高原鼠兔（Ochotona curzoniae）是兔形目、鼠兔科，為青藏高原特有種，廣泛分佈於海拔3,000-5,200公尺的高原草原與高原荒漠區。本研究利用粒線體細胞色素b序列，分析高原鼠兔在青藏鐵路沿線之族群結構，並探討鐵路是否對兩側族群之基因交流造成屏障效應。野外採樣於2009年及2010年8月，在西大灘、崑崙山口、可可西里二號橋、風火山隧道及沱沱河等地區之10個採樣點，共捕獲29隻個體。定序結果共有26個單倍基因型，細胞色素b序列平均長度1,190 bp，有68個變異位，平均遺傳距離1.7%。鐵路同側族群間基因固定係數（Fst）和基因交流係數（Nm）分別為0.299及3.136；異側族群間基因固定係數和基因交流係數分別為0.799及0.139。親緣關係樹及TCS圖皆呈現2個主要系群，系群分佈與地理位置大致相關，分別為鐵路西側群及鐵路東側群。在族群遺傳的分析中顯示，鐵路異側族群間呈現顯著的遺傳分化，同側族群則無。由於鐵路異側族群間的地理距離遠小於同側族群間的距離，因此其分化模式與距離隔離理論（isolation by distance）不符，推測青藏鐵路可能對鐵路兩側的高原鼠兔族群形成屏障效應，並導致兩側族群間基因交流降低而產生遺傳分化，且此遺傳分化的程度預期將隨著隔離的時間拉長而增加。

Plateau pika (Ochotonidae: Ochotona curzoniae) is widespread in Qinghai-Tibetan Plateau (QTP). It is endemic to QTP and restricted to high altitude area, ranging from 3,000 to 5,200 m above sea level. In this study, I examined the genetic structure of O. curzoniae along the Qinghai-Tibetan Railway (QTR) using mitochondrial cytochrome b sequences, and investigated whether QTR had become a barrier of gene flow to populations of O. curzoniae on its two sides. In total, I found 26 haplotypes of cyt b sequences from 29 individuals, of which the mean length was 1,190 bp including 68 informative sites, and the mean genetic distance was 1.7%. Two major clades were revealed in phylogenetic trees as well as TCS haplotype network. In general, the relative positions of haplotypes in the clades were corresponded to their geographic distribution. Most haplotypes of clade I were from east side, while all the haplotypes of clade II were from west side of QTR. Significant population differentiation was revealed between populations from the opposite sides of QTR, but not the same side. Due to the far smaller geographical distances between sampling sites between opposite sides than those of the same side, the differentiation pattern was not consistent with the theory of isolation by distance. Therefore, QTR might have resulted as a barrier to gene flow between populations of O. curzoniae living on opposite sides of QTR. The degree of genetic differentiation between populations of O. curzoniae on opposite sides of QTR will probably further increase in the future.

論文審定書.................................................................................................i
誌謝............................................................................................................ii
摘要...........................................................................................................iii
Abstract....................................................................................................iv
Contents.....................................................................................................v
Figure Legend..........................................................................................vi
Table Legend...........................................................................................vii
Introduction..............................................................................................1
Materials and Methods............................................................................5
Results......................................................................................................10
Discussion................................................................................................13
References................................................................................................18
Figures.....................................................................................................27
Tables.......................................................................................................33
Appendix.................................................................................................39

Avise, J. C. 2000. Phylogeography: the History and Formation of Species. Harvard University Press, Cambridge, Massachusetts, U.S.A.
Bagchi, S., T. Namgail and M. E. Ritchie. 2006. Small mammalian herbivores as mediators of plant community dynamics in the high-altitude rangelands of Trans-Himalaya. Biological Conservation 127: 438-442.
Bauert, M. R., M. Kalin, M. Baltisberger and P. J. Edwards. 1998. No genetic variation detected within isolated relict populations of Saxifraga cernua in the Alps using RAPD markers. Molecular Ecology 7: 1519-1527.
Cantatore, P., M. Roberti, G. Pesole, A. Ludovico, F. Milella, M. N. Gadaleta and C. Saccone. 1994. Evolutionary analysis of cytochrome b sequences in some Perciformes: evidence for a slower rate of evolution than in mammals. Journal of Molecular Evolution 39: 589-597.
Clement, M., D. Posada and K. A. Crandall. 2000. TCS: a computer program to estimate gene genealogies. Molecular Ecology 9: 1657-1659.
Clevenger, A. P., B. Chruszcz and K. E. Gunson. 2001. Highway mitigation fencing reduces wildlife-vehicle collisions. Wildlife Society Bulletin 29: 646-653.
Crochet, P.-A. 2000. Genetic structure of avian populations – allozymes revisited. Molecular Ecology 9: 1463-1469.
Dobson, F. S., A. T. Smith and X. G. Wang. 1998. Social and ecological influences on dispersal and philopatry in the plateau pika (Ochotona curzoniae). Behavioral Ecology 9: 622-635.
Dobson, F. S., A. T. Smith and X. G. Wang. 2000. The mating system and gene dynamics of plateau pikas. Behavioural Processes 51: 101-110.
Ehrich, D. and N. C. Stenseth. 2001. Genetic structure of Siberian lemmings (Lemmus sibiricus) in a continuous habitat: large patches rather than isolation by distance. Heredity 86: 716-730.
Epps, C. W., P. J. Palsboll, J. D. Wehausen, G. K. Roderick, R. R. Ramey II and D. R. McCullough. 2005. Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep. Ecology Letters 8: 1029-1038.
Excoffier, L. and H. E. L. Lischer. 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.
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.
Floyd, C. H., D. H. Van Vuren and B. May. 2005. Marmots on great basin mountaintops: using genetics to test a biogeographic paradigm. Ecology 86: 2145-2153.
Forman, R. T. T. and L. E. Alexander. 1998. Roads and their major ecological effects. Annual Review of Ecological Systems 29: 207-231.
Funk, W. C., A. E. Greene, P. S. Corn and F. W. Allendorf. 2005. High dispersal in a frog species suggests that it is vulnerable to habitat fragmentation. Biology Letters 1: 13-16.
Gauer, L. and S. Cavalli-Molina. 2000. Genetic variation in natural populations of mate (Ilex paraguariensis A. St.-Hil., Aquifoliaceae) using RAPD markers. Heredity 84: 647-656.
Goossens, B., L. Chikhi, P. Taberlet L. P. Waits and D. Allaine. 2001. Microsatellite analysis of genetic variation among and within Alpine marmot populations in the French Alps. Molecular Ecology 10: 41-52.
Grant, W. S. 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.
Gutzwiller, K. J. and W. C. Barrow. 2003. Influences of roads and development on bird communities in protected Chihuahuan Desert landscapes. Biological Conservation 113: 225-237.
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.
Hels, T. and E. Buchwald. 2001. The effect of road kills on amphibian populations. Biological Conservation 99: 331-340.
Irwin, D. M., T. D. Kocher and A. C. Wilson. 1991. Evolution of the cytochrome b gene of mammals. Journal of Molecular Evolution 32: 128-144.
Kaczensky, P., F. Knauer, B. Krze, M. Jonozovic, M. Adamic and H. Gossow. 2003. The impact of high speed, high volume traffic axes on brown bears in Slovenia. Biological Conservation 111: 191-204.
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 animals and sequencing with conserved primers. Proceedings of the National Academy of Sciences USA 86: 6196-6200.
Kyle, C. J. and C. Strobeck. 2003. Genetic homogeneity of Canadian mainland marten populations underscores the distinctiveness of Newfoundland pine martens (Martes Americana atrata). Canadian Journal of Zoology 81: 57-66.
Lai C. H. and A. T. Smith. 2003. Keystone status of plateau pikas (Ochotona curzoniae): effect of control on biodiversity of native birds. Biodiversity and Conservation 12: 1901-1912.
Le Corre, V., S. Dumolin-Lapegue and A. Kremer. 1997. Genetic variation at allozyme and RAPD loci sessile oak Quercus petraea (Matt.) Liebl.: the role of history and geography. Molecular Ecology 6: 519-529.
Lee, P. L. M., R. B. Bradbury, J. D. Wilson, N. S. Flanagan, L. Richardson, A. J. Perkins and J. R. Krebs. 2001. Microsatellite variation in the yellowhammer Emberiza citrinella: population structure of a declining farmland bird. Molecular Ecology 10: 1633-1644.
Librado, P. and J. Rozas. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451-1452.
Lugo, A. E. and H. Gucinski. 2000. Function, effects, and management of forest roads. Forest Ecology and Management 133: 249-262.
Miller, D. J. and S. R. Craig. 1997. Rangelands and Pastoral Development in the Hindu Kush-Himalayas. International Centre for Integrated Mountain Development, Kathmandu, Nepal.
Nei, M. 1987. Molecular Evolutionary Genetics. Columbia University Press, New York, USA.
Nei, M. and S. Kumar. 2000. Molecular Evolution and Phylogenetics. Oxford University Press, New York, USA.
Nesbo, C. L., C. Magnhagen and K. S. Jakobsen. 1998. Genetic differentiation among stationary and anadromous perch (Perca fluviatilis) in the Baltic Sea. Hereditas 129: 241-249.
Neumann, K., H. Jansman, A. Kayser, S. Maak and R. Gattermann. 2004. Multiple bottlenecks in threatened western European populations of the common hamster Cricetus cricetus (L.). Conservation Genetics 5: 181-193.
Page, R. D. M. and E. C. Holmes. 1998. Molecular Evolution: A Phylogenetic Approach. Blackwell Science Press, London, U.K.
Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology Evolution 25: 1253-1256.
Reed, R. A., J. Johnson-Barnard and W. L. Baker. 1996. Contribution of roads to forest fragmentation in the Rocky Mountains. Conservation Biology 10: 1098-1106.
Reh, W. and A. Seitz. 1990. The influence of land use on the genetic structure of populations of the common frog Rana temporaria. Biological Conservation 54: 239-249.
Reid, W. V. and K. R. Miller. 1989. Keeping Options Alive: the Scientific Basis for Conserving Biodiversity. World Resources Institute, Washington, DC.
Rico, A., P. Kindlmann and F. Sedlacek. 2007. Barrier effects of roads on movements of small mammals. Folia Zoologica 56: 1-12.
Saarinen, K., A. Valtonen, J. Jantunen and S. Saarnio. 2005. Butterflies and diurnal moths along road verges: Does road type affect diversity and abundance? Biological Conservation 123: 403-412.
Smith, A. T. 2008. The world of pikas. pp. 89-102. in P. C. Alves, N. Ferrand and K. Hacklander, eds. Lagomorph Biology: Evolution, Ecology, and Conservation. Springer-Verlag, New York, USA.
Smith, A. T. and J. M. Foggin. 1999. The plateau pika (Ochotona curzoniae) is a keystone species for biodiversity on the Tibetan plateau. Animal Conservation 2: 235-240.
Sumner, J., T. Jessop, D. Paetkau and C. Moritz. 2004. Limited effect of anthropogenic habitat fragmentation on molecular diversity in a rain forest skink, Gnypetoscincus queenslandiae. Molecular Ecology 13: 259-269.
Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
Tamura, K., D. Peterson, N. Peterson, G. Stecher, M. Nei and S. Kumar. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
Trizio, I., B. Crestanello, P. Galbusera, L. A. Wauters, G. Tosi, E. Matthysen and H. C. Hauffe. 2005. Geographical distance and physical barriers shape the genetic structure of Eurasian red squirrels (Sciurus Vulgaris) in the Italian Alps. Molecular Ecology 14: 469-481.
Van der Grift, E. A. 1999. Mammals and railroads: impacts and management implications. Lutra 42: 77-98.
Wang, G. X., Q. B. Wu, Y. B. Wang and Z. G. Guo. 2005. The impacts of railroad engineering on the alpine grassland ecosystem in the Qinghai-Tibet Plateau. Science and Technology Review 1: 8-13.
Wang, M. and A. Schreiber. 2001. The impact of habitat fragmentation and social structure on the population genetics of roe deer (Capreolus capreolus L.) in Central Europe. Heredity 86: 703-715.
Whittaker, R. H., S. A. Levin and R. B. Root. 1973. Niche, habitat, and ecotope. The American Naturalist 107: 321-338.
Wolff, K., S. El-Akkad and R. J. Abbott. 1997. Population substructure in Alkanna orientalis (Boraginaceae) in the Sinai Desert, in relation to its pollinator behaviour. Molecular Ecology 6: 365-372.
Wright, S. 1943. Isolation by distance. Genetics 28: 114-138.
Yang, S. M., H. Y. Huai, Y. L. Zhang, B. F. Yin, L. Zhou and W. H. Wei. 2006. Effects of railway traffic on the community structure of rodents in warm steppe along the Qinghai-Tibet Railway. Acta Theriologica Sinica 26: 267-273.
Yang, Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11: 367-372.
Zhang, Y. Q. 2002. Negative impact of Qinghai-Tibetan Railway construction on ecological environment of Qinghai-Tibetan Plateau. Bulletin of Soil and Water Conservation 22: 50-53.
Zhou, L., B. F. Yin, S. M. Yang, H. Y. Huai, S. P. Li, Y. L. Zhang and W. H. Wei. 2006. Effects of Qinghai-Tibet Highway on genetic differentiation of plateau pika (Ochotona curzoniae). Acta Ecologica Sinica 26: 3572-3577.