臺灣博碩士論文加值系統

本研究以分子特徵來探討煙管蝸科的膨腹煙管蝸Hemiphaedusa ventriosa (Schmacker & Boettger, 1891) 的分類地位與親緣地理學。本研究採集恆春半島17個樣點，共定序171隻膨腹煙管蝸，以粒線體DNA中的16S 核糖體RNA (16S rRNA) 之基因片段為遺傳標記，重建出單倍型 (haplotype) 的親緣關係樹。本研究結果顯示曾與膨腹煙管蝸視為同一種的白口煙管蝸Hemiphaedusa similaris (Adams, 1867) 屬於不同分支。此外，不同地區的膨腹煙管蝸在殼形上雖然有變異，但是從親緣樹來看仍然歸類在同一類群，因此確立了膨腹煙管蝸屬於獨立物種的地位。族群遺傳結構的分析顯示整體遺傳歧異度 (Hd值、π值) 都屬於偏高的數值，顯示膨腹煙管蝸有大且穩定的族群並擁有久遠的演化歷史，或是具有高度分歧之族群二次接觸後，造成譜系混雜的結果。由AMOVA分析結果顯示，膨腹煙管蝸族群有高度遺傳分化，推究其原因可能是物種本身較低的擴散能力以及地理隔離，使得族群間缺乏基因交流，造成較高的遺傳分化現象。在族群變動分析中，Tajima’s D中性假說測試結果顯示族群沒有受到選汰的影響，也沒有經歷族群擴張；而核苷酸變異分佈檢測結果顯示膨腹煙管蝸A、B兩大群曾經歷族群擴張。總結而論，膨腹煙管蝸族群擁有高度遺傳分化，形成A、B兩大族群，在應用上可以作為許多領域的基礎研究，像是生物學、保育遺傳學或是地質學等等。

The taxonomy and phylogeography of the clausilid land snail Hemiphaedusa ventriosa (Schmacker & Boettger, 1891) were studied by using molecular characteristics. Sequences of mtDNA 16S rRNA were examined from 171 individuals collected from 17 locations in Hengchun Peninsula as one molecular marker to build the phylogenetic trees of haplotypes showing that H. ventriosa differs from H. similaris (Adams, 1867), which were considered to be the same species. Hemiphaedusa ventriosa, along with geographical variations on shell morphology, are clustered on single clade. Therefore, we can identify H. ventriosa is an independent species. In addition, population genetic structure analysis shows high overall genetic diversities (Hd, π) indicating it is a large stable population with long evolutionary history or secondary contact between differentiated lineages. The result of AMOVA shows the existence of high genetic divergence among populations, which may be caused by the lack of gene flow resulted from weak mobility of the land snail or geographic isolation. The analyses of Tajima’s D and mismatch distribution show inconsistency on historic population expansion. Overall, populations of H. ventriosa have high divergence and differentiate into two groups. In applications, this research could offer the base information for other research areas like biology, conservation genetics or geology.

謝誌 I
第一章 前言 3
1.1研究物種介紹 3
1.1.1分類階層和簡介 3
1.1.2分類問題與歷史 4
1.2親緣地理學 5
1.3破碎化理論 7
1.4恆春半島的地形地貌 7
1.4.1簡介 7
1.4.2地形破碎化 9
1.5粒線體DNA與分子演化 11
1.6研究方向 12
第二章 材料與方法 13
2.1採樣 13
2.2純化及擴增DNA片段 13
2.2.1純化DNA 13
2.2.2擴增DNA片段-聚合酶連鎖反應 (PCR) 14
2.3資料分析 16
2.3.1序列整理 16
2.3.2親緣關係分析 16
2.3.3族群遺傳結構分析 18
2.3.4族群遺傳分析 19
2.3.5族群變動分析 19
第三章 結果 21
3.1親緣地理關係重建 21
3.2核苷酸組成分析 22
3.3族群內遺傳變異分析 22
3.4族群間遺傳變異分析 23
3.5族群變動分析 26
第四章 討論 27
4.1膨腹煙管蝸的親緣關係 27
4.1.1以分子角度看分類問題 27
4.1.2探討地理上膨腹煙管蝸族群間的親緣關係 29
4.2膨腹煙管蝸的遺傳結構與變異 31
4.3膨腹煙管蝸的族群分化與變動歷史 32
4.4 延伸應用 33
第五章 結論 34
第六章 參考文獻 35
第七章 圖與表 41

王鑫，(1992)。墾丁國家公園地形景觀簡介。內政部營建署員工消費合作社。
李光周，王　鑫，黃增泉，林曜松，楊榮宗。(1985)。墾丁國家公園史前文化及生態資源 屏東縣春鄉：墾丁國家公園管理處。
陳文山，李偉彰，黃能偉，顏一勤，楊志成，楊小青，陳勇全，宋時驊。(2005)。恆春半島增積岩體的構造與地層特性：全新世恆春斷層的活動性. 西太平洋地質科學 50：129-154.
陳芊蓉，(2013)。班卡拉蝸牛(腹足綱：南亞蝸牛科)的親緣地理學。(碩士論文)，大葉大學。
陳盈先，(2014)。細葉山螞蝗親緣地理。(碩士論文)，國立台南大學生態科學與技術學系環境生態碩士班。
陳盈蓉。(2007)。褐樹蛙(Buergeria robusta)的親緣地理學研究。(碩士論文)，國立臺灣師範大學。
陳慶昌，嚴明鉦，王世宇，(2007)，台灣與東亞之夏季季風降雨變化。大氣科學，35(4)：305-352。
維基百科編者。(2016)。臺灣清治時期。維基百科，自由的百科全書：https://zh.wikipedia.org/w/index.php?title=%E8%87%BA%E7%81%A3%E6%B8%85%E6%B2%BB%E6%99%82%E6%9C%9F&oldid=40202102
謝伯娟，黃重期，吳書平。(2006)。台灣蝸牛圖鑑。台北：行政院農業委員會林務局。
Avise, J. C. (2009). Phylogeography: retrospect and prospect. Journal of Biogeography, 36(1): 3-15.
Bermingham, E., and Moritz, C. (1998). Comparative phylogeography: concepts and applications. Molecular Ecology, 7(4): 367-369.
Brown, W. M., George, M., and Wilson, A. C. (1979). Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences, 76(4): 1967-1971.
Brown, W. M., Prager, E. W., Wang, A., and Wilson, A. C. (1982). Mitochondrial DNA sequences of primates: Tempo and mode of evolution. Journal of Molecular Evolution, 18:225-239.
Bouchet P. and Rocroi, J. P. (2005). Classification and nomenclator of gastropod families. Malacologia, 47(1-2):1-397.
Czech B., K. P. R., and Devers, P. K. (2000). Economic associations among causes of species endangerment in the United States. BioScience, 50: 593-601.
Cox, C. B., and Moore, P. D. (2005). Biogeography: An Ecological and Evolutionary Approach, 7th ed. Blackwell, Oxford.
Excoffier, L., and Lischer, H. E. L. (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10: 564-567.
Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 9(4):783-791.
Frankham, R., Ballou, J. D., and Briscoe, D. A. (2010). Introduction to Conservation Genetics, Cambridge University Press, New York.
Fu, Y. X. (1997). Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147(2): 915-925.
Grant, W.S. and Bowen, B.W. (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.
Graur, D., and Li, W. H. ( 2000). Fundamentals of Molecular Evolution. 2nd ed. Sunderland: MA.
Hall, T. A. (1999). BioEdit: A user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
Hillis, D. M., C. Moritz, and Mable, B. K. (1996). Molecular Systematics. USA: Sinauer Associates.
Hwang, C.-C., Chen, M.-C., and Ger, M.-J. (2016). Taxonomy of Hemiphaedusa similaris Adams, 1867 (Gastropoda: Clausiliidae) from southern Taiwan. Bulletin of Malacology, Taiwan, 39: 13.
Futuyma, D. J. (1998). Evolutionary Biology. Sunderland, MA.: Sinauer.
Posada, D., and Crandall, K. A. (1998). Modeltest: testing the model of DNA substitution. Bioinformatics, 149: 817-818.
Palumbi, S.R., Martin, A., Romano, S., McMillan, W.O., Stice, L., and Grabowski, G. (1991) The Simple Fool's Guide to PCR, Version 2. University of Hawaii Zoology Department, Honolulu.
Kameda, Y., Kawakita, A., and Kato, M. (2007). Cryptic genetic divergence and associated morphological differentiation in the arboreal land snail Satsuma (Luchuhadra) largillierti (Camaenidae) endemic to the Ryukyu Archipelago, Japan. Molecular Phylogenetics and Evolution, 45: 519-533.
Kimura, M. (1968). Genetic variability maintained in a finite population due to mutational production of neutral and nearly neutral isoalleles. Genetics Research, 11(03): 247-270.
Kimura, M. (1980). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16:111-120.
Kumar, S., Stecher, G., and Tamura, k. (2015). MEGA7: Molecular Evolutionary Genetics Analysis version 7.0. Molecular Biology and Evolution.
Librado, P., and Rozas., J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25: 1451-1452.
Nei, M. (1987). Molecular Evolutionary Genetics. New York: Columbia University Press.
Nei, M., Tajima, F., and Tateno, Y. (1983). Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data. Journal of Molecular Evolution, 19(2):153-70.
Neiber, M. T., and Hausdorf, B. (2015). Phylogeography of the land snail genus Circassina (Gastropoda: Hygromiidae) implies multiple Pleistocene refugia in the western Caucasus region. Molecular Phylogenetics and Evolution, 93: 129-142.
Ouborg, N. J., Piquot, Y., and van Groenendael, J. M. (1999). Population genetics, molecular markers and the study of dispersal in plants. Journal of Ecology, 87(4): 551-568.
Palumbi, S. R. (1996) Nucleic acids II: the polymerase chain reaction. In:
Molecular Systematics, 2nd ed., Hillis, D.M., C. Moritz, B.K. Mable (eds.) Pp. 205-247. Sunderland, MA: Sinauer Associates Inc. Bouchet P. and Rocroi, J. P. (2005). Classification and nomenclator of gastropod families. Malacologia, 47(1-2): 1-397.
Pfenninger, M., and Posada, D. (2002). Phylogeographic history of the land
snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution, 56: 1776-1788.
Rogers, A. R., and Harpending, H. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9: 552-569.
Ronquist, F., Teslenko, M,. van der Mark P., Ayres, DL., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, MA., and Huelsenbeck, JP. (2012). MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3): 539-542.
Saitou, N., and Nei., M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4: 406-425.
Shimizu, Y., and Ueshima, R. (2000). Historical biogeography and interspecific mtDNA introgression in Euhadra peliomphala (the Japanese land snail). Heredity, 85: 84-96.
Slatkin, M., and Hudson, R. R. (1991). Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics, 129(2): 555-562.
Swofford, D. L. (2002). Phylogenetic analysis using parsimony (* and other methods). Version 4. Sunderland, MA: Sinauer Associates.
Tajima, F. (1989). Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123(3): 585-595.
Thompson, J. D., Higgins, D. G., and Gibson., T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22: 4673-4680.
Truett, G. E., Heeger, P., Mynatt, R. L., Truett, A. A., Walker, J. A., and Warman, M. L. (2000).Preparation of PCR-quality mouse genomic DNA with hot sodium hydroxide and tris (HotSHOT).
Wright, S. (1965). The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution, 19: 395-420.
Xia, X., and Xie, Z. (2001). DAMBE: Data analysis in molecular biology and evolution. Journal of Heredity, 92: 371-373.