Complete mitochondrial DNA sequence of Aulopus japonicus (Teleostei: Aulopiformes), a basal Eurypterygii: Longer DNA sequences and higher-level relationships

Ichthyological Research

Volumn 48, Issue 3, 2001, Pages 213-223

  Kawaguchi, Akira ^a,b   Miya, Masaki ^c   Nishida, Mutsumi ^b  

^a FUKUI PREFECTURAL UNIVERSITY   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

^c NATURAL HISTORY MUSEUM AND INSTITUTE   (Japan)

Author keywords

Aulopiformes; Complete mtDNA sequence; Mitogenomics; Phylogeny; Teleostei

Indexed keywords

AULOPIFORMES; AULOPODIDAE; AULOPUS JAPONICUS; EURYPTERYGII; PISCES; TELEOSTEI; VERTEBRATA;

EID: 0035539901     PISSN: 13418998     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10228-001-8139-0     Document Type: Article

References (35)

1. Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature (Lond) 290:457-465
2. Baldwin CC, Johnson GD (1996) Interrelationships of Aulopiformes. In: Interrelationships of fishes. Stiassny MLJ, Parenti LR, Johnson GD (eds) Academic Press, San Diego, pp 355-404
3. Chang Y-S, Huang F-I, Lo T-B (1994) The complete nucleotide sequence and gene organization of carp (Cyprinus carpio) mitochondrial genome. J Mol Evol 38:138-155
4. Cheng S, Chang S-Y, Gravitt P, Respess R (1994) Long PCR. Nature (Lond) 369:684-685
5. Doda JN, Wright CT, Clayton DA (1981) Elongation of displacement-loop strands in human and mouse mitochondrial DNA is arrested near specific template sequences. Proc Natl Acad Sci USA 78:6116-6120
6. Gutell RR, Gray MW, Schnare MN (1993) A compilation of large subunit (23S and 23S-like) ribosome RNA structures. Nucleic Acids Res 21:3055-3074
7. Hendy MD, Penny D (1989) A framework for the quantitative study of evolutionary trees. Syst Zool 38:297-309
8. Hillis DM (1998) Taxonomic sampling, phylogenetic accuracy, and investigator bias. Syst Biol 47:3-8
9. Hillis DM, Huelsenbeck JP (1992) Signal, noise, and reliability in molecular phylogenetic analyses. J Hered 83:189-195
10. Hixson JE, Wong TW, Clayton DA (1986) Both the conserved stem loop and divergent 5́-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. J Biol Chem 261:2384-2390
11. Inoue J, Miya M, Tsukamoto K, Nishida M (2000) Complete mitochondrial DNA sequence of the Japanese sardine, Sardinops melanostictus. Fish Sci 66:924-932
12. Inoue J, Miya M, Aoyama J, Ishikawa S, Tsukamoto K, Nishida M (2001) Complete mitochondrial DNA sequence of the Japanese eel, Anguilla japonica. Fish Sci 67:118-125
13. 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
14. Johnson GD, Patterson C (1996) Relationships of lower teleostean fishes. In: Stiassny MLJ, Parenti LR, Johnson GD (eds) Interrelationships of fishes. Academic Press, San Diego, pp 251-332
15. Kumazawa Y, Nishida M (1993) Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J Mol Evol 37:380-398
16. Lê HLV, 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
17. Lecointre G, Nelson G (1996) Clupeomorpha, sister group̀ of Ostariophysi. In: Stiassny MLJ, Parenti LR, Johnson GD (eds) Interrelationships of fishes. Academic Press, San Diego, pp 193-207
18. Mindell DP, Sorenson MD, Dimcheff DEM, Hasegawa M, Ast JC, Yuri T (1999) Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes. Syst Biol 48:138-152
19. Miya M, Nishida M (1998) Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx. Mol Phylogenet Evol 10:11-12
20. 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
21. Miya M, Nishida M (2000a) Molecular systematics of the deep-sea fish genus Gonostoma Stomiiformes: Gonostomatidae): two paraphyletic clades and resurrection of Sigmops. Copeia 2000:378-389
22. 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
23. Naylor GJP, Brown WM (1998) Amphioxus mitochondrial DNA, chordate phylogeny, and the limits of inference based on comparisons of sequences. Syst Biol 47:61-76
24. Nelson G (1989) Phylogeny of major fish groups. In: Fernholm B, Bremer K, Jornvall H (eds) The hierarchy of life. Excerpta Medica, Amsterdam, pp 325-336
25. Nelson JS (1984) Fishes of the world, 2nd edn. Wiley, New York
26. Nelson JS (1994) Fishes of the world, 3rd edn. Wiley, New York
27. Rosen DE (1973) Interrelationships of higher euteleostean fishes. In: Greenwood PH, Miles RS, Patterson C (eds) Interrelationships of fishes. Academic Press, London, pp 397-413
28. Stepien CA, Kocher TD (1997) Molecules and morphology in studies of fish evolution. In: Kocher TD, Stepien CA (eds) Molecular systematics of fishes. Academic Press, San Diego, pp 1-11
29. Stiassny MLJ, Parenti LR. Johnson GD (eds) (1996) Interrelationships of fishes. Academic Press, San Diego
30. Swofford DL (1993) PAUP: phylogenetic analysis using parsimony, ver. 3.1.1. Smithsonian Institute, Washington, DC
31. Swofford DL (1998) PAUP*: phylogenetic analysis using parsimony (*and other methods), ver. 4.0. Sinauer Associates, Sunderland, MA
32. Templeton AR (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of human and the apes. Evolution 37:221-244
33. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The Clustal X Windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
34. Walberg MW, Clayton DA (1981) Sequence and properties of the human KB cell and mouse L cell D-loop regions of mitochondrial DNA. Nucleic Acids Res 9:5411-5421
35. Zardoya R, Carrido-Pertierra A, Bautista JM (1995) The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. J Mol Evol 41:942-951