鰍科（Cobitidae）為中國各區分布最廣的一科，其中花鰍屬（Cobitis）更分布於整個中國之東部，而中華花鰍（C. sinensis）便為其中最為廣泛分布之物種，且因中華花鰍其擴散能力限於河系分布，故為研究親緣地理之好材料。本研究自南中國地區，包括台灣之31條主要河川、35個採樣點採取共158個樣本，利用粒線體細胞色素b基因序列來探討族群遷徙及歷史重建重要的依據。本研究結果顯示35個族群及個體間分子序列有相當之差異，根據親緣分析結果中華花鰍具六個高遺傳變異的系群，且系群內遺傳多樣性亦相當高。藉由地理分布發現，此六大系群呈異域分布，此六大系群的分歧時間約為4,100,000到2,200,000年前，而且並非直接分歧，而是經歷一個或多個中間族群。本研究亦發現南中國地區之中華花鰍起源於長江流域，經由三條擴散路徑使得族群擴散至整個南中國地區：一、於上新世(Pliocene)中期，從長江流域至海南亞區之流域；二、於上新世中期，從長江流域至珠江流域，在上新世晚期從珠江流域經苗栗台地進入台灣中西部及東北部；三、上新世末期，從長江流域至閩江流域及浙閩南部之獨立水系，在更新世晚期再經由浙閩南部之獨立水系至台灣南部。並推論第三紀(Tertiary)末期至第四紀(Quaternary)南中國地區頻繁的地質活動為影響中華花鰍親緣地理分布的主因。利用Bayesian analysis估算系群的溯祖時間及有效族群量，發現六個系群的溯祖時間約為2,620,930至835,390年，且其有效族群量與其分布範圍成正比。在族群動態分析結果顯示，珠江族群於更新世(Pleistocene)中期(約800,000年前)便發生顯著之族群擴張現象，而其他族群如浙閩南部及台灣則是於更新世晚期發生族群擴張（約430,000-223,000年前）。根據系群之溯祖時間、分歧時間及擴張時間的分析結果均支持地質歷史中所呈現，上新世之後北半球進入多次週期性的冰河事件。此外，本研究認為台灣系群因位於族群拓張路徑的邊緣、族群承載量較大陸系群少且其遷移率亦較少，促使surfing mutations現象的發生，以及在沒有天擇及拓荒者效應作用下，促使新的變異能快速在族群中普遍擴散到廣大的系群分布地為影響台灣系群演化歷史的主因。

We examined the phylogeographic structure of the Siberian spiny loach, Cobitis sinensis, in East and South China based on the molecular variation of the complete mitochondrial DNA cytochrome b gene. The C. sinensis populations can be divided into six haplogroups: one with loach from Yangtz River, one from North ZheMin, third from South ZheMin, fourth from Pearl River, fifth from Hainan, and the least from Taiwan. We estimated that the six groups diverged from each other c. 4,100,000 – 2,200,000 years ago, and these groups did not diverge directly via intermediary population or a series of intermediary population. Based on the phylogeographical patterns and molecular dating, three migratory routes: 1: from Yangtz River to Hainan in the Pliocene (Tertiary); 2: from Yangtz River via Pearl River to Taiwan in the Pliocene (Tertiary); 3: from Yangtz River to ZheMin subregion afterward, independently, were identified. The populations in Taiwan originated form at least two mainland refugia during the last glacial period. Our results support that the tectonic actives during Quaternary are major factors in the phylogeographic pattern of C. sinensis in South China. Using Bayesian analysis with a coalescent population model to analyse the temporal pattern of formation of different lineages and estimate effective population size, we find that the C.sinensis lineages formed about 2,620,930 - 835,390 years before present and the effective population size depend on the lineage’s distributed deme size. In this study, the short time to the most recent common ancerstor (TMRCA) and low diversity support Taiwan clade’s colonization is relatively recent, but its long divergence time between original clade did not support. We consider that C. sinensis in Taiwan to the edge of the wave, lower deme size, and lower migration rate favor the survival of a new mutation. This surfing mutation phenomenon influences the colonization’ history of Taiwan C. sinensis to reach very frequencies and eventually occupy a large area without selection or founder effect.

Abdo, Z., Minin, V.N., Joyce, P. & Sullivan, J. Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phyloheny estimation. Molecular Biology and Evolution 22, 691-703. 2005.
Adsersen, H. Research on island:classic, recent, and prospective approaches. In P.M. Vitousek, L.L. Loop, and H. Adsersen (eds.), Islands: biological diversity and ecosystem function, 7-21. Spring-Verlag, Berlin, Germany. 1995.
Avise, J.C. Molecular Markers, Natural History and Evolution. Chapman & Hall, New York, NY. 1994.
Avise, J.C. Phylogeography: the History and Formation of Species. Harvard University Press, Cambridge, MA. 2000.
Avise, J.C. Molecular Markers, Natural History, and Evolution. Sinauer, Sunderland, MA. 2004.
Avise, J.C., Arnold, J., BallJr, R.M., Bermingham, E., Lamb, T., Neigel, E., Reeb, C.A. & Saunder, N.C. Intraspecific phylogeography: the mitochrondrial DNA bridge between population genetics and systematics. Ann. Rev. Ecol. Syst., 18, 489-522. 1987.
Ayala, F.J. Vagaries of the molecular clock. Proc. Natl. Acad. Sci. USA, 94, 7776-7783. 1997.
Banarescu, P. In: Zoogeography of Fresh Waters, Vol. 1. AULA-Verlag, Wiesbaden. 1990.
Banarescu, P. In: Zoogeography of Fresh Waters, Vol. 2. AULA-Verlag, Wiesbaden. 1991.
Banarescu, P. Distribution and Dispersal of Freshwater Animals in North America and Eurasia. Aula-Verlag: Wiesbaden. 1992.
Banarescu, P. & Coad, B.W. Cyprinids of Eurasia. In: Cyprinid Fishes. Systematics, Biology and Exploitation. Fish and Fisheries Series, Vol. 3. (eds. Winfield IJ, Nelson JS), pp. 127–155. Chapman & Hall, London, Stanford University Press, Stanford. 1991.
Beerli, P., Hotz, H. & Uzzell, T. Geologically dated sea barriers calibrate a protein clock for Aegean water frogs. Evolution, 50, 1676-1687. 1996
Bermingham, E. & Martin, A.P. Comparative mtDNA phylogeography of Neotropical freshwater fishes: testing shared history to infer the evolutionary landscape pf lower Central America. Molecular Ecology, 7, 499-519. 1998.
Bermingham, E., McCafferty, S.S. & Martin, A.P. Fish biogeography and molecular clocks: perspectives from the Panamanian Isthmus. In. Molecular Systematics of Fishes. (eds Kocher TD, Stepien CA) pp.113-128. Academic Press, San Diego. 1997.
Bernatchez, L. & Wilson, C.C. Comparative phylogeography of Nearctic and Palearctic fishes. Mol. Ecol. 7(4), 431-452. 1998.
Berrebi, P., Boissin, E., Fang, F. & Cattaneo-Berrebi, G. Intron polymorphism (EPIC-PCR) reveals phylogeographic structure of Zacco platypus in China: a possible target for aquaculture development. Heredity, 94, 589-598. 2005.
Berrebi, P., Retif, X., Fang, F. & Zhang, C.G. Population structure and systematics of Opsariichthys bidens (Osteichthyes: Cyprinidae) in south-east China using a new nuclear marker: the introns (EPIC-PCR). Biological Journal of the Linnean Society, 87, 155-166. 2006.
Blin, N. & Stafford, D.W. A general method for isolation of high molecular weight DNA from eukaryotes. Nucleic Acids Research, 3, 2303–2308. 1976.
Brown, J.H. & Lomolino, M.V. Biogeography end. Sinauer Associates, Sunderland, Massachusetts. 1998.
Brown, J.H. & Gibson, A.C. Biogeography. Mosby Company, St. Louis. 1983.
Bruyn, M.D., Wilson, J.C. & Mather, P.B. Reconciling geography and genealogy: phlogeography of giant freshwater prawns from the lake carpentaris region, Molecular Ecology, 13, 3515-3526. 2004.
Caicedo, A.L. & Schaal, B.A. Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene. Molecular Ecology, 13, 1871-1882. 2004.
Cavender, T.M. & Coburn, M.M. Phylogenetics relationships of North American Cyprinidae. In: Mayden, R.L. (Ed.), Systematics, Historical Ecology, and North American Freshwater Fishes. Chapman & Hall, Londom, pp. 293-327. 1992.
Chang, Y. S., Huang, F.L. & Lo, T.B. The complete nucleotide sequence of carp （Cyprinus carpio）mitochondrial genome. J. Mol. Evol. 38, 138-155. 1994.
Chen, J.Y. Study on biogeohraphy and phylogeny of rhacophorid frogs in Taiwan. Master’s Thesis, National Taiwan Normal University. 1995.
Chen, Y. & Cao, W. & Zheng, C. Ichthyofauna of the Zhujiang River with a discussion on zoogeographical divisions for freshwater fishes. Acta Hydrobiology Sinica, 10, 228-236. 1986.
Chen, I.S. & Chang, Y.C. A Photographic Guide to the Inlandwater Fishes of Taiwan. Vol. 1. Cypriniformes. Sueichan Press, Taiwan. 2005.
Chen, X.L., Chiang T.Y., Lin, H.D., Zheng, H.S., Shao, K.T., Zhang, Q & Hsu K.C. Mitochondrial DNA Phylogeography of Glyptothorax fokiensis and G. hainanensis in Asia. Journal of Fish biology, 70, 1-19. 2007.
Chiang, T.Y. Lineages sorting accounting for the disassociation between chloroplast and mitochrondrial lineages in oaks of southern France. Genome, 43, 1090-1094. 2000.
Chiang, T.Y. & Schaal, B.A. Molecular evolution and phylogeny of the atpB-rbcL spacer of chloroplast DNA in true mosses. Genome, 43, 417–426. 2000.
Clifford, S. L., McGinnity, P. & Ferguson, A. Genetic changes in an Atlantic salmon population resulting from escaped juvenile farm salmon. Journal of Fish biology, 52(1), 118-127. 1997.
Crandall, K.A. & Templeton, A.R. Empirical tests of some predictions from coalescent theory with application to intraspecific phylogeny reconstructure. Genetics, 134, 959-969. 1993.
Crawford, D.J. Plant molecular systematics:macromolecular approaches. John Wiley, New York, USA. 1990.
Culling, M.A., Jako, K., Boron, A., Vasilev, V.P., Cote, I.M. & Hewitt, G.M. European colonization by the spined loach (Cobitis taenis) from Ponto-Caspian refugia based on mitochrondrial DNA variation. Molecular Ecology, 15, 173-190. 2006.
Cunningham, C.W. Can three incongruence tests predict when data should be combined? Molecular Biology and Evolution, 14, 733-740. 1997.
Curnutt, J.L., Pimm, S.L. & Maurer, B.A. Population variability of sparrows in space and time. Oikos, 76,131-144. 1996.
Currat, M., Excoffier, L., Maddison, W., Otto, S.P., Nicolas, R., Whitlock, M.C. & Yeaman, S. Comment on “Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens” and “Microcephalin, a gene regulating brain size, continues to evolve adaptively in Humans”. Science, 313, 172a. 2006.
Doadrio, I. & Perdices, A. Phylogenetic relationships among the Ibro-African cobitids (Cobitis, Cobitidae) based on cytochrome b sequence data. Molecular Phylogenetics and Evolution, 37, 484-493. 2005.
Drummond, A.J. & Rambaut, A. BEAST, version 1.3. University of Oxford, Oxford, UK. 2005.
Dynesius, M. & Jansson, R. Evolutionary consequences of changes in species; geographical distributions driven by Milankovitch climate oscillations. Proceedings of the National Academy of Sciences USA, 97, 9115-9120. 2000.
Edmonds, C.A., Lillie, A.S. & Cavalli-Sforza, L.L. Mutations arising in the wave front of an expanding population. Proc. Natl. Acad. Sci. USA 101, 975-979. 2004.
Edwards, S.V. & Beerli, P. Perspective: gene divergence, population divergence, and variance in coalescence time in phylogeographic studies. Evolution, 54,6, 1839 -1854. 2000
Emerson, B.C. Evolution on oceanic island: molecular phylogenetic approaches to understanding patters and process. Mol. Ecol. 11, 951-966. 2002.
Excoffier, L. Analysis of Molecular Variance. Version 1.55. Genetics and Biometry Laboratory, University of Geneva. 1993.
Excoffier, L. & Smouse, P.E. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species, molecular variance parsimony. Genetics, 136, 343-359. 1994.
Excoffier, L., Smouse, P.E. & Quattro, J.M. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA data. Genetics 131, 479-491. 1992.
Felsenstein, J. PHYLIP (Phylogeny Inference Package) Version 3.6a2. Distributed by the author. Department of Genetics, University of Washington, Seattle. 1993.
Fu, Y.X . Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics, 147, 915–925. 1997.
Fu, Y.X. & Li, W.H. Statistical tests of neutrality of mutations. Genetics, 133, 693-704. 1993.
Futuyma, D.J. Evolutionary biology, 2nd ed. Sinauer, Sunderland, Massachusetts, USA. 1997.
Griswold, C.K. & Baker, A.J. Time to the most recent common ancestor and divergence times of populations of common chaffinches (Fringilla coelebs) in Europe and North Africa: insights into Pleistocene refugia and current levels of migration. Evolution, 56, 143-153. 2002.
Gyllenberg, M. & Hanski, I. Single-Species metapopulation dynamics – a structured model. Theoretical Population Biology, 42, 35-61. 1992.
Hasegawaet, M.H., Kishino, H. & Yano, T. Dating of the human-ape splitting by a molecular clock of mitochrondrial DNA. J. Mol. Evol. 21, 160-174. 1985.
Hey, J. & Nielsen R. Multilocus methods for estimating population size, migration rates, and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747-760. 2004.
Higgins, D.G., Bleasby, A.J. & Fuchs, R. CLUSTAL V: improved software for multiple sequence alignment. CABIOS 8: 189-191. 1992.
Hikida, T. & Ota, H. Biogeography of reptiles in the subtropical East Asia Island. Pp. 11-28. In K.Y. Lue and T.H. Chen (eds.) Proceeding the symposiumon the phylogeny, biogeography and conservation of fauna and flora of East Asian region. National Science Council, Taipei. 1997.
Humphries, C.J.& Parenti, L.R. Cladistic biogeography. Clarendon Press, Oxford, UK. 1986.
Hundson, R.R, Slatkin, M. & Maddison, W.P. Estimation of levels of gene flow from DNA sequence data. Genetics, 132,583-59. 1992.
Janko, K., Culling, M.A., Rάb, P. &Kotlik, P. Ice age cloning-comparison of Quaternary evolutionary histories of sexual and clonal forms of spiny loaches (Cobitis; Teleostei) using the analysis of mitochrondrial DNA variation. Molecular Ecology, 14, 10, 2991-3004. 2005.
Jennings, W.B. & Edwards, S.V. Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution, 59,9, 2033-2047. 2005.
Johns, G.C. & Avise, J.C. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology Evolution, 15, 1481-1490. 1998.
Jukes, T.H. & Cantor, C.R. Evolution of protein molecules. In Mammalian protein metabolism. (ed. Monro HN) pp. 21–132. Academic Press, New York. 1969.
Kimura, M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Mol. Evo., 16: 111-120. 1980.
Kimura, M. Quaternary paleogeography of Ryukyu Arc. J. Geo. 105, 259-285. 1996.
Kirkpatrick, M. & Barton, N.H. Evolution of a species’ range. American Naturalist, 150,1-23. 1997.
Kizaki, K., Oshrio, I. Paleogeography of the Ryukyu Islands. Marine Science Monthly, 9, 542-549. 1977.
Klopfstein, S., Currat, M. & Excoffier, L. The fate of mutations surfing on the wave of a range expansion. Mol. Biol. Evol. 23 (3), 482-490. 2006.
Knowles, L.L. & Maddison, W.P. Statistical phylogeography. Molecular Ecology, 11, 2623-2635. 2002.
Kotlik, P. & Berrebi, P. Phylogeography of the barbel (Barbus barbus) assessed by mitochondrial DNA variation. Molecular Ecology, 10, 2177-2185. 2001.
Kumar, S., Tamura, K., Jakobsen, I.B. & Nei, M. MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics, 17, 1244–1245. 2001.
Lande, R. Population dynamics and extinction in heterogeneous environments: the northern spotted owel. In : Bird population studies. Relevance to conservation and management (eds. Perrins CM, Lebreton J-D, Hirons GJM, pp. 566-580. Oxford University Press, Oxford. 1991.
Lawton, J.H. Range, population abundance and conservation. Trends in Ecology and Evolution, 8, 409-413.
Lesica, P. & Allendorf, F.W. When are peripheral-populations valuable for conservation. Conservation Biology, 9, 753-760. 1995.
Li, S.Z. Studies on zoogeographical divisions for fresh water fishes of China. Science Press, Bsijing, China. 1981.
Li, S.H., Huang, Y.J. & Brown, J.L. Isolation of tetranucleotide microsatellite from the Mexican jay Aphelocoma ultramarina. Mol. Eco. 6(5), 499-501. 1997.
Li, W.H. & Zharkikh, A. Statistical tests of DNA phylogenies. Systemstic Biology 44: 49-63. 1997.
Lin, C.C. An outline of Taiwan’s Quaternary geohistory with a special discussion of the relation between natural history and cultural history in Taiwan. Bulletin of the Department of Archaeology and Anthropology, 23, 7-44. 1966.
Lin, S.M., Chen, C.A. Lue, K.Y. Molecular phylogeny and biogeography of the grass lizards genus Takydromus (Reptilia: Lacertidae) of East Asia. Molecular Phylogenetics and Evolution, 22, 276-288. 2002.
Liu, H.T. & Su, T.T. Pliocene fishes from Yushe basin, Shanxi. Vert. Parasiat., 6, 1-25. 1962.
Lomolino, M.V. & Channell, R. Splendid isolation – patterns of geographic range collapse in endangered mammals. Journal of Mammalogy, 76, 335-347. 1995.
MacArthur, R.H. Geographical Ecology-Patterns in the Distributionn of Species. Princeton: Princeton University Press. 1972.
Mesquita, N., Hanfling, B., Carvalho, G.R. &Coelho, M.M. Phylogeography of the cyprinid Squalius aradensis and implications for conservation of the endemic freahwater fauna of southern Portugal. Molecular Ecology, 14, 1939-1954. 2005.
Meyer, A. Evolution of mitochondrial DNA in fishes. In The Biochemistry and Molecular Biology of Fishes. Vol. 2, (eds. Hochachka PW, Mommsen TP), pp.1-38. Elsevier, Amsterdam. 1993.
Montoya-Burgos, J.I. Historical biogeography of the catfish genus Hypostomas (Siluriformes: Loricariidae), with implications on the diversification of Neotropical ichthyofauna. Molecular Ecology, 12, 1855-1867. 2003.
Mori, T. Studies on the geographical distribution of freshwater fishes of Eastern Asia. Pp.88. 1936.
Muller-Dombois, D. Island ecosystem: what is unique about their ecology? In Muller-Dombois, D., Bridges, K.W., and Carson, H.L. (eds.) Island Ecosystem, Stroudsburg: Hutchinson, 485-501. 1981.
Nei, M. & Tajima, F. Maximum likelihood estimation of the number of nucleotide substitutions from restriction sites data. Genetics, 105, 207–217. 1983.
Nelson, C. & Platnick, N.L. Biogeography.Carolina Biology Reader. 1984.
Nielsen, R & Wakeley, J. Distinguishing migration from isolation: a Markov Chain Monte Carlo approach. Genetics, 158, 885-896. 2001.
Numachi, K. I., Kobayashi, T., Chang, K.H. & Lin, Y.S. Genetic identification and differentiation of the Formosan salmon, Oncorhynchus masou formosanus, by restriction analysis of mitochondrial DNA. Bull. Inst. Zool. Acad. Sinica 29(3, supplement), 61-72. 1990.
Oshima, M. III. Contribution to the study of the fresh water fishes of the island of Formosa. Annals of the Carnegie Museum. V. 12:169-328, Pls:XLVIII-LIII. 1919.
Page, R.D.M. Temporal congruence revisited: Comparison of mitochrondrial DNA sequence divergence in cospeciation pocket gophers and their chewing lice. Systematic Biology, 45, 151-167. 1996.
Page, B.M. & Suppe, J. The Pliocene lichi mélange of Taiwan: Its plate tectonic and olistostromal origin. Am. J. Sci., 281, 193-227. 1981.
Perdics, A., Cunha, C. & Coelho, M.M. Phylogenetic structure of Zacco platypus (Teleostei, Cyprinidae) populations on the upper and middle Chang Jiang (=Yangtze) drainage inferred from cytochrome b sequences. Molecular Phylogenetics Evolution, 31, 192-203. 2004
Posada, D. & Crandall, K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818. 1998.
Posada, D., Crandall, K.A. & Templeton, A.R. GEODIS: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology 9, 487-488. 2000.
Perduces, A & Doadrio, I. The molecular systematics and biogeography of the European cobitids based on mitochrondial DNA sequences. Molecular Phylogenetics and Evolution, 19, 468-478. 2001.
Quattro, J. M., Leberg, P. L., Douglas, M.E. & Vrijenhoek, R.C. Molecular evidence for a unique evolutionary lineage of endangered Sonoran desert fish (genus Poeciliopsis). CONSERV. BIOL. 10(1): 128-135. 1996.
Rainboth, W.J. Cyprinid of South Asia. In: Cyprinid Fishes. Systematics, Biology and Exploitation. Fish and Fisheries Series, Vol. 3. (eds. Winfield IJ, Nelson JS) pp. 156–210. Chapman & Hall, London. 1991.
Rambaut, A. & Drummond, AJ. TRACER, version 1.2. University of Oxford, Oxford, UK. 2004.
Randi, E., Tabarroni, C. & Kark, S. The role of history vs. demography in shaping genetic population structure across an ecotone: chukar partridges (Alectoris chukar) as a case study. Diversity and Distributions, 12, 714-724. 2006
Refseth, U.H., Nesbo,C.L., Stacy, J.E., Vollestad, L.A., Fjeld, E. & Jakobsen, K.S. Genetic evidence for different migration routes of freshwater fish into Norway revealed by analysis of current perch (Perca fluviatilis) populations in Scandinavia. Mol. Eco. 7 (8), 1015-1027. 1998.
Reusch, T.B.H., Wegner, K.M. & Kalbe, M. Rapid genetic divergence in postglacial populations of three spine sticklebackl (Gasterosteus aculeatus): the role of habit type, drainage and geographical proximity. Molecular Ecology, 10, 2435-2445. 2001.
Rogers, A.R. Genetic evidence for a Pleistocene population explosion. Evolution 49, 608-615. 1995.
Roger, A.R. & Harpending, H. Population growth makes waves in the distribution of pairwise genetic differences. Molecular Biology and Evolution, 9, 552-569. 1992.
Rozas, J. & Rozas, R. DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15, 174–175. 1999.
Sanderson, M.J. A nonparametric approach to estiming divergence times in the absence of rate constancy. Molecular Biology and Evolution, 14, 1218-1231. 1997.
Sanderson, M.J. r8s: Analysis of rates (‘‘r8s’’) of evolution (and other stuff), version 1.5. Section of Evolution and Ecology, Univ. of California, Davis. Distributed at http://ginger.ucdavis.edu/r8s/.2002.
Sivasunder, A., Bermingham, E. & Orti, G. Population structure and biogeography of migratory freshwater fishes (Prochilodus: Characiformes) in major South American rivers. Molecular Ecology, 10, 407-417. 2001.
Slatkin, M. Gene flow in natural population. Ann. Rev. Ecol. Syst. 16: 393-430.
Swofford DL. 1999. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4.0. Sinauer Associates, Sunderland, Massachusetts. 1985.
Sponer, R. & Roy, M.S. Phylogeographic analysis of the brooding brittle star Amphipholis squamate (Echinodermata) along thecoast of New Zealand reveals high cryptic genetic variation and cryptic dispersal potential. Evolution, 56, 1954-1967. 2002.
Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585-595. 1989.
Tang, Q., Liu, H., Mayden, R. & Xiong, B. Comparison of evolutionary rates in the mitochondrial DNA cytochrome b gene and control region and their implications for phylogeny of the Cobitoidea (Teleostei: Cypriniformes). Molecular Phylogenetics and Evolution, 39, 347-357. 2006.
Tchang, H.C., Chen, T.C. & Hung, K.C. The new geological structures in coastal line of South China. Earthquake Press, Beijing. 1990.
Templeton, A.R. Nested clade analyses of phylogeographic data: testing hypothesis about gene flow and population history. Molecular Ecology, 7, 381–397. 1998.
Templeton, A.R. Statistical phylogeography: methods of evaluating and minimizing inference errors. Molecular Ecology 13, 789–809. 2004.
Templeton, A.R., Routman, E. & Phillips, C.A. Separating population structure from population history: a cladistic analysis the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140, 767–782. 1995.
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. & Higgins, D.G. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acid Research, 24, 4876–4882. 1997.
Tsukada, M. Late Pleistocene vegetation and climate in Taiwan (Formosa). Anthropology, 5, 546-548. 1966.
Tzeng, C.S. Distribution of the freshwater fishes of Taiwan. Journal of Taiwan Museum, 39, 127-146. 1986.
Tzeng, C.S., Hui, C.F., Shen, S.C. & Huang, P.C. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome : conservation and variations among vertebrates. Nucleic Acids Res. 20: 4853-4858. 1992.
Tzeng, C.S., Shen, S.C. & Huang, P.C. Mitochondrial DNA identity of Crossostoma (Homalopteridae, Pisces) from two river systems of the same geographical origin. Bull. Inst. Zool. Acad. Sinica 29(1), 11-19. 1990.
Ujiie, H. Geographical history of the Ryukyu Island Arc. Pp. 251-255. In H. Ujiie (ed.) Nature of Okinawa; Geomorphology and geology. Hirugisha, Naha. 1990.
Vucetich, J.A. & Waite, T.A. Spatial patterns of demography and genetic processes across the species’ range: Null hypotheses for landscape conservation genetics. Conservation Genetics, 4, 639-645. 2003.
Wallace, A.R. Island Life. London:Macmillan. 1880.
Wang, H.Y., Tsai, M.P., Yu, M.J. & Lee, S.C. Influence of glaciation on divergence patterns of the endemic minnow, Zacco pachycaphalus, in Taiwan. Molecular Ecology, 8, 1879-1888. 1999.
Wang, J.P., Hsu, K.C. & Chiang, T.Y. Mitochondrial DNA phylogeography of Acrossocheilus paradoxus (Cyprinidae) in Taiwan. Moleular Ecology, 9, 1483-1494. 2000.
Wang, J.P., Lin, H.D., Huang, S., Pan, C.H., Chen, X.L. & Chiang, T.Y. Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes. Molecular Phylogenetics and Evolution, 31, 1143-1156. 2004.
Water, J.M. & Roy, M.S. Marine biogeography of southern Australia: phylogeographical structure in a temperate sea-star. Journal of Biogeography, 30, 1787-1796. 2003.
Waters, J.M., Craw, D., Youngson, J.H. & Wallis, G.P. Genes meet geology: fish phylogeographic pattern reflects ancient, rather than modern, drainage connections. Evolution, 55, 1844-4851. 2001.
Watterson, G.A. On the number of segregating sites in genetical models without recombination. Theoretical Population Biology, 7, 256-276. 1975.
Wright, S. Evolution in Mendelian populations. Genetics 16, 97-159. 1931.
Wright, S. The genetical structure of population structure. Ann. Eugen. 15, 323-354. 1951.
Wright, S. The interpretation of population structure F-statistics with special regard to systems of mating. Evolution 19, 395-420. 1965.
Wu, C.I & Li, W.H. Evidence for higher rates of nucleotide substitution in rodents than in man. Proceedings of the National Academy of Sciences of the United states of America, 82, 1741–1745. 1985.
Xiao, W., Zhang, Y. & Liu, H. Molecular systematics of Xenocyprinae (Teleostei: Cyprinidae): taxonomy, biogeography, and coevolution of a special group restricted in East Asia. Molecular Phylogenetics Evolution, 18, 163–173. 2001.
Yang, Z. On the estimation of ancestral population sizes of modern humans. Genetic Research, 69, 111-116. 1997.
Yeh, W.S., Yang ,Y.J. & Lin, Y.S. Phylogeographic structure of Rhacophorus moltrechti (Amphiia: Anura) in Taiwan. The Symposium on the Phylogeny, Biogeography, and Conservation of Fauna and Flora of east Asian region, pp. 29-44. 1997.
Zhang, D.X. & Hewitt, G.M. Nuclear integrations: challenges for mitochondrial DNA markers. Trends in Ecology and Evolution, 11, 247–251. 1996.
Zheng, H.S. “Freshwater fish fauna and biogeography of eight rivers in east Guangdong, China,” Master dissertation. Institute of Zoology, the South China Normal University. 2004.
Zhou, J. The Cyprinidae fossils from middle Miocene of Shanwang. Vert. Palasiat., 28, 95-127. 1990.
王慎之。台灣近海產小沙丁魚屬魚類類緣關係之研究。國立台灣海洋大學海洋生物研究所碩士論文。1993。
王子元。台灣與鄰近地區腹吸鰍族魚類之親緣關係研究。國立清華大學生命科學研究所碩士論文。1997a。
王昱人。台灣鉤吻鮭與日本櫻花鉤吻鮭遺傳多樣性之研究。國立清華大學生命科學研究所碩士論文。1997b。
李思忠。中國淡水魚類的分布區劃。科學出版社。北京。1981。
林朝棨。台灣地形。台灣省文獻委員會印行。台北。1957。
林朝棨。概說台灣第四紀的地史觀討論其自然史和文化史的關係。國立台灣大學考古人類學刊。 28：7-44。1966。
林思民。青將魚粒線體去氧核醣核酸控制區（D-loop）之研究。國立清華大學生命科學研究所碩士論文。1995。
桑自剛。利用粒線體去氧核醣核酸序列分析日本鰻之族群結構。國立台灣海洋大學漁業科學研究所碩士論文。1992。
張春霖。中國淡水魚類分布。地理學報, 20(3), 279-284。1954。
张虎男，陈伟光，黄坤荣等. 华南沿海新构造运动与地质环境.北京：地震出版社,1990。
張廖年鴻。利用粒線體去氧核醣核酸片段探討雀鯛科魚類之類緣關係。國立台灣海洋大學。海洋生物研究所碩士論文。1996。
陳正平。利用形態及粒線體去氧核醣核酸的12S rRNA序列探討天竺鯛科魚類分類與類緣關係。國立台灣大學海洋研究所博士論文。1996。
曾晴賢。台灣產平鰭鰍科魚類之研究。文化大學海洋所碩士論文。1981。
曾晴賢。台灣纓口鰍之粒線體基因組和台灣產平鰭鰍科魚類之分子演化的研究。國立台灣大學動物學研究所博士論文。1992。
黃國峰。台灣水域盲鰻粒線體去氧核醣核酸與系統分類之研究。國立中山大學海洋生物研究所碩士論文。1990。
趙松喬。台灣海峽。地理知識。9(10):435-438。1958。
簡春潭。台灣周邊海域鯛亞科（鱸形目：鯛科）魚類種間親緣關係及種內族群遺傳之研究。國立台灣海洋大學漁業科學研究所博士論文。995。
魏柏林,冯绚敏，陈定国等，东南沿海地震活动特征.北京：地震出版社，2001。