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Osteobrama peninsularis has been reported in southern Indian drainages, particularly in the Krishna River drainage. This study provides new findings of O. peninsularis in two distant locations: the Kangsabati River (Suvarnarekha River drainage) in West Bengal and Wyra Lake (Godavari River drainage) in Telangana. This marks the first record of O. peninsularis in eastern India, specifically in West Bengal. The species can be distinguished from other Osteobrama members by its 28--31 branched anal-fin rays and 55--60 lateral line scales, along with other unique morphological features. Mitochondrial cytochrome oxidase C subunit I gene sequences from specimens collected in Suvarnarekha and Godavari River drainages cluster together in the phylogenetic analysis, indicating that the clade of O. peninsularis is distinct and maintains significant genetic distance from its congeners. [ABSTRACT FROM AUTHOR]

Abstract 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.

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]

The assembly of complete and circularized mitochondrial genomes (mitogenomes) is essential for population genetics, phylogenetics and evolution studies. Recently, Song et al. developed a seed-free tool called MEANGS for de novo mitochondrial assembly from whole genome sequencing (WGS) data in animals, achieving highly accurate and intact assemblies. However, the suitability of this tool for marine fish remains unexplored. Additionally, we have concerns regarding the overlap sequences in their original results, which may impact downstream analyses. In this Letter to the Editor, the effectiveness of MEANGS in assembling mitogenomes of cartilaginous and ray-finned fish species was assessed. Moreover, we also discussed the appropriate utilization of MEANGS in mitogenome assembly, including the implementation of the data-cut function and circular detection module. Our observations indicated that with the utilization of these modules, MEANGS efficiently assembled complete and circularized mitogenomes, even when handling large WGS datasets. Therefore, we strongly recommend users employ the data-cut function and circular detection module when using MEANGS, as the former significantly reduces runtime and the latter aids in the removal of overlapped sequences for improved circularization. Furthermore, our findings suggested that approximately 2× coverage of clean WGS data was sufficient for MEANGS to assemble mitogenomes in marine fish species. Moreover, due to its seed-free nature, MEANGS can be deemed one of the most efficient software tools for assembling mitogenomes from animal WGS data, particularly in studies with limited species or genetic background information. [ABSTRACT FROM AUTHOR]

Aquaporin (Aqp) 10 is a member of the aquaglyceroporin subfamily of water channels, and human Aqp10 is permeable to solutes such as glycerol, urea, and boric acid. Tetrapods have a single aqp10 gene, whereas ray-finned fishes have paralogs of this gene through tandem duplication, whole-genome duplication, and subsequent deletion. A previous study on Aqps in the Japanese pufferfish Takifugu rubripes showed that one pufferfish paralog, Aqp10.2b, was permeable to water and glycerol, but not to urea and boric acid. To understand the functional differences of Aqp10s between humans and pufferfish from an evolutionary perspective, we analyzed Aqp10s from an amphibian (Xenopus laevis) and a lobe-finned fish (Protopterus annectens) and Aqp10.1 and Aqp10.2 from several ray-finned fishes (Polypterus senegalus , Lepisosteus oculatus , Danio rerio , and Clupea pallasii). The expression of tetrapod and lobe-finned fish Aqp10s and Aqp10.1-derived Aqps in ray-finned fishes in Xenopus oocytes increased the membrane permeabilities to water, glycerol, urea, and boric acid. In contrast, Aqp10.2-derived Aqps in ray-finned fishes increased water and glycerol permeabilities, whereas those of urea and boric acid were much weaker than those of Aqp10.1-derived Aqps. These results indicate that water, glycerol, urea, and boric acid permeabilities are plesiomorphic activities of Aqp10s and that the ray-finned fish-specific Aqp10.2 paralogs have secondarily reduced or lost urea and boric acid permeability. [ABSTRACT FROM AUTHOR]

Alcichthys elongatus is the only species in the genus, and this work is the first to provide a comprehensive mitogenome analysis of this species. The A. elongatus mitogenome was 16,712 bp long, with biased A + T content (52.33%), and featured thirteen protein-coding genes (PCGs), twenty-two tRNAs, two rRNAs, and the control region (D-loop). The H strand encoded twenty-eight genes (twelve PCGs, fourteen tRNA, and two rRNA) and the control region, whereas the L strand encoded the remaining nine genes (ND6 and eight tRNA). Except for COXI, which started with GTG, all PCG sequences started with ATG and ended with TAA (ND4L, ND5, COXI, ATP8) or TAG (ND1, ND6) termination codons, with some (ND2, ND3, ND4, COXII, COXIII, ATP6, Cytb) having an incomplete termination codon. Except for tRNA-serine-1 (trnS), the majority of the tRNAs exhibited characteristic cloverleaf secondary structures. Based on 13 PCGs, phylogenetic analysis placed A. elongatus in the same clade as Icelus spatula. This genomic data will be useful for species identification, phylogenetic analysis, and population genetics. [ABSTRACT FROM AUTHOR]

Fish (Elasmobranchia and Actinopterygii) inhabit the majority of aquatic habitats globally. They are crucial for human nutrition but they may be negatively affected by parasitic protists and metazoan parasites. Fish parasites are also an extraordinary group of animals because of their ecological and evolutionary importance and unique adaptations to parasitism. They also play a key role in ecosystem functioning. In the present special issue, 13 review and research articles on major groups of fish parasites are provided to document the current advancement in our understanding of different aspects of their biology, ecology and associations with their fish hosts. The existing gaps in our knowledge of these peculiar animals are mapped and future trends in their research outlined. [ABSTRACT FROM AUTHOR]

The tapeworms of fishes (Chondrichthyes and Actinopterygii) account one-third (1670 from around 5000) of the total tapeworm (Platyhelminthes: Cestoda) species diversity. In total 1186 species from 9 orders occur as adults in elasmobranchs (sharks, rays and chimaeras), and 484 species from 8 orders mature in ray-finned fishes (referred to here as teleosts). Teleost tapeworms are dominated by freshwater species (78%), but only 3% of elasmobranch tapeworms are known from freshwater rays of South America and Asia (Borneo). In the last 2 decades, vast progress has been made in understanding species diversity, host associations and interrelationships among fish tapeworms. In total, 172 new species have been described since 2017 (149 from elasmobranchs and 23 from teleosts; invalidly described taxa are not included, especially those from the Oriental region). Molecular data, however, largely limited to a few molecular markers (mainly 28S rDNA, but also 18S and cox 1), are available for about 40% of fish tapeworm species. They allowed us to significantly improve our understanding of their interrelationships, including proposals of a new, more natural classification at the higher-taxonomy level (orders and families) as well as at the lower-taxonomy level (genera). In this review, we summarize the main advances and provide perspectives for future research. [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 globin gene family encodes oxygen-binding hemeproteins conserved across themajor branches of multicellular life. The origins and evolutionary histories of complete globin repertoires have been established for many vertebrates, but there remain major knowledge gaps for ray-finned fish. Therefore, we used phylogenetic, comparative genomic and gene expression analyses to discover and characterize canonical "non-blood" globin family members (i.e., myoglobin, cytoglobin, neuroglobin, globin-X, and globin-Y) across multiple ray-finned fish lineages, revealing novel gene duplicates (paralogs) conserved from whole genome duplication( WGD) andsmall-scaleduplication events. Our key findings were that: (1) globin-Xparalogs in teleosts havebeenretained from the teleost-specific WGD, (2) functional paralogs of cytoglobin, neuroglobin, and globin-X, but notmyoglobin, have been conserved from the salmonid-specific WGD, (3) triplicate lineage-specificmyoglobin paralogs are conserved in arowanas (Osteoglossiformes), which arose by tandem duplication and diverged under positive selection, (4) globin-Y is retained in multiple early branching fish lineages that diverged before teleosts, and (5) marked variation in tissue-specific expression of globin gene repertoires exists across ray-finned fish evolution, including several previously uncharacterized sites of expression. In this respect, our data provide an interesting link between myoglobin expression and the evolution of air breathing in teleosts. Together, our findings demonstrate greatunrecognized diversity in the repertoire and expression of nonblood globins that has arisen during ray-finned fish evolution. [ABSTRACT FROM AUTHOR]

Determining the phylogenetic relationship of two extant lineages of lobe-finned fish, coelacanths and lungfishes, and tetrapods is important for understanding the origin of tetrapods. We analyzed data sets from two previous studies along with a newly collected data set, each of which had varying numbers of species and genes and varying extent of missing sites. We found that in all the data sets the sister relationship of lungfish and tetrapods was constructed with the use of cartilaginous fish as the outgroup with a high degree of statistical support. In contrast, when ray-finned fish were used as the outgroup, which is taxonomically an immediate outgroup of lobe-finned fish and tetrapods, the sister relationship of coelacanth and tetrapods was supported most strongly, although the statistical support was weaker. Even though it is generally accepted that the closest relative is an appropriate outgroup, our analysis suggested that the large divergence of the ray-finned fish as indicated by their long branch lengths and different amino acid frequencies made them less suitable as an outgroup than cartilaginous fish. [ABSTRACT FROM AUTHOR]

The emergence of the steroid system is coupled to the evolution of multicellular animals. In vertebrates in particular, the steroid receptor repertoire has been shaped by genome duplications characteristic to this lineage. Here, we investigate for the first time the composition of the androgen receptor-signaling pathway in ray-finned fish genomes by focusing in particular on duplicates that emerged from the teleost-specific whole-genome duplication. We trace lineage- and species-specific duplications and gene losses for the genomic and nongenomic pathway of androgen signaling and subsequently investigate the sequence evolution of these genes. In one particular fish lineage, the cichlids, we find evidence for differing selection pressures acting on teleost-specific whole-genome duplication paralogs at a derived evolutionary stage. We then look into the expression of these duplicated genes in four cichlid species from Lake Tanganyika indicating, once more, rapid changes in expression patterns in closely related fish species. We focus on a particular case, the cichlid specific duplication of the rac1 GTPase, which shows possible signs of a neofunctionalization event. [ABSTRACT FROM AUTHOR]

Current research on the thalamus and related structures in the zebrafish diencephalon identifies an increasing number of both neurological structures and ontogenetic processes as evolutionary conserved between teleosts and mammals. The patterning processes, for example, which during the embryonic development of zebrafish form the thalamus proper appear largely conserved. Yet also striking differences between zebrafish and other vertebrates have been observed, particularly when we look at mature and histologically differentiated brains. A case in point is the migrated preglomerular complex of zebrafish which evolved only within the lineage of ray-finned fish and has no counterpart in mammals or tetrapod vertebrates. Based on its function as a sensory relay station with projections to pallial zones, the preglomerular complex has been compared to specific thalamic nuclei in mammals. However, no thalamic projections to the zebrafish dorsal pallium, which corresponds topologically to the mammalian isocortex, have been identified. Merely one teleostean thalamic nucleus proper, the auditory nucleus, projects to a part of the dorsal telencephalon, the pallial amygdala. Studies on patterning mechanisms identify a rostral and caudal domain in the embryonic thalamus proper. In both, teleosts and mammals, the rostral domain gives rise to GABAergic neurons, whereas glutamatergic neurons originate in the caudal domain of the zebrafish thalamus. The distribution of GABAergic derivatives in the adult zebrafish brain, furthermore, revealed previously overlooked thalamic nuclei and redefined already established ones. These findings require some reconsideration regarding the topological origin of these adult structures. In what follows, I discuss how evolutionary conserved and newly acquired features of the developing and adult zebrafish thalamus can be compared to the mammalian situation. [ABSTRACT FROM AUTHOR]

Data partitioning, the combined phylogenetic analysis of homogeneous blocks of data, is a common strategy used to accommodate heterogeneities in complex multilocus data sets. Variation in evolutionary rates and substitution patterns among sites are typically addressed by partitioning data by gene, codon position, or both. Excessive partitioning of the data, however, could lead to overparameterization; therefore, it seems critical to define the minimum numbers of partitions necessary to improve the overall fit of the model. We propose a new method, based on cluster analysis, to find an optimal partitioning strategy for multilocus protein-coding data sets. A heuristic exploration of alternative partitioning schemes, based on Bayesian and maximum likelihood (ML) criteria, is shown here to produce an optimal number of partitions. We tested this method using sequence data of 10 nuclear genes collected from 52 ray-finned fish (Actinopterygii) and four tetrapods. The concatenated sequences included 7995 nucleotide sites maximally split into 30 partitions defined a priori based on gene and codon position. Our results show that a model based on only 10 partitions defined by cluster analysis performed better than partitioning by both gene and codon position. Alternative data partitioning schemes also are shown to affect the topologies resulting from phylogenetic analysis, especially when Bayesian methods are used, suggesting that overpartitioning may be of major concern. The phylogenetic relationships among the major clades of ray-finned fish were assessed using the best data-partitioning schemes under ML and Bayesian methods. Some significant results include the monophyly of “Holostei” (Amia and Lepisosteus), the sister-group relationships between (1) esociforms and salmoniforms and (2) osmeriforms and stomiiforms, the polyphyly of Perciformes, and a close relationship of cichlids and atherinomorphs. [ABSTRACT FROM PUBLISHER]

Abstract: Extensive evidence exists for a genome duplication in the fish lineage leading to the species-rich clade of the teleosts, comprising > 99% of the known actinopterygian (ray-finned) fish species. Our previous studies of the neuropeptide Y receptor (NPYR) gene family suggested an ancestral gnathostome repertoire of 7 genes in 3 subfamilies. However, studies in the zebrafish have earlier identified only 5 NPYR genes, despite the expected increase in gene number due to the teleost tetraploidization. Notably, receptors Y1, Y5 and Y6 were missing in the zebrafish genome database and only Y8 had been duplicated. We report here an investigation of the evolutionary history of the Y1 subfamily (Y1, Y4, Y6 and Y8) and the Y5 receptor. Seven basal actinopterygian species and a shark were investigated and a total of 22 gene fragments were cloned and analyzed. Our results show that subtypes Y1, Y5 and Y6 still exist in species representing basal actinopterygian lineages (bichir, sturgeon, gar and bowfin) as well as in some basal teleost lineages. Surprisingly we identified a zebrafish Y1 receptor, the first Y1 receptor found in euteleosts. Thus, these findings confirm the ancestral gnathostome repertoire of 7 NPYR genes and show that many of these receptors are present in basal actinopterygians as well as some basal teleosts. NPYR losses seem to have occurred relatively recently in euteleosts because Y1, Y5 and Y6 are absent in the genome databases of two pufferfishes as well as medaka and stickleback and Y5 and Y6 are absent in the zebrafish database. A duplicate of Y8 seems to be the only remaining receptor gene resulting from the teleost tetraploidization. The unexpected absence of the two appetite-stimulating receptors Y1 and Y5 in some euteleosts, along with our discovery of duplicates of the peptide ligands NPY and PYY, has implications for the role of the NPY system in euteleost feeding behavior. [Copyright &y& Elsevier]

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]