| 研究生: |
陳怡雁 Chen, Yi-Yen |
|---|---|
| 論文名稱: |
鈴木草屬(唇形科),台灣及琉球特有屬,之親緣地理學研究 Phylogeography of Suzukia (Lamiaceae),a Genus Endemic to Taiwan and Ryukyus |
| 指導教授: |
蔣鎮宇
Chiang, Tzen-Yuh |
| 學位類別: |
碩士 Master |
| 系所名稱: |
生物科學與科技學院 - 生物學系 Department of Biology |
| 論文出版年: | 2004 |
| 畢業學年度: | 92 |
| 語文別: | 中文 |
| 論文頁數: | 67 |
| 中文關鍵詞: | 族群遺傳 、嶼那國島 、鈴木草 、親緣地理 |
| 外文關鍵詞: | Suzukia, phylogeography, yonaguni, G3PDH, population structure, trnD-T |
| 相關次數: | 點閱:128 下載:1 |
| 分享至: |
| 查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
鈴木草屬在分類地位上為唇形科(Lamiaceae),屬東亞特有植物,僅分佈於台灣及日本琉球群島,為多年生草本,具匍匐莖,葉寬卵形,粗鋸齒緣,腋生疏散總狀花序,密被腺毛,唇瓣花,色紫豔,具蜜腺,蜜蜂等昆蟲為其主要之傳粉媒介;全世界一屬兩種,目前被世界保育組織IUCN (The world conservation union)列為瀕臨滅絕之稀有植物。本研究以葉綠體 DNA 之trnD-trnT 基因間之
非轉譯區間(non-coding spacer)片段與合成甘油三磷酸脫氫酵素 G3PDH(glyceraldehyde-3-phosphate dehydrogenase) 基因片段為遺傳標示物來探討鈴木草屬間的親緣地理關係。根據兩遺傳標示物之結果顯示,鈴木草屬具高的遺傳歧異度;在葉綠體DNA 所建構之親緣演化樹狀圖中,鑑定出兩演化支系,其中一支系包含大部分的台灣鈴木草族群,而另一支系則由所有的琉球鈴木草族群及台灣鈴木草的金馬隧道族群組成,然而細胞核DNA 演化樹狀圖中金馬隧
道族群與其他台灣鈴木草族群群聚,顯現金馬隧道族群可能為以琉球鈴木草為母系,以台灣鈴木草為父系起源之種間雜交。台灣鈴木草因海拔環境差異分成山系族群與沿海族群,此二族群顯示高度遺傳分化;相對地,嶼那國島之琉球鈴木草族群間則具頻繁基因交流,但族群間不符合isolation-by-distance 模式。根據葉綠體DNA 所構築的親緣網狀圖(minimum spanning network)顯示嶼那國
島琉球鈴木草族群與台灣鈴木草之低海拔族群擁有較古老祖先型,依據分子時鐘(molecular clock)推估,分布於低海拔的台灣鈴木草與琉球鈴木草之共同祖先,於距今約一百一十萬年前分別進入琉球群島及台灣後分歧並種化。台灣鈴木草的種化伴隨族群向高海拔地區之輻射適應,而造成山系與海系之族群分化。綠島之琉球鈴木草的拓殖約發生在距今九十三萬年前。相對於葉綠體DNA顯現台灣鈴木草與琉球鈴木草為二個單系群(金馬隧道族群除外),G3PDH 基因
片段因受制衡性選擇(balancing selection)影響,種及族群皆程現paraphyly,此外,台灣鈴木草、綠島之琉球鈴木草及嶼那國島之琉球鈴木草之異基因合子(heterozygote)比例各為0.8、0、0.2。
Suzukia Kudo, a genus of the Lamiaceae with two species, is endemic to Taiwan (S.shikikunensis Kudo) and the Ryukyu Islands (S. luchuensis Kudo). Plants of Suzukia are perennial herbs, with long-creeping stems. Inflorescences of short or elongated racemes possess showy flowers that attract pollinators, mostly honey bee, to visit. Due to its limited population number and size, Suzukia has been listed as an endangered taxon by IUCN. In
this study, we investigated the genetic structure and hylogeographic pattern of the genus Suzukia based on the sequences of the trnD-trnT noncoding spacer of the chloroplast DNA and G3PDH (glyceraldehyde-3-phosphate dehydrogenase) gne of the nuclear DNA. In both genes high levels of genetic diversity were detected in Suzukia. Chloroplast DNA genealogy identified two lineages, one exclusively consisting of most populations of S.shikikunensis, while the other containing S. luchuensis and the Chinma population of S.shikikunensis. Nevertheless, the Chinma population is phylogenetically close to S.shikikunensis in the nuclear DNA phylogeny, indicating a hybrid origin of this population.In S. shikikunensis, populations of mountain areas were significantly differentiated from the coastal populations of Taiwan. In contrast, there existed frequent gene flow between subpopulations of Yonaguni Island. In the cpDNA minimum spanning network, coastal populations of S. shikikunensis and S. luchuensis possessed ancestral polymorphisms.Based on a molecular clock, splitting from a hypothetical common distributed at low elevations may have occurred about 1.1 million years ago. Speciation followed in Taiwan and Ryukyus, respectively. Coupled with peciation, adaptive radiation to middle and high
elevations may have led to high levels of genetic diversity in S. shikikunensis. The colonization of S. luchuensis in Green Island was dated to 0.93 million years ago. In contrast to chloroplast DNA data, G3PDH gene represent paraphyly of species and populations of the both species due to effects of balancing selection. In addition, the heterozygote ratio of S. shikikunensis, S. luchuensis in Green Island and in Yonaguni were 0.8, 0 and 0.2, respectively。
Avise, J. C. (1994). Molecular Markers, Natural History and Evolution. New York.
Avise, J. C. (1998). "The history and purview of phylogeography: a personal reflection."
Molecular Ecology 7(4): 371-379.
Avise, J. C. (2000). Phylogeography: The History and Formation of Species.
Massachusetts London, Harvard University Press.
Avise, J. C., R. M. Arnold, Ball E. Bermingham, T. Lamb, E. Neigel, C. A. Reeb and N. C.
Saunder (1987). "Instraspecific phylogeography : the mitochondrial DNA bridge
between population genetics and systematics." Annual Review Ecology Systematic
18: 489-522.
Barry, C. C. and P. D. Moore (2000). Biogeography. London, Blackwell Science.
Bush, M. B. and R. J. Whittaker (1993). "Non-equilibration in island theory of Krakatau."
Journal of Biogeography 20: 453-457.
Byrne, M. and G. F. Moran (1994). "Population divergence in chloroplast genome of
Eucalyptus nitens." Heredity 73: 18-28.
Byrne, R. (1980). Man and the variable vulnerability of island life-A study of recent
vegetation change in the Bahamas. Washington D. C., Smithsonian Institution.
Case, T. J., D. T. Bolger and A. D. Richman (1992). Reptilian extinctions: the last ten
thousand years, Chapman and Hall, New York.
Chiang, T. Y., Y. C. Chiang, Y. J. Chen, C. H. Chou, S. Havanond and T. N. Hong (2001).
"Phylogeography of kandelia candel in East Asiatic mangroves based on nucleotide
variation of chloroplast and mitochondrial DNAs." Molecular Ecology 10:
2697-2710.
Chiang, Y. C., B. A. Schaal, X. J. Ge and T. Y. Chiang (2004). "Range expansion leading to
departures from neutrality in the nonsymviotic hemoglobin gene and the cpDNA
trnL-trnF intergenic spacer in Trema dielsiana (Ulmaceae)." Molecular
Phylogeny and Evolution 31: 929-942.
Crawford, D., E. Ruiz, T. Tepe, P. Aqeveque and F. Gonzalez (2001). "Allozyme diversity
in endemic flowering plant species of the Juan Fernandez Archipelago, Chile:
ecological and historical factors with implications for conservation." American
Journal of Botany 88: 2156-2203.
Cruzan, M. B., M. L. Arnold, S. E. Carney, K. R. Wollenberg, M. L. Arnold, S. E. Carney
and K. R. Wollenberg (1993). "CpDNA ingeritance in interspecific crosses and irs
effect on evolutionary inference in Louisiana irises." American Journal of Botany
80: 344.
42
Demesure, B., N. Sodzi and R. J. Petit (1995). "A set of universal primers for amplification
of popumorphic non-coding regions of mitochondrial and chloroplast DNA in
plants." Molecular Ecology 4: 129-131.
Doyle, J. L. and K. L. Doyle (1987). "A rapid DNA isolation procedure for small quantities
of fresh leaf tissue." Phytochem. Bull. 19: 11-15.
Excoffier, L. and 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., P. E. Smouse and J. M. Quattro (1992). "Analysis of molecular variance
inferred from metric distances among DNA haplotypes: application to human
mitochondrial DNA data." Genetics 131: 479-491.
Felsnstein, J. (1985). "Confidence limits on phylogenies: an approach using the bootstrap."
Evolution 39: 783-791.
Frankham, R. (1997). "Do island populations gave less genetic variation than mainland
populations." Heredity 78: 311-327.
Frankham, R. and D. A. Briscoe (2002). Introduction to conservation genetics. New York,
Cambridge.
Futuyma, D. J. (1986). Evolutionary Biology. Sunderland, Sinauer.
Ge, X. J., Y. C. Chiang, C. H. Chou and T. Y. Chiang (2002). "Nested clade analysis of
Dunnia sinensis (Rubiaceae), a monotypic genus from China based on organelle
DNA sequence." Consevation genetics 3: 351-362.
Grant, W. A. and B. W. Bowen (1998). "Shallow population histories in deep evolutionary
lineages of marine fishes: insights from sardines and anchovies and lessons for
conservation." Journal of Heredity 89: 415-426.
Hamrick, J. L. and M. J. W. Godt (1989). Allozyme diversity in plant species. Sunderland,
Sinauer.
Hare, M. P. (2001). "Prospects for nuclear gene phylogeography." Trends in Ecology &
Evolution 16(12): 700-706.
Hellis, D. M. and J. J. Bull (1993). "An empirical test of bootstrapping as a method
assessing confidence in phylogenetic analysis." Systmatic Biology 41(187-192).
Hillis, D. M., C. Moritz and B. K. Mable (1996). Molecular systematics, 2nd Edn. Sinauer,
Sunderland.
Hsieh, T.-H. (2000). "Suzukia Kudo (Lamiaceae) in Taiwan." Taiwania 45(3): 217-225.
Huang, S., Y. C. Chiang, B. A. Schaal, C. H. Chou and T. Y. Chiang (2001). "Organelle
DNAs phylogeography of Cycas taitungensis, a relict species in Taiwan."
Molecular Ecology 11: 2669-2682.
Hudson, R. R. (1998). "Island models and the coalescent process." Molecular Ecology 7(4):
43
413-418.
Kimura, M. (1980). "Asimple method for estimation evolutionary rates of base
substitutions through comparative studies of nucleotide sequences." Journal of
Molecular Evolution 16: 111-120.
Kimura, M. (1983). The neutral theory of molecular evolution. Cambridge, Cambridge
University Press.
Kimura, M. (1996). "Quaternary paleogeography of the Ryukyu Arc." Journal of
Geography 105: 259-295.
Kizaki, K. and I. Oshiro (1977). "Paleogeography of the Ryukyu Islands." Marine Science
Monthly 9: 542-549.
Krauss, S. L. (1994). "Restricted gene flow within the morphologically complex species
Persoonia mollis (Proteaceae) : contrasting evidence from the mation system and
pollen dispersal." Heredity 73: 142-154.
Kudo (1930). "Materials for a Flora of Formosa. I." Journal Society Tropical Agriculture 2:
145-146.
Kumar, S., K. , I. B. Tamura, Jakobsen and M. Nei (2001). MEGA2: Molecular
Evolutionary Genetics Analysis software, Bioinformatics.
Li, W. H. (1997). Molecular Evolution, Sunderland, MA.
Li, W. H. (2000). Fundamentals of Molecular Evolution. Sunderland, Sinauer Associates,
Inc.
Lu, S. Y., K. H. Hong, S. L. Liu, Y. P. Cheng, W. L. Wu and T. Y. Chiang (2002). "Genetic
variation and population differentiation of Michelia formosana (Magnoliaceae)
based on cpDNA variation and RAPD fingerprints: relevance to post-Pleistocene
recolonization." Journal of Plant Research 115(1119): 203-216.
Lu, S. Y., C. I. Peng, Y. P. Cheng, K. H. Hong and T. Y. Chiang (2001). "Chloroplast DNA
phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of
Taiwan." Genome 44(5): 797-807.
MacArthur, R. H. and E. O. Wilson (1972). Geogrphical Ecology-Pattern in the
distribution of species., Princeton University Press.
MacIntyre, R. J. (1985). Molecular evolutionary genetics. New York, Plenum Press.
Maki, M., T. yamashiro and S. Matsumura (2003). "High levels of genetic diversity in
island populations of the island endemic Suzukia luchuensis (Labiatae)." Heredity
91: 300-306.
Malcolm, L. and J. Hunter (2002). Fundamentals of Conservation Biology. Orono,
Blackwell.
Maskas, S. D. and M. B. Cruzan (2000). "Patterns of intraspecific diversification in the
Piriqueta caroliniana complex in southeastern North America and the Bahamas."
44
Evolution 54: 815-827.
Moritz, C. (1994). "Defining evolutionary significant units for conservation." Trends of
Ecology and Evolution 9: 373-375.
Moritz, C. and P. Bermingham (1998). "Comparative phylogeography: concepts and
applications." Molecular Ecology 7: 367-370.
Nei, M. and F. Tajima (1983). "Maximum likelihood estimation of number of nucleotide
substitution from restriction site data." Genetics 105: 207-217.
Ohsawa, T. A. (1997). In evolution and diversification of land plants., Springer.
Olsen, K. M. (2002). "Population history of Manihot esculenta (Euphorbiaceae) inferred
from nuclear DNA sequences." Molecular Ecology 11(5): 901-911.
Olsen, K. M. and B. A. Schaal (1999). "Evidence on the origin of cassava: Phylogeography
of Manihot esculenta." Proceedings of the National Academy of Sciences of the
United States of America 96(10): 5586-5591.
Ota, H. (1998). "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 40(2):
189-204.
Ouborg, N. J., Y. Piquot and J. M. V. Groenendael (1999). "Population genetics, molecular
markers and the study of dispersal in plants." Journal of Ecology 87: 551-568.
Posada, D., K. A. Crandall and A. R. Templetion (2000). "Geodis: a program for the
cladistic nested analysis of the geographical distribution of genetic haplotypes."
Molecular Ecology 9: 487-488.
Posada, K. and K. Crandall (1998). "Modeltest: testing the model of DNA substitution."
Bioinformatics 14: 817-818.
Rauscher, J. T. (2002). "Molecular phylogenetics of the Espeletia complex (Asteraceae):
evidence from nrDNA ITS sequence on the closest relatives of an Andean adaptive
radiation." American Journal of Botany 7: 1074-1084.
Rosenberg, M. S. and S. Kumer (2003). "Heterogeneity of Nucleotide Frequencies Among
Evolutionary Lineages and Phylogenetic Inference." Molecular Biology and
Evolution 20(4): 610-621.
Rozas, J. and R. Rozas (1999). "DnaSP version 3.0: an integrated program for molecular
population genetics and molecular evolution analysis." Bioinformatics 15: 174-175.
Saitou, N., and M. Nei (1987). "The neighbor-joining method: a new method for
reconstructing phylogenetic trees." Molecular Biology and Evolution 4: 406-425.
Sanchez-Baracaldo, P. (2004). "Phyogeentics and biogeography of the neotropical fern
genera Jamesonia and Eriosorus (Pteridaceae)." American Journal of Botany 91:
274-284.
45
Schaal, B. A., D. A. Hayworth, K. M. Olsen, J. T. Rauscher and W. A. Smith (1998).
"Phylogeographic studies in plants: problems and prospects." Molecular Ecology
7(4): 465-474.
Slatkin, M. (1985). "Gene flow in natural populations." Annual Review of Ecology,
Evolution and Sysmatics 16: 394-430.
Smith, F. D. M., R. M. May, R. Pellew, T. H. Johnson and K. R. Walter (1993). " How
much do we know about the
current extinction rate?" Trends of Ecology and Evolution 8(extinction of the endemic
Hawaiian avifauna): 375-378.
Stuessy, T. F. (1998). Evolution and Speciation of Island Plants., Cambridge University
Press: Cambridge.
Tajima, F. (1989). "DNA polymorphism in a subdivided population: the expected number
of segregating sites in the two-subpopulation model." Genetics 122: 957-966.
Takahata, N. (1989). "Gene genealogy in three related populations: consistency probablity
between gene and population trees." Genetics 146: 427-441.
Templeton, A. R. (1998). "Nested clade analyses of phylogeographic data: testing
hypotheses about gene flow and population history." Molecular Ecology 7(4):
381-397.
Templeton, A. R. (2004). "Statistical phylogeography: methods of evaluating and
minimizing inference errors." Molecular Ecology 10: 1-21.
Templeton, A. R., E. Routman and C. A. Phillips (1995). "Separating population structure
from population history: a cladistic analyses of the geographical distribution of
mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrnium."
Genetics 140: 767-782.
Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin and D. G. Higgins (1997). "The
clustal X windows interface: flexible strategies for multiple sequence alignment
aided by quality analysis tools." Nuclear Acid Research 24: 4876-4882.
Wang, W. P., C. Y. Hwang, T. P. Lin and S. Y. Hwang (2003). "Historical biogeography and
phylogenetic relationships of the genus Chamaecyparis (Cupressaceae) inferred
from chloroplast DNA polymorphism." Plant Systematics and Evolution 241:
13-28.
Wen, J. (1999). "Evolution of eastern asian and eastern north american disjunct
distributions in flowering plants." Annual Review of Ecology, Evolution and
Sysmatics 30: 421-455.
Whittaker, R. J. (1998). Island biogeography : Ecology, Evolution and Conservation. New
York, Oxford University Press.
Wright, S. (1931). "Evolution in Mendelian populations." Genetics 28: 114-138.
46
Wright, S. (1943). "Isolation by distance." Genetics 16: 114-138.
Wright, S. (1978). Evolution and genetics of populations. Chicago, University of Chicago
press.
Wu, W. L., B. A. Schaal, C. Y. Hwang, M. D. Hwang, Y. C. Chiang and T. Y. Chiang
(2003). "Characterization and adaptive evolution of alpha-tubulin genes in the
Miscanthus sinensis complex (Poaceae)." American Journal of Botany 90(10):
1513-1521.
Yeh, F. C., J. Shl, R. Yang, J. Hong and Z. Ye (1994). "Genetic diversity and multilocus
associations in Cunninghamia lanceolata (Lamb.)." Theory Application Genetics 88:
465-471.
Zuckerkandl, E. and L. Poauling (1965). Evolutionary divergence and convergence in
protein. In Evolving genes and proteins. New York, Academic Press.