Natural History Museum and Institute, Chiba, Japan;
Ocean Research Institute, University of Tokyo, Tokyo, Japan
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Abstract |
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Introduction |
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For fish mitogenomes, one practical method is a PCR-based approach that employs a long PCR technique and many versatile PCR primers and is accurate and faster than sequencing cloned mitochondrial DNA (mtDNA) (Miya and Nishida 1999
; for bird mitogenomes, see Sorenson et al. 1999
). In fact, complete mtDNA sequences for 12 teleost species have already been determined using this method (Miya and Nishida 1999, 2000b
; Inoue et al. 2000, 2001a, 2001b, 2001c, 2001d
; Ishiguro, Miya, and Nishida 2001
; Kawaguchi, Miya, and Nishida 2001
). Furthermore, including the additional species determined during the present study, the number of complete mtDNA sequences determined using this method (total 50) has become compatible with those determined in other studies for whole vertebrates, including fishes (total 69; Pollock et al. 2000
), indicating a certain utility of our approach in moderate-scale evolutionary genomic studies. Thus, technical difficulties in obtaining mitogenomic data from various fishes within a relatively short period of time had been overcome, although there still remained problems as to whether or not they were suitable for inferring phylogenies, thus providing a basis for further comparative evolutionary analyses.
To address this problem, Miya and Nishida (2000b)
explored the phylogenetic utility and limits of individual and concatenated mitochondrial genes for reconstructing higher-level relationships, using the complete mtDNA sequences of eight teleosts (of noncontroversial relative phylogenetic positions). They demonstrated that nucleotide sequences from concatenated protein-coding (no third codon positions) plus transfer RNA (tRNA; stem regions only) genes (hereinafter called "mitogenomic data") were most able to reproduce the expected phylogeny of teleosts with high statistical support, unlike most individual genes. Accordingly, mitogenomic data can be expected to resolve the persistent controversies over the higher-level relationships of teleosts. Subsequently, Inoue et al. (2001d)
resolved the interrelationships of five major lineages of basal teleosts (Osteoglossomorpha, Elopomorpha, Clupeomorpha, Ostariophysi, and Protacanthopterygii, given various rankings), for which five alternative phylogenetic hypotheses had previously been proposed on the basis of both morphological and molecular data, using mitogenomic data. Thus, the mitogenomic data not only are able to reproduce the expected phylogeny of teleosts (Miya and Nishida 2000b
), but can also resolve specific phylogenetic questions for higher-level relationships of teleosts (Inoue et al. 2001d
), the most diversified group of all vertebrates, comprising over 23,500 extant species (J. S. Nelson 1994
).
Higher teleosts have been collectively called Acanthomorpha, Acanthopterygii, or Percomorpha, depending on their limits (fig. 1 ; Rosen 1973
; Lauder and Liem 1983
; J. S. Nelson 1984, 1994
; Stiassny 1986
; Stiassny and Moore 1992
; Johnson 1993
; Johnson and Patterson 1993
; Stiassny, Parenti, and Johnson 1996
). If higher teleosts are equated with the most comprehensive group, Acanthomorpha (Rosen 1973
), they comprise about 14,650 species placed in 20 orders, 296 families, and 2,615 genera (calculated from J. S. Nelson 1994
). Their interrelationships have long been controversial and so complex that G. Nelson (1989)
described them as the "(unresolved) bush at the top of the tree," which is still evident, as seen in figure 1
. A strict consensus tree (fig. 1C
) generated from two recently proposed hypotheses on higher teleostean relationships (Johnson and Patterson 1993
[fig. 1A
]; J. S. Nelson 1994
[fig. 1B
]) clearly included unresolved "bushes" (fig. 1C
). As a first step toward resolution of higher teleostean phylogenies containing such enormous taxonomic diversity, this study attempted (1) to circumscribe a well-supported monophyletic group encompassing such "bushes" (=Percomorpha) and (2) to determine the phylogenetic position of such a monophyletic group relative to other major lineages using mitogenomic data. By doing so, we hoped to clarify where the phylogenetic problems lay, thus providing a basis and guidelines for subsequent resolution of the "bushy top." Clearly, this study was not intended to resolve intrarelationships of the bushy top, as such an investigation would require wider and more extensive taxonomic sampling.
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Materials and Methods |
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For circumscription of the upper bushes, we chose at least one species each to represent all of the major lineages above Paracanthopterygii (=Acanthopterygii; fig. 2
); of those major lineages that occupied the three most basal positions in either Johnson and Patterson's (1993)
or J. S. Nelson's (1994)
hypotheses (see fig. 1A and B
; Mugiliformes, Atherinomorpha, Stephanoberyciformes, Beryciformes, and Zeioidei), we added one to three species so as to locate their phylogenetic positions more correctly, assuming possible cases in which they would be placed outside the upper bushes. For more accurate determination of the relative phylogenetic positions of the upper bushes, we chose two to three species from all major lineages up to the Paracanthopterygii in order to break up possible long branches (fig. 2
). Final rooting was done using a clupeid, Sardinops melanostictus, with reference to the recent mitogenomic analysis of basal teleostean phylogeny by Inoue et al. (2001d)
. All species used in this study are listed in table 1
, along with references and DDBJ/EMBL/GenBank accession numbers.
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Mitochondrial DNA Purification by Long PCR
The mitogenomes of the 38 species were amplified in their entirety using a long PCR technique (Cheng et al. 1994
; Miya and Nishida 1999
). Seven fish-versatile long PCR primers (S-LA-16S-L, L2508-16S, L12321-Leu, H12293-Leu, H15149-CYB, H1065-12S, and S-LA-16S-H; for locations and sequences of these primers, see Miya and Nishida 2000b
; Inoue et al. 2000, 2001d
; Ishiguro, Miya, and Nishida 2001
; Kawaguchi, Miya, and Nishida 2001
) were used in various combinations so as to amplify the entire mitochondrial genome in a single reaction or two reactions. When long PCR using the above primers proved to be unsuccessful for a certain segment, species-specific primers were alternatively designed with reference to the partial nucleotide sequences from either 16S rRNA, ND5, or cytochrome b (cyt b) genes, determined from total DNA with the fish-versatile primers listed below.
Long PCR was done in a Perkin-Elmer Model 9700 thermal cycler, with reactions being carried out with 30 cycles of a 25-µl reaction volume containing 13.25 µl sterile distilled H2O, 2.5 µl 10x LA PCR buffer (Takara), 4.0 µl dNTP (4 mM), 2.5 µl each primer (5 µM), 0.25 µl of 2.5 U LA Taq (Takara), and 1 µl template. The thermal cycle profile was that of "shuttle PCR": denaturation at 98°C for 10 s, with annealing and extension combined at the same temperature (68°C) for 1620 min. Long PCR products were electrophoresed on a 1.0% L 03 agarose gel and later stained with ethidium bromide for band characterization via ultraviolet transillumination. The long PCR products were diluted with sterile TE buffer (1:10100) for subsequent use as PCR templates.
PCR and Sequencing
A total of 182 fish-versatile PCR primers were used in various combinations to amplify contiguous, overlapping segments of the entire mitochondrial genome for each of the 38 species (for primer locations and sequences of these primers, see Miya and Nishida 1999, 2000b
; Inoue et al. 2000, 2001a, 2001b, 2001c, 2001d
; Ishiguro, Miya, and Nishida 2001
; Kawaguchi, Miya, and Nishida 2001
). Species-specific primers were designed in cases in which no appropriate fish-versatile primers were available. A list of PCR primers used for a specific species is available from M.M. on request.
PCR was done in a Perkin-Elmer Model 9700 thermal cycler, and reactions were carried out with 3032 cycles of a 15-µl reaction volume containing 8.3 µl sterile, distilled H2O, 1.5 µl 10x PCR buffer (Takara), 1.2 µl dNTP (4 mM), 1.5 µl of each primer (5 µM), 0.07 µl Taq DNA polymerase (Z Taq, Takara), and 1 µl template (diluted long PCR products). All PCR products overlapped by approximately 50300 bp.
The thermal cycle profile was as follows: denaturation at 98°C for 1 s; annealing at 5053°C, depending on primer specificity, for 5 s; and extension at 72°C for 1020 s, depending on the expected size of the PCR products. The PCR products were electrophoresed on a 1.0% L 03 agarose gel (Takara) and stained with ethidium bromide for band characterization via ultraviolet transillumination.
Double-stranded DNA products, purified using a Pre-Sequencing Kit (USB), were subsequently used for direct cycle sequencing with dye-labeled terminators (Applied Biosystems Inc.). Primers used were the same as those for PCR. All sequencing reactions were performed according to the manufacturer's instructions. Labeled fragments were analyzed on a Model 373S/377 DNA sequencer (Applied Biosystems Inc.). All DNA sequence electropherograms were carefully checked to see whether or not they included the mitochondrial pseudogenes in the nuclear genome (for checkpoints, see Mindell et al. 1999
). As pointed out by Mindell et al. (1999)
, features that were consistent with mitochondrial origin were (1) the presence of a conserved reading frame in protein-coding genes among all taxa, with decreasing rates of variability at third, first, and second codon positions, respectively; (2) the absence of extra stop codons, frameshifts, or unusual amino acid substitutions; and (3) no sequence changes resulting in losses of known secondary structure in tRNA and rRNA genes.
Phylogenetic Analysis
The DNA sequences were edited with EditView, version 1.0.1; AutoAssembler, version 2.1 (Applied Biosystems); and DNASIS, version 3.2 (Hitachi Software Engineering). Individual gene sequence alignments for the 48 teleosts were initiated with Clustal X (Thompson et al. 1997
) with default gap penalties and adjusted manually using DNASIS. Amino acids were used for alignments of the protein-coding genes and secondary-structure models (Kumazawa and Nishida 1993
) for alignment of tRNA genes. Since unambiguous alignments of the two rRNA genes (12S and 16S) on the basis of secondary-structure models (e.g., Miya and Nishida 1998, 2000a
; Yamaguchi et al. 2000
) were not feasible, 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 (Zardoya and Meyer 1996
; Miya and Nishida 2000b
). Also, tRNA loops and other ambiguous alignment regions, such as the 5' and 3' ends of several protein-coding genes, were excluded from the analyses. In addition, third codon positions in the protein-coding genes that would positively mislead an analysis of higher-level relationships of teleosts (Miya and Nishida 2000b
) were excluded from the analyses, leaving 7,002 and 908 available nucleotide positions from the 12 protein-coding and 22 tRNA genes, respectively. Amino acid sequences were not used in phylogenetic analysis, as the resulting trees were not well resolved, with many internal branches being supported by relatively low bootstrap values compared with those obtained by nucleotide sequences. Also, there was no noticeable improvement in tree statistics or bootstrap values when greater weight was given to amino acid replacements, which required more nucleotide changes, by using the PROTPARS weight matrix for amino acids provided in MacClade (Maddison and Maddison 1992
). Similarly, although Naylor and Brown (1997, 1998)
suggested that isoleucine (I), leucine (L), and valine (V) were the amino acids responsible for phylogenetic inconsistency, exclusion of these three amino acids through conversion of L and V into I from the data matrix (see Cao et al. 1998
; Mindell et al. 1999
) did not improve the tree statistics or the bootstrap values.
MacClade, version 3.08 (Maddison and Maddison 1992
) was used in various phases of the phylogenetic analyses, such as preparing data matrices in NEXUS format, exporting tree files, and exploring alternative tree topologies. Aligned sequence data in NEXUS format are available from M.M. on request.
All phylogenetic analyses were performed using PAUP 4.0b4a (Swofford 1998
). Heuristic maximum-parsimony (MP) analyses were conducted with tree bisection-reconnection branch swapping and 100 random-addition sequences. Support for internal branches was assessed using 500 bootstrap replications, with 20 random-addition sequences performed in each replication. All phylogenetically uninformative sites were ignored. Gaps were considered as missing data rather than as fifth characters, to prevent those longer than one or two bases from being taken as representing multiple events (Swofford 1993
).
Heuristic maximum-likelihood (ML) analyses were conducted to determine the statistically most likely phylogeny with the following parameters: substitution model set at transition/transversion ratio = 2; the HKY85 (Hasegawa, Kishino, and Yano 1985
) two-parameter model variant for unequal base frequencies; empirical base frequencies; starting branch lengths obtained using the Rogers-Swofford approximation method; and molecular clock not enforced. Nucleotide positions, including gaps, were all excluded.
Tests of alternative phylogenetic hypotheses were accomplished using the constraint tree option in PAUP 4.0b4a (Swofford 1998
). Differences in tree topologies were compared between the unconstrained and the constrained MP trees, with tree length differences being statistically evaluated using the Templeton (1983)
test implemented in PAUP 4.0b4a (Swofford 1998
).
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Results |
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Although the gene arrangements of most species were identical to those in typical vertebrates, those of five species (Sigmops gracile, Chauliodus sloani, Myctophum affine, Diaphus splendidus, and Caelorinchus kishinouyei) were unique among vertebrate mitogenomes. To date, only two patterns of gene rearrangements have been found in teleosts (S. gracile [=Gonostoma gracile] [Miya and Nishida 1999
]; Conger myriaster and their allies [Inoue et al. 2001c
]). Notwithstanding, the five species listed above exhibited gene arrangements that differed completely from the two examples. These unique mitogenomes will be described elsewhere, with discussions of their phylogenetic utility and the possible mechanisms generating such gene arrangements.
Phylogenetic Analysis
Heuristic MP analysis of the nucleotide sequences from the concatenated 12 protein-coding (no third codon positions) and 22 tRNA (stem regions only) genes yielded a single most-parsimonious tree (fig. 3
) with a length of 22,932 steps (consistency index = 0.245; retention index = 0.345; rescaled consistency index = 0.087). Many internal branches were supported by moderate (60%79%) to high (80%100%) bootstrap values, except for a within-monophyletic group that was taken to represent upper bushes (fig. 3
), with the observation of many unbisected long branches (fig. 4
) probably being due to the lower-density taxonomic sampling compared with their taxonomic diversity (fig. 2
).
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Discussion |
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It appears that adequate resolution of higher-level relationships of any organism will require longer DNA sequences (Miya and Nishida 2000b
). If so, the question remains as to which types of genes or genomes are useful in reconstructing the higher-level relationships of teleosts. It remains unclear whether or not mitochondrial or nuclear genes are generally more efficacious for such a purpose, although the transition from an apparently unsolvable problem to a solvable problem has come about mainly from the availability of complete mtDNA sequences in mammals (Penny et al. 1999
; Springer et al. 1999
). Additional complete mtDNA sequences have also been expected to be useful in answering some questions about fish relationships (Stepien and Kocher 1997
). Inoue et al. (2001d)
, in fact, resolved the interrelationships of five major lineages of basal teleosts, for which five alternative phylogenetic hypotheses had been proposed on the basis of both morphological and molecular data, using mitogenomic data. Accordingly, mitogenomic data can be expected to resolve the persistent controversies over higher teleostean relationships, which are apparently more complex and difficult than those for basal teleosts (G. Nelson 1989
). Below is a brief discussion of phylogenetic issues for the higher teleosts from the standpoint of both global and local taxonomic congruence between the MP tree obtained in this study (fig. 3
; statistically indistinguishable from the ML tree) and previously proposed hypotheses, most of them based on morphological analyses. Our discussions of phylogenetic issues are restricted to recent major contributions and are not intended to be exhaustive.
Global Congruence
Recently, two major hypotheses on higher teleostean relationships have been proposed (Johnson and Patterson 1993
[fig. 1A
]; J. S. Nelson 1994
[fig. 1B
]). Johnson and Patterson (1993)
presented a cladogram (their fig. 24) summarizing their "views" on acanthomorph interrelationships on the basis of their own extensive, comparative anatomical survey. Although they provided many putative synapomorphies (a total of 34 characters) substantiating their hypothesis, along with detailed discussions on their validity, they did not construct a character matrix including all of the species that they examined. Alternatively, their "views" were corroborated by MP analysis of an abbreviated character matrix comprising 39 anatomical features taken from 16 acanthomorph species (their fig. 25). Johnson and Patterson (1993
, p. 621) stated that the number of taxa examined by them and ideally included in their sample far exceeded the limits of available parsimony programs at that time. Major topological differences between the present MP tree (fig. 3
) and that of Johnson and Patterson (1993)
were in the placements of zeiforms, stephanoberyciforms, and beryciforms (for details, see below). When topological constraints of Johnson and Patterson's (1993)
tree (those of Johnson [1992]
and Olney, Johnson, and Baldwin [1993]
being followed below Lampridiformes) were enforced, two minimum-length trees that required an additional 413 steps were found, with the differences being highly significant (z = -11.847, P < 0.0001; z = -10.428, P < 0.0001).
J. S. Nelson (1994)
subsequently presented different views on higher teleostean relationships in his comprehensive guide to fish classification (now in its third edition), which has been used as a standard reference and has been highly influential in systematic ichthyology. Although his hypothesis was presented in the form of two separate, sequential cladograms (J. S. Nelson 1994
, pp. 194, 215), he failed to provide any relevant evidence or corroborative statements for such relationships. His hypothesis seemed to have been based on the conventionally accepted views on acanthomorph relationships advocated by Rosen (1973)
and subsequently reviewed by Lauder and Liem (1983)
, with partial modifications being made where he agreed with Johnson and Patterson's (1993)
radically different views. When topological constraints of J. S. Nelson's (1994)
tree were enforced, one minimum-length tree that required an additional 588 steps was found, with the difference being highly significant (z = -13.977, P < 0.0001).
Basal Relationships
Basal interrelationships of the four major lineages (fig. 5
) generally followed previously proposed hypotheses (Rosen 1973
; Lauder and Liem 1983
; Fink 1984
; Johnson 1992
), with Ostariophysi, Protacanthopterygii, Stomiiformes, and Aulopiformes sequentially diverging in this sequence. Notwithstanding, the monophyly of each taxon, particularly Ostariophysi and Protacanthopterygii, should be substantiated on the basis of more extensive taxonomic sampling, considering their heterogeneous compositions. It should be noted that two comprehensive major clades within the teleosts, Neoteleostei and Eurypterygii, were strongly supported, with bootstrap values of 93% and 96%, respectively.
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Monophyly and Interrelationships of Zeiformes and Paracanthopterygii
The monophyly and interrelationships of Zeiformes have long been one of the most problematic issues in systematic ichthyology (for details, see Johnson and Patterson 1993
, p. 592599). Zeiformes currently comprise two suborders, Zeioidei and Caproidei (J. S. Nelson 1994
), although recent authors have questioned the reality of a relationship between those two groups (e.g., Johnson and Patterson 1993
). In the present tree, monophyly of the two zeioid species was strongly supported by a bootstrap value of 100%. However, a caproid, Antigonia capros, was convincingly placed within a well-supported monophyletic group (bootstrap value = 83%) at the top of the tree (fig. 3
). When topological constraints were enforced on the monophyly of zeiforms (including caproids), one minimum-length tree that required an additional 111 steps was found, with the difference being highly significant (z = -4.267, P = 0.0008). The superficial similarity between the two groups, such as the laterally flattened and extremely deep body (see fig. 2
), would surely have misled phylogenetic inferences based on morphology.
At no time has convincing evidence been demonstrated regarding zeiform affinities with other higher teleosts. Rosen (1984)
suggested a close affinity to Tetraodontiformes, although this idea has not been generally accepted (Johnson and Patterson 1993
). In fact, when topological constraints on the monophyly of tetraodontiforms + zeiforms (including caproids) were enforced, one minimum-length tree that required an additional 84 steps was found, with the difference being highly significant (z = -2.793, P = 0.0052). In a total-evidence analysis of the combined molecular and morphological data, Wiley, Johnson, and Dimmick (2000)
found that two zeids and two gadiforms formed a well-supported monophyletic group (bootstrap value = 94%), which has never before been proposed. However, this sister group relationship has been reproduced in the present analysis with a high bootstrap value of 94%. Evidently, the extremely disparate morphologies of the two groups (see fig. 7
) has deterred most systematic ichthyologists from exploring such a possibility.
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Monophyly of Beryciformes and Stephanoberyciformes
The limits of Beryciformes have undergone considerable reduction, with the currently recognized Polymixiiformes, Stephanoberyciformes, and Trachichthyiformes (sensu Moore 1993
) having been removed from the group during the past 30 years (for details, see Moore 1993
; Johnson and Patterson 1993
). All of these groups, however, with the exception of polymixiiforms (fig. 7
), formed a weakly supported monophyletic group (fig. 8
), although the two major components (Stephanoberyciformes and Beryciformes; sensu J. S. Nelson 1994
; Johnson and Patterson 1993
) within the lineage were not monophyletic because a berycid (Beryx splendens) was confidently placed as a sister species of the two melamphaids represented (Scopelogadus mizolepis + Poromitra oscitans) with a bootstrap value of 100%. Such a close affinity has not previously been asserted with confidence (but see Colgan, Zhang, and Paxton 2000
), apparently owing to the disparate morphologies and ecology of the component taxa. When topological constraints on the monophyly of stephanoberyciforms and beryciforms were enforced, one minimum-length tree, requiring an additional 67 and 86 steps, respectively, was found for each, with the differences being highly significant (z = -7.183, P < 0.0001; z = -7.786, P < 0.0001, respectively).
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Conclusions |
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The present study was based on unprecedentedly long DNA sequences (>15 kb) from many purposefully chosen species that represented the overall diversity of the higher teleosts. The resultant trees were well resolved and provided a number of new insights into higher teleostean phylogeny, many of them quite unexpected from previous analyses, including both morphology-based cladistic analyses and molecular phylogenetic studies. Also, the present study clearly identified major phylogenetic problems. In particular, the limits and interrelationships of the Paracanthopterygii, the Zeiformes, the Beryciformes, and the Stephanoberyciformes should be reconsidered, this being the most obvious "next investigative step." By doing so, the Percomorpha could be circumscribed more accurately, leading to the resolution of that group.
It should also be noted that this study not only embodies the recent expectation of Pollock et al. (2000)
that increasing the mitogenomic data set would be likely to have a large impact on confidence in the resolution of tree structure, but also indicates the practicality of our PCR-based approach for sequencing fish mitogenomes during moderate-scale evolutionary genomic research under limited resources. Although our long PCR primers were originally designed for fish mitogenomes, they should be effective for other vertebrates, including humans, with little or no modification (Miya and Nishida 2000b
). By using long PCR products (917 kb) as purified templates of mtDNA for subsequent full-nested PCR (5001,500 bp), a number of published primers (e.g., Kocher et al. 1989
; Palumbi 1996
; Miya and Nishida 1999, 2000b
; Sorenson et al. 1999
) may work well for various vertebrate mitogenomes. Direct sequencings of these contiguous, overlapping PCR products that cover the entire mitogenomes have proven to be successful, providing consistent results (Miya and Nishida 1999, 2000b
; Sorenson et al. 1999
; Mindell et al. 1999
). Also, with the aid of commercially available sequence editors, the complete mtDNA sequence and associated information (e.g., location of features) from a single species are obtainable within a few weeks or so from DNA extraction to submission of the data to DNA databases, such as DDBJ/EMBL/GenBank. Thus, our PCR-based approach is feasible in a single laboratory equipped with standard experimental facilities for molecular biology with a moderate level of manpower and funds. We believe that similar kinds of moderate-scale evolutionary genomics should be conducted in parallel with larger-scale evolutionary genomics employing genome technologies capable of producing sequence data in large quantities (Pollock et al. 2000
), which would consequently cover the entire vertebrate biodiversity in the near future.
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Acknowledgements |
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Footnotes |
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1 Keywords: mitogenomics
teleosts
complete mtDNA sequence
long PCR
taxonomic sampling
higher-level relationships
2 Address for correspondence and reprints: Masaki Miya, Department of Zoology, Natural History Museum and Institute, Chiba, 955-2 Aoba-cho, Chuo-ku, Chiba 260-8682, Japan. miya{at}chiba-muse.or.jp
.
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