Please use this identifier to cite or link to this item: http://hdl.handle.net/11455/20232
標題: 以粒線體控制區與細胞色素氧化酶 I 探討台灣山區澤蟹屬之親緣關係
Phylogeny of Taiwanese montane freshwater crabs genus Geothelphusa by mitochondrial control region and COI
作者: 巫國志
Wu, Kuo-Chih
關鍵字: 細胞色素氧化酶I
Control region (CR)
澤蟹屬
親緣關係
COI
Geothelphusa
Phylogeny
出版社: 生命科學系所
引用: 王巍、朱華、胡紅霞、田照輝、董穎, 2009。五種鱘魚粒線體控制區異質性與系統發育分析。動物學研究。30: 487-496。 吳惠仙、徐雪娜、薛俊增、董双林、王芳, 2009。中國沿海三疣梭子蟹的遺傳結構和親緣關係分析。海洋學研究。27(3): 48-53。 林朝棨、周瑞燉, 1974。臺灣地質。台灣省文獻委員會。450頁。 施志昀、李伯雯, 2009。臺灣淡水蟹圖鑑。晨星出版。221頁。 施志昀、游祥平, 1999。臺灣的淡水蟹。國立海洋生物博物館。114頁。 施習德, 2002。甲殼類的分子生態學。科學月刊。388: 307-314 。 張瑞宗, 2008。日本絨螯蟹 (Eriocheir japonica) 遺傳多樣性之研究。國立清華大學生物資訊與結構生物研究所碩士論文。 許桂菁, 2007。後冰河時期南中國中華花鰍 ( Cobitis sinensis ) 之遷移路徑。國立成功大學生物學研究所博士論文。 陳培源, 2006。臺灣地質。台灣省應用地質技師公會。495頁。 陳溫柔, 2007。臺灣地區澤蟹屬蟹類親緣關係暨西南部惡地區域厚圓澤蟹之適應策略研究。國立中山大學生物科學系博士論文。 郭瓊華, 2001。臺灣蜓蜥族群遺傳結構之研究。國立臺灣師範大學生物學系碩士論文。 蕭程友, 2007。臺灣絨螯蟹 (Eriocheir formosa) 遺傳多樣性之研究。國立清華大學生物資訊與結構生物研究所碩士論文。 戴愛雲, 1999。中國動物誌。節肢動物門: 甲殼動物亞門: 軟甲綱: 十足目: 束腹蟹科, 溪蟹科。科學出版社。501頁。 羅偵源, 2004。東亞島嶼淡水蟹的分子親緣地理關係。國立中興大學生命科學系研究所碩士論文。 Arbelaez-Coetes, E., Nyari, A.S. & Navarro-Siguenza, A.G. (2010). The differential effect of lowlands on the phylogeographic pattern of a Mesoamerican montane species (Lepidocolaptes affinis, Aves: Furnariidae). Molecular Phylogenetics and Evolution 2010: 658-668. Arif, I.A. & Khan, H.A. (2009). Molecular markers for biodiversity analysis of wildlife animals: a brief review. Animal Biodiversity and Conservation 32: 9-17. Brown, W.M., George, M., JR. & Wilson, A.C. (1979). Rapid evolution of animal mitochondrial DNA. Proceedings of the National Academy of Sciences of the United States of America 76: 1967-1971. Buroker, N.E., Brown, J.R., Gilbert, T.A., ƠHara, P.J., Beckenbach, A.T., Thomas, W.K. & Smith, M.J. (1990). Length heteroplasmy of sturgeon mitochondrial DNA: an illegitimate elongation model. Genetics 124: 157-163. Chen, C.L.A., Ablan, M.C.A., McManus, J.W., Bell, J.D., Tuan, V.S., Cabanban, A.S. & Shao, K.T. (2004). Variable numbers of tandem repeats (VNTRs), heteroplasmy, and sequence variation of the mitochondrial control region in threespot dascyllus, Dascyllus trimaculatus (Perciformes: Pomacentridae). Zoological Studies 43: 803-812. Cho, E.M., Min, G.S., Kanwal, S., Hyun, Y.S., Sun, W.P. & Chung, K.W. (2009). Phylogenetic analysis of mitochondrial DNA control region in the swimming crab, Portunus trituberculatus. Animal Cells and Systems 13: 305-314. Chu, K.H., Li, C.P., Tam, Y.K. & Lavery, S. (2003) Application of mitochondrial control region in population genetic studies of the shrimp Penaeus. Molecular Ecology Notes 3: 120-122. Chu, K.H., Tong, J.G. & Chan, T.Y. (1999). Mitochondrial cytochrome oxidase I sequence divergence in some Chinese species of Charybdis (Crustacea: Decapoda: Portunidae). Biochemical Systematics and Ecology 27: 461-468. Chow, S., Suzuki, N., Imai, H. & Yoshimura, T. (2006). Molecular species identification of spiny lobster phyllosoma larvae of the genus Panulirus from the northwestern pacific. Marine Biotechnology 8: 260-267. Cox, C.B. & Moore, P.D. (2005). Biogeography: An ecological and evolutionary approach, 7/e. Blackwell Publishing Ltd. 438 pages. Diniz, F.D., Maclean, N., Ogawa, M., Cintra, I.H.A. & Bentzen, P. (2005). The hypervarariable domain of the mitochondrial control region in atlantic spiny lobsters and its potential as a marker for investigating phylogeographic structuring. Marine Biotechnology 7: 462-473. Eberhard, J.R., Wright, T.F. & Bermingham, E. (2001). Duplication and concerted evolution of the mitochondrial control region in the parrot genus Amazona. Molecular Biology and Evolution 18: 1330-1342. Edgar, R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acid Reserch 32: 1792-1797. Farris, J.S., Kallersjo, M., Kluge, A.G. and Bult, C. (1994). Testing significance of congruence. Cladistics 10: 315-319. Folmer, O., M. Black, W. Hoeh, R. Lutz & R. Vrijenhoek, (1994). DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294-299. Galtier, N., Nabholz, B., Glemin, S. & Hurst, G.D.D. (2009). Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18: 4541-4550. Garcia-Paris, M., Good, D.A., Parra-Olea, G. & Wake, D.B. (2000). Biodiversity of Costa Rican salamanders: Implications of high levels of genetic differentiation and phylogeographic structure for species formation. Proceedings of the National Academy of Sciences of the United States of America 97: 1640-1647. 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. Hebert, P.D.N., Cywinska, A., Ball, S.L. & deWaard, J.R. (2003) Biological identification through DNA barcode. Proceedings of the Royal Society of London, Series B 270: 313-321. Hills, D.M. (1987). Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics 18: 23-42. Hills, D.M. & Bull, J.J. (1993). An empirical test of bootstrapping as a method assessing confidence in phylogenetic analysis. Systematic Biology 41: 182-192. Hirayama, M., Mukai, T., Miya, M., Murata, Y., Sekiya, Y., Yamashita, T., Nishida, M., Watabe, S., Oda, S. & Mitani, H. (2010). Intraspecific variation in the mitochondrial genome among local populations of Medaka Oryzias latipes. Gene 457: 13-24. Hubert, N., Hanner, R., Holm, E., Mandrak, N.E., Taylor, E., Burridge, M., Watkinson, D., Dumont, P., Curry, A., Bentzen, P., Zhang, J., April, J. & Bernatchez, L. (2008). Identifying Canadian freshwater fishes through DNA barcodes. PLoS ONE 3: e2490. Kimura, M. (2000). Paleogeography of Ryukyu islands. Tropics 10: 5-24 Kolpakov, R., Bana, G. & Kucherov, G. (2003). Mreps: efficient and flexible detection of tandem repeat in DNA. Nucleic Acids Reserch 31: 3672-3678. Krebs, J.E., Goldstein, E.S. & Kilpatrick, S.K. (2009). Lewin`s genes X. Jones and Bartlett Publishers, LLC. 930 pages. Lai, J.S. & Lue, K.Y. (2008). Two new Hynobius (Caudata: Hynobiidae) salamanders from Taiwan. Herpetologica 64: 63-80. Lewis, D.L., Farr, C.L., Farquhar, A.L. & Kaguni, L.S. (1994). Seqeence, organization, and evolution of the A+T region of Drosophila melanogaster mitochondrial DNA. Molecular Biology and Evolution 11: 523-538. Mancini, E., Biase, A.D., Mariottini, P., Bellini, A. & Audisio, P. (2008). Structure and evolution of the mitochondrial control region of the pollen beetle Meligethes thalassophilus (Coleoptera: Nitidulidae). Genome 51: 196-207. McMillen-Jackson, A.L. & Bert, T.M. (2004). Genetic diversity in the mtDNA control region and population structure in the pink shrimp Farfantepenaeus duorarum. Journal of Crustacean Biology 24: 1101-1109. Minei, H. (1968). Freshwater crabs of Japan. Nature Study 14: 94-99. [In Japanese] Minei, H., (1974). Potamoid crabs of Taiwan, with description of one new species (Crustacea, Decapoda). Journal of the Faculty of Agriculture, Kyushu University 18: 239 251. Mullis, K., Faloona, F., Scharf, S., Saiki, R., Horn, G. & Erhlich, H. (1986). Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harbor Symposia on Quantitative Biology 51: 263-273. Mundy, N.I., Winchell, C.S. & Woodruff, D.S. (1996). Tandem repeats and heteroplasmy in the mitochondrial DNA control region of the loggerhead shrike (Lanius ludovicianus). Journal of Heredity 87: 21-26. Ng, P.K.L., Guinot, D. & Davie, P.J.F. (2008). Systema brachyurorum: part I. An annotated checklist of extant brachyuran crabs of the world. The Raffles Bulletin of Zoology 17: 1-286. Ng, P.K.L., Shih, H.T., Naruse, T. and Shy, J.Y. (2010). Using molecular tools to establish the type locality and distribution of the endemic taiwanese freshwater crab Geothelphusa chiui Minei, 1974 (Crustacea: Brachyura: Potamidae), with notes on the genetic diversity of Geothelphusa from eastern Taiwan. Zoological Studies 49(4): 544-555. Nylander, J.A.A. (2005). MrModeltest, Version 2.2. Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden. Oliveira-Neto, J.F., Boeger, W.A., Pie, M.R., Ostrensky, A. & Hungria. D.B. (2007a). Genetic structure of populations of the mangrove crab Ucides cordatus (Decapoda: Ocypodidae) at local and regional scales. Hydrobiologia 583: 69-76. Oliveira Neto, J.F., Pie, M.R., Boeger, W.A., Ostrensky, A. & Baggio, R.A. (2007b). Population genetics and evolutionary demography of Ucides cordatus (Decapoda : Ocypodidae). Marine Ecology 28: 460 469. Oliveira Neto, J.F., Pie, M.R., Chammas, M.A., Ostrensky, A. & Boeger, W.A. (2008). Phylogeography of the blue land crab, Cardisoma guanhumi (Decapoda: Gecarcinidae) along the Brazilian coast. Journal of the Marine Biological Association of the United Kingdom 88: 1417 1423. Page, R.D.M. & Holmes, E.C. (1998). Molecular Evolution: A phylogeny approach. Blackwell Science Ltd. 352 pages. Pie, M.R., Oliveira-Neto, J.F., Boeger, W.A., Ostrensky, A. & Baggio, R.A. (2008). The organization of the mitochondrial control region in 2 brachyuran crustaceans: Ucides cordatus (Ocypodidae) and Cardisoma guanhumi (Gecarcinidae). Journal of Heredity 99: 432-437. Pride, D.T. (2004). Swaap 1.0.3. (http://asiago.stanford.edu/SWAAP/SwaapPage.htm) Ray, N. & Adams, J.M. (2001). A GIS-based vegetation map of the world at the Last Glacial Maximum (25,000-15,000 BP). Internet Archaeology 11: 1-44. Ray, D.A. & Densmore, L.D. (2003). Repetitive Sequences in the Crocodilian mitochondrial control region: poly-A sequence and heteroplasmic tandem repeats. Molecular Biology and Evolution 20: 1006–1013. Roman, J. & Palumbi, S.R. (2004). A global invader at home: population structure of the green crab, Carcinus maenas, in Europe. Molecular Ecology 13: 2891–2898. Saccone, C., Attimonelli, M. & Sbisa, E. (1987). Structure elements highly preserved during the evolution of the D-loop-containing region in vertebrate mitochondrial DNA. Journal of Molecular Evolution 26: 205-211. Saccone, C., Pesole, G. & Sbisa, E. (1991). The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. Journal of Molecular Evolution 33: 83-91. Saito, S., Tamura, K. & Aotsuka, T. (2005). Replication origin of mitochondrial DNA in Insects. Genetics 171: 1695-1705. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406-425. Savolainen, P., Arvestad, L. & Lundeberg, J. (2000). mtDNA tandem repeats in domestic dogs and wolves: mutation mechanism studied by analysis of the sequence of imperfect repeats. Molecular Biology and Evolution 17: 474-488. Sbisa, E., Tanzariello, F., Reyes, A., Pesole, G. & Saccone, C. (1997). Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Genes 205: 125-140. Schubart, C.D., Diesel, R. & Hedges, S.B. (1998). Rapid evolution to terrestrial life in Jamaican crabs. Nature 393: 363-365. Schubart, C.D. & Huber M.G.J. (2006). Genetic comparisons of German population of the stone crayfish, Austropotamobius torrentium (Crustacea: Astacidae). Bulletin Francais de la Peche et de la Pisciculture 380-381: 1019-1028. Schubart, C.D., Neigel, J.E. & Felder, D.L. (2000a). Molecular phylogeny of mud crabs (Brachyura: Panopeidae) from the northwestern Atlantic and the role of morphological stasis and convergence. Marine Biology 137: 11-18. Schubart, C.D., Neigel, J.E. & Felder, D.L. (2000b). Use of the mitochondrial 16S rRNA gene for phylogenetic and population studies of Crusracea. Crustacean Issues 12: 817-830. Segawa, R.D. & Aotsuka, T. (2005). The mitochondrial genome of the Japanese freshwater crab, Geothelphusa dehaani (Crustacea: Brachyura): Evidence for its evolution via gene duplication. Gene 355: 28-39. Shih, H.T., Ehsan, K., Peter, J.F.D. & Liu M.Y. (2009a). Genetic evidence for the recognition of two fiddler crans, Uca iranica and U. albimana (Crustacea: Brachyura: Ocypodidae), from the northwestern Indian Ocean, with note on the U. lacteal species-complex. Hydrobiologia 635: 373-382. Shih, H.T., Fang, S.H. & Ng, P.K.L. (2007a). Phylogeny of the freshwater crabs genus Somanniathelphusa Bott (Decapoda: Parathelphusidae) from Taiwan and the coastal region of China, with notes on their biogeography. Invertebrate Systematics 21: 29-37. Shih, H.T., Hung, H.C., Schubart, C.D., Chen, C.A. & Chang, H.W. (2006). Intraspecific genetic diversity of the endemic freshwater crab Candidiopotamon rathbunae (Decapoda, Brachyura, Potamidae) reflects five million years of the geological history of Taiwan. Journal of Biogeography 33: 980–989. Shih, H.T. & Ng, P.K.L. (2011). Diversity and biogeography of freshwater crabs (Crustacea: Brachyura: Potamidae, Gecarcinucidae) from East Asia. Systematics and Biodiversity 9: 1-16. Shih, H.T., Ng, P.K.L., Chang, H.W. (2004). Systematics of the genus Geothelphusa (Crustacea, Decapoda, Brachyura, Potamidae) from southern taiwan: a molecular appraisal. Zoological Studies 43: 561-570. Shih, H.T., Ng, P.K.L., Naruse, T., Shokita, S. & Liu, M.Y. (2011a). Pleistocene speciation of freshwater crans (Crustacea: Potamidae: Geothelphusa) from northern Taiwan and southern Ryukyus, as revealed by phylogenetic relationships. Zoologische Anzeiger 250: 457-471. Shih, H.T., Ng, P.K.L., Schubart, C.D. & Chang, H.W. (2007b). Phylogeny and phylogeography of the genus Geothelphusa (Crustacea: Decaoida, Brachyura, Potamidae) in Southwestern Taiwan based on two mitochondrial genes. Zoological Science 24: 57-66. Shih, H.T. & Suzuki, H. (2008). Taxonomy, phylogeny, and biogeography of the endemic mudflat crab Helice/Chasmagnathus Complex (Crustacea: Brachyura: Varunidae) from east asia. Zoological Studies 47: 114-125. Shih, H.T., Yeo, D.C.J. & Ng, P.K.L. (2009b). The collision of the Indian plate with Asia: molecular evidence for its impact on the phylogeny of freshwater crabs (Brachyura: Potamidae). Journal of Biogeography 36: 703-719. Shih, H.T., Zhou, X.M., Chen, G.X., Chien, I.C. & Ng, P.K.L. (2011b). aRecent vicariant and dispersal events affecting the phylogeny and biogeography of East Asian freshwater crab genus Nanhaipotamon (Decapoda: Potamidae). Molecular Phylogenetics and Evolution 58: 427-438. Sibuet, J.C. & Hsu, S.K. (2004). How was Taiwan created? Tectonophysics 379: 159– 181. Simon, C., Frati, F., Beckenbach, A., Crespi, B., Liu, H. & Flook, P. (1994). Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and compilation of conserved polymerase chain reaction primer. Annals of Entomological Society America 87: 651-701. Snall, N., Huoponen, K., Savontaus, M.L. & Ruohomaki, K. (2002). Tandem repeats and length variation in the mitochondrial DNA control region of Epirrita autumnata (Lepidoptera: Geometridae). Genome 45: 855-861. Sugihara, K., Yui, R., Ibaragi, Y. & Matsuura, E.T. (2006). Complete nucleotide sequence of the A+T-rich region of Drosophila mauritiana mitochondrial DNA. Genes & Genetic Systems 81: 21-28. Sun, H.Y., Zhou, K.Y. & Song, D.X. (2005). Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis (Brachyura: Thoracotremata: Grapsoidea) reveals a novel gene order and two target regions of gene rearrangements. Gene 349: 207-217. Swofford, D.L. (2003). PAUP* 4.0b 10. Phylogenetic Analysis Using Parsimony (*and Other Methods). Sinauer Associates, Sunderland, MA. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. & Kumar, S. (2011). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731–2739. Teng, L.S. (1990). Geotectonic evolution of late Cenozoic arc-continent collision in Taiwan. Tecionophysics 183: 57-76. Tofffoli, D., Hrbek, T., de Araujo, M.L.G., de Almeida, M.P., Charvet-Almeida, P. & Farias, I.P. (2008). A test of the utility of DNA barcoding in the radiation of the freshwater stingray genus Potamotrygon (Potamotrygonidae, Myliobatiformes). Genetics and Molecular Biology 31: 324-336. Vila, M. & Bjorklund, M. (2004). The utility of the neglected mitochondrial control region for evolutionary studies in Lepidoptera (Insecta). Journal of Molecular Evolution 58: 280-290. Watson, J.D. & Crick, F.H.C. (1953). Molecular structure of nucleic acid. Nature 171: 737-738. Yamaguchi, T. & Takamatsu, Y. (1980). Ecological and morphological studies on the Japanese freshwater crab, Geothelphusa dehaani. Kumamoto Journal of Science, Biology 15(1): 1-27. Yan, H.Y. (2000). Threatened fishes of the world: Oncorhynchus masou formosanus (Jordan & Oshima, 1919) (Salmonidae). Environmental Biology of Fishes 57: 314. Yeo, D.C.J., Ng, P.K.L., Cumberlidge, N., Magalhaes, C., Daniels, S.R. & Campos, M.R. (2008). Global diversity of crabs (Crustacea: Decapoda: Brachyura) in freshwater. Hydrobiologia 595: 275–286. Zhang, D.X. & Hewitt, G.M. (1997). Insect mitochondrial control region: a review of its structure, evolution and usefulness in evolutionary studies. Biochemical Systematics and Ecology 25: 99-120. Zhang, D.X., Szymura, J.M. & Hewitt, G.M. (1995). Evolution and structural conservation of the control region of insect mitochondrial DNA. Journal of Molecular Evolution 40: 382-391. Zhang, D.Z., Ding, G., Wang, G., Tang, B. & Sun, H. (2011). Structure and variable numbers of tandem repeats (VNTRs) of the mitochondrial control region in mitten crab Eriocheir (Crustacean: Brachyura). Molecular Biology Reports 38: 4935-4940. Zhao, L., Zheng, Z.M., Zhou, Z. & Wang, L. (2011). Comparative analysis of the mitochondrial control region in orthoptera. Zoological Studies 50: 385-393.
摘要: 本研究利用粒線體控制區 (CR) 以及細胞色素氧化酶 I (COI) 序列探討台灣山區澤蟹屬物種之親緣關係, 以及控制區序列在台灣澤蟹屬物種上的變異程度。控制區序列可分為三區域: 兩側區域較保守, 可能與存有調控粒線體 DNA複製的序列有關; 中間區域在不同物種間具有高變異性, 此與大量的插入與缺失以及串聯重複序列 (tandem repeats, TRs) 有關。然而相近物種間, 中間區域仍具有高相似度, 且其串聯重複序列單元也具有類似的組成。因此控制區可能不適用在整個台灣澤蟹屬內的親緣關係研究上, 但運用在關係接近的物種研究中, CR 仍具有與 COI 相近的解析力。此外, 影響 CR 長度高變異的主因是串聯重複序列的拷貝數, 形成原因主要是複製滑動 (replication slippage)。在拷貝數的數量方面, 山區類群多於低海拔類群物種, 可能與山區類群能夠適應較高海拔的生活環境有關。基於 COI 與控制區之親緣樹, 台灣山區澤蟹可分成北群與南群,大致符合雪山山脈以及中央山脈的地理位置。此外, 水系的分布與地形的阻隔也可能是造成各物種分布受限的原因。
The mitochondrial control region (CR) and cytochrome oxidase I (COI) markers were used to study the phylogeny among Taiwanese montane freshwater crabs (genus Geothelphusa), and the variation of CR among Taiwanese freshwater crabs. The CR of these crabs can be devided into three segments. Two side segments are more conserved than the central one, which may contain sequences related to the regulation of mtDNA replication. However, the central segment is highly variable among crabs, including a lot of indels and tandem repeats (TRs). Nevertheless the sequences and tandem repeat unit of the central segment are similar among closely related species. In conclusion, it is suggested that the CR sequences are too variable to study the whole phylogeny among Taiwanese freshwater crabs, but this marker is suitable for closely related species, and it has similar resolution with COI. Moreover, the variation of CR length is caused by the copy number of tandem repeats due to replication slippage. The montane species always have more copy number than those in lower altitude which may be related with the adaptation in higher altitude. Based on the phylogenetic tree of the combined COI and CR, Taiwanese montane species can be divided into the northern and southern clades, corresponded to the Syueshan Range and Central Range more or less, respectively. The river and mountain barriers may be other reasons for the narrower distributional range of each montane species.
URI: http://hdl.handle.net/11455/20232
其他識別: U0005-2607201217112200
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-2607201217112200
Appears in Collections:生命科學系所

文件中的檔案:

取得全文請前往華藝線上圖書館



Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.