Shinjuku, Japan
Shinjuku, Japan

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Campbell M.A.,Massey University | Lopez J.A.,University of Alaska Fairbanks | Satoh T.P.,Collection Center | Chen W.-J.,National Taiwan University | Miya M.,Natural History Museum and Institute
Gene | Year: 2014

We present the first study to use whole mitochondrial genome sequences to examine phylogenetic affinities of the flatfishes (Pleuronectiformes). Flatfishes have attracted attention in evolutionary biology since the early history of the field because understanding the evolutionary history and patterns of diversification of the group will shed light on the evolution of novel body plans. Because recent molecular studies based primarily on DNA sequences from nuclear loci have yielded conflicting results, it is important to examine phylogenetic signal in different genomes and genome regions. We aligned and analyzed mitochondrial genome sequences from thirty-nine pleuronectiforms including nine that are newly reported here, and sixty-six non-pleuronectiforms (twenty additional clade L taxa [Carangimorpha or Carangimorpharia] and forty-six secondary outgroup taxa). The analyses yield strong support for clade L and weak support for the monophyly of Pleuronectiformes. The suborder Pleuronectoidei receives moderate support, and as with other molecular studies the putatively basal lineage of Pleuronectiformes, the Psettodoidei is frequently not most closely related to other pleuronectiforms. Within the Pleuronectoidei, the basal lineages in the group are poorly resolved, however several flatfish subclades receive consistent support. The affinities of Lepidoblepharon and Citharoides among pleuronectoids are particularly uncertain with these data. © 2014 Elsevier B.V.All rights reserved.


Iwasaki W.,University of Tokyo | Fukunaga T.,University of Tokyo | Isagozawa R.,University of Tokyo | Yamada K.,RNAi Incorporated | And 7 more authors.
Molecular Biology and Evolution | Year: 2013

Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface. © The Author 2013.


Miya M.,Natural History Museum and Institute | Pietsch T.W.,University of Washington | Orr J.W.,National Oceanic and Atmospheric Administration | Arnold R.J.,University of Washington | And 6 more authors.
BMC Evolutionary Biology | Year: 2010

Background. The teleost order Lophiiformes, commonly known as the anglerfishes, contains a diverse array of marine fishes, ranging from benthic shallow-water dwellers to highly modified deep-sea midwater species. They comprise 321 living species placed in 68 genera, 18 families and 5 suborders, but approximately half of the species diversity is occupied by deep-sea ceratioids distributed among 11 families. The evolutionary origins of such remarkable habitat and species diversity, however, remain elusive because of the lack of fresh material for a majority of the deep-sea ceratioids and incompleteness of the fossil record across all of the Lophiiformes. To obtain a comprehensive picture of the phylogeny and evolutionary history of the anglerfishes, we assembled whole mitochondrial genome (mitogenome) sequences from 39 lophiiforms (33 newly determined during this study) representing all five suborders and 17 of the 18 families. Sequences of 77 higher teleosts including the 39 lophiiform sequences were unambiguously aligned and subjected to phylogenetic analysis and divergence time estimation. Results. Partitioned maximum likelihood analysis confidently recovered monophyly for all of the higher taxa (including the order itself) with the exception of the Thaumatichthyidae (Lasiognathus was deeply nested within the Oneirodidae). The mitogenomic trees strongly support the most basal and an apical position of the Lophioidei and a clade comprising Chaunacoidei + Ceratioidei, respectively, although alternative phylogenetic positions of the remaining two suborders (Antennarioidei and Ogcocephaloidei) with respect to the above two lineages are statistically indistinguishable. While morphology-based intra-subordinal relationships for relatively shallow, benthic dwellers (Lophioidei, Antennarioidei, Ogcocephaloidei, Chaunacoidei) are either congruent with or statistically indistinguishable from the present mitogenomic tree, those of the principally deep-sea midwater dwellers (Ceratioidei) cannot be reconciled with the molecular phylogeny. A relaxed molecular-clock Bayesian analysis of the divergence times suggests that all of the subordinal diversifications have occurred during a relatively short time period between 100 and 130 Myr ago (early to mid Cretaceous). Conclusions. The mitogenomic analyses revealed previously unappreciated phylogenetic relationships among the lophiiform suborders and ceratioid familes. Although the latter relationships cannot be reconciled with the earlier hypotheses based on morphology, we found that simple exclusion of the reductive or simplified characters can alleviate some of the conflict. The acquisition of novel features, such as male dwarfism, bioluminescent lures, and unique reproductive modes allowed the deep-sea ceratioids to diversify rapidly in a largely unexploited, food-poor bathypelagic zone (200-2000 m depth) relative to the other lophiiforms occurring in shallow coastal areas. © 2010 Miya et al; licensee BioMed Central Ltd.


Satoh T.P.,Collection Center | Sato Y.,National Institute of Genetics | Masuyama N.,University of Tokyo | Masuyama N.,Resonarch Co. | And 2 more authors.
BMC Genomics | Year: 2010

Background: Mitochondrial (mt) gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years. It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order.Results: Based on the analysis of codon usage and tRNA gene positions, we suggest that tRNA gene order of the typical vertebrate mt-genomes may be important for their translational efficiency. The vertebrate mt-genome encodes 2 rRNA, 22 tRNA, and 13 transmembrane proteins consisting mainly of hydrophobic domains. We found that the tRNA genes specifying the hydrophobic residues were positioned close to the control region (CR), where the transcription efficiency is estimated to be relatively high. Using 47 vertebrate mt-genome sequences representing jawless fishes to mammals, we further found a correlation between codon usage and tRNA gene positions, implying that highly-used tRNA genes are located close to the CR. In addition, an analysis considering the asymmetric nature of mtDNA replication suggested that the tRNA loci that remain in single-strand for a longer time tend to have more guanine and thymine not suffering deamination mutations in their anticodon sites.Conclusions: Our analyses imply the existence of translational constraint acting on the vertebrate mt-gene arrangement. Such translational constraint, together with the deamination-related constraint, may have contributed to long-term maintenance of gene order. © 2010 Satoh et al; licensee BioMed Central Ltd.


Coccato A.,Ghent University | Karampelas S.,Gubelin Gem Laboratory | Worle M.,Collection Center | Van Willigend S.,Swiss National Museum | Petrequin P.,University of Franche Comte
Journal of Raman Spectroscopy | Year: 2014

Raman spectroscopy was used for the characterization of seven gem quality green 'jade' samples and three green 'jade' samples of archaeological importance. The results were also compared with those acquired by other nondestructive techniques such as classical gemology, energy-dispersive X-ray fluorescence (EDXRF), ultraviolet-visible-near infrared (UV-Vis-NIR) in absorption, Fourier transform infrared spectroscopy (FTIR) in absorption and micro-FTIR in reflectance. Five samples of gem quality and two samples of archaeological interest were found to be 'jadeite jade', whereas two samples of gem quality and one sample of archaeological interest were 'omphacite jade'. Raman spectroscopy is found to be the most efficient method for their characterization. The results were confirmed with EDXRF and micro-FTIR in reflectance. Data acquired using classical gemology, UV-Vis-NIR absorption and FTIR absorption spectroscopy were similar on 'omphacite jade' and 'jadeite jade'. Copyright © 2014 John Wiley & Sons, Ltd.


Song H.Y.,University of Tokyo | Satoh T.P.,Collection Center | Mabuchi K.,University of Tokyo
Mitochondrial DNA | Year: 2012

We determined the complete mitochondrial genome (mitogenome) sequence of the dragonet Callionymus curvicornis. The total length of C. curvicornis mitogenome is 16,406 bp, which consists of 13 proteincoding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region. It has the typical vertebrate mitochondrial gene arrangement. This is the first report of a complete mitochondrial genome in the fish suborder Callionymoidei. © 2012 Informa UK, Ltd.


Yamanoue Y.,University of Tokyo | Setiamarga D.H.E.,University of California at San Diego | Matsuura K.,Collection Center
Journal of Fish Biology | Year: 2010

The pelvic fins of teleosts are paired appendages that are considered to be homologous to the hind limbs of tetrapods. Because they are less important for swimming, their morphology and function can be flexibly modified, and such modifications have probably facilitated the adaptations of teleosts to various environments. Recently, among these modifications, pelvic-fin loss has gained attention in evolutionary developmental biology. Pelvic-fin loss, however, has only been investigated in a few model species, and various biological aspects of pelvic fins in teleosts in general remain poorly understood. This review summarizes the current state of knowledge regarding pelvic fins, such as their structure, function and evolution, to elucidate their contribution to the considerable diversity of teleosts. This information could be invaluable for future investigations into various aspects of pelvic fins, which will provide clues to understanding the evolution, diversity and adaptations of teleosts. © 2010 The Fisheries Society of the British Isles.


Nakae M.,Collection Center | Sasaki K.,Kochi University
Journal of Morphology | Year: 2010

The lateral line system and its innervation in ten tetraodontiform families and five outgroup taxa were examined. Although some homology issues remained unresolved, tetraodontiforms were characterized by having two types (at least) of superficial neuro-masts (defined by the presence or absence of supporting structures) and accessory lateral lines and neuromasts (except Molidae in which "accessory" elements were absent). The preopercular line in Tetraodontiformes was not homologous with that of typical teleosts, because the line was innervated by the opercular ramule that was newly derived from the mandibular ramus, the condition being identical to that in Lophiidae. Within Tetraodonti-formes, the number of neuromasts varied between 70 and 277 in the main lines and between 0 and 52 in accessory elements. Variations were also recognized in the presence or absence of the supraorbital commissure, mandibular line, otic line, postotic line, ventral trunk line, and some lateral line nerve rami, most notably the dorsal branch of the opercular ramule, being absent in Aracanidae, Ostra-ciidae, Tetraodontidae, Diodontidae, and Molidae. Morphological characteristics derived from the lateral line system and its innervation provided some support for a sister relationship of tetraodontiforms with lophiiforms. © 2009 Wiley-Liss, Inc.


Asaoka R.,Kochi University | Nakae M.,Collection Center | Sasaki K.,Kochi University
Ichthyological Research | Year: 2011

Components of the lateral line system and their innervation were studied in Odontobutis obscura (Odontobutidae) and Pterogobius elapoides (Gobiidae), which are benthic and pelagic species, respectively. Innervation of the superficial neuromasts constituting the trunk lateral line system by way of three continuous longitudinal series (dorsal, middle, and ventral series: ld, lm, and lv series, respectively) became apparent for the first time. Innervation patterns indicated that the ld and lv series represented a mixture of displaced rows (from lm series) and new additional rows. In O. obscura, the ld and lv series were poorly developed, whereas both series were well developed in the pelagic P. elapoides, possibly as an adaptation to receive stimuli from above and below. Two extremely elongated nerve branches derived from the lateral ramus of the posterior lateral line nerve innervated the ld and lv series, respectively, in P. elapoides. Homologies of the neuromast rows on the head and body were discussed on the basis of their innervation patterns. © 2010 The Ichthyological Society of Japan.


Yamanaka Y.,Kochi University | Nakae M.,Collection Center | Fukuda E.,Kochi University | Sasaki K.,Kochi University
Ichthyological Research | Year: 2010

Branching patterns of the horizontal septum lateral line nerves (HSN) were studied in 123 teleostean species (including literature records) assigned to 96 families in 28 orders, primarily to indentify the group characterized by the presence of the dorsal longitudinal collector nerve (DLCN) for innervation of the trunk lateral line. In nonacanthomorphs, DLCN was absent, the trunk lateral line being mostly innervated by branches directly detached from HSN or those derived from the collector nerve running parallel to the former. In acanthomorphs, the dorsally arched trunk lateral line, typical of the group, was uniformly innervated by DLCN, indicating that presence of the latter was a synapomorphy of the group. Within the latter, DLCN was absent in Gasterosteiformes (Fistularia and Macroramphosus), Mugilidae, Atherinomorpha, Champsodontidae, Blenniidae, Callionymidae, Gobioidei, Istiophoridae, Gempylidae, Cynoglossidae, Ostraciidae, and Molidae. Monophyly of the Mugilidae plus Atherinomorpha was discussed based on the specialized innervation pattern. © The Ichthyological Society of Japan 2009.

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