臺灣博碩士論文加值系統

摘要
鬼鼠(Bandicota indica)為分布於東南亞最大型的鼠科動物，亦是台灣體型最大的鼠類動物，普遍分布於較低海拔地區，Swinhoe (1870)曾提出鬼鼠可能是1630年荷蘭人殖民時引進台灣的，但是缺乏歷史記載的證據。以遺傳學的角度來看，物種在拓殖到新環境時，應該會受到創立者效應或瓶頸效應的影響而呈現較低的遺傳多樣性。因此透過探討不同地理分布族群的遺傳結構，以及各族群間的分化程度與親緣關係，可追溯物種的演化歷史。本研究選用粒線體核苷酸之控制區域(d-loop)及細胞色素b基因(cytb)的序列建構親緣關係樹，以探討台灣地區鬼鼠的族群遺傳變異，並以基因單型的網狀關係圖以及不相合分布分析檢驗鬼鼠是否具有短期內引進物種的遺傳特性，並檢驗與福建、廣東和越南樣本的親緣關係。控制區域片段序列(700 bp)及細胞色素b基因完整序列(1140 bp)的親緣關係分析可將台灣的樣本分為台灣型與花蓮型兩大群，兩型間遺傳距離遠，族群分化指數高且基因交流指數低，AMOVA分析亦顯示大部分的變異是存在於兩型之間。台灣型在cytb的單型網狀關係圖呈現分支較多的結構，與短期內引進種的情形不太一致。不相合分佈分析中具有族群擴張的現象且未受瓶頸效應影響。此外台灣型與福建的單型具有高度相近的親緣關係，顯示台灣型的鬼鼠可能是從大陸地區拓殖而來。而花蓮型單型在cytb所呈現的高遺傳多樣性指數，可能與多次入侵有關，來源初步可以排除福建、廣東及越南南部等地區。未來應該針對越南北部以及其他東南亞地區進行更多樣本的分析以釐清與花蓮型單型的親緣關係。

Abstract
Bandicota indica is the largest muridae animal distributed in Southeast Asia, and also the biggest rodent generally habitat at lower elevation area in Taiwan. Swinhoe (1870) speculated that this rat had been introduced to Taiwan by the Dutch in the 17th century, but lacking the historical evidence. From the view of the genetics, species colonize a new environment should affect by the founder effect or the bottleneck effect, exhibiting a lower genetic diversity. The evolutionary history of the species could be traced by understand the genetic variations, population divergence and phylogenetic relationships of the populations in different geographical regions. In this study, I used the d-loop region and cytochrome b gene sequences of the mitochondrial DNA to reconstruct the phylogenetic trees in order to understand the population genetic structure of Bandicota indica in Taiwan, and examine the phylogenetic relationships of samples from Fujian, Guangdong, and Vietnam. I used the haplotypes network and mismatch distribution analysis to examine any genetic pattern of the recent introduced species in Bandicota indica. The phylogenetic analysis of the d-loop partial sequence (700 base pairs) and cytochrome b gene complete sequence (1140 base pairs) can separate the Taiwan samples into two groups, Taiwan type and Hualien type. The genetic distance and sequence divergence were high between two types. Most of the variance is between two types in AMOVA analysis and the gene flow was low. The large divergent star-like structure in cytochrome b gene haplotypes network of Taiwan types was not consist with the pattern of recent introduced species. The unimodal displays in mismatch distribution analysis revealed the population expansion of Taiwan types, and closely relationships between Taiwan types and Fujian haplotypes suggest that the rat might have been colonized from mainland. The high genetic diversity of cytochrome b sequences in Hualien types might be resulted from the multiple introduction events. In this study, however, I excluded the Fujian, Guangdong, and Southern Vietnam as the possible origin of the Hualien types. Futher investigation on relationships among populations of Hualien and Northern Vietnam and other regions of Southeast Asia should be conducted in detail with more samples.

目錄
中文摘要‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥Ⅰ
英文摘要‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥Ⅲ
一、前言‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥1
二、材料與方法‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥7
1. 樣本採集‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥7
2. 去氧核糖核苷酸(DNA)分析‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥7
3. 序列片段增幅反應(PCR)及定序‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥8
(1) 控制區域(d-loop) ‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥8
(2) 細胞色素b基因(cytochrome b gene, cytb gene) ‥‥‥‥‥‥‥‥9
4. 序列分析‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥10
(1) 排序(alignment)及定義單型(haplotype) ‥‥‥‥‥‥‥‥‥‥‥10
(2) 繪製親緣關係樹(phylogenetic tree) ‥‥‥‥‥‥‥‥‥‥‥‥10
(3) 核苷酸多樣性、單型多樣性與遺傳變異‥‥‥‥‥‥‥‥‥‥‥11
(4) 單型的網狀結構(haplotype network)‥‥‥‥‥‥‥‥‥‥‥‥12
(5) 不相合分佈分析(mismatch distribution analysis) ‥‥‥‥‥‥‥12
三、 結果‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
1. 序列資料‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
(1) 控制區域片段序列資料‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
(2) 細胞色素b基因序列資料‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥13
2. 分子親緣關係‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥14
(1) 控制區域片段序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥14
(2) 細胞色素b基因序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥15
3. 遺傳變異‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥17
(1) 控制區域片段序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥17
(2) 細胞色素b基因序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥19
4. 單型網狀關係‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥20
(1) 控制區域片段序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥20
(2) 細胞色素b基因序列‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥21
5. 不相合分佈(mismatch distribution) ‥‥‥‥‥‥‥‥‥‥‥‥‥‥22
四、討論‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥24
1. 鬼鼠的親緣地理‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥24
2. 台灣地區鬼鼠之引進的可能性‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥30
五、參考文獻‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥35
六、表目‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥42
七、圖目‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥43
八、表和圖‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥44
九、附錄一‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥62
十、附錄二‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥68
十一、附錄三‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥70
十二、作者資訊‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥‥74

參考文獻
王博優。1970。蔗園野鼠藥劑防除之研究：I、發生消長與食性。台糖研究所研究彙報。
王博優。1977。蔗園鼠類組成之研究。台糖研究所研究彙報。
朱巧雯。2006。台灣地區兩種葉鼻蝠科蝙蝠之遺傳變異。私立東海大學生命科學系碩士論文。
何傳坤、劉克竑、陳浩維。1998。台中縣清水鎮清水遺址調查暨考古發掘報告。行政院文化建設委員會委託，國立自然科學博物館執行。台中。
林良恭。1981。台灣哺乳類研究。私立東海大學生物研究所碩士論文。
茅秀娟。2003。臺灣西南部新化丘陵地區齧齒動物化石牙齒之研究。國立成功大學地球科學系碩士論文。
范雪春、鄭國珍。2006。福建第四紀哺乳動物化石考古發現與研究。科學出版社。北京。
許富雄。1989。台北縣貢寮鄉草生地小黃腹鼠及鬼鼠之族群生態研究。國立台灣大學動物學研究所碩士論文。
張榮祖、金善科、全國強、李思華、葉宗耀、王逢桂、張曼麗。1997。中國哺乳動物分布。中國林業出版社。北京。
張育誠。2007。台灣黑腹絨鼠族群分化之研究。私立東海大學生命科學系碩士論文。
黑田長禮。1940。原色日本哺乳類圖說。三省堂。東京。(日文)
楊尚達。1998。台灣地區小家鼠粒線體控制區序列變異及族群遺傳之研究。國立台灣大學動物學研究所碩士論文。
壽振黃。1964。中國經濟動物志-獸類。科學出版社。北京。
鄭錫奇。1990。鬼鼠之生殖與生態研究。國立台灣大學動物學研究所碩士論文。
鄭維新。2007。台灣地區小黃腹鼠與亞洲家鼠之地理變異及親緣地理學研究。國立嘉義大學生物資源學系研究所碩士論文。
韓德芬、張森水。1978。建德發現的一枚人的犬齒化石及浙江第四紀哺乳動物群新資料。古脊椎動物與古人類。16：255-263。
儲瑞華、曹又仁、莊媛茹、陳皇奇、林曜松、吳海音。2007。台灣地區外來種緬甸小鼠的族群遺傳結構與生物地理起源。特有生物研究。9：1-11。
Allen, G. M. 1938. The Mammals of China and Mongolia. Part 2. The American Museum of Natural History, New York.
Aplin, K. P., P. R. Brown, J. Jacob, C. Krebs, and G. R. Singleton. 2003. Field Methods for Rodent Studies in Asia and the Indo-Pacific. Australian Centre for International Agricultural Research, Canberra, Austalia.
Avise, J. C. 1994. Molecular Markers, Natural History and Evolution. Chapman and Hall, New York.
Avise, J. C. 2000. Phylogeography: the History and Formation of Species. Harvard University Press, London.
Avise, J. C., J. Arnold, J. R. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb, and N. C. Saunders. 1987. Intraspecic phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522.
Capula, M. 1994. Population genetics of a colonizing lizard: loss of genetic variability in introduced populations of Podarcis sicula. Experientia 50: 691-696.
Chen, S. F., S. J. Rossiter, C. G. Faulkes, and G. Jones. 2006. Population genetic structure and demographic history of the endemic Formosan lesser horseshoe bat (Rhinolophus monoceros). Molecular Ecology 15: 1643-1656.

Clement, M., D. Posada, and K. A. Crandall. 2000. TCS: A computer program to estimate gene genealogies. Version 1.21. Molecular Ecology 9: 1657-1659.
Corbet, G. B., and J. E. Hill. 1992. The Mammals of the Indomalayan Region: A Systematic Review. Oxford University Press, Oxford.
Cox, G. W. 2004. Alien Species and Evolution: The Evolutionary Ecology of Exotic Plants, Animals, Microbes and Interacting Native Species. Island Press, Washington, D.C.
Ellerman, J. R., and T. C. S. Morrison-Scott. 1951. Checklist of Palaearctic and Indian Mammals 1758 to 1946. British Museum, London.
Excoffier, L., G. Laval, and S. Schneider. 2005. Arlequin (version 3.0): An integrated software for population genetics data analysis. Evolutionary Bioinformatics Online 1: 47-50.
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 restriction data. Genetics 131: 479-491.
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
Ficetola, G. F., A. Bonin, and C. Miaud. 2008. Population genetics reveals origin and number of founders in a biological invasion. Molecular Ecology 17: 773-782.
Fu, Y.-X., and W.-H. Li. 1993. Statistical tests of neutrality of mutations. Genetics 133: 693-709.
Gaubert, P., J. Godoy, I. delCerro, and F. Palomares. 2009. Early phases of a successful invasion: mitochondrial phylogeography of the common genet (Genetta genetta) within the Mediterranean Basin. Biological Invasions 11: 523-546.

Grant, W., 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.
Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52: 696-704.
Gündüz, İ., J.-C. Auffray, J. Britton-Davidian, J. Catalan, G. Ganem, M. G. Ramalhinho, M. L. Mathias, and J. B. Searle. 2001. Molecular studies on the colonization of the Madeiran archipelago by house mice. Molecular Ecology 10: 2023-2029.
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Research Symposium Series 41:95-98.
Hawley, D. M., D. Hanley, I. J. Lovette, and A. A. Dhondt. 2006. Molecular evidence for a founder effect in invasive house finch (Carpodacus mexicanus) populations experiencing an emergent disease epidemic. Molecular Ecology 15: 263-275
Hingston, M., S. M. Goodman, J. U. Ganzhorn, and S. Sommer. 2005. Reconstruction of the colonization of southern Madagascar by introduced Rattus rattus. Journal of Biogeography 32:1549-1559.
Hudson, R. R., D. D. Boos, and N. L. Kaplan. 1992. A statistical test for detecting geographic subdivision. Molecular Biology and Evolution 9: 138-151.
Kimura, M. 1983. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
Kocher, T. D., W. K. Thomas, A. Meyer, S. V. Edwards, S. Paabo, F. X. Villablanca, and A. C. Wilson. 1989. Dynamics of mitochondrial DNA evolution in mammals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences 86: 6196-6200.

Kolbe, J. J., R. E. Glor, L. R. G. Schettino, A. C. Lara, A. Larson, and J. B. Losos. 2004. Genetic variation increases during biological invasion by a Cuban lizard. Nature 431: 177-181.
Kumar, S., J. Dudley, M. Nei, and K. Tamura. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.
Kuroda, N.1938. A List of the Japanese Mammals. Published by the Author, Tokyo.
Lekagul, B., and J. A. McNeely. 1977. Mammals of Thailand. Association for the Conservation of Wildlife, Bangkok.
Librado, P., and J. Rozas. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Lin, H.-D., K.-C. Hsu, K.-T, Shao, Y.-C. Chang, J.-P. Wang, C.-J. Lin, and T.-Y. Chiang. 2008. Population structure and phylogeography of Aphyocypris kikuchii (Oshima) based on mitochondrial DNA variation. Journal of Fish Biology 72: 2011-2025.
Liu, W, A. Lathrop, J. Fu, D. Yang, and R. W. Murphy. 2000. Phylogeny of east asian bufonids inferred from mitochondrial DNA sequences (Anura: amphibia). Molecular Phylogenetics and Evolution 14: 423-435.
Marshall, J. T. Jr. 1977. Family Muridae: rats and mice. Pp: 397-485. In “Mammals of Thailand”. Lekagul, B. and J. A. McNeely, editors. Association for the Conservation of Wildlife, Bangkok.
Martin, Y., G. Gerlach, C. Schlötterer, and A. Meyer. 2000. Molecular phylogeny of European Muroid rodents based on complete cytochrome b sequences. Molecular Phylogenetics and Evolution 16: 37-47.
Nei, M., T. Maruyama, and R. Chakraborty. 1975. The bottleneck effect and genetic variability in population. Evolution 29: 1-10.

Oshida, T., L. K. Lin, R. Masuda, and M. C. Yoshida. 2000. Phylogenetic relationships among Asian species of Petaurista (Rodentia, Sciuridae), inferred from mitochondrial cytochrome b gene sequences. Zoological Science 17: 123-128.
Oshida, T., K. Ikeda, K. Yamada, and R. Masuda. 2001. Phylogeography of the Japanese giant flying squirrel, Petaurista leucogenys, based on mitochondrial DNA control region sequences. Zoological Science 18: 107-114.
Oshida, T., L. K. Lee, L. K. Lin, and Y. J. Chen. 2006. Phylogeography of Pallas’s saquirrel in Taiwan: geographical isolation in an arboreal small mammal. Journal of Mammalogy 87: 247-254.
Posada, D., and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 917-818.
Posada, D., and K. A. Crandall. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends in Ecology and Evolution 16: 37-45.
Rogers, A. R. 1995. Genetic evidence for a Pleistocene population explosion. Evolution 49: 608-615.
Rogers, A. R., and H. C. Harpending. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution 9: 552-569.
Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
Shimada, T., K. P. Aplin, T. Joghara, L.-K. Lin, V. Herbreteau, J.-P. Gonzalez, and H. Suzuki. 2007. Complex phylogeographic structuring in a continental small mammal from East Asia, the rice field mouse, Mus caroli (Rodentia, Muridae). Mammal Study 32: 49-62.
Swinhoe, R. 1870. Catalogue of the mammals of China (south of the River Yangtsze) and of the island of Formosa. Proceedings of the Scientific Meetings of Zoological Society of London 1870:615-673.

Tajima, E. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
Toda, M., M. Nishida, M. Matsui, K. Y. Lue, and H. Ota. 1998. Genetic variation in the Indian rice frog, Rana limnocharis (Amphibia: Anura) in Taiwan, as revealed by allozyme data. Herpetologica 54: 73-82.
Tokuda, M. 1941. A revised monograph of the Japanese and Manchou-Korean Muridae. Biogeographica 4: 1-155.
Valiente, A. G., F. Juanes, P. Nunẽz, and E. Garcia-Vazquez. 2007. Is genetic variability so important? Non-native salmonids in South America. Journal of Fish Biology 71:1–12
Wilson, D. E., and D. M. Reeder. 2005. Mammal Species of the World: A Taxonomic and Geographic Reference. Third edition. The Johns Hopkins University Press, Baltimore.
Xia, X., and Z. Xie. 2001. DAMBE: Data analysis in molecular biology and evoluiton. Journal of Heredity 92: 371-373.
Yuan, S. L., L. K. Lin, and T. Oshida. 2006. Phylogeography of the mole-shrew (Anourosorex yamashinai) in Taiwan: implications of interglacial refugia in a high-elevation small mammal. Molecular Ecology 15: 2119-2130.
Zou, F., H. C. Lim, B. D. Marks, R. G. Moyle, and F. H. Sheldon. 2007. Molecular phylogenetic analysis of the Grey-cheeked Fulvetta (Alcippe morrisonia) of China and Indochina: A case of remarkable genetic divergence in a "species". Molecular Phylogenetics and Evolution 44: 165-174.