龍膽屬（Gentiana L.）植物，屬於龍膽科（Gentianaceae），龍膽族（Gentianaeae）。台灣本地產龍膽屬植物可分為多年生草本及一年生草本兩類，本論文研究材料黃斑龍膽（Gentiana flavomaculata）及鴛鴦湖龍膽（G. flavomaculata var. yuanyanghuensis）均為台灣特有種之一年生草本。黃斑龍膽及鴛鴦湖龍膽在形態上及地理分布上略有區隔，但兩類群又呈現極高的相似度，因此本研究擬以葉綠體 rps4基因探討台灣產黃斑龍膽及鴛鴦湖龍膽是否在分子分類上，可藉由分子遺傳證據將之有效區分，同時亦結合微衛星DNA序列探討其族群分化情形，分析其遺傳多樣性特徵。結果顯示，黃斑龍膽與鴛鴦湖龍膽之間的核苷酸歧異度僅有0.2%，在多樣性分析方面，於兩種龍膽的所有葉綠體片段中，共只得到8個單套型核酸（haplotype, h），且以聚類樹形分析法（neighbor-joining tree, NJ tree）利用kimura雙參數模式進行黃斑龍膽與鴛鴦湖龍膽族群的親緣演化樹建構，結果顯現兩者呈現出具有共用單型的現象。再根據AMOVA分析，葉綠體DNA與微衛星DNA的結果呈現一致結果，在種間鴛鴦湖龍膽與黃斑龍膽之間的遺傳分化指數相當非常低（ΦCT = 0.064, cpDNA; ΦCT =0.057, microsatellite DNA），顯示兩者並沒有遺傳上顯著的分化情形結合以上特徵，表示黃斑龍膽以及鴛鴦湖龍膽的族群間尚保有基因交流的機制，在分子分類上，尚無法支持成為有效的獨立種，因此本研究建議黃斑龍膽與鴛鴦湖龍膽在分子層級上，應暫處理為種下階級較為合適。

Gentiana L. is belonged to Gentianaceae, Gentianaeae. The Gentiana in Taiwan includes perennial and annual herbaceous species. Both Gentiana flavomaculata and G. flavomaculata var. yuanyanghuensis are annual and endemic in Taiwan. Though there are some distributional and morphological differences between these two species, however, highly similarity still exists among taxons. In order to test whether G. flavomaculata and G. flavomaculata var. yuanyanghuensis were genetically differentiated and genetic diversity characteristics, chloroplast rps4 was combined with microsatellite DNA to discuss phylogenetic structure and genetic differentiation. The result showed only 0.2 % nucleotide diversity between G. flavomaculata and G. flavomaculata var. yuanyanghuensis and eight haplotypes were found among all chloroplast segments, which were highly shared by two species according to Neighbor - Joining K2P tree. The AMOVA showed congruent result of chloroplast and microsatellite and low genetic differentiation among species (ΦCT = 0.064, cpDNA; ΦCT =0.057, microsatellite DNA ), implying genetic exchange mechanism among populations of these two specie, and these two species could not be spported as different species phylogenetically. As a result, we suggested G. flavomaculata and G. flavomaculata var. yuanyanghuensis should temporarily be treated as a infra-species based on phylogenetic evidence.

楊建夫（2001）。台灣的山脈。台灣地理百科。
陳志雄（1996）。台灣產龍膽屬的分類研究。國立台灣師範大學生命科學研究所碩士論文。
陳志雄（2001）。龍膽屬內小龍膽組的親緣關係研究。國立台灣師範大學生命科學研究所博士論文。
黃啟俊（2006）。台灣產玉山杜鵑複合群之親緣地理學研究。國立成功大學生命科學研究所碩士論文。
Allen, M. P., C. P. Mason, E. de Miguel, & J. Stelzer. 1995. Structure of molecular liquids. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52: 25-28.
Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigl, C. A. Reeb, & N. C. Saunders. 1987. The mitochondrial DNA bridge between populations genetics and systematics. Annual Review of Ecology and Systematics 3: 457-498.
Avise, J. C. 2000. Phylogeography: the History and Formation of Species. Harvard University Press, Cambridge, MA.
Baker, A. J. 2002. Molecular methods in ecology. Malden, MA, Blackwell Science. 208-226.
Beerli, P. 1998. "Estimation of migration rates and population sizes in geographically structured populations.". Advances in molecular ecology. NATO-ASI workshop (G. Carvalho, Ed.) IOS, Amsterdam.
Beerli, P., & J. Felsenstein. 1999. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics 152(2): 763-73.
Beerli, P., & J. Felsenstein. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences of the USA 98(8): 4563-4568.
Beerli, P. 2004. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology 13: 827-836.
Beerli, P. 2006. Comparison of a Bayesian and maximum likelihood inference of population genetic parameters. Bioinformatics 22(3): 341-345.
Beerli, P. 2008. Migrate version 3.0 - maximum likelihood and Bayesian estimator of gene flow using the coalescent. Distributed over the internet at http://popgen.scs.edu/migrate.html.
Benson, G. 1999. Tandom Repeats Finder: a program to analyze DNA sequences. Nucleic Acid Research. 27: 573-580.
Budowle, B., R. Chakraborty, A. M. Giusti, A. J. Eisenberg, & R. C. Allen. 1991. Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE. Am J Hum Genet 48: 137-144.
Bowcock, A. M., A. Ruiz-Linares, J. Tomfohrde, E. Minch, J. R. Kidd, & C.-S. L. L. 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
Callen, D.F., A.D. Thompson, Y. Shen, H.A. Phillips, R.I. Richards, J.C. Mulley, & G.R. Sutherland. 1993. Incidence and origin of “null” alleles in the (AC)n microsatellite markers. American Journal of Human Genetics 52(5): 922-927.
Carvalho, G.R. 1993. Evolutionary aspects of fish distributions: genetic variability and adaptation. Journal of Fish Biology 43(Suppl. A): 53-73.
Carvalho, G.R., & T.F. Cross. 1998. Enhancing fish production through introductions and stocking: genetic perspectives. In: Cowx. I.G. (Ed.), Stocking and Introduction of Fish. Blackwell Science, Oxford, 329-338.
Chiang, T.Y., Y.C. Chiang, Y.J. Cheng, C.H. Chou, S. Havanond, T.N. Hong & S. Huang. 2001. Phylogeography of Kandelia candel in East Asiatic mangroves based on nucleotide variation of chloroplast and mitochondria DNAs. Molecular Ecology 10: 2697-2710.
Chung, J.D., T.P. Lin, Y.L. Chen, Y.P. Cheng & S.Y. Huang. 2007. Phylogeographic study reveals the origin and evolutionary history of a Rhododendron species complex in Taiwan. Molecular Phylogenetics and Evolution 42: 14-24.
Comes, H.P., & J.W. Kadereit. 1998. The effect of Quaternary climatic changes on plant distribution and evolution. Trends in Plant Science 3(11): 432-438
Corander, J., P. Waldmann, & M.J. Sillanpaa. 2003. Bayesian Analysis of Genetic Differentiation Between Populations. Genetics 163: 367-374.
Cornuet, J.M., & G. Luikart. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001-2014.
Corriveau, J. L., & A. W. Coleman. 1988. Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. American Journal of Botany 75(10): 1443-1458.
Dib, C., S. Faure, C. Fizames, D. Samson, N. Drouot, A. Vignal, P. Millasseau, S. Marc, J. Hazan, E. Seboun, M. Lathrop, G. Gyapay, J. Morissette, & J. Weissenbach. 1996. A comprehensive genetic map of the human genome based on 5,264 microsatellites. Nature 380: 152-154.
Dietrich, W. F., J. Miller, R. Steen, M. A. Merchant, D. Damron-Roles, Z. Husain, R. Dredge, M. J. Daly, K. A. Ingalls, & T. J. O’Connor. 1996. A comprehensive genetics map of the mouse genome. Nature 380:149-152.
Doyle, J.J., & J.L. Doyle. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochemical Bullitin 19: 11-15.
Ellstrand, N.C., & D.R. Elam. 1993. Population genetic consequences of small population size: implications for plant conservation. Annual Review of Ecology and Systematics 24: 217-242.
Exoffier, L., & P.E. Smouse. 1994. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics 136: 343-359.
Excoffier, L., G. Larval, & S. Schneider. 2005. Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics 1: 47-50.
Felsenstein, J. 1985. Confidence Limits on Phylogenetics: An Approach Using the Bootstrap. Evolution 39: 783-791.
Franklin, I.R. 1980. Evolutionary change in small populations. In: Soule’, M.E., Wilcox, B.A. (Eds.), Conservation Biology: An Evolutionary Ecological Perspective. Sinauer Associates, Sunderland, 134-148.
Frascaria, N., L. Maggia, M. Michaud, & J. Bousquet. 1993. The rbcL gene sequence from chestnut indicates a slow rate of evolution in the Fagaceae. Genome 36: 668-671.
Fu, Y.X., & W.H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-704.
Fu, Y.X. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking, and background selection. Genetics 147: 915-925.
Gifford, M. E., R. Powell, A. Larson & R. L. Gutberlet. 2004. Population structure and history of a phenotypically variable teiid lizard (Ameiva chrysolaema) from Hispaniola: the influence of a geologically complex island. Molecular Phylogenetics and Evolution 32: 735-748.
Goldstein, D.B., & C. Schlötterer. 1999. Microsatellite: evolution and applications. Oxford University Press, Oxford.
Gottelli, D., C. Sillero-Zubiri, G. D. Applebaum, M.S. Roy, D. J. Girman, J. Garcia-Moreno, E. A. Ostrander, & R. K. Wayne. 1994. Molecular genetics of the most endangered canid: the Ethiopian wolf Canis simensis. Molecular Ecology 3: 301-312.
Grant, W.S., & B. W. Bowen. 1998. Shallow population histories in deep evolutionary lineages of marine fishes: insights from sardines and anchovies and lessons for conservation. The Journal of Heredity 89: 735-748.
Graur, D., & W.H. Li. 2000. Fundamentals of Molecular Evolution. Sinaurer Associates Inc. Sunderland, MA.
Hayata, B. 1908. Flora Montana Formosae. Journal of the College of Science, Imperial University, Tokyo, 25(19): 165-168.
Hayata, B. 1917. General Index to the Flora of Formosa. Bureau of Productive Industries Government of Formosa Taihoku. 48-49.
Hennequin, S., A. Ebihara, M. Ito, K. Iwatsuki, & J. Y. Dubuisson. 2003. Molecular systematic of the fern genus Hymenophyllum s.l. (Hymenophyllaceae) based on chloroplastic coding and noncoding regions. Molecular Phylogenet Evol. 27: 283-301.
Hewitt, G.M. 1996. Some genetic consequences of ice ages, and their role in divergence and speciation. Biological Journal of the Linnean Society 58: 247-276.
Ho, T.N. 1985. A study on the genus Gentiana of China. Acta Phytotax. Sin 23(1): 43-52.
Ho, T.N. 1988. Flora Reipublicae Popularis Sinicae. Tomus 62. Science Press, Beijing. 1-146.
Ho, T.N., & J.S. Pringle. 1995. Gentianaceae. In Editorial Committee, Flora of China, vol 16, Gentianaceae Through Boraginaceae, Science Preee (Beijing) and Missouri Bot. Gard. 1-139.
Huang S.F., S.Y. Huang, J.C. Wang & T.P. Lin. 2004. Phylogeography of Trochodendron aralioodes (Trochodendraceae) in Taiwan and its adjacent areas. Journal of Biogepgraphy. 31: 1251-1259.
Hudson, R.R., M. Slatkin, & W.P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
Jukes, T.H., & D. R. Cantor. 1969. Evolution of protein molecules in Mammalian Protein Metabolism. Edited by H.N. Munro. Academic Press, New York. 21-132
Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Molecular Ecology 16: 111-120.
Kuhner, M.K. 2006. LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics 22: 768-770.
Lande, R., & S. Shannon. 1996. The role of genetic variation in adaptation and population persistence in a changing environment. Evolution 50: 434-437.
Liu, T.S., & C.C. Kuo. 1970. Studies on the Taiwan species of Gentianoideae. Ann. Taiwan Mus. 13: 98-130.
Liu, T.S., & C.C. Kuo. 1974. A taxonomic revision of the species of Gentianaceae in Taiwan. Bull. Exp. Forest N.T.U. 114: 165-216.
Liu, T.S., & C.C. Kuo. 1978. Gentianaceae. In H. L. Li et al. Flora of Taiwan. Epoch. Publ. Co. Taipei. 4: 161-201.
Liu, T. K., Y.G. Chen, W.S. Chen, & S.H. Jiang. 2000. Rats of cooling and denudation of the Early Pengli Orogency, Taiwan, as assessed by fission-track constraints. Tectonophysics 320: 69-82.
Lowe, A., C. Moule, M. Trick, & K. Edwards. 2004. Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theoretical and Applied Genetics. 108: 1103-1112.
Lunt, D.H., W.F. Hutchinson, & G.R. Carvalho. 1999. An efficient method for PCR-based isolation of microsatellite arrays (PIMA). Molecular Ecology. 8: 891-894.
Lynch, M., & B. G. Milligan. 1994. Analysis of population genetics structure with RAPD markers. Mol Ecol 3: 91-99.
Masamune, G. 1943. Miscellaneous notes on the flora of Eastern Asia ⅩⅩⅤ. Trans. Nat. Hist. Soc. Form. 33: 108-111.
Mogensen, H.L. 1996. The hows and whys of cytoplasmic inheritance in seed plants. American Journal of Botany 83: 383–404.
Moritz, C. 1994. Defining “Evolutionarily Significant Units” for conservation. Tree. 9: 373-375.
Moritz, C. 1995. Uses of molecular phylogenies for conservation. Philosophical Transactions: Biological Sciences. 349: 113-118.
Moritz, C. 1999. Conservation units and translocations: strategies for conserving evolutionary process. Hereditas 130: 217-228.
Muschner, V.C., A.P. Lorenz, A.C. Cervi, S.L. Bonatto, T.T. Souza-Chies, F.M. Salzano, & L.B. Freitas. 2003. A first molecular phylogenetic analysis of Passiflora (Passifloraceae). American Journal of Botany 90: 1229-1238.
Nei, M., & F. Tajima. 1983. Maximum likelihood estimation of number of nucleotide substitution from restriction site data. Genetics 105: 207-217.
Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
Nelson, G. & N. Platnick, 1984. Systematics and evolution. In M.-W. Ho and P. T. Saunders (eds), Beyond Neo-Darwinism. An integration to the new evolutionary paradigm. Academic Press, London, 143-158.
O’Conell, M., & J.M. Wright. 1997. Microsatellite DNA in fishes. Reviews in Fish Biology and Fisheries. 7: 331-363.
O’Reilly, P., & J. M. Wright. 1995. The evolving technology of DNA fingerprinting and its application to fisheries and aquaculture. Journal of Fish Biology 47.
Ota, T., & M. Kimura. 1973. A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetic Research 22: 201-204.
Paetkau, D., W. Calvert, I. Stirling, & C. Strobeck. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol 4: 347-354.
Palmer, J.D. 1985. Comparative organization of chloroplast genomes. Annual Review of Genetics. 19: 325-354.
Pritchard, J.K., M. Stephens, & P. Donnelly. 2000. Inference of Population Structure Suing Multilocus Genotype Data. Genetics. 155: 945-959.
Raymond, M., & F. Rousset. 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heridity. 86: 248-249.
Rogers, A.R., & H. C. Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution. 9: 552-569.
Rogers, A.R. 1995. Genetic evidence for a Pleistocene population explosion. Evolution. 49: 608-615.
Rousset, F. 1996. Equilibrium values of measures of population subdivision for stepwise mutation processes. Genetics. 142: 1357-1362.
Rozas, J., J.C. Sanchez-Delbarrio, X. Messenguer, & R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 19: 2496-2497.
Rozen, S., & H.J. Skaletsky. 2000. PRIMER 3.0. In: Krawetz, S., Misener, S. Methods and Protocols: Methods in Molecular Biology. New Jersey: Human Press. 365-386.
Ryder, O.A. 1986. Species conservation and systematic: the dilemma of subspecies. Trends in Ecology and Evolution. 1: 9-10
Schaal, B. A. & K. M. Olsen. 2000. Gene genealogies and population variation in plants. Proceedings of the National Academy of Sciences USA. 97: 7024-7029.
Schneider, S., D. Roessli, & L. Excoffier. 2000. Arlequin ver. 2000: A software for population genetics data analysis. Geneva, Switzerland: University of Geneva.
Slatkin, M. 1985. Rare alleles as indicators of gene flow. Evolution. 39: 53-65.
Suen, T. C., & M. C. Hung. 1990. Multiple cis- and trans-acting elements involved in regulation of the neu gene. Mol Cell Biol 10: 6306-6315.
Tajima, F. 1989. Statistical method for resting the neutral mutation hypothesis by DNA polymorphism. Genetics. 123: 585-595.
Tamura, K., J. Dudley, M. Nei, & S. Kumar. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Molecular Biology and Evolution. 24(8): 1596-1599.
Taylor, R. J., T. F. Patterson, & R. J. Harrod. 1994. Systematics of Mexican Sqruce-Revisited. Systematic Botany 19: 47-59.
Templeton, A. R. 1994. Biodiversity at molecular genetic level: experiences from disparate macroorganisms. In: Hantsworth, D.L. (Ed.), Biodiversity, Measurement and Estimation. Chapman & Hall, The Royal Society, London. 59-64.
Thompson, J.D., T.J. Gibson, F. Plewniak, F. Jeanmougin, & D.G. Higgins. 1997. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 24: 4876-4882.
Werner, O., & J. Guerra. 2004. Molecular Phylogeography of the Moss Tortula muralis Hedw. (Pottiaceae) Based on Chloroplast rps4 Gene Sequence Data. Plant Biology. 6: 147-157.
Wright, S. 1951. The genetic structure of populations. Ann. Eugenics. 15: 323-354.
Wright, S. 1965. The interpretation of population structure by F-stastics with special regard to systems of mating. Evolution. 19: 395-420.
Wright, S. 1978. Evolution and the Genetics of Populations, Vol. 4. Variability Within and Among Natural Populations. Univ. Chicago Press, Chicago.
Yamamoto, Y. 1936. Observation ad floram Formosanam ⅩⅡ. Journal of the Society of Tropical Agriculture. 8: 63-75.
Yeh, F.C., R.C. Yang, & T. Boyle. 1999. POPGENE (version 1.3.1). Microsoft Window-Bases Freeware for Population Genetic Analysis. University of Alberta and the Center for International Forestry Research, Edmonton, AB, Canada. Available at: http://www.ualberta.ca/~fyeh/
Ying, S.S. 1989. Systematic study on Gentianaceae of Taiwan. Quarterly Journal of the Experimental Forest of National Taiwan University. 3(2): 87-111.