Genome structures resolve the early diversification of teleost fishes.

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes.

BACKGROUND: Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae. METHODS AND RESULTS: To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively. CONCLUSIONS: This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes.

A new species of the rare genus Myroconger Günther, 1870 (Anguilliformes: Myrocongridae) from Brazilian waters, tropical western Atlantic.

The family Myrocongridae comprises some of the rarest and least known benthopelagic eel species. It is composed of a single genus, Myroconger Günther, 1870, and five valid species: M. compressus Günther, 1870, from the Atlantic Ocean; M. gracilis Castle, 1991, M. prolixus Castle Béarez, 1995, and M. nigrodentatus Castle Béarez, 1995, from the Pacific Ocean; and M. seychellensis Karmovskaya, 2006, from the Indian Ocean. Herein, we report on an additional species from the Atlantic Ocean, Myroconger pietschi n. sp., based on a specimen obtained on the Aracati Bank, North Brazilian ridge, off Ceará State, western South Atlantic. Myroconger pietschi can be diagnosed by having 190 anal-fin rays, a short pectoral fin (16.6% HL), the posterior portion of the ethmovomerine teeth arranged in a single row, teeth on lower and upper pharyngeal tooth plate 24 and 27, and 10 branchiostegal rays.

A new arrowtooth eel of genus emMeadia/em (Synaphobranchidae: Ilyophinae) from Vietnam, South China Sea.

Meadia minor sp. nov., a scaless ilyophine eel, is described on the basis of 10 specimens collected from off Quy Nhon, central coast of Vietnam. It can be distinguished from its congeners in having a relatively long trunk (21.3-25.0% TL) which is longer than head length; a short and blunt snout (21.4-23.7% HL); gill opening close to pectoral-fin base; interbranchial space broad (20.7-26.2% HL); dorsal-fin origin above posterior third of pectoral fin; body depth 24-28 times in TL; total vertebrae 118-122; mean vertebral formula 7-33-121; and a small body size, reaching 330 mm TL. The generic status of the new species is discussed. Short descriptions of two congeners are provided.

Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes.

The structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

A new species of the genus Cirrhimuraena (Anguilliformes: Ophichthidae) from the Bay of Bengal, India.

A new species of the genus Cirrhimuraena (Anguilliformes: Ophichthidae), Cirrhimuraena indica sp. nov., is described based on eight specimens collected from the Paradip (Odisha) and Petuaghat harbours (West Bengal) along the Bay of Bengal. The species is distinct in having the upper jaw fringed with 16-17 cirri before posterior nostril and 4-5 in between the anterior and posterior nostrils on the side; dorsal fin originates above the level of gill opening, predorsal length is 9.3-10.9 in total length; the head is relatively large, the length is 9.3-9.8 in total length; no infraorbital pores are observed between the nostrils; teeth are numerous, small, conical and in bands on each jaw; pores are present before the gill opening 10-11 and before anus 47-48; pectoral-fin length is 2.4-2.8 in head length; predorsal vertebrae are 8-10, pre-anal vertebrae 43-47 and total vertebrae 164-169. In the maximum likelihood tree analysis for COI gene, the new species belongs to the same clade as the other congener of Cirrhimuraena chinensis and is separated from the species morphologically and genetically.

A review of the genus Strophidon (Anguilliformes: Muraenidae), with description of a new species.

Strophidon McClelland is a muraenid genus with characteristic appearance of a very elongated body, a large mouth cleft and anteriorly placed eyes. The nomenclature and taxonomic history of species within Strophidon are contentious and its members are easily misidentified. In the present study, species of the genus Strophidon are revised based on morphological and molecular data, and five species are considered valid, including S. dawydoffi Prokofiev, S. dorsalis (Seale), S. sathete (Hamilton), S. ui Tanaka and a new species, S. tetraporus. Strophidon tetraporus sp. nov. is described based on 15 specimens from Indonesia, the Philippines, Taiwan and Vietnam with the unique characteristic of the constant presence of the fourth infraorbital pore among species of Strophidon. The intraspecific variation of vertebral formula within S. dorsalis is discussed based on molecular data. Muraena macrurus Bleeker and Thyrsoidea longissima Kaup are synonyms of S. sathete that can be distinguished from the most similar congener S. ui by a longer tail, smaller eyes and more inner maxillary and inner dentary teeth. A key to identify species of Strophidon is provided. The distribution and maximum size of each species are also re-evaluated.

De novo European eel transcriptome provides insights into the evolutionary history of duplicated genes in teleost lineages.

Paralogues pairs are more frequently observed in eels (Anguilla sp.) than in other teleosts. The paralogues often show low phylogenetic distances; however, they have been assigned to the third round of whole genome duplication (WGD), shared by all teleosts (3R), due to their conserved synteny. The apparent contradiction of low phylogenetic difference and 3R conserved synteny led us to study the duplicated gene complement of the freshwater eels. With this aim, we assembled de novo transcriptomes of two highly relevant freshwater eel species: The European (Anguilla anguilla) and the Japanese eel (Anguilla japonica). The duplicated gene complement was analysed in these transcriptomes, and in the genomes and transcriptomes of other Actinopterygii species. The study included an assessment of neutral genetic divergence (4dTv), synteny, and the phylogenetic origins and relationships of the duplicated gene complements. The analyses indicated a high accumulation of duplications (1217 paralogue pairs) among freshwater eel genes, which may have originated in a WGD event after the Elopomorpha lineage diverged from the remaining teleosts, and thus not at the 3R. However, very similar results were observed in the basal Osteoglossomorpha and Clupeocephala branches, indicating that the specific genomic regions of these paralogues may still have been under tetrasomic inheritance at the split of the teleost lineages. Therefore, two potential hypotheses may explain the results: i) The freshwater eel lineage experienced an additional WGD to 3R, and ii) Some duplicated genomic regions experienced lineage specific rediploidization after 3R in the ancestor to freshwater eels. The supporting/opposing evidence for both hypotheses is discussed.

Phylogenetic interrelationships of the eel families Derichthyidae and Colocongridae (Elopomorpha: Anguilliformes) based on the pectoral skeleton.

A cladistic analysis of the eel families Derichthyidae and Colocongridae is herein proposed for the first time on the basis of morphological data. We discovered dozens of new phylogenetic characters derived from a detailed analysis of the pectoral skeleton, an anatomical system neglected by most previous studies. Our maximum parsimony analysis indicates that Colocongridae sensu lato is paraphyletic, with its two constituent genera Coloconger and Congriscus appearing as successive sister groups of derichthyids. Monophyly of the family Derichthyidae, which has been questioned by some studies, is herein strongly supported by 10 unambiguous synapomorphies. We also stress the importance of the appendicular skeleton as a useful source of phylogenetic information for the resolution of systematic problems within Anguilliformes.

Assemblage structure, vertical distributions and stable-isotope compositions of anguilliform leptocephali in the Gulf of Mexico.

In August 2007, October 2008 and September-October 2010, 241 Tucker trawl and plankton net tows were conducted at the surface to depths of 1377 m at six locations in the northern and eastern Gulf of Mexico (GOM) to document leptocephalus diversity and determine how assemblage structure, larval size, abundance and isotopic signatures differ across the region and with depth. Overall, 2696 leptocephali representing 59 distinct taxa from 10 families were collected. Five families accounted for 96% of the total catch with Congridae and Ophichthidae being the most abundant. The top four most abundant species composed 59% of the total catch and included: Ariosoma balearicum, Paraconger caudilimbatus, Rhynchoconger flavus and Ophichthus gomesii. Four anguilliform species not previously documented in the GOM as adults or leptocephali were collected in this study, including Monopenchelys acuta, Quassiremus ascensionis, Saurenchelys stylura and one leptocephalus only known from its larval stage, Leptocephalus proboscideus. Leptocephalus catches were significantly greater at night than during the day. Catches at night were concentrated in the upper 200 m of the water column and significantly declined with increasing depth. Leptocephali abundances and assemblages were significantly different between sites on the upper continental slope (c. 500 m depth) and sites on the middle to lower continental slope (c. 1500-2300 m). Sites on the lower continental slope had a mixture of deep-sea demersal, bathypelagic and coastal species, whereas upper-slope sites contained several numerically dominant species (e.g., A. balearicum, P. caudilimbatus) that probably spawn over the continental shelf and upper slope of the GOM. Standard lengths of the four dominant species differed between sites and years, indicating heterochronic reproduction and potential larval source pools within and outside of the GOM. Stable-isotope analyses (δ13 C and δ15 N) conducted on 185 specimens from six families revealed that leptocephali had a wide range of isotopic values at the family and size-class levels. Species in the families Muraenidae, Congridae and Ophichthidae had similar δ15 N values compared with the broad range of δ15 N values seen in the deep-sea families Nemichthyidae, Nettastomatidae and Synaphobranchidae. Stable-isotope values were variably related to length, with δ15 N values being positively size correlated in ophichthids and δ13 C values being negatively size correlated in A. balearicum and P. caudilimbatus. Results suggest that leptocephali feed in various water depths and masses, and on different components of POM, which could lead to niche partitioning. Ecological aspects of these important members of the plankton community provide insight into larval connectivity in the GOM as well as the early life history of Anguilliformes.

Genetic identification of eggs from four species of Ophichthidae and Congridae (Anguilliformes) in the northern East China Sea.

We report the first genetic identification of eggs of four species of Anguilliformes caught in the northern East China Sea during August 2016, where leptocephali and adults have been collected. The species were Ophisurus macrorhynchos and Echelus uropterus belonging to the Ophichthidae, and Ariosoma majus and Gnathophis heterognathos belonging to the Congridae. The eggs were identified using three molecular genetic markers (mitochondrial 12S rRNA, 16S rRNA, and cytochrome c oxidase subunit 1), sequences obtained from local adult specimens, and geographical distribution data. All eggs were in the early or middle developmental stages. For all species except A. majus, the eggs were found near the range of small leptocephali in the East China Sea and the southern Korean Peninsula, which indicates these species had spawned along the continental near these areas during the summer.

Dysomma alticorpus, a new species of cutthroat eel from the Gulf of Aqaba, Red Sea (Teleostei: Synaphobranchidae).

The cutthroat eel Dysomma alticorpus n. sp. is described based on a single specimen collected in a trammel net at a depth of 350m off Eilat, Israel, Gulf of Aqaba, Red Sea. The new species belongs to the Dysomma anguillare species complex, which comprises species possessing a well-developed pectoral fin, intermaxillary teeth, a uniserial row of 7-15 large compound teeth in the lower jaw (which may be followed by a few smaller teeth), and an anteriorly situated anus with the trunk shorter than the head length. It is characterised by a combination of the following characters: origin of the dorsal fin well anterior to the base of the pectoral fin, predorsal length 13.8% TL; preanal length 22.8% TL; three compound teeth on the vomer; head pores: IO 4, SO 3; M 6; POP 0; AD 1, F 0, ST 0; lateral-line pores: predorsal 4, prepectoral 8, preanal 14, total 57-58, the last at the posterior two-thirds of the total length; MVF 7-16-115; total vertebrae 115. Dysomma alticorpus n. sp. is compared with other species of the genus. A revised key to the species of the genera Dysomma and Dysommina is provided.

Can an eel be a flatfish? Observations on enigmatic asymmetrical heterenchelyids from the Guinea coast of West Africa.

Morphological asymmetry is described in the heterenchelyid mud eel Pythonichthys cf. macrurus from inshore coastal waters of Guinea, West Africa. The intensity of asymmetry differs between two examined specimens, with the more extreme case exhibiting strong asymmetry in both external and internal features, including unilateral depigmentation, reductive degeneration and embedding of a blind-side eye, skewed jaws with reduced dentition and tooth loss. The extent and nature of asymmetry suggests that this individual probably lived primarily on its left lateral side, not unlike sinistral pleuronectiform flatfishes.

Morphology and Species Composition of Southern Adriatic Sea Leptocephali Evaluated Using DNA Barcoding.

Leptocephali are the characteristic larvae of the superorder Elopomorpha that are difficult to identify at the species level. In this study, we used DNA barcoding (i.e. short genetic sequences of DNA used as unique species tags) coupled with classical taxonomic methods to identify leptocephali in the southern Adriatic Sea. This information will provide an assessment of the biodiversity of the eel larvae in this region. A total of 2,785 leptocephali were collected, and using external morphology were assigned to seven morphotypes: Ariosoma balearicum, Conger conger, Gnathophis mystax, Facciolella sp., Nettastoma melanurum, Dalophis imberbis and Chlopsis bicolor. Collectively, these seven morphotypes are considered to be a good proxy for the Anguilliformes community (the main order of the Elopomorpha) in the southern Adriatic Sea (to date, seven families and sixteen species have been recorded in this region). Interestingly, the higher number of G. mystax larvae collected suggests an increased abundance of this genus. To validate the morphological identifications, we sequenced 61 leptocephali (at a 655 bp fragment from the cytochrome oxidase subunit 1 mitochondrial region) and developed barcode vouchers for the seven morphotypes. Using genetic information from reference databases, we validated three of these morphotypes. Where reference sequences were unavailable, we generated barcodes for both adult and juvenile forms to provide additional genetic information. Using this integrated approach allowed us to characterize a new species of Facciolella in the Adriatic Sea for the first time. Moreover, we also revealed a lack of differentiation, at the species level, between G. mistax and G. bathytopos, a western Atlantic Ocean species. Our morphological and barcode data have been published in the Barcoding of the Adriatic Leptocephali database. This work represents the first contribution to a wider project that aims to create a barcode database to support the assessment of leptocephali diversity in the Mediterranean Sea.

A new species of elongate unpatterned moray eel of the genus Gymnothorax (Muraenidae: Muraeninae) from the Bay of Bengal.

An elongate, brown unpatterned moray eel, Gymnothorax indicus sp. nov., is described based on four specimens collected from the northern Bay of Bengal. The new species is differentiated from other elongate, unpatterned moray eels in having the following combination of characters: anus at about mid-point of body, preanal length 2.0 in total length; snout blunt and short; dorsal fin margin black, 5 mandibular pores; maxillary teeth uniserial, sharp and depressible, total vertebrae 194 (MVF: 9-79-194).

A giant anguilliform leptocephalus Thalassenchelys foliaceus Castle & Raju is a junior synonym of Congriscus maldivensis (Norman 1939).

A single specimen of giant leptocephalus Thalassenchelys foliaceus Castle & Raju 1975 was caught in subtropical waters of the western North Pacific Ocean. Mitochondrial coI gene sequence divergence between T. foliaceus and Congriscus maldivensis (Norman 1939) was 0·64 ± 0·27% (mean ± s.e.), and the myomere and vertebral counts of these species were similar, indicating T. foliaceus is a junior synonym of C. maldivensis.

Evolution of the locomotory system in eels (Teleostei: Elopomorpha).

BACKGROUND: Living anguilliform eels represent a distinct clade of elongated teleostean fishes inhabiting a wide range of habitats. Locomotion of these fishes is highly influenced by the elongated body shape, the anatomy of the vertebral column, and the corresponding soft tissues represented by the musculotendinous system. Up to now, the evolution of axial elongation in eels has been inferred from living taxa only, whereas the reconstruction of evolutionary patterns and functional ecology in extinct eels still is scarce. Rare but excellently preserved fossil eels from the Late Cretaceous and Cenozoic were investigated here to gain a better understanding of locomotory system evolution in anguilliforms and, consequently, their habitat occupations in deep time. RESULTS: The number of vertebrae in correlation with the body length separates extinct and extant anguilliforms. Even if the phylogenetic signal cannot entirely be excluded, the analyses performed here reveal a continuous shortening of the vertebral column with a simultaneous increase in vertebral numbers in conjunction with short lateral tendons throughout the order. These anatomical changes contradict previous hypotheses based on extant eels solely. CONCLUSIONS: The body curvatures of extant anguilliforms are highly flexible and can be clearly distinguished from extinct species. Anatomical changes of the vertebral column and musculotendinous system through time and between extinct and extant anguilliforms correlate with changes of the body plan and swimming performance and reveal significant shifts in habitat adaptation and thus behaviour. Evolutionary changes in the skeletal system of eels established here also imply that environmental shifts were triggered by abiotic rather than biotic factors (e.g., K/P boundary mass extinction event).

A new species of Apterichtus (Anguilliformes: Ophichthidae) from the Marquesas Islands.

A new finless ophichthid eel, Apterichtus succinus sp. nov., is described based on a single specimen collected from the Marquesas Islands. The new species closely resembles A. klazingai Weber, 1913 in the shape and coloration of its head and its total vertebral count. The former differs from the latter in having more preopercular pores (4 vs. 3), fewer preanal vertebrae (54 vs. 56-63), a single tooth on the prevomer (generally absent), a shorter head (14.8 in TL vs. 12-14 in TL), and larger spots on its head and nape. Three species of Apterichtus (A. succinus, A. klazingai, and Apterichtus mysi McCosker & Hibino, 2015) are recognized from the Marquesas Islands.

Phylogenetic relationships of twenty Gymnothorax species based on cytochrome b sequence data.

To study the phylogenetic relationships of the genus Gymnothorax (moray eels) distributed in South China Sea, polymerase chain reactions were performed, and the amplification products were sequenced by cloning into the PMD18T-vector (TaKaRa). The entire gene sequences encoding cytochrome b (1140 bp) for 16 Gymnothorax (G. flavimarginatus, G. meleagris, G. undulates, G. reticularis, G. reevesi, G. melanospilus, G. rueppeliae, G. javanicus, G. chilospilus, G. pseudothyrsoideus, G. fimbriatus, G. hepaticus, G. berndti, G. curostus, G. favagineus, and G. margaritophorus) were obtained. Four additional Gymnothorax sequences from GenBank were also included. The nucleotide composition, genetic distances, and base substitution saturation analysis were calculated using the MEGA 5.0 Software. Phylogenetic analysis was performed using maximum-parsimony, maximum-likelihood (ML), and neighbor-joining (NJ). The results were as follows: 1) base-substitution saturation analysis suggested that both in third codon positions, and the full-length cytochrome b data set, Ts are not saturated, but Tv substitutions may be saturated, 2) the genus Gymnothorax, native to the South China Sea, is divided into four distinct clades, with two clades in the NJ and ML trees, and 3) according to our experimental data, G. melanospilus (Bleeker, 1855) and G. favagineus (Bloch and Schneider, 1801) are the same species.

Complete mitogenome of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae).

In this study, the complete mitogenome sequence of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome, with the length of 16,558 bp for G. formosus and 16,521 bp for S. tigrina, shows 78% identity to each other. Both mitogenomes follow the typical vertebrate arrangement, including 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region of D-loop. The length of D-loop is 927 bp (G. formosus) and 850 bp (S. tigrina), which is located between tRNA-Pro and tRNA-Phe. The overall GC content is 45.5% for G. formosus and 47.9% for S. tigrina. Complete mitogenomes of G. formosus and S. tigrina provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for moray eel.