, Niemela J, Dianmo L. Nested distribution of amphibians in the Zhoushan archipelago, China:can selective extinction cause nested subsets of species? Oecologia,1998,113:557-564.
Yu G., Chen X, Ni J, Cheddadi R, Guiot J, Han H, Harrison S P, Huang C, Ke M, Kong Z, Li S, Li W, Liew P, Liu G, Liu J, Liu Q, Liu K B, Prentice IC, Qui W, Ren G., Song C, Sugita S, Sun X, Tang L, Van Campo E, Xia Y, Xu Q, Yan S, Yang X, Zhao J, Zheng Z. Palaeovegetation of China:a pollen data-based synthesis for the mid-Holocene and last glacial maximum. Journal of Biogeography,2000,27:635-664.
Yumoto T. Pollination systems of a warm temperature evergreen broad-leaved forest in Yakushima Islands. Ecological Research,1987,2:133-145.
Zhou W J, An S, Head D J. Stratigraphic division of Holocene loess in China. Radiocarbon,1994,36:37-46.
陈善元,张亚平.家养动物起源研究的遗传学方法及其应用科学通报,2006,51：2469-2475.
葛颂.1998.植物群体遗传结构研究的回顾和展望.李承森(主编),植物科学进展(第一卷).北京：高等教育出版社.
王慰,黄胜利,丁国剑,黄有军,黄坚钦,郑炳松.盐胁迫下舟山新木姜子1年生苗形态变化及生理反应.浙江林学院学报,2007,24：168-172.
王中生,安树青,冷欣,丁方明,郑建伟,陈琳.岛屿植物舟山新木姜子居群遗传多样性的RAPD分析.生态学报,2004,24：414-422.
刘占林,赵桂仿.居群遗传学原理及其在珍稀濒危植物保护中的应用.生物多样性,1999,7：340-346.
廖日京.1988.台湾樟科植物之学名订正.
邹喻苹,葛颂,王晓东.2001.系统与进化植物学中的分子标记.北京：科学出版社.
傅立国等.1992.中国植物红皮书第一册.北京.科学出版社.
葛颂.1994.同工酶和植物进化生物学研究.陈家宽,杨继(编著),植物进化生物学.武汉：武汉大学出版社.
沈浪,陈小勇,李媛媛.生物冰期避难所与冰期后的重新扩散.生态学报,2002,22：1984-1990.
田欣,李德铢.DNA序列在植物系统学研究中的应用.云南植物研究,2002,24：170-184.
汪松,解焱.2004.中国物种红色名录.北京：高等教育出版社.