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The freshwater leaf fish

The freshwater leaf fish Pristolepis rubripinnis belongs to the family Pristolepididae, restricted to Pamba and Chalakudy rivers of Kerala, India. In the present study, we sequenced the complete mitogenome of P. rubripinnis and analysed its phylogeny in the order Anabantiformes. The 16622-bp long genome comprised of 13 protein-coding genes, two rRNA genes, 22 transfer RNAs (tRNAs) genes and had a noncoding control region. All the protein-coding genes, tRNA and rRNA were located on the heavy strand, except nad6 and eight tRNAs (glutamine, alanine, asparagine, cysteine, tyrosine, serine, glutamic acid and proline) transcribed from L strand. The genome exhibited an overlapping between atp8 and atp6 (2 bp), nad4 and nad4l (2 bp), tRNAIle and tRNAGln. (1 bp), tRNAThr and tRNAPro (1 bp). Around 157 bp, an intergenic spacer was identified. The overall GC-skews and AT-skews of the H-strand mitogenome were -0.35 and 0.079, respectively, revealing that the H-strand consisted of equal amounts of A and T and that the overall nucleotide composition was C skewed. All tRNA genes exhibited cloverleaf secondary structures, while the secondary structure of tRNASer lacked a discernible dihydrouridine stem. The phylogenetic analysis of available mitogenomes of Anabantiformes revealed a sister group relationship between Pristolepididae and Channidae. The whole mitogenome of Pristolepis rubripinnis will form a molecular resource for further taxonomic and conservation studies on this endemic freshwater fish.

The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish

The Tetraodontidae (pufferfishes), is primarily a family of marine and estuarine fishes with a limited number of freshwater species. Freshwater invasions can be observed in South America, Southeast Asia and central Africa. In the present study, we have analysed the complete mitogenome of freshwater pufferfish, Carinotetraodon travancoricus (dwarf pufferfish or Malabar pufferfish) endemic to southwest India. The genome is 16487 bp in length and consist of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region like all the other vertebrate mitogenomes. The protein-coding genes ranged from 165 bp (ATP synthase subunit 8) to 1812 bp (NADH dehydrogenase subunit 5) and comprised of 11310 bp in total, constituting 68.5% of the complete mitogenome. Some overlaps have been observed in protein-coding genes by a total of 7 bp. The AT skew (0.032166) and GC skew (-0.29746) of the mitogenome indicated that heavy strand consists equal amount of A and T, but the overall base composition was mainly C skewed. The noncoding D-loop region comprised 869 bp. The conserved motifs ATGTA and its complement TACAT associated with thermostable hairpin structure formation were identified in the control region. The phylogenetic analysis depicted a sister group relationship of C. travancoricus with euryhaline species Dichotomyctere nigroviridis and D. ocellatus with 100% bootstrap value rather than with the other freshwater members of Carinotetraodon species from Southeast Asia. The data from this study will be useful for proper identification, genetic differentiation, management and conservation of the dwarf Indian pufferfish.

The genus Mola of ocean sunfishes (family Molidae) is currently composed of three species: Mola mola (Linnaeus 1758), Mola ramsayi (Giglioli 1883), and Mola tecta Nyegaard et al. 2017. For a comprehensive revision of the genus, both literature survey and morphological investigations of Molidae were conducted. We found Mola alexandrini (Ranzani 1839) to be synonymous with M. ramsayi and we herein redescribe M. alexandrini based on the rediscovered dried holotype and 21 other fresh and preserved specimens. Mola alexandrini can be distinguished from other species of Mola by the following combination of characters in adults: head profile with bump; chin with bump; body scales rectangular; clavus rounded, supported by 14–24 (mode 17) clavus fin rays and 8–15 (12) ossicles on the rear margin. A neotype of M. mola is designated for comparison with M. alexandrini, as these two species have long been confused.

The taxonomy of the ocean sunfishes (Molidae) has a complicated history. Currently, three genera and four species are recognized, including two in the genus Mola (M. mola and M. ramsayi). In 2009, a genetic study revealed a potential third species, Mola species C, in Southeast Australian waters. Concentrating on this region, we obtained samples and morphological data from 27 Mola sp. C specimens, genetically confirmed the existence of this species (mtDNA D-loop and cytochrome c oxidase 1), and established its morphology across a size spectrum of 50–242 cm total length. Mola sp. C is diagnosed by clavus meristics [15–17 fin rays (13–15 principal, 2 minor), 5–7 ossicles, paraxial ossicles separate], clavus morphology (prominent smooth band back-fold, rounded clavus edge with an indent), and body scale morphology (raised conical midpoints, non-branching). This species does not develop a protruding snout, or swollen dorso- or ventrolateral ridges. Body proportions remain similar with growth. A review of the historic literature revealed that Mola sp. C is a new, hitherto undescribed species, M. tecta, which we describe and diagnose, and that it is the first proposed addition to the genus Mola in 125 years. Its core distribution is likely in the temperate waters of the Southern Hemisphere.

Recent molecular and morphological studies suggest the existence of at least three species of Mola (Mola spp. A, B and C). Currently, only Mola mola and Mola ramsayi are formally accepted and species A, B or C have not been assigned to these thus far. In this study, a large ocean sunfish in the western Mediterranean Sea was analysed molecularly and morphologically, identified as Mola sp. A and a detailed account of the specimen's parasite load is reported.

We employed molecular systematic analysis based on mitochondrial D-loop sequences to identify two specimens of ocean sunfish from Omani coastal waters that had previously been identified morphologically as Mola mola (Linnaeus, 1758) and M. ramsayi (Giglioli, 1883). Of the three molecular species that are recognized globally, Mola sp. A, Mola sp. B, and Mola sp. C, we confirmed that both specimens from Oman are Mola sp. A. This result suggested a broader distribution of this species than had ever been thought, but it also revealed a discrepancy between morphological and genetic characters in Mola taxonomy. We reexamined the morphology of the two specimens from Oman to clarify the extent to which the key morphological features correspond with molecular genetic identifications, and discovered errors in the original reports on both specimens.

The acropomatid genus Verilus is redescribed as a senior synonym of Apogonops and Neoscombrops with description of a new species and a taxonomic revision of the five species that were formerly classified in these genera. This genus is characterized by the following combination of characters: a canine tooth (rarely two) near symphysis of premaxilla of upper jaw but lacking a row of conical teeth on anterior part of outer premaxillary margin; a canine tooth (rarely two) near symphysis of dentary with only villiform or a row of conical teeth posteriorly; three anal-fin spines; 10 dorsal-fin spines; pelvic-fin spine smooth; luminous organ absent. This genus comprises six species: Verilus sordidus (type species, western Atlantic Ocean); Verilus anomalus (off southern and eastern coast of Australia); Verilus atlanticus (western Atlantic Ocean); Verilus cynodon (south-western Indian Ocean); Verilus pacificus (north-western and central Pacific Ocean); Verilus starnesi sp. nov. (Coral Sea off Chesterfield Islands, New Caledonia). These species are distinguishable from one another by dentition on the lower jaw, numbers of pectoral-fin rays, gill rakers and lateral-line scales, features of the proximal-middle radial of the first anal-fin pterygiophore, presence or absence of basioccipital fossa and body depth.

Eight Southeast Asian freshwater puffers–Tetraodon biocellatus, T. cochinchinensis, T. cutcutia, T. palembangensis, T. turgidus, Carinotetraodon irrubesco, C. lorteti, and C. travancoricus—spawned in captivity at the Shimonoseki Marine Science Museum Aquarium, and the larvae were reared for more than 180 days. Tetraodon cochinchinensis, T. cutcutia, T. palembangensis, and T. turgidus spawned large eggs in batches and protected them; Carinotetraodon travancoricus spawned and protected a few eggs, larger than those of congeners; and T. biocellatus, C. irrubesco, and C. lorteti spawned smaller eggs that were scattered and unprotected. Larval growth was faster in T. cochinchinensis, T. cutcutia, T. palembangensis, and T. turgidus and slower in T. biocellatus, C. irrubesco, C. lorteti, and C. travancoricus.

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.

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). Unambiguously aligned sequences (13,872 bp) from those 16 species plus 78 percomorphs and two outgroups (total 96 species) were subjected to partitioned Bayesian and maximum likelihood analyses. The resulting trees revealed a highly supported clade comprising seven families in Syngnathoidei (Gasterosteiformes), Dactylopteridae (Scorpaeniformes), Mullidae in Percoidei and two families in Callionymoidei (Perciformes). We herein proposed to call this clade “Syngnathiformes” following the latest nuclear DNA studies with some revisions on the included families.

Pufferfishes belonging to the genus Tetraodon form one of the largest groups in the family Tetraodontidae. This group consists of more than 20 species distributed across freshwater, as well as brackish and coastal waters, of Africa and Southeast Asia. However, their phylogenetic and evolutionary relationships are still ambiguous. In the present study, mitochondrial genes encoding 16S rRNA and cytochrome b were sequenced for 17 Tetraodon species collected from various areas mentioned above. Supermatrix analysis based on the complete sequences of the two genes from Tetraodon species was performed using a tree with 50 tetraodontid species (including 7 Tetraodon species) as a backbone. The obtained phylogenetic tree classified Tetraodon species into three groups, correlating well with their habitats, such as Asian freshwater, Asian brackish water, and African freshwater. We also showed that salinity tolerance of Asian freshwater species T. cochinchinensis was apparently lower than that of Asian brackish water species T. nigroviridis, suggesting that the speciation of Tetraodon species in the Asian freshwater group was caused by the molecular evolution associated with osmotic regulation.

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.

The acropomatid, Amia (Amioides) grossidens Smith and Radcliffe 1922, was originally described from a single specimen collected off Luzon Island, the Philippines. Although this species was regarded as belonging to Synagrops, it is distinguished from Synagrops by the dentition of the upper jaw, number of dorsal fin spines, and additionally from other acropomatid genera by 14 caudal vertebrae and a posttemporal spine. Therefore, this species should be placed in a monotypic genus Amioides, with elevation of the subgenus to generic rank, compared with diagnostic characters of seven other genera, and this genus and species were herein redescribed based on the holotype.

A poorly known acropomatid, Verilus sordidus Poey 1860, is redescribed based on six specimens from the western central Atlantic. We present diagnostic characters to differentiate this species from Neoscombrops atlanticus Mochizuki and Sano 1984, which has been confused with this species, and designate a neotype of V. sordidus. This species is distinguishable from N. atlanticus by the proximal-middle radial of the first anal-fin pterygiophore being slender with no trough or hollow on the anterodorsal portion (vs. hollow in N. atlanticus), several canine teeth posterior to the large canine teeth on either side of the symphysis of the lower jaw (vs. villiform teeth posterior to enlarged canines), and by the modal numbers of pectoral-fin rays, lateral-line scales, and gill rakers on the lower limb of the first arch.

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.

Phylogenetic analyses were conducted using complete nucleotide sequences of the D-loop in the mitochondrial genome of Mola specimens, collected mainly in Japanese waters, to clarify the genetic features and distribution patterns of Mola sunfishes. Two significantly distinct groups (designated A and B) were present in the genus, with a considerable net nucleotide sequence divergence between the two (8.4%). The two groups occurred sympatrically around the Japanese coast, as previously suggested by Sagara et al. (2005). Group A occurred mostly on the Pacific coast of eastern Japan, while group B was widely distributed along the Kuroshio Current, strongly suggesting different migration routes for each group. The morphological characteristics of the two group specimens were differentiated via the head bump, body proportions and shape of the clavus. Through the addition of Mola sequence data taken from outside Japan to our phylogenetic analyses, three independent groups, including groups A and B, were found, each with a wide geographical distribution, which suggests the presence of at least three independent species within the genus Mola.

Although the fugu Takifugu rubripes has attracted attention as a model organism for genomic studies because of its compact genome, it is not generally appreciated that there are approximately 25 closely related species with limited distributions in the waters of East Asia. We performed molecular phylogenetic analyses and constructed a time tree using whole mitochondrial genome sequences from 15 Takifugu species together with 10 outgroups to examine patterns of diversification. The resultant time tree showed that the modern Takifugu species underwent explosive speciation during the Pliocene 1.8-5.3 Ma, which is comparable with that of the Malawi cichlids and tropheine cichlids in Lake Tanganyika. Considering their limited distributions and remarkable variations in coloration, morphology, and behavior, the results of the present study strongly suggest that Takifugu species are strong candidates as a model system for evolutionary studies of speciation mechanisms in marine environments where few such organisms are available.

The poorly known acropomatid fish, Acropoma lecorneti Fourmanoir 1988 was originally described from a single specimen off the west coast of New Caledonia. However, the brief original description and apparent subsequent loss of the holotype made the taxonomic status of the species problematic. A second specimen, collected in good condition from off Okinawa Island, Japan, enabled the species to be redescribed with detailed emphasis on morphological characters. It is easily distinguishable from other species of Acropoma by an O-shaped luminous gland, the slender proximal radial of 1st anal-fin pterygiophore lacking a trough or hollow, and the pale-colored anus located closer to the pelvic-fin origin than to that of the anal fin.

A poorly known acropomatid, Rhomboserranus gracilispinis Fowler, 1943, was originally described on the basis of specimens from the Philippines. Since the recognition of Rhomboserranus as a junior synonym of Doederleinia, R. gracilispinis had been considered a valid species of Doederleinia. Examination of the holotype of R. gracilispinis and other type series of nominal species of Doederleinia showed them to be included in the single species D. berycoides (Hilgendorf, 1879). The sole representative of Doederleinia is distributed from Japan to northwestern Australia. This species is distinguishable from other acropomatids by the following combination of characters: head and body red; nine dorsal-fin spines; three anal-fin spines; no luminous organ; a row of conical teeth with a large canine tooth medially on lower jaw; large conical teeth on anterior part of outer margin with two or three large canine teeth on inner margin on upper jaw; and anus situated just anterior to origin of anal fin.

We determined the whole mitochondrial genome sequence for spotted green pufferfish, Tetraodon nigroviridis (Teleostei: Tetraodontiformes). The genome (16,488 bp) contained 37 genes (two ribosomal RNA genes, 22 transfer RNA genes, and 13 protein-coding genes) plus control region as found in other vertebrates, with the gene order identical to that of typical vertebrates. The sequence was used to estimate phylogenetic relationships and divergence times among major lineages of fishes, including representative model organisms in fishes. We employed partitioned Bayesian approaches for these two analyses using two datasets that comprised concatenated amino acid sequences from 12 protein-coding genes (excluding the ND6 gene) and concatenated nucleotide sequences from the 12 protein-coding genes (without 3rd codon positions), 22 transfer RNA genes, and two ribosomal RNA genes. The resultant trees from the two datasets were well resolved and largely congruent with those from previous studies, with spotted green pufferfish being placed in a reasonable phylogenetic position. The approximate divergence times between spotted green pufferfish and model organisms in fishes were 85 million years ago (MYA) vs. torafugu, 183 MYA vs. three-spined stickleback, 191 MYA vs. medaka, and 324 MYA vs. zebrafish, all of which were about twice as old as the divergence times estimated by their earliest occurrences in fossil records.

Malakichthys Doderlein, 1883, comprises seven species: type species Malakichthys griseus Doderlein 1883, from southern Japan to north-western Australia; Malakichthys barhatits Yamanoue & Yoseda, 2001, from southern Japan, the South China Sea, north-western Australia and the Coral Sea; Malakichthys elegans Matsubara & Yamaguti, 1943, from southern Japan south to the Arafura Sea; Malakichthys levis Yamanoue & Matsuura, 2001, from northern Australia; Malakichthys mochizuki Yamanoue & Matsuura, 2001, from the Coral Sea; Malakichthys similis sp. nov. from the Bohol Sea, Philippines; Malakichthys wakiyae Jordan & Hubbs, 1925, from southern Japan and Taiwan. Species of Malakichthys are very similar to each other in general appearance but are distinguishable by spination on the lower jaw, features of the proximal-middle radial of the first anal-fin pterygiophore, the number of anal-fin soft rays and body depth.

We determined the complete nucleotide sequences of the mitochondrial genomes for the three currently recognized species of ocean sunfish: Mola mola, Masturus lanceolatus, and Ranzania laevis (Tetraodontiformes: Molidae). Each genome contained the 37 genes as found in teleosts, with the typical gene order in teleosts. Bayesian, maximum-likelihood, and maximum-parsimony analyses were conducted with the data set comprising concatenated nucleotide sequences from 36 genes (excluding the ND6 gene) of three molids and four outgroups (three tetraodontiforms plus a caproid). The resultant trees supported monophyly of the Molidae and its intrarelationships ((Mola, Masturus), Ranzania), which were congruent with previous morphology-based hypotheses.

Neoscombrops annectens Gilchrist, 1922, described from off Natal, South Africa, has long been regarded as a valid species. Although Acropoma cynodon Regan, 1921, also described from off Natal, was found to be Neoscombrops, they were regarded as distinct species, distinguishable by body depth and body color. Examination of many specimens, including the holotype of A. cynodon and neotype of N. annectens, revealed that the differences are within the range of intraspecific variation. N. cynodon is redescribed as a senior synonym of N. annectens.

Acropoma boholensis sp. nov. is described on the basis of two specimens collected from Dumaguete city market, Negros Island, Philippines. It is distinguished from other species of Acropoma by the following combination of characters: anus situated closer to the origin of pelvic fin than to that of anal fin; luminous gland extending from isthmus to anal fin base; scales cycloid except weakly ctenoid scales around anterior part of lateral line and on ventral side of body; proximal radial of first anal fin pterygiophore lacking trough or hollow; body depth 31%–33% SL; head length 40%–42% SL; length of orbit 13%–14% SL.

A new acropomatid, Malakichthys barbatus, is described on the basis of 27 specimens (76.3–180.1 mm SL) collected from Suruga Bay to Tosa Bay, along the southern Pacific coast of Japan. The new species is unique in having numerous pairs of spines on the chin (a pair of spines in other congeners). Although the new species resembles M. elegans in having a slender body (the depth less than 35% SL), the former is further distinguishable from the latter in having a slender first proximal radial of the anal fin with no hollow (broad with a cone-shaped hollow in M. elegans), 43–48 lateral line scales (48–51), modally 21 gill rakers on the lower arm (modally 23), and a dark blotch on the opercle (no remarkable blotch).

Balistoid fishes have a unique and reduced pelvic fin structure, which does not exhibit paired structures. The pelvic complex exhibits reductive trends, but its rudimentary structure was retained among balistoids, and its unidirectional and parsimonious reduction in more derived lineages has been hypothesized based on morphology. We investigated the evolution of pelvic complex reduction in balistoids using whole mitochondrial genome (mitogenome) data from 33 species (27 newly determined during the study) that represent the entire morphological diversity of balistoids. Partitioned maximum likelihood and Bayesian analyses were conducted with two datasets that comprised concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]) plus 22 transfer RNA and two ribosomal RNA genes. The resultant trees were well resolved and largely congruent, with most internal branches having high support values. The mitogenomic datasets strongly supported monophylies of both balistids and monacanthids, but rejected previous hypotheses on the intra-relationships in each family. The present tree topology revealed that highly reduced pelvic complexes had multiple origins, and optimization of the traits on the resultant tree strongly suggested the non-unidirectional and independent reduction of pelvic complexes in balistoids. The evolution of balistoid pelvic structure is very different among fishes that exhibit its reductive trends, and this uniqueness in pelvic evolution may be a link to their reproductive behaviors.

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. We subjected the unambiguously aligned mitogenome sequences to partitioned maximum likelihood and Bayesian phylogenetic analyses. The resulting phylogenies recovered a monophyletic Atherinomorpha within the Percomorpha, and demonstrated its phylogenetic affinity to the percomorph fishes (including cichlids) spawning demersal eggs with filaments. This study, further, provided the first molecular evidence for the monophyly of the respective atherinomorph orders (Atheriniformes, Beloniformes, and Cyprinodontiformes) with high posterior probabilities and mostly high bootstrap values, providing an important basis for the future studies on the phylogeny and evolution of this diverse group.

Tetraodontiformes includes approximately 350 species assigned to nine families, sharing several reduced morphological features of higher teleosts. The order has been accepted as a monophyletic group by many authors, although several alternative hypotheses exist regarding its phylogenetic position within the higher teleosts. To date, acanthuroids, zeiforms, and lophiiforms have been proposed as sister-groups of the tetraodontiforms. The monophyly and sister-group status was investigated using whole mitochondrial genome (mitogenome) sequences from 44 purposefully-chosen species (26 sequences newly-determined during the study) that fully represent the major tetraodontiform lineages plus all the groups that have been hypothesized as being close relatives. Partitioned Bayesian analyses were conducted with the three datasets that comprised concatenated nucleotide sequences from 13 protein-coding genes (with and without, or with RY-coding, 3rd codon positions), plus 22 transfer RNA and two ribosomal RNA genes. The resultant trees were well resolved and largely congruent, with most internal branches being supported by high posterior probabilities. Mitogenomic data strongly supported the monophyly of tetraodontiform fishes, placing them as a sister-group of either Lophiiformes plus Caproidei or Caproidei only. The sister-group relationship between Acanthuroidei and Tetraodontiformes was statistically rejected using Bayes factors. These results were confirmed by a reanalysis of the previously published nuclear RAG1 gene sequences using the Bayesian method. Within the Tetraodontiformes, however, monophylies of the three superfamilies were not recovered and further taxonomic sampling and subsequent efforts should clarify these relationships.

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. However, members of the 15 families are either coastal or oceanic pelagic in their ecology with diverse modes of life, suggesting that they represent a previously undetected adaptive radiation in the pelagic realm. Time-calibrated phylogenies imply that scombrids originated from a deep-ocean ancestor and began to radiate after the end-Cretaceous when large predatory epipelagic fishes were selective victims of the Cretaceous-Paleogene mass extinction. We name this clade of open-ocean fishes containing Scombridae “Pelagia” in reference to the common habitat preference that links the 15 families.

Pufferfishes of the Family Tetraodontidae are the most speciose group in the Order Tetraodontiformes and mainly inhabit coastal waters along continents. Although no members of other tetraodontiform families have fully discarded their marine lives, approximately 30 tetraodontid species spend their entire lives in freshwaters in disjunct tropical regions of South America, Central Africa, and Southeast Asia. To investigate the interrelationships of tetraodontid pufferfishes and thereby elucidate the evolutionary origins of their freshwater habitats, we performed phylogenetic analysis based on whole mitochondrial genome sequences from 50 tetraodontid species and closely related species (including 31 newly determined sequences). The resulting phylogenies reveal that the family is composed of four major lineages and that freshwater species from the different continents are independently nested in two of the four lineages. A monophyletic origin of the use of freshwater habitats was statistically rejected, and ancestral habitat reconstruction on the resulting tree demonstrates that tetraodontids independently entered freshwater habitats in different continents at least three times. Relaxed molecular-clock Bayesian divergence time estimation suggests that the timing of these invasions differs between continents, occurring at 0–10 million years ago (MA) in South America, 17–38 MA in Central Africa, and 48–78 MA in Southeast Asia. These timings are congruent with geological events that could facilitate adaptation to freshwater habitats in each continent.

Background The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084). Results The resultant tree topologies from the two data sets were congruent, with many internal branches showing high support values. The mitogenomic data strongly supported monophyly of all families and subfamilies (except the Tetraodontinae) and sister-group relationships of Balistidae + Monacanthidae and Tetraodontidae + Diodontidae, confirming the results of previous studies. However, we also found two unexpected basal splits into Tetraodontoidei (Triacanthidae + Balistidae + Monacanthidae + Tetraodontidae + Diodontidae + Molidae) and Triacanthodoidei (Ostraciidae + Triodontidae + Triacanthodidae). Conclusion This basal split into the two clades has never been reported and challenges previously proposed hypotheses based on both morphology and nuclear gene sequences. It is likely that the basal split had involved ecological diversification, because most members of Tetraodontoidei exclusively occur in shallow waters (freshwater, brackish and coastal waters, and open seas), while those of Triacanthodoidei occur mainly in relatively deep waters along continental shelves and slopes except for more derived ostraciids. This suggests that the basal split between the two clades led to subsequent radiation into the two different habitats.

Background The lancelet Asymmetron inferum (subphylum Cephalochordata) was recently discovered on the ocean floor off the southwest coast of Japan at a depth of 229 m, in an anaerobic and sulfide-rich environment caused by decomposing bodies of the sperm whale Physeter macrocephalus. This deep sulfide-rich habitat of A. inferum is unique among the lancelets. The distinguishing adaptation of this species to such an extraordinary habitat can be considered in a phylogenetic framework. As the first step of reconstruction of the evolutionary processes in this species, we investigated its phylogenetic position based on 11 whole mitochondrial genome sequences including the newly determined ones of the whale-fall lancelet A. inferum and two coral-reef congeners. Results Our phylogenetic analyses showed that extant lancelets are clustered into two major clades, the Asymmetron clade and the Epigonichthys + Branchiostoma clade. A. inferum was in the former and placed in the sister group to A. lucayanum complex. The divergence time between A. inferum and A. lucayanum complex was estimated to be 115 Mya using the penalized likelihood (PL) method or 97 Mya using the nonparametric rate smoothing (NPRS) method (the middle Cretaceous). These are far older than the first appearance of large whales (the middle Eocene, 40 Mya). We also discovered that A. inferum mitogenome (mitochondrial genome) has been subjected to large-scale gene rearrangements, one feature of rearrangements being unique among the lancelets and two features shared with A. lucayanum complex. Conclusion Our study supports the monophyly of genus Asymmetron assumed on the basis of the morphological characters. Furthermore, the features of the A. inferum mitogenome expand our knowledge of variation within cephalochordate mitogenomes, adding a new case of transposition and inversion of the trnQ gene. Our divergence time estimation suggests that A. inferum remained a member of the Mesozoic and the early Cenozoic large vertebrate-fall communities before shifting to become a whale-fall specialist.