Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences

Yamanoue, Yusuke; Miya, Masaki; Matsuura, Keiichi; Yagishita, Naoki; Mabuchi, Kohji; Sakai, Harumi; Katoh, Masaya; Nishida, Mutsumi

doi:10.1016/j.ympev.2007.03.008

Cited by 87 publications

(85 citation statements)

References 46 publications

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“…In recent years, helped by the development of long polymerase chain reaction (long-PCR) methods for amplification of mtDNA genes and complete mt genomes, comparative analyses of mt genome sequences and organizations are widely used to study phylogenetic relationships of animal taxa. The unique characters of mt DNA, such as its small size, simple structure, maternal inheritance, fast evolutionary rate, and high informational content, have made mt DNA a very attractive subject of research (Miyata et al, 1982;Brown, 1983;Moritz et al, 1987;Wolstenholme, 1992;Avis, 1994;Castro et al, 1998;Saccone et al, 1999;Yamanoue et al, 2007;Zhou et al, 2009). More than 1200 complete mt genome sequences are currently available in GenBank, including mt sequences from various vertebrate groups.…”

Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

Chao¹,

Li²,

Geng³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. This is the first report of a complete mitochondrial genome sequence from Himalayan marmot (Marmota himalayana, class Marmota). We determined the M. himalayana mitochondrial (mt) genome sequence by using long-PCR methods and a primerwalking sequencing strategy with genus-specific primers. The complete mt genome of M. himalayana was 16,443 bp in length and comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a typical control region (CR). Gene order and orientation were identical to those in mt genomes of most vertebrates. The heavy strand showed an overall A+T content of 63.49%. AT and GC skews for the mt genome of the M. himalayana were 0.012 and -0.300, respectively, indicating a nucleotide bias against T and G. The control region was 997 bp in size and displayed some unusual features, including absence of repeated motifs and two conserved sequence blocks (CSB2 and CSB3), which is consistent with observations from two other rodent species, Sciurus vulgaris and Myoxus glis. Phylogenetic analysis of complete mt DNA sequences without the control region including 30 taxa of Rodentia was performed with Maximum-Likelihood (ML) and Bayesian Inference (BI) methods and provided strong support for Sciurognathi polyphyly and Hystricognathi monophyly. This analysis also provided evidence that M. himalayana mt DNA was closely related to that from Sciurus vulgaris (Sciuridae) and was similar to mt DNA from Myoxus glis.

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Section: Introductionmentioning

confidence: 99%

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

Chao¹,

Li²,

Geng³

et al. 2014

Genet. Mol. Res.

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“…Saitoh et al, 2006;Yamanoue et al, 2007), and a significant amount of sequence data is available in GenBank and other DNA databases, these genes are very useful and convenient markers to clarify the evolutionary history of fishes at various phylogenetic levels (e.g. Sasaki et al, 2006;Kuriiwa et al, 2007;Pérez et al, 2007;Timm et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses

et al. 2009

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Sparid fishes consist of approximately 115 species in 33 genera that are broadly distributed in tropical and temperate coastal waters. Although several phylogenetic analyses were conducted based on specific molecular markers, their classification remains unresolved. Here, we present the most comprehensive molecular phylogeny of the family Sparidae to date, based on cytochrome b (cyt-b) genes. We determined 18 sequences of sparids and conducted phylogenetic analyses among 72 individuals representing 66 sparids with 23 outgroup species. Phylogenetic trees were constructed according to partitioned Maximum Likelihood (ML) and Bayesian methods. The phylogenetic analyses were conducted on two different data sets (including all positions; RY-coding). The phylogenetic trees showed monophyly of the family Sparidae with a different taxon, centracanthid Spicara. The subfamilies in the Sparidae in all trees are non-monophyletic and do not agree with current classification of the subfamilies. The genera Acanthopagrus, Cheimerius, Dentex, Diplodus, Pagellus, Pagrus, and Spicara are also non-monophyletic and their classifications should be revised based on the phylogenetic relationships and reinvestigation of morphological characters. The sparids are divided into three major clades, A, B and C, respectively in the ML tree based on all codon positions, whereas clade C was paraphyletic in the other trees. The species in clade C are known to be present in the eastern Pacific to western Atlantic, whereas those in clades A and B are distributed in various oceanic regions. Some sub-clades in clades A and B consist of species that are distributed in defined local regions. We further investigated evolutionary patterns of 87 morphological characters by ancestral character-state reconstruction according to the parsimony criteria. The results suggested high evolutionary plasticity of the characters in sparids, indicating that it causes species-diversity and taxonomic confusion at various taxonomic levels, and that such convergent evolution may occur more frequently also in other coastal fishes.

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“…However, they used few taxa: one species of Caproidae, two species of Tetraodontiformes, and six species of Lophiiformes. Yamanoue et al (2007) analyzed more species of the three groups and provided a robust phylogenetic topology that placed the Caproidei as sister to the Lophiiformes, and the two groups as a clade that is sister to the Tetraodontiformes. Nakae and Sasaki (2010) studied the lateral-line system and its innervations of nine species of tetraodontiforms (representing all families examined except for the Molidae) and a single species each from the Lophiidae, Zeidae, Caproidae, and Siganidae.…”

Section: Systematicsmentioning

confidence: 99%

“…Molecular studies by various authors have generally supported the monophyly of tetraodontiform families (Holcroft 2005;Alfaro et al 2007;Yamanoue et al 2007Yamanoue et al , 2008, although conflicts exist between the constructed topologies of familial relationships by morphological and molecular analyses (Figs. 7, 8).…”

Section: Systematicsmentioning

confidence: 99%

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Taxonomy and systematics of tetraodontiform fishes: a review focusing primarily on progress in the period from 1980 to 2014

Matsuura

2014

Ichthyol Res

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When the first Indo-Pacific Fish Conference (IPFC1) was held in Sydney in 1981, there were still many problems in the generic-and species-level taxonomy of all tetraodontiform families except for the recently reviewed Triacanthodidae and Triacanthidae. The period from IPFC1 to IPFC9 (1981IPFC9 ( -2013) was a time of great progress in the taxonomy and systematics of the Tetraodontiformes: many review and revisional papers have been published for various genera and species, with descriptions of many new taxa occurring mainly on coral reefs and in tropical freshwaters; and cladistic analyses of morphological characters have been performed to clarify phylogenetic relationships of various families and molecular analyses have greatly progressed to provide detailed phylogenetic relationships of families, genera, and even species. The purpose of this paper is to provide a review on developments in the taxonomy and systematics of the Tetraodontiformes, focusing primarily on contributions since 1980 (when James C. Tyler's monumental work was published) through the period of IPFCs, including pertinent publications before 1980. This paper recognizes 412 extant species in the 10 families of living Tetraodontiformes, with the allocation of species and genera as follows: Triacanthodidae including 23 species in 11 genera, Triacanthidae seven species in four genera, Balistidae 37 species in 12 genera, Monacanthidae 102 species in 27 genera, Aracanidae 13 species in six genera, Ostraciidae 22 species in five genera, Triodontidae monotypic, Tetraodontidae 184 species in 27 genera, Diodontidae 18 species in seven genera, and Molidae five species in three genera. Phylogenetic relationships of the families have been clarified by morphological and molecular analyses and have provided well-supported sister relationships of the families: Triacanthodidae and Triacanthidae, Balistidae and Monacanthidae, and Tetraodontidae and Diodontidae. However, there remain problems with the phylogenetic positions of the Triodontidae and Molidae due to conflicts of differing positions in morphological and molecular studies (e.g., Molidae has been placed differently among molecular studies).

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Phylogenetic position of tetraodontiform fishes within the higher teleosts: Bayesian inferences based on 44 whole mitochondrial genome sequences

Cited by 87 publications

References 46 publications

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

Complete mitochondrial genome sequence of Marmota himalayana (Rodentia: Sciuridae) and phylogenetic analysis within Rodentia

Comprehensive phylogeny of the family Sparidae (Perciformes: Teleostei) inferred from mitochondrial gene analyses

Taxonomy and systematics of tetraodontiform fishes: a review focusing primarily on progress in the period from 1980 to 2014

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