Rhodopsin gene evolution in early teleost fishes.

Rhodopsin mediates an essential step in image capture and is tightly associated with visual adaptations of aquatic organisms, especially species that live in dim light environments (e.g., the deep sea). The rh1 gene encoding rhodopsin was formerly considered a single-copy gene in genomes of vertebrates, but increasing exceptional cases have been found in teleost fish species. The main objective of this study was to determine to what extent the visual adaptation of teleosts might have been shaped by the duplication and loss of rh1 genes. For that purpose, homologous rh1/rh1-like sequences in genomes of ray-finned fishes from a wide taxonomic range were explored using a PCR-based method, data mining of public genetic/genomic databases, and subsequent phylogenomic analyses of the retrieved sequences. We show that a second copy of the fish-specific intron-less rh1 is present in the genomes of most anguillids (Elopomorpha), Hiodon alosoides (Osteoglossomorpha), and several clupeocephalan lineages. The phylogenetic analysis and comparisons of alternative scenarios for putative events of gene duplication and loss suggested that fish rh1 was likely duplicated twice during the early evolutionary history of teleosts, with one event coinciding with the hypothesized fish-specific genome duplication and the other in the common ancestor of the Clupeocephala. After these gene duplication events, duplicated genes were maintained in several teleost lineages, whereas some were secondarily lost in specific lineages. Alternative evolutionary schemes of rh1 and comparison with previous studies of gene evolution are also reviewed.

First record of Gauguin's blunt-nose lizardfish, Trachinocephalus gauguini Polanco, Acero Betancur 2016 (Teleostei: Synodontidae) outside the Marquesas Archipelago.

Trachinocephalus gauguini Polanco, Acero Betancur, 2016 was described based on eighteen specimens collected from off the Marquesas Islands, the only location where this species has been recorded until now. Through morphological and molecular examination of Trachinocephalus specimens collected from an exploratory cruise conducted in June 2014 under the Tropical Deep-Sea Benthos program along the northern coast of the New Ireland Province, Papua New Guinea, we demonstrate the presence of this species in Papua New Guinea waters. This new record suggests a wide distribution for this rarely collected species in the western Pacific Ocean.

New case of lateral asymmetry in fishes: A new subfamily, genus and species of deep water clingfishes from Papua New Guinea, western Pacific Ocean.

The unusual clingfish Protogobiesox asymmetricus n. gen, n. sp. is described on the basis of four specimens collected in deep water off the north coast of Papua New Guinea in 2012. The species is characterized by its 9-10 dorsal rays, 8 anal rays, 17-24 pectoral-fin rays, 15 principal caudal-fin rays, 3 gills, third arch with 3 gill rakers, 34-35 total vertebrae, with asymmetrical lateral bending starting behind the skull, bent at an angle of 85°-92°; skull asymmetrical in frontal view; skin naked, surface of head and body without striae; disc without adhesive papillae. A new subfamily Protogobiesocinae is described for this species and Lepadicyathus mendeleevi Prokofiev, 2005, which is redescribed. The new subfamily is compared within the family; keys to the subfamilies of Gobiesocidae and the species within the new subfamily are presented; its phylogenetic relationship to other gobiesocids is inferred based on a multi-locus DNA dataset.

Phylogeny of the Elopomorpha (Teleostei): evidence from six nuclear and mitochondrial markers.

The Elopomorpha (eels and relatives) is a morphologically diverse group of predominantly marine teleost fishes comprising about 1000 species placed in 25 families. It is one of the three major living teleost lineages along with the Osteoglossomorpha and Clupeocephala. Among a few morphological synapomorphies that have been offered as evidence for the monophyly of the Elopomorpha, the remarkable leptocephalus larvae stand out. Several studies aiming at reconstructing the elopomorph phylogeny using morphological or molecular characters led to inconsistent results. In this study, we have tested previous hypotheses regarding inter- and intra-relationships of the Elopomorpha using a multi-locus dataset composed of three nuclear and three mitochondrial genes. Our analyses were based on likelihood phylogenetic reconstruction methods using different character-weighting data matrices and gene partition schemes to assess reliability of our findings. Our results confirm the respective monophyly of the Elopomorpha, Osteoglossomorpha and Clupeocephala. The majority of our analyses identify the Elopomorpha as the sister group of a clade containing the rest of the Teleostei. Within the Elopomorpha, the Elopiformes is the sister group of the remaining taxa. The Albuliformes sensuForey et al. (1996) and the Notacanthiformes are never sister-taxa in our phylogenetic trees, in contradiction with the recent mitogenomic hypothesis and current classification. Our results place the Notacanthiformes as the sister group of the Anguilliformes, including Saccopharyngiformes. Among anguilliforms, the families Congridae and Muraenesocidae are not monophyletic. The recently discovered anguilliform "living fossil" family Protanguillidae is not the sister group of the remaining Anguilliformes, instead, the sister group of the Synaphobranchidae. Based on the results presented here, we propose a revised classification for the Elopomorpha, comprised of four orders, including a resurrected Notacanthiformes but surrendering the Saccopharyngiformes. Within Anguilliformes, we recognized four monophyletic suborders named Protanguilloidei, Muraenoidei, Anguilloidei, and Congroidei.