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Our new study of the species originally included in the genus Allolepidotus led to the taxonomic revision of the halecomorph species from the Triassic of Perledo, Italy. The morphological variation revealed by the analysis of the type material is sufficient to confirm four different taxa represented in the Perledo Formation. We correct the misunderstanding about the type species of Allolepidotus, which is A. ruppelii and not "A." bellottii as considered in the literature over the past two decades. The latter species was originally placed in the genus Semionotus. Fossils from the Kalkschieferzone of Besnasca/Ca' del Frate (Viggiù-Varese, Italy) and Meride (Ticino, Switzerland) which were referred to Allolepidotus, rather represent a species of Eoeugnathus. Therefore, we transfer the species Semionotus bellottii to that genus and propose the new combination E. bellottii. The second and only other species originally included in the genus Allolepidotus is transferred here to the new genus Perledovatus. The holotype of P. nothosomoides new comb. has been mechanically prepared, revealing additional anatomical information that allows to place this taxon in the halecomorph family Subortichthyidae. The other halecomorph species named from the Perledo Formation, Pholidophorus oblongus and Pholidophorus curionii, have been treated as junior synonyms of E. bellottii, but our analysis indicates that they represent distinct separate taxa. However, due to the loss of the type specimens, it is not possible to decide whether they might have been conspecific with other ray-finned fishes from the Middle Triassic of the Alps. [ABSTRACT FROM AUTHOR]

With the rapid development of next-generation sequencing technologies and bioinformatics, over 50 ray-finned fish genomes by far have been sequenced with high quality. The genomic work provides abundant genetic resources for deep understanding of divergence, evolution and adaptation in the fish genomes. They are also instructive for identification of candidate genes for functional verification, molecular breeding, and development of novel marine drugs. As an example of other omics data, the Fish-T1K project generated a big database of fish transcriptomes to integrate with these published fish genomes for potential applications. In this review, we highlight the above-mentioned recent investigations and core topics on the ray-finned fish genome research, with a main goal to obtain a deeper understanding of fish biology for theoretical and practical applications. [ABSTRACT FROM AUTHOR]

The proteasome subunit beta type 8 ( PSMB8) gene encodes a catalytic subunit of immunoproteasome that plays a central role in the processing of antigenic peptides presented by major histocompatibility complex class I molecules. The A- and F-type alleles defined by the 31st amino acid residue determining cleaving specificity have been identified from ray-finned fish, amphibia, and reptiles. These two types show extremely long-term trans-species polymorphism in Polypteriformes, Cypriniformes, and Salmoniformes, suggesting the presence of very ancient lineages termed A and F. To elucidate the evolution of the PSMB8 dimorphism in basal ray-finned fish, we analyzed Pantodon buchholzi (Osteoglossiformes), seven species of Anguilliformes, and Hypomesus nipponensis (Osmeriformes). Both A and F lineage sequences were identified from P. buchholzi and H. nipponensis, confirming that these two lineages have been conserved by basal ray-finned fish. However, both the A- and F-type alleles found in Anguilliformes species belonged to the F lineage irrespective of their types. This apparently suggests that the A lineage was lost in the common ancestor of Anguilliformes, and recovery of the A type within the F lineage occurred in Anguilliformes. The apparent loss of the F lineage and recovery of the F type within the A lineage have already been reported from tetrapods and higher teleosts. However, this is the first report on the reverse situation and reveals the dynamic evolution of the PSMB8 dimorphism. [ABSTRACT FROM AUTHOR]

Meyer and Wilson's (1990) 12S rRNA phylogeny unites lungfish and tetrapods to the exclusion of the coelacanth. These workers also provide a list of morphological features shared in common between modern lungfish and tetrapods, and they conclude that these traits were probably present in their last common ancestor. However, the exquisite fossil records of the abundant extinct lungfishes and rhipidistians show that at least 13 out of Meyer and Wilson's 14 supposed ancestral traits were not present in the last common ancestor of lungfishes and tetrapods. Using extant taxa to infer ancestral morphologies is fraught with difficulties; just like molecular sequences, ancestral character states of morphological traits may be severely overprinted by subsequent modifications. Modern lungfish are air-breathing nonmarine forms, yet their Devonian forebears were marine fish that did not breathe air. Fossils dating from the time of origin of tetrapods in the Devonian offer the only hope of understanding the morphological innovations that led to tetrapods; morphological analysis of the 'living fossils,' the coelacanth and lungfish, only lends confusion. [ABSTRACT FROM AUTHOR]