請用此 Handle URI 來引用此文件: http://hdl.handle.net/11455/22883
標題: 羅漢魚在東亞的親緣地理及族群分化
The phylogeography and population differentiation of Pseudorasbora parva in East Asia
作者: 雷蕾
Lei, Lei
關鍵字: Cytochrome b
細胞色素b
D loop
mismatch distribution
molecular clock
Taiwan
Cyprinidae
D環
控制區
分佈落差分析
分子時鐘
台灣
鯉科
出版社: 生命科學系所
引用: Aris-Brosou, S. & Excoffier, L. (1996) The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. Molecular Biology and Evolution, 13, 494-504. Boggs, S., Wang, W.-C., Lewis, F.S. & Chen, J.-C. (1979) Sediment properties and water characteristics of the Taiwan shelf and slope. Acta Oceanographica Taiwanica, 10, 10-49. Cavender, T.M. (1991) The fossil record of the Cyprinidae. In: WinWeld, I.J., Nelson, J.S. (Eds.), Cyprinid Fishes: Systematics, Biology and Exploitation Chapman & Hall, London, pp. 34-54. Chen, I.-S. & Fang, L.-S. (1999) The freshwater and estuarine fishes of Taiwan. National Museum of Marine Biology and Aquarium Press, Pingtung, Taiwan. (in Chinese) Cheng, H.-L., Huang, S., & Lee, S.-C. (2005 a) Morphogogical and molecular variation of Rhinogobius rubromaculatus (Pisces: Gobiidae) from Taiwan. Zoological studies, 44, 119-129. Cheng, H.-L., Huang, S., & Lee, S.-C. (2005 b) Population genetics of the edemic goby, Rhinogobius maculafasciatus (Pisces: Gobiidae) from Taiwan. Zoological studies, 44, 329-336. Chen, I.-S., Wu, J.-H. & Hsu, C.-H. (2008) The taxonomy and phylogeny of Candidia (teleostei: Cyprinidae) from Taiwan, with description of a new species and comments on a new genus. The Raffles Bulletin of Zoology, 19, 203-214. Excoffier, L., Laval, G. & Schneider, S. (2005) Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1, 47-50. Excoffier, L., Smouse, P.E. & Quattro, J.M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics, 131, 479-491. Farris, J.S., Källerjsö M., Kluge A.G. & Bult, C. (1994) Testing significance of congruence. Cladistics, 10, 315-319. Fu, Y.-X. (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915-925. Froese, R. & Pauly, D. (2009) FishBase. World Wide Web electronic publication. www.fishbase.org, version (09/2009). Garrigan, D. & Hedrick, P.W. (2003) Perspective: detecting adaptive molecular polymorphism: lessons from the MHC. Evolution, 57, 1707-1722. Gozlan, R.E., St-Hilarire, S., Feist, S.W., Martin, P. & Kent, M.L. (2005) Disease threat to European fish. Nature, 435, 1046. Gu, X., Fu, Y.-X. & Li, W.-H. (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Molecular Biology and Evolution, 12, 546-557 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. Harpending, H.C. (1994) Signature of ancient population growth in a low resolution mitochondrial DNA mismatch distribution. Human Biology, 66, 591-600. Hasegawa, M., Kishino, H. & Yano, T. 1985 Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160-174. Hewitt, G.M. (1996) Some genetic consequences of Ice Ages, and their role in divergence and speciation. Biological Journal of the Linnean Society, 58, 247-276. Hewitt, G.M. (2000) The genetic legacy of the Quaternary Ice Ages. Nature, 405, 907-913. Huelsenbeck, J.P. & Ronquist, F. (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755. Jobb, G., von Haeseler, A. & Strimmer, K. (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evolutionary Biology, 4, 18. Ju, L., Wang, H. & Jiang, D. (2007) Simulation of the Last Glacial Maximum climate over East Asia with a regional climate model nested in a general circulation model. Palaeogeography Palaeoclimatology and Palaeoecology, 248, 376-390. Lambeck, K., Esat, T.M. & Potter, E.K. (2002) Links between climate and sea levels for the past three million years. Nature, 419, 199-206. Li, G.-Y., Wang, X.-Z., Zhao, X.-V., Zhang, J., Zhang, C.-G. & He, S.-P. (2009) Speciation and phylogeography of Opsariichthys bidens (Pisces: Cypriniformes: Cyprinidae) in China: analysis of the cytochrome b gene of mtDNA from diverse populations. Zoological Studies, 48, 569-583. Li, W.-H., Wu, C.-I. & Luo, C.-C. (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Molecular Biology and Evolution, 2, 150-174. Librado, P. & Rozas, J. (2009) DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 25, 1451-1452. Liu, J.-X., Gao, T.-X., Wu, S.-F., & Zhang, Y.-P. (2007) Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in marine fish, Chelon haematocheilus (Temminck & Schelegel, 1845). Molecular Ecology, 16, 275-288. Liu, H.-T. & Su T.-T. (1962) Pliocene fishes from Yushe Basin, Shansi. Vertebrate Palasiatica, 6, 1-47. Nelson, J.S. (2006) Fishes of the world (4th ed), pp.142. John Wiley Press, New York. Nylander, J.A.A. (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University. Ota, H. (1998) Geographic patterns of endemism and speciation in amphibians and reptiles of the Ryukyun Archipelago, Japan, with reference to their palaeogeographical implications. Researches on Population Ecology, 40, 189-204. Peck, D. & Congdon, B. (2004). Reconciling historical processes and population structure in the sooty tern Sterna fuscata. Journal of Avian Biology, 35, 327-335. Perdices, A., Cunha, C. & Coelho, M.M. (2004) Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (= Yangtze) drainage inferred from cytochrome b sequences. Molecular Phylogenetics and Evolution, 31, 192-203. Posada, D. & Crandall, K.A. (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818. Rogers, A. R. & Harpending, H. C. (1992). Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569. Sanderson, M.J. (1997) A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218-1231. Schneider, S. & Excoffier, L. (1999) Estimation of past demographic parameters from the distribution of pairwise differences when the mutation rates vary among sites. Application to human mitochondrial DNA. Genetics, 152, 1079-1089. Swofford, D.L. (2001) PAUP*: Phylogenetic analysis using parsimony (*and other methods), version 4.0b10. Sinauer Associates, Sunderland, MA. Tajima, F. (1989) Statistical methods to test for nucleotide mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595. Tamura, K., Dudley, J., Nei, M. & Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599. Tamura, K. & Nei, M. (1993) Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10, 512-526. Tatusova, T.A. & Madden, T.L. (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS microbiology letters, 174, 247-250. Templeton, A.R., Routman E. & Philips, C.A. (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of Mitochondria DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140, 767-782. Thompson, J.D., Higgins, D.G. & Gibson, T.J. (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. Wang, C.-F. (2005) Studies on genetic diversity and morphological variance of Candida barbatus (Cypriniformes: Cyprinidae) in Taiwan rivers. Master thesis. National Taiwan University, Taipei, Taiwan. Wang, H.-Y., Hsu, K.-C., & Chiang, T.-Y. (2000). Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Molecular Ecology, 9, 1483-1494. Wang, H.-Y., Tsai, M.-P., Yu, M.-J., & Lee, S.-C. (1999). Influence of glaciation on divergence patterns of the endemic minnow, Zacco pachycephalus, in Taiwan. Molecular Ecology, 8, 1879-1888. Wang, J-P., Lin, H.-D., Huang, S., Pan, C.-H., Chen, X.-L., & Chiang, T.-Y. (2004). Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes. Molecular Phylogenetics and Evolution, 31, 1143-1156. Wang, X.-Z., Li, J.-B. & He, S.-P. (2006) Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences. Molecular Phylogenetics and Evolution, 42, 157-170. Weir, B. S. & Cockerham, C. C. (1984) Estimating F-statistics for the analysis of population structure. Evolution, 38, 1358-1370. Xia, X. & Xie, Z. (2001) DAMBE: data analysis in molecular biology and evolution. Journal of Heredity, 92, 371-373. Zhang, H., Yan, J., Zhang, G. & Zhou, K. (2008) Phylogeography and demographic history of Chinese black-spotted frog populations (Pelophylax nigromaculata): evidence for independent refugia expansion and secondary contact. BMC Evolutionary Biology, 8, 21. Zwickl, D. J. (2006) Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin.
摘要: 羅漢魚(Pseudorasbora parva)是一種廣泛分佈於台灣,中國大陸,日本以及韓國的小型鯉科魚類。由於屬於初級淡水魚,因此牠們的分布會受到水域鹽度以及地形等天然界線的影響。為了研究牠們在東亞地區的親緣地理和族群分化模式,我們利用聚合酶連鎖反應(PCR)的方法將167隻羅漢魚,兩隻長麥穗魚(P. elongate),三隻卜米麥穗魚(P. pumila)的粒線體細胞色素b (cytochrome b, 簡稱cyt b) DNA序列全長增幅出來。利用貝氏方法(Bayesian)、最大或然率法(maximaum likelihood)、最大簡約法(maximum parsimony)以及鄰接法(neighbor-joining)所重建演化樹都支持有五個主要的粒線體支系(lineage)存在,其中包括了日本(L1)、韓國(L2)、台灣的台東(L3)、中國大陸南部+日本(L4)以及中國大陸東北部+台灣(L5)。這五個支系彼此之間的演化距離(GTR + I + G 模式)為2.26%到8.14%。L1位於演化樹的最基部,接著是L2、L3、L4和L5。我們另外挑出一些個體,增幅出D環基因(D-loop,簡稱DL)並與牠們各自的cyt b接起來重建新的演化樹,結果cyt b與cyt b-DL所構築的演化樹的樹形是一致的。估計L1、L2、L3、L4和L5各自的分化時間分別是在0.62–1.14、0.46–0.96、0.27–0.64、0.19–0.52和0.12–0.38 百萬年前(Mya),這表示這幾個粒線體支系很可能是在更新世分歧的。利用cyt b DNA序列進行分佈落差分析(mismatch distribution)顯示,台灣、中國大陸、韓國和日本的羅漢魚都呈現多峰型(multimodal),這表示各地理群中可能有多個遺傳支系或者羅漢魚的族群數量很穩定。以分子變異分析(analysis of molecular variance, AMOVA)分析族群變異的組成顯示,發生於地理群間、地理群內(=族群間)和族群內的遺傳變異分別是50.85%, 22.85%和 26.29%。Φst的數值呈現顯著,表示地理區的族群分化顯著。我們推測台灣島、朝鮮半島和日本列島可能是羅漢魚在冰河時期的庇護所(refugia)。而中國大陸東北及西南部是另外兩個庇護所。
Pseudorasbora parva is a small cyprinid distributed in Taiwan, mainland China, Korea, and Japan. It is primarily a freshwater fish, and its dispersal is limited by water salinity and geographical barrier. To infer phylogeography and population differentiation of P. parva in East Asia, complete cytochrome b (cyt b) DNA sequences of 167 individuals of P. parva, two individuals of P. elongate, and three individuals of P. pumila were amplified by polymerase chain reaction (PCR) and subsequently sequenced. Phylogenetic trees reconstructed with Bayesian, maximum likelihood, maximum parsimony, and neighbor-joining methods all support the existence of five major mitochondrial lineages, including lineages of Japan (L1), Korea (L2), Taitung of Taiwan (L3), south China + Japan (L4), and northeast China + Taiwan (L5) with evolutionary distances (GTR + I + G model) ranging from 2.26 to 8.14%. The L1 is at the most basal position of the tree following by the L2, L3, L4, and L5. The topology of the tree is congruent with that of the tree reconstructed with a combination of cyt b and D loop DNA sequences in a reduced data set. The estimated divergence times were 0.62-1.14, 0.46-0.96, 0.27-0.64, 0.19-0.52, and 0.12-0.38 Mya for L1, L2, L3, L4, and L5, respectively, suggesting that the five mitochondrial lineages are most likely a late Pleistocene split. Mismatch distributions are multimodal for the cyt b DNA sequences of P. parva in Taiwan, mainland China, Korea, and Taiwan, suggesting that either the existence of multiple genetic lineages in each geographical population or the populations are stable. Analyses of molecular variance (AMOVA) for the geographical groups of Taiwan, China, Korea, and Japan showed that 50.85%, 22.85%, and 26.29% of genetic variances were derived from among geographical population, among populations (= within geographical groups), and within populations, respectively and the Φst was significant suggesting that genetic differentiation among geological populations was occurred. We proposed that Taiwan, Korea peninsula, and Japan archipelago were refugia for P. parva during the ice age. In addition, the northeast and southeast China were two refugia in mainland China.
URI: http://hdl.handle.net/11455/22883
其他識別: U0005-1112200912212900
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-1112200912212900
顯示於類別:生命科學系所

文件中的檔案:
沒有與此文件相關的檔案。


在 DSpace 系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。