Mitogenomic circumscription of a novel percomorph fish clade mainly comprising “Syngnathoidei” (Teleostei)

Song, Ha Yeun; Mabuchi, Kohji; Satoh, Taku; Moore, Jon A.; Yamanoue, Yusuke; Miya, Masaki; Nishida, Mutsumi

doi:10.1016/j.gene.2014.03.040

Cited by 29 publications

(32 citation statements)

References 48 publications

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“…Redraws from Miya et al (2010) based on multiple nuclear genes (Betancur et al 2013b;Campbell et al 2013a). Finally, it should be noted that our mitogenomic studies have consistently recovered eight major clades within the Percomorpha with the exception of Ophidiiformes and Batrachoidiformes despite differences in taxonomic coverage Mabuchi et al 2007;Yamanoue et al 2007;Kawahara et al 2008;Yagishita et al 2009;Song et al 2014). Kawahara et al (2008) labeled those eight clades A to H and these clades are labeled (or named) in the latest two studies based on multiple nuclear genes as shown in Table 2.…”

Section: Further Resolution Of Percomorph Relationshipsmentioning

confidence: 89%

“…25). No previous molecular phylogenetic studies have sampled all of those families (see table 2 in Song et al 2014), and this previously unrecognized clade found across four different percomorph suborders with diverse morphologies (Fig. 25) represents another example of unique patterns of diversification in percomorphs with no trace of morphological synapomorphies.…”

Section: Further Resolution Of Percomorph Relationshipsmentioning

confidence: 96%

“…Based on the results from Kawahara et al (2008) on the relationships of the 11 gasterosteiform families, together Yamanoue et al (2008) with those from previous molecular phylogenetic studies, Song et al (2014) attempted to circumscribe a novel clade mainly comprising Syngnathoidei using the mitogenomic data. They sampled a wide variety of percomorphs that have been suggested to have close affinities with syngnathoids and performed Bayesian and maximum likelihood analyses.…”

Section: Further Resolution Of Percomorph Relationshipsmentioning

confidence: 99%

“…Exceptions are those of the Percomorpha, in which all terminal taxa are taken from a revised classification of bony fishes adopted by DeepFin (http://deepfin.org). Numerals indicate those 83 studies according to the temporal sequence of the publications: 1 Miya and Nishida (1999); 2 Lee et al (2001); 12 Inoue et al (2003a); 13 Miya et al (2003); 14 Saitoh et al (2003); 15 Ishiguro et al (2003); 16 Inoue et al (2003b); 17 ; 18 ; 19 Inoue et al (2004); 20 Yamanoue et al (2004); 21 Mabuchi et al (2004); 22 Minegishi et al (2005); 23 Inoue et al (2005); 24 Miya et al (2005); 25 Ishiguro et al (2005); 26 Lavoué et al (2005); 27 Miya et al (2006); 28 Yamanoue et al (2006); 29 Mabuchi et al (2006); 30 Satoh et al (2006); 31 Saitoh et al (2006); 32 Mabuchi et al (2007); 33 Lavoué et al (2007); 34 Mayden et al (2007); 35 Yamanoue et al (2007); 36 Miya et al (2007); 37 Kawahara et al (2008); 38 Mayden et al (2008); 39 Imoto et al (2013); 75 Lavoué et al (2013); 76 Poulsen et al (2013); 77 Tang et al (2013); 78 Miya et al (2013); 79 Campbell et al (2013b); 80 Iwasaki et al (2013); 81 Song et al (2014); 82 Lavoué et al (2014); 83 Campbell et al (2014) clades that must...…”

Section: Introductionmentioning

confidence: 99%

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The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

Miya

Nishida

2014

Ichthyol Res

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This review summarizes the achievements and novel perspectives that our fish mitochondrial genome (mitogenome) project has brought to molecular phylogenetics and evolution of fishes during the last 15 years (1999)(2000)(2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014). To date, we have assembled &1,340 whole mitogenome sequences from fishes, publishing 83 mitogenomic papers on all major fish lineages (except agnathans). Those papers have been cited 5,303 times in total as of 30 September 2014 and have been featured in many textbooks and scientific articles as well as various media. These results have not only had a significant impact on the scientific community, but also attracted considerable attention from the general public. The success of the project largely owes to our own development of a novel, PCRbased approach for sequencing whole mitogenomes (ca. 16,500 bp), which opened a new avenue toward addressing higher-level relationships of fishes based on longer DNA sequences from a number of taxa. Shortly after the development of the method, we explicitly demonstrated the phylogenetic utility of mitogenomic data and actually resolved a long-standing issue in basal teleostean relationships. On the basis of those encouraging results from the initial studies, we published a series of four mitogenomic papers in 2003, which together encompass the whole of actinopterygian diversity and provided a ''big picture'' phylogenetic framework for the group. Those four studies offered a useful phylogenetic basis for subsequent studies (i.e., with a different choice of outgroups and targeted taxa) and have facilitated massive sequencing efforts for a wide variety of fishes from chondrichthyians to higher teleosts living in diverse habitats from freshwaters to the deep sea. We highlight some of the 83 mitogenomic papers by subject and briefly refer to the phylogenetic and evolutionary significances of those studies. Finally, we argue that intensive taxonomic sampling from an interface between species and populations together with the massive character sampling from mitogenome sequences using next-generation sequencing (NGS) technologies would enable simultaneous attempts to delimit species boundaries and to reconstruct evolutionary relationships at much finer scale, eventually unraveling the fish part of the Tree of Life in a bottom-up manner with more accurate estimations of species diversity.

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Section: Further Resolution Of Percomorph Relationshipsmentioning

confidence: 89%

Section: Further Resolution Of Percomorph Relationshipsmentioning

confidence: 96%

Section: Further Resolution Of Percomorph Relationshipsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

Miya

Nishida

2014

Ichthyol Res

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“…It is listed as least concern in the IUCN Red List of Threatened Species (Carpenter et al 2015). Their phylogenetic position of this group, the family Dactylopteridae was changed from Scorpaeniformes to Syngnathiformes by Nelson (2016) based on the molecular evidence (Betancur et al 2013;Near et al 2013;Song et al 2014); however, their taxonomic position remains controversial. In the current study, we first determined the complete mitochondrial DNA sequence of D. volitans and to analyze the phylogenetic relationship of this species with members of Syngnathiformes.…”

Section: Mitochondrial Genome; Syngnathiformes; Dactylopteridae; Dactmentioning

confidence: 99%

Characterization of the complete mitochondrial genome of Dactylopterus volitans (Syngnathiformes, Dactylopteridae)

Song

Choi

et al. 2019

Mitochondrial DNA Part B

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The complete mitochondrial genome was determined for the flying gurnard Dactylopterus volitans belonging to the family Dactylopteridae. The total length of the D. volitans mitochondrial genome is 16,632 bp, which consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. It has the typical vertebrate mitochondrial gene arrangement. Phylogenetic analysis using mitochondrial genomes of 20 species showed that D. volitans formed a well-supported monophyletic group with other Dactylopteridae species. ARTICLE HISTORY

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Evolutionary History of Syngnathid Fishes

Lin¹

2021

Encyclopedia of Life Sciences

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The family Syngnathidae diverged from other teleosts approximately 48 Mya; they originated from Indo‐Pacific regions and then diversified and spread globally. Subsequently, a unique animal group, fishes with ‘male pregnancy’, emerged. Together with their morphological traits, syngnathid fishes established a specialised evolutionary position. Interestingly, all 300 species in this family lost their pelvic fin, which is directly correlated to the absence of the tbxt4 gene. In this family, pregnancy relies on the attached brood pouch in males, and the structure of the pouch varies dramatically within the family owing to their independent evolutionary history. Some species, such as seahorses, have a fully enclosed brood pouch with robust functions. The phylogenomics and adaptive evolution of the species in the family Syngnathidae might elucidate further mechanisms involved in their morphology and male pregnancy. Key Concepts Phylogeny and evolutionary morphology in the family Syngnathidae. Syngnathidfishes represent the endless beauty of the evolution of marine organisms. Syngnathids origin from the Indian‐Pacific and spread globally. Comparative genomics elucidate the genetic basis of the specialized morphology of syngnathids. ‘Male pregnancy’ could be implemented in syngnathids by evolving a complex brood structure and the evolution of genes.

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Mitogenomic circumscription of a novel percomorph fish clade mainly comprising “Syngnathoidei” (Teleostei)

Cited by 29 publications

References 48 publications

The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

The mitogenomic contributions to molecular phylogenetics and evolution of fishes: a 15-year retrospect

Characterization of the complete mitochondrial genome of Dactylopterus volitans (Syngnathiformes, Dactylopteridae)

Evolutionary History of Syngnathid Fishes

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