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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]

Obtaining reliable estimates of the effective number of breeders (Nb) and generational effective population size (Ne) for fishery‐important species is challenging because they are often iteroparous and highly abundant, which can lead to bias and imprecision. However, recent advances in understanding of these parameters, as well as the development of bias correction methods, have improved the capacity to generate reliable estimates. We utilized samples of both single‐cohort young of the year and mixed‐age adults from two geographically and genetically isolated stocks of the Australasian snapper (Chrysophrys auratus) to investigate the feasibility of generating reliable Nb and Ne estimates for a fishery species. Snapper is an abundant, iteroparous broadcast spawning teleost that is heavily exploited by recreational and commercial fisheries. Employing neutral genome‐wide SNPs and the linkage‐disequilibrium method, we determined that the most reliable Nb and Ne estimates could be derived by genotyping at least 200 individuals from a single cohort. Although our estimates made from the mixed‐age adult samples were generally lower and less precise than those based on a single cohort, they still proved useful for understanding relative differences in genetic effective size between stocks. The correction formulas applied to adjust for biases due to physical linkage of loci and age structure resulted in substantial upward modifications of our estimates, demonstrating the importance of applying these bias corrections. Our findings provide important guidelines for estimating Nb and Ne for iteroparous species with large populations. This work also highlights the utility of samples originally collected for stock structure and stock assessment work for investigating genetic effective size in fishery‐important species. [ABSTRACT FROM AUTHOR]

This study investigates the genetic diversity and population structure of the greasyback shrimp, Metapenaeus ensis (De Haan, 1844), within the Tam Giang - Cau Hai lagoon, Vietnam, by analyzing mtCOI genes from 91 individuals collected across four populations in nine sampling locations. High genetic diversity was found, with 34 unique haplotypes and 38 genetic variations identified. Most genetic variation occurred within populations (AMOVA), suggesting high gene flow. Low and non-significant Fst values and close genetic distances confirmed minimal differentiation among populations. These findings provide the first insights into M. ensis population genetics in this lagoon, informing conservation and management efforts. Understanding genetic diversity is crucial for sustainable management and conservation of marine species. This research aids in understanding population resilience, potential impacts of overfishing, and may assist in developing sustainable harvest strategies of this economically important shrimp species. [ABSTRACT FROM AUTHOR]

This article summarizes the Special Issue of Evolutionary Applications focused on "Advances in Salmonid Genetics." Contributions to this Special Issue were primarily presented at the Coastwide Salmonid Genetics Meeting, held in Boise, ID in June 2023, with a focus on Pacific salmonids of the west coast region of North America. Contributions from other regions of the globe are also included and further convey the importance of various salmonid species across the world. This Special Issue is comprised of 22 articles that together illustrate major advances in genetic and genomic tools to address fundamental and applied questions for natural populations of salmonids, ranging from mixed‐stock analyses, to conservation of genetic diversity, to adaptation to local environments. These studies provide valuable insight for molecular ecologists since salmonid systems offer a window into evolutionary applications that parallel conservation efforts relevant and applicable beyond salmonid species. Here, we provide an introduction and a synopsis of articles in this Special Issue, along with future directions in this field. We present this Special Issue in honor of Fred Utter, a founder and leader in the field of salmonid genetics, who passed away in 2023. [ABSTRACT FROM AUTHOR]

Kryptolebias marmoratus (Kmar), a teleost fish of the order Cyprinodontiformes, has a suite of unique phenotypes and behaviors not observed in other fishes. Many of these phenotypes are discrete and highly plastic—varying over time within an individual, and in some cases reversible. Kmar and its interfertile sister species, K. hermaphroditus, are the only known self‐fertile vertebrates. This unusual sexual mode has the potential to provide unique insights into the regulation of vertebrate sexual development, and also lends itself to genetics. Kmar is easily adapted to the lab and requires little maintenance. However, its internal fertilization and small clutch size limits its experimental use. To support Kmar as a genetic model, we compared alternative husbandry techniques to maximize recovery of early cleavage‐stage embryos. We find that frequent egg collection enhances yield, and that protease treatment promotes the greatest hatching success. We completed a forward mutagenesis screen and recovered several mutant lines that serve as important tools for genetics in this model. Several will serve as useful viable recessive markers for marking crosses. Importantly, the mutant kissylips lays embryos at twice the rate of wild‐type. Combining frequent egg collection with the kissylips mutant background allows for a substantial enhancement of early embryo yield. These improvements were sufficient to allow experimental analysis of early development and the successful mono‐ and bi‐allelic targeted knockout of an endogenous tyrosinase gene with CRISPR/Cas9 nucleases. Collectively, these tools will facilitate modern developmental genetics in this fascinating fish, leading to future insights into the regulation of plasticity. Research Highlights: A forward genetic screen in the self‐fertile fish, Kryptolebias marmoratus, identified useful mutants for use as markers and to enhance egg output.Optimization of husbandry further improved egg yield for embryo manipulation.New resources enabled targeted gene knockout in K. marmoratus using CRISPR/Cas9. [ABSTRACT FROM AUTHOR]

Fishing has the potential to influence the life‐history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large‐effect loci linked with ecologically important life‐history traits, such as age at maturity in Atlantic salmon (Salmo salar), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93‐year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping‐by‐sequencing approach (GT‐seq), we discovered strong within‐season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within‐season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life‐history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life‐history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature. [ABSTRACT FROM AUTHOR]

Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts. [ABSTRACT FROM AUTHOR]

Habitat fragmentation is among the main threats to freshwater fish biodiversity, with expected effects including genetic impacts due to disturbance of migration and declining population size. Major concern falls on highly exploited species such as Prochilodus magdalenae, a migratory characiform fish endemic to the Magdalena River basin supporting much of the Colombian artisanal fishery, whose migration route was interrupted by the Ituango hydroelectric project in the Cauca River. To determine the potential effects of fragmentation, this study evaluated the population genetics of this species on both geographical (upstream and downstream of the dam) and temporal (before and after the construction) scales by using 11 species-specific microsatellite markers. Contrary to expectation, genetic diversity and structure remained relatively stable. This study provided no evidence of genetic impacts on P. magdalenae associated with fragmentation over the short term (4–10 years, 5–12 generations) despite persisting threats, genetic evidence of bottleneck, and a high degree of inbreeding, showing the ability of this species to withstand disturbance of its habitat. [ABSTRACT FROM AUTHOR]

The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP (http://bioinfo.ihb.ac.cn/fishsnp), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information. [ABSTRACT FROM AUTHOR]

We integrate multidisciplinary observations to provide a regional-scale synthesis of river drainage reconfiguration in Southland (New Zealand) between the Miocene and the Holocene. Distributions of sedimentary clasts, including alluvial gold, garnets and chromite, are combined with freshwater fish genetics, surface geomorphology, and basement geology to constrain river drainage directions and interconnections through time. River evolution in much of the South Island has been dominated by localised tectonic uplift linked to distant Alpine Fault tectonism. In the southeast, the rise of ranges between Central Otago and Southland severed initial long-distance southward drainage and gold transport and isolated fish species. Plio-Pleistocene range uplift caused the recycling of older alluvial gold deposits into the new Southland river systems. The most significant Southland drainage reorientations have occurred through the Pleistocene, in parallel with similar processes in Central Otago. In particular, the Pomahaka River has evolved geomorphologically from a Southland-linked catchment to become a major tributary of the Clutha catchment, with associated biological evolution of distinctive endemic freshwater fish. [ABSTRACT FROM AUTHOR]

Simple Summary: As an endemic and vulnerable fish from the upper Yangtze River in China, Schizothorax kozlovi holds significant scientific and ecological importance, yet it has received little attention so far. In this paper, we reported the characterization of the mitochondrial genome of S. kozlovi, and further investigated the phylogenetic relationships of Schizothorax. The results showed that the mitochondrial genome of S. kozlovi had a total size of 16,585 bp, a circular arrangement, and contained 13 PCGs, 22 tRNAs, two rRNAs, and two non-coding regions. Moreover, the phylogenetic analyses demonstrated that Schizothorax could be classified into four clades, and S. kozlovi was closely related to Schizothorax chongi. The present study enriched the basic biological data for S. kozlovi and provided fundamental references for the conservation of S. kozlovi and Schizothorax. Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of S. kozlovi has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of S. kozlovi and investigated the phylogenetic relationships of Schizothorax. The complete mitochondrial genome of S. kozlovi was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (−0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the Schizothorax into four clades and did not support the classification of Schizothorax based on morphology. The phylogenetic status of S. kozlovi was closely related to that of S. chongi. The present study provides valuable genomic information for S. kozlovi and new insights in phylogenetic relationships of Schizothorax. These data could also offer fundamental references and guidelines for the management and conservation of S. kozlovi and other species of Schizothorax. [ABSTRACT FROM AUTHOR]

CD4 T helper cells are an important group of cells in the immune system of vertebrates and express CD4 receptor on the cell surface. In mammals, the CD4 receptor is encoded by a single copy gene, whilst in fish, two copies of cd4 genes, namely cd4-1 and cd4-2, are found. In this study, the ectodomains of grass carp (Ctenopharyngodon idella, Ci) CD4-1 and CD4-2 were expressed in the E. coli cells and used to generate monoclonal antibodies in mice. Western blotting, confocal microscopy and flow cytometry were performed to characterize the monoclonal antibodies. It has been shown that the CiCD4-1 and CiCD4-2 monoclonal antibodies had good specificity to react with the recombinant ectodomains of CiCD4-1 and CiCD4-2 expressed in the CHO-S cells and the native CD4 molecules of grass carp. The CiCD4-1 monoclonal antibody did not recognize CiCD4-2 and verse versa. In addition, the CD4-1 and CD4-2 monoclonal antibodies specifically recognized the CD4-1 and CD4-2 receptors expressed in the HEK293 cells and native molecules of fish cells. Further, the percentages of lymphocytes in immune tissues of healthy fish were analyzed by flow cytometry. It was found that 17.6% of lymphocytes were CD4-1+ cells and 22.5% were CD4-2+ in the head kidney. In the spleen, 13.1% of lymphocytes were CD4-1+ and 18.6% were CD4-2+ while 7.3% of blood lymphocytes were CD4-1+ cells and 8.8% were CD4-2+ cells. The availability of the CD4-1 and CD4-2 monoclonal antibodies provides antibody-based tools for further elucidation of the functions of CD4 T cells in grass carp. [ABSTRACT FROM AUTHOR]

The giant freshwater prawn Macrobrachium rosenbergii distributed from tropical to subtropical regions, is a warm-water species, and its survival temperature is 14–35 °C, which greatly limits its culture cycle and culture area in China. Therefore, it is urgent to cultivate a new high quality, high yield variety with improved cold-resistance, but the genetic parameters for cold-resistance traits are unknown in M. rosenbergii. In this study, the cold-resistance of adult M. rosenbergii populations was tested using the indoor artificial cooling method. Individuals were selected from 139 families of Shufeng G3 generation and cultured for 200 days. A linear mixed model was constructed by ASReml-R to evaluate the genetic parameters of the cold-resistance trait (cooling degree hours, CDH) and growth traits (body weight, BW, and body length, BL) based on the restricted maximum likelihood (REML) method. The results show that the heritability of CDH was low (0.12±0.05), while the growth traits (BW and BL) had low to moderate heritability, with 0.20±0.06 for BW and 0.06±0.04 for BL. The phenotypic and genetic correlation between BW and BL was significantly positive, but significantly negative phenotypic and genetic correlations were detected between CDH and BW and between CDH and BL. Furthermore, the analysis of the differences between cold-resistance and phenotypic traits showed that the female reproductive status, exoskeleton hardness and claw number of adult prawns had a great influence on the cold-resistance of M. rosenbergii (P<0.05), indicating that adults with claws and hard exoskeletons are preferred as parents in subsequent breeding selection. The present results can be attributed to the selection and breeding of a new cold-resistant variety of M. rosenbergii. [ABSTRACT FROM AUTHOR]

The differentiation and developmental trajectory of fish gonads, significantly important for fish breeding, culture, and production, has long been a focal point in the fields of fish genetics and developmental biology. However, the mechanism of gonadal differentiation in leopard coral grouper (Plectropomus leopardus) remains unclear. This study investigates the 17β-Hydroxysteroid Dehydrogenase (Hsd17b) gene family in P. leopardus, with a focus on gene characterization, expression profiling, and functional analysis. The results reveal that the P. leopardus's Hsd17b gene family comprises 11 members, all belonging to the SDR superfamily. The amino acid similarity is only 12.96%, but conserved motifs, such as TGxxxGxG and S-Y-K, are present in these genes. Hsd17b12a and Hsd17b12b are unique homologs in fish, and chromosomal localization has confirmed that they are not derived from different transcripts of the same gene, but rather are two independent genes. The Hsd17b family genes, predominantly expressed in the liver, heart, gills, kidneys, and gonads, are involved in synthesizing or metabolizing sex steroid hormones and neurotransmitters, with their expression patterns during gonadal development categorized into three distinct categories. Notably, Hsd17b4 and Hsd17b12a were highly expressed in the testis and ovary, respectively, suggesting their involvement in the development of reproductive cells in these organs. Fluorescence in situ hybridization (FISH) further indicated specific expression sites for these genes, with Hsd17b4 primarily expressed in germ stem cells and Hsd17b12a in oocytes. This comprehensive study provides foundational insights into the role of the Hsd17b gene family in gonadal development and steroidogenesis in P. leopardus, contributing to the broader understanding of fish reproductive biology and aquaculture breeding. [ABSTRACT FROM AUTHOR]

Age‐at‐maturity and iteroparity are two life history variations of steelhead trout (Oncorhynchus mykiss) that are believed to increase population resilience and stability. While repeat‐spawning individuals are thought to have historically made up a substantial portion of the reproductive population in the Columbia River and the majority of females still attempt outmigration as kelts, return rates of repeat‐spawner are low throughout the basin and below 1% for the furthest migrating stocks. Notably, outmigrating adults exhibit variation in rematuration phenology, displaying either "consecutive" (reproduce immediately the following season) or "skip" (delay spawning for future seasons) spawning patterns. Here, we use low coverage whole genome sequencing of consecutive versus skip spawning female Columbia River steelhead from two populations to test for genomic differences between these two iteroparous phenotypes. We identified genomic regions on several chromosomes which were associated with the phenology of iteroparity, including a region on chromosome 25 containing two genes, estradiol receptor beta (ERβ) and glycoprotein hormone beta‐5 (GPHB5), which, in mammals, are estrogen‐sensitive and expressed in reproductive tissues. Allele frequencies in this ERβ/GPHB5 region differed among female steelhead of different age at maturity, but not males. These genes also shared an island of linkage disequilibrium with the SIX6 gene, 600Kbp away on the same chromosome, a region of known association with age‐at‐maturity. These observations contribute to growing evidence that age‐at‐maturity and the phenology of iteroparity are determined by overlapping physiological processes and genetic pathways. [ABSTRACT FROM AUTHOR]

Microphysogobio longidorsalis is endemic to South Korea and inhabits small areas of the Namhangang, Bukhangang, and Imjingang Rivers in the Hangang River water system. Endemic species usually are more vulnerable than species with a wide distribution. Notably, there is a lack of basic conservation data for M. longidorsalis. We analyzed 19 microsatellite loci in six populations of M. longidorsalis in South Korea to characterize their population structure and genetic diversity. The genetic diversity of the microsatellites was 0.741–0.779, which is lower than that of other freshwater fishes. The pairwise genetic differentiation of microsatellite (FST) values ranged from 0.007 to 0.041, suggesting low genetic differentiation between the populations. The Jojongicheon stream population (CP) had an effective population size of <100. Therefore, conservation efforts are required to prevent inbreeding depression in M. longidorsalis. Discriminant analysis of principal components showed that the Hangang River water system would be a single management unit (MU). Our findings provide fundamental genetic insights for the formulation of conservation strategies for M. longidorsalis. [ABSTRACT FROM AUTHOR]

Aquaculture plays a crucial role in meeting the increasing global demand for food and protein sources. However, its expansion is followed by increasing challenges, such as infectious disease outbreaks and antibiotic misuse. The present study focuses on the genetic and functional analyses of two Lacticaseibacillus paracasei (BF3 and RT4) and two Lactiplantibacillus plantarum (BF12 and WT12) strains isolated from a rotifer cultivation tank used for turbot larviculture. Whole-genome sequencing (WGS) and bioinformatics analyses confirmed their probiotic potential, the absence of transferable antibiotic resistance genes, and the absence of virulence and pathogenicity factors. Bacteriocin mining identified a gene cluster encoding six plantaricins, suggesting their role in the antimicrobial activity exerted by these strains. In vitro cell-free protein synthesis (IV-CFPS) analyses was used to evaluate the expression of the plantaricin genes. The in vitro-synthesized class IIb (two-peptide bacteriocins) plantaricin E/F (PlnE/F) exerted antimicrobial activity against three indicator microorganisms, including the well-known ichthyopathogen Lactococcus garvieae. Furthermore, MALDI-TOF MS on colonies detected the presence of a major peptide that matches the dimeric form of plantaricins E (PlnE) and F (PlnF). This study emphasizes the importance of genome sequencing and bioinformatic analysis for evaluating aquaculture probiotic candidates. Moreover, it provides valuable insights into their genetic features and antimicrobial mechanisms, paving the way for their application as probiotics in larviculture, which is a major bottleneck in aquaculture. [ABSTRACT FROM AUTHOR]

This document titled "Arabic Abstracts" is a compilation of abstracts from various authors and institutions in the field of aquaculture. The authors come from diverse backgrounds and countries such as Australia, Norway, China, Italy, Bangladesh, and more. The abstracts cover a range of topics including aquaculture disease control, marine sciences, fish genetics, fishery management, and more. This resource provides a snapshot of current research in the field and may be useful for library patrons conducting research on specific aquaculture topics. [Extracted from the article]

Reconstructing a well-supported phylogenetic relationship among species is a prerequisite for biological and evolutionary researches. Chondrichthyes (sharks, rays, skates and chimaeras) serves as an important clade of highly commercial, ecological, evolutionary, and conservation significance. Yet the genome-scale data of chondrichthyans are lacking, which largely restrict phylogeny, evolution, and conservation investigations of these species. Recently reported 1105 orthologous exon markers generated for ray-finned fishes are powerful tools for phylogenomics inferences. Given the relatively close relationship between cartilaginous and ray-finned fish species, we purposed to verify whether these 1105 genomic exon markers generated for ray-finned fishes were applicable for chondrichthyan phylogenomics. In this study, we collected publically available 10 genomes and 30 transcriptomes of chondrichthyans to conduct the phylogenomics analysis. Phylogenomics analyses based on the 1105 genomic exon markers and the Benchmarking Universal Single-Copy Orthologs (BUSCO) approach were performed to reconstruct phylogenetic relationships of investigated chondrichthyans. We also attempted to apply these exon markers for phylogeny of 26 jawed fish species. Our results revealed well-supported and almost identical phylogenetic relationships of chondrichthyans, confirming the applicability of genomic exon markers of ray-finned fishes in chondrichthyan phylogeny. Moreover, phylogenomics analyses of 26 jawed fish species further confirmed the application of these genomic exon markers in both cartilaginous and lobe-finned fish phylogeny. Our results highlighted the wide-ranging utility of genomic markers of ray-finned fishes in phylogenetic inference of cartilaginous and lobe-finned fish species and provided substantial and background information for the evolutionary biology and conservation of chondrichthyans and related fish species. [ABSTRACT FROM AUTHOR]

Repetitive DNA make up a considerable fraction of most eukaryotic genomes. In fish, transposable element (TE) activity has coincided with rapid species diversification. Here, we annotated the repetitive content in 100 genome assemblies, covering the major branches of the diverse lineage of teleost fish. We investigated if TE content correlates with family level net diversification rates and found support for a weak negative correlation. Further, we demonstrated that TE proportion correlates with genome size, but not to the proportion of short tandem repeats (STRs), which implies independent evolutionary paths. Marine and freshwater fish had large differences in STR content, with the most extreme propagation detected in the genomes of codfish species and Atlantic herring. Such a high density of STRs is likely to increase the mutational load, which we propose could be counterbalanced by high fecundity as seen in codfishes and herring. [ABSTRACT FROM AUTHOR]

How various factors, including demography, recombination or genome duplication, may impact the efficacy of natural selection and the burden of deleterious mutations,is a central question in evolutionary biology and genetics. In this study, we show that key evolutionary processes, including variations in i) effective population size (Ne) ii) recombination rates and iii) chromosome inheritance, have influenced the genetic load and efficacy of selection in Coho salmon (Oncorhynchus kisutch), a widely distributed salmonid species on the west coast of North America. Using whole genome resequencing data from 14 populations at different migratory distances from their southern glacial refugium, we found evidence supporting gene surfing, wherein reduced Ne at the postglacial recolonization front, leads to a decrease in the efficacy of selection and a surf of deleterious alleles in the northernmost populations. Furthermore, our results indicate that recombination rates play a prime role in shaping the load along the genome. Additionally, we identified variation in polyploidy as a contributing factor to within-genome variation of the load. Overall, our results align remarkably well with expectations under the nearly neutral theory of molecular evolution. We discuss the fundamental and applied implications of these findings for evolutionary and conservation genomics. Author summary: Understanding how historical processes, such as past glaciations, may have impacted variations in population size and genetic diversity along the genome is a fundamental question in evolution. In this study, we investigated how recent postglacial demographic expansion has affected the distribution of deleterious genetic variants and the resulting deleterious mutation load in Coho salmon (Oncorhynchus kisutch), throughout its native range in North America. By sequencing the entire genome of 71 Coho salmon, we reveal that postglacial expansion has led to allele surfing, a process where alleles increase in frequency in populations that are expanding or colonizing new environments. Here, allele surfing resulted in an increased deleterious mutation load at the colonization front. Furthermore, we demonstrated that the efficacy of natural selection scales with variation in effective population size among populations. We showed that the specific genomic features of Coho salmon, namely variation in local recombination rate and variation in chromosomal inheritance, strongly impacted the segregation of deleterious mutations. [ABSTRACT FROM AUTHOR]

Atlantic salmon (Salmo salar) in Northeastern US and Eastern Canada has high economic value for the sport fishing and aquaculture industries. Large differences exist between the genomes of Atlantic salmon of European origin and North American (N.A.) origin. Given the genetic and genomic differences between the 2 lineages, it is crucial to develop unique genomic resources for N.A. Atlantic salmon. Here, we describe the resources that we recently developed for genomic and genetic research in N.A. Atlantic salmon aquaculture. Firstly, a new single nucleotide polymorphism (SNP) database for N.A. Atlantic salmon consisting of 3.1 million putative SNPs was generated using data from whole-genome resequencing of 80 N.A. Atlantic salmon individuals. Secondly, a high-density 50K SNP array enriched for the genic regions of the genome and containing 3 sex determination and 61 putative continent of origin markers was developed and validated. Thirdly, a genetic map composed of 27 linkage groups with 36K SNP markers was generated from 2,512 individuals in 141 full-sib families. Finally, a chromosome-level de novo genome assembly from a male N.A. Atlantic salmon from the St. John River aquaculture strain was generated using PacBio long reads. Information from Hi-C proximity ligation sequences and Bionano optical mapping was used to concatenate the contigs into scaffolds. The assembly contains 1,755 scaffolds and only 1,253 gaps, with a total length of 2.83 Gb and N50 of 17.2 Mb. A BUSCO analysis detected 96.2% of the conserved Actinopterygii genes in the assembly, and the genetic linkage information was used to guide the formation of 27 chromosome sequences. Comparative analysis with the reference genome assembly of the European Atlantic salmon confirmed that the karyotype differences between the 2 lineages are caused by a fission in chromosome Ssa01 and 3 chromosome fusions including the p arm of chromosome Ssa01 with Ssa23, Ssa08 with Ssa29, and Ssa26 with Ssa28. The genomic resources we have generated for Atlantic salmon provide a crucial boost for genetic research and for management of farmed and wild populations in this highly valued species. [ABSTRACT FROM AUTHOR]

Hybrid, polyploid, and clonal fishes are found naturally in wild populations, but they can also be induced artificially by cross-breeding and chromosome manipulation. The dojo loach Misgurnus anguillicaudatus includes various naturally occurring as well as artificially induced hybrid, polyploid, and clonal biotypes. This review aims to organize the results from previous works that used the dojo loach as the model animal for a better understanding of the interrelationship among the constitution of chromosome sets, the meiotic configuration, and the resultant gametogenesis. Autopolyploids with an even number of extra sets of homologous chromosomes were observed to be fertile. However, autopolyploids with an odd number of extra sets of homologous chromosomes and allopolyploids (polyploid hybrids) with exotic non-homologous chromosomes were found to exhibit a broad range of sterility ranging from retarded gonadal development to the production of aneuploid gametes with various abnormal characteristics. Sterile biotypes often showed meiotic configurations, including univalents. Past hybridization events likely triggered the atypical reproduction phenomena, such as the formation of unreduced isogenic gametes by doubling each chromosome for sister chromosome pairing, the elimination of a non-homologous chromosome set by meiotic hybridogenesis, and clonal development by spontaneous gynogenesis of unreduced eggs. The results obtained by studying a series of works using the dojo loach as the model organism highlight the mechanisms of sterility in hybrids and polyploids as well as of unisexuality in isogenic clones. These results contribute to the understanding of basic and aquaculture-oriented reproductive biology and genetics in fishes. [ABSTRACT FROM AUTHOR]

Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10−9 and µ = 4.29 × 10−9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular. [ABSTRACT FROM AUTHOR]

During the evolution of astacin metalloprotease family genes, gene duplication occurred, especially in the lineage of teleosts, in which several types of astacins containing six conserved cysteines (c6ast) emerged. One of them is patristacin, originally found in syngnathid fishes, such as pipefishes and seahorses. Patristacin is expressed in the brood pouch and is present on the same chromosome as other c6ast (pactacin and nephrosin) genes. We first surveyed all the genes from 33 teleost species using a genome database, and characterized the genes by phylogenetic analysis. Pactacin and nephrosin gene homologs were found from all the examined species with only few exceptions, while patristacin gene homologs were found from only several lineages. The patristacin gene homologs were found as multicopy genes in most species of Percomorpha, one of the diverged groups in teleosts. Further diversification of the gene occurred during the evolution of Atherinomorphae, one of the groups in Percomorpha. Fishes of Atherinomorphae possess two types of patristacin, belonging to subclades 1 and 2. Among the Atherinomorpha, we chose the southern platyfish to examine the patristacin gene expression. Platyfish possess eight patristacin gene homologs, called XmPastn1, 2, 3, 4, 5, 7, 10, and 11. Of these genes, only XmPastn2 belongs to subclade 1, while the other seven belong to subclade 2. Only XmPastn2 showed strong expression in several organs of adult platyfish, as observed in reverse‐transcription polymerase chain reaction of RNA extracts. Cells expressing XmPastn2 were predominantly mucus‐secreting cells found in epidermis around the jaw, as revealed by in‐situ hybridization. This result suggests that XmPastn2 is secreted and may contribute to mucus formation or secretion. Research highlights: Neprhosin and pactacin genes were already established in Euteleostei. However, the patristacin gene appeared during the evolution of Euteleostei, and further diversification into two groups (subclades 1 and 2) occurred during evolution. [ABSTRACT FROM AUTHOR]

Flowerhorn fish has been known as a breed of fish produced by artificial hybridization between several cichlid fish. Other ornamental cichlid fish generally known to be crossed to make flowerhorn variant includes Amphilophus citrinelus, Amphilophus labiatus, Vieja melanurus, and Amphilophus trimaculatus. Our study identified a variety of flowerhorn samples with distinct morphotypes, dubbed as Cencu (LH1CC), Kamfa (LH2KF), Thai Silk (LH3TS), Kirin (LH4KR), Parrot (LH5PR), and Vieja (LH6VJ) using mtDNA COI-based DNA barcoding. Molecular analysis and phylogenetics showed that all sample had 0% genetic divergence and conspecific with A. trimaculatus sequence. Hence, we concluded that despite having varied morphotypes, all flowerhorn samples were identified as A. trimaculatus and were a variation of flowerhorn from A. trimaculatus lineage. The findings should be used as a precaution as the fish is identified as an invasive species. [ABSTRACT FROM AUTHOR]

Indonesian leaffish Pristolepis grooti, an endemic species, are distributed in the region of Sumatra, Riau, Bangka Belitung and Kalimantan. However, there has been a decline in the population recently. This research purposed to investigate the mitochondrial DNA cytochrome c oxidase subunit I (COI) gene, the genetic distance, the genetic tree of the leaffish and characterize the chemical physics of water of its habitat in the Kelekar River Muara Enim Regency and the Ogan River, Ogan Ilir Regency. The method used in species authentication was DNA isolation, amplification using PCR (Polymerase Chain Reaction) and sequencing of COI gene. The size of the COI mtDNA gene fragment was 704 bp (PM 1, PM 4, PP 2 and PP 4) and 723 bp (PM 2, PM 3, PP 1 and PP 3). A cryptic diversity of the species P. grooti is found based on the genetic distance value of 4.5-6%, both in the Kelakar and Ogan Rivers. The phylogenetic tree of the leaffish of this study formed 2 separate sub-clusters with a bootstrap value of 50%. The properties of water qualities in the two rivers included temperatures 28.3-31.8°C, pH 5.6-8.3, dissolved oxygen 4.82-10.89 mg L-1, alkalinity 10-28 mg L-1 CaCO3, water transparency 16-45 cm, ammonia 0.47-0.70 mg L-1, water current 0.17-0.30 m s-1 and TDS 7-44 mg L-1. [ABSTRACT FROM AUTHOR]

Schizothorax kozlovi is an endemic and vulnerable fish species found in the upper Yangtze River in China. Over the past few years, the population resources of S. kozlovi have been nearly completely depleted owing to multiple contributing threats. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of S. kozlovi has still received little attention. In this study, we analyzed the characterization of the mitochondrial genome of S. kozlovi and investigated the phylogenetic relationships of Schizothorax. The complete mitochondrial genome of S. kozlovi was 16,585 bp in length, which contained thirty-seven genes (thirteen protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)) and two non-coding regions for the origin of light strand (OL) and the control region (CR). There were nine overlapping regions and seventeen intergenic spacers regions in the mitochondrial genome. The genome also showed a bias towards A + T content (55.01%) and had a positive AT-skew (0.08) and a negative GC-skew (−0.20). All the PCGs employed the ATG or GTG as the start codon and TAA, TAG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1 which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that the topologies of the phylogenetic tree divided the Schizothorax into four clades and did not support the classification of Schizothorax based on morphology. The phylogenetic status of S. kozlovi was closely related to that of S. chongi. The present study provides valuable genomic information for S. kozlovi and new insights in phylogenetic relationships of Schizothorax. These data could also offer fundamental references and guidelines for the management and conservation of S. kozlovi and other species of Schizothorax.

Breeding program in order to increase genetic improvement in blue tilapia have not been widely carried out at brackish water ponds. This study aimed to evaluate the increase in growth and genetic gain of F-4 blue tilapia from family selection in ponds with 25-30 gL-1 salinity. The parent used for the formation of F-4 is the selected parent F-3 and as a control using the non-selected parent F-3. Spawning was carried out in a full-sib mating design using the family selection method. The ratio of male and female broodstock is 1: 2. Spawning and nursery activities of F-4 blue tilapia are carried out in freshwater. The enlargement test was carried out in the net cage 5m x2.5m x1 m which was installed in the ponds with a salinity of 25-35 g l-1 for 120 days, at a stocking density of 10 fish m-2. At the end of maintenance, a selection process is carried out on the weight traits. Parameters observed included growth, survival, and genetic values. The results showed that the growth and survival in the F-4 blue tilapia population, male and female selected populations, had a higher value than in the non-selected population. The realized heritability value of the population growth character of the F-4 blue fish is in the high category. The difference in the average weight of the selected blue tilapia and the control was equivalent to an increase in genetic value added by 15.06% (male population) and 17.92% (female population). [ABSTRACT FROM AUTHOR]

Accurate species identification is essential to assess biodiversity and species richness in ecosystems threatened by rapid and recent environmental changes, such as warming in most Antarctic waters. The Lepidonotothen species complex comprises demersal notothenioid fishes which inhabit the shelf areas of the Antarctic Peninsula, the Scotia Arc and sub‐Antarctic islands with a circum‐Antarctic distribution. Species determination in this group has often been problematic. In particular, whether Lepidonotothen squamifrons and Lepidonotothen kempi are valid as separate species has been questioned. In this study, we analysed the genetic variation among four nominal southern polar species within this complex (L. kempi, L. squamifrons, Nototheniops larseni, Nototheniops nudifrons) by means of three different markers (ND2 and tRNA mitochondrial genes and a panel of 16 nuclear microsatellites). We tested whether individuals morphologically assigned to L. kempi showed genetic separation from L. squamifrons. Our analyses indicated a lack of differentiation between L. kempi and L. squamifrons. However, a genetically distinct population was found for L. squamifrons at the Shag Rocks islands near South Georgia. Antarctic and sub‐Antarctic islands are known to be home to many cryptic species and further studies will elucidate if the genetically differentiated population we found potentially originated from this context and can be considered an incipient species. Our analysis contributes to further characterize the species composition of the most abundant fish suborder in the Southern Ocean, which is among the regions most threatened by climate change. [ABSTRACT FROM AUTHOR]

The study on the phenotypic polymorphism of Heterotis niloticus was undertaken from February to May 2020 in the rain forest region of Cameroon. The main objective was to contribute to a better understanding of the genetic diversity of this adapted species for adequate breeding and preservation strategies. More specifically, the investigation aimed at evaluating the variability of phenotypic, morphometric and meristic features according to the study sites. Further, it was also in order to analyse the phenotypic variability, the structure, as well as the phylogenetic relationships among the Heterotis niloticus subpopulations. A total of 125 adult individuals were collected in three localities and characterized. Two (2) phaneroptic traits were observed, while 16 morphometric traits were measured and 5 meristic characters were counted. The results showed that there is a colour variability of eyes and body in Heterotis niloticus from the study area with a predominance of golden eyes (97.60%) and grey body (96.80%). The number of scales on the lateral line was higher in the individuals collected in Mbalmayo (38.67±1.46) than those in Ayos (37.70±0.95). Discriminant factor analyses and phylogenetic analyses revealed that the overall population studied is made up of 3 morphotypes cohabiting in the three localities; thus it was possible to establish the phylogenetic relationships that exist between them. Morphotypes 1 and 2 are closer while morphotypes 2 and 3 are far apart, showing a tendency of splitting genetic make up. The recorded diversity suggests that Heterotis niloticus from the study area constitutes a natural genetic resource having the interesting variability for further improvement and sustainable management. L'étude sur le polymorphisme phénotypique de Heterotis niloticus a été réalisée de février à mai 2020 dans la zone forestière du Cameroun. L'objectif était de contribuer à une meilleure connaissance de la diversité phénotypique de cette espèce adaptée afin de développer des stratégies idoines pour son élevage et sa préservation. Plus spécifiquement, l'étude visait à évaluer la variabilité des caractéristiques phénotypiques, morphométriques et méristiques en fonction des localités identifiées. Il s'agissait plus loin d'analyser la variabilité phénotypique, la structure, ainsi que les relations phylogénétiques entre les sous-populations de Heterotis niloticus. Un total de 125 individus adultes a été collecté dans trois localités et caractérisé. Deux (2) caractères phnotypiques ont été observés, tandis que 16 caractères morphométriques ont été mesurés et 5 caractères méristiques comptés. Les résultats ont montré qu'il existe une variabilité colorée des yeux et du corps chez Heterotis niloticus de la zone d'étude, avec une prédominance des yeux dorés (97,60%) et du corps gris (96,80%). Le nombre d'écailles sur la ligne latérale était plus élevé chez les individus collectés à Mbalmayo (38,67±1,46) par rapport à ceux d'Ayos (37,70±0,95). Les analyses des facteurs discriminants et phylogénétiques ont révélé que l'ensemble de la population étudiée est composée de 3 morphotypes cohabitant dans les trois localités; il a donc été possible d'établir les relations phylogénétiques qui existent entre eux. Les morphotypes 1 et 2 sont plus proches l'un de l'autre tandis que les morphotypes 2 et 3 sont éloignés l'un de l'autre, montrant une tendance à la scission de la structure génétique. La diversité évaluée suggère que Heterotis niloticus de la zone d'étude constitue une ressource génétique naturelle ayant un niveau de variabilité intéressante pour des perspectives d'amélioration ultérieure et d'une gestion durable. [ABSTRACT FROM AUTHOR]

An essential factor for aquatic conservation is genetic diversity or population divergence, which in natural populations reflects the interplay between geographical isolation with restricted gene flow and local evolution of populations. The long geological history of Africa may induce stronger among‐population divergence and lower within‐population divergence in fish populations of African watersheds. As an example, we studied population structure of the African snakehead fish Parachanna obscura. Our study aimed: (1) to develop a set of highly polymorphic microsatellite markers suitable for the analysis of genetic diversity among P. obscura and (2) to study the genetic diversity and structure of P. obscura populations from the West Africa region and mostly from Côte d'Ivoire, with respect to the effects of climate region and geographical distance on the genetic differentiation. A total of 259 specimens from 15 locations of P. obscura were collected over the West Africa region reflecting a high variability of pairwise geographical distances and variability of hydrological connectivity of the area. We developed a set of 21 polymorphic microsatellite markers for studying population genetics of the fish. The results showed relatively low intragenetic diversity for all the 15 locations, certainly attributable to confinement of fish in segregated catchments, resulting in limited gene flow. We also found evidence for local adaptation processes, suggested by five out of 21 microsatellite loci being under putative selection, according to BAYESCAN analysis. In turn, there was strong genetic differentiation (FST > 0.5) among fish from most locations, reflecting the allopatric development in watersheds without hydraulic connectivity. Neighbor‐joining dendrogram, Principal Coordinate Analysis, and analysis of ancestral groups by STRUCTURE suggested that the 15 locations can be divided into three clusters, mainly matching the dominant climate zones and the segregation of the watersheds in the region. The distinct genetic structure of the fish from the 15 locations obtained in this study suggests that conservation and sustainable management actions of this fish resource should avoid genetic mixing of potentially locally adapted populations. [ABSTRACT FROM AUTHOR]

Aeromonas hydrophila is a Gram-negative pathogen that can infect various fish, including largemouth bass (Micropterus salmoides), which have caused huge economic losses. In present study, largemouth bass anti-A. hydrophila antibodies were produced, then a highly immunogenic outer membrane proteins, AHA_3793, was identified by combined western blotting and mass spectrometry analysis. Moreover, AHA_3793 was expressed, and its immunogenicity was further verified by western blotting. Subsequently, the protective efficacy of AHA_3793 were evaluated in largemouth bass. The results showed that rAHA_3793 could produce a relative percentage survival (RPS) of 61.76% for largemouth bass against A. hydrophila challenge. ELISA analysis showed the specific serum antibodies of largemouth bass against rAHA_3793 and A. hydrophila in vaccinated group in weeks 4 and 5 after immunization were significantly higher than those in control group, which suggested that rAHA_3793 induced production of specific serum antibodies against rAHA_3793 and A. hydrophila. The qRT-PCR analysis showed that expressions of CD4-2 and MHC IIα were also significantly up-regulated after immunization. These results collectively demonstrated that rAHA_3793 could induce a strong humoral immune response of largemouth bass, and then produce high immune protection effects against A. hydrophila infection. [ABSTRACT FROM AUTHOR]

Populations of the bottlenose wedgefish (Rhynchobatus australiae) in the Indo-West Pacific (IWP) have declined by nearly 80% in recent decades. In response, IWP countries are establishing sanctuaries to provide refuge for the fish. However, little is known about the genetic stock structure of the fish in the region. Hence, this study analysed partial sequences (610 base pairs) of the cytochrome oxidase subunit (COI) gene from eight bottlenose wedgefish populations in the IWP to assess the genetic stock structure of the fishery. The sequences revealed that Western Indian Ocean (WIO) populations are genetically distinct from those in the West Pacific (WP) (FCT = 0.24, p = 0.01) and Australia (FCT = 0.88, p = 0.01). Similarly, WP populations were genetically distinct from Australian populations (FCT = 0.42, p = 0.01). This suggests that the IWP contains three genetically distinct stocks of the bottlenose wedgefish: the WIO, WP, and Australia. The indices of genetic diversity and population size showed that the WIO stock has low genetic diversity and population size when compared to the WP and Australia. This shows that efforts to establish elasmobranch sanctuaries in the IWP should take into account the three identified stocks, with priority given to the WIO. [ABSTRACT FROM AUTHOR]

The document provides information about continuing education courses offered at a fisheries conference. The courses cover a range of topics including data visualization, data analysis, genetics, Bayesian inference, and science communication. The instructors come from various institutions and organizations, ensuring diverse perspectives. The courses are offered at different times throughout the conference, and fees vary depending on membership status. [Extracted from the article]

Supportive breeding programmes are becoming increasingly crucial for the conservation of many declining freshwater fishes such as the European common nase, Chondrostoma nasus. However, small relict populations are genetically highly vulnerable, and supportive breeding can have a detrimental impact on the genetic composition of the cultured offspring (e.g. as a result of inbreeding, genetic drift, and adaptation to captivity).This study monitored the genetic effects of a continuing supportive breeding programme of common nase by comparing the genetic diversity of two wild spawning populations with the respective wild offspring and the progeny from captive breeding originating from spawners of the two wild populations, considering genetic variability, genetic differentiation, and inbreeding effects using nine microsatellite markers.Despite low genetic differentiation, the offspring from captive breeding and from one of the natural populations (River Sims) were remarkably different genetically, as indicated by pairwise analyses of genetic divergence (FST from 0.028 to 0.070; Jost's DEST from 0.080 to 0.205) and the discriminant analysis of principal components. The mean number of alleles and mean allelic richness in the captive‐bred offspring and also in the wild offspring of the River Sims were lower than for wild populations of spawners and natural offspring of the River Mangfall, and signs of inbreeding effects were detected (F = 0.106 for captive bred and 0.048 for natural offspring).The observed effects can probably be attributed to the limited number of spawners (two females and three males) used for captive breeding. In addition, the results support previous evidence on recruitment problems of the Sims population, such as a reduced hatching success.Collecting fertilized eggs from the wild and rearing them in captivity (repatriation approach) could be an alternative to stripping a limited number of spawners and thereby to improve the conservation of genetic diversity of natural populations. [ABSTRACT FROM AUTHOR]

Eighty nine (42%) of Canada's 215 freshwater fish species have been assessed as at risk by the Committee on the Status of Endangered Wildlife in Canada. This study examines genomic population structure of the at-risk Grass Pickerel (Esox americanus vermiculatus), a small (≤ 33 cm) predatory fish that in Canada has a range spanning approximately 114,000 km2 of southern Ontario. Within this range it occupies approximately ten sites that are mostly shallow, weedy, and slow-flowing. Its populations and habitat are declining. This study defines population clusters and quantifies genomic diversity within and between populations based on > 5500 loci and > 950 SNPs from genomes of 66 individuals representing the subspecies' entire Canadian range. Ordination and STRUCTURE analyses revealed four major geographic/genomic clusters centered in the Georgian Bay-Severn River, southeastern shore of Lake Huron, Niagara Peninsula, and upper St. Lawrence River. Major clusters were distinguished by relatively high Hudson Fst values (0.205–0.480), with Georgian Bay-Severn River being consistently most distinct. The Niagara Peninsula major cluster contained an additional three discernable sub-clusters differentiated by Fst values as great or greater than major clusters, despite spanning only ca. 200 km2. Genomically distinct Niagara sub-clusters occurred in Abino Drain, Big Forks Creek, and Tea Creek. Samples from sites between both major and minor clusters exhibited admixture from adjacent clusters. Despite current management of Grass Pickerel under a single designatable unit throughout its Canadian range, we map considerable geographic population structure that should help guide the designation of additional conservation units. [ABSTRACT FROM AUTHOR]

This study was designed to generate the full-length transcriptome of Coilia nasus using single-molecule long read isoform sequencing (SMRT-seq) technology. RNAs of brains, ovaries, and testes of C. nasus conditioned in both seawater and freshwater except for gut which was only from the fish conditioned in freshwater, were isolated. All the RNAs were pooled together equally for SMRT sequencing. One SMRT cell produced 64.18 Gb clean data, including 765,184 circular consensus (CCS) reads and 616,126 full-length non-chimeric (FLNC) reads. Finally, 93,793 non-redundant transcripts were obtained after clustered and polished. Structural analysis of the 93,793 non-redundant transcripts predicted 8242 alternative splicing events, a total of 229,825 SSR and 72,037 complete CDS. A total of 8437 lncRNA were identified. 84,617 transcripts were annotated in NR, Swissprot, GO, COG, KOG, eggnog, Pfam and KEGG database totally. This is the first full-length transcriptome of Coilia nasus, including transcripts appeared in the case of seawater, which will facilitate exploration of genetic data and life story of Coilia nasus. [ABSTRACT FROM AUTHOR]

Salmon lice have plagued the salmon farming industry and have negatively impacted salmon populations in the wild. In response, researchers have generated high density genetic maps, genome assemblies, transcriptomes, and whole-genome resequencing data to better understand this parasite. In this study, we used long-read sequencing technology to update the previous genome assemblies of Atlantic Ocean salmon lice with a more contiguous assembly and a more comprehensive gene catalog of Pacific Ocean salmon lice. We were also able to further characterize genomic features previously identified from other studies by using published resequenced genomes of 25 Atlantic and 15 Pacific salmon lice. One example was further characterizing the ZW sex chromosomes. For both the Atlantic and Pacific Ocean salmon lice subspecies, we found that the female W-chromosome is only a small fraction of the Z-chromosome and that the vast majority of theWand Z-chromosome do not contain conserved regions (i.e. pseudoautosomal regions). However, conserved orthologous protein sequences can still be identified between the W- and Z-chromosomes. [ABSTRACT FROM AUTHOR]

Suitable reference genes are one of the necessary conditions for obtaining reliable results by real-time fluorescence quantitative PCR (qPCR). In this study, the expression of the 10 common candidate reference genes (18s rRNA, rps27, cnbp, rpl7, ube2, hsp-at, gapdh, β-actin, rpl13a, 1-ef1a) at different developmental stages of gonad and embryo of Takifugu bimaculatus were analyzed by qPCR. And the expression stability of these reference genes is analyzed by GeNorm, NormFinder and Bestkeeper softwares. The results showed that the expression stability of 1-ef1a was the highest (p < 0.05) combined with the results of three analysis softwares, and the optimal number of reference genes was 3, which were 1-ef1a, hsp-at and rps27. Based on this result, we analyzed the expression of objective genes (foxl2 and dmrt1) at different developmental stages (early, medium-term and late) of gonads and embryos (eye vesicle stage, motility stage, heart anlage stage, retinal pigmentation stage, newly hatched larva) of T. bimaculatus by qPCR. Among which the highest expression level of foxl2 was in the middle stage of ovary (p < 0.05), and dmrt1 was expressed in the early stage of testis with the highest level (p < 0.05). The expression levels of foxl2 and dmrt1 in the early stages of embryonic development were low or even almost non-existent, and had a slight increase in the late embryonic development (newly hatched larva). The expression profile of objective genes are consistent with their roles in the development of gonads and embryos, which indicates that 1-ef1a, hspat and rps27 are the suitable reference gene combination for detecting the expression of objective genes by qPCR in gonads and embryos of T. bimaculatus. This research also provides the reliability data for screening the reference genes by qPCR in fish. [ABSTRACT FROM AUTHOR]

Non‐motile strains of Yersinia ruckeri, known as Y. ruckeri biotype 2, now dominate amongst clinical isolates retrieved from rainbow trout internationally. Due to an acute increase in the number of yersiniosis cases in Norway in recent years, followed by introduction of widespread intraperitoneal vaccination against the disease, an investigation on the prevalence of Y. ruckeri biotype 2 in Norwegian aquaculture was conducted. We biotyped 263 Y. ruckeri isolates recovered from diseased salmonids in Norway between 1985 and 2020. A total of seven biotype 2 isolates were identified, four of which were collected between 1985 and 1987, and three of which belong to the current epizootic clone, isolated from two different sea‐farms in 2017. Whole‐genome sequencing revealed single non‐synonymous nucleotide polymorphisms in the flagellar genes flhC in isolates from the 1980s, and in fliP in isolates from 2017. In both variants, motility was restored both by complementation with wild‐type alleles in trans and via spontaneous mutation‐driven reversion following prolonged incubation on motility agar. While biotype 2 strains do not yet seem to have become broadly established in Norwegian aquaculture, the seven isolates described here serve to document a further two independent cases of Y. ruckeri biotype 2 emergence in salmonid aquaculture. [ABSTRACT FROM AUTHOR]

The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3–1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies. [ABSTRACT FROM AUTHOR]

Simple Summary: Stock enhancement aggressively replenishes depleted wild finfish populations. However, stock enhancement of black sea bream in Taiwan with complex genetic sources, especially when successful, maintains genetic diversity but dramatically changes the genetic structure within and among wild populations. Stock enhancement, used for replenishing depleted wild finfish populations, is an aggressive approach. Stock enhancement projects in Taiwan involve black sea bream (Acanthopagrus schlegelii), a major commercial species. During 2004–2015, even management agencies conducted stock enhancement projects, leading to numerous private releases that have not been recorded. Stock enhancement by a private hatchery without accurate genetic records may lead to a genetic structure change in wild populations. Using allele frequencies at nine microsatellite loci, we studied the genetic effects of stock enhancement in 19 samples collected from populations in the hatcheries and the wild. In 458 individuals from nine hatchery samples, most populations showed weak but significant genetic differences and complex clusters in structure analysis, indicating dramatic stock change within and among hatcheries. The 10 wild populations (n = 773) also had a complex genetic composition and were genetically different among sampling sites and times. However, a simple and clear cluster in structure analysis was found for only one sampling site, which had no release history. Thus, stock enhancement with complex genetic sources helps maintain genetic diversity but dramatically changes the genetic structure within and among wild populations, especially when stock enhancement is successful. [ABSTRACT FROM AUTHOR]

Hatchery production and fisheries stocking is a widespread and high profile management practice because it allows recreational fisheries to continue in threatened species. Human-mediated transfer of fish across the geographic boundaries of intraspecies lineages or closely related species can cause introgression and occasionally outbreeding depression. Hybridization can be difficult to detect due to limited morphological differences among close lineages and the relatively low power of traditional genetic datasets. Here we showcase the use of genomic techniques to detect admixture of the economically important and threatened golden perch (Macquaria ambigua) in the Murray-Darling Basin, southeast Australia. We detected admixture through a genome-wide dataset of 6,862 single nucleotide polymorphisms (SNPs) across 174 Murray-Darling sourced fish and 15 fish from each of two neighbouring basins: the Lake Eyre and Fitzroy basins. Individuals with partial ancestry from both neighboring basins were detected using genomics throughout the Murray-Darling, suggesting the release of individuals and introgression into the Murray-Darling Basin. Importantly, a traditional microsatellite dataset was unreliable for identifying admixed individuals. The SNP-detected admixed individuals were also found in Murray-Darling impoundments, where fish are solely sourced from government-managed hatcheries, suggesting that some broodstock in hatcheries might have non-endemic ancestry. Stocking programs for golden perch release over one million fingerlings each year, and so could impact the genetic variation in the wild. We advocate for using genomics to check the ancestry of broodstock and for increasing collaboration between managers and academics—as done here—to better integrate the power of genomics into biodiversity management and conservation. [ABSTRACT FROM AUTHOR]

Stock enhancement is one of the potential management strategies for the fishery. To better understand the impaction of stock enhancement, we simulated an experiment for lined seahorse (Hippocampus erectus) and evaluated the genetic structure after stock enhancement. In this study, we found the numbers of alleles (N A ) and heterozygosity (H O ) of stock enhancement strains were lower than those of the wild collections, while the inbreeding coefficient (F IS ) and relatedness index were higher. Within the 3 generations of stock enhancement strain, the N A , H O and polymorphism information content (PIC) didn't change significantly. In addition, the F ST value indicated that the genetic differentiation between the stock enhancement strains and the first wild collection reached an intermediate level, which could lead to substructuring in wild populations. Overall, these findings revealed a potential genetic risk associated with the release of hatchery strains into wild populations. [ABSTRACT FROM AUTHOR]

Through this paper, we aim to report the research within the group of poeciliid fishes and compare it to the current state of the art genomic research. We also want to show the importance of combining the two fields, one zoological and the other molecular, for the development of knowledge. The sequencing of the Saccharomyces cerevisiae genome was a major milestone in genomics and has since led to the sequencing of many other eukaryotic genomes, including those of humans, mice, and many other species. With the genomic era, genome sequencing began in many vertebrates, including poeciliid fishes. Poeciliids are a diverse family of freshwater fish that includes popular aquarium fish such as guppies, mollies, and swordtails. There are two species of Poeciliid fish whose genomes have been sequenced: Poecilia reticulata Peters, 1859 and Xiphophorus maculatus (Günther, 1866). Moreover, we have the mitochondrial genome sequenced in several other poeciliid species: Poecilia formosa (Girard, 1859), Xiphophorus variatus (Meek, 1904), Xiphophorus hellerii Heckel, 1848, Xiphophorus couchianus (Girard, 1859), Poecilia parae Eigenmann, 1894, Poecilia latipinna (Lesueur, 1821), Poecilia mexicana Steindachner, 1863. These genome sequences provide valuable resources for researchers studying the genetics of poeciliid fish and their evolutionary history. By sequencing an animal's genome, we can identify the genes and genetic variants responsible for various traits such as disease susceptibility, growth rate, and behavior. This knowledge can be used to develop new therapies and treatments, improve breeding strategies, and enhance animal welfare. [ABSTRACT FROM AUTHOR]

Esterase enzymes catalyse the formation and breakdown of carboxylic acid esters of alcohols. The present work aimed to study the electrophoretic banding patterns of esterase isozymes in fresh water fish Channa punctatus The results revealed that the electrophoretic esterase banding patterns varied in different tissues i.e. gill, liver, intestine, muscle, and brain of fish c. puctatus Esterase patterns were separated on thin layer 1.5mm (thickness) polyacrylamide gels (SDS-7.5 ) and stained with α-naphthyl acetate used as substrate. Three different esterase bands were detected and named as Esi-1; Est-2; and Est-3; with different relative mobilities such as 0.6 ±0.05; 0.4±0.05; 0.3±0.05. All the three esterase bands were found in all tissues i.e. gill, liver, intestine, muscle and brain. Among the three esterases Est-1 is found in all the tissues. Est-2 and Est-3 were found in all the tissues. Studies on esterases of fishes and other organisms revealed similar type of patterns of esterase were noticed in one or the other tissue of all the animals. [ABSTRACT FROM AUTHOR]