Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications

Molecular Phylogenetics and Evolution

Volumn 38, Issue 3, 2006, Pages 648-658

  Akasaki, Tetsuya ^a   Nikaido, Masato ^a   Tsuchiya, Kotaro ^b   Segawa, Susumu ^b   Hasegawa, Masami ^c   Okada, Norihiro ^a,d  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b TOKYO UNIVERSITY OF MARINE SCIENCE AND TECHNOLOGY   (Japan)

^c INSTITUTE OF STATISTICAL MATHEMATICS   (Japan)

^d NATIONAL INSTITUTES OF NATURAL SCIENCES   (Japan)

Author keywords

Cephalopods; Evolution; Gene rearrangement; Mitochondria

Indexed keywords

MITOCHONDRIAL DNA; PRIMER DNA;

ANIMAL; ARTICLE; CEPHALOPOD; CLASSIFICATION; GENE ORDER; GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; CEPHALOPODA; DNA PRIMERS; DNA, MITOCHONDRIAL; GENE ORDER; LIKELIHOOD FUNCTIONS; PHYLOGENY;

CEPHALOPODA; COLEOIDEA; DECAPODIFORMES; LOLIGO BLEEKERI; OCTOPODA; OCTOPUS; OCTOPUS OCELLATUS; OEGOPSIDA; SEPIA OFFICINALIS; SEPIIDA; SEPIIDAE; SEPIOTEUTHIS LESSONIANA; TEUTHIDA; TODARODES PACIFICUS; WATASENIA SCINTILLANS;

EID: 33244495720     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2005.10.018     Document Type: Article

References (47)

1. Adachi, J., Hasegawa, M., 1996a. MOLPHY: Programs for molecular phylogenetics ver. 2.3, Computer Science Monographs, No. 28. Institute of Statistical Mathematics, Tokyo.
2. J. Adachi, and M. Hasegawa Model of amino acid substitution in proteins encoded by mitochondrial DNA J. Mol. Evol. 42 1996 459 468
3. H. Akaike A new look at the statistical model identification IEEE Trans. Autom. Contr. AC19 1974 716 723
4. F.E. Anderson Preliminary cladistic analysis of relationships among loliginid squids (Cephalopoda: Myopsida) based on morphological data Am. Malac. Bull. 12 1/2 1996 113 128
5. F.E. Anderson Phylogeny and historical biogeography of the loliginid squids (Mollusca: Cephalopoda) based on mitochondrial DNA sequence data Mol. Phylogenet. Evol. 15 2000 191 214
6. F.E. Anderson Phylogenetic relationships among loliginid squids (Cephalopoda: Myopsida) based on analyses of multiple data sets Zool. J. Linnean Soc. 130 2000 603 633
7. N. Blin, and D.W. Stafford A general method for isolation of high molecular weight DNA from eukaryotes Nucleic Acids Res. 3 1976 2303 2308
8. S.V. Boletzky Biology of early life stages in cephalopod mulluscs Adv. Mar. Biol. 44 2003 144 184
9. L. Bonnaud, R. Boucher-Rodoni, and M. Monnerot Relationship of some coleoid cephalopods established by 3′ end of the 16S rDNA and cytochrome oxidase 3 gene sequence comparison Am. Malac. Bull. 12 1/2 1996 87 90
10. L. Bonnaud, R. Boucher-Rodoni, and M. Monnerot Phylogeny of Cephalopods inferred from mitochondrial DNA sequences Mol. Phylogenet. Evol. 7 1997 44 54
11. J.L. Boore, and W.M. Brown Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicate Genetics 138 2 1994 423 443
12. J.L. Boore, and W.M. Brown Mitochondrial genomes and the phylogeny of Mollusks NAUTILUS Suppl. 2 1994 61 78
13. J.L. Boore, and W.M. Brown Big trees from little genomes: mitochondrial gene order as a phylogenetic tool Curr. Opin. Genet. Dev. 8 1998 668 674
14. J.L. Boore, M. Medina, and L.A. Rosenberg Complete sequence of two highly rearranged molluscan mitochondrial genomes, those of the scaphopod Graptacme eborea and of the bivalve Mytilus edulis Mol. Biol. Evol. 21 2004 1492 1503
15. D.B. Carlini, K.S. Reece, and J.G. Graves Actin gene family evolution and the phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) Mol. Biol. Evol. 17 2000 1353 1370
16. M. Dowton, and A.D. Austin Evolution dynamics of a mitochondrial rearrangement "Hot Spot" in the Hymenoptera Mol. Biol. Evol. 16 1999 298 309
17. M. Dowton, L.R. Castro, and A.D. Austin Mitochondrial gene rearrangements as phylogenetic characters in the invertebrates: the examination of genome 'morphology' Invert. Systematics 16 2002 345 356
18. H. Dreyer, and G. Steiner The complete sequence and gene organization of the mitochondrial genome of the gadilid scaphopod Siphonondentalium labatum (Mollusca) Mol. Phylogenet. Evol. 31 2004 605 617
19. J. Felsenstein Evolutionary trees from DNA sequences: a maximum likelihood approach J. Mol. Evol. 17 1981 368 376
20. N. Goldman, and Z. Yang A codon-based model of nucleotide substitution for protein-coding DNA sequences Mol. Biol. Evol. 11 1994 725 736
21. R. Grantham Amino acid difference formula to help explain protein evolution Science 185 1974 862 864
22. M. Hasegawa, and H. Kishino Accuracies of the simple methods for estimating the bootstrap probability of a maximum likelihood tree Mol. Biol. Evol. 11 1994 142 145
23. D.T. Jones, W.R. Taylor, and J.M. Thornton The rapid generation of mutation data matrices from protein sequences Comput. Appl. Biosci. 8 1992 275 282
24. H. Kishino, and M. Hasegawa Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea J. Mol. Evol. 29 1989 170 179
25. H. Kishino, T. Miyata, and M. Hasegawa Maximum likelihood inference of protein phylogeny, and the origin of chloroplasts J. Mol. Evol. 31 1990 151 160
26. Y. Kumazawa, H. Ota, M. Nishida, and T. Ozawa The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions Genetics 150 1998 313 329
27. D.V. Lavrov, J.L. Boore, and W.M. Brown Complete mtDNA sequences of two Millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss Mol. Biol. Evol. 19 2002 163 169
28. A.R. Lindgren, G. Giribet, and M.K. Nishiguchi A combined approach to the phylogeny of Cephalopoda (Mollusca) Cladistics 20 2004 454 486
29. J.R. Macey, T.J. Papenfuss, J.V. Kuehl, H.M. Fourcade, and J.L. Boore Phylogenetic relationships among amphisbaenian reptiles based on complete mitochondrial genomic sequences Mol. Phylogenet. Evol. 33 2004 22 31
30. T. Miyata, S. Miyazawa, and T. Yasunaga Two types of amino acid substitutions in protein evolution J. Mol. Evol. 12 3 1979 219 236
31. Y. Murata, M. Nikaido, T. Sasaki, Y. Cao, Y. Fukumoto, M. Hasegawa, and N. Okada Afrotherian phylogeny as inferred from complete mitochondrial genomes Mol. Phylogenet. Evol. 28 2003 253 260
32. M. Nickisch-Rosenegk, W.M. Brown, and J.L. Boore Complete sequence of the mitochondrial genome of the tapeworm Hymenolepis diminuta: gene arrangements indicate that Platyhelminths are Eutrochozoans Mol. Biol. Evol. 18 2001 721 730
33. A. Rokas, and W.H. Holland Rare genomic changes as a tool for phylogenetics Trends Ecol. Evol. 15 2000 454 459
34. C. Saccone, C.D. Giorgi, C. Gissi, and G. Pesole Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system Gene 238 1999 195 209
35. T. Sasaki, M. Nikaido, H. Hamilton, M. Goto, H. Kato, N. Kanda, L.A. Pastene, Y. Cao, M. Hasegawa, R.E. Fordyce, and N. Okada Mitochondrial phylogenetics and evolution of Mysticete Whales System. Biol. 54 2005 77 90
36. J. Sasuga, S. Yokobori, M. Kaifu, T. Ueda, K. Nishikawa, and K. Watanabe Gene contents and organization of a mitochondrial DNA segment of the squid Loligo bleekeri J. Mol. Evol. 48 1999 692 702
37. H. Shimodaira, and M. Hasegawa Multiple comparisons of log-likelihoods with applications to phylogenetic inference Mol. Biol. Evol. 16 1999 1114 1116
38. H. Shimodaira, and M. Hasegawa CONSEL: a program for assessing the confidence of phylogenetic tree selection Bioinformatics 17 2001 1246 1247
39. H. Shimodaira An approximately unbiased test of phylogenetic tree selection System. Biol. 51 2002 492 508
40. J. Strugnell, M. Norman, J. Jackson, A.J. Drummond, and A. Cooper Molecular phylogeny of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach; the effect of data partitioning on resolving phylogenies in a Bayesian framework Mol. Phylogenet. Evol. 37 2 2005 426 441
41. J.D. Taylor Origin and Evolutionary Radiation of the Mollusca 1996 Oxford Science Publications pp. 41-42
42. K. Tomita, S. Yokobori, T. Oshima, T. Ueda, and K. Watanabe The Cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes J. Mol. Evol. 54 2002 486 500
43. Z. Yang Among-site rate variation and its impact on phylogenetic analyses TREE 11 1996 367 372
44. Z. Yang PAML: a program package for phylogenetic analysis by maximum likelihood CABIOS 13 1997 555 556
45. Z. Yang, R. Nielsen, and M. Hasegawa Models of amino acid substitution and applications to mitochondrial protein evolution Mol. Biol. Evol. 15 1998 1600 1611
46. S. Yokobori, N. Fukuda, M. Nakamura, T. Aoyama, and T. Oshima Long-term conservation of six duplicated structural genes in Cephalopod mitochondrial genomes Mol. Biol. Evol. 21 2004 2034 2046
47. R.E. Young, M. Vecchione, and D.T. Donovan The evolution of coleoid Cephalopods and their present biodiversity and ecology Cephalopod biodiversity ecology, and evolution S. Afr. J. Mar. Sci. 20 1998 393 420