Evolution Of Fishes Research Articles

Fish body size influenced by multiple drivers

There is evidence that organisms have become smaller during the past periods of global warming. Global change has substantial effects on biodiversity, with body size reduction being the third most common response to global warming. Body size allometry in ectotherms needs to be explored further; the objectives of this study were to better understand the mechanisms regulating body size in fish by testing: 1) Bergmann's rule with temperature and elevation, 2) additional environmental drivers, 3) the role of isolation, 4) ecoevolutionary hypotheses comparing native and exotic species and 5) the role of migration propensity in comparing migratory and resident species. We analyzed an extensive dataset of Chilean fish composed of 75 198 records which included 25 species from 12 different families between latitudes −28.80 to −51.42 using linear mixed models to discern the best environmental variables contributing to body size changes, as well as incorporating factors related to dispersal capabilities, biogeographic isolation and levels of exotic/native interactions. Bergmann's rule is supported by changes in elevation, and our study shows that freshwater fish body size also increases with increasing environmental heterogeneity and productivity. In general, inland native fish tend to be smaller than coastal ones, supporting the island rule with evidence of gigantism or dwarfism in selected species. Ecological variables affecting fish body size do not differ between native and exotic fish unless other factors are considered, such as dispersal capacity (migrating vs resident fish) or mechanisms related to their isolation. Although temperature is not a direct driver of body size in Chilean fish, heterogeneity, productivity, geography, migratory ability and species origin may affect body size. A better understanding of the mechanisms driving body size in ectotherms will aid in determining management priorities in the face of global climate disruption.

Nursery origin of yellowfin tuna in the western Atlantic Ocean: significance of Caribbean Sea and trans-Atlantic migrants

Natural geochemical markers in the otolith of yellowfin tuna (Thunnus albacares) were used to establish nursery-specific signatures for investigating the origin of fish captured in the western Atlantic Ocean (WAO). Two classes of chemical markers (trace elements, stable isotopes) were used to first establish nursery-specific signatures of age-0 yellowfin tuna from four primary production zones in the Atlantic Ocean: Gulf of Mexico, Caribbean Sea, Cape Verde, and Gulf of Guinea. Next, mixture and individual assignment methods were applied to predict the origin of sub-adult and adult yellowfin tuna from two regions in the WAO (Gulf of Mexico, Mid Atlantic Bight) by relating otolith core signatures (corresponding to age-0 period) to baseline signatures of age-0 fish from each nursery. Significant numbers of migrants from Caribbean Sea and eastern Atlantic Ocean (EAO) production zones (Gulf of Guinea, Cape Verde) were detected in the WAO, suggesting that fisheries in this region were subsidized by outside spawning/nursery areas. Contributions from local production (Gulf of Mexico) were also evident in samples from both WAO fisheries, but highly variable from year to year. High levels of mixing by yellowfin tuna from the different production zones and pronounced interannual trends in nursery-specific contribution rates in the WAO emphasize the complex and dynamic nature of this species’ stock structure and population connectivity. Given that geographic shifts in distribution across national or political boundaries leads to governance and management challenges, this study highlights the need for temporally resolved estimates of nursery origin to refine assessment models and promote the sustainable harvest of this species.

Genome-Wide Identification of Trachinotus ovatus Antimicrobial Peptides and Their Immune Response against Two Pathogen Challenges.

Golden pompano, Trachinotus ovatus, as a highly nutritious commercially valuable marine fish, has become one of the preferred species for many fish farmers due to its rapid growth, wide adaptability, and ease of feeding and management. However, with the expansion of aquaculture scale, bacterial and parasitic diseases have also become major threats to the golden pompano industry. This study, based on comparative genomics, shows the possibility of preferential evolution of freshwater fish over marine fish by analyzing the phylogenetic relationships and divergence times of 14 marine fish and freshwater fish. Furthermore, we identified antimicrobial peptide genes from 14 species at the genomic level and found that the number of putative antimicrobial peptides may be related to species evolution. Subsequently, we classified the 341 identified AMPs from golden pompano into 38 categories based on the classification provided by the APD3. Among them, TCP represented the highest proportion, accounting for 23.2% of the total, followed by scolopendin, lectin, chemokine, BPTI, and histone-derived peptides. At the same time, the distribution of AMPs in chromosomes varied with type, and covariance analysis showed the frequency of its repeat events. Enrichment analysis and PPI indicated that AMP was mainly concentrated in pathways associated with disease immunity. In addition, our transcriptomic data measured the expression of putative AMPs of golden pompano in 12 normal tissues, as well as in the liver, spleen, and kidney infected with Streptococcus agalactiae and skin infected with Cryptocaryon irritans. As the infection with S. agalactiae and C. irritans progressed, we observed tissue specificity in the number and types of responsive AMPs. Positive selection of AMP genes may participate in the immune response through the MAPK signaling pathway. The genome-wide identification of antimicrobial peptides in the golden pompano provided a complete database of potential AMPs that can contribute to further understanding the immune mechanisms in pathogens. AMPs were expected to replace traditional antibiotics and be developed into targeted drugs against specific bacterial and parasitic pathogens for more precise and effective treatment to improve aquaculture production.

Comparative Mitogenome Analyses Uncover Mitogenome Features and Phylogenetic Implications of the Reef Fish Family Holocentridae (Holocentriformes).

To understand the molecular mechanisms and adaptive strategies of holocentrid fish, we sequenced the mitogenome of eight species within the family Holocentridae and compared them with six other holocentrid species. The mitogenomes were found to be 16,507-16,639 bp in length and to encode 37 typical mitochondrial genes, including 13 PCGs, two ribosomal RNAs, and 22 transfer RNA genes. Structurally, the gene arrangement, base composition, codon usage, tRNA size, and putative secondary structures were comparable between species. Of the 13 PCGs, nad6 was the most specific gene that exhibited negative AT-skews and positive GC-skews. Most of the genes begin with the standard codon ATG, except cox1, which begins with the codon GTG. By examining their phylogeny, Sargocentron and Neoniphon were verified to be closely related and to belong to the same subfamily Holocentrinae, while Myripristis and Ostichthys belong to the other subfamily Myripristinae. The subfamilies were clearly distinguished by high-confidence-supported clades, which provide evidence to explain the differences in morphology and feeding habits between the two subfamilies. Selection pressure analysis indicated that all PCGs were subject to purifying selection. Overall, our study provides valuable insight into the habiting behavior, evolution, and ecological roles of these important marine fish.

Ecology, evolution and conservation of tidepool fishes of the Americas

Ecology, evolution and conservation of tidepool fishes of the Americas

Detection of clinically relevant carbapenemase encoding genes in carbapenem-resistant Enterobacter cloacae complex and Klebsiella pneumoniae isolated from farmed freshwater fish.

The present study was aimed to detect clinically relevant carbapenemase encoding genes in carbapenem-resistant Enterobacter cloacae complex (CR-ECC), Klebsiella pneumoniae (CR-KP), and Serratia plymuthica (CR-SP) isolated from farmed freshwater fish. Out of 243 spatially diverse freshwater fish samples analysed, 5.3% were contaminated with CR-ECC, 1.6% with CR-KP, and 0.4% with CR-SP. The CR-ECC was further identified as E. asburiae (38.5%), E. mori (23.1%), E. cloacae (15.4%), E. hormaechei (15.4%), and E. kobei (7.7%) by 16S rRNA gene sequencing. The CR-ECC were resistant to carbapenems and cefoxitin, whereas CR-KP and CR-SP were multi-drug resistant (MDR). The CR-ECC harboured the carbapenemase gene blaIMI alone or in combination with blaTEM, blaEBC, blaCIT, blaACC, and tet(E). Whereas, CR-KP harboured carbapenemase gene, blaNDM-5 along with blaOXA-48, blaSHV, blaOXA-1, blaCTX-M-15, tet(A), sul1, and qnrB. No carbapenemase-encoding genes were detected in CR-SP. The MLST analysis showed that CR-KP belonged to ST231 and ST1561 lineages, while CR-ECC did not show exact match with any reported STs. The plasmid replicons predominantly detected were IncF and IncI1. Broth mating assays of CR-KP and CR-ECC with recipient Escherichia coli J53 indicated that blaNDM-5 was transferable but not blaIMI. This study highlights the low-level contamination of carbapenem-resistant Enterobacterales (CRE) harbouring clinically relevant carbapenemase-encoding genes in farmed freshwater fish from India. The CR-ECC of fish origin did not show the potential to spread carbapenem resistance.

Microstructures, geochemistry, and geochronology of mica fish: Review and advances

Shear zones are one of the most conspicuous structures in orogenic and rifting settings, accommodating high strain, rock displacement and influencing magma emplacement and fluid flow. Since shear zones may be simultaneously or sequentially affected by multiple processes involving mineral reactions, variations in pressure-temperature conditions, fluid-rock interaction, and diffusion, determining the timing of such structures has been one of the major challenges for modern geochronology. Although low- (up to lower greenschist facies) and high-temperature shear zones (above amphibolite facies) are well-dated through low- and high-closure temperature minerals, medium-temperature shear zones developed within the critical temperature window of ∼450–550 °C, in which conventional chronometers such as 40Ar/39Ar and Rb–Sr applied to mica fish may or may not record the timing of deformation for multiple reasons (e.g., grain size, cooling rate, mineral composition, fluid activity, deformation, neo- and recrystallization). Here, we review the current knowledge on the evolution of mica fish and the effect of deformation on its chemical and isotopic systems. We evaluate the effect on the widely deployed in situ 40Ar/39Ar technique. Furthermore, we demonstrate the potential to assess mica fish evolution applying high-spatial resolution microstructural and chemical mapping techniques such as electron backscatter diffraction (EBSD), time-of-flight secondary ion mass spectrometry (ToF–SIMS) and in situ Rb–Sr via triple quadrupole inductively coupled plasma mass spectrometry (TQ-ICP-MS) to a case study of medium-temperature mylonites from the well-characterized Taxaquara shear zone, SE Brazil. We show that mica fish display complex microstructures with variable strain intensity, commonly with low strain inner cores and high strain edges and along kink planes. Strain shadows in mica fish are commonly characterized by low-strain fine-grained muscovite, suggesting recrystallization coeval with ductile deformation. Despite being intensely deformed, muscovite fish Rb–Sr retain the protolith age (c. 600 Ma), whereas recrystallized fine-grained muscovite yields the timing of deformation (c. 550–540 Ma). Synthetic shear bands cross-cutting coarse-grained muscovite fish induce muscovite recrystallization consistent with their distinct chemistry, with recrystallized muscovite characterized by higher Fe–Mg and lower Na suggesting fluid-assisted recrystallization under lower temperature compared to the muscovite fish host. We propose that these shear bands across mica fish play an important role by accommodating grain size reduction and subsequent deformation, leading to the formation of smaller individual mica fish. Grain size reduction, likely enhanced by dynamic precipitation (i.e., coeval crystal-plastic deformation and dissolution-precipitation creep), appears as the key recrystallization mechanism that allows low strain muscovite in strain shadows and shear bands to record the timing of deformation in medium-temperature shear zones, consistent with qualitative Sr diffusion modelling.

Whole-genome Comparisons Identify Repeated Regulatory Changes Underlying Convergent Appendage Evolution in Diverse Fish Lineages.

Fins are major functional appendages of fish that have been repeatedly modified in different lineages. To search for genomic changes underlying natural fin diversity, we compared the genomes of 36 percomorph fish species that span over 100 million years of evolution and either have complete or reduced pelvic and caudal fins. We identify 1,614 genomic regions that are well-conserved in fin-complete species but missing from multiple fin-reduced lineages. Recurrent deletions of conserved sequences in wild fin-reduced species are enriched for functions related to appendage development, suggesting that convergent fin reduction at the organismal level is associated with repeated genomic deletions near fin-appendage development genes. We used sequencing and functional enhancer assays to confirm that PelA, a Pitx1 enhancer previously linked to recurrent pelvic loss in sticklebacks, has also been independently deleted and may have contributed to the fin morphology in distantly related pelvic-reduced species. We also identify a novel enhancer that is conserved in the majority of percomorphs, drives caudal fin expression in transgenic stickleback, is missing in tetraodontiform, syngnathid, and synbranchid species with caudal fin reduction, and alters caudal fin development when targeted by genome editing. Our study illustrates a broadly applicable strategy for mapping phenotypes to genotypes across a tree of vertebrate species and highlights notable new examples of regulatory genomic hotspots that have been used to evolve recurrent phenotypes across 100 million years of fish evolution.

Karakteristik Morfometrik Hampala macrolepidota Kuhl & Van Hasselt, 1823 di Indonesia

Hampala macrolepidota is a native fish in Indonesia that has potential as an ornamental fish and a consumption fish. The research aims were to determine the geographical classifying of fish and to analyze morphometric characteristics of H.macrolepidota morphology. The research was conducted at Fish Biosystematics Laboratory, Biosystematics and Evolution Research Center-BRIN Cibinong. Sample measured were 371 wet-preserved specimens of H. macrolepidota from various water lotic and lentic habitats in Indonesia using standard morphometric and truss morphometric methods. The collected data was analyzed using significance test with Wilk’s Lambda. Research result showed there is a tendency standard morphometrics is more accurate than truss morphometrics for classified H.macrolepidota according to their distribution area in Indonesia. This shows that H. macrolepidota on the islands of Sumatera, Jawa, and Kalimantan have a high similarity is due to the fact that the three islands are part of the Sunda Shelf.

A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae.

Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches.

Effects of Salinity on Fertilization, Hatching, and Larval Performance of Longfin Smelt Spirinchus thaleichthys

Understanding the spawning and rearing habitats of fishes is critical to effective fisheries management and conservation. Longfin smelt Spirinchus thaleichthys is an imperiled migratory fish that is believed to spawn and rear in habitats of varying salinities; however, optimal conditions for each stage remain unknown. Here, we examined the effects of variation in salinity on egg fertilization, hatch success, and larval growth and survival. Eggs that were fertilized in freshwater (0.4 ppt) exhibited a significantly higher fertilization rate (81%) than those fertilized in brackish water (62% at 5 ppt), with no detectible effects of fish origin or female size. In contrast to fertilization rates, once the eggs were fertilized, their hatching rates were not affected by the fertilization salinity, incubation salinity, nor their interaction; however, hatching success and larval survival both increased with increasing maternal body mass. Larval growth rate appeared to be independent of salinity and maternal size. Taken together, the results indicate that fertilization is possible at a range of salinities, but optimal at lower salinities for longfin smelt; however, embryos and larvae can perform well across a range of salinities. Furthermore, results indicated that larger mothers produced high-quality offspring, a finding that supports the “bigger is better” paradigm in fisheries science and management. These results likely explain, in part, the spawning and rearing behaviors of wild longfin smelt and suggest that the conservation culture program would likely be optimized by utilizing freshwater fertilization and larger females as broodstock.

Selection on standing genetic variation mediates convergent evolution in extremophile fish.

Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish in the Poecilia mexicana species complex have independently evolved sulfide tolerance several times. Despite clear evidence for convergence at the phenotypic level in these fishes, it is unclear if the repeated evolution of hydrogen sulfide tolerance is the result of similar genomic changes. To address this gap, we used a targeted capture approach to sequence genes associated with sulfide processes and toxicity from five sulfidic and five nonsulfidic populations in the species complex. By comparing sequence variation in candidate genes to a reference set, we identified similar population structure and differentiation, suggesting that patterns of variation in most genes associated with sulfide processes and toxicity are due to demographic history and not selection. But the presence of tree discordance for a subset of genes suggests that several loci are evolving divergently between ecotypes. We identified two differentiation outlier genes that are associated with sulfide detoxification in the mitochondria that have signatures of selection in all five sulfidic populations. Further investigation into these regions identified long, shared haplotypes among sulfidic populations. Together, these results reveal that selection on standing genetic variation in putatively adaptive genes may be driving phenotypic convergence in this species complex.

Gelatine adhesives from mammalian and fish origins for historical art objects conservation: How do microstructural features determine physical and mechanical properties?

Gelatine adhesives aka ‘animal glues’ are water-soluble biopolymers used in historic objects such as wooden cabinets and panel paintings since ancient times. This paper investigates the correlations between microstructural features, namely triple helices, and macroscopic properties of four different types of gelatine adhesives, prevalently used in conservation practices, irrespective of the animal origin. These adhesives include bovine bone, bovine skin, rabbit skin, and fish glues. Thin adhesive films were produced via solution casting methods in controlled climate conditions and their thermal and mechanical properties, and moisture sensitivity were investigated. XRD as a non-destructive characterisation method demonstrated good agreement with DSC in the quantification of gelatine adhesive (animal glue) triple helix content irrespective of the animal origin. Linear correlations between triple helices and gel (Bloom) strength and tensile strain energy to failure (toughness) were found for all adhesive types. Dynamic vapour sorption experiments demonstrated that lower triple helix content is correlated with higher moisture sensitivity of the adhesives. Moreover, the effect of environmental RH on the thermal behaviour of adhesives was investigated by DSC. The results demonstrated that the increase in environmental RH causes a reduction in the adhesives' glass transition and denaturation temperatures whilst triple helix content did not alter. Bovine bone glue with the lowest triple helix content showed the least toughness and highest moisture sensitivity, whilst fish glue with the highest triple helix content was identified as the most flexible glue.

Phylogeography and demographic history of the cyprinid fish Barbodes semifasciolatus: implications for the history of landform changes in south mainland China, Hainan and Taiwan

Hainan Island and Taiwan Island are adjacent to the southern margin of mainland China and Vietnam. During glacial periods, global sea levels dropped, allowing that the land bridges connected the continental island and mainland, connecting rivers and providing dispersal opportunities that shaped the origin and diversification of freshwater fishes. Barbodes semifasciolatus is distributed in various water systems of Vietnam, Hainan, Taiwan, and southern mainland China and is restricted to the southern region of the Min River. Our study aimed to evaluate the genetic diversity and phylogeography of B. semifasciolatus using the mtDNA cyt b gene (1,141 bp). A total of 107 haplotypes were identified from 395 specimens in 23 populations, and high haplotype diversity (1.000) and low nucleotide diversity (0.0134) were detected. Mitochondrial phylogenetic analysis and haplotype network analyses revealed three major lineages according to geographical distribution. Lineage A was mainly distributed in Hainan Island, Vietnam and the southern region of the Pearl River in mainland China. Lineage B was distributed only in southeastern Hainan Island. Lineage C was distributed in the coastal rivers of mainland China and Taiwan. We suggest that the river in the Guangdong region is a colonization route in South Taiwan and that the populations distributed in the Pearl River region moved southward to Hainan Island and Vietnam based on the network and Bayesian binary MCMC (BBM) analysis. Our demographic history results indicated that the populations of B. semifasciolatus experienced a bottleneck event following a recent population expansion (DECINC model) supported by ABC analysis. We suggest that sea-level changes exerted pronounced effects on the demography of B. semifasciolatus on the continental island and in the mainland during the late Pleistocene glacial cycles.

Fisheries products traceability using batch code

The importance of product quality and food safety for consumers would be reached by apply traceability product. Indonesia's geographical archipelago has long supply chain of fisheries which cause all supply chain data getting difficult to trace from upstream to end of consumer. The problem of this research is how to apply traceability of seafood products from their origin through to end customer by using traceability system. The method used is apply batch code identifier to represent vessel information, catch data, and landing site. System applies automatic detection of landing site coordinates using global positioning system, and along with batch code stored to cloud server. The batch code moved along with the fish movement in each supply chain. Once fish received by processors, system get access cloud server to get proper batch code. Finally, each product is labeled with QR Code containing product information and batch code. While products sent to customers, label scanned and system provide fish origin information and show the maps of the vessel landing location. The testing results shows label can be scanned at maximum distance of 40 cm in dry surface and flat and curved position, and at a maximum distance of 25 cm in flat position, wet and frozen conditions. Label can be scanned at maximum distance 20 cm in a curved position and wet and frozen conditions.

Phenotypic and genomic dissection of colour pattern variation in a reef fish radiation.

Coral reefs rank among the most diverse species assemblages on Earth. A particularly striking aspect of coral reef communities is the variety of colour patterns displayed by reef fishes. Colour pattern is known to play a central role in the ecology and evolution of reef fishes through, for example, signalling or camouflage. Nevertheless, colour pattern is a complex trait in reef fishes-actually a collection of traits-that is difficult to analyse in a quantitative and standardized way. This is the challenge that we address in this study using the hamlets (Hypoplectrus spp., Serranidae) as a model system. Our approach involves a custom underwater camera system to take orientation- and size-standardized photographs in situ, colour correction, alignment of the fish images with a combination of landmarks and Bézier curves, and principal component analysis on the colour value of each pixel of each aligned fish. This approach identifies the major colour pattern elements that contribute to phenotypic variation in the group. Furthermore, we complement the image analysis with whole-genome sequencing to run a multivariate genome-wide association study for colour pattern variation. This second layer of analysis reveals sharp association peaks along the hamlet genome for each colour pattern element and allows to characterize the phenotypic effect of the single nucleotide polymorphisms that are most strongly associated with colour pattern variation at each association peak. Our results suggest that the diversity of colour patterns displayed by the hamlets is generated by a modular genomic and phenotypic architecture.

Otoliths of the deepest-living fishes

Bony fishes have a well-developed acoustic and vestibular sense, which is registered in the highly specialized otolithic end-organ containing a pair of three aragonitic otoliths. Usually, the largest otolith is the sagitta, which is considered to be primarily responsible for sound detection and is known to be morphologically diverse and specific across species and higher taxonomic levels. We investigated sagittal otoliths of abyssal and hadal fishes of three families containing taxa adapted to these deep habitats: the Liparidae (snailfishes), Macrouridae (rattails), and Ophidiidae (cusk eels). The purpose of our study was to ascertain whether specific depth-dependent effects on otolith size or morphology could be observed in comparison to the shallower-living counterparts in these groups. We were able to identify a trend toward size reduction in otoliths with depth and certain “simplifications” in otolith morphology. However, we also observed that such trends would only become detectable when studying otoliths within well-defined clades because of the many complexities that occur in otolith morphologies that are unrelated to habitat depth. We propose future work to study freshly caught hadal liparids for the physiology of the otolith end-organ and macula acustica to learn more about the functioning of the organ in fishes living at great depths. Together these findings provide new insights into the drivers of otolith diversity and the evolution of fishes into deep-sea environments.

Mathematical Formulation to Differentiate between Naturally Occurred and Artificially Added Formaldehyde in the Ice Stored of Lizardfish (Saurida tumbil)

The practice of formaldehyde abuse as a food preservative, especially in fishery products, is commonly occurred. However, the differentiation of the formaldehyde origin in fish is difficult to be performed. Meanwhile, physical observation is not sufficient to determine the additional formaldehyde in fishery products. This study aimed to formulate a quantitative method to detect the origin of formaldehyde in fish. The formulation was developed based on the differences in some chemical properties (Formaldehyde (FA), Trimethylamine (TMA) and Trimethylamine oxide (TMAO) of fish treated with and without formaldehyde addition. The fish used as samples were beloso fish/lizardfish (Saurida tumbil). Fish were prepared with and without the addition of formaldehyde and then stored in ice for 21 days. The content of FA, TMA, and TMAO of gill and flesh during storage were analyzed every 3 days to determine the difference in the trend of distribution patterns of two fish treatments. The data were statistically processed to produce two mathematical formulas to identify the origin of formaldehyde. The results reveal that detection of the origin of formaldehyde in fish could be done using two approaches: the diffusion rate approach (validation 75-100%) and the ratio of formaldehyde, TMA, and TMAO (validation 96,47%).Keywords: Formaldehyde, fishery product, food preservative, mathematical formalulation, Surida tumbil

A chromosome-level genome assembly of Hong Kong catfish (Clarias fuscus) uncovers a sex-determining region

BackgroundHong Kong catfish (Clarias fuscus) is an ecologically and economically important species that is widely distributed in freshwater regions of southern China. Hong Kong catfish has significant sexual growth dimorphism. The genome assembly of the Hong Kong catfish would facilitate study of the sex determination and evolution mechanism of the species.ResultsThe first high-quality chromosome-level genome of the Hong Kong catfish was constructed. The total genome was 933.4 Mb, with 416 contigs and a contig N50 length of 8.52 Mb. Using high-throughput chromosome conformation capture (Hi-C) data, the genome assembly was divided into 28 chromosomes with a scaffold N50 length of 36.68 Mb. A total of 23,345 protein-coding genes were predicted in the genome, and 94.28% of the genes were functionally annotated in public databases. Phylogenetic analysis indicated that C. fuscus and Clarias magur diverged approximately 63.7 million years ago. The comparative genome results showed that a total of 60 unique, 353 expanded and 851 contracted gene families were identified in Hong Kong catfish. A sex-linked quantitative trait locus identified in a previous study was located in a sex-determining region of 30.26 Mb (0.02 to 30.28 Mb) on chromosome 13 (Chr13), the predicted Y chromosome. This QTL region contained 785 genes, of which 18 were identified as sex-related genes.ConclusionsThis study is the first to report the chromosome-level genome assembly of Hong Kong catfish. The study provides an excellent genetic resource that will facilitate future studies of sex determination mechanisms and evolution in fish.

A fish for Phoebe: a new actinopterygian from the Upper Carboniferous Coal Measures of Saddleworth, Greater Manchester, UK, and a revision of Kansasiella eatoni

Abstract The origin of crown Actinopterygii has been dated to near the Devonian-Carboniferous boundary, but poor phylogenetic signal occludes the origin of modern actinopterygian biodiversity. Scarcity of comparative endoskeletal anatomy from this period likely contributes to the uncertainty. For example, only a handful of neurocrania have been described from the Carboniferous period despite an abundance of fossil taxa. Here we present a new actinopterygian, Phoebeannaia mossae gen. et sp. nov., from the Bashkirian Coal Measures of Saddleworth, Greater Manchester, UK, represented by an exceptionally preserved neurocranium and associated dermal bones. Morphological similarities to the Virgilian Kansasiella eatoni prompted comparative study and construction of a new neurocranial character matrix. Subsequent systematic analysis enabled identification of a cluster of similar Late Palaeozoic neurocrania, exploration of trends in braincase evolution across time, and investigation of potential causes of cladistic instability. Our neurocranial dataset reliably places this new specimen on the neopterygian stem near Kansasiella, but it struggles to incorporate extant taxa such as Polypteriformes, leading to uncertainty in branching pattern and inferred neurocranial transformation series. This work triples the number of complete Carboniferous neurocrania described with modern microcomputed tomography and provides a framework for future testing of large-scale hypotheses regarding the diversification and origin of ray-finned fishes.