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Fishways are built on obstacles to restore the connectivity between aquatic habitats. Our study investigated how species-specific fishways interact with interindividual trait differences among fish. We compared several groups of glass eels (Anguilla anguilla) climbing two types of fishways with those remaining below the water impoundments. We analyzed relative body condition factor, body length, mass, and in vitro activities and gene transcription levels of several enzymes involved in the energy metabolism (LDH, CS, CCO, PK). Differences among groups indicated that glass eel fish ladders can be size- specific, according to the type of substrate covering the surface of apparatus. Moreover, we found that climbing specific glass eel ladders can require higher endurance-related metabolic traits, triggering increased aerobic capacities. Increased aerobic efforts together with potential size selectivity of fishways should be taken into account when designing such devices and choosing appropriate location on eel migratory pathways. Les passes a poissons sont construites sure les obstacle pour restaurer la connectivity entre les habitats aquatiques. Notre etude s'interessait a la maniere dont les passes specifiques a une espece interagissent avec la variability individuelle des poissons. Nous avons compare des groupes d'anguillettes (Anguilla anguilla) escaladant deux types de passes installees sur des obstacles aquatiques. Nous avons analyse le facteur de condition relatif, taille, poids, ainsi que l'activite in vitro et le niveau de transcription genetique des plusieurs enzymes impliquees dans le metabolisme energetique (LDH, CS, CCO, PK). Les differences entre les groupes montrent que le substrat de ces passes peut etre specifique a la taille du poisson. De plus, nous avons trouve que l'escalade des echelles a anguilles peut demander un effort musculaire particulier, lie aux capacites aerobies des individus. Les efforts aerobies accrus ainsi qu'une selectivite potentielle des passes doit etre prise en compte lors de la conception de ce type de dispositifs tout comme leur emplacement geographique le long du trajet migratoire de l'anguille., Introduction Diadromous migrations are challenging life-history stages, particularly for semelparous species with a single opportunity to secure lifetime fitness (Dingle 1996). Animals traveling through freshwater corridors to reach their breeding [...]

Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.

In vertebrates, the somatotropic axis comprising the pituitary gland, liver and muscle plays a major role in myogenesis. Its output in terms of muscle growth is highly affected by nutritional and environmental cues, and thus likely epigenetically regulated. Hydroxymethylation is emerging as a DNA modification that modulates gene expression but a holistic characterization of the hydroxymethylome of the somatotropic axis has not been investigated to date. Using reduced representation 5-hydroxymethylcytosine profiling we demonstrate tissue-specific localization of 5-hydroxymethylcytosines at single nucleotide resolution. Their abundance within gene bodies and promoters of several growth-related genes supports their pertinent role in gene regulation. We propose that cytosine hydroxymethylation may contribute to the phenotypic plasticity of growth through epigenetic regulation of the somatotropic axis., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Growth is a complex trait whose variability within a population cannot be explained solely by genetic variation. Epigenetic regulation is often suggested as an important factor shaping the phenotype, but its association with growth can be highly context- and species-dependent. Nevertheless, the mechanisms involved in epigenetic regulation of growth in fish are poorly understood. We have used reduced representation bisulphite sequencing to determine the genome-wide CpG methylation patterns in male and female Nile tilapia of different sizes but at the same early stage of domestication. The average CpG methylation level in the reduced genome representation was 63% across groups but many sites displayed group-specific methylation patterns. The number of differentially methylated (DM) CpGs was much higher when the interaction between sex and weight was included rather than when these factors were considered separately. There were 1128 DM CpGs between large and small females and 970 DM CpGs between large and small males. We have found many growth-related genes associated with DM CpGs, namely map3k5 and akt3 in females and gadd45g and ppargc1a in males. Only 5% of CpG locations associated with growth were common to both sexes. In particular, the autophagy-related gene atg14 displayed a high association of methylation with growth exclusively in males. The sexually dimorphic association between atg14 methylation and growth may uncover novel metabolic mechanisms at play during mouth brooding in Nile tilapia females. Taken together, our data suggest that epigenetic regulation of growth in Nile tilapia involves different gene networks in males and females.

Selectivity of recreational angling on fish behaviour was studied by examining whether capture order or lure type (natural v. artificial bait) in ice-fishing could explain behavioural variation among perch Perca fluviatilis individuals. It was also tested if individually assessed personality predicts fish behaviour in groups, in the presence of natural predators. Perca fluviatilis showed individually repeatable behaviour both in individual and in group tests. Capture order, capture method, condition factor or past growth rate did not explain variation in individual behaviour. Individually determined boldness as well as fish size, however, were positively associated with first entrance to the predator zone ( i.e. initial risk taking) in group behaviour tests. Individually determined boldness also explained long-term activity and total time spent in the vicinity of predators in the group. These findings suggest that individual and laboratory-based boldness tests predict boldness of P. fluviatilis in also ecologically relevant conditions, i.e. in shoals and in the presence of natural predators. The present results, however, also indicate that the above-mentioned two angling methods may not be selective for certain behavioural types in comparison to each other. [ABSTRACT FROM AUTHOR]

Background: European eel is a panmictic species, whose decline has been recorded since the last 20 years. Among human-induced environmental factors of decline, the impact of water dams during species migration is questioned. The main issue of this study was to pinpoint phenotypic traits that predisposed glass eels to successful passage by water barriers. The approach of the study was individual-centred and without any a priori hypothesis on traits involved in the putative obstacles selective pressure. We analyzed the transcription level of 14,913 genes., Results: Transcriptome analysis of three tissues (brain, liver and muscle) from individuals sampled on three successive forebays separated by water obstacles indicated different gene transcription profiles in brain between the two upstream forebays. No differences in gene transcription levels were observed in liver and muscle samples among segments. A total of 26 genes were differentially transcribed in brain. These genes encode for, among others, keratins, cytokeratins, calcium binding proteins (S100 family), cofilin, calmodulin, claudin and thy-1 membrane glycoprotein. The functional analysis of these genes highlighted a putative role of cytoskeletal dynamics and synaptic plasticity in fish upstream migration., Conclusion: Synaptic connections in brain are solicited while eels are climbing the obstacles with poorly designed fishways. Successful passage by such barriers can be related to spatial learning and spatial orientation abilities when fish is out of the water.

Embryonic temperature has a lasting impact on muscle phenotype in vertebrates, involving complex molecular mechanisms that encompass both protein-coding and non-coding genes. Circular RNAs (circRNAs) are a class of regulatory RNAs that play important roles in various biological processes, but the effect of variable thermal conditions on the circRNA transcriptome and its long-term impact on muscle growth plasticity remains largely unexplored. To fill this knowledge gap, we performed a transcriptomic analysis of circRNAs in fast muscle of Nile tilapia (Oreochromis niloticus) subjected to different embryonic temperatures (24°C, 28°C and 32°C) and then reared at a common temperature (28°C) for 4 months. Nile tilapia embryos exhibited faster development and subsequently higher long-term growth at 32°C compared to those reared at 28°C and 24°C. Next-generation sequencing data revealed a total of 5,141 unique circRNAs across all temperature groups, of which 1,604, 1,531, and 1,169 circRNAs were exclusively found in the 24°C, 28°C and 32°C groups, respectively. Among them, circNexn exhibited a 1.7-fold (log2) upregulation in the 24°C group and a 1.3-fold (log2) upregulation in the 32°C group when compared to the 28°C group. Conversely, circTTN and circTTN_b were downregulated in the 24°C groups compared to their 28°C and 32°C counterparts. Furthermore, these differentially expressed circRNAs were found to have multiple interactions with myomiRs, highlighting their potential as promising candidates for further investigation in the context of muscle growth plasticity. Taken together, our findings provide new insights into the molecular mechanisms that may underlie muscle growth plasticity in response to thermal variation in fish, with important implications in the context of climate change, fisheries and aquaculture. [ABSTRACT FROM AUTHOR]

An earlier study of ours investigating the effect of dietary lipid levels on the choline requirement of Atlantic salmon showed increasing severity of intestinal steatosis with increasing lipid levels. As choline is involved in epigenetic regulation by being the key methyl donor, pyloric caeca samples from the study were analysed for epigenetic effects of dietary lipid and choline levels. The diets varied in lipid levels between 16% and 28%, and choline levels between 1.9 and 2.3 g/kg. The diets were fed for 8 weeks to Atlantic salmon of 25 g of initial weight. Using reduced representation bisulfite sequencing (RRBS), this study revealed that increasing dietary lipid levels induced methylation differences in genes involved in membrane transport and signalling pathways, and in microRNAs important for the regulation of lipid homoeostasis. Increasing choline levels also affected genes involved in fatty acid biosynthesis and transport, lipolysis, and lipogenesis, as well as important immune genes. Our observations confirmed that choline is involved in epigenetic regulation in Atlantic salmon, as has been reported for higher vertebrates. This study showed the need for the inclusion of biomarkers of epigenetic processes in studies that must be conducted to define optimal choline levels in diets for Atlantic salmon. [ABSTRACT FROM AUTHOR]

Genome scans provide a comprehensive method to explore genome‐wide variation associated with traits under study. However, linking individual genes to broader functional groupings and pathways is often challenging, yet crucial for understanding the evolutionary mechanisms underlying these traits. This task is particularly relevant for multi‐trait processes such as domestication, which are influenced by complex interactions between numerous genetic and non‐genetic factors, including epigenetic regulation. As various traits within the broader spectrum of domestication are selected in concert over time, this process offers an opportunity to identify broader functional overlaps and understand the integrated genetic architecture underlying these traits. In this study, we analyzed approximately 600,000 SNPs from a Pool‐Seq experiment comparing eight natural‐origin and 12 farmed populations of European seabass in the Mediterranean Sea region. We implemented two genome scan approaches and focused on genomic regions supported by both methods, resulting in the identification of 96 candidate genes, including nine CpG islands, which highligt potential epigenetic influences. Many of these genes and CpG islands are in linkage groups previously associated with domestication‐related traits. The most significantly overrepresented molecular function was "oxidoreductase activity". Furthermore, a dense network of interactions was identified, connecting 22 of the candidate genes. Within this network, the most significantly enriched pathways and central genes were involved in "chromatin organization", highlighting another potential epigenetic mechanism. Altogether, our findings underscore the utility of interactome‐assisted pathway analysis in elucidating the genomic architecture of polygenic traits and suggest that epigenetic regulation may play a crucial role in the domestication of European seabass. [ABSTRACT FROM AUTHOR]

Somatic growth in vertebrates is mainly controlled by the growth hormone (GH)/insulin-like growth factor I (IGF-I) axis. The role of epigenetic mechanisms in regulating this axis in fish is far from being understood. This work aimed to optimize and evaluate the use of short-term culture of pituitary and liver explants from a farmed fish, the gilthead seabream Sparus aurata, for studying epigenetic mechanisms involved in GH/IGF-I axis regulation. Our results on viability, structure, proliferation, and functionality of explants support their use in short-term assays. Pituitary explants showed no variation in gh expression after exposure to the DNA methylation inhibitor decitabine (5-Aza-2'-deoxycytidine; DAC), despite responding to DAC by changing dnmt3bb and tet1 expression, and TET activity, producing an increase in overall DNA hydroxymethylation. Conversely, in liver explants, DAC had no effects on dnmts and tets expression or activity, but modified the expression of genes from the GH-IGF-I axis. In particular, the expression of igfbp2a was increased and that of igfbp4, ghri and ghrii was decreased by DAC as well as by genistein, which is suggestive of impaired growth. While incubation of liver explants with S-adenosylmethionine (SAM) produced no clear effects, it is proposed that nutrients must ensure the methylation milieu within the liver in the fish to sustain proper growth, which need further in vivo verification. Pituitary and liver explants from S. aurata can be further used as described herein for the screening of inhibitors or activators of epigenetic regulators, as well as for assessing epigenetic mechanisms behind GH-IGF-I variation in farmed fish. [ABSTRACT FROM AUTHOR]

River flow intermittence is a natural phenomenon intensified by human activities, such as water abstraction and the effects of climate change. A growing number of rivers are predicted to experience intermittent flows, which may impact the diversity and abundance of freshwater species. Dry riverbeds directly diminish the availability of habitats for freshwater organisms, and suitable environments can turn into ecological traps with reduced survival rates, posing a significant threat to population persistence. Even though fish movements can enable drought-affected populations to persist, little is known about individual fish movement between intermittent and perennial reaches. Here, we study the movement of individual PIT-tagged Italian riffle dace (Telestes muticellus) in an intermittent and perennial river reach before, during and after two severe drying events. A high proportion of fish from the intermittent reach survived the drying riverbed through directed upstream migration. This was manifested in fish living in the intermittent reach of the river displaying significantly higher linear ranges, and net travelled distances during the monitoring period than fish in the perennial reach, which remained resident with limited linear range and net distances travelled. This finding underscores the importance of conserving longitudinal river connectivity in the face of increased water scarcity and intermittent flow patterns. [ABSTRACT FROM AUTHOR]

The article "Where Have All the Good Editors Gone? - A Necessary Polemic" addresses the issue of poor editing in aquaculture journals. The author criticizes the publication of papers with fake bibliographies and inadequate identification of studied organisms, which lack commentary or peer review. They also question the absence of "Letters to the Editor" sections and the use of product names instead of scientific terms. The article emphasizes the importance of accurate species characterization and proper nomenclature in scientific research. The author argues for the need for knowledgeable editors who can set scientific standards and suggests the inclusion of "Letters to the Editor" to encourage discussion and debate. [Extracted from the article]

Optimising the design of passage facilities to restore fluvial connectivity for juvenile European eel (Anguilla anguilla) is a key priority within conservation efforts for the species, across the majority of its freshwater range. Employing an experimental setup that simulated gravity-fed upstream eel passes, this study demonstrated that novel V-profile passes, which incorporate two lateral slopes (15°), performed better than laterally flat passes over the flow rates tested (0.2–0.6 L s−1). For the small eel size used (60–80 mm length), the bristle substrate consistently outperformed studs, but the lateral slope had a greater effect on passage metrics than the substrate choice. Our findings strongly support the use of V-shaped channels for upstream migrating eel at fish passage facilities, particularly in scenarios where flow rates may be elevated and/or fluctuating, such as for gravity-fed passes. [ABSTRACT FROM AUTHOR]

Early embryonic development is crucially important but also remarkably diverse among animal taxa. Axis formation and cell lineage specification occur due to both spatial and temporal control of gene expression. This complex system involves various signaling pathways and developmental genes such as transcription factors as well as other molecular interactants that maintain cellular states, including several types of epigenetic marks. 5mC DNA methylation, the chemical modification of cytosines in eukaryotes, represents one such mark. By influencing the compaction of chromatin (a high-order DNA structure), DNA methylation can either repress or induce transcriptional activity. Mammals exhibit a reprogramming of DNA methylation from the parental genomes in the zygote following fertilization, and later in primordial germ cells (PGCs). Whether these periods of methylation reprogramming are evolutionarily conserved, or an innovation in mammals, is an emerging question. Looking into these processes in other vertebrate lineages is thus important, and teleost fish, with their extensive species richness, phenotypic diversity, and multiple rounds of whole genome duplication, provide the perfect research playground for answering such a question. This review aims to present a concise state of the art of DNA methylation reprogramming in early development in fish by summarizing findings from different research groups investigating methylation reprogramming patterns in teleosts, while keeping in mind the ramifications of the methodology used, then comparing those patterns to reprogramming patterns in mammals., (© 2024 Wiley Periodicals LLC.)

Background: Broodstock nutritional programming improves the offspring utilization of plant-based diets in gilthead sea bream through changes in hepatic metabolism. Attention was initially focused on fatty acid desaturases, but it can involve a wide range of processes that remain largely unexplored. How all this can be driven by a different genetic background is hardly underlined, and the present study aimed to assess how broodstock nutrition affects differentially the transcriptome and genome-wide DNA methylome of reference and genetically selected fish within the PROGENSA® selection program. Results: After the stimulus phase with a low fish oil diet, two offspring subsets of each genetic background received a control or a FUTURE-based diet. This highlighted a different hepatic transcriptome (RNA-seq) and genome-wide DNA methylation (MBD-seq) pattern depending on the genetic background. The number of differentially expressed transcripts following the challenge phase varied from 323 in reference fish to 2,009 in genetically selected fish. The number of discriminant transcripts, and associated enriched functions, were also markedly higher in selected fish. Moreover, correlation analysis depicted a hyper-methylated and down-regulated gene expression state in selected fish with the FUTURE diet, whereas the opposite pattern appeared in reference fish. After filtering for highly represented functions in selected fish, 115 epigenetic markers were retrieved in this group. Among them, lipid metabolism genes (23) were the most reactive following ordering by fold-change in expression, rendering a final list of 10 top markers with a key role on hepatic lipogenesis and fatty acid metabolism (cd36, pitpna, cidea, fasn, g6pd, lipt1, scd1a, acsbg2, acsl14, acsbg2). Conclusions: Gene expression profiles and methylation signatures were dependent on genetic background in our experimental model. Such assumption affected the magnitude, but also the type and direction of change. Thus, the resulting epigenetic clock of reference fish might depict an older phenotype with a lower methylation for the epigenetically responsive genes with a negative methylation-expression pattern. Therefore, epigenetic markers will be specific of each genetic lineage, serving the broodstock programming in our selected fish to prevent and mitigate later in life the risk of hepatic steatosis through changes in hepatic lipogenesis and fatty acid metabolism. [ABSTRACT FROM AUTHOR]

Background: Tilapia is one of the most essential farmed fishes in the world. It is a tropical and subtropical freshwater fish well adapted to warm water but sensitive to cold weather. Extreme cold weather could cause severe stress and mass mortalities in tilapia. The present study was carried out to investigate the effects of cold stress on the up-regulation of antifreeze protein (AFP) genes in Nile tilapia (Oreochromis niloticus). Two treatment groups of fish were investigated (5 replicates of 15 fish for each group in fibreglass tanks/70 L each): 1) a control group; the fish were acclimated to lab conditions for two weeks and the water temperature was maintained at 25 °C during the whole experimental period with feeding on a commercial diet (30% crude protein). 2) Cold stress group; the same conditions as the control group except for the temperature. Initially, the temperature was decreased by one degree every 12 h. The fish started showing death symptoms when the water temperature reached 6–8 °C. In this stage the tissue (muscle) samples were taken from both groups. The immune response of fish exposed to cold stress was detected and characterized using Differential Display-PCR (DD-PCR). Results: The results indicated that nine different up-regulation genes were detected in the cold-stressed fish compared to the control group. These genes are Integrin-alpha-2 (ITGA-2), Gap junction gamma-1 protein-like (GJC1), WD repeat-containing protein 59 isoform X2 (WDRP59), NUAK family SNF1-like kinase, G-protein coupled receptor-176 (GPR-176), Actin cytoskeleton-regulatory complex protein pan1-like (PAN-1), Whirlin protein (WHRN), Suppressor of tumorigenicity 7 protein isoform X2 (ST7P) and ATP-binding cassette sub-family A member 1-like isoform X2 (ABCA1). The antifreeze gene type-II amplification using a specific PCR product of 600 bp, followed by cloning and sequencing analysis revealed that the identified gene is antifreeze type-II, with similarity ranging from 70 to 95%. The in-vitro transcribed gene induced an antifreeze protein with a molecular size of 22 kDa. The antifreeze gene, ITGA-2 and the WD repeat protein belong to the lectin family (sugar–protein). Conclusions: In conclusion, under cold stress, Nile tilapia express many defence genes, an antifreeze gene consisting of one open reading frame of approximately 0.6 kbp. [ABSTRACT FROM AUTHOR]

A refugial population of the endangered delta smelt (Hypomesus transpacificus) has been maintained at the Fish Conservation and Culture Laboratory (FCCL) at UC Davis since 2008. Despite intense genetic management, fitness differences between wild and cultured fish have been observed at the FCCL. To investigate the molecular underpinnings of hatchery domestication, we used whole-genome bisulfite sequencing to quantify epigenetic differences between wild and hatchery-origin delta smelt. Differentially methylated regions (DMRs) were identified from 104 individuals by comparing the methylation patterns in different generations of hatchery fish (G1, G2, G3) with their wild parents (G0). We discovered a total of 132 significant DMRs (p < .05) between G0 and G1, 132 significant DMRs between G0 and G2, and 201 significant DMRs between G0 and G3. Our results demonstrate substantial differences in methylation patterns emerged between the wild and hatchery-reared fish in the early generations in the hatchery, with a higher proportion of hypermethylated DMRs in hatchery-reared fish. The rearing environment was found to be a stronger predictor of individual clustering based on methylation patterns than family, sex or generation. Our study indicates a reinforcement of the epigenetic status with successive generations in the hatchery environment, as evidenced by an increase in methylation in hypermethylated DMRs and a decrease in methylation in hypomethylated DMRs over time. Lastly, our results demonstrated heterogeneity in inherited methylation pattern in families across generations. These insights highlight the long-term consequences of hatchery practices on the epigenetic landscape, potentially impacting wild fish populations., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

DNA methylation is an epigenetic alteration that impacts gene expression without changing the DNA sequence affecting an organism's phenotype. This study utilized a reduced representation bisulfite sequencing (RRBS) approach to investigate the patterns of DNA methylation in genetically selected Clarias magur stocks. RRBS generated 249.22 million reads, with an average of 490,120 methylation sites detected in various parts of genes, including exons, introns, and intergenic regions. A total of 896 differentially methylated regions (DMRs) were identified; 356 and 540 were detected as hyper-methylated and hypo-methylated regions, respectively. The DMRs and their association with overlapping genes were explored using whole genome data of magur, which revealed 205 genes in exonic, 210 in intronic, and 480 in intergenic regions. The analysis identified the maximum number of genes enriched in biological processes such as RNA biosynthetic process, response to growth factors, nervous system development, neurogenesis, and anatomical structure morphogenesis. Differentially methylated genes (DMGs) such as myrip, mylk3, mafb, egr3, ndnf, meis2a, foxn3, bmp1a, plxna3, fgf6, sipa1l1, mcu, cnot8, trim55b, and myof were associated with growth and development. The selected DMGs were analyzed using real-time PCR, which showed altered mRNA expression levels. This work offers insights into the epigenetic mechanisms governing growth performance regulation in magur stocks. This work provides a valuable resource of epigenetic data that could be integrated into breeding programs to select high-performing individuals., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Background: The combination of the increasing demand of freshwater crayfish exports, the reduced population sizes due to overfishing, the crayfish plague epidemics and the habitat degradation, have led to unrecorded translocations of Pontastacus leptodactylus in Greek lakes., Methods and Results: In the present study, the genetics of five narrow clawed crayfish (P. leptodactylus) populations were studied, namely three translocated populations inhabiting in Northern Greece, one native Greek population from Evros river and one potential progeny source population from Turkey. Nine microsatellite loci previously designed for the specific species were investigated, in order to assess the levels of genetic diversity and further to confirm the origin of these translocated populations some decades after the translocation events. Our results confirmed that the source population for the translocated Greek population is the Turkish lake Eğirdir. Further, despite the low values of the number of alleles, heterozygosity, and F ST the populations were generally diverse, providing evidence for local adaptation., Conclusions: The low values of F IS for the translocated populations in combination with the high values of gene flow, possibly indicate the existence of re-introducing events. Apart from the translocated populations, high levels of genetic diversity and heterozygosity were observed in Evros population, suggesting it as a possible unit for future conservation purposes both as a donor population for reintroduction purposes as well as a unique gene pool protection source. To the best of our knowledge this is the first study dealing with the genetic composition of Greek P. leptodactylus populations from Nothern Greece, operating as a first step towards the development of proper management practices for restocking events and monitoring of translocated populations., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

The biology of fish sperm, an important topic in the research of reproduction and fisheries from basic science to evolutionary and applied aspects, has implications for aquaculture management, fish breeding and biological conservation. The quality of spermatozoa plays a vital role in fish fertility, and directly affects the health and performance of offspring. Environmental factors that affect determinants of spermatozoa quality usually reflected in the DNA methylation pattern of the spermatozoa epigenome, which may change offspring's performance. The aim of the present study was to conduct a review on existing data about DNA methylation in fish spermatozoa as a biological tool for identifying the quality of offspring based on their phenotypes and performances. Furthermore, this study provides valuable knowledge from fundamental to applied sciences dealing with enhancement of breeding selection, fish reproduction and environmental adaptation. The review also describes the individual parts related to DNA methylation in fish, including overview of the methods which can be used to study DNA methylation, DNA methylation dynamics and epigenetic inheritance; identification of DNA methylation changes in sperm function in response to internal and external environment constraints, and potential relationships between DNA methylation and physiological regulation of spermatozoa quality determinants. Overall, the present study revealed that our knowledge about intergenerational inheritance of the performance and adaptability of fish through sperm DNA methylation is very limited, and no general conclusion could be approached from literature mostly due to non‐standardized experimental protocol or analytical tools. [ABSTRACT FROM AUTHOR]

Management of inland recreational fisheries would benefit from stock abundance and size structure data. Feasibly standardised angling methods such as ice fishing could produce representative catch‐per‐unit‐effort (CPUE) information on the abundance of different‐sized fish in small lakes. Here, we first used standard Nordic multimesh gillnets to obtain number‐per‐unit‐effort (NPUE), biomass‐per‐unit‐effort (BPUE) and size structure data on Eurasian perch (Perca fluviatilis) stocks in 11 small boreal lakes in summer. Second, the same lakes were ice‐fished by voluntary anglers using a pre‐defined, loosely standardised protocol to obtain angling‐based NPUE, BPUE, and length frequency distributions. Effects of environmental variables such as water oxygen concentration and light penetration on angling catch rates were controlled statistically. Neither perch Nordic gillnet NPUE nor BPUE corresponded to ice‐fishing CPUEs. However, the length distribution of the catch did not differ between methods. Our results imply that traditional ice fishing applying natural baits is relatively unselective for fish size and could produce valid length‐based indicators for management purposes while angling CPUE was poorly related to Nordic gillnet CPUE. [ABSTRACT FROM AUTHOR]

Despite significant population declines and targeted European Union regulations aimed at Anguilla anguilla conservation, little attention has been given to their status at their easternmost range. This study applies wide‐scale integrated monitoring to uncover the present‐day eel distribution in Cyprus' inland freshwaters. These are subject to increasing pressures from water supply requirements and dam construction, as seen throughout the Mediterranean. We applied environmental DNA metabarcoding of water samples to determine A. anguilla distribution in key freshwater catchments. In addition, we present this alongside 10 years of electrofishing/netting data. Refuge traps were also deployed to establish the timing of glass eel recruitment. These outputs are used together, alongside knowledge of the overall fish community and barriers to connectivity, to provide eel conservation and policy insights. This study confirm the presence of A. anguilla in Cyprus' inland freshwaters, with recruitment occurring in March. Eel distribution is restricted to lower elevation areas, and is negatively associated with distance from coast and barriers to connectivity. Many barriers to connectivity are identified, though eels were detected in two reservoirs upstream of dams. The overall fish community varies between freshwater habitat types. Eels are much more widespread in Cyprus than previously thought, yet mostly restricted to lowland intermittent systems. These findings make a case to reconsider the requirement for eel management plans. Environmental DNA‐based data collected in 2020 indicate that "present‐day" eel distribution is representative of 10‐year survey trends. Suggesting that inland freshwaters may act as an unrealized refuge at A. anguilla's easternmost range. Conservation efforts in Mediterranean freshwaters should focus on improving connectivity, therefore enabling eels to access inland perennial refugia. Thus, mitigating the impact of climate change and the growing number of fragmented artificially intermittent river systems. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes. [ABSTRACT FROM AUTHOR]

The economic costs of non-indigenous species (NIS) are a key factor for the allocation of efforts and resources to eradicate or control baneful invasions. Their assessments are challenging, but most suffer from major flaws. Among the most important are the following: (1) the inclusion of actual damage costs together with various ancillary expenditures which may or may not be indicative of the real economic damage due to NIS; (2) the inclusion of the costs of unnecessary or counterproductive control initiatives; (3) the inclusion of controversial NIS-related costs whose economic impacts are questionable; (4) the assessment of the negative impacts only, ignoring the positive ones that most NIS have on the economy, either directly or through their ecosystem services. Such estimates necessarily arrive at negative and often highly inflated values, do not reflect the net damage and economic losses due to NIS, and can significantly misguide management and resource allocation decisions. We recommend an approach based on holistic costs and benefits that are assessed using likely scenarios and their counter-factual. [ABSTRACT FROM AUTHOR]

Morphology and feature selection are key approaches to address several issues in fisheries science and stock management, such as the hypothesis of admixture of Caspian common carp (Cyprinus carpio) and farmed carp stocks in Iran. The present study was performed to investigate the population classification of common carp in the southern Caspian basin using data mining algorithms to find the most important characteristic(s) differing between Iranian and farmed common carp. A total of 74 individuals were collected from three locations within the southern Caspian basin and from one farm between November 2015 and April 2016. A dataset of 26 traditional morphometric (TMM) attributes and a dataset of 14 geometric landmark points were constructed and then subjected to various machine learning methods. In general, the machine learning methods had a higher prediction rate with TMM datasets. The highest decision tree accuracy of 77% was obtained by rule and decision tree parallel algorithms, and "head height on eye area" was selected as the best marker to distinguish between wild and farmed common carp. Various machine learning algorithms were evaluated, and we found that the linear discriminant was the best method, with 81.1% accuracy. The results obtained from this novel approach indicate that Darwin's domestication syndrome is observed in common carp. Moreover, they pave the way for automated detection of farmed fish, which will be most beneficial to detect escapees and improve restocking programs. [ABSTRACT FROM AUTHOR]

The astonishing diversity of brain sizes observed across the animal kingdom is typically explained in the context of trade‐offs: the benefits of a larger brain, such as enhanced cognitive ability, are balanced against potential costs, such as increased energetic demands. Several hypotheses have been formulated in this framework, placing different emphasis on ecological, behavioural, or physiological aspects of trade‐offs in brain size evolution. Within this body of work, there exists considerable taxonomic bias towards studies of birds and mammals, leaving some uncertainty about the generality of the respective arguments. Here, we test three of the most prominent such hypotheses, the 'expensive tissue', 'social brain' and 'cognitive buffer' hypotheses, in a large dataset of fishes, derived from a publicly available resource (FishBase). In accordance with predictions from the 'expensive tissue' and the 'social brain' hypothesis, larger brains co‐occur with reduced fecundity and increased sociality in at least some Classes of fish. Contrary to expectations, however, lifespan is reduced in large‐brained fishes, and there is a tendency for species that perform parental care to have smaller brains. As such, it appears that some potential costs (reduced fecundity) and benefits (increased sociality) of large brains are near universal to vertebrates, whereas others have more lineage‐specific effects. We discuss our findings in the context of fundamental differences between the classically studied birds and mammals and the fishes we analyse here, namely divergent patterns of growth, parenting and neurogenesis. As such, our work highlights the need for a taxonomically diverse approach to any fundamental question in evolutionary biology. [ABSTRACT FROM AUTHOR]

Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes may have also facilitated early self-domestication in humans. Here, we argue that fish species, which have been recently domesticated, can provide model systems to study epigenetic drivers in human self-domestication. To test this, we used in silico approaches to compare genes with epigenetic changes in early domesticates of European sea bass with genes exhibiting methylation changes in anatomically modern humans (comparison 1), and neurodevelopmental cognitive disorders considered to exhibit abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome, and autism spectrum disorders (comparison 2). Overlapping genes in comparison 1 were involved in processes like limb morphogenesis and phenotypes like abnormal jaw morphology and hypopigmentation. Overlapping genes in comparison 2 affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. These findings pave the way for future studies using fish species as models to investigate epigenetic changes as drivers of human self-domestication and as triggers of cognitive disorders. [ABSTRACT FROM AUTHOR]

Resident microbial communities that can support various host functions play a key role in their development and health. In fishes, microbial symbionts are vertically transferred from the parents to their progeny. Such transfer of microbes in mouthbrooder fish species has not been reported yet. Here, we employed Nile tilapia (Oreochromis niloticus) to investigate the vertical transmission of microbes across generations using a 16S rRNA amplicon sequencing approach, based on the presence of bacteria in different generations. Our analysis revealed that the core microbiome in the buccal cavity and posterior intestine of parents shapes the gut microbiome of the progeny across generations. We speculate that the route of this transmission is via the buccal cavity. The identified core microbiome bacteria, namely Nocardioides, Propionibacterium , and Sphingomonas have been reported to play an essential role in the health and development of offspring. These core microbiome members could have specific functions in fish, similar to mammals. [ABSTRACT FROM AUTHOR]

Dams and other anthropogenic barriers have caused global ecological and hydrological upheaval in the blink of the geological eye. In the present article, we synthesize 307 studies in a systematic review of contemporary evolution following reduced connectivity and habitat alteration on freshwater fishes. Genetic diversity loss was more commonly observed for small populations impounded in small habitat patches for many generations behind low-passability barriers. Studies show that impoundments can cause rapid adaptive evolution in migration timing, behavior, life history, temperature tolerance, and morphology, as well as reduce phenotypic variance, which can alter adaptive potential and ecological roles. Fish passage structures can restore migratory populations but also create artificial selection pressures on body size and migration. The accelerating pace of dam removals and the paucity of data for fishes other than salmonids, other vertebrates, invertebrates, and tropical and southern hemisphere organisms highlights the urgent need for more studies on the rapid evolutionary effects of dams. [ABSTRACT FROM AUTHOR]

Invasive alien species (IAS) are leading to the homogenisation of taxonomic and functional biodiversity, with negative consequences for key ecosystem processes in fresh water. Invasive signal crayfish (Pacifastacus leniusculus) is expected to disrupt detritus‐based food webs by affecting leaf breakdown and/or by decreasing invertebrate density and diversity through predation. The combination of per‐capita and abundance effects of P. leniusculus in invaded ecosystems is still largely unknown.A four‐week field experiment was established in Rabaçal and Tuela Rivers (NE Portugal) to assess effects of P. leniusculus on invertebrate taxonomic and functional diversity and leaf litter breakdown following a gradient of invasion. We controlled the presence and absence of crayfish by placing the animals and leaf litter inside cages at six sites (three sites per river) according to the crayfish in situ abundance (absent, low, high). Cages were covered with coarse‐ or fine‐mesh net to allow or prevent invertebrates from accessing the leaves.Results showed that higher crayfish in situ abundance led to a decrease in abundance, richness and Shannon diversity of invertebrates and to changes in the communities' structures. Higher crayfish abundance led also to a decrease in invertebrate functional redundancy and an increase in the percentage of invertebrate taxa with resistance forms. Leaf litter breakdown increased with crayfish presence and decreased at sites with higher crayfish abundance.Overall, signal crayfish changed the community structure of invertebrates, with potential severe long‐term effects on native communities and leaf litter breakdown. Given the widespread distribution of signal crayfish (and other crayfish species), their ecological impacts should be assessed carefully, especially in pristine freshwater ecosystems such as those described here. [ABSTRACT FROM AUTHOR]

Temperature is one of the most important factors governing the activity of ectothermic species, and it plays an important but less studied role in the manifestation of invasive species impacts. In this study, we investigated temperature-specific feeding and metabolic rates of invasive and native crayfish, and evaluated how temperature regulates their ecological impacts at present and in future according to different climatic scenarios by bioenergetics modelling. We conducted a series of maximum food consumption experiments and measured the metabolic rates of cold-adapted native noble crayfish (Astacus astacus) and invasive signal crayfish (Pacifastacus leniusculus) originally from a warmer environment over a temperature gradient resembling natural temperatures in Finland. The maximum feeding rates and routine metabolic rates (RMR) of native noble crayfish were significantly higher at low temperatures (< 10 °C than the rates of invasive signal crayfish. The RMRs of the species crossed at 18 °C, and the RMRs of signal crayfish were higher at temperatures above 18 °C. These findings indicate that the invader's thermal niche has remained stable, and the potential impacts per capita are lower at suboptimal cold temperatures than for the native species. Our bioenergetics modelling showed that the direct annual predation impact of noble and signal crayfish seem similar, although the seasonal dynamics of the predation differs considerably between species. Our results highlight that the temperature-specific metabolic and feeding rates of species need to be taken into account in the impact assessment instead of simple generalisations of the direction or magnitude of impacts. [ABSTRACT FROM AUTHOR]

Fish distributions in river systems are known to be affected by large dams and other artificial cross‐river structures such as weirs that prevent their movements and migrations. However, little is known about the cumulative effect of low‐height barriers on fish distributions. Although fishes like eels and lampreys, which include endangered species, have a unique type of ability to climb or attach to obstacles, the strength of their anguilliform swimming locomotion style is generally lower than in other fishes. To investigate the cumulative effects of small barriers irrespective of their distances from the river mouth on riverine distributions of endangered eels, the individual density of Japanese eels and habitat characteristics of five model river systems having differences in numbers, size and positional patterns of small barriers were surveyed and analysed using a generalized linear mixed model approach. The results clearly showed that a continuum of small barriers and the distance from the river mouth affected the riverine distributions of Japanese eels, and that these effects were eel size‐ or stage‐dependent. The density of small eels decreased as the cumulative height of barriers downstream of each station increased, while that of large eels decreased as the distance from the river mouth increased. Small individuals dispersed in a wide range of habitats before the end of their upstream migration phase, suggesting that small barriers have an impact on their ideal distributions, life‐history patterns (becoming residents or nomads shifting growth habitats to estuaries) and sex differentiation. This study and existing information indicate that conservation/restoration actions are needed to maintain or improve riverine connectivity for migratory species, especially those having lower swimming ability and a benthic growth phase in freshwater ecosystems that are at risk even when migration barriers are not very high. [ABSTRACT FROM AUTHOR]

There is increasing evidence that personality traits may drive dispersal patterns of animals, including invasive species. We investigated, using the widespread signal crayfish Pacifastacus leniusculus as a model invasive species, whether effects of personality traits on dispersal were independent of, or affected by, other factors including population density, habitat, crayfish size, sex and limb loss, along an invasion gradient. Behavioural traits (boldness, activity, exploration, willingness to climb) of 310 individually marked signal crayfish were measured at fully-established, newly-established and invasion front sites of two upland streams. After a period at liberty, recaptured crayfish were reassessed for behavioural traits (newly-established, invasion front). Dispersal distance and direction of crayfish movement, local population density, fine-scale habitat characteristics and crayfish size, sex and limb loss were also measured. Individual crayfish exhibited consistency in behavioural traits over time which formed a behavioural syndrome. Dispersal was both positively and negatively affected by personality traits, positively by local population density and negatively by refuge availability. No effect of size, sex and limb loss was recorded. Personality played a role in promoting dispersal but population density and local habitat complexity were also important determinants. Predicting biological invasion in animals is likely to require better integration of these processes. [ABSTRACT FROM AUTHOR]

Millions of dams impair watershed connectivity across the globe and have severely affected migratory fish populations. Fishways offer upstream passage opportunities, but artificial selection may be imposed by these structures. Using juvenile American eel Anguilla rostrata as a model species, we consider whether individual differences in behaviour (i.e. personality) and fish size can predict passage success.We evaluated the expression of bold and exploratory behaviours using open field and emergence assays in the laboratory. Then we assessed the propensity for individuals to volitionally climb through an experimental fishway to understand if personality and fish size could predict climbing success.We demonstrate personality in juvenile eels, and swimming speed in the open field was negatively associated with climbing propensity. Slower swimmers were up to 60% more likely to use the passage device suggesting that more exploratory eels incurred greater passage success. For successful climbers, climbing time was negatively associated with fish length.Synthesis and applications. Our results suggest fish may segregate at barriers based on personality and size. Preventing a subset of individuals from accessing upstream habitat is likely to have negative consequences for fish populations and aquatic ecosystems. Selection may be alleviated by increasing passage opportunities, maximizing fishway attraction and avoiding inefficient passage solutions. [ABSTRACT FROM AUTHOR]

It is well known that fishing is size‐selective, but harvest may also inadvertently target certain behavioral types or personalities. Changes in the abundance of behavioral types within a population have implications for fisheries management, including affecting catch rates, individual growth, and food web dynamics. Using streamside behavioral assays, we quantified the repeatability of behaviors in a population of Baikal grayling (Thymallus baicalensis) in northern Mongolia, a popular sport fish and important local predator. We assessed whether different angling techniques (i.e., fly or spinning gear) collected different behavioral types and whether variation in behavior was associated with body condition or diet (i.e., using stable isotope analysis). Surprisingly, we found no evidence for consistent individual differences in several behaviors within this population. Furthermore, differences in mean behaviors were not predicted by angling gear, body condition, or carbon and nitrogen isotopic signatures. We suggest that since this is a fished population, the range of behavioral variability in the population may have been reduced through previous behaviorally selective harvest. This might explain both the lack of difference in mean behaviors between fish caught by both gear types and the lack of evidence for consistent individual differences in behavior within the sampled population. [ABSTRACT FROM AUTHOR]

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter , Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring. [ABSTRACT FROM AUTHOR]

Invasive non‐native species represent a leading threat to global freshwater biodiversity and non‐native crayfish species frequently cause extensive ecological damage. However, the extent to which their impact: (1) depends on invader identity and (2) differs from the natural state with native crayfish remains unclear. Comparison of the functional responses of invasive and native species represents a promising approach in this regard.Here, we explored whether four invasive crayfish species (calico crayfish Faxonius immunis, spiny‐cheek crayfish Faxonius limosus, signal crayfish Pacifastacus leniusculus, and marbled crayfish Procambarus virginalis) in European freshwaters and the most widespread native species (noble crayfish Astacus astacus) overlap in function in their potential effects on key resources of benthic food webs. First, the impact on gammarids and zebra mussels was assessed by means of comparative functional response analysis using the functional response ratio as impact metric; second, the consumption of macrophytes (Chara sp.) and detritus (leaf litter) was quantified and compared using feeding experiments.Both invader‐ and resource‐specific effects were observed. Invasive calico crayfish and signal crayfish exhibited the strongest per capita effects on gammarids and zebra mussels, respectively, with functional response ratios being 2‐fold higher than those of native noble crayfish. Marbled crayfish showed an intermediate effect on both prey species, whereas spiny‐cheek crayfish had lower impacts than noble crayfish. In the feeding experiment, calico crayfish consumed the highest amount of detritus, while the consumption of macrophytes did not differ among the five crayfish species.Our work demonstrates as‐yet unrecognised differences in functional responses among the four North American crayfish invaders and the European noble crayfish. The lack of congruence across the observed impacts suggests a mostly species‐specific pattern and stresses the importance of species and resource identity when considering the ecological impact of crayfish. An initial assessment of invader‐specific potential impacts positions calico crayfish and signal crayfish among the most impactful invaders. [ABSTRACT FROM AUTHOR]

Background: Olive flounder (Paralichthys olivaceus) is one of the major cultured fish species in Asia including Korea. However, the mass mortality of olive flounder caused by various pathogens leads to huge economic loss. The pathogens that lead to fish mortality include parasites, bacteria, and viruses that can cause various kinds of diseases. Objective: The purpose of this study was to investigate the protein expression patterns in the gills and spleens of olive flounder after artificial infection. We hypothesized that proteomics levels in gills and spleen may be differentially expressed depending on infectious agents. Methods: To investigate the expression pattern of proteins in gills and spleens, olive flounders were experimentally infected with VHSV (virus), S. parauberis (bacteria), or M. avidus (pathogenic ciliate). Proteins were extracted from the gills and spleens of infected olive flounder. We used 2-DE analysis with LC–MS/MS to investigate proteome changes in infected olive flounders. Results: The results of the LC–MS/MS analyses showed different protein expression profiles depending on pathogenic sources and target organs. Proteins related to cytoskeletal structure like keratin, calmodulin and actin were mostly expressed in the infected gills. Proteins involved in the metabolism pathway like glycolysis were expressed mainly in the spleens. The protein profiles of S. parauberis and VHSV infection groups had many similarities, but the profile of the M. avidus infection group was greatly different in the gill and spleen. Conclusion: Our results indicate that measures according to the characteristics of each pathogen are necessary for disease prevention and treatment of farmed fish. [ABSTRACT FROM AUTHOR]

Catadromous fish species can be defined important organisms for their ecological, economical, and cultural value. Because of a complex life cycle, catadromous fish species are exhibited to the cumulative effect of multiple anthropogenic threats that resulted in worldwide decline since the beginning of the 20th century. Among the most iconic catadromous species, the European eel Anguilla anguilla has aroused considerable interest, and to date, many aspects of its life cycle remain relatively unknown. Although conspicuous efforts by the research to ensure the perpetuation of the species were conducted, the identification of the best tools to reduce the threats that affect eels remains challenging. In this narrative review, the state of the knowledge and main threats about the life cycle, the habitat occupancy, the recruitment, and migration patterns of the European eel have been reported. [ABSTRACT FROM AUTHOR]