Mothocya kaorui n. sp. (Crustacea: Isopoda: Cymothoidae), a fish-parasitic isopod with unique antennules from the Izu Islands, Japan.

A new species of fish-parasitic isopod in the family Cymothoidae is described from the Izu Islands, Japan. Mothocya kaorui n. sp.

Complete mitochondrial genomes of two sand diver species (Perciformes, Trichonotidae): novel gene orders and phylogenetic position within Gobiiformes.

The complete mitochondrial genome sequences of two species of the family Trichonotidae, (Shimada and Yoshino 1984) and (Steindachner 1867), were determined using a polymerase chain reaction-based method. The genomes ranged from 16,517 to 17,235 bp in length and included 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and two non-coding regions (control region and origin of the light strand replication) as in other vertebrates. However, they shared a unique gene order among vertebrates with multiple gene switching and insertions.

Complete mitochondrial genome sequence of (Pempheriformes: Glaucosomatidae) with implications based on the phylogenetic position.

The complete mitochondrial genome sequence of pearl perch () was determined using a PCR-based method. The genome was 16,529 bp in length and included 37 genes (13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes) and two non-coding regions (control region and origin of the light strand replication). A maximum likelihood analysis was conducted to confirm the phylogenetic position of this species using almost all the data available on Pempheriformes in the database.

Evolutionary affinities of the unfathomable Parabrotulidae: Molecular data indicate placement of Parabrotula within the family Bythitidae, Ophidiiformes.

Fishes are widely diverse in shape and body size and can quite rapidly undergo these changes. Consequently, some relationships are not clearly resolved with morphological analyses. In the case of fishes of small body size, informative characteristics can be absent due to simplification of body structures.

Structure and variation of the mitochondrial genome of fishes.

Background: The mitochondrial (mt) genome has been used as an effective tool for phylogenetic and population genetic analyses in vertebrates. However, the structure and variability of the vertebrate mt genome are not well understood. A potential strategy for improving our understanding is to conduct a comprehensive comparative study of large mt genome data.

Molecular phylogeny of Percomorpha resolves Trichonotus as the sister lineage to Gobioidei (Teleostei: Gobiiformes) and confirms the polyphyly of Trachinoidei.

The percomorph fish clade Gobiiformes is a worldwide, tropical and temperate radiation with species occupying nearly all aquatic, and some semi-terrestrial, habitats. Early molecular phylogenetic studies led to the discovery of Gobiiformes, which contains Gobioidei, the gobies and sleepers, and a clade (Apogonoidei) consisting of Apogonidae and Kurtus, the cardinalfishes and nurseryfishes. Gobioidei is consistently resolved as monophyletic in molecular studies, and includes eight families whose members range from waterfall climbing stream gobies to several prominent lineages inhabiting coral reefs.

Identification of the notothenioid sister lineage illuminates the biogeographic history of an Antarctic adaptive radiation.

Background: Antarctic notothenioids are an impressive adaptive radiation. While they share recent common ancestry with several species-depauperate lineages that exhibit a relictual distribution in areas peripheral to the Southern Ocean, an understanding of their evolutionary origins and biogeographic history is limited as the sister lineage of notothenioids remains unidentified. The phylogenetic placement of notothenioids among major lineages of perciform fishes, which include sculpins, rockfishes, sticklebacks, eelpouts, scorpionfishes, perches, groupers and soapfishes, remains unresolved.

Mitochondrial genomic investigation of flatfish monophyly.

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.

Mitogenomic circumscription of a novel percomorph fish clade mainly comprising "Syngnathoidei" (Teleostei).

Percomorpha, comprising about 60% of modern teleost fishes, has been described as the "(unresolved) bush at the top" of the tree, with its intrarelationships still being ambiguous owing to huge diversity (>15,000 species). Recent molecular phylogenetic studies based on extensive taxon and character sampling, however, have revealed a number of unexpected clades of Percomorpha, and one of which is composed of Syngnathoidei (seahorses, pipefishes, and their relatives) plus several groups distributed across three different orders. To circumscribe the clade more definitely, we sampled several candidate taxa with reference to the previous studies and newly determined whole mitochondrial genome (mitogenome) sequences for 16 percomorph species across syngnathoids, dactylopterids, and their putatively closely-related fishes (Mullidae, Callionymoidei, Malacanthidae).

Evolutionary origin of the Scombridae (tunas and mackerels): members of a paleogene adaptive radiation with 14 other pelagic fish families.

Uncertainties surrounding the evolutionary origin of the epipelagic fish family Scombridae (tunas and mackerels) are symptomatic of the difficulties in resolving suprafamilial relationships within Percomorpha, a hyperdiverse teleost radiation that contains approximately 17,000 species placed in 13 ill-defined orders and 269 families. Here we find that scombrids share a common ancestry with 14 families based on (i) bioinformatic analyses using partial mitochondrial and nuclear gene sequences from all percomorphs deposited in GenBank (10,733 sequences) and (ii) subsequent mitogenomic analysis based on 57 species from those targeted 15 families and 67 outgroup taxa. Morphological heterogeneity among these 15 families is so extraordinary that they have been placed in six different perciform suborders.

MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

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.

Mitogenomic sequences and evidence from unique gene rearrangements corroborate evolutionary relationships of myctophiformes (Neoteleostei).

Background: A skewed assemblage of two epi-, meso- and bathypelagic fish families makes up the order Myctophiformes - the blackchins Neoscopelidae and the lanternfishes Myctophidae. The six rare neoscopelids show few morphological specializations whereas the divergent myctophids have evolved into about 250 species, of which many show massive abundances and wide distributions. In fact, Myctophidae is by far the most abundant fish family in the world, with plausible estimates of more than half of the oceans combined fish biomass.

Complete mitochondrial genome sequence of the dragonet Callionymus curvicornis (Perciformes: Callionymoidei: Callionymidae).

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 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region.

Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation.

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.

Evolutionary history of anglerfishes (Teleostei: Lophiiformes): a mitogenomic perspective.

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.

Mitogenomic evaluation of the unique facial nerve pattern as a phylogenetic marker within the percifom fishes (Teleostei: Percomorpha).

Percomorpha has been described as the "(unresolved) bush at the top" of the teleostean phylogenies and its intrarelationships are intrinsically difficult to solve because of its huge diversity (>15,000 spp.) and ill-defined higher taxa. Patterns of facial nerves, such as those of the ramus lateralis accessorius (RLA), have been considered as one of the candidate characters to delimit a monophyletic group within the percomorphs.

Deep-sea mystery solved: astonishing larval transformations and extreme sexual dimorphism unite three fish families.

The oceanic bathypelagic realm (1000-4000 m) is a nutrient-poor habitat. Most fishes living there have pelagic larvae using the rich waters of the upper 200 m. Morphological and behavioural specializations necessary to occupy such contrasting environments have resulted in remarkable developmental changes and life-history strategies.

Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences.

Series Atherinomorpha, with its plentiful number of species and highly diversified ecological and morphological characters, is the most successful fish group at the surface layer of the ocean and many freshwater habitats, comprising 1552 species classified into three orders, six suborders, 21 families, and 193 genera. The group includes one of the most important research model organisms, the medaka (Oryzias latipes), together with diverse fishes with morphological, physiological, and ecological specializations, such as highly developed pectoral fins to glide, self-fertilization, and live-bearing. In this study, we examined the whole mitochondrial genomes (mitogenomes) from 17 species representing all of the three orders and six suborders within Atherinomorpha, with data from 70 additional percomorph species as ingroups, and two non-percomorph outgroup species.

Interrelationships of the 11 gasterosteiform families (sticklebacks, pipefishes, and their relatives): a new perspective based on whole mitogenome sequences from 75 higher teleosts.

The fishes currently recognized as members of the order Gasterosteiformes (sticklebacks, pipefishes, and their relatives) number 278 species, classified into two suborders (Gasterosteoidei and Syngnathoidei), 11 families and 71 genera. Members of this group exhibit unique appearances, many of which are derived from armored bodies with bony plates in various forms. Although recent molecular phylogenetic studies have repeatedly questioned the monophyly of this order, none of the studies examined all of the representative families and the phylogenetic reality of the group has remained unclear.

Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences.

The gene order of mitochondrial genomes (mitogenomes) has been employed as a useful phylogenetic marker in various metazoan animals, because it may represent uniquely derived characters shared by members of monophyletic groups. During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) based on whole mitogenome sequences, we found that two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi: family Macrouridae) revealed a unusually identical gene order (translocation of the tRNA(Leu (UUR))). Both are members of the same family, although their external morphologies differed so greatly (e.

Gene rearrangements and evolution of tRNA pseudogenes in the mitochondrial genome of the parrotfish (Teleostei: Perciformes: Scaridae).

Genomic size of animal mitochondrial DNA is usually minimized over time. Thus, when regional duplications occur, they are followed by a rapid elimination of redundant material. In contrast to this general view, we report here long-sustained tRNA pseudogenes in the mitochondrial genome (mitogenome) of teleost fishes of the family Scaridae (parrotfishes).

Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences.

A recent preliminary study using complete mitochondrial DNA sequences from 48 species of teleosts has suggested that higher teleostean phylogenies should be reinvestigated on the basis of more intensive taxonomic sampling. As a second step towards the resolution of higher teleostean phylogenies, which have been described as the "(unresolved) bush at the top of the tree," we reanalyzed their relationships using mitogenomic data from 100 purposefully chosen species that fully represented all of the higher teleostean orders, except for the Batrachoidiformes. Unweighted and weighted maximum parsimony analyses were conducted with the data set that comprised concatenated nucleotide sequences from 12 protein-coding genes (excluding 3rd codon positions) and 21 transfer RNA (tRNA) genes (stem regions only) from each species.