本研究定序出台灣及鄰近地區鯉科魚丹亞科魚類的粒線體D-loop DNA序列，及台灣產五種珊瑚粒線體基因組，並利用這些序列所含有的訊息，來探討魚丹亞科魚類在台灣海峽兩岸的族群演化，以及分析各種珊瑚粒線體基因序列，建構珊瑚蟲綱之分子類緣關係，並找出適合做為分子鑑定的基因片段。由於台灣縱紋獵及粗首馬口獵在恆春半島地區的形態皆有明顯的分化，進一步以粒線體D-loop序列分析，發現台灣縱紋獵共可區分出六個地理區族群，其中同樣以恆春半島的差異最為顯著。而大陸西南沿岸河系的平頜獵及馬口魚，在福建及閩北浙江之間有明顯的區隔。這些結果顯示隨著冰河期海平面下降，海峽兩岸的魚丹亞科魚類會經由海峽底部露出的河系進行播遷，並受到山脈和海峽地形高低走勢的影響，產生不同程度的族群分化。本研究並利用粒線體D-loop序列建構魚丹亞科物種的分子類緣關係樹，發現與現行之分類系統有部份的差異，而有再檢討的必要。在珊瑚粒線體基因體DNA序列的分析中，六放及八放珊瑚的基因排序相當穩定，石珊瑚ND5基因皆含有一個大型的group I intron，另外圓管星珊瑚COI基因中含有一個較小的intron，並存在一個LAGLI-DADG基因家族的ORF。分子類緣關係分析中，本研究新定序的物種中，樹珊瑚科、真葉珊瑚科、鹿角珊瑚科及鞭珊瑚科皆為新定序出基因體的科，各大分類系群的結構則相當穩定。各別基因的分析中，除了COI、COIII、Cyt b及ND3外，其他基因的同類置換皆趨向飽和，異類置換中，除了12S和ATP8呈現明顯的飽和外，其他都未趨向飽和，本結果將可做為未來珊瑚分子鑑種的片段選擇參考。

Population studies and species identification based on morphological characteristics are often ambiguous. A different approach, e.g. molecular information, may be used to clarify the ambiguities . In this thesis, two categories of organisms, fish and corals, were chosen for study. The Danioninae, Candidia barbata and Opsariichthys pachycephalus, are extremely diversified morphologically among the Henchun peninsula and the northern Taiwan populations. Six geographic population of C. barbata were found using the mitochondrial D-loop DNA sequences. The sequences data also confirmed that the Henchun peninsula population was the most divergent group. On the other side of Taiwan strait, Opsariichthys bidens and Zacco platypus in northern Fujian province were also found to be divergent. It is likely that the Danioninae fishes migrated through the basins due to lowering of sea level during glacial stages. The discrepancies of morphological classification and molecular phylogenetics should be re-examined. The five coral mitochondrial genomes sequenced were Euphyllia ancora (19084 bp), Tubastrea aurea (18770 bp), Stylophora pistillata (17169 bp), Montipora aequituberculata (17886 bp), and Junceella fragilis (18724 bp). The gene organization of Octocorallia and Hexacorallia were highly conserved. All the stony corals contain a group I intron in the ND5 gene. In addition, the COI gene of Tubastrea aurea contains an extra intron, which consists an ORF of the LAGLI-DADG gene family. Of all the genes analysed, the transition rates were saturated except COI, COIII, Cytb and ND3; on the other hand, only 12S and ATP8 were saturated for the transversion rates. The results might refer to new gene markers for future species identification of corals.

壹、粒線體基因與物種演化之研究
一、粒線體的起源與演化 …………………………………………………………… 1
二、粒線體基因體的多樣性 ……………………………………………………….... 1
三、粒線體基因體在高階動物分類的應用 ………………………………………… 2
四、粒線體D-loop序列在動物族群類緣關係的應用 ……………………………... 3
五、本論文的研究目的 ……………………………………………………………… 4
六、參考文獻 ………………………………………………………………………… 4

貳、從台灣海峽隔離探討鯉形目魚丹亞科之族群演化
一、 前言
1. 台灣島的形成與地質構造 ………………………………………………………… 7
2. 更新世至今的冰河期現象 ………………………………………………………… 9
3. 冰河週期對生物的影響 …………………………………………………………… 10
4. 以粒線體做為在族群地理類緣關係研究的工具 ………………………………… 12
5. 台灣的分子地理類緣關係論文 …………………………………………………… 13
6. 台灣海峽兩岸的獵屬及近緣魚類 ………………………………………………… 14
7. 本論文研究目的 …………………………………………………………………… 15

二、材料與方法
1. 物種選擇 …………………………………………………………………………... 17
2. 標本採集與保存 …………………………………………………………………… 17
3. 形態測量 …………………………………………………………………………… 17
4. 粒線體D-loop DNA定序 ………………………………………………………….. 18
5. DNA序列分析 ……………………………………………………………………... 19
三、結果
1. 台灣縱紋獵的形態分化 …………………………………………………………… 21
1-1 台灣縱紋獵 ………………………………………………………………………. 21
1-2. 屏東縱紋獵 ……………………………………………………………………… 26
1.3 附記 ……………………………………………………………………………….. 29
2. 粗首馬口獵的形態分化 …………………………………………………………… 31
2-1. 粗首馬口獵 ……………………………………………………………………… 31
2-2. 高屏馬口獵 ……………………………………………………………………… 36
2.3 附記 ……………………………………………………………………………….. 39
3. 台灣縱紋獵之分子類緣關係 ……………………………………………………… 41
3-1. 台灣縱紋獵族群D-loop序列特性及多樣性
3-2. 台灣縱紋獵分子類緣關係分析
4. 大陸東南沿海地區馬口魚及平頜獵之分子類緣關係 …………………………… 43
4-1. 族群D-loop序列特性及多樣性
4-2. 大陸東南地區產馬口魚及平頜獵分子類緣關係分析
5. 獵屬及近緣魚類之分子類緣關係 ………………………………………………… 44
5.1 獵屬近緣種的檢索表
5-2. 獵屬近緣種D-loop序列特性及多樣性
5-3. 獵屬近緣種分子類緣關係

四、討論
1. 台灣縱紋獵的形態分化 …………………………………………………………… 46
2. 粗首馬口獵的形態分化 …………………………………………………………… 47
3. 台灣縱紋獵之分子類緣關係 ……………………………………………………… 49
3-1. 台灣縱紋獵的起源與分布
3-2. 台灣縱紋獵的分子生物地理學
3-3. 從分子鐘的計算來推估台灣縱紋獵的播遷歷史
3-4. 台灣更新世末期地理環境對台灣縱紋獵分布的影響
3-5. 台灣縱紋獵內部的種化
3-6. 台灣縱紋獵的水系特有族群保育
4. 大陸東南沿海地區馬口魚及平頜獵之分子類緣關係 …………………………… 53
5. 獵屬及近緣魚類之分子類緣關係 ……………………………………………….... 54
5-1. 縱紋獵屬組成物種分析
5-2. 獵屬之分類
5-3. 馬口獵屬組成物種分析及其多樣性
5-4. 獵屬及近緣種之命名問題

五、結論 ………………………………………………………………………………... 57
六、參考文獻 …………………………………………………………………………. 59

參、台灣產五種珊瑚粒線體之研究
一、前言
1. 珊瑚的定義及分類 ………………………………………………………………… 77
2. 珊瑚生態與多樣性 ………………………………………………………………… 78
3. 珊瑚的演化與分子類緣關係研究 ………………………………………………… 79
4. 珊瑚粒線體基因的研究 …………………………………………………………… 80
5. 台灣的珊瑚論文研究 ……………………………………………………………… 81
6. 本論文研究目的 …………………………………………………………………… 82
7. 本研究使用物種介紹 ……………………………………………………………… 83

二、材料與方法
1. 樣品取得與保存 …………………………………………………………………… 86
2. DNA的萃取 ………………………………………………………………………... 86
3. 珊瑚粒線體DNA短片段增幅反應 ………………………………………………. 87
4. 長片段DNA增幅及定序 …………………………………………………………. 88
5. DNA序列分析 ……………………………………………………………………... 89

三、結果
1. Long PCR法增幅粒線體DNA ……………………………………………………... 91
2. 珊瑚粒線體基因體的組成、大小及特性 ………………………………………… 91
3. 基因排序與基因間隔 ……………………………………………………………… 92
4. Protein coding基因及核糖體基因 …………………………………………………. 93
5. 轉譯起始碼及終止碼 ……………………………………………………………… 94
6. tRNA基因 ………………………………………………………………………….. 95
7. 珊瑚粒線體基因的飽和度測試 …………………………………………………… 95
8. 分子類緣關係分析 ………………………………………………………………… 95

四、討論
1. 本研究的具體成果 ………………………………………………………………... 97
2. 本研究珊瑚粒線體定序的正確性 ………………………………………………... 97
3. 珊瑚粒線體基因體的特性 ………………………………………………………... 98
4. 珊瑚粒線體基因體具有的特殊序列 ……………………………………………... 98
5. 以珊瑚粒線體基因做為鑑種的工具 …………………………………………….. 99
6. 珊瑚的分子類緣關係 ……………………………………………………………. 100

五、參考文獻 ………………………………………………………………………... 103
肆、總結 ………………………………………………………………………… 113

Boore, J.L. 1999. Animal Mitochondrial Genomes. Nucleic Acids Research, 27(8):1767-1780.
Burger, G., D.V. Lavrov, L. Forget, and B.F. Lang. 2007. Sequencing complete mitochondrial and plastid genomes. Nature Protocols, 2(3):603-614.
Chen, I.S., C.H. Hsu, C.F. Hui, K.T. Shao, P.J. Miller and L.S. Fang. 1998. Sequence length and variation of mitochondrial control region from two freshwater gobiid fishes belonging to Rhinogobius (Teleostei: Gobiidae). Journal of Fish Biology, 53(1):179-191.
Chu, J.H., Y.S. Lin, H.Y. Wu. 2007. Evolution and dispersal of three closely related macaque species, Macaca mulatta, M. cyclopis, and M. fuscata, in the eastern Asia. Molecular Phylogenetics and Evolution. 43:418-429.
Clayton, D.A. 1982. Replication of Animal Mitochondrial DNA. Cell, 28:693-705.
Coskun, P.E., E. Ruiz-Pesini, and D.C. Wallace. 2003. Control Region mtDNA Variants: Longevity, Climatic Adaptation, and a Forensic Conundrum. PNAS, 100(5):2174-2176.
Gray, M.W., G. Burger, and B.F. Lang. 2001. The Origin and Earily Evolution of Mitochondria. Genome Biology, 2(6):reviews1018.1-1018.5.
Haen, K.M., B.F. Lang, S.A. Pomponi, and D.V. Lavrov. 2007. Glass Sponge and Bilaterian Animals Share Derived Mitochondrial Genomic Features: A Common Ancestry or Parallel Evolution? Mol. Biol. Evol., 24(7):1518-1527.
Lang, B.F., D.V. Lavrov, and G. Burger. 2004. Mitochondrial Genome, Evolution. Encyclopedia of Biological Chemistry, 2:703-708.
Lavrov, D.V. W.M. Brown, and J.L. Boore. 2000. A Novel type of RNA Editing Occurs in the Mitochondrial tRNA of the Centipede Lithobius forficatus. PNAS, 97(25):13738-13742.
Lavrov, D.V. and W.M. Brown. 2001. Trichinella spiralis mtDNA: A Nematode Mitochondrial Genome That Encodes a Putative ATP8 and Normally Structured tRNAs and Has a Gene Arrangement Relatable to Those of Coelomate Metazoans. Genetics, 157:621-637.
Lavrov, D.V., J.L. Boore, and W.M. Brown. 2002. Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss. Mol. Biol. Evol., 19(2):163-169.
Lavrov, D.V., W.M. Brown, and J.L. Boore. 2004. Phylogenetic Position of the Pentastomida and (pan)crustacean relationships. Proc. R. Soc. Lond. B, 271:537-544.
Lavrov, D.V. and B.F. Lang. 2005. Poriferan mtDNA and Animal Phylogeny Based on Mitochondrial Gene Arrangements. Syst. Biol., 54(4):651-659.
Lavrov, D.V., L. Forget, M. Kelly, and B.F. Lang. 2005. Mitochondrial Genomes of Two Demosponges Provide Insights into An Early Stage of Animal Evolution. Mol. Biol. Evol., 22(5):1231-1239.
Lavrov, D.V. and B.F. Lang. 2005. Transfer RNA Gene Recruitment in Mitochondrial DNA. TRENDS in Genetics, 21(3):129-133.
Lavrov, D.V. 2007. Key Transitions in Animal Evolution: a Mitochondrial DNA Perspective. Integrative and Comparative Biology Advance Access Publishd, 1-10.
Lee, W.J., J. Conroy, W.H. Howell, and T.D. Kocher. 1995. Structure and Evolution of Teleost Mitochondrial Control Region. J. Mol. Evol., 41:54-66.
Medina, M., A.G. Collins, T.L. Takaoka, J.V. Kuehl, and J.L. Boore. 2006. Naked corals: Skeleton loss in Scleractinia. PNAS, 103(24):9096-9100.
Saitoh, K., T. Sado, R.L. Mayden, N. Hanzawa, K. Nakamura, M. Nishida, and M. Miya. 2006. Mitogenomic Evolution and Interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): The First Evidence Toward Resolution of Higher-Level Relationships of the World’s Largest Freshwater Fish Clade Based on 59 Whole Mitogenome Sequences. J. Mol. Evol., 63:826-841.
Wang, J.P., H.D. Lin, S. Huang, C.H. Pan, X.L. Chen and T.Y. Chiang. 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. and D.V. Lavrov. 2007. Mitochondrial Genome of the Homoscleromorph Oscarella carmela (Porifera, Demospongiae) Reveals Unexpected Complexity in the Common Ancestor of Sponges and Other Animals. Mol. Biol. Evol., 24(2):363-373.

Ashiwa, H. and K. Hosoya. 1998. Osteology of Zacco pachycephalus, sensu Jordan and Evermann (1903), with special reference to its systematic position. Environmental Biology of Fishes, 52:163-171.
Banarescu, P. 1968. Revision of the genera Zacco and Opsariichthys (Pisces, Cyprinidae). Vestn. Cesk. Spol. Zool, 32(4):305-311, Pls. 1-2.
Banarescu, P. 1997. The status of some nominal genera of Eurasian Cyprinidae (Osteichthyes, Cypriniformes). Rev. Roum. Biol. Ser. Biol. Anim, 42(1):19-30.
Bird, M.I., L.K. Fifield, T.S. Teh, C.H. Chang, N. Shirlaw, and K. Lambeck. 2007. An inflection in the rate of early mid-Holocene eustatic sea-level rise: A new sea-level curve from Singapore. Estuarine, Coastal and Shelf Science, 71:523-536.
Bleeker, P. 1863. Systema Cyprinoideorum revisum. Neder. Tijdschr. Dierk, 1:187-218.
Boggs, S., Jr., W.C. Wang, F.S. Lewis, and J.C. Chen. 1979. Sediment properties and water characteristics of the Taiwan shelf and slope. Acta Oceanogr. Taiwan, 10:10-49.
Bose, M. 2006. Geomorphic altitudinal zonation of the high mountains of Taiwan. Quaternary International, 147:55-61.
Briolay, J, N. Galtier, R.M. Brito, and Y. Bouvet. 1998. Molecular Phylogeny of Cyprinidae Inferred from cytochrome b DNA Sequences. Molecular Phylogeny and Evolution, 9(1):100-108.
Boulay, S., C. Colin, A. Trentesaux, F. Pluquet, J. Bertaux, D. Blamart, C. Buehring and P. Wang. 2003. Mineralogy and sedimentology of Pleistocene sediment in the South China Sea (ODP Site 1144). In: Prell, W.L., P. Wang, P. Blum, D. K. Rea, and S.C. Clemens, (Eds.), Proceeding of the Ocean Drilling Program, Scientific Results, 184:1-21.
Brito, R.M., J. Briolay, N. Galtier, Y. Bouvet, and M.M. Coelho. 1997. Phylogenetic Relationships within Genus Leuciscus (Pisces, Cyprinidae) in Portuguese FreshWaters, Based on Mitochondrial DNA Cytochrome b Sequences. Molecular Phylogeny and Evolution, 8(3):435-442.
Chakraborty, A., M. Sakai and Y. Iwatsuki. 2006. Museum fish specimens and molecular taxonomy: A comparative study on DNA extraction protocols and preservation techniques. J. Appl. Ichthyol., 22:160-166.
Chen, Y.Y. 1982. A revision of opsariichthine cyprinid fishes. Oceanol. Limnol. Sin., 13(3):293-299. (In Chinese)
Chen, I.S., C.H. Hsu, C.F. Hui, K.T. Shao, P.J. Miller and L.S. Fang. 1998. Sequence length and variation of mitochondrial control region from two freshwater gobiid fishes belonging to Rhinogobius (Teleostei: Gobiidae). Journal of Fish Biology, 53(1):179-191.
Chen, I.S. and L.S. Fang. 1999. The freshwater and estuarine fishes of Taiwan. National Museum of Marine Biology & Aquarium. 287 pp.
Chen, Y.G. and T.K. Liu. 2000. Holocene uplift and subidence along an active tectonic margin aouthwestern Taiwan. Quaternary International, 19:923-930.
Chen, I.S., P.J. Miller, H.L. Wu and L.S. Fang, 2002. Taxonomy and mitochondrial sequence evolution in non-diadromous species of Rhinogobius (Teleostei: Gobiidae) of Hainan Island, southern China. Marine & Freshwater Research, 53:259-273.
Chen, I.S. and Y.C. Chang. 2005. A photographic Guide to the Inlandwater Fishes of Taiwan. Vol. I. Cypriniformes. 284 pp.
Chen, Y.G., J.B.H. Shyu, Y. Ota, W.S. Chen, J.C. Hu, B.W. Tsai, and Y. Wang. 2004. Active structures as deduced from geomorphic features: a case in Hsinchu Area, northwestern Taiwan. Quaternary International, 115-116:189-199.
Chen, M.T., C.C. Huang, U. Pflaumann, C. Waelbroeck, M. Kucer. 2005. Estimating glacial western Pacific sea-surface temperature: methodological overview and data compilation of surface sediment planktic foraminifer faunas. Quaternary Science Reviews. 24:1049-1062.
Chu, J.H., Y.S. Lin, H.Y. Wu. 2007. Evolution and dispersal of three closely related macaque species, Macaca mulatta, M. cyclopis, and M. fuscata, in the eastern Asia. Molecular Phylogenetics and Evolution. 43:418-429.
Cortey. M. and J.L. Garcia-Martin. 2002. Evidence for phylogeographically informative sequence variation in the mitochondrial control region of Atlantic brown trout. Journal of Fish Biology, 60:1058-1063.
Cui. Z, C. Yang, G. Liu, W. Zhang, S. Wang, and Q. Sung. 2002. The Quaternary glaciation of Shesan Mountain in Taiwan and glacial classification in monsoon areas. Quaternary International, 97-98:147-153.
Durand, J.D., A.R. Templeton, B. Guinand, A. Imsiridou and Y. Bouvet. 1999. Nested clade and phylogeographic analyses of the chub, Leuciscus cephalus (Teleostei: Cyprinidae), in Greece: Implications for Balkan Peninsula biogeography. Molecular Phylogenetics and Evolution, 13(3):566-580.
Durand J.D., Tsigenopoulos, C.S., Unlu E., and P. Berrebi. 2002. Phylogeny and Biogeography of the Family Cyprinidae in the Middle East Inferred from Cytochrome b DNA-Evolutionary Significance of This Region. Mol. Phylogenet. Evol., 22:91-100.
Eberli, G.P. 2000. The Record of Neogene Sea-level Changes in the Prograding Carbonates along the Bahamas Transect-LEG 166 Synthesus. pp. 167-177. In: Swart, P.K., G.P. Eberli, M.J. Malone, and J.F. Sarg (Eds.) Proceedings of the Ocean Drilling Program, Scientific Results, Vol. 166.
Excoffier, L. and P.E. Smouse, 1994. Using allele frequencies and geographic subdivision to reconstruct gene trees within a species: molecular variance parsimony. Genetics, 136:343-359.
Falk, T.M., G.G. Teugels, E.K. Abban, W. Villwock and L. Renwrantz. 2003. Phylogeographic patterns in populations of the black-chinned tilapia complex (Teleostei, Cichlidae) from coastal areas in West Africa: support for the refuge zone theory. Molecular Phylogenetics and Evolution, 27:81-92.
Froese, R. and D. Pauly. Editors. 2007.FishBase. World Wide Web electronic publication. www.fishbase.org, version (05/2007).
Froufe, E., I. Magyary, I. Lehoczky and S. Weiss, 2002. mtDNA sequence data supports an Asian ancestry and single introduction of the common carp into the Danube Basin. Journal of Fish Biology, 61:301-304.
Gilles, A., G. Lecointre, E. Faure, R. Chappaz, and G. Brun. 1998, Mitochondrial Phylogeny of the European Cyprinids: Implications for Their Systematics, Reticulate Evolution, and Colonization Time. Molecular Phylogeny and Evolution, 10(1):132-143.
Gilles, A., G. Lecointre, A. Miquelis, M. Loerstcher, R. Chappaz, and G. Brun. 2001. Partial Combination Applied to Phylogeny of European Cyprinids Using the Mitochondrial Control Region. Mol. Phylogenet. Evol., 19:22-33.
Guinand, B., Y. Bouvet and B. Brohon. 1996. Spatial aspects of genetic differentiation of the European chub in the Rhone River basin. Journal of Fish Biology, 49:714-726.
Gunther, A. 1868. Catalogue of the fishes in the British Museum. Catalogue of the Physostomi, containing the families Heteropygii, Cyprinidae, Gonorhynchidae, Hyodontidae, Osteoglossidae, Clupeidae,... [thru]... Halosauridae, in the colelction of the British Museum. Cat. Fishes v. 7: i-xx + 1-512.
Gunther, A. 1873. Report on a collection of fishes from China. Ann. Mag. Nat. Hist., 12:239-250.
Hanfling, B. and R. Brandl. 1998. Genetic and morphological variation in a common European cyprinid, Leuciscus cephalus within and across Central European drainages. Journal of Fish Biology, 52:706-715.
Hantoro, W.S. 1997. Quaternary sea level variations in the Pacific-Indian ocean gateways: Response and impact. Quaternary International, 37:73-80.
Hantoro, W.S. H. Faure, R. Djuwansah, L. Faure-Denard, and P.A. Pirazzoli. 1995. The Sunda and Sahul continental platform: Lost lad of the last glacial continent in S.E. Asia. Quaternary International, 29-30:129-134.
Haq, B. U., J. Hardenbol and P. R. Vail. 1987. Chronology of fluctuating sea levels since the Triassic. Science, 235(4793):1156-1167.
Hebenstreit, R. 2006. Present and former equilibrium line altitudes in the Taiwanese high mountain range. Quaternary International, 147.70-75.
Hebenstreit, R., M. Bose, and A. Murray. 2006. Late Pleistocene and early Holocene glaciations in Taiwanese mountains. Quaternary International, 147:76-88.
Hope, G., A.P. Kershaw, S.v.d. Kaars, S. Xiangjun, P. M. Liew, L.E. Heusser, H. Takahara, M. McGlone, N. Miyoshi and P.T. Moss, 2004. History of vegetation and habitat change in the Austral-Asian region. Quaternary International, 118-119:103-126.
Hosoya, K., H. Ashiwa, M. Watanabe, K. Mizuguchi and T. Okazaki. 2003. Zacco sieboldii, a species distinct from Zacco temminckii (Cyprinidae). Ichthyological Research, 50:1-8.
Hsieh, M.L., P.M. Liew and M.Y. Hsu, 2004. Holocene tectonic uplift on the Hua-tung coast, eastern Taiwan. Quaternary International, 115-116: 47-70.
Huang, C.Y., P.M. Liew, M. Zhao, T.C. Chang, C.M. Kuo, M.T. Chen, C.H. Wang, and L.F. Zheng. 1997. Deep sea and lake records of the Southeast Asian paleomonsoons for the last 25 thousand years. Earth and Planetary Science Letters, 146:59-72.
Huang, M.T., E.H.S. Tsao and H.T. Yu. 2004. Conservation genetics of Zacco pachycephalus by microsatellite DNA locus analyses (in Chinese with English abstract). Endemic Species Research, 6(1):17-27.
Imsiridou, A., Y. Karakousis, and C. Triantaphyllidis. 1997. Genetic Polymorphism and Differentiation Among Chub Leuciscus cephalus L. (Pisces, Cyprinidae) Population of Greece. Biochemical Systematics and Ecology, 25(6):537-546.
Imsiridou, A., A.P. Apostolidis, J.D. Durand, J. Briolay, Y. Bouvet, and C. Triantaphyllids. 1998. Genetic differentiation and phylogenetic relationships among Greek Chub Leuciscus cephalus L. (Pisces, Cyprinidae) populations as revealed by RFLP analysis of mitochondrial DNA. Biochemical Systematics and Ecology, 26:415-429.
Jang, M.H., M.C. Lucas, and G.J. Joo. 2003. The fish fauna of mountain streams in South Korean national parks and its significance to conservation of regional freshwater fish biodiversity. Biological Conservation, 114:115-126.
Johns, G.C. and J.C. Avise. 1998. A comparative summary of genetic distances in the vertebrates from the mitochondrial cytochrome b gene. Molecular Biology and Evolution, 15:1481-1490.
Jordan, D.S. and B.W. Evermann. 1902. Notes on a collection of fishes from the island of Formosa. Proc. U. S. Natl. Mus., 25(1289):315-368.
Jordan, D.S. and R.E. Richardson. 1909. A catalogue of the fishes of the islands of Formosa, of Taiwan, based on the collections of Dr. Hans Sauter. Memoirs Carnegie Museum, 4(4):159-204.
Ju, L., H. Wang, and D. Jiang. 2007. Simulation of the Last Glacial Maximum climate over East Asia with a regional climate model nested in a general circulation model. Palaeogeography, Palaeoclimatology, Palaeoecology, 248:376-390.
Jukes, T. H. and C. R. Canter. 1969. Evolution of protein molecules. pp. 21-132. In: Munro, H. N. (ed.), Mammalian Protein Metabolism, III. Academic Press. New York.
Kimura, S. 1934. Description of the fishes collected from the Yangtze-kiang, China, by the late Dr. K. Kishinouye and his party in 1927-1929. J. Shanghai Sci. Inst., 1:11-247.
Kohlmann, K., R. Gross, A. Murakaeva, and P. Kersten. 2003. Genetic variability and structure of common carp (Cyprinus carpio) populations throughout the distribution range inferred from allozyme, microsatellite and mitochondrial DNA markers. Aquat. Living Resour., 16:421-431.
Koller, O. 1927. Fische von der Insel Hai-nan. Ann. Naturhist. Mus. Wien., 41:25-49.
Kotlik, P. and P. Berrebi. 2002. Genetic subdivision and biogeography of the Danubian rheophilic barb Barbus petenyi inferred from phylogenetic analysis of mitochondrial DNA variation. Molecular Phylogenetics and Evolution, 24:10-18.
Kumar, S., K. Tamura and M. Nei. 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics, 5:150-163.
Lambeck, K., T.M. Esat and E.K. Potter. 2002. Links between climate and sea levels for the past three million years. Nature, 419:199-206.
Liew, P.M., C.M. Kuo, S.Y. Huang, and M.H. Tseng. 1998. Vegetation change and terrestrial carbon storage in eastern Asia during the Last Glacial Maximum as indicated by a new pollen record from central Taiwan. Global and Planetary Change, 16-17:85-94.
Liew, P.M., M.L. Hsieh and B.H. Shyu. 2004. An overview of coastal development in a Young Mountain Belt-Taiwan. Quaternary International, 115-116:39-45.
Liew, P.M., S.Y. Huang, and C.M. Kuo. 2006. Pollen stratigraphy, vegetation and environment of the last glacial and Holocene—A record from Toushe Basin, central Taiwan. Quaternary International, 147:16-33.
Liu, T.K., Y.G. Chen, W.S. Chen, and S.H. Jiang. 2000. Rates of cooling and denudation of the Early Penglai Orogeny, Taiwan, as assessed by fission-track constraints. Tectonophysics, 320:69-82.
Liu, H., C.S. Tzeng, and H.Y. Teng. 2002. Sequence variations in the mitochondrial DNA control region and their implications for the phylogeny of the Cypriniformes. Can. J. Zool., 80:569-581.
Lourie, S.A. and A.C.J. Vincent. 2004. A marine fish follows Wallace’s Line: the phylogeography of the three-spot seahorse (Hippocampus trimaculatus, Syngnathidae, Teleostei) in Southeast Asia. Journal of Biogeography, 31:1975-1985.
Machordom, A. and I. Doadrio. 2001. Evidence of a Cenozoic Betic-Kabilian connection based on freshwater fish phylogeography (Luciobarbus, Cyprinidae). Mol. Phylogenet. Evol., 18:252-263.
Malhi, R.S., G. Rhett, and A.M. Bell. 2006. Mitochondrial DNA evidence of an early Holocene population expansion of threespine sticklebacks from Scotland. Molecular Phylogenetics and Evolution, 40:148-154.
McConnell, S.K.J. 2004. Mapping aquatic faunal exchanges across the Sunda shelf, South-East Asia, using distributional and genetic data sets from the cyprinid fish Barbodes gonionotus (Bleeker, 1850). Journal of Natural History, 38:651-670.
McCulloch, M., G. Mortimer, T. Esat, X. Li, B. Pillans, and J. Chappell. 1996. High resolution windows into early Holocene climate: Sr/Ca coral records from Huon Peninsula. Earth and Planetary Science Letters, 138:169-178.
Meijaard, E. 2003. Mammals of south-east Asian islands and their Late Pleistocene environments. Journal of Biogeography, 30:1245-1257.
Mihara, M., T. Sakai, K. Nakao, L. de O. Martins, K. Hosoya and J.I. Miyazaki. 2005. Phylogeography of Loaches of the Genus Lefua (Balitoridae, Cypriniformes) Inferred from Mitochondrial DNA Sequences. Zoological Science, 22:157-168.
Nei, M. and F. Tajima. 1983. Maximum likelihood estimation of the number of neucleitude substitutions from restriction sites data. Genetics, 105:207-217.
Nelson, J. 1994. Fishes of the World. John Wiley and Sons, pp. I-viii, 1-386.
Okazaki, T., S.R. Jeon and T. Kitagawa. 2002. Genetic Differentiation of Piscivorous Chub (genus Opsariichthys) in Japan, Korea and Russia. Zoological Science, 19:601-610.
Ono,Y., T. Aokib, H. Hasegawac, and L. Dali. 2005. Mountain glaciation in Japan and Taiwan at the global Last Glacial Maximum. Quaternary International, 138-139:79-92.
Ota, Y. and M. Yamaguchi. 2004. Holocene coastal uplift in the western Pacific Rim in the context of late Quaternary uplift. Quaternary International, 120:105-117.
Page, B. M. and J. Suppe. 1981. The Pliocene Lichi melange of Taiwan: Its plate-tectonic and olistostromal origin. American Jourmal of Science, 281:193-227.
Perdices, A. and I. Doadrio. 2001. The molecular systematics and biogeography of the European cobitids based on mitochondrial DNA sequences. Mol. Phylogenet. Evol., 19:468-478.
Perdices, A., I. Doadrio, P. S. Economidis, J. Bohlen and P. Banarescu. 2003. Pleistocene effect on the European freshwater fish fauna: double origin of the cobitid genus Sabanejewia in the Danube basin (Osteichthyes: Cobitidae). Molecular Phylogenetics and Evolution, 26:289-299.
Perdices, A., C. Cunha, and M.M. Coelho. 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.
Perdices, A., D. Sayanda, M.M. Coelho. 2005. Mitochondrial diversity of Opsariichthys bidens (Teleostei, Cyprinidae) in three Chinese drainages. Molecular Phylogenetics and Evolution, 37:920-927.
Raymo, M. E. 1994. The initiaion of northern hemisphere glaciation. Annual Reviews of Earth and Planetary Sciences, 22:353-383.
Regan, C. T. 1908. Description of new fishes from Lake Candidius, Formosa, collected by Dr. A. Moltrecht. Ann. Mag. Nat. Hist., 2:358-360.
Rosas, J. and R. Rosas. 1999. DnaSP version 3.0: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics, 15:174-175.
Sado, T. and S. Kimura. 2002a. Developmental morphology of the cyprinid fish, Candidia barbatus. Ichth. Research, 49(4):350-354.
Sado, T. and S. Kimura. 2002b. Descriptive morphology of the eggs, larvae, and juveniles of two cyprinid fishes belonging to the Zacco temminckii species' group. Ichthyological Research, 49:245-252.
Saitou, N. and M. Nei. 1987. The Neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol. Biol. Evol., 4:406-425.
Shi, Y. 2002. Characteristics of late Quaternary monsoonal glaciation on the Tibetan Plateau andin East Asia. Quaternary International, 97-98:79-91.
Shieh, Y.T., C.H. Wang, M.P. Chen, and Y.L. Yung. 1997. The Last Glacial Maximun to Holocene environment changes in the southern Okinawa Trough. Journal of Asian Earth Sciences, 15(1):3-8.
Song, S.R., C.M. Liu, C.H. Chen, and W. Lo. 2004. Pumice layers in marine terraces: implications for tectonic uplift rates on the east and northeast coasts of Taiwan over the last hundreds of years. Quaternary International, 115-116:83-92.
Sota, T., T. Mukai, T. Shinozaki, H. Sato and K. Yodoe. 2005. Genetic Differentiation of the Gobies Gymnogobius castaneus and G. taranetzi in the Region Surrounding the Sea of Japan as Inferred from a Mitochondrial Gene Genealogy. Zoological Science, 22:87-93.
Steinke, S., H.Y. Chiu, P.S. Yu, C.C. Shen, H. Erlenkeuser, L. Lowemark, and M.T. Chen. 2006. On the influence of sea level and monsoon climate on the southern South China Sea freshwater budget over the last 22,000 years. Quaternary Science Reviews, 25:1475-1488.
Swofford, D.L. 1998. PAUP: Phylogenetic analysis using parsimony, 4.03. Illinois Natural History survey. Champaign.
Temminck, C. J. and H. Schlegel. 1846. Pisces, Fauna Japonica. Lunduni Batavorum, Leiden., 10-14:173-269.
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. Nuc. Acids Res., 22:4673-4680.
Tougard, C. 2001. Biogeography and migration routes of large mammal faunas in South-East Asia during the last Middle Pleistocene: focus on the fossil and faunas from Thaland. Palaeogeography, Palaeoclimatology, Palaeoecology, 68:337-358.
Tzeng, M.C., T.Y. Chiang and J.P. Wang. 1999. Population structure of Acrossocheilus paradoxus Gunther (Cyprinidae). Endemic Species Research, 1:20-25. (in Chinese with English abstract)
Tzeng, C.S, Y.S. Lin, S.M. Lin, T.Y. Wang, and F.Y. Wang. 2006. The Phylogeography and Population Demographics of Selected Freshwater Fishes in Taiwan. Zoological Studies, 45(3):285-297.
Ujiie, H. and Y. Ujiie. 1999. Late Quaternary course changes of the Kuroshio Current in the Ryukyu Arc region, northwestern Pacific Ocean. Marine Micropaleontology, 37:23-40.
Unmark, P.J. 2001. Biogeography of Australian freshwater fishes. Journal of Biogeography, 28:1053-1089.
Voris, H.K. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. Journal of Biogeography, 27:1153 1167.
Wang, H.Y., S.C. Lee and M.J. Yu. 1997. Genetic evidence to clarify the systematic status of the genera Zacco and Candidia (Cypriniformes: Cyprinidae). Zool. Studies, 36(3):170-177. (In English with Chinese summary.)
Wang, H.I., M.P. Tsai, M.J. Yu and S.C. Lee. 1999a. Influence of glaciation on divergence patterns of the endemic minnow, Zacco pachycephalus, in Taiwan. Molecular Ecology, 8: 1879-1888.
Wang, L., M. Sarnthein, H. Erlenkeuser, J. Grimalt, P. Grootes, S. Heilig, E. Ivanova, M. Kienast, C. Pelejero, and U. Pflaumann. 1999b. East Asian monsoon climate during the Late Pleistocene: high-resolution sediment records from the South China Sea. Marine Geology, 156:245-284.
Wang, J.P., K.C. Hsu and T.Y. Chiang. 2000. Mitochondrial DNA phylogeography of Acrossochilus paradoxus (Cyprinidae) in Taiwan. Molecular Ecology, 9:1483-1494.
Wang, J.P., H.D. Lin, S. Huang, C.H. Pan, X.L. Chen and T.Y. Chiang. 2004. Phylogeography of Varicorhinus barbatulus (Cyprinidae) in Taiwan based on nucleotide variation of mtDNA and allozymes. Molecular Phylogenetics and Evolution, 31:1143-1156.
Wei, K. Y. 2002. Environmental changes during the late quaternary in Taiwan and adjacent seas: An overview of recent results of the past decade (1990-2000). Western Pacific Earth Sciences, 2(2):149-160.
Woodruff, D.S. 2003. Neogene marine transgressions, palaeogeography and biogeographic transitions on the Thai–Malay Peninsula. Journal of Biogeography, 30:551-567.
Xia, X. and. Z. Xie. 2001 DAMBE: Data analysis in molecular biology and evolution. Journal of Heredity, 92:371-373.
Yamaguchi, M. and Y. Ota. 2004. Tectonic interpretations of Holocene marine terraces, east coast of Coastal Range, Taiwan. Quaternary International, 115-116:71-81.
Yim, W.W.S., G. Huang, M.R. Fontugne, R.E. Hale, M. Paterne, P.A. Pirazzoli, and W.N.R. Thomas. 2006. Postglacial sea-level changes in the northern South China Sea continental shelf: Evidence for a post-8200 calendar yr BP meltwater pulse. Quaternary International, 145-146:55-67.
Zhu, S.Q. 1995. Synopsis of freshwater fishes of China. Jiangsu Science and Technology Publishing House: i-v + 1-549. (In Chinese with English summary)
王子元。1996。台灣與鄰近地區腹吸鰍族魚類之親緣關係研究。碩士論文。生命科學系。國立清華大學。45頁。
王子元。2004a。東亞地區爬鰍科的分類、演化與親緣地理學。博士論文。生命科學系。國立清華大學。96頁。
王弘毅。1995。臺灣溪流中獵屬與馬口魚屬(鯉形目: 鯉科)的系統分類與遺傳結構之研究。碩士論文。54頁。東海大學。
王信和。2002。臺灣南部大樹-大社地區之層序與古沉積環境分析應用。碩士論文。地球物理研究所。國立海洋大學。63頁。
王晨帆。2004c。臺灣鬚獵(鯉形目:鯉科)的親緣地理及形態變異之研究。碩士論文。動物學研究所。國立臺灣大學。64頁。
王智文。2004b。台灣及大陸東南地區中華花鰍(Cobitis sinensis)種群形態系統分類、分子地理親緣與生殖生態之研究。碩士論文。海洋生物研究所。國立中山大學。76頁。
朱元鼎。1984。福建魚類誌 (下卷)。福建科學技術出版社。福州。699頁。
朱育民。2000。台灣產瓢鰭蝦虎屬之形態分類與mtDNA分子演化及日本瓢鰭蝦虎生殖生態之研究。碩士論文。海洋資源學系。研究所。國立中山大學。118頁。
西田睦、鹿谷法一、諸喜田茂充。2003。琉球列島之陸水生物。東海大學出版會。神奈川縣。572頁。
伍漢霖、邵廣昭、賴春福。1999。拉漢世界魚類名典。水產出版社。基隆。1,028頁。
何杰騰。2003。利用遺傳標記及形態鑑定台灣的外來種鱘。碩士論文。動物學研究所。國立臺灣大學。110頁。
吳瑞賢、陳義雄、邵廣昭、徐基新、方力行。2001。Molecular phylogeography of freshwater cyprinid, Candidia barbata from Taiwan。九十年度魚類學會年會既論文發表會。中華民國魚類學會。台北市。22頁。
宋時驊。2000。末次冰期以來高雄地區沉積層序之研究。碩士論文。地質科學研究所。國立臺灣大學。122頁。
李偉彰。1991。臺灣南部西恆春台地更新統之沉積環境研究。碩士論文。地質研究所。國立台灣大學。79頁。
沈世傑。1993。台灣魚類誌。台大動物系。台北。1-960頁。
沈康寧。2006。以微衛星DNA探討澳洲東部三種淡水鰻(澳洲花鰻、澳洲短鰭鰻和紐西蘭大鰻)的族群遺傳結構及其演化史。博士論文。動物學研究研究所。臺灣大學。102頁。
林育萱。2002。應用RAPD解析保種之台灣本土塘蝨魚種源基因以排除疑為雜交種之研究。碩士論文。水產養殖學系。國立海洋大學。118頁。
林思民。1994。青將魚粒線體去氧核醣核酸控制區(D-loop)之研究。碩士論文。生命科學研究所。國立清華大學。
林思民。2002。臺灣及鄰近地區草蜥屬的親緣關係與親緣地理學研究（有鱗目：蜥蜴科）。博士論文。生物研究所。國立臺灣師範大學。207頁。
林偉恩。2006。西太平洋邊緣烏魚粒線體DNACytochromeb序列變異及族群遺傳之研究。碩士論文。生物科學研究所。國立高雄師範大學。63頁。
林殿順。1990。臺灣西南部麓山帶上新-更新統之沉積岩相與沉積環境演化。碩士論文。地質研究所。國立台灣大學。93頁。
姜宏偉。1999。由岩心沈積物之有機碳同位素研究來探討台灣西部平原區晚更新世以來的海岸環境變遷。碩士論文。地質學研究所。國立臺灣大學。61頁。
俞何興、陳汝勤。1996。台灣海域之沉積盆地。渤海堂。台北。230頁。
洪東耀。2004。以粒線體DNA探討台灣產鱨類生物地理學。碩士論文。生命科學系。國立清華大學。44頁。
徐澔德。1998。上次冰期以來屏東平原南部之沈積環境。碩士論文。地質學研究所。國立臺灣大學。212頁。
馬國欽。2005。台灣獵屬魚類(鯉目:鯉科)之系統分類、族群遺傳結構及生物親緣地理研究。博士論文。動物學研究研究所。臺灣大學。114頁。
張韻嫻。2002。台灣地區流域面積高度積分之研究。碩士論文。地理學系。國立高雄師範大學。139頁。
陳于高。1992a。晚更新世以來南臺灣地區海水面變化與新構造運動研究。博士論文。地質研究所。國立台灣大學。158頁。
陳俊廷。1999a。洞穴碳酸鈣微量化學的初步研究：更新世晚期台灣氣候的變化。碩士論文。地球科學系。國立成功大學。102頁。
陳彥傑。2003。台灣山脈的構造地形指標特性--以面積高度積分、地形碎形參數與河流坡降指標為依據。博士論文。地球科學系。國立成功大學。129頁。
陳振華。1992b。由晚期新生代沈積物之岩象學與構造地層學研究探討台灣中西部褶皺逆衝帶之演化。博士論文。地質學系。國立台灣大學。
陳新言。2000a。高身白甲魚（Onychostomaalticorpus）族群間親緣地理學之研究。碩士論文。生命科學系。國立清華大學。
陳義雄。1993。臺灣產褐吻蝦虎相似種群系統分類之研究。碩士論文。海洋資源學系。國立中山大學。112頁。
陳義雄、方力行。1999。台灣淡水及河口魚類誌。國立海洋生物博物館籌備處。屏東。287頁。
陳義雄。2001。台灣淡水魚類的調查研究史、地理分布特性及生態保育策略與展望。台灣文獻。52(3):45-60。
陳義雄、王智文。2001。Molecular phylogenetic study of freshwater loach, Cobitis sinensis complex from Taiwan。九十年度魚類學會年會既論文發表會。中華民國魚類學會。台北市。22頁。
陳義雄、張詠青、方力行。2001。Morphological and molecular evolution of cyprinid genus, Squalidus from Taiwan。九十年度魚類學會年會既論文發表會。中華民國魚類學會。台北市。22頁。
陳義雄、張詠青。2005。台灣淡水魚類原色圖鑑 鯉形目。水產出版社。基隆市。
陳聖宗。2000b。台灣與鄰近地區小鰾鮈分子親緣關係之研究。碩士論文。生命科學系。國立清華大學。57頁。
陳燕珍。1999b。東亞地區水筆仔族群的遺傳變異之研究。碩士論文。生物研究所。國立臺灣師範大學。62頁。
彭志雄。1997。台北盆地晚第四紀沉積環境。碩士論文。地質學系。國立台灣大學。77頁。
彭慧蘭。2002。台北盆地古沉積環境分析。碩士論文。海洋科學系。國立海洋大學。85頁。
曾可欣。2001。台灣西南部陸上及海域之構造演化。碩士論文。地球科學研究所。國立臺灣師範大學。68頁。
曾美珍。2002。以微衛星DNA研究日本鰻之族群結構。博士論文。動物學研究所。國立臺灣大學。127頁。
曾晴賢。1991。臺灣纓口鰍之粒線體基因組和臺灣產平鰭鰍科魚類之分子演化的研究。博士論文。動物學研究所。國立台灣大學。171頁。
游淑惠。2000。台灣四周海域灰鰭鯛種群遺傳分化之研究。碩士論文。50頁。國立臺灣師範大學。
黃世彬。2005。中國韓江流域吻蝦虎魚(Rhinogobius)的分類研究。碩士論文。野生動物保育研究所。屏東科技大學。85頁。
黃美慈。2002。台灣溪哥的族群遺傳研究-微隨體基因座的應用。碩士論文。動物學研究所。國立臺灣大學。100頁。
黃郁婷。2000。嘉南平原曾文溪流域晚第四系之沉積環境暨層序初探。碩士論文。地質科學研究所。國立臺灣大學。89頁。
楊貴生。1991。廣東淡水魚類誌。廣東科技出版社。廣東。589頁。
葉昌憲。1993。臺灣水鹿粒線體DNA序列之分析。碩士論文。生物學研究所。國立師範大學。
褚耀鈺。1990。臺灣沿岸產大鱗鯔，當鱗鯔及烏魚之種群關係之研究。碩士論文。71頁。國立台灣大學。
劉名允。2005。沼蝦屬分子系統分類及台灣的粗糙沼蝦親緣地理和族群遺傳探討。博士論文。生命科學系。國立清華大學。73頁。
鄭光佑。2001。台灣西部麓山帶前緣流域面積高度積分之構造意義研究。碩士論文。地理學系。國立高雄師範大學。101頁。
儲瑞華。2004。台灣獼猴的親緣地理與族群遺傳學研究。博士論文。生態學與演化生物學研究所。臺灣大學。143頁。
繁玉萍。2000。台灣島形成過程對台灣淡水魚族群遺傳結構影響之研究。碩士論文。生命科學系。國立清華大學。53頁。
簡春潭。1995。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。博士論文。國立海洋大學。

Adams, K.L. and J.D. Palmer. 2003. Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Molecular Phylogenetics and Evolution, 29:380-395.
Allen, G.R. and R. Steene. 1994. Indo-Pacific Coral Reef field guide. Tropical Reef Research. Singapore, pp. 1-378.
Beagley, C..T., R.Okimoto, and D.R. Wolstenholme. 1998. The Mitochondrial Genome of the Sea Anemone Metridium senile (Cnidaria): Introns, a Paucity of tRNA Genes, and a Near-Standard Genetic Code. Genetics, 148:1091-1108.
Beaton, M.J., A.J. Roger, and T. Cavalier-Smith. 1998. Sequence Analysis of the Mitochondrial Genome of Sarcophyton glaucum: Conserved Gene Order Among Octocorals. Journal of Molecular Evolution, 47:697-708.
Berntson, E.A., S.C. France, and L.S. Mullineaux. 1999. Phylogenetic Relationships within the Class Anthozoa (Phylum Cnidaria) Based on Nuclear 18S rDNA Sequences. Molecular Phylogenetics and Evolution, 13(2): 417-433.
Boore, J.L. and W.M. Brown. 1998. Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. Current Opinion in Genetics and Development, 8:668-674
Bridge, D., C.W. Cunningham, B. Schierwater, R. DeSalle, and L.W. Buss. 1992. Class-level relationships in the phylum Cnidaria: Evidence from mitochondrial genome structure. Proc. Natl. Acad. Sci. USA, 89:8750-8753.
Bridge, D., C.W. Cunningham, R. DeSalle, and L.W. Buss. 1995. Class-Level Relationships in the Phylum Cnidaria: Molecular and Morphological Evidence. Molecular Biology Evolution, 12(4):679-689.
Brugler, M.R. and S.C. France. 2007. The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria:Anthozoa:Antipatharia) supports classification of antipatharians within the subclass Hexacorallia. Molecular Phylogenetics and Evolution, 42:776-788.
Burger, G., D.V. Lavrov, L. Forget, and B.F. Lang. 2007. Sequencing complete mitochondrial and plastid genomes. Nature Protocols, 2(3):603-614.
Calderon, I., J. Garrabou, and D. Aurelle. 2006. Evaluation of the utility of COI and ITS markers as tools for population genetic studies of temperate gorgonians. Journal of Experimental Marine Biology and Ecology, 336:184-197.
Chen, C.A., D.M. Odorico, M.T. Lohuis, J.E.N. Veron, and D.J. Miller. 1995. Systematic Relationships within the Anthozoa (Cnidaria: Anthozoa) Using the 5' -end of the 28S rDNA. Molecular Phylogenetics and Evolution, 4(2):175-183.
Chen, C.A., D.J. Miller, N.V. Wei, C.F. Dai, and H.P. Yang. 2000. The ETS/IGS Region in a Lower Animal, the Seawhip, Junceella fragilis (Cnidaria: Anthozoa: Octocorallia): Compactness, Low Variation and Apparent Conservation of a Pre-rRNA Processing Signal with Fungi. Zoological Studies, 39(2):138-143.
Chen, C.A., C.C. Wallace, and J. Wolstenholme. 2002a. Analysis of the mitochondrial 12S rRNA gene supports a two-clade hypothesis of the evolutionary history of scleractinian corals. Molecular Phylogenetics and Evolution, 23:137-149.
Chen, C.A, N.V. Wei, and C.F. Dai. 2002b. Genotyping the Clonal Population Structure of a Gorgonian Coral, Junceella fragilis (Anthozoa: Octocorallia: Ellisellidae) from Lanyu, Taiwan, Using Simple Sequence Repeats in Ribosomal Intergenic Spacer. Zoological Studies, 41(3):295-302.
Collins, A.G., P. Cartwright, C.S. McFadden, and B. Scherwater. 2005. Phylogenetic Context and Basal Metazoan Model Systems1. Integr. Comp. Biol., 45:585-594.
Daly, M., D.G. Fautin and V.A. Cappola. 2003. Systematics of the Hexacorallia (Cnidaria: Anthozoa). Zoological Journal of the Linnean Society, 139:419-437.
Fabricius, K. and P. Alderslade. 2001. Soft Corals and Sea Fans. Astralian Institute of Marine Science, pp. i-viii, 1-264.
Fautin, D.G. 2002. Reproduction of Cnidaria. Can. J. Zool. 80:1735-1754.
France, S.C. and L.L. Hoover. 2002. DNA sequences of the mitochondrial COI gene have low levels of divergence among deep-sea octocorals (Cnidaria: Anthozoa). Hydrobiologia, 471:149-155.
Fukami, H., M. Omori, and M. Hatta. 2000. Phylogenetic Relationships in the Coral Family Acroporidae, Reassessed by Inference from Mitochondrial Genes. Zoological Science, 17: 689-696.
Fukami, H., A.F. Budd, and G. Paulay, A. Sole’-Cava, C.A. Chen, K. Iwao and N. Knowlton. 2004. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Nature, 427: 832-835.
Fukami, H. and N. Knowlton. 2005. Analysis of complete mitochondrial DNA sequences of three members of the Montastraea annularis coral species complex (Cnidaria, Anthozoa, Scleractinia). Coral Reefs, 24:410-417.
Fukami ,H., C.A. Chen, C.Y. Chiou, N. Knowlton. 2007. Novel Group I Introns Encoding a Putative Homing Endonucleasein the Mitochondrial cox1 Gene of Scleractinian Corals. J. Mol. Evol., 64:591–600.
Goddard, M.R., J. Leigh, A.J. Roger, and A.J. Pemberton. 2006. Invasion and Persistence of a Selfish Gene in the Cnidaria. PLoS ONE, 1(1):e3.
Haussermann, V. and G. Forsterra. 2003. First evidence for coloniality in sea anemones. Marine Ecology Progress Series, 257:291-294.
Hellberg, M.E. 2006. No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation. BMC Evolutionary Biology, 2006, 6:24.
Kumar, S., K. Tamura and M. Nei, 2004. MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics, 5:150-163.
Le Goff-Vitry, M.C, A.D. Rogers, and D. Baglow. 2004. A deep-sea slant on the molecular phylogeny of the Scleractinia. Molecular Phylogenetics and Evolution, 30:167-177.
Liu, S.Y., C.F. Dai, T.Y. Fan and H.T. Yu. 2005a. Cloning and characterization of microsatellite loci in a gorgonian coral, Junceella juncea (Anthozoa; Octocorallia; Ellisellidae) and its application in clonal genotyping. Mar. Biotechnol., 7:26-32.
Liu, S. Y., H. T. Yu, T. Y. Fan and C. F. Dai. 2005b. Genotyping the clonal structure of a gorgonian coral, Junceella juncea (Anthozoa: Octocorallia), using microsatellite loci. Coral Reefs 24:352-358.
Lowe, T.M. and S.R. Eddy. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res, 25:955-964.
Ma’rquez, L.M., D.J. Miller, J.B. MacKenzie, and M.J.H. van Oppen. 2003. Pseudogenes Contribute to the Extreme Diversity of Nuclear Ribosomal DNA in the Hard Coral Acropora. Molecular Biology Evolution, 20(7):1077-1086.
Magalon, H., M. Adjeroud, and M. Veuille. 2005. Patterns of genetic variation do not correlate with geographical distance in the reef-building coral Pocillopora meandrina in the South Pacific. Molecular Ecology, 14:1861-1868.
McFadden, C.S., I.D. Tullis, M.B. Hutchinson, K. Winner, and J.A. Sohm. 2004. Variation in Coding (NADH Dehydrogenase Subunits 2, 3, and 6) and Noncoding Intergenic Spacer Regions of the Mitochondrial Genome in Octocorallia (Cnidaria: Anthozoa). Marine Biotechnology, 6:516-526.
McFadden, C.S., S.C. France, J.A. Sanchez, and P. Alderslade. 2006. A molecular phylogenetic analysis of the Octocorallia (Cnidaria: Anthozoa) based on mitochondrial protein-coding sequences. Molecular Phylogenetics and Evolution, 41:513-527.
Medina, M., A.G. Collins, T.L. Takaoka, J.V. Kuehl, and J.L. Boore. 2006. Naked corals: Skeleton loss in Scleractinia. PNAS, 103(24):9096-9100.
Miya, M., Takeshima, H., Endo,H., Ishiguro, N.B., Inoue, J.G., Mukai, T., Satoh, T.P., Yamaguchi, M., Kawaguchi, A., Mabuchi, K., Shirai, S.M., Nishida, M., 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences Mol. Phylogenet. Evol. 26, 121-138.
Pont-Kingdon, G.A., N.A. Okada, J.L. Macfarlane, C.T. Beagley, D.R. Wolstenholme, T. Cavalier-Smith, and G.D. Clark-Walker. 1995. A coral mitochondrial mutS gene. Nature, 375:109-111.
Pont-Kingdon, G., N.A. Okada, J.L. Macfarlane, C.T. Beagley, C.D. Watkins-Sims, T. Cavalier-Smith, G.D. Clark-Walker, and D.R. Wolstenholme. 1998. Mitochondrial DNA of the Coral Sarcophyton glaucum Contains a Gene for a Homologue of Bacterial MutS: A Possible Case of Gene Transfer from the Nucleus to the Mitochondrion. Journal of Molecular Evolution, 46:419-431.
Reimer, J.D., S. Ono, A. Iwama, K. Takishita, J. Tsukahara, and T. Maruyama. 2006. Morphological and Molecular Revision of Zoanthus (Anthozoa: Hexacorallia) from Southwestern Japan, with Descriptions of Two New Species. Zoological Science, 23:261-275.
Romano, S.L. and S.R. Palumbi. 1997. Molecular Evolution of a Portion of the Mitochondrial 16S Ribosomal Gene Region in Scleractinian Corals. Journal of Molecular Evolution, 45:397-411.
Saitou, N. and M. Nei. 1987. The Neighbor-joining method: a new method for reconstructing phylogenetic tree. Mol. Biol. Evol., 4:406-425.
Sa'nchez, J.A., C.S. McFadden, S.C. France, and H.R. Lasker 2003a. Molecular phylogenetic analyses of shallow-water Caribbean octocorals. Marine Biology, 142:975-987.
S'anchez, J.A., H.R. Lasker, and D.J. Taylor. 2003b. Phylogenetic analyses among octocorals (Cnidaria): mitochondrial and nuclear DNA sequences (lsu-rRNA, 16S and ssu-rRNA, 18S) support two convergent clades of branching gorgonians. Molecular Phylogenetics and Evolution, 29:31-42.
Sankoff, D., G. Leduc, N. Antoine, B. Paquin, B.F. Lang. and R. Cedergren. 1992. Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proc. Natl. Acad. Sci. USA, 89:6575-6579.
Shao, Z., S. Graf, O.Y. Chaga, and D.V. Lavrov. 2006. Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule encoding a putative DNA-dependent DNA polymerase. Gene, 381:92-101.
Shearer, T.L., M.J.H. van Oppen, S.L. Romano, and G.W. Rheide. 2002. Slow mitochondrial DNA sequence evolution in the Anthozoa (Cnidaria). Molecular Ecology, 11, 2475-2487.
Sinniger, F., P. Chevaldonne, and J. Pawlowsk. 2007. Mitochondrial Genome of Savalia savaglia (Cnidaria, Hexacorallia) and Early Metazoan Phylogeny. Journal of Molecular Evolution, 64:196-203.
Stanley Jr., G.D. 2003. The evolution of modern corals and their early history. Earth-Science Reviews, 60:195-225.
Swofford, D.L. 1998. PAUP: Phylogenetic analysis using parsimony, 4.03. Illinois Natural History survey. Champaign.
van Oppen, M.J.H., B.L. Willis and D.J. Miller. 1999. Atypically low rate of cytochrome b evolution in the scleractinian coral genus Acropora. Proc. R. Soc. Lond. B., 266:179-183.
van Oppen, M.J.H., J. Catmull, B. J. McDonald, N.R. Hislop, P.J. Hagerman, and D.J. Miller. 2000. The Mitochondrial Genome of Acropora tenuis (Cnidaria; Scleractinia) Contains a Large Group I Intron and a Candidate Control Region. Journal of Molecular Evolution, 55:1-13.
Veron, J.E.N. 2000. Corals of the World. Australian Institute of Marine Science, Volumes 1-3. pp. 1410.
Vollmer, S.V. and S.R. Palumbi. 2004. Testing the utility of internally transcribed spacer sequences in coral phylogenetics. Molecular Ecology, 13:2763-2772.
Walker, T.A. and G.D. Bull. 1983. A newly discovered method of reproduction in gorgonian coral. Marine Ecology - Progress Series, 12:137-143.
Waeschenbach, A., M.J. Telford, and J.S. Porter. 2006. The complete mitochondrial genome of Flustrellidra hispida and the phylogenetic position of Bryozoa among the Metazoa. Molecular Phylogenetics and Evolution, 40:195-207.
Xia, X. and. Z. Xie. 2001 DAMBE: Data analysis in molecular biology and evolution. Journal of Heredity, 92:371-373.
于名振。2001。動物系統分類綱要。水產出版社。基隆。1-1002頁。
方力行。1989。珊瑚學。黎明文化事業。台北。1-178頁。
王選昶。2000環境因子對於紅管星珊瑚Tubastraea aurea 與黑樹管星珊瑚T. diaphana族群分布的初步研究。碩士論文。海洋生物研究所。國立海洋大學。58頁。
何俊忠。2002墾丁海域巨枝軸孔珊瑚（Acropora grandis） 白化現象與水文條件之關係。碩士論文。海洋資源學系研究所。國立中山大學。63頁。
吳岱穎2003 溫度與光度對萼柱珊瑚(Stylophora pistillata)光合作用的影響。碩士論文。海洋研究所。臺灣大學。46頁。
林俊諭。1998臺灣南部珊瑚礁魚類群聚時空變遷之研究。碩士論文。海洋生物研究所。國立海洋大學。87頁。
林科含。2004。台灣南部海域五種孵育幼生型珊瑚釋放幼生的時機：季節性、月週期與日夜週期。碩士論文。海洋生物研究所。國立中山大學。69頁。
林益正。1992。二種造礁珊瑚族群遺傳結構之研究。碩士論文。海洋生物研究所。國立中山大學。42頁。
林榕珊。2005養殖環境對造礁珊瑚生理的影響：生態缸與裸缸的比較。碩士論文。海洋研究所。臺灣大學。48頁。
段文宏。2003。珊瑚排卵與內分泌之關係。博士論文。海洋生物研究所。國立臺灣海洋大學。105頁。
洪聖雯。2005。台灣珊瑚群聚分布及氣候變遷對其衝擊之研究。碩士論文。海洋研究所。臺灣大學。104頁。
胡中瀚。2005。自漸新世以來南海的板塊活動與南沙群礁演化之關係。碩士論文。應用地球科學研究所。國立臺灣海洋大學。74頁。
孫虓天。1998。由珊瑚紀錄重建全新世大暖期之南台灣氣候。碩士論文。地質學研究所。國立臺灣大學。55頁。
張朝欽。2003。以多組分子遺傳標誌探討表孔珊瑚屬的分子親緣關係。碩士論文。海洋研究所。臺灣大學。51頁。
張崑雄、戴昌鳳。1987。墾丁國家公園海域珊瑚礁及海洋生物生態研究—海域珊瑚類的分佈及群聚生態學之研究。墾丁國家公園管理處。屏東。1-77頁。
張琬蘭。2002。白鞭珊瑚的生長策略。碩士論文。海洋研究所。國立臺灣大學。45頁。
張簡淑惠。1994。眾多指形軟珊瑚共存細菌親緣分析研究。碩士論文。海洋資源學系。國立中山大學。
陳玉珮。2004a。台灣產八放珊瑚Briareum excavatum及Junceella fragilis所含天然化合物之研究。碩士論文。海洋資源學系研究所。國立中山大學。132頁。
陳威錚。2004b。台灣產軟珊瑚Klyxum simplex和印尼產海綿Halichondria sp.所含化學成份之研究。碩士論文。海洋資源學系研究所。國立中山大學。94頁。
陳建維。2005。利用微隨體基因座探討軸孔珊瑚種間界線與族群遺傳之研究。碩士論文。海洋研究所。臺灣大學。51頁。
曾智麟。2000。中間軸孔珊瑚(Acropora intermedia)的共生藻變動與白化的復原。碩士論文。海洋生物研究所。國立中山大學。54頁。
童亞瑄。2003溫度對萼柱珊瑚(Stylophora pistillata)和尖枝列孔珊瑚(Seriatopora hystrix)生長與存活影響的比較： 中型生態箱研究。碩士論文。海洋研究所。臺灣大學。32頁。
黃家培1992。軟珊瑚共生細菌的特性研究。碩士論文。海洋資源學系。國立中山大學。
楚涵。2002。台灣地區珊瑚礁魚類之群聚構造、種類鑑定及初期生活史之研究。碩士論文。動物學研究所。國立臺灣大學。92頁。
楊雅雯。2000。印度太平洋石珊瑚之共生藻的親緣分析與共生多型性。碩士論文。海洋生物研究所。國立中山大學。46頁。
樊同雲。1995臺灣南北部海域葉片形珊瑚的生活史與族群動態。博士論文。海洋學系國立台灣大學。173頁。
戴昌鳳。1998。墾丁國家公園海域珊瑚群聚變遷之研究。墾丁國家公園管理處。屏東。1-78頁。
戴昌鳳。1999。墾丁國家公園海域珊瑚群聚變遷之研究(第二年)。墾丁國家公園管理處。屏東。1-72頁。
鄭名君。2005。肉質軟珊瑚屬與葉形軟珊瑚屬之分子親緣關係研究。碩士論文。海洋研究所。臺灣大學。46頁。
蕭聖代。2002。澳洲球形海綿完整粒線體DNA序列及分析研究。碩士論文。海洋資源學系研究所。國立中山大學。108頁。
魏汝薇。2000軸孔珊瑚核糖體第二轉錄區間的分子演化：平行系效應與祖先多型性的證據。碩士論文。海洋研究所。國立臺灣大學。34頁。
魏汝薇。2006軸孔珊瑚種間關係的探討。博士論文。海洋研究所。臺灣大學。82頁。