Mitogenomic evidence for the monophyly of elopomorph fishes (Teleostei) and the evolutionary origin of the leptocephalus larva

Molecular Phylogenetics and Evolution

Volumn 32, Issue 1, 2004, Pages 274-286

  Inoue, Jun G ^a   Miya, Masaki ^b   Tsukamoto, Katsumi ^a   Nishida, Mutsumi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

Author keywords

Elopomorpha; Leptocephalus larvae; Mitogenome; Partitioned Bayesian analysis

Indexed keywords

RIBOSOME RNA; RNA; TRANSFER RNA;

ANIMAL; ARTICLE; BAYES THEOREM; DNA SEQUENCE; FISH; GENETICS; GENOME; MOLECULAR EVOLUTION; PHYLOGENY; POLYMERASE CHAIN REACTION; PRENATAL DEVELOPMENT; SPECIES DIFFERENCE; TIME;

ANIMALS; BAYES THEOREM; EVOLUTION, MOLECULAR; FISHES; GENOME; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA; RNA, RIBOSOMAL; RNA, TRANSFER; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; TIME FACTORS;

ALBULIFORMES; ANGUILLIFORMES; ELOPIFORMES; ELOPOMORPHA; PISCES; SACCOPHARYNGIFORMES; TELEOSTEI;

EID: 3042697196     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2003.11.009     Document Type: Article

References (68)

1. Arratia G. Basal teleosts and teleostean phylogeny. Palaeo Ichthyologica. 7:1997;5-168
2. Berg L.S. Classification of fishes, both recent and fossil. Trav. Inst. Zool. Acad. Sci. USSR. 5:1940;87-517
3. Böhlke E.B. Fishes of the Western North Atlantic. Part 9. 1989;Sears Foundation for Marine Research, New Haven
4. Bond C.E. Biology of Fishes. second ed. 1996;Saunders College Publishing, Philadelphia
5. Chang Y.-S., Huang F.-I., Lo T.-B. The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J. Mol. Evol. 38:1994;138-155
6. Cheng S., Higuchi R., Stoneking M. Complete mitochondrial genome amplification. Nat. Genet. 7:1994;350-351
7. Delarbre C., Spruyt N., Delmarre C., Gallut C., Barriel V., Janvier P., Laudet V., Gachelin G. The complete nucleotide sequence of the mitochondrial DNA of the dogfish, Scyliorhinus canicula. Genetics. 150:1998;331-344
8. Filleul A., Lavoué S. Basal teleosts and the question of elopomorph monophyly. Morphological and molecular approaches. C. R. Acad. Sci. Paris Life Sci. 324:2001;393-399
9. Forey P.L. Relationships of elopomorphs. Greenwood P.H., Miles R.S., Patterson C. Interrelationships of Fishes. 1973;351-368 Academic Press, London
10. Forey P.L., Littlewood D.T.J., Ritchie P., Meyer A. Interrelationships of elopomorph fishes. Stiassny M.L.J., Parenti L.R., Johnson G.D. Interrelationships of Fishes. 1996;175-191 Academic Press, San Diego
11. Gosline W.A. Functional Morphology and Classification of Teleostean Fishes. 1971;The University Press of Hawaii, Honolulu
12. Greenwood P.H. Notes on the anatomy and classification of elopomorph fishes. Bull. Br. Mus. (Nat. Hist.) Zool. 32:1977;65-102
13. Greenwood P.H., Rosen D.E., Weitzman S.H., Myers G.S. Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bull. Am. Mus. Nat. Hist. 131:1966;339-456
14. Hillis D.M. Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst. Biol. 47:1998;3-8
15. Huelsenbeck J.P., Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 17:2001;754-755
16. Hulet W.H., Robins C.R. The evolutionary significance of the leptocephalus larva. Böhlke E.B. Fishes of the Western North Atlantic. Part 9. Vol. 2:1989;669-677 Sears Foundation for Marine Research, New Haven
17. Hurst C.D., Bartlett S.E., Davidson W.S., Bruce I.J. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene. 239:1999;237-242
18. Inoue J.G., Miya M. Phylogeny of the basal teleosts, with special reference to the Elopomorpha. Jpn. J. Ichthyol. 48:2001;75-91. (in Japanese with English abstract)
19. Inoue J.G., Miya M., Tsukamoto K., Nishida M. Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish. Sci. 66:2000;924-932
20. Inoue J.G., Miya M., Aoyama J., Ishikawa S., Tsukamoto K., Nishida M. Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica. Fish. Sci. 67:2001;118-125
21. Inoue J.G., Miya M., Tsukamoto K., Nishida M. 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. 52:2001;311-320
22. Inoue J.G., Miya M., Tsukamoto K., Nishida M. Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fish. Sci. 67:2001;828-835
23. Inoue J.G., Miya M., Tsukamoto K., Nishida M. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol. 20:2001;275-285
24. Inoue J.G., Miya M., Tsukamoto K., Nishida M. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish" Mol. Phylogenet. Evol. 26:2003;110-120
25. Inoue J.G., Miya M., Tsukamoto K., Nishida M. Evolution of the deep-sea gulper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels. Mol. Biol. Evol. 20:2003;1917-1924
26. Ishiguro N.B., Miya M., Nishida M. Complete mitochondrial DNA sequence of ayu Plecoglossus altivelis. Fish. Sci. 67:2001;474-481
27. Ishiguro N.B., Miya M., Nishida M. Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the " Protacanthopterygii" Mol. Phylogenet. Evol. 27:2003;476-488
28. Jamieson B.G.M. Fish Evolution and Systematics: Evidence from Spermatozoa. 1991;Cambridge University Press, Cambridge
29. Kawaguchi A., Miya M., Nishida M. Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: longer DNA sequences and higher-level relationships. Ichthyol. Res. 48:2001;213-223
30. Kumazawa Y., Nishida M. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37:1993;380-398
31. Lauder G.V., Liem K.F. The evolution and interrelationships of the actinopterygian fishes. Bull. Mus. Comp. Zool. 150:1983;95-197
32. Lê H.L.V., Lecointre G., Perasso R. A 28S rRNA-based phylogeny of the gnathostomes: first steps in the analysis of conflict and congruence with morphologically based cladograms. Mol. Phylogenet. Evol. 2:1993;31-51
33. Lecointre G., Nelson G. Clupeomorpha, sister-group of Ostariophysi. Stiassny M.L.J., Parenti L.R., Johnson G.D. Interrelationships of Fishes. 1996;193-207 Academic Press, San Diego
34. Lee J.-S., Miya M., Lee Y.-S., Kim C.G., Park E.-H., Aoki Y., Nishida M. The complete DNA sequence of the mitochondrial genome of the selffertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish. Gene. 280:2001;1-7
35. Löytynoja A., Milinkovitch M.C. A hidden Markov model for progressive multiple alignment. Bioinformatics. 19:2003;1505-1513
36. Maddison D.R., Maddison W.P. MacClade Ver. 4.05. 2002;Sinauer, Sunderland, MA
37. Mattei X. Spermatozoon ultrastructure and its systematic implications in fishes. Can. J. Zool. 69:1991;3038-3055
38. Miller R.E., Buckley T.R., Manos P.S. An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Syst. Biol. 51:2002;740-753
39. Miya M., Nishida M. 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. 1:1999;416-426
40. Miya M., Nishida M. Use of mitogenomic information in teleostean molecular phylogenetics: a tree-based exploration under the maximum-parsimony optimality criterion. Mol. Phylogenet. Evol. 17:2000;437-455
41. Miya M., Kawaguchi A., Nishida M. 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. 18:2001;1993-2009
42. Miya, M., Takeshima, H., Endo, H., et al., 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26, 121-138
43. Nelson G.J. Relationships of clupeomorphs, with remarks on the structure of the lower jaw in fishes. Greenwood P.H., Miles R.S., Patterson C. Interrelationships of Fishes. 1973;333-349 Academic Press, London
44. Nelson G. Phylogeny of major fish groups. Fernholm B., Bremer K., Jörnvall H. The Hierarchy of Life. 1989;325-336 Elsevier, Amsterdam
45. Nelson J.S. Fishes of the World. third ed. 1994;Wiley, New York
46. Nybelin O. On the caudal skeleton in Elops with remarks on other teleostean fishes. Acta Reg. Soc. Sci. Litt. Goth. Zool. 7:1971;1-52
47. Obermiller L.E, Pfeiler E. Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences. Mol. Phylogenet. Evol. 26:2003;202-214
48. Ortí G., Meyer A. The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences. Syst. Biol. 46:1997;75-100
49. Patterson C., Rosen D.E. Review of ichthyodectiform and other Mesozoic teleost fishes and the theory and practice of classifying fossils. Bull. Am. Mus. Nat. Hist. 158:1977;81-172
50. Pfeiler E. Acidic glycosaminoglycans in marine teleost larvae: evidence for a relationship between composition and negative charge density in elopomorph leptocephali. Comp. Biochem. Physiol. 119B:1998;137-144
51. Posada D., Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics. 14:1998;817-818
52. Regan, C.T., 1929. Fishes. In: Encyclopaedia Britannica, vol. 9, 14th ed. London and New York, pp. 305-336
53. Robins C.R. The phylogenetic relationships of the anguilliform fishes. Böhlke E.B. Fishes of the Western North Atlantic. Part 9. vol. 1:1989;9-23 Sears Foundation for Marine Research, New Haven
54. Ronquist, F., Huelsenbeck, J.P., 2003. Mr Bayes 3: Bayesian phylogenetic inference under mixed models. 19, 1572-1574
55. Saitoh K., Miya M., Inoue J.G., Ishiguro N.B., Nishida M. Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography. J. Mol. Evol. 56:2003;464-472
56. Shimodaira H., Hasegawa M. Multiple comparisons of log-likelihoods with application s to phylogenetic inference. Mol. Biol. Evol. 16:1999;1114-1116
57. Smith D.G. Guide to the leptocephali (Elopiformes, Anguilliformes, and Notacanthiformes). NOAA Tech. Rep. NMFS Circ. 424:1979;1-39
58. Smith D.G. Elopiformes, Notacanthiformes and Anguilliformes: relationships. Moser H.G., Richards W.J., Cohen D.M., Fahay M.P., Kendall A.W. Jr., Richardson S.L. Ontogeny and Systematics of Fishes. 1984;94-102 Am. Soc. Ichthyol. Herpetol. Spec. Publ. Lawrence, KS
59. Stepien C.A., Kocher T.D. Molecules and morphology in studies of fish evolution. Kocher T.D., Stepien C.A. Molecular Systematics of Fishes. 1997;1-11 Academic Press, San Diego
60. Swofford D.L. PAUP*: Phylogenetic Analysis Using Parsimony. (* and Other Methods), Version 4.0b10. 2002;Sinauer Associates, Sunderland, MA
61. Templeton A.R. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of human and apes. Evolution. 37:1983;221-244
62. Tchernavin V. A living bony fish which differs substantially from all living and fossil Osteichthyes. Nature. 158:1946;667
63. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680
64. Tzeng C.-S., Hui C.-F., Shen S.-C., Huang P.C. The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Res. 20:1992;4853-4858
65. Wang C.-H., Kuo C.-H., Mok H.-K., Lee S.-C. Molecular phylogeny of elopomorph fishes inferred from mitochondrial 12S ribosomal RNA sequences. Zool. Scr. 32:2003;231-241
66. Yang Z. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:1994;105-111
67. Zardoya R., Garrido-Pertierra A., Bautista J.M. The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J. Mol. Evol. 41:1995;942-951
68. Zardoya R., Meyer A. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13:1996;933-942