Major patterns of higher teleostean phylogenies: A new perspective based on 100 complete mitochondrial DNA sequences

Molecular Phylogenetics and Evolution

Volumn 26, Issue 1, 2003, Pages 121-138

  Miya, Masaki ^a   Takeshima, Hirohiko ^b   Endo, Hiromitsu ^c   Ishiguro, Naoya B ^b   Inoue, Jun G ^b   Mukai, Takahiko ^b   Satoh, Takashi P ^b   Yamaguchi, Motoomi ^b   Kawaguchi, Akira ^b   Mabuchi, Kohji ^b   Shirai, Shigeru M ^d   Nishida, Mutsumi ^b  

^a NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c KOCHI UNIVERSITY   (Japan)

^d FISHERIES RESEARCH AGENCY   (Japan)

Author keywords

Complete mtDNA sequence; Higher level relationships; Long PCR; Mitogenomics; Taxonomic sampling; Teleostei

Indexed keywords

ANIMALS; DNA, MITOCHONDRIAL; FISHES; GENOME; PHYLOGENY; SEQUENCE ANALYSIS, DNA; VARIATION (GENETICS);

ACANTHOMORPHA; ACANTHOPTERYGII; ATELEOPODIFORMES; BATRACHOIDIFORMES; BERYCIFORMES; CTENOSQUAMATA; EURYPTERYGII; LAMPRIDIFORMES; LOPHIIFORMES; NEOTELEOSTEI; OPHIDIIFORMES; PARACANTHOPTERYGII; PERCOMORPHA; POLYMIXIIFORMES; STEPHANOBERYCIFORMES; TELEOSTEI; ZEIFORMES;

EID: 0037215848     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00332-9     Document Type: Article

References (84)

1. Anderson, M.E., Hubbs, C.L., 1981. Redescription and osteology of the northeastern Pacific fish Derepodichthys alepidotus (Zoarcidae). Copeia 1981, 341-352.
2. Banister, K.E., 1970. The anatomy and taxonomy of Indostomus paradoxus Prashad & Mukerji. Bull. Brit. Mus. (Nat. Hist.) Zool. 19, 179-209.
3. Berg, L.S., 1940. Classification of fishes both recent and fossil. Trav. Inst. Zool. Acad. Sci. USSR 5, 87-517.
4. Bertelsen, E., Marshall, N.B., 1984. Mirapinnatoidei: Development and relationships. In: Ontogeny and Systematics of Fishes. In: Moser, H.G., Richards, W.J., Cohen, D.M., Fahay, M.P., Kendall Jr., A.W., Richardson, S.L. (Eds.),. Spec. Publ. No. 1. Am. Soc. Ichthyol. Herpetol, Lawrence, KA, pp. 380-383.
5. Bremer, K., 1988. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 44, 360-370.
6. Carroll, R.L., 1988. Vertebrate Paleontology and Evolution. Freeman, New York.
7. Chang, Y.S., Huang, F.L., Lo, T.B., 1994. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38, 138-155.
8. Chapleau, F., 1993. Pleuronectiform relationships: A cladistic reassessment. Bull. Mar. Sci. 52, 516-540.
9. Cheng, S., Chang, S.-Y., Gravitt, P., Respess, R., 1994. Long PCR. Nature 369, 684-685.
10. Colgan, D.J., Zhang, C.-G., Paxton, J.R., 2000. Phylogenetic investigations of the Stephanoberyciformes and Beryciformes, particularly whalefishes (Euteleostei: Cetomimidae), based on partial 12S rDNA and 16S rDNA sequences. Mol. Phylogenet. Evol. 17, 15-25.
11. Donoghue, M.J., Olmstead, R.G., Smith, J.F., Palmer, J.D., 1992. Phylogenetic relationships of the Dipsacales based on rbcL sequences. Ann. Miss. Bot. Gard. 79, 333-345.
12. Farris, J.S., Albert, V.A., Källersjö, M., Lipscomb, D., Kluge, A.G., 1996. Parsimony jackknifing outperforms neighbor-joining. Cladistics 12, 99-124.
13. Fraser, T.H., 1972. Some thoughts about the teleostean fish concept - The Paracanthopterygii. Jpn. J. Ichthyol. 19, 232-242.
14. Freihofer, W.C., 1970. Some nerve patterns and their systematic significance in teleostean fishes. Proc. Calif. Acad. Sci. 38, 215-264.
15. Gayet, M., 1980a. Sur la découverte dans le crétacé de hadjula (Liban) du plus ancien caproidae connu. Compte Rendu Hebdomadaire des Śeances de l'Académie des Sciences, Paris 290D, 447-448.
16. Gayet, M., 1980b. Découverte dans le crétacé de hadjula (Liban) du plus ancien caproidae connu. Étude anatomique et phylogénétique. Bull. Mus. Nat. Hist. Natur. Paris 4, 259-269.
17. Gosline, W.A., 1970. A reinterpretation of the teleostean fish order Gobiesociformes. Proc. Calif. Acad. Sci. 38, 363-382.
18. Gosline, W.A., 1971. Functional Morphology and Classification of Teleostean Fishes. Univ. of Hawaii Press, Honolulu.
19. 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. Mus. Nat. Hist. 131, 339-456.
20. Helfman, G.S., Collette, B.B., Facey, D.E., 1997. The Diversity of Fishes. Blackwell Science, Massachusetts.
21. Hennig, W., 1966. Phylogenetic Systematics. Univ. of Illinois Press, Urbana.
22. Hillis, D.M., 1998. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47, 3-8.
23. Inoue, J.G., Miya, M., 2001. Phylogeny of the basal teleosts, with special reference to the Elopomorpha. Jpn. J. Ichthyol. 48, 75-91 (in Japanese with English abstract).
24. Inoue, J.G., Miya, M., Aoyama, J., Ishikawa, S., Tsukamoto, K., Nishida, M., 2001a. Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica. Fish. Sci. 67, 118-125.
25. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2000. Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish. Sci. 66, 924-932.
26. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2001b. 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, 311-320.
27. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2001c. A mitogenomic perspective on the basal teleostean phylogeny: Resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol. 20, 275-285.
28. Inoue, J.G., Miya, M., Tsukamoto, K., Nishida, M., 2001d. Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fish. Sci. 67, 828-835.
29. Ishiguro, N., Miya, M., Nishida, M., 2001. Complete mitochondrial DNA sequence of ayu, Plecoglossus altivelis. Fish. Sci. 67, 474-481.
30. Johansen, S., Bakke, I., 1996. The complete mitochondrial DNA sequence of Atlantic cod (Gadus morhua): Relevance to taxonomic studies among codfishes. Mol. Mar. Biol. Biotechnol. 5, 203-214.
31. Johnson, G.D., 1992. Monophyly of the euteleostean clades - Neoteleostei, Eurypterygii, and Ctenosquamata. Copeia 1992, 8-25.
32. Johnson, G.D., 1993. Percomorph phylogeny: progress and problems. Bull. Mar. Sci. 52, 3-28.
33. Johnson, G.D., Patterson, C., 1993. Percomorph phylogeny: A survey of acanthomorphs and a new proposal. Bull. Mar. Sci. 52, 554-626.
34. Johnson, R.K., Bertelsen, E., 1991. The fishes of the family Giganturidae: Systematics, development, distribution and aspects of biology. DANA Rep. 91, 1-45.
35. Kawaguchi, A., Miya, M., Nishida, M., 2001. Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: Longer DNA sequences and higher-level relationships. Ichthyol. Res. 48, 213-223.
36. Kocher, T., Stepien, C.A. (Eds.), 1997. Molecular Systematics of Fishes. Academic Press, San Diego.
37. Kumazawa, Y., Nishida, M., 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37, 380-398.
38. Kumazawa, Y., Yamaguchi, M., Nishida, M., 1999. Mitochondrial molecular clocks and the origin of euteleostean biodiversity: Familial radiation of perciforms may have predated the Cretaceous/Tertiary boundary. In: Kato, M. (Ed.), The Biology of Biodiversity. Springer-Verlag, Tokyo, pp. 35-52.
39. Lauder, G.V., Liem, K.F., 1983. The evolution and interrelationships of the actinopterygian fishes. Bull. Mus. Comp. Zool. 150, 95-197.
40. Maddison, W.P., Maddison, D.R., 2000. MacClade Ver. 4. Sinauer, Sunderland, MA.
41. Mindell, D.P., Sorenson, M.D., Dimcheff, D.E.M., Hasegawa, M., Ast, J.C., Yuri, T., 1999. Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst. Biol. 48, 138-152.
42. Miya, M., Nishida, M., 1998. Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx. Mol. Phylogenet. Evol. 10, 11-22.
43. Miya, M., Nishida, M., 1999. Organization of the mitochondrial genome of a deep-sea fish Gonostoma gracile (Teleostei: Stomiiformes): First example of transfer RNA gene rearrangements in bony fishes. Mar. Biotechnol. 1, 416-426.
44. Miya, M., Nishida, M., 2000a. Molecular phylogeny of the deep-sea fish genus Gonostoma (Teleostei: Stomiiformes): Two paraphyletic clades and resurrection of Sigmops. Copeia 2000, 378-389.
45. Miya, M., Nishida, M., 2000b. Use of mitogenomic information in teleostean molecular phylogenetics: A tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17, 437-455.
46. 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.
47. Mooi, R.D., Johnson, G.D., 1997. Dismantling the Trachinoidei: Evidence of a scorpaenoid relationship for the Champsodontidae. Ichthyol. Res. 44, 143-176.
48. Moore, J.A., 1993. Phylogeny of the Trachichthyiformes (Teleostei: Percomorpha). Bull. Mar. Sci. 52, 114-136.
49. Nakabo, T. (Ed.), 2000. Fishes of Japan with Pictorial Keys to the Species, Second Ed. Tokai Univ. Press, Tokyo.
50. Nelson, G., 1989. Phylogeny of major fish groups. In: Fernholm, B., Bremer, K., Jörnvall, H. (Eds.), The Hierarchy of Life. Excerpta Medica, Amsterdam, pp. 325-336.
51. Nelson, J.S., 1976. Fishes of the World. Wiley, New York.
52. Nelson, J.S., 1984. Fishes of the World, Second Ed. Wiley, New York.
53. Nelson, J.S., 1994. Fishes of the World, Third Ed. Wiley, New York.
54. Nixon, K., 1999. The parsimony ratchet: A rapid means for analyzing large data sets. Cladistics 15, 407-414.
55. Olney, J.E., Johnson, G.D., Baldwin, C.C., 1993. Phylogeny of lampridiform fishes. Bull. Mar. Sci. 52, 137-169.
56. Parenti, L.R., 1993. Relationships of atherinomorph fishes (Teleostei). Bull. Mar. Sci. 52, 170-196.
57. Patterson, C., Rosen, D.E., 1989. The Paracanthopterygii revisited: Order and disorder. In: Cohen, D.M. (Ed.), Papers on the Systematics of Gadiform Fishes. Nat. Hist. Mus. Los Angeles Co, Los Angeles, pp. 5-36.
58. Paxton, J.R., 1989. Synopsis of the whalefishes (family Cetomimidae) with descriptions of four new genera. Rec. Aust. Mus. 41, 135-206.
59. Posada, D., Crandall, K.A., 1998. Modeltest: Testing the model of DNA substitution. Bioinformatics 14, 817-818.
60. Regan, C.T., 1913. The osteology and classification of the teleostean fishes of the order Scleroparei. Ann. Mag. Nat. Hist. 11, 169-184.
61. Romer, A.S., 1945. Vertebrate Paleontology, Second Ed. Chicago Univ. Press, Chicago.
62. Rosen, D.E., 1973. Interrelationships of higher teleostean fishes. In: Greenwood, P.H., Miles, R.S., Patterson, C. (Eds.), Interrelationships of Fishes. Academic Press, London, pp. 397-513.
63. Rosen, D.E., 1985. An essay on euteleostean classification. Am. Mus. Novit. 2827, 1-57.
64. Rosen, D.E., Patterson, C., 1969. The structure and relationships of the paracanthopterygian fishes. Bull. Am. Mus. Nat. Hist. 141, 357-474.
65. Saitoh, K., Hayashizaki, K., Yokoyama, Y., Asahida, T., Toyohara, H., Yamashita, Y., 2000. Complete nucleotide sequence of Japanese flounder (Paralichthys olivaceus) mitochondrial genome: Structural properties and cue for resolving teleostean relationships. J. Heredity 91, 271-278.
66. Sikes, D.S., Lewis, P.O., 2001. PAUPRat: A Tool to Implement Parsimony Ratchet Searches Using PAUP*, Dept. Ecol. Evol. Biol., Univ. of Connecticut.
67. Soltis, D.E., Soltis, P.S., Nickrent, D.L., Johnson, L.A., Hahn, W.H., Hoot, S.B., Sweere, J.A., Kuzoff, R.K., Kron, K.A., Chase, M.W., Swensen, S.M., Zimmer, E.A., Chaw, S.M., Gillespie, L.J., Kress, W.J., Sytsma, K.J., 1997. Angiosperm phylogeny inferred from 18S ribosomal DNA sequences. Ann. Miss. Bot. Gard. 84, 1-49.
68. Soltis, D.E., Soltis, P.S., Chase, M.W., Mort, M.E., Albach, D.C., Zanis, M., Savolainen, V., Hahn, W.H., Hoot, S.B., Fay, M.F., Axtell, M., Swensen, S.M., Prince, L.M., Kress, W.J., Nixon, K.C., Farris, J.S., 2000. Angiosperm phylogeny inferred from 18S rDNA, rbcL, and atpB sequences. Bot. J. Linn. Soc. 133, 381-461.
69. Stepien, C.A., Kocher, T.D., 1997. Molecules and morphology in studies of fish evolution. In: Kocher, T.D., Stepien, C.A. (Eds.), Molecular Systematics of Fishes. Academic Press, San Diego, pp. 1-11.
70. Stiassny, M.L.J., 1986. The limits and relationships of the acanthomorph teleosts. J. Zool. London (B) 1986, 411-460.
71. Stiassny, M.L.J., 1993. What are grey mullets? Bull. Mar. Sci. 52, 197-219.
72. Stiassny, M.L.J., Moore, J.A., 1992. A review of the pelvic girdle of acanthomorph fishes, with comments on hypotheses of acanthomorph interrelationships. Zool. J. Linn. Soc. 104, 209-242.
73. Stiassny, M.L.J., Parenti, L.R., Johnson, G.D. (Eds.), 1996. Interrelationships of Fishes. Academic Press, San Diego.
74. Swofford, D.L., 1993. PAUP: Phylogenetic Analysis Using Parsimony, Ver. 3.1.1. Smiths. Inst, Washington DC.
75. Swoord, D.L., 2001. PAUP*: Phylogenetic Analysis Using Parsimony (* and Other Methods), Version 4.0. Sinauer Associates, Sunderland, MA.
76. Templeton, A.R., 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of human and the apes. Evolution 37, 221-244.
77. Tucker, D.W., 1954. Report on the fishes collected by S.Y. 'Rosaura' in the North and Central Atlantic, 1937-38. Part IV. Families Carcharhinidae, Torpedinidae, Rosauridae (nov.), Salmonidae, Alepocephalidae, Searsidae, Clupeidae. Bull. Brit. Mus. (Nat. Hist.) 2, 163-214.
78. Tzeng, C.S., Hui, C.F., Shen, S.C., Huang, P.C., 1992. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Res. 20, 4853-4858.
79. Wiley, E.O., 1981. Phylogenetics: The Theory and Practice of Phylogenetic Systematics. Wiley, New York.
80. Wiley, E.O., Johnson, G.D., Dimmick, W.W., 2000. The interrelationships of acanthomorph fishes: A total evidence approach using molecular and morphological data. Biochem. Syst. Ecol. 28, 319-350.
81. Yamaguchi, M., Miya, M., Okiyama, M., Nishida, M., 2000. Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae). Mol. Phylogenet. Evol. 15, 103-114.
82. Yang, Z., 1994. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods. J. Mol. Evol. 39, 306-314.
83. Zardoya, R., Meyer, A., 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13, 933-942.
84. Zardoya, R., Garrido-Pertierra, A., Bautista, J.M., 1995. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 41, 942-951.