* Ocean Research Institute, University of Tokyo, Tokyo, Japan
Department of Zoology, Natural History Museum & Institute, Chiba, Japan
Correspondence: E-mail: jinoue{at}ori.u-tokyo.ac.jp.
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Abstract |
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Key Words: gulper eels complete mtDNA sequence gene rearrangement mitogenomics deep sea higher-level relationships
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Introduction |
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During the course of molecular phylogenetic studies of the Elopomorpha (eels and their allies) using mitogenomic data, we found an unusual mitochondrial gene order for one of the gulper eels, Eurypharynx pelecanoides (fig. 1). This article describes novel gene organization in the mitogenomes of two species of gulper eels, E. pelecanoides and Saccopharynx lavenbergi. We employed a polymerase chain reaction (PCR)-based approach developed by Miya and Nishida (1999) for sequencing the complete mitogenomes of these fishes. To explore the origin of such unique mitogenomes, we subjected the mitogenomic data to phylogenetic analysis, and we discuss here the possible mechanisms generating such a gene arrangement in the two gulper eels.
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Materials and Methods |
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Polymerase Chain Reaction and Sequencing
The entire mitogenomes of two gulper eels were amplified using a long-PCR technique (Cheng, Higuchi, and Stoneking 1994). Five fish-universal and three species-specific long-PCR primers (S-LA-16S-L + H12293-Leu and L12321-Leu + S-LA-16S-H for E. pelecanoides; L250816S + Sala-ND4-H and Sala-CO1-L + Sala-ND1-H for S. lavenbergi; fig. 1) were used to amplify the entire mitogenome of each eel in two reactions. The entire mitogenomes of the other four E. pelecanoides individuals were amplified with three fish-universal primers and one species-specific long-PCR primer (L250816S + Eupe-ND2-H and L12321-Leu + S-LA-16S-H). Four species-specific primers (Eupe-ND2-H for E. pelecanoides; Sala-CO1-L, Sala-ND1-H, and Sala-ND4-H for S. lavenbergi) were alternatively designed with reference to the partial nucleotide sequences from the ND2 gene of E. pelecanoides and the COI, ND1, and ND4 genes of S. lavenbergi determined from each total DNA using fish-universal primers.
The long-PCR products were diluted with TE buffer (1:20) for subsequent use as PCR templates, except for a region intervening between the two long-PCR primers (between S-LA-16S-H and S-LA-16S-L, and H12293-Leu and L12321-Leu for E. pelecanoides; fig. 1), in which total genomic DNA was used alternatively.
A total of 82 fish-universal primers (Miya and Nishida 1999, 2000; Inoue et al. 2000, 2001a, 2001b, 2001c, 2001d; Ishiguro, Miya, and Nishida 2001; Kawaguchi, Miya, and Nishida 2001) were used in various combinations to amplify contiguous, overlapping segments of the entire mitogenome for each of the two species. Species-specific primers were designed in cases where no appropriate fish-universal primers were available. A list of PCR primers used for a specific species is available from J.G.I. upon request. Long-PCR and subsequent PCR reactions were carried out as previously described (e.g., Miya and Nishida 1999; Inoue et al. 2003).
Double-stranded PCR products, purified using a Pre-Sequencing Kit (USB), were subsequently used for direct cycle sequencing using dye-labeled terminators (Applied Biosystems). The primers used were the same as those for PCR. All sequencing reactions were performed according to the manufacturer's instructions. Labeled fragments were analyzed by means of a Model 377 DNA sequencer (Applied Biosystems).
Sequence Analysis
DNA sequences were analyzed using the computer software package program DNASIS version 3.2 (Hitachi Software Engineering). Locations of the 13 protein-coding genes were determined by comparisons of DNA or amino acid sequences of bony fish mitogenomes. The 22 tRNA genes were identified by their cloverleaf secondary structures (Kumazawa and Nishida 1993) and anticodon sequences. The two rRNA genes were identified by sequence similarity and secondary structure (Gutell, Gray, and Schnare 1993). Sequence data are available from DDBJ/EMBL/GenBank with accession numbers AB046473 and AB046475AB046490 for E. pelecanoides, and AB047825 for S. lavenbergi.
Phylogenetic Analysis
The data matrices from Inoue et al. (2001d) and Miya, Kawaguchi, and Nishida (2001) were combined and redundant taxa were eliminated. Mitogenomic sequences from the two gulper eels and two teleosts (Gymnothorax kidako, AP002976 [Inoue et al. 2003] and Salmo salar, U12143 [Hurst et al. 1999]) were added. Because unambiguous alignments of the two rRNA genes on the basis of secondary structure models were not feasible (Miya and Nishida 2000), they were not used in the analyses. The ND6 gene was not used in the phylogenetic analyses because of its heterogeneous base composition and consistently poor phylogenetic performance (e.g., Zardoya and Meyer 1996; Miya and Nishida 2000). Also, tRNA loops, tRNASer(AGY) (unstable inferred secondary structures in some species), and other ambiguously aligned regions, such as the 5' and 3' ends of several protein-coding genes, were excluded form the analyses. In addition, 3rd codon positions in the protein-coding genes that could positively mislead an analysis of higher-level relationships of actinopterygians (Miya and Nishida 2000) were excluded from the analyses, leaving 7,984 available nucleotide positions from the 12 protein-coding genes and 21 tRNA genes.
Bayesian phylogenetic analyses were conducted using MrBayes 2.01 (Huelsenbeck and Ronquist 2001). The general time reversible model with some sites assumed to be invariable and with variable sites assumed to follow a discrete gamma distribution (GTR + I + ; Yang 1994) was selected as the best-fit model of nucleotide substitution (ModelTest version 3.06; Posada and Crandall 1998). We set the maximum likelihood parameters in MrBayes as follows: "lset nst = 6" (GTR), "rates = invgamma" (I +
), and "basefreq = estimate" (estimated proportion of base types from the data). The Markov chain Monte Carlo process was set so that four chains (three heated and one cold) ran simultaneously. We conducted two independent runs for 1 million generations, with trees being sampled every 100 generations, each of which started from a random tree. Two independent analyses converged on similar log-likelihood scores and reached "stationarity" (lack of improvement in ML scores) at no later than 120,000 generations. Thus, the first 1,200 trees were discarded from each analysis, and the remaining 17,602 combined samples from two independent analyses were used to generate a 50% majority rule consensus tree, with the percentage of samples recovering any particular clade representing that clade's posterior probability (Huelsenbeck and Ronquist 2001).
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Results |
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The E. pelecanoides mitogenome contains three noncoding regions longer than 200 bp (fig. 2; see also Supplementary Materials online; noncoding region [nc1 and 2] and control region [CR]). The nc1, located between tRNASer(UCN) and tRNAAsp genes, and the nc2, located between the tRNAAsp and COII genes, contain two and four pseudogenes corresponding to degenerating copies of tRNAAsp gene, respectively. A noncoding region (1,818 bp) located between the cyt b and tRNAPhe genes appears to correspond to the control region. The S. lavenbergi mitogenome also contains three noncoding regions longer than 200 bp (noncoding region [nc] and control regions [CR1 and CR2]). The nc, located between the tRNALeu(CUN) and ND5 genes, contains at least two pseudogenes corresponding to degenerating copies of the tRNALeu(CUN) gene. CR1 (992 bp), located between two tRNA gene clusters (TP and IM regions), and CR2 (> 837 bp), located between cyt b and tRNAPhe genes, appear to correspond to the control region, and they have completely identical sequences over 800 bp, indicating that they are undergoing concerted evolution (see Kumazawa et al. 1998).
With the exception of the two duplicated control regions (CR1 and CR2) in the S. lavenbergi mitogenome, the mitogenomes from the two deep-sea gulper eels exhibit an identical gene order (fig. 2). However, the mitochondrial gene order of the two gulper eels differs greatly from that of all other vertebrates known to date. When some tRNA genes were excluded from the comparisons (fig. 2), we identified five gene blocks (A, tRNAGlutRNAGln; B, ATP8-ND3; C, tRNALeu(CUN)ND6; D, tRNAIletRNALys; and E, tRNAArgtRNASer(AGY) gene regions), the gene order of which is identical to that of typical vertebrates.
Phylogenetic Positions of Two Gulper Eels
Figure 3 is a 50% majority rule consensus tree of the 17,602 combined samples from two independent Bayesian analyses of the 59 mitochondrial nucleotide sequences from the concatenated 12 protein-coding (no 3rd codon positions), plus 21 tRNA genes (stem regions only) using the GTR + I + model of sequence evolution (Yang 1994). With the exception of a few nodes within the Neoteleostei, most internal branches were supported by high Bayesian posterior probabilities (
95%). It should be noted that the resultant tree explicitly demonstrates not only that the two gulper eels form a sister-group relationship with a high posterior probability (100%), but also that they are deeply nested within the Anguilliformes (true eels), strongly suggesting that they have been derived from an eel-like ancestor.
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Discussion |
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Phylogenetic Implications on the Origin of Novel Gene Order
To deduce the evolution of the gene arrangements in the two gulper eels, inference for the ancestral organization based on a reliable phylogenetic framework is required. Although the gulper eels have been included in the Elopomorpha based solely on a distinct pelagic larval form, termed the leptocephalus, no one has corroborated their phylogenetic position using character matrices derived from morphological or molecular data (Inoue and Miya 2001).
Bayesian analysis using the mitogenomic data from 59 species which fully represent teleostean fish diversity (fig. 3) not only corroborated that the novel gene order of the two gulper eels originated in a common ancestor of the two species, but also demonstrated that their origin was independent from those of the other novel gene orders. It also appears that the novel gene order of Conger myriaster, another member of the Elopomorpha, has an origin independent from that of gulper eels. It should be noted that Anguilla japonica, which has the typical vertebrate gene order, was confidently placed as a sister species of the two gulper eels. The most parsimonious reconstruction of the gene rearrangement events on the phylogenetic tree indicated that the aberrant gene order of the two gulper eels is derived from that of typical vertebrates.
Possible Mechanism for the Gene Rearrangement in Gulper Eels
Two major mechanisms have been proposed to explain the gene rearrangements in vertebrate mitogenomes (Lee and Kocher 1995; Kumazawa et al. 1996). One is the tandem duplication of gene regions as a result of slipped strand mispairing, followed by the deletions of genes (Moritz and Brown 1986; Levinson and Gutman 1987). Although the dynamics of mitochondrial gene arrangements have not been explained in some invertebrates (e.g., Kurabayashi and Ueshima 2000; Machida et al. 2002; Tomita et al. 2002), vertebrate mitochondrial gene rearrangements may well be explained by such a mechanism (Desjardins and Morais 1990; Quinn and Wilson 1993; Kumazawa and Nishida 1995; Kumazawa et al. 1996; Mindell, Sorenson, and Dimcheff 1998; Miya and Nishida 1999; Inoue et al. 2001b), and its feasibility is also supported by the frequent polymorphic duplications of mtDNA sequences (e.g., Stanton et al. 1994; Gach and Brown 1997; Mindell, Sorenson, and Dimcheff 1998; Miya and Nishida 1999). The other suggested mechanisms invoke the illicit priming of replication by tRNAs and the resultant integration of tRNA genes around the control region (Cantatore et al. 1987; Jacobs et al. 1989).
Although the second model is not excluded at this point, the first model is favored as the mechanism of gene rearrangement in the gulper eel mitogenomes. Assuming that a long DNA fragment in the tRNAIleCR region of the typical organization is duplicated (fig. 4), subsequent deletions of redundant genes would give rise to the rearranged gene organization in gulper eels. Such tandem duplication and subsequent deletions most parsimoniously resulted in the observed gene order and associated intergenic spacers in these two gulper eels.
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If four of five contiguous gene blocks were duplicated together in a common ancestor of the two species, and if subsequent deletion of genes occurred before the speciation, the assumed duplicated portions of gulper eels, ranging from the tRNAIle gene to CR of the typical organization, were extending beyond 12 kb (fig. 1). Prior to this study, the putative duplicated regions of ever-known vertebrate rearrangement were 4 kb at best. Moreover, all the known tandemly repeated coding sequences were restricted to regions adjacent to the CR, IQM, or WANCY regions, possibly reflecting occasional imprecise termination of replications beyond their origins. The duplicated region in the gulper eel mitogenome was much greater than that of ever-known vertebrate rearrangements and involved almost the entire mitogenome (fig. 1).
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Acknowledgements |
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Footnotes |
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Literature Cited |
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Anderson, S., A. T. Bankier, and B. G. Barrell, et al. (14 co-authors). 1981. Sequence and organization of the human mitochondrial genome. Nature 290:457-465.[ISI][Medline]
Anderson, S., M. H. L. de Bruijn, A. R. Coulson, I. C. Eperon, F. Sanger, and I. G. Young. 1982. Complete sequence of bovine mitochondrial DNA conserved features of the mammalian mitochondrial genome. J. Mol. Biol. 156:683-717.[ISI][Medline]
Banister, K. E., (Ed.). 1987. The encyclopaedia of animals, Vol. 13. Andromeda Oxford, London, p. 43.
Bertelsen, E., J. G. Nielsen, and D. G. Smith. 1989. Suborder Saccopharyngoidei: families Saccopharyngidae, Eurypharyngidae, and Monognathidae. Pp. 636655 in E. B. Böhlke, ed. Fishes of the western North Atlantic. Part 9. Vol. 1. Orders Anguilliformes and Saccopharyngiformes. Sears Foundation for Marine Research, New Haven, Conn.
Bibb, M. J., R. A. Van Etten, C. T. Wright, M. W. Walberg, and D. A. Clayton. 1981. Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167-180.[ISI][Medline]
Boore, J. L. 1999. Animal mitochondrial genomes. Nucleic Acids Res. 27:1767-1780.
Cantatore, P., M. N. Gadaleta, M. Roberti, C. Saccone, and A. C. Wilson. 1987. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature 329:853-855.[CrossRef][ISI][Medline]
Cheng, S., R. Higuchi, and M. Stoneking. 1994. Complete mitochondrial genome amplification. Nat. Genet. 7:350-351.[ISI][Medline]
Desjardins, P., and R. Morais. 1990. Sequence and gene organization of the chicken mitochondrial genome. J. Mol. Biol. 212:599-634.[ISI][Medline]
1991. Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome. J. Mol. Evol. 32:153-161.[ISI][Medline]
Gach, M. H., and W. M. Brown. 1997. Characteristics and distribution of large tandem duplications in brook stickleback (Culaea inconstans) mitochondrial DNA. Genetics 145:383-394.
Greenwood, P. H., D. E. Rosen, S. H. Weitzman, and G. S. Myers. 1966. Phyletic studies of teleostean fishes, with a provisional classification of living forms. Bull. Am. Mus. Nat. Hist. 131:339-456.
Gutell, R. R., M. W. Gray, and M. N. Schnare. 1993. A compilation of large subunit (23S and 23S-like) ribosome RNA structures: 1993. Nucleic Acids Res. 21:3055-3074.[ISI][Medline]
Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:754-755.
Hurst, C. D., S. E. Bartlett, W. S. Davidson, and I. J. Bruce. 1999. The complete mitochondrial DNA sequence of the Atlantic salmon, Salmo salar. Gene 239:237-242.[CrossRef][ISI][Medline]
Inoue, J. G., and M. Miya. 2001. Phylogeny of the basal teleosts, with special reference to the Elopomorpha. Jpn. J. Ichthyol. 48:75-91 [in Japanese with English abstract].
Inoue, J. G., M. Miya, J. Aoyama, S. Ishikawa, K. Tsukamoto, and M. Nishida. 2001a. Complete mitochondrial DNA sequence of the Japanese eel Anguilla japonica. Fish. Sci. 67:118-125.[CrossRef][ISI]
Inoue, J. G., M. Miya, K. Tsukamoto, and M. Nishida. 2000. Complete mitochondrial DNA sequence of the Japanese sardine Sardinops melanostictus. Fish. Sci. 66:924-932.[CrossRef][ISI]
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.[ISI][Medline]
2001c. Complete mitochondrial DNA sequence of the Japanese anchovy Engraulis japonicus. Fish. Sci. 67:828-835.[CrossRef][ISI]
2001d. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Mol. Phylogenet. Evol. 20:275-285.[CrossRef][ISI][Medline]
2003. Basal actinopterygian relationships: a mitogenomic perspective on the phylogeny of the "ancient fish.". Mol. Phylogenet. Evol. 26:110-120.[CrossRef][ISI][Medline]
Ishiguro, N., M. Miya, and M. Nishida. 2001. Complete mitochondrial DNA sequence of ayu Plecoglossus altivelis. Fish. Sci. 67:474-481.[CrossRef][ISI]
2003. Basal euteleostean relationships: a mitogenomic perspective on the phylogenetic reality of the "Protacanthopterygii.". Mol. Phylogenet. Evol. 27:476-488.[CrossRef][ISI][Medline]
Jacobs, H. T., S. Asakawa, T. Araki, K. Miura, M. J. Smith, and K. Watanabe. 1989. Conserved tRNA gene cluster in starfish mitochondrial DNA. Curr. Genet. 15:193-206.[ISI][Medline]
Janke, A., G. Feldmaier-Fuchs, W. K. Thomas, A. von Haeseler, and S. Pääbo. 1994. The marsupial mitochondrial genome and the evolution of placental mammals. Genetics 137:243-256.
Kawaguchi, A., M. Miya, and M. Nishida. 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.[CrossRef][ISI]
Kumazawa, Y., and M. Nishida. 1993. Sequence evolution of mitochondrial tRNA genes and deep-branch animal phylogenetics. J. Mol. Evol. 37:380-398.[ISI][Medline]
1995. Variation in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. Mol. Biol. Evol. 12:759-772.[Abstract]
Kumazawa, Y., H. Ota, M. Nishida, and T. Ozawa. 1996. Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-regionlike sequences duplicated and inserted into a tRNA gene cluster. Mol. Biol. Evol. 13:1242-1254.[Abstract]
1998. The complete nucleotide sequence of a snake (Dinodon semicarinatus) mitochondrial genome with two identical control regions. Genetics 150:313-329.
Kurabayashi, A., and R. Ueshima. 2000. Complete sequence of the mitochondrial DNA of the primitive opisthobranch gastropod Pupa strigosa: systematic implication of the genome organization. Mol. Biol. Evol. 17:266-277.
Lee, W.-J, and T. D. Kocher. 1995. Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. Genetics 139:873-887.
Levinson, G., and G. A. Gutman. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.[Abstract]
Macey, J. R., A. Larson, N. B. Ananjeva, Z. Fang, and T. J. Papenfuss. 1997. Two novel gene orders and the role of light-strand replication in rearrangement of the vertebrate mitochondrial genome. Mol. Biol. Evol. 14:91-104.[Abstract]
Machida, R. J., M. U. Miya., M. Nishida, and S. Nishida. 2002. Complete mitochondrial DNA sequence of Tigriopus japonicus (Crustacea: Copepoda). Mar. Biothechnol. 4:406-417.[CrossRef]
Masuda, H., K. Amaoka, C. Araga, T. Uyeno, and T. Yoshino. 1984. The fishes of the Japanese archipelago. Tokai University Press, Tokyo.
Mindell, D. P., M. D. Sorenson, and D. E. Dimcheff. 1998. Multiple independent origins of mitochondrial gene order in birds. Proc. Natl. Acad. Sci. USA 95:10693-10697.
Miya, M., and M. Nishida. 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.[ISI][Medline]
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.[CrossRef][ISI][Medline]
Miya, M., A. Kawaguchi, and M. Nishida. 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., H. Takeshima, and H. Endo, et al. (12 co-authors). 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol. Phylogenet. Evol. 26:121-138.[CrossRef][ISI][Medline]
Moritz, C., and W. M. Brown. 1986. Tandem duplications of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425-1427.[ISI][Medline]
Pääbo, S., W. K. Thomas, K. M. Whitfield, Y. Kumazawa, and A. C. Wilson. 1991. Rearrangements of mitochondrial transfer RNA genes in marsupials. J. Mol. Evol. 33:426-430.[ISI][Medline]
Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.[Abstract]
Quinn, T. W., and D. P. Mindell. 1996. Mitochondrial gene order adjacent to the control region in crocodile, turtle, and tuatara. Mol. Phylogenet. Evol. 5:344-351.[CrossRef][ISI][Medline]
Quinn, T. W., and A. C. Wilson. 1993. Sequence evolution in and around the mitochondrial control region in birds. J. Mol. Evol. 37:417-425.[ISI][Medline]
Robins, C. R. 1989. The phylogenetic relationships of the anguilliform fishes. Pp. 923 in E. B. Böhlke, ed. Fishes of the western North Atlantic. Part 9. Vol. 1. Orders Anguilliformes and Saccopharyngiformes. Sears Foundation for Marine Research, New Haven, Conn.
Roe, B. A., D.-P. Ma, R. K. Wilson, and J. F.-H. Wong. 1985. The complete nucleotide sequence of the Xenopus laevis mitochondrial genome. J. Biol. Chem. 260:9759-9774.
Saitoh, K, M. Miya, J. G. Inoue, N. B. Ishiguro, and M. Nishida. 2003. Mitochondrial genomics of ostariophysan fishes: perspectives on phylogeny and biogeography. J. Mol. Evol. 56:464-472.[CrossRef][ISI][Medline]
Stanton, D. J., L. L. Daehler, C. C. Moritz, and W. M. Brown. 1994. Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA. Genetics 137:233-241.
Sumida, M., Y. Kanamori, H. Kaneda, Y. Kato, M. Nishioka, M. Hasegawa, and H. Yonekawa. 2001. Complete nucleotide sequence and gene rearrangement of the mitochondrial genome of the Japanese pond frog Rana nigromaculata. Genes Genet. Syst. 76:311-325.[CrossRef][ISI][Medline]
Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (*and other methods). Version 4.0b10. Sinauer Associates, Sunderland, Mass.
Tchernavin, V. 1946. A living bony fish which differs substantially from all living and fossil Osteichthyes. Nature 158:667.
Tomita, K., S. Yokobori, T. Oshima, T. Ueda, and K. Watanabe. 2002. The cephalopod Loligo bleekeri mitochondrial genome: multiplied noncoding regions and transposition of tRNA genes. J. Mol. Evol. 54:486-500.[CrossRef][ISI][Medline]
Whitfield, P. 1998. Encyclopedia of animals. Marshall Editions, London.
Yang, Z. 1994. Estimating the pattern of nucleotide substitution. J. Mol. Evol. 39:105-111.[ISI][Medline]
Zardoya, R., and A. Meyer. 1996. Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Mol. Biol. Evol. 13:933-942.