請用此 Handle URI 來引用此文件:
http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59670
完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 陳韋仁 | |
dc.contributor.author | Jhen-Nien Chen | en |
dc.contributor.author | 陳貞年 | zh_TW |
dc.date.accessioned | 2021-06-16T09:32:26Z | - |
dc.date.available | 2017-02-17 | |
dc.date.copyright | 2017-02-17 | |
dc.date.issued | 2017 | |
dc.date.submitted | 2017-02-15 | |
dc.identifier.citation | Alfaro, M.E., Santini, F., Brock, C., Alamillo, H., Dornburg, A., Rabosky, D.L., Carnevale, G., Harmon, L.J., 2009. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc. Natl. Acad. Sci. U. S. A. 106, 13410–4.
Alfaro, M.E., Santini, F., Brock, C.D., 2007. Do reefs drive diversification in marine teleosts? Evidence from the pufferfish and their allies (Order Tetraodontiformes). Evolution. 61, 2104–2126. Amores, A., Suzuki, T., Yan, Y.L., Pomeroy, J., Singer, A., Amemiya, C., Postlethwait, J.H., 2004. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Res. 14, 1–10. Aoyama, J., 2009. Life history and evolution of migration in catadromous eels ( Genus Anguilla ). Aqua-Bio. 2, 1–42. Archer, S., Hope, A., Partridge, J.C., 1995. The molecular basis for the green-blue sensitivity shift in the rod visual pigments of the European eel. Proc. Biol. Sci. 262, 289–295. Arnegard, M.E., Zwickl, D.J., Lu, Y., Zakon, H.H., 2010. Old gene duplication facilitates origin and diversification of an innovative communication system--twice. Proc. Natl. Acad. Sci. U. S. A. 107, 22172–22177. Arratia, G., 1987. Anaethalion and similar teleosts (Actinopterygii, Pisces) from the Late Jurassic (Tithonian) of Southern Germany and their relationships. Palaeontogr. Abteilung 200, 1–44. Arratia, G., 1997. Basal teleosts and teleostean phylogeny, Palaeo Ichthyologica Volume 7. Arratia, G., 1999. The monophyly of Teleostei and stem-group teleosts. Consensus and disagreements, in: Arratia, G., Schultze, H.P. (Eds). Mesozoic fishes 2 – systematics and fossil record. Munich: Dr. Friedrich Pfeil, 265–334. Arratia, G., 2000. Remarkable teleostean fishes from the Late Jurassic of southern Germany and their phylogenetic relationships. Foss. Rec. Mitt. Mus. Nat.kd. Berl., Geowiss. Reihe 3, 137–179. Avise, J.C., 2004. Molecular merkers, Natural History and Evolution. 2nd edition. Sinauer Associates, Inc. Belouze A., Gayet M., Atallah C. 2003. The first Anguilliformes: II. Paraphyly of the genus Urenchelys Woodward, 1900 and phylogenetic relationships. Geobios 36, 351-378. Bernardi, G., 2013. Speciation in fishes. Mol. Ecol. 22, 5487–5502. Bertelsen, E., Nielsen, J., Smith, D., 1989. Suborder Saccopharyngoidei: families Saccopharyngidae, Eurypharyngidae, and Monognathidae, in: Bohlke, E. (Ed.), Fishes of the Western North Atlantic, Part 9, Vol 1. Sears Foundation for Marine Research, Yale University, New Haven, pp. 636–655. Bishop, R., Torres, J., 1999. Leptocephalus energetics: metabolism and excretion. J. Exp. Biol. 202, 2485–2493. Braasch, I., Gehrke, A.R., Smith, J.J., Kawasaki, K., Manousaki, T., Pasquier, J., Amores, A., Desvignes, T., Batzel, P., Catchen, J. et al., 2016. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nat. Genet. 48, 427–437. Chen, J.-N., Lopez, J.A., Lavoue, S., Miya, M., Chen, W.-J., 2014. Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers. Mol. Phylogenet. Evol. 70, 152–61. Chen, J.-N., Samadi, S., Chen, W.-J., 2015. Elopomorpha (Teleostei) as a New Model Fish Group for Evolutionary Biology and Comparative Genomics, in: Pontarotti, P. (Ed.), Evolutionary Biology: Biodiversification from Genotype to Phenotype. Springer International Publishing, Cham, pp. 329–344. Chen, W.-J., 2001. La repetitivite des clades comme critere de fiabilite: application a la phylogenie des Acanthomorpha (Teleostei) et des Notothenioidei (acanthomorphes antarctiques). University of Paris VI. Chen, W.-J., Bonillo, C., Lecointre, G., 2003. Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa. Mol. Phylogenet. Evol. 26, 262–288. Chen, W.-J., Mayden, R., 2009. Molecular systematics of the Cyprininoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: further evidence from six nuclear genes. Mol. Phylogenet. Evol. 52, 544–549. Chen, W.-J., Mayden, R.L., 2010. A phylogenomic perspective on the new era of ichthyology. Bioscience 60, 421–432. Chen, W.-J., Miya, M., Saitoh, K., Mayden, R.L., 2008. Phylogenetic utility of two existing and four novel nuclear gene loci in reconstructing Tree of Life of ray-finned fishes: the order Cypriniformes (Ostariophysi) as a case study. Gene 423, 125–34. Chen, W.-J., Santini, F., Carnevale, G., Chen, J.-N., Liu, S.-H., Lavoue, S., Mayden, R.L., 2014. New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha). Front. Mar. Sci. 1, 53. Chen, W.-J., Mayden, R.L., 2012. Phylogeny of suckers (Teleostei: Cypriniformes: Catostomidae): further evidence of relationships provided by the single-copy nuclear gene. Zootaxa. 3586, 195–210. Christoffels, A., Koh, E.G.L., Chia, J.M., Brenner, S., Aparicio, S., Venkatesh, B., 2004. Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes. Mol. Biol. Evol. 21, 1146–1151. Collin, S.P., Darwin, C., 2005. Opsins : Evolution in Waiting. Curr. Biol. 15, 794–796. Coppe, A., Pujolar, J.M., Maes, G.E., Larsen, P.F., Hansen, M.M., Bernatchez, L., Zane, L., Bortoluzzi, S., 2010. Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. BMC Genomics 11, 635. Dehal, P., Boore, J.L., 2005. Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol. 3(10), e314. De Schepper N., De Kegel B., Adriaens D. 2007. Morphological specializations in Heterocongrinae (Anguilliformes: Congridae) related to burrowing and feeding. Journal of Morphology 268: 343-356. DeVaney, S.C., 2008. The interrelationships of fishes of the order Stomiiformes. Unpublished Ph.D. Ecology and Evolutionary Biology Department, University of Kansas, Lawrence, KS. Dornburg, A., Friedman, M., Near, T.J., 2015. Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei). Mol. Phylogenet. Evol. 89, 205–218. Duboule, D., 2007. The rise and fall of Hox gene clusters. Development 134, 2549–2560. Edgar, R.C., 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797. Eschmeyer, W.N., Fong, J.D., (version Oct. 2016) Catalog of fishes, http://research.calacademy.org/ichthyology/catalog/fishcatmain.asp. Faircloth, B.C., Sorenson, L., Santini, F., Alfaro, M.E., 2013. A phylogenomic perspective on the radiation of ray-finned fishes based upon targeted sequencing of ultraconserved elements (UCEs). PLoS One 8, e65923. Felsenstein, J., 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 39, 783–791. Filleul, A., Lavoue, S., 2001. Basal teleosts and the question of elopomorph monophyly. Morphological and molecular approaches. Comptes Rendus l’Academie des Sci. - Ser. III - Sci. la Vie 324, 393–399. Forey, P., Littlewood, D., Ritchie, P., Meyer, A., 1996. Interrelationships of elopomorph fishes, Interrelationships of Fishes. Woodhead Publishing Limited. Froese, R., Pauly, D., 2016. FishBase. www.fishbase.org, version (10/2016) Glasauer, S.M.K., Neuhauss, S.C.F., 2014. Whole-genome duplication in teleost fishes and its evolutionary consequences. Mol. Genet. Genomics 289, 1045–60. Gosline, W.A., 1971. Functional morphology and classification of Teleostean Fishes. The University Press of Hawaii, Honolulu. Greenwood, P.H., Rosen, D.E., Weitzman, S.H., Myers, G.S., 1966. Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bull. Am. Museum Nat. Hist. 131, 339–456. Guo, B., Gan, X., He, S., 2010. Hox genes of the Japanese eel Anguilla japonica and Hox cluster evolution in teleosts. J. Exp. Zool. B. Mol. Dev. Evol. 314, 135–47. Henkel, C. V, Burgerhout, E., de Wijze, D.L., Dirks, R.P., Minegishi, Y., Jansen, H.J., Spaink, H.P., Dufour, S., Weltzien, F.-A., Tsukamoto, K. et al. 2012a. Primitive duplicate Hox clusters in the European eel’s genome. PLoS One 7, e32231. Henkel, C. V, Dirks, R.P., de Wijze, D.L., Minegishi, Y., Aoyama, J., Jansen, H.J., Turner, B., Knudsen, B., Bundgaard, M., Hvam, K.L., Boetzer, M. et al. 2012b. First draft genome sequence of the Japanese eel, Anguilla japonica. Gene 511, 195–201. Hidaka, K., Tsukamoto, Y., Iwatsuki, Y., 2016. Nemoossis, a new genus for the eastern Atlantic long-fin bonefish Pterothrissusbelloci Cadenat 1937 and a redescription of P. gissu Hilgendorf 1877 from the northwestern Pacific. Ichthyol. Res. 1–9 Hoegg, S., Brinkmann, H., Taylor, J.S., Meyer, A., 2004. Phylogenetic timing of the fish-specific genome duplication correlates with the diversification of teleost fish. J. Mol. Evol. 59, 190–203. Hope, A.J., Partridge, J.C., Dulai, K.S., Hunt, D.M., 1997. Mechanisms of wavelength tuning in the rod opsins of deep-sea fishes. Proc. Royal. Soc. B. Biol. Sci. 264, 155–163. Howe, K., Clark, M.D., Torroja, C.F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E., Humphray, S., McLaren, K., Matthews, L. et al., 2013. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503. Hulet, W., Robins, C., 1989. The evolutionary significance of the leptocephalus larva, in: Bohlke, E. (Ed.), Fishes of the Western North Atlantic, Leptocephali Part 9, Vol 2. Sears Foundation for Marine Research, Yale University, New Haven, pp. 669–677. Hunt, D.M., Dulai, K.S., Partridge, J.C., Cottrill, P., Bowmaker, J.K., 2001. The molecular basis for spectral tuning of rod visual pigments in deep-sea fish. J. Exp. Biol. 204, 3333–3344. Inoue, J.G., Miya, M., Miller, M.J., Sado, T., Hanel, R., Hatooka, K., Aoyama, J., Minegishi, Y., Nishida, M., Tsukamoto, K., 2010. Deep-ocean origin of the freshwater eels. Biol. Lett. 6, 363–6. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2004. Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva. Mol. Phylogenet. Evol. 32, 274–86. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2003. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the “ancient fish.” Mol. Phylogenet. Evol. 26, 110–120. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2001. Complete mitochondrial DNA sequence of Conger myriaster (Teleostei: Anguilliformes): novel gene order for vertebrate mitochondrial genomes and the phylogenetic implications for anguilliform families. J. Mol. Evol. 52, 311–20. Johnson, G.D., Ida, H., Sakaue, J., Sado, T., Asahida, T., Miya, M., 2012. A “living fossil” eel (Anguilliformes: Protanguillidae, fam. nov.) from an undersea cave in Palau. Proc. Royal. Soc. B. Biol. Sci. 279, 934–43. Kai, W., Nomura, K., Fujiwara, A., Nakamura, Y., Yasuike, M., Ojima, N., Masaoka, T., Ozaki, A., Kazeto, Y., Gen, K. et al. 2014. A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel (Anguilla japonica) provides insights into genome evolution after the teleost-specific genome duplication. BMC Genomics 15, 233. Kocher, T.D., 2004. Adaptive evolution and explosive speciation: the cichlid fish model. Nat. Rev. Genet. 5, 288–298. Kurogi, H., Chow, S., Yanagimoto, T., Konishi, K., Nakamichi, R., Sakai, K., Ohkawa, T., Saruwatari, T., Takahashi, M., Ueno, Y., Mochioka, N., 2015. Adult form of a giant anguilliform leptocephalus Thalassenchelys coheni Castle and Raju 1975 is Congriscus megastomus (Gunther 1877). Ichthyol. Res. 63(2), 239-246. Kurosawa, G., Takamatsu, N., Takahashi, M., Sumitomo, M., Sanaka, E., Yamada, K., Nishii, K., Matsuda, M., Asakawa, S., Ishiguro, H. et al. 2006. Organization and structure of hox gene loci in medaka genome and comparison with those of pufferfish and zebrafish genomes. Gene 370, 75–82. Lauder, G.V., Liem, K.F., 1983. Patterns of diversity and evolution in ray-finned fishes, in: Norrhcutt, R.G., Davis, R.. (Eds.), Fish Neurobiology. University of Michigan Press, Ann Arbor, pp. 1–24. Le, H.L., Lecointre, G., Perasso, R., 1993. A 28S rRNA-based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms. Mol. Phylogenet. Evol. 2, 31-51. Li, C., Lu, G., Orti, G., 2008. Optimal data partitioning and a test test case for ray-finned fishes (Actinopterygii) based on ten nuclear loci. Syst. Biol. 57, 519–539. Lim, J., Chang, J.L., Tsai, H.J., 1997. A second type of rod opsin cDNA from the common carp (Cyprinus carpio). Biochim. Biophys. Acta - Gene Struct. Expr. 1352, 8–12. Lopez, J.A., Chen, W.-J., Orti, G., 2004. Esociformes phylogeny. Copeia. 2004(3), 449–464. Lopez, J.A., Wesrneat, W.M., Hanel, R., 2007. The phylogenetic affinities of the mysterious Anguilliformes genera Coloconger and Thalassenchelys as supported by mtDNA sequences. Copeia 2007, 959–966. Maddison, W.P., Maddison, D.R., 2011. Mesquite: A molecular system for evolution analysis Version 2.75. Magnoli, D., Zichichi, R., Laura, R., Guerrera, M.C., Campo, S., de Carlos, F., Suarez, A.A., Abbate, F., Ciriaco, E., Vega, J.A., Germana, A., 2012. Rhodopsin expression in the zebrafish pineal gland from larval to adult stage. Brain Res. 1442, 9–14. Mano, H., Kojima, D., Fukada, Y., 1999. Exo-rhodopsin: a novel rhodopsin expressed in the zebrafish pineal gland. Mol. Brain Res. 73, 110–118. Masuda, H., K. Amaoka, C. Araga, T. Uyeno and T. Yoshino, 1984. Family Albulidae. in: The fishes of the Japanese Archipelago. 1, pp.21. Mayden, R., 1999. Systematics, Historical Ecology, and North American Freshwater Fishes., in: Systematic Biology. 42(3), pp. 398–402. McGinnis, W., Krumlauf, R., 1992. Homeobox genes and axial patterning. Cell 68, 283–302. Miller, M., 2009. Ecology of Anguilliform Leptocephali: remarkable transparent fish larvae of the ocean surface layer. Aqua-BioScience Monogr. 2, 1–94. Miller, M.A., Pfeiffer, W., Schwartz, T., 2010. Creating the CIPRES Science Gateway for inference of large phylonenetic trees., in: Proceedings of the Gateway Computing Evironments Workshop (GCE). pp. 1–8. Miya, M., Kawaguchi, A., Nishida, M., 2001. Mitogenomic exploration of higher teleostean phylogenies: a case study for moderate-scale evolutionary genomics with 38 newly determined complete mitochondrial DNA sequences. Mol. Biol. Evol. 18, 1993–2009. Miya, M., Nishida, M., 2000. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17, 437–455. Morrow, J.M., Lazic, S., Chang, B.S.W., 2011. A novel rhodopsin-like gene expressed in zebrafish retina. Vis. Neurosci. 28, 325–35. Morrow, J.M., Lazic, S., Fox, M.D., Kuo, C., Schott, R.K., Gutierrez, E. de A., Santini, F., Tropepe, V., Chang, B.S.W., 2016. A second visual rhodopsin gene, rh1-2 , is expressed in zebrafish photoreceptors and found in other ray-finned fishes. J. Exp. Biol. doi: 10.1242/jeb.145953. Nakabo, T., 2013. Fishes of Japan with pictorial keys to the species, 3rd edition. Tokai University Press. Near, T.J., Eytan, R.I., Dornburg, A., Kuhn, K.L., Moore, J. a, Davis, M.P., Wainwright, P.C., Friedman, M., Smith, W.L., 2012. Resolution of ray-finned fish phylogeny and timing of diversification. Proc. Natl. Acad. Sci. U. S. A. 109, 13698–13703. Nelson, G.J., 1973. Relationships of clupeomorphs, with remarks on the structure of the lower jaw in fishes, in: Greenwood, P.H., Miles, R.S., Patterson, C. (Eds.), Interrelationships of Fishes. Academic Press, London, pp. 333–349. Nelson, J.S., 1984. Fishes of the World, Third ed. Jhon Wiley & Sons Inc., New York. Nelson, J.S., 2006. Fishes of the World, Fourth ed. John Wiley & Sons Inc., New York. Grande, T.C, Nelson, J.S., Wilson, M.V.H., 2016. Fishes of the World, Fifth ed. Jhon Wiley & Sons Inc., New York. Obermiller, L.E., Pfeiler, E., 2003. Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences. Mol. Phylogenet. Evol. 26, 202–214. Ohno, S., 1970. Evolution by Gene Duplication. Springer. Orti, G., Meyer, A., 1997. The radiation of Characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences. Syst. Biol. 46, 75–100. Patterson, C., 1998. Comments on basal teleosts and teleostean phylogeny, by Gloria Arratia. Am. Soc. Ichthyol. Herpetol. 1998, 1107–1109. Patterson, C., Rosen, D.E., 1977. Review of Ichthyodectiform and other Mesozoic teleost fishes and the theory and practice of classifying fossils. Bull. Am. Museum Nat. Hist. 158, 81–172. Pfeiler, E., 1999. Developmental physiology of elopomorph leptocephali. Comp. Biochem. Physiol. - A Mol. Integr. Physiol. 123, 113–128. Pointer, M. A., Carvalho, L.S., Cowing, J. A., Bowmaker, J.K., Hunt, D.M., 2007. The visual pigments of a deep-sea teleost, the pearl eye Scopelarchus analis. J. Exp. Biol. 210, 2829–2835. Rambaut, A., 1996. Sequence Alignment Editor Version 1.0.1. Rennison, D.J., Owens, G.L., Taylor, J.S., 2012. Opsin gene duplication and divergence in ray-finned fish. Mol. Phylogenet. Evol. 62, 986–1008. Righton, D., Walker, A. M., 2013. Anguillids: conserving a global fishery. J. Fish Biol. 83, 754–765. Robins, C.R., 1989. The phylogenetic relationships of the anguilliform fishes, in: Bohlke, E.B. (Ed.), Fishes of the Western North Atlantic, Part 9, Vol 1. Sears Foundation for Marine Research, pp. 9–23. Rubinoff, D., Holland, B.S., 2005. Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference. Syst. Biol. 54, 952–961. Sabbah, S., Laria, R.L., Gray, S.M., Hawryshyn, C.W., 2010. Functional diversity in the color vision of cichlid fishes. BMC Biol. 8, 133. Saitoh, K., Shao, T., Mayden, R.L., Hanzawa, K., Nishida, M., Miya, M., 2006. Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world’s largest freshwatr fish clade based 59 whole mitogenome sequences. J. Mol. Evol. 63, 826–841. Santini, F., Harmon, L.J., Carnevale, G., Alfaro, M.E., 2009. Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes. BMC Evol. Biol. 9, 194. Santini, F., Kong, X., Sorenson, L., Carnevale, G., Mehta, R.S., Alfaro, M.E., 2013. A multi-locus molecular timescale for the origin and diversification of eels (Order: Anguilliformes). Mol. Phylogenet. Evol. 69, 884–94. Seehausen, O., Terai, Y., Magalhaes, I.S., Carleton, K.L., Mrosso, H.D.J., Miyagi, R., van der Sluijs, I., Schneider, M. V, Maan, M.E., Tachida, H. et al. 2008. Speciation through sensory drive in cichlid fish. Nature 455, 620–626. Shen, S.-C., Lee, S.-C., Shao, K.-T., Chen, C.-W., Chen, C.-T., 1993. Elopomorpha, in: Fishes of Taiwan. Department of Zoology, National Taiwan University, Taiwan. Shiao, J.C., Itoh, S., Yurimoto, H., Iizuka, Y., Liao, Y.C., 2014. Oxygen isotopic distribution along the otolith growth axis by secondary ion mass spectrometry: Applications for studying ontogenetic change in the depth inhabited by deep-sea fishes. Deep. Res. Part I Oceanogr. Res. Pap. 84, 50–58. Smith, D.G., 1989. Class Actionopterygii, in: Carpenter, K.E., Niem, V.H. (Eds). FAO species idintification guide for fishery purpose, the living marine resources of the Western Central Pacific. 3, 1619-1697. Stamatakis, A., Hoover, P., Rougemont, J., 2008. A rapid bootstrap algorithm for the RAxML web server. Syst. Biol. 57, 758–771. Swofford, D.L., 2002. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods), Verson 4. Sinaure Assoc. Sunderland, MA. Talavera, G., Vila, R., 2011. What is the phylogenetic signal limit from mitogenomes? The reconciliation between mitochondrial and nuclear data in the Insecta class phylogeny. BMC Evol. Biol. 11, 315. Tang, K.L., Fielitz, C., 2012. Phylogeny of moray eels (Anguilliformes: Muraenidae), with a revised classification of true eels (Teleostei: Elopomorpha: Anguilliformes). Mitochondrial DNA 24, 55–66. Taylor, S.M., Loew, E.R., Grace, M.S., 2011. A rod-dominated visual system in leptocephalus larvae of elopomorph fishes (Elopomorpha: Teleostei). Environ. Biol. Fishes 92, 513–523. Terakita, A., 2005. The opsins. Genome Biol. 6, 213. doi:10.1186/gb-2005-6-3-213 Van de Peer, Y., Maere, S., Meyer, A., 2009. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–32. Venkatesh, B.Y. V, Ing, Y.A.N.A.N., Renner, S.Y.B., 1999. Late changes in spliceosomal introns define clades in vertebrate evolution. Proc. Natl. Acad. Sci. U. S. A. 96, 10267–10271. Volff, J.-N., 2005. Genome evolution and biodiversity in teleost fish. Heredity. 94, 280–94. Wang, C.-H., Kuo, C.-H., Mok, H.-K., Lee, S.-C., 2003. Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences. Zool. Scr. 32, 231–241. Wang, F.Y., Tang, M.Y., Yan, H.Y., 2011. A comparative study on the visual adaptations of four species of moray eel. Vision Res. 51, 1099–1108. Wiley, E.O., Johnson, G.D., 2010. A teleost classification based on monophyletic groups, in: Nelson, J.S., Schultz, H.-P., Wilson, M.V.H. (Eds.), Origin and Phylogenetic Interrelationships of Teleostei. Verlag Dr. Friedrich Pfeil, Munchen, Germany, pp. 123–182. Wiley, R.H., 1981. Social structure and individual ontogenies: problems of description, mechanism, and evolution. Perspect. Ethol. 4 (5), 105-133. Woltering, J.M., Durston, A.J., 2006. The zebrafish hoxDb cluster has been reduced to a single microRNA. Nat. Genet. 38, 601–602. Yang, Z.B., 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39, 105–111. Yokoyama, S., 1997. Molecular genetic basis of adaptive selection: examples from color vision in vertebrates. Annu. Rev. Genet. 31, 315–36. Yokoyama, S., Tada, T., Zhang, H., Britt, L., 2008. Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc. Natl. Acad. Sci. U. S. A. 105, 13480–5. Zhang, H., Futami, K., Horie, N., Okamura, A., Utoh, T., Mikawa, N., Yamada, Y., Tanaka, S., Okamoto, N., 2000. Molecular cloning of fresh water and deep-sea rod opsin genes from Japanese eel Anguilla japonica and expressional analyses during sexual maturation. FEBS Lett. 469, 39–43. Zhang, H., Futami, K., Yamada, Y., Horie, N., Okamura, A., Utoh, T., Mikawa, N., Tanaka, S., Olamoto, N., Oka, H.P., 2002. Isolation of freshwater and deep-sea type opsin genes from the common Japanese conger. J. Fish Biol. 61, 313–324. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/59670 | - |
dc.description.abstract | 海鰱總目(鰻魚及其近親)為一群形態多樣性高、主要生活在海水的魚類類群,包含至少一千個物種,25個科,四或五個目(海鰱目,北梭魚目,背棘鰻目,鰻鱺目及囊鰓鰻目)。其類群擁有高度的棲地多樣性,分佈在沙岸,珊瑚礁,遠洋及深海等棲地。海鰱總目為現生硬骨魚三大分群之一(其他二者為骨舌魚總目及鯡型總目)。過去數篇研究利用外部形態或分子證據欲重建海鰱總目之親緣關係及系統分類,並無一致結果,這限制了海鰱總目相關的演化研究。為提倡海鰱總目作為一模式魚群以應用於魚類演化及其基因體研究範疇,在此論文中將全面性地探討海鰱總目的親緣關係假說。第一,利用多基因分子資料建構一完整海鰱總目之親緣關係,藉以釐清海鰱總目在硬骨魚中的分類地位及其中目之間的親緣關係與分類。結果顯示,海鰱總目為所有其他硬骨魚的姊妹群並包含四個主要單系群或目,而其中鰻鱺目可進一步被分成四個亞目。第二,接續前部份研究結果,利用相似的研究方法針對鰻鱺目中最大的亞目類群(康吉鰻亞目)建構親緣關係樹,結果發現在康吉鰻亞目中廣泛存在多個多系群科。本論文基於此重建之親緣關係樹,進一步討論康吉鰻亞目的分類修訂。第三,以本論文所建構的親緣關係及海鰱總目為研究重心,深入探討視紫質基因在脊椎動物中的演化。本研究分析了227條來自179種脊椎動物的視紫質基因及其類似基因序列,並針對在脊椎動物演化過程中,數個關於基因演化的假說進行分析(包含基因複製和基因遺失事件),並討論其結果。本研究發現在大部分鰻鱺目物種(除鯙科外)的基因體中,均可發現兩對視紫質基因。根據分析結果推測,在過去早期硬骨魚的演化歷史中,共發生兩次基因複製事件。一次發生在所有硬骨魚的共同祖先,與演化史上“魚類特定基因體複製“事件相符;另一次則發生於鯡型總目的共同祖先。而在此兩次基因複製事件之後,其中一複製的視紫質基因在某些特定魚類類群的基因體中因未被保留而遺失。最後,本論文期許海鰱總目能成為研究魚類演化及其基因體研究的模式魚群,而此篇論文即能作為之後旨在更了解海鰱總目或其他硬骨魚的演化歷史及其生物多樣性研究的重要參考。 | zh_TW |
dc.description.abstract | Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine teleost fishes which comprising more than 1000 species classified in 25 families and four or five orders (i.e. Elopiformes, Albuliformes, Notacanthiformes, Anguilliformes and Saccopharyngiformes). The elopomorph fishes are also ecologically diversified as their habitats include sandy shore, coral reef, pelagic ocean, and deep-sea benthos. Elopomorpha is one of the three major living teleost lineages along with the Osteoglossomorpha and Clupeocephala. Several studies aiming at reconstructing the elopomorph phylogeny using morphological and/or molecular characters led to inconsistent results, precluding us from further investigation of their evolution. To promote the Elopomorpha as a model fish group in the evolutionary and genomic studies, new phylogenetic hypotheses (at different taxonomic levels) are presented in this dissertation. First, the phylogenetic position of the Elopomorpha related to other teleosts and the inter-ordinal phylogeny within the Elopomorpha were investigated using a large multi-gene dataset with an extensive taxonomic sampling. The results show that Elopomorpha is the sister group of the rest of the Teleostei and the Elopomorpha comprises four main monophyletic groups or orders. Within the Anguilliformes, four main lineages (suborders) were presented. Second, the phylogeny of the most speciose suborder, the Congroidei, was examined using similar multi-gene approaches but with different taxon samplings focusing on congroids. The result demonstrates an extensive polyphyly at the familial level within the Congroidei. According to the reconstructed phylogeny, a revised classification of the Congroidei is presented and discussed. Third, with the new phylogenetic framework established in this dissertation and the Elopomorpha as the focus, a thorough perspective of the rhodopsin gene (rh1) evolution within the vertebrates was presented. 227 sequences of rh1 and rh1-like from 179 vertebrate species were included in the analysis. Several hypotheses concerning the rh1 evolutionary events like gene duplication/lost event during the evolution of the vertebrates were evaluated. In this study, two paralogous copies of rh1 were found in the genomes of the most of anguilliforms (except the Muraenidae). According to the analyses, rh1 was likely duplicated two times during the early evolutionary of the Teleostei, one occurred close to the origin of teleosts corresponding to the Fish-Specific Genome Duplication and the other in the common ancestor of the Clupeocephala. After those gene duplication events, one copy was secondarily lost in some specific teleost lineages. Eventually, I expect that the Elopomoprha as a potential model fish group for evolutionary and genomic studies in fishes and hopefully this study could provide a guide for researches which intend to better understanding of the evolution and of biodiversity of the Elopomorpha and other early teleost fishes. | en |
dc.description.provenance | Made available in DSpace on 2021-06-16T09:32:26Z (GMT). No. of bitstreams: 1 ntu-106-F99241214-1.pdf: 12906118 bytes, checksum: b8ea7169cc038d941e3c987732ace3b4 (MD5) Previous issue date: 2017 | en |
dc.description.tableofcontents | 誌謝 i
中文摘要 ii Abstract iv Chapter 1 General Introduction 1 1.1 Elopomorpha 1 1.2 Phylogeny and Classification of the Elopomorpha 3 1.3 Elopomorpha as a Model Group to Study Evolutionary Genomics, Especially, the Species Diversification in Relation to Gene Duplication 6 1.4 Rhodopsin gene in the Teleostei 7 1.5 Purpose of this dissertation 10 Chapter 2 Phylogeny of the Elopomorpha 16 2.1 Introduction 16 2.2 Materials and Methods 17 2.2.1 Taxonomic sampling 17 2.2.2 Genetic markers acquisition 17 2.2.3 Analytical methods 19 2.3 Results 21 2.3.1 Characteristics of sequence data 21 2.3.2 A paralogous copy of the egr3 nuclear gene in elopomorphs 21 2.3.3 Phylogenetic inference 22 2.4 Discussion 23 2.4.1 Basal teleost phylogentic relationships and the position of the Elopomoprha 23 2.4.2 The ordinal relationships within the Elopomorpha 25 2.4.3 Interfamilial relationships within the Anguilliformes and the phylogenetic position of the family Protanguillidae 27 Chapter 3 Multiple-gene study reveals extensive family-level polyphyly in the eel suborder Congroidei 38 3.1 Introduction 38 3.2 Materials and Methods 39 3.2.1 Sample collection and species identification 39 3.2.2 Genetic markers 40 3.3 Result and discussion 41 Chapter 4 Rhodopsin gene evolution within the Elopomorpha (Teleostei) 51 4.1 Introduction 51 4.2 Materials and Methods 51 4.2.1 Sequences acquisition and data collection 51 4.2.2 Sequence alignment, data matrix 52 4.2.3 Phylogenetic analysis 53 4.2.4 Hypothesis evaluation of dynamic process of rhodopsin gene evolution 53 4.2.5 Ancestral state reconstruction of rhodopsin gene 54 4.3 Results 55 4.3.1 Rhodopsin gene tree 55 4.3.2 Gene orthology and hypotheses of gene evolution 56 4.3.3 Ancestral state reconstruction (ASR) 57 4.4 Discussion 58 4.4.1 The exo-rhodopsin in the ray-finned fishes 58 4.4.2 Rh1-dso and rh1-fwo in the Elopomorpha 59 4.4.3 Gene duplication in the Teleostei 60 Chapter 5 Conclusions 73 References 76 Appendix I. The sample list and the sequences used in Chapter 2. 90 Appendix II. The primers used in this dissertation. 95 Appendix III. Species and the sequence detail in Chapter 3. 96 Appendix IV. Sample (sequence) list used in Chapter 4. 98 Appendix V. Descriptive statistics of each codon of rhodopsin gene sequences. 105 Appendix VI. Amino acid sequences of Elops rh1-dso and rh1-fwo. 106 Appendix VII. Publications 111 | |
dc.language.iso | en | |
dc.title | 海鰱總目之系統分類及其視紫質基因的演化 | zh_TW |
dc.title | Systematics and rhodopsin gene evolution in the Elopomorpha (Teleostei) | en |
dc.type | Thesis | |
dc.date.schoolyear | 105-1 | |
dc.description.degree | 博士 | |
dc.contributor.oralexamcommittee | 邵廣昭,莫顯蕎,戴昌鳳,韓玉山 | |
dc.subject.keyword | 海鰱總目,康吉鰻亞目,分子系統分類,分類,視紫質基因,基因演化,模式魚群, | zh_TW |
dc.subject.keyword | Elopomorpha,Congroidei,Molecular systematics,Classification,Rhodopsin gene,Gene evolution,Model fish group, | en |
dc.relation.page | 111 | |
dc.identifier.doi | 10.6342/NTU201700464 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2017-02-15 | |
dc.contributor.author-college | 理學院 | zh_TW |
dc.contributor.author-dept | 海洋研究所 | zh_TW |
顯示於系所單位: | 海洋研究所 |
文件中的檔案:
檔案 | 大小 | 格式 | |
---|---|---|---|
ntu-106-1.pdf 目前未授權公開取用 | 12.6 MB | Adobe PDF |
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。