本論文的第一部份為研究東亞特有植物昆欄樹族群之遺傳結構，來探討該物種之遺傳變異度及基因流傳情形等微演化的情形。第二部份則利用分子歧異度的証據，來重新界定昆欄樹與其相關類群的分子親緣關係。
使用同功異構酵素、逢機擴大多型性核酸技術及ITS序列分析，探討東亞特有植物昆欄樹族群之遺傳結構。前者分析十九個族群，而ITS序列分析則分析二十個族群，共選取了十六個台灣本島之族群、兩個日本本島族群，及琉球群島的西表島與奄美大島（ITS序列分析）族群樣本。綜合三種遺傳標示的結果，昆欄樹族群內具有高的遺傳變異，主要導因於其特殊雌、雄差別成熟的花期及昆蟲傳粉行為所造成。族群間高度的遺傳歧異，則與地理的阻隔有相當的關連性。由於地質年代上長久的隔離，造成台灣與日本、奄美大島親緣關係較遠，而與近期隔離的西表島親緣關係較近。在同功異構酵素、逢機擴大多型性核酸技術及ITS序列分析中，都顯示出日本/奄美大島群及台灣/西表島群為區隔的兩群。因此，遺傳分化已經存在這兩大群，其間只有極少的基因流傳存在，明顯屬於地理割裂的隔離分化。而在台灣島內不同地理分區及山脈的阻隔，與族群間的遺傳分化有相關。台灣中部的族群，累積較多遺傳變異及具有較多的古老的祖先型，可能是冰期時昆欄樹族群的避難所，於冰期後再散佈到其他各地;而台灣南部里龍山及北部陽明山具有較低的遺傳變異，可能是冰期後昆欄樹族群散佈的邊緣地帶。我們的結果顯示日本與台灣族群間，適合隔離分化模型， 但台灣島內族群間並不符合此一模式，這些論點二組數據分析的結果皆相一致。
利用細胞核內5.8 S rDNA及葉綠體trnL（UAA）intron DNA、rbcL-atpb基因區間片段等序列，來測定分布於東亞的低等金縷梅類植物7科7個代表種的分子親緣關係。並加入高等金縷梅類胡桃科胡桃屬（Juglans）、榛木科千金榆屬（Carpinus）及虎皮楠科虎皮楠屬（Daphniphyllum）一併作對照分析，而以木蘭科烏心石屬（Michelia）為外群，用以界定其分子親緣關係。有關低等金縷梅類植物的分子親緣，綜合以上三組序列資料之比對分析，再加上已發表之18S rRNA （Hoot and Crane, 1996）及rbcL（Feng et al., 1998）序列分析之結果可歸納出下列結論： 1. 低等及高等金縷梅類植物來自共同祖先，而低等金縷梅類植物是並系群。2. Cercidiphyllum與金縷梅科關係密切，不應放在昆欄樹目，本研究結果支持將其併入金縷梅科（Hoot and Crane, 1996）。3. Tetracentron 應併入昆欄樹科。4. Euptelea和Trochodendron-Tetracentron 關係疏遠，反較近於Platanus。5. Platanus和金縷梅科關係疏遠，不同於形態研究所認定具共同祖先之看法。

Trochodendron aralioides Sieb. & Zucc., a species of the monotypic family Trochodendraceae is an evergreen tree characterized by vesselless wood. This primitive angiosperm is restricted to the East Asia in distribution. The purpose of this study is to investigate the population structure of this narrow distributed species and to explore the phylogeny of T. aralioides and its allies.
Multiple data of allozyme, and nucleotide sequences of the internal transcribed spacers (ITS) of ribosomal DNA were used to investigate genetic structure. Nineteen (allozyme) and twenty (ITS) populations were analyzed, including 16 from Taiwan, four from the main islands of Japan, Iriomote Island and Amami-O-shima. Genetic variability at the species level was comparable to that of narrow distributed species. In comparisons of allozyme, and ITS DNA sequences, the following results are concluded: first, genetic diversity was largely distributed within, rather than among, populations. Plants with protogynous and protandrous sexuality are highly self-incompatible, which probably promotes outcrossing and contributes to the high levels of heterozygosity within populations. Second, populations of T. aralioides were grouped into two distinct clusters, i.e., Japan/Amami-O-shima and Taiwan/Iriomote Island, indicating historical division undergone genetic differentiation. Populations of Iriomote Island was closely related to northern Taiwan. Those of glacial history of this area. Third, based on AMOVA analysis and no share an ITS haplotype, suggesting that geographic barriers have impeded gene flow. The genetic differentiation maybe due to geographic vicariance. Fourth, the isolation by distance model does not fit populations in Taiwan, but suitably describes the relationship between populations of T. aralioides in Japan and Taiwan.
In the second part, the phylogeny of representative species from seven families of the lower Hamamelidae was examined based on DNA sequences of 5.8S rDNA, trnL (UAA) intron and rbcL-atpb intergenic spacer. Three genera of the higher Hamamelidae, Juglans, Carpinus and Daphniphyllum were included. Cladistic analyses suggested paraphyly of the lower Hamamelidae, rooted at Michelia of Magnoliaceae. The 50% majority-rule consensus most parsimonious tree, maximum-likelihood tree and neighbor-joining tree were reconstructed using PAUP based on combined datas. All of the parsimonious trees of 1098 steps, with a CI and an RI of 0.837 and 0.691, respectively, were recovered. All reconstructed trees suggested that the lower Hamamelidae are a paraphyletic group. The Cercidiphyllaceae are most closely related to Hamamelidaceae, suggesting that Cercidiphyllaceae be placed in the Hamamelidales. Trochodendraceae and Tetracentraceae are very close as indicated by a bootstrap value of 100%. The Eupteleaceae phylogenetially are closely related with the Platanaceae.

Archie, J. W. 1989. Homoplasy excess ratios: new indices for measuring levels of homoplasy in phlogenetics systemics and a critique of the consistency index. Syst. Zool. 38: 253-269.
Baldwin, B.G. 1993. Molecular phylogenetics of Calycadenia (Compositae) based on ITS sequences of nuclear ribosomal DNA: Chromosomal and morphological evolution reexamined. Am. J. Bot. 80: 222-238.
Baldwin B.G., Sanderson, M.J., Porter J.M., Wojciechowski, M.F., Campbell, C.S. and Donoghue, M.J. 1995. The ITS region of nuclear ribosomal DNA: a valuable source of evidance on angiosperm phylogeny. Ann. Missouri Bot. Gard. 82: 247-277.
Blair, D., Agatsuma, T., Watanobe, T. and Okamoto, M. 1997. Geographical genetic structure within the human lung fluke, Paragonimus westermani, detected from DNA sequences. Parasitology 115: 411-417.
Brunsfeld, S.J., Soltis, D.E. and Soltis, P.S. 1991. Patterns of genetic variation in Salix section Longifoliae (Salicaceae). Amer. J. Bot. 78: 853-869.
Castelloe, J. and Templeton, A. R. 1994. Root probabilities for intraspecific gene trees under neutral coalescent theory. Molec. Phylogen. and Evol. 3: 102-113.
Chaw, S.M. 1992. Pollination, breeding syndromes and systematics of Trochodendron aralioides Sieb. & Zucc. (Trochodendraceae), a relictual species in eastern Asia. In C.I. Peng, ed., Phytogeography and Botanical Inventory of Taiwan, Institute of Botany, Academia Sinica Monograph Series No.12, Taipei, Taiwan, pp. 63-77.
Chen, L.F.O., Kuo, H.Y., Chen, M.H., Lai, K.N. and Chen, S.C.G. 1997. Reproducibility of the differential amplification between leaf and root DNAs in soybean revealed by RAPD markers. Theor. Appl. Genet. 95: 1033-1043.
Chiang, T.Y. and Schaal, B.A. 1999. Phylogeography of north American populations of the moss species Hylocomium splendens based on the nucleotide sequence of internal transcribed spacer 2 of nuclear ribosomal DNA. Molec. Ecol. 8: 1037-1042.
Clegg, M.T. 1980. Measuring plant mating systems. Bioscience 30: 814-818.
Cornuet, J.M. and Luikart, G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
Croizat, L. 1964. Space, Fime, From: the biological synthesis. Published by the author, Caracas, Venezuela, 4 Vols.
Cronquist, A. 1981. An Integrated System of Classification of Flowering Plants, Columbia University Press, New York.
Cronquist, A. 1988. The evolution and classification of flowering plants. 2nd ed New York Botanical Garden, New York.
Crow, J.F. and Kimura, M. 1970. An introduction to population genetics theory. Harper and Row, New York.
Endress, P.K. 1993. The Families and Genera of Vascular Plants II. Flowering Plants, In K. Kubitzki, ed., Springer-Verlag Berlin Heidelberg, Germany, pp. 599-602.
Excoffier, L., Smouse, P. and Quattro, J. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
Felsenstein, J. 1995. PHYLIP, The phylogenetic inference Package, version 3.57c. Seattle, Washington: University of Washington.
Frankham, R. 1997. Do island populations have less genetic variation than mainland populations? Heredity 78:311-327.
Fritz, G.N., Conn, J., Cockburn, A. and Seawright, J. 1994. Sequence analysis of the ribosomal DNA internal transcribed spacer 2 from populations of Anopheles nuneztovari (Diptera: Culicidae). Molec. Biol. Evol. 11: 406-416.
Fu, Y.X. and Li, W.H. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.
Golding, G.B. 1987. The detection of deleterious selection using ancestors inferred from a phylogenetic history. Genetics Research 49: 71-82.
Gottlieb, L.D. 1977. Electrophoretic evidence and plant systematics. Ann. Missouri Bot. Gard. 64: 161-180.
Gottlieb, L.D. 1981a. Electrophoretic evidence and plant populations. In J. Reingold, J.B. Harborn, T. Swain (eds.). Progress in phytochemistry. vol.8, Pergamon press, New York.
Gottlieb, L.D. 1981b. Electrophoretic evidence and plant populations. Prog. Phycochem. 7: 1-47.
Goudet, J., Raymond, M., de Meeus, T. and Rousset, F. 1996. Testing differentiation in diploid populations. Genetics 144: 1933-1940.
Hamrick, J.L. and Allard, R.W. 1972. Microgeographical variation in allozyme
frequencies in Avena barbata. Evolution 33: 521-533.
Hamrick, J.L., Linhart, Y.B. and Mitton, J.B. 1979. Relationships between life history characteristics and electrophoretically detectable genetic variation in plants. Ann. Rev. Ecol. Syst. 10: 173-200.
Hamrick, J.L. and Godt, M.J.W. 1989. Allozyme diversity in plant species. In A.D.H. Brown, M.T. Clegg, A.L. Kahler and B.S. Wies eds., Plant Population Genetic, Breeding and Genetic Resources, Sinauer Associates, Inc., Sunderland, Massachusetts, pp. 43-63.
Hamrick, J.L., Godt, M.J.W. and Sherman-Broyles, S.L. 1992. Factors influencing levels of genetic diversity in woody plant species. In W.T. Adams, S.H. Strauss, D.L. Copes and A.R. Griffin eds., Population Genetics of Forest Trees, Dordrecht, The Netherlands: Kluwer Academic: 95-124.
Hansen, M., Henry, Y. and Sall, T. 1998. Error rates and polymorphism frequencies for three RAPD protocols. Plant. Mol. Biol. Rep. 16: 139-146.
Hartl, D.C. and Clark, A.G. 1989. Principles of population genetics 2ed. Sinauer associates, Inc. sunderland, Massachusetts.
Hedrick, P.W. 1984. Population biology: The evolution and ecology of population. pp. 445. Jones And Bartlett, Inc.U.S.A.
Heywood, V.H. 1978. ed. Flowering Plants of the World, Mayflower Books Inc., New York.
Higgins, D.G., Bleasby, A.J. and Fuchs, R. 1992. Clustal V: improved software for mutiple sequence alignment. CABIOS. 8: 189-191.
Hills, D.M. and Moritz, C. 1990. Molecular systematics. Sinauer Associates, Sunderland, Mass.
Hsieh, C.F. and Shen, C.F. 1994. Introduction to the flora of Taiwan, 1: geography, geology, climate, and soils. In T.C. Huang et al., eds., The Flora of Taiwan, second edition, Vol.1: 1-18, 597-608; published by the Editorial Committee of the Flora of Taiwan, Second Edition, Taipei, Taiwan.
Huehrsen, K.R., De Wet, J.R. and Walbot, V. 1992. Transient expression analysis in plant using firefly luciferase reporter gene. Methods in Enzymology 216: 397-414.
Keng, H. 1959. Androdioecism in the flowers of Trochodendron aralioides. J. Arnold Arbor. 40: 158-160.
Kephart, S.R. 1990. Starch gel electrophoresis of plant isozymes: a comparative analysis of techniques. Amer. J. Bot. 77: 693-712.
Khandka, D.K., Tuna, M., Tal, M., Nejidat, A. and Golan-Goldhirsh A. 1997. Variability in the pattern of random amplified polymorphic DNA. Electrophoresis 18: 2852-2856.
Kimura, M. 1980. A sample method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Molec. Evol. 16: 111-120.
Kimura, M. 1983. Rare variant alleles in the light of the neutral theory. Mol. Biol. Evol. 1: 84-93.
Kizaki, K. and Oshiro, I. 1977. Paleogeography of the Ryukyu islands. Mar. Sci. Mon. 9: 542-549.
Krimbas, C. B. 1992. The inversion polymorphism of Drosophila subobscura. In: C. B. Krimbas, J. R. Powell (eds.) Drosophila Inversion Polymorphism. CRC Press, Florida. pp. 128-220.
Kumar, S., Tamura, K. and Nei, M. 1993."MEGA: Molecular Evolutionary Genetics Analysis" (user manual), version 1.01, The Pennsylvania State University, University Park, PA.
Ledig, F. T. 1986. Heterozygosity, heterosis, and fitness in outbreeding plants. In M. E. Soule ed., Conservation Biology: the science of scarcity and diversity, Sinauer Associates, Inc., Sunderland, MA, pp.77-104.
Lewontin, R.C. 1974. The Genetics Basis of Evolutionary Change. Columbia University Press, New York.
Li, C.C. 1955. Population genetics. Univ. of Chicago Press, Chicago,Illinois.
Li, C.C. and Horvitz, D.G. 1953. Some methods of estimating the inbreeding coefficient. Amer. J. Hum. Genet. 5:107-117.
Liengsiri, C., Piewluang, C. and Boyle, T.J.B. 1990. Starch gel electrophoresis of tropical trees - a mannual. Asean-Canada Forest Tree Seed Center.
Lin, T.P., Cheng, Y.P. and Huang, S.G. 1997. Allozyme variation in four geographic areas of Cinnamomum kanehirae. J. Hered. 88: 433-438.
Liston, A., Robinson, W.A., Oliphant, J.M. and Alvarez-Buylla E.R. 1996. Length variation in the nuclear ribosomal DNA internal transcribed spacer of non-flowering seed plants. Systematic Bot. 21: 109-120.
Liu, T. 1968. Studies on the classification of the climax vegetation communities of Taiwan. I. Classification of the climax formations of the vegetation of Taiwan. Bull. Taiwan For. Res. Ins. 166: 1-25.
Loveless, M.D. and Hamrick, J.L. 1984. Ecological determinants of genetic structure in plant population. Ann. Rev. Ecol. Syst. 15: 65-95.
Manly, B. F. J. 1985. The statistics of natural selection. Chapman & Hall, London.
Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Can. Res. 27: 209-220.
Maruyama, T. and Nei, M. 1981. Genetic variability maintained by mutation and
overdominant selection in finite population. Genetics 98: 441-459.
Max, K.N., Mouchaty, S.K. and Schwaegerle, K.E. 1999. Allozyme and morphological variation in two subspecies of Dryas octopetala (Rosaceae) in Alaska. Amer. J. Bot. 86: 1637-1644.
Miller, M.P. 1997. Tools For Population Genetics Analysis (TFPGA) 1.3: A Windows program for the analysis of allozyme and molecular population genetic data.
Mitton, J.B., Linhart, Y.B., Sturgeon, K.B. and Hamrick, J.L. 1979. Allozyme polymorphisms detected in mature needle tissue of ponderosa pine. J. Hered. 70: 86-89.
Muster, W., Boon, K., van der Sande, C.A.F.M., van Herrikhuizan, H. and Planta, R.J. 1990. Functional analysis of transcribed spacers of yeast ribosomal DNA. EMBO 9: 3989-3996.
Nei, M. 1972. Genetic distance between populations. Am. Nat. 106: 283-292.
Nei, M. 1973. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. U.S.A. 70: 3312-3323.
Nei, M. 1977. F-statistics and analysis of gene diversity in subdivided populations. Ann. Hum. Genet. 41: 225-233.
Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89: 583-590.
Nei, M. 1987. Molecular Evolution Genetics. Columbia University Press, New York, USA.
Nei, M. and Tajima, F. 1981. DNA polymorphism detectable by restriction endonucleases. Genetics 97: 145-163.
Newman, P.L. 1985. Variation amongst isozymes of Rhynchosporium secalis. Pl. Pathol. 34: 329-337.
O'Donnel, K. 1992. Ribosomal DNA internal transcribed spacers are highly divergent in the phytopathogenic ascomycete Fusarium sambucinum (Gibberella pulicares). Curr. Genet. 22: 213-220.
Ohta, T. 1982a. Linkage disequilibrium with the island model. Genetics 101: 139-155.
Ohta, T. 1982b. Linkage disequilibrium due to random drift in finite subdivided populations. Proc. Natl. Acad. Sci. USA 79: 1940-1944.
Prakash, S., LewontinR.C. and Hubby, J.L. 1969. A molecular approach to the study of genetic heterozygosity in natural populations. Ⅳ. Pattern of genic variation in centrol, marginal and isolated populations of Drosophila pseudoobscura. Genetics 61: 841-858.
Price, M.V. and Waster, N.M. 1982. Experimental studies of pollen carryover: Hummingbirds and Ipomopsis aggregata. Oecologia 54: 353-358.
Quijada, A., Liston, A., Delgado, P., Vazquez-Lobo, A. and Alvarez-Buylla, E. R. 1998. Variation in the nuclear ribosomal DNA internal transcribed spacer (ITS) region of Pinus rzedowskii revealed by PCR-RFLP. Theor. Appl. Genet. 96: 539-544.
Ratter, J.A. and Milne, C. 1973. Chromosome number of some primitive angiosperms . Notes R. Bot.Gard. Edinb. 32:423-428.
Raymond, M. and Rousset, F. 1995a. GENEPOP (Version 1.2): Population genetics software for exact tests and ecumenicism. J. Hered. 86: 248-249.
Raymond, M., and Rousset, F. 1995b. An exact test for population differentiation. Evolution 49: 1280-1283.
Rozas, J., and Rozas, R. 1999. DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15: 174-175.
Sang, T., Crawford, D.J., Kim, S.C. and Stuessy, T. F. 1994. Radiation of the endemic genus Dendroseris (Asteraceae) of the Juan Fernandez islands: Evidence from sequences of the ITS regions of the nuclear ribosomal DNA. Am. J. Bot. 81: 1491-1501.
Sang, T., Crawford, D.J. and Stuessy, T.F. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. USA 92: 6813-6817.
Saitou, U. and Nei, M. 1987. The neighbor-joining methods: A new method for reconstructing phylogenetics tree. Mol. Evol. Biol. 4: 406-425.
Scaltsoyiannes, A., Tsaktsira, M. and Drouzas, A.D. 1999. Allozyme differentiation in the Mediterranean firs (Abies, Pinaceae). A first comparative study with phylogenetic implications. Pl. Syst. Evol. 216: 289-307.
Schaal, B. A. 1975. Population structure and local differentiation in Liastris cylindracea. Amer. Natur. 109: 511-528
Schaal, B.A. 1980.Measurement of gene flow in Lupinus texensis. Nature 284: 450-451.
Schaal, B.A., Leverich, W.J. and Rogstad, S.H. 1991. A comparison of methods for assessing genetic variation in plant conservation biology. In Falk, D. A. and K. E. Holsinger.(eds), Genetics and Conservation of Rare Plants. Oxford Univ. Press, New York, Oxford. 123-134.
Schaal, B.A., Hayworth, D.A., Olsen, K.M., Rauscher, J.T. and Smith, W.A. 1998. Phylogeographic studies in plants: problems and prospects. Molec. Ecol. 7: 465-474.
Schemske, D.W. 1984. Population structure and local selection in Impatiens (Balsaminaceae ), a selfing annual. Evolution 38: 817-832.
Schneider, S., Kueffer, J. M., Roessli, D. and Excoffier, L. 1997. ARLEQUIN ver 1.1: A software for population genetic data analysis. University of Geneva Press, Switzerland.
Schumaker, K.E. and Babble, G.R. 1980. Patterns of allozymic similarity in ecologically central and marginal populations of Hordeum jubatum in Utah. Evolution 34: 110-116.
Shure, M., Wessler, S. and Fedoroff, N. 1983. Molecular identification and isolation of the Waxy Loous in Maize. Cell 35: 225-233.
Silvertown, J.W. and Lovett Doust, J. 1993. Introduction to plant population biology. In J.W. Silvertown and J. Lovett Doust eds., Oxford, Boston, Blackwell Sciemtific, pp. 32-33.
Slatkin, M. 1985. Rare alleles as indicators of gene flow. Evolution 39: 53-65.
Slatkin, M. 1987. Gene flow and the geographic structure of natural population. Science.236: 787-792.
Soltis, D.E., Haufler, C.H., Darrow, D.C. and Gastony, G.J. 1983. Starch gel electrophoresis of ferns: a compilation of grinding buffers, gel and electrode buffers, and staining schedules. Amer. Fern J. 73: 9-27.
Soltis, P.S. and Kuzoff, R.K. 1993. ITS sequence variation within and among populations of Lomatium grayi and L. laevigatum (Umbelliferae). Molec. Phylo. Evol. 2: 166-170.
Su, H. J. 1984a. Studies on the climate and vegetation types of the natural forests in Taiwan (I) analysis of the variations in climatic factors. Quart. J. Chin. For. 17: 1-14.
Su, H.J. 1984b. Studies on the climate and vegetation types of the natural forests in Taiwan (II) Altitudinal vegetation zones in relation to temperature gradient. Quart. J. Chin. For. 17: 57-73.
Su, H.J. 1992. Vegetation of Taiwan: Altitudinal vegetation zones and geographical climatic regions. In C. I. Peng ed., The biological resources of Taiwan: a status report, Institute of Botany, Academia Sinica, Taipei, pp.39-54.
Sue, C.Y., Fang, K. and Huang, S. 2000. Patterns of genetic variation of Alnus formosana in Taiwan. Taiwania 45(1): 95-106.
Suh, Y., Thien, L.B., Reeve, H.E. and Zimmer, E.A. 1993. Molecular evolution and phylogenetic implications of internal transcribed spacer sequences of ribosomal DNA in Winteraceae. Am. J. Bot. 80: 1042-1055.
Swofford, D.L. and Selander, R.B. 1989. BIOSYS-1. University of Illinois Urbana-Champaign.
Swofford, D.L. 1998. PAUP. Phylogenetic Analysis Using Parsimony version 4.0b3a. Sinauer Associates, Sunderland, Massachusetts.
Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
Takhtajan, A. 1980. Outline of the classification of flowering plants (Magnoliophyta). Bot Rev. 46: 225-359.
Templeton, A.R., Routman, E. and Phillips, C.A. 1995. Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA sequence data. III. Cladogram estimation. Genetics 140: 767-782.
Teng, L.S. 1987. Stratigraphic records of the late Cenozoic penglai orogeny of Taiwan. Acta Geol. Taiwanica 25: 205-224.
Tomaru, N., Mitsutsuji, T., Takahashi, M., Tsumura, Y., Uchida, K. and Ohba, K. 1997. Genetic diversity in Fagus crenata (Japanese beech): influence of the distributional shift during the late-Quaternary. Heredity 78: 241-251.
Torres, R.A., Ganal, M. and Hemleben, V. 1990. GC balance in the internal transcribed spacers ITS-1 and ITS-2 of nuclear ribosomal RNA genes. J. Mole. Evol. 30: 170-181.
Tsumura, Y. and Ohba, K. 1993. Genetic structure of geographical marginal populations of Cryptomeria japonica. Can. J. For. Res. 23: 859-863.
van der Sande, C.A.F.M., Kwa, M., van Nues, R.W., van Herrikhuizen, H., Raue, H.A. and Planta, R.J. 1992. Functional analysis of internal transcribed spacer 2 of Saccharomyces cerevisiae ribosomal DNA .J. Molec. Biol. 223: 899-910.
van der. Stappen, J. and van. Campenhout, S. 1998. Sequencing of the internal transcribed spacer region ITS1 as a molecular tool detecting variation in the Stylosanthes guianensis species complex. Theor. Appl. Genet. 96: 869-877.
van Nues, R.W., Rientjes, J.M.J., van der Sande, C.A.F.M., Zerp, S. F., Slutter, C., Venema, J., Planta, R.J. and Raue, H.A. 1994. Separate structural elements within internal transcribed spacer 1 of Saccharomyces cerevisiae precursor ribosomal RNA direct the formation of 17S and 26S rRNA. Nucl. Acids Res. 22: 912-919.
Vogler, A.P. and DeSalle, R. 1994. Evolution and phylogenetic information content of the ITS1 region in the tiger beetle Cicindela dorsalis. Molec. Biol. Evol. 11: 393-405.
Watterson, G. A. 1975. On the number of segregating sites in genetical models without recombination. Theor. Pop. Biol. 7: 256-276.
Weir, B. S. 1979. Inferences about linkage disequilibrium, Biometrics 35: 235-254.
Weir, B.S. and Cockerham, C.C. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
Weir, B.S. 1990. Genetic Data Analysis. Methods for Discrete Population Genetic Data. Sinauer Associates, Inc., Sunderland, Massachusetts.
White, T.J., Bruns, T., Lee, S. and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. Innis, D. Gelfand, J. Sninsky, and White, Eds.,"PCR Protocols: A Guide to mathods and Applications". Academic Press, San Diego. pp. 315-322.
Willams, P.L. and Fitch, W.M. 1989. Finding the minimalchang in a given tree. In C.I. Fernholm eds., The hierachy of life, pp. 453-469. Elsevier Science Publishers B.V.
Wojciechowski, M.F., Sanderson, M.J., Boldwin, B.G. and Donoghue, M.J. 1993. Monophyly of aneuploid Astragalus (Fabaceae): Evidence from nuclear ribosomal DNA internal transcribed spacer sequence. Am. J. Bot. 80: 711-722.
Wolfe, K.H., Li, W.H. and Sharp, P.M. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84: 9054-9058.
Workman, P.L. and Niswander, J.D. 1970. Population studies on southwestern Indian tribes. II. Local genetic differentiation in the Papago. Amer. J. Hum. Genet. 22: 24-29.
Wright, S. 1931. Evolution in Mendelian population. Genetics 16: 97-159.
Wright, S. 1943. Isolation by distance. Genetics 28: 114-138.
Wright, S. 1946. Isolation by distance under diverse systems of mating. Genetics
31:39-59.
Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19: 395-420.
Wright, S. 1978. Evolution and the genetics of population, vol. 4. Variability within and among natural populations. University of Chicago Press, Chicago.
Wu J.E., Huang, S., Wang, J.C. and Tong, W.F. 2001. Allozyme variation and genetic structure of population of Trochodendron aralioides, a monotypic and narrow geographic genus. In press in Journal of plant research
Yeh, F.C. and Boyle, T. 1996. Popgene version 1.1. University Alberta and Center for International Forestry Research.
Yeh, F.C. and Boyle, T.J.B. 1997. Population genetic analysis of codominant and dominant markers and quantitative traits. Belg. J. Bot. 129: 157.
王文采，1989。中國植物區系中的一些間斷分布現象。植物研究9（1）：1-16。
王介鼎，1995。台灣穗花杉族群同位酵素變異之研究。國立台灣大學森林學研究所碩士論文。
王斯範，1997。紅檜與台灣扁柏的同功酉每遺傳、基因座連鎖與異交率研究。
國立台灣大學植物學研究所碩士論文。
李 恒，1994。獨龍江地區種子植物區系的性質和特徵。雲南植物研究 增刊VI ：1-100.
李鎮宇，1993。紅檜五個族群同位酵素變異之研究。國立台灣大學森林學研
究所碩士論文。
呂春森，1992。台灣杉的族群遺傳結構。私立輔仁大學生物學研究所碩士論文。
洪培元，1992。不同種源台灣櫸同功酉每變異之研究。國立台灣大學森林學系研究所碩士論文。
孫于卿，1998。台東蘇鐵族群遺傳結構分析。國立台灣大學森林學系研究所碩士論文，1-50頁。
陳美蓮，1995。台灣的筆筒樹族群遺傳結構之研究。國立台灣師範大學生物學研究所碩士論文。
陳怡旴，1997。水筆仔族群內的基因流傳研究。國立台灣師範大學生物學研
究所碩士論文。
黃 生，1991。基因流傳與族群分化。生物科學，35(1)：19-32。
楊莉芬，1993。台灣扁柏族群之遺傳結構。國立中興大學植物學研究所碩士論文。
楊國禎，1996。台灣的柳屬植物種間與種內變異之研究。國立台灣大學植物學研究所博士論文。
劉業經、呂福原、歐辰雄，1988。台灣樹木誌。Pp. 122-124頁。
中國科學院植物研究所等，1978。中國植物化石，第3冊：中國新生代植物，科學出版社 第30 頁。

Angiosperm Phylogeny Group 1998. An ordinal classification for the families of flowering plants. Ann. Missouri Bot. Gard. 85: 531-553.
Archie, J.W. 1989, Homoplasy excess ratios: new indices for measuring levels of homoplasy in phlogenetics systemics and a critique of the consistency index. Syst. Zool. 38: 253-269.
Avise, J. C. 1994. Molecular Markers, Natural History and Evolution. Chapman &Hall, New York.
Bayer P.J. and Starr,J.R. 1998. Tribal phylogeny of the Asteraceae based on two noncoding chloroplast sequences, the trnL intron and trnL/trnF intergenic spacer. Ann. Missouri Bot. Gard. 85(2): 242-256.
Bernardi, G., Olofsson, B., Filipski, J., Zerial, M., Salinas, J., Cuny, G., Meunier-Rotival, M. and Rodier, F. 1985. The mosaic genome of warm-blooded vertebrates. Science 228: 953-958.
Chase, M.W., Soltis, D.E., Olmstead, R.G., Morgan, D., Les, D.H., Mishler, B.D., Duvall, M.R., Price, R.A., Hills, H.G., Qiu, Y.L., Kron, K.A., Rettig, J.H., Conti, E., Palmer, J.D., Manhart, J.R., Sytsma, K.J., Michaels, H.J., Kress, W.J., Karol, K.G., Clark, W.D., Hedren, M., Gaut, B.S., Jansen, R.K., Kim, K.J., Wimpee, C.F., Smith, J.F., Furnier, G.R., Strauss, S.H., Xiang, Q.Y., Plunkett, G.M., Soltis, P.S., Swensen, S.M., Williams, S.E., Gadek, P.A., Quinn, C.J., Eguiarte, L.E., Golenberg, E., Learn Jr., G.H., Graham, S.W., Barrett, S.C.H., Dayanandan, S. and Albert, V.A. 1993. Phylogenetics of seed plants: An analysis of nucleotide sequences from the plastid gene rbcL. Ann. Missouri Bot. Gard. 80: 528-580.
Chaw, S.M., Long, H., Wang, B.S., Zharkikh, A. and Li, W.H. 1993. The phylogentic positions of Taxaceae based on 18S rRNA sequences. J. Molec. Evol. 37: 624-630.
Chaw, S.M., Zharkikh, A., Sung, H.M., Lau, T.C. and Li, W.H. 1997. Molecular phylogeny of extant gymnosperms and seed plant evolution: anlysis of nuclear 18S rRNA sequences. Molec. Biol. Evol. 14 (1): 56-68.
Chiang, T.Y., and Schaal, B.A. 2000. Molecular evolution and the atpb-rbcL spacer of chloroplast DNA in the true mosses. Genome 43: 417-426..
Clegg, M.T., Gaut, B.S., Jr. Learn, G.H. and Morton, B.R. 1994. Rates and patterns of chloroplast DNA evolution. Proc. Natl. Acad. Sci. USA 91: 6795-6801.
Crane, P.R., Friis, E.M. and Pedersen, K.R. 1986. Lower Cretaceous angiosperm flower: fossil evidence on early radiation of dicotyledons. Science 232: 852-854.
Crane, P.R. 1989. Paleobotanical evidence on the early radiation of nonmagnoliid dicotyledons. Pl. Syst. Evol. 162 : 165-191.
Cronquist, A. 1981. An integrated system of classification of flowering plants. Columbia University Press, New York
Crayn, D.M. and Quinn,C.J. 2000. The evolution of the atpb-rbcL intergenic spacer in the epacrids (Ericales) and its systematic and evolution implications. Molec, Phylo. Evol. 16(2): 238-252.
Dahlgren, R. 1980. A revised system of classification of the angiosperms. Bot. J. Linn. Soc. 80: 91-124.
Endress, P.K. 1986. Floral structure, systematics and phylogeny in Trochodendrales. Ann. Missouri Bot. Gard. 73 : 297-324.
Endress, P.K. 1989. Aspects of evolutionary differentiation of the Hamamelidaceae and the lower Hamamelididae. Pl. Syst. Evol. 162: 193-211.
Felsenstein, J. 1995. PHYLIP, The phylogenetic inference Package, version 3.57c. Seattle, Washington: University of Washington.
Feng, Y.X., Wang, X.Q., Pan, K.Y. and Hong, D.Y. 1998. A reevaluation of the systematic positions of the Cercidiphyllaceae and Daphniphyllaceae based on rbcL gene sequence analysis, with reference to the relationship in the lower Hamamelidae. Acta Phytotax. Sin. 36(5): 411-422.
Fujii, N., Ueda, K., Watano, Y. and Shihimizu, T. 1997. Intraspecific sequence variation of chloroplast DNA in Pedicularis chamissonis Steven (Scrophulariaceae) and geographic structuring of the Japanese "Alpine" plants. J. Pl. Res. 110: 195-207.
Gaut, B.S., Muse, S.V., Clark W.D. and Clegg, M.T. 1992. Relative rate of nucleotide substitution at the rbcL locus of monocotyledous plants. J. Molec. Evol. 35: 292-303.
Gielly, L. and Taberlet, P. 1994. The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Molec. Biol. Evol. 11: 769-777.
Gielly, L. and Taberlet, P. 1996a. Chloroplast DNA sequencing to resolve plant phylogenies between closely related taxa. In "Molecular Genetic Approaches in Conservation." ed. by T. B. Smith and R. K. Wayne (eds.) Oxford University Press, New York. pp. 143-153.
Gielly, L. and Taberlet, P. 1996b. A phylogeny of the European gentians inferred from chloroplast trnL (UAA) intron sequences. Bot. J. Linn. Soc. 120: 57-75.
Higgins, D.G., Bleasby, A. J. and Fuchs, R. 1992. Clustal V: improved software for mutiple sequence alignment. CABIOS. 8: 189-191.
Hoot, S.B. and Crane, P.R. 1996. A comparison of results from 18S nuclear ribosomal DNA sequences with two chloroplast genes (atpβ and rbcL) within the lower Hamamelidae and Ranunculidae. Amer. J. Bot. 83 (Suppl. 6): 212.
Hoot S.B. and Douglas A.W. 1998. Phylogeny of the Proteaceae based on atpB and atpB-rbcL intergenic spacer region sequences. Australian Systematic Botany. 11(3-4): 301-320.
Jordan, W.C., Courtney, M.W. and Neigel, J.E. 1996. Low levels of intraspecfic genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). Amer. J. Bot. 83: 430-439.
Kamiya, K., Harada, K., Ogino, K., Kajita, T., Yamazaki, T., Lee, H.S. and Ashton, P.S. 1998. Molecular phylogeny of Dipterocarp species using nucleotide sequences of two non-coding regions in chloroplast DNA. Tropics 7: 195-207.
Kelchner, S.A., and Clark, L.G. 1997. Molecular evolution and phylogenetic utility of the choloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molec. Phylo. Evol. 8:385-397.
Kimura, M. 1980. A sample method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Molec. Evol. 16: 111-120.
Kita, Y., Ueda, K. and Kadota, Y. 1995. Molecular phylogeny and evolution of the Asian Aconitum subgenus Aconitum (Ranunculaceae). J. Pl. Res. 108: 429-442.
Kumar, S., Tamura, K. and Nei, M. 1993. "MEGA: Molecular Evolutionary Genetics Analysis" (user manual), version 1.01, The Pennsylvania State University, University Park, PA.
Loconte, H. and Stevenson, D.M. 1991. Cladistics of the Magnoliidae. Cladistics 7: 267-296.
Li, J., Bogle, A.L. and Donoghue, M.J. 1999. Phylogenetic relationships in the Hamamelidoideae inferred from sequences of TRN non-coding regions of chloroplast DNA. Harv. Pap. Bot. 4(1): 343-356.
Lu, A.M., Li, J.Q. and Xu, K.X. 1991. A phylogenetic analysis of families in the Hamamelidae. Acta Phytotax. Sin. 29(6):481-493.
Manen, J.F. and Natali, A. 1995. Comparison of the evolution of ribolose-1, 5-bisphosphate carboxylase (rbcL) and atpB-rbcL non-coding spacer sequences in a recent plant group, the tribe Rubieae (Rubiaceae). J. Molec. Evol. 41: 920-927.
Martin, W., Gierl, A. and Saedler, H. 1989. Molecular evidence for pre-Cretaceous angiosperm origins. Nature 339: 46-48.
Niedenzu, C.G. and Engler, A. 1930. Myrothamnaceae. In "Die Naturlichen Pflanzenfamilien 18a (2nd.)." ed. by Engler A. and K. Prantl(eds.) Engelmann. Leipzig. pp. 262-265.
Page, R.D.M. and Holmes, E.C. 1998. Inferring molecular phylogeny. In "Molecular Evolution-A Phylogenetic Approach" ed by R. D. M. Page and E. C. Holmes(eds.) Blackwell Science, Oxford. pp. 172-227.
Praglowski, J. 1974. The pollen morphology of the Trchodendraceae, Tetracentraceae, Cercidiphyllaceae, and Eupteleaceae, with reference to taxonomy. Pollen Spores 16: 449-467.
Renner S.S. 1998. Phylogenetic affinities of Manimiaceae based on cpDNA gene and spacer sequences. Perspective in plant Ecology, Evolution and Systematics. 1(1): 67-77.
Saitou, U. and Nei, M. 1987. The neighbor-joining methods: A new method for reconstructing phylogenetics tree. Mol. Evol. Biol. 4: 406-425.
Sang, T., Crawford, D.J. and Stuessy, T.F. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proc. Natl. Acad. Sci. USA 92: 6813-6817.
Savolainen, V., Manen, J.K., Douzery, E. and Spichiger, R. 1994. Molecular phylogeny of families related to Celastrales based on rbcL 5' flanking sequences. Molec. Phylo. Evol. 3: 27-37.
Schwarzwalder, R.N.Jr. and Dilcher, D.L. 1991. Systematic placement of the Platanaceae in the Hamamelidae. Ann. Missouri. Bot. Gard. 78: 962-969.
Schwarzbach, A.E. and Ricklefs, R.E. 2000. Systematic affinities of Rhizophoraceae and Anisophylleaceae, and intergeneric relationships within Rhizophoraceae, based on chloroplast DNA, nuclear ribosomal DNA, and morphology. Amer. J. Bot. 87(4): 547-564.
Shure, M., Wessler, S. and Fedoroff, N. 1983. Molecular identification and isolation of the Waxy Loous in Maize. Cell 35: 225-233.
Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.J., Hoot, S.B., Sweere, J.A., Kuzoff, R.K., Kron, K.A., Chase, M.W., Swensen, S.M., Zimmer, E.A., Chaw, S.M., Gillespie, L.J., Kress, W.J. and Sytsma, K.J. 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann. Missouri Bot. Gard. 84: 1-49.
Swofford, D.L. 1998. PAUP. Phylogenetic Analysis Using Parsimony version 4.0b3a Sinauer Associates, Sunderland, Massachusetts.
Taberlet, P., Gielly, L., Pautou, G. and Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Pl. Molec. Biol. 17: 1105-1109.
Takhtajan, A. 1969. Flowering Plant: Orgin and Dispersal. Transl. from the Russian by C. Jeffrey, Kew. Oliver and Bord. Edinburgh.
White, T.J., Bruns, T., Lee, S. and Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In"PCR Protocols: A Guide to mathods and Applications" ed by M. Innis, D. Gelfand, J. Sninsky, and T. J. White (eds.) Academic Press, San Diego. pp. 315-322.
Willams, P.L. and Fitch, W.M. 1989. Finding the minimalchang in a given tree. In "The hierachy of life." P. Fernholm eds. Elsevier Science Publishers B.V. pp.453-469
Wolfe, K.H., Li, W.H. and Sharp, P.M. 1987. Rate of nucleotide substitution vary greatly among plant mitochondria, chloroplast, and nuclear DNAs. Proc. Natl. Acad. Sci. USA 84: 9054-9058.
吳瑞娥，童武夫和王震哲1999. 利用trnL intron序列分析低等金縷梅類植物分子親緣。師大生物學報34 : 137-149。
邵廣昭 1992. 分子生物技術在動物系統分類上之應用。生物科學35 : 1-12。
趙淑妙 1992. 分子生物技術在研究植物親緣關係的應用。生物科學35 : 13-33。
路安民，李建強和陳之端 1993. 低等金縷梅類植物的起源和散布。植物分類學報31(6) : 489-504.