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Many critical aquatic habitats are in close proximity to human activity (i.e., adjacent to residences, docks, marinas, etc.), and it is vital to monitor biodiversity in these and similar areas that are subject to ongoing urbanization, pollution, and other environmental disruptions. Environmental DNA (eDNA) metabarcoding is an accessible, non-invasive genetic technique used to detect and monitor species diversity and is a particularly useful approach in areas where traditional biodiversity monitoring methods (e.g., visual surveys or video surveillance) are challenging to conduct. In this study, we implemented an eDNA approach that used a combination of three distinct PCR primer sets to detect marine vertebrates within a canal system of Biscayne Bay, Florida, an ecosystem representative of challenging sampling conditions and a myriad of impacts from urbanization. We detected fish species from aquarium, commercial, and recreational fisheries, as well as invasive, cryptobenthic, and endangered vertebrate species, including charismatic marine mammals such as the protected West Indian manatee, Trichechus manatus. Our results support the potential for eDNA analyses to supplement traditional biodiversity monitoring methods and ultimately serve as an important tool for ecosystem management. This approach minimizes stress or disturbance to organisms and removes the intrinsic risk and logical limitations of SCUBA diving, snorkeling, or deploying sensitive equipment in areas that are subject to high vessel traffic and/or low visibility. Overall, this work sets the framework to understand how biodiversity may change over different spatial and temporal scales in an aquatic ecosystem heavily influenced by urbanization and validates the use of eDNA as a complementary approach to traditional ecological monitoring methods., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Fish ear bones, known as otoliths, are often collected in fisheries to assist in management, and are a common sample type in museum and national archives. Beyond their utility for ageing, morphological and trace element analysis, otoliths are a repository of valuable genomic information. Previous work has shown that DNA can be extracted from the trace quantities of tissue remaining on the surface of otoliths, despite the fact that they are often stored dry at room temperature. However, much of this work has used reduced representation sequencing methods in clean lab conditions, to achieve adequate yields of DNA, libraries and ultimately single-nucleotide polymorphisms (SNPs). Here, we pioneer the use of small-scale (spike-in) sequencing to screen contemporary otolith samples prepared in regular molecular biology (in contrast to clean) laboratories for contamination and quality levels, submitting for whole-genome resequencing only samples above a defined endogenous DNA threshold. Despite the typically low quality and quantity of DNA extracted from otoliths, we are able to produce whole-genome libraries and ultimately sets of filtered, unlinked and even putatively adaptive SNPs of ample numbers for downstream uses in population, climate and conservation genomics. By comparing with a set of tissue samples from the same species, we are able to highlight the quality and efficacy of otolith samples from DNA extraction and library preparation, to bioinformatic preprocessing and SNP calling. We provide detailed schematics, protocols and scripts of our approach, such that it can be adopted widely by the community, improving the use of otoliths as a source of valuable genomic data., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

The use of environmental DNA (eDNA) is becoming prevalent as a novel method of ecological monitoring. Although eDNA can provide critical information on the distribution and biomass of particular taxa, the DNA sequences of an organism remain unaltered throughout its existence, which complicates the accurate identification of crucial events, including spawning. Therefore, we examined DNA methylation as a novel source of information from eDNA, considering that the methylation patterns in eggs and sperm released during spawning differ from those of somatic tissues. Despite its potential applications, little is known about eDNA methylation, including its stability and methods for detection and quantification. Therefore, we conducted tank experiments and performed methylation analysis targeting 18S rDNA through bisulphite amplicon sequencing. In the target region, eDNA methylation was not affected by degradation and was equivalent to the methylation rate of genomic DNA from somatic tissues. Unmethylated DNA, abundant in the ovaries, was detected in the eDNA released during fish spawning. These results indicate that eDNA methylation is a stable signal reflecting targeted gene methylation and further demonstrate that germ cell-specific methylation patterns can be used as markers for detecting fish spawning., (© 2024 John Wiley & Sons Ltd.)

Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages., (© 2024. The Author(s).)

Migration independently evolved numerous times in animals, with a myriad of ecological and evolutionary implications. In fishes, perhaps the most extreme form of migration is diadromy, the migration between marine and freshwater environments. Key and long-standing questions are: how many times has diadromy evolved in fishes, how frequently do diadromous clades give rise to non-diadromous species, and does diadromy influence lineage diversification rates? Many diadromous fishes have large geographic ranges with constituent populations that use isolated freshwater habitats. This may limit gene flow between some populations, increasing the likelihood of speciation in diadromous lineages relative to nondiadromous lineages. Alternatively, diadromy may reduce lineage diversification rates if migration is associated with enhanced dispersal capacity that facilitates gene flow within and between populations. Clupeiformes (herrings, sardines, shads, and anchovies) is a model clade for testing hypotheses about the evolution of diadromy because it includes an exceptionally high proportion of diadromous species and several independent evolutionary origins of diadromy. However, relationships among major clupeiform lineages remain unresolved, and existing phylogenies sparsely sampled diadromous species, limiting the resolution of phylogenetically informed statistical analyses. We assembled a phylogenomic dataset and used multi-species coalescent and concatenation-based approaches to generate the most comprehensive, highly resolved clupeiform phylogeny to date, clarifying associations among several major clades and identifying recalcitrant relationships needing further examination. We determined that variation in rates of sequence evolution (heterotachy) and base-composition (nonstationarity) had little impact on our results. Using this phylogeny, we characterized evolutionary patterns of diadromy and tested for differences in lineage diversification rates between diadromous, marine, and freshwater lineages. We identified 13 transitions to diadromy, all during the Cenozoic Era (10 origins of anadromy, 2 origins of catadromy, and 1 origin of amphidromy), and 7 losses of diadromy. Two diadromous lineages rapidly generated nondiadromous species, demonstrating that diadromy is not an evolutionary dead end. We discovered considerably faster transition rates out of diadromy than to diadromy. The largest lineage diversification rate increase in Clupeiformes was associated with a transition to diadromy, but we uncovered little statistical support for categorically faster lineage diversification rates in diadromous versus nondiadromous fishes. We propose that diadromy may increase the potential for accelerated lineage diversification, particularly in species that migrate long distances. However, this potential may only be realized in certain biogeographic contexts, such as when diadromy allows access to ecosystems in which there is limited competition from incumbent species., (© The Author(s) 2024. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

This study employed Environmental DNA (eDNA) barcoding technology to delve into the influence of the tributaries and mainstem on fish diversity and spatiotemporal distribution in a hotspot fish conservation area in the upper Yangtze River. A total of 123 fish species were detected, belonging to 7 orders, 19 families, and 77 genera. The composition of fish species in tributaries is similar to that in mainstem, with higher fish community diversity in tributaries during the spring and summer. Exploration of fish ecotypes revealed significant differences between mainstem and tributaries. The fish community is mainly influenced by key environmental factors such as water temperature, dissolved oxygen, electrical conductivity, and ammonia nitrogen, with a higher impact of these factors on tributaries than on mainstem. In conclusion, while tributaries and mainstem in the Jiangjin section exhibit similarities in fish community composition, there are notable differences in community structure and diversity. Therefore, the protection of not only mainstem but also tributaries and their associated fish habitats is crucial for promoting the overall health and sustainability., (© 2024. The Author(s).)

DNA transposons are diverse in fish genomes and have been described to generate genomic evolutionary novelties. hAT transposable element data are scarce in Teleostei genomes, making it challenging to conduct comparative genomic studies to understand their neutrality or function. This study aimed to perform a genomic and molecular characterization of hAT copies to assess the diversity of these elements and associate changes in these sequences to genomic and karyotypic novelties in Apareiodon sp. The data revealed that hAT TEs are highly abundant in the Apareiodon sp. genome, with few possibly autonomous copies. Highly conserved sequences with likely functional transposases were observed in nine hAT elements. A great diversity of hAT subgroups was observed, especially from Ac, Charlie, Blackjack, Tip100, hAT6, and hAT5, and a similar wave of hAT genomic invasion was identified in the genome for these six groups of hAT sequences. The data also revealed a distinct number of microsatellites within degenerated hAT copies. hAT sites were demonstrated to be dispersed in the Apareiodon sp. chromosomes and not involved in W chromosome-specific region differentiation. In conclusion, the genomic analysis revealed a great diversity of hAT elements, possible autonomous copies, and differentiation of degenerated transposable elements into tandem sequences., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Global marine biodiversity loss impairs entire ecosystems and their stability. Robust biodiversity estimates are key to inform policies and management strategies, and need to consider the contribution of diverse habitats, including those for which estimates of biodiversity are scattered or totally absent. This study assessed the fish diversity associated with three main coastal habitats (rocky bottoms, Posidonia oceanica meadows, sandy bottoms), and their role in shaping the overall coastal fish diversity, also in relation to potential environmental and anthropogenic drivers affecting patterns of fish diversity in coastal areas. Using underwater visual census, we sampled 62 sites distributed on the three habitats, for a total of 496 replicates. We assessed the contribution of each habitat to β-diversity, divided into Local Contribution to β-diversity (LCBD), a comparative indicator of the contributions to β-diversity of each habitat, and Species Contribution to β-diversity (SCBD), which measures the relative importance of each species in affecting β-diversity. Finally, we modelled species diversity in relation to potential environmental and anthropogenic drivers. Overall, 72 species were recorded, with the highest species richness observed on rocky bottoms (56 species, 16 unique to this habitat), followed by P. oceanica (38 species, 0 unique) and sandy bottoms (32 species, 14 unique). Sandy bottom assemblages had a significantly higher contribution to LCBD than P. oceanica meadows and rocky bottoms, and two of the five species with the highest contribution to SCBD are exclusively associated with sandy bottoms. Finally, sea surface temperature, sea surface salinity, and habitat were highlighted as significant predictors of species richness. Our findings, aside from highlighting the environmental drivers of coastal fish diversity in the Mediterranean Sea, unravel the potential key role of sandy bottoms in contributing to overall coastal fish diversity and can inform conservation planning., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Despite significant advancements in ichthyoplankton collection and data processing, challenges persist in the taxonomic identification of these organisms, particularly their eggs. To overcome these challenges, a novel technique has been developed to facilitate the identification of live eggs collected directly in wild. This user-friendly technique includes the collection, processing of the material, and field incubation. Sampling must be conducted using a pelagic net towed at low speed, preferably during early evening. The material processing involves pre-sorting and sorting to remove eggs and larvae. The separated eggs, kept in an aerated bowl, can be identified based on their morphological and meristic characteristics. Unidentified eggs can be placed in plastic bags with oxygen and incubated directly in the aquatic environment for 48-72 h. After this incubation period, the hatched larvae at the yolk-sac or preflexion stage, are identified to the lowest possible taxonomic level. Depending on the study's purpose, hatched larvae and field-collected larvae can be transported to research centers for further development, released back into the natural environment, or fixed to complete the collection. The application of this technique supports management and monitoring programs by identifying spawning areas through egg identification, forming broodstock, and replenishing threatened species, thereby enhancing scientific collections of ichthyoplankton. Additionally, it reduces mortality in ichthyoplankton techniques, including endangered species. Therefore, we believe that this novel taxonomic technique for identifying live ichthyoplankton represents a paradigm shift in the monitoring, management, and conservation of fish, as well as in ecological stewardship and advances in this area of research., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Marine sponges have recently emerged as efficient natural environmental DNA (eDNA) samplers. The ability of sponges to accumulate eDNA provides an exciting opportunity to reconstruct contemporary communities and ecosystems with high temporal and spatial precision. However, the use of historical eDNA, trapped within the vast number of specimens stored in scientific collections, opens up the opportunity to begin to reconstruct the communities and ecosystems of the past. Here, we define the term 'heDNA' to denote the historical environmental DNA that can be obtained from the recent past with high spatial and temporal accuracy. Using a variety of Antarctic sponge specimens stored in an extensive marine invertebrate collection, we were able to recover information on Antarctic fish biodiversity from specimens up to 20 years old. We successfully recovered 64 fish heDNA signals from 27 sponge specimens. Alpha diversity measures did not differ among preservation methods, but sponges stored frozen had a significantly different fish community composition compared to those stored dry or in ethanol. Our results show that we were consistently and reliably able to extract the heDNA trapped within marine sponge specimens, thereby enabling the reconstruction and investigation of communities and ecosystems of the recent past with a spatial and temporal resolution previously unattainable. Future research into heDNA extraction from other preservation methods, as well as the impact of specimen age and collection method, will strengthen and expand the opportunities for this novel resource to access new knowledge on ecological change during the last century., (© 2024 The Author(s). Molecular Ecology Resources published by John Wiley & Sons Ltd.)

Sciadonus alphacrucis Melo, Gomes, Møller & Nielsen, 2022 is a rare deep-sea species, previously known from only two specimens collected off São Paulo State, southeastern Brazil, in the western South Atlantic. Herein, we report a new specimen of S. alphacrucis collected on the continental slope off Santa Catarina State, southern Brazil, thereby extending its known distribution by 420 km. Additionally, we provide the new meristic and morphometric data, the molecular identification using sequences of the cytochrome c oxidase subunit I (COI), an updated distribution map, and a discussion of troglomorphic traits., (© 2024 Fisheries Society of the British Isles.)

Boreal lakes experience pronounced seasonal variation in abiotic factors, especially light, temperature, and oxygen. A deep boreal humic lake was sampled year-round to test putative changes in total fish catch, species composition, catch-per-unit-effort (CPUE), habitat use, fish size, and condition. Monthly sampling was conducted in Lake Pääjärvi, southern Finland, during one full year in 2020-2021 as well as in March and August 2021 and 2022. The fish community was dominated by cyprinid species in all months, but the percentage of percid fish caught increased during the warm summer period. Most fish were caught in littoral habitats and the highest catches occurred in summer, but some species (e.g., ruffe, Gymnocephalus cernua, and pikeperch, Sander lucioperca) remained abundant in the winter catch. The body size of fish was larger in the winter catch, while condition factor was higher in summer for most species. Fish species proportions in total catch, CPUE, and average size of fish were closest to the annual mean values in September, which may be used as the optimal period to monitor fish communities of similar deep boreal lakes. Our findings highlight the need for year-round research to reveal the impacts of rising temperatures and diminishing ice-covered periods in fish communities and lake food webs., (© 2024 The Author(s). Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish-tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri) 1 and African 2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren's genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus' limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren-Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Background: For the past 25 years, the ITS rDNA (ITS1-5.8S-ITS2) of Gyrodactylidae has been crucial for species identification, description, and phylogeny. This family includes 25 genera parasitizing marine and freshwater fish, initially distinguished by morphological differences in attachment and/or male copulatory organs. Gyrodactylus Nordmann, 1832, the most species-rich genus, has approximately 500 described species and an additional 25,000 species suspected. The genus is not monophyletic, and the functionally adaptive nature of morphological diagnostic characters complicates the delimitation of new genera., Methods: A phylogeny based on ITS rDNA was proposed to address these challenges, using only complete sequences of primitive taxa. Fifty-four sequences were aligned with the MUSCLE v5.1 algorithm, creating a 1590 ps long matrix. Maximum Likelihood (ML) and Bayesian Inference (BI) methods with the models TVM+F+G4 and SYM+G4 for ITS1-ITS2 and 5.8S, respectively, were inferred using IQ-TREE v2.3.5 and BEAST v2.7.6.0., Results: The findings revealed eleven main lineages. Four of them are proposed for classification into new genera: Cichlidarus gen. nov., Iraqemembranatus gen. nov., Macracanthus gen. nov., and Rysavyius gen. nov. Elevating the subgenus G . ( Gyrodactylus ) to genus rank was supported., Conclusions: The presented phylogeny provides a foundation for developing a classification system within Gyrodactylidae that is both reasonable and comprehensive.

Endemic fish species have long supported the livelihoods of local communities in the Rufiji River Basin (RRB). However, destructive fishing practices have led to a concerning decline in endemic fish stocks. To assess these changes, this study employed key informant interviews, focus group discussions (FGDs), and fishery surveys to assess the historical and contemporary distribution of endemic fishes within the RRB. DNA barcoding was also used to verify species identities. Out of 37 reported fish species, 33 species (54.55% endemic and 45.45% exotic to RRB) were confirmed through DNA barcoding and morphological characteristics. About 5 species including, Heterobranchus longifilis, Citharinus congicus, Labeo congoro, Mormyrus longirostris, and Labeobarbus leleupanus were rarely found in the field, despite being classified as Least Concern by IUCN. Additionally, five species that were reported to be present in the RRB by experienced fishers were not captured during sampling. This highlights the need for validation of the existence of such species through eDNA metabarcoding. Moreover, due to the rarity of some species in the area, their IUCN assessment should be revisited., Competing Interests: The author have declared that no competing interests exist., (Copyright: © 2024 Saiperaki et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

To complete the life cycle, species exhibit corresponding functional traits in morphology, physiology, ecology, etc . The eigenvalues, variation, and distribution of functional traits are the functional components of biodiversity, namely functional diversity, could maintain the service function and healthy operation of ecosystems. The application of functional diversity broadens our understanding of biodiversity and its temporal and spatial variations, and provides a breakthrough to the problem of how to combine morphological structure with ecological function. I reviewed the research process of functional diversity from the perspective of proposing, calculating, and applying the parameters of functional diversity, as well as the application of functional diversity from different purposes and perspectives. I put forward the challenges and countermeasures of related studies. In the future, researches should pay attention to establish a set of effective trait indicators, discover the internal and external mechanisms driving functional diversity variations, and map the redistribution of traits under environmental changes.

This study was carried out to analyze the fatty acid and amino acid compositions of three economically important freshwater fish species, Mali (Wallago attu), Raho (Labeo rohita), and Mahseer (Tor putitora), indigenous to Indus River, Pakistan.. Amino acid profiling was done by high-performance liquid chromatography (HPLC) while gas chromatography (GC) was used for fatty acid analysis. Glutamic acid, aspartic acid, arginine, alanine, leucine, lysine and isoleucine were the most predominant amino acid while palmitic acid (C16:0), oleic acid (C18:1c), palmitoliec acid (C16:1c), linolenic acids (C18:2c) and docosahexaenoic acids (DHA C22:6) were the notable fatty acids present in these species. Our results indicated that all species have comparable nutritional composition and are good source of healthy human diet. Our findings will help the people to make informed choice while selecting fish for consumption and will pave the way for future researchers in planning new strategies to enhance the growth and production of commercial fish species. It will also be helpful for theFrom the current finding it was concluded that all fish species under discussion are rich in amino acids and fatty acids. These species contain essential amino acids and important fatty acid such as omega3 and omega 6, thus raising the nutritional quality of these species.

The living coelacanth Latimeria (Sarcopterygii: Actinistia) is an iconic, so-called 'living fossil' within one of the most apparently morphologically conservative vertebrate groups. We describe a new, 3-D preserved coelacanth from the Late Devonian Gogo Formation in Western Australia. We assemble a comprehensive analysis of the group to assess the phylogeny, evolutionary rates, and morphological disparity of all coelacanths. We reveal a major shift in morphological disparity between Devonian and post-Devonian coelacanths. The newly described fossil fish fills a critical transitional stage in coelacanth disparity and evolution. Since the mid-Cretaceous, discrete character changes (representing major morphological innovations) have essentially ceased, while meristic and continuous characters have continued to evolve within coelacanths. Considering a range of putative environmental drivers, tectonic activity best explains variation in the rates of coelacanth evolution., (© 2024. The Author(s).)

Freshwater ecosystems are crucial for global biodiversity through supporting plant and animal species and providing essential resources. These ecosystems are under significant threat, particularly in island environments such as Madagascar. Our study focuses on the Amboaboa River basin, home to the rare and endemic fish species Rheocles derhami, last recorded in 2013. To assess the status of this and other threatened fish species including Ptychochromis insolitus and Paretroplus gymnopreopercularis, and to understand freshwater fish population dynamics in this biodiversity hotspot, we conducted a comprehensive survey using both environmental DNA (eDNA) and traditional fishing methods. While traditional methods effectively captured a diverse range of species, including several invasive aliens and the critically endangered endemic species that were the focus of this study, the eDNA approach detected only a fraction of these introduced species and struggled to identify some critically endangered endemics at the species level. This highlights the value of combining methods to enhance species detection. We also investigated the trade-offs associated with multi-primer assessments in eDNA analysis, focusing on three different primer combinations targeting the 12S mitochondrial gene: MiFish, Tele02, and Riaz. Additionally, we provided 12S reference barcodes for 10 species across 9 genera of fishes from the region to increase the coverage of the public reference databases. Overall, our study elucidates the current state of freshwater biodiversity in the Amboaboa River basin and underscores the value of employing multiple methods for effective conservation strategies., (© 2024. The Author(s).)

Elucidating cellular architecture and cell-type evolution across species is central to understanding immune system function and susceptibility to disease. Adaptive immunity is a shared trait of the common ancestor of cartilaginous and bony fishes. However, evolutionary features of lymphocytes in these two jawed vertebrates remain unclear. Here, we present a single-cell RNA sequencing atlas of immune cells from cartilaginous (white-spotted bamboo shark) and bony (zebrafish and Chinese tongue sole) fishes. Cross-species comparisons show that the same cell types across different species exhibit similar transcriptional profiles. In the bamboo shark, we identify a phagocytic B cell population expressing several pattern recognition receptors, as well as a T cell sub-cluster co-expressing both T and B cell markers. In contrast to a division by function in the bony fishes, we show close linkage and poor functional specialization among lymphocytes in the cartilaginous fish. Our cross-species single-cell comparison presents a resource for uncovering the origin and evolution of the gnathostome immune system., (© 2024. The Author(s).)

The gastric stomach is a hallmark of vertebrate evolution, yet is missing in nearly 25% of living fish species and some mammals. New work by Kato et al. shows how a cassette of genes relating to acid production, pepsins, cell adhesion, and developmental control are repeatedly lost in animals that have also lost their stomachs., Competing Interests: Declaration of interests The author declares no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Seafood fraud has become a global issue, threatening food security and safety. Adulteration, substitution, dilution, and incorrect labeling of seafood products are fraudulent practices that violate consumer safety. In this context, developing sensitive, robust, and high-throughput molecular tools for food and feed authentication is becoming crucial for regulatory purposes. Analytical approaches such as proteomics mass spectrometry have shown promise in detecting incorrectly labeled products. For the application of these tools, genome information is crucial, but currently, for many marine species of commercial importance, such information is unavailable. However, when combining proteomic analysis with spectral library matching, commercially important fish species were successfully identified, differentiated, and quantified in pure muscle samples and mixtures, even when genome information was scarce. This study further tested the previously developed spectral library matching approach to differentiate between 29 fish species from the North Sea and examined samples including individual fish, laboratory-prepared mixtures and commercial products. For authenticating libraries generated from 29 fish species, fresh muscle samples from the fish samples were matched against the reference spectral libraries. Species of the fresh fish samples were correctly authenticated using the spectral library approach. The same result was obtained when evaluating the laboratory-prepared mixtures. Furthermore, processed commercial products containing mixtures of two or three fish species were matched against these reference spectral libraries to test the accuracy and robustness of this method for authentication of fish species. The results indicated that the method is suitable for the authentication of fish species from highly processed samples such as fish cakes and burgers. The study shows that current and future challenges in food and feed authentication can efficiently be tackled by reference spectral libraries method when prospecting new resources in the Arctic., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: The author, Dr. J. D. Rasinger, is currently employed with the European Food Safety Authority (EFSA) in the Food Ingredients and Packaging Unit (FIP). However, the present article is published under the sole responsibility of the author Dr. J. D. Rasinger and may not be considered as an EFSA scientific output. The positions and opinions presented in this article are those of the author alone and are not intended to/do not necessarily represent the views/any official position of EFSA. The author’s main contributions to this article were made before joining EFSA when still employed at the Institute of Marine Research. The other authors declare no conflict of interest., (Copyright © 2024 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Fish welfare is a critical issue that needs to be addressed by the rapidly growing aquaculture industry. Scientific knowledge regarding the natural behaviors of species and the conditions in which they are kept in farms is essential for improving their welfare in aquaculture. To provide a consistent overview of the welfare of farmed fish, the organization fair-fish has created the online platform fair-fish database, which gathers ethological knowledge categorized into profiles of farmed aquatic species. The WelfareChecks on this platform are profiles based on criteria that are rated based on the likelihood and potential of the species to experience a high level of welfare in aquaculture systems, together with the certainty about the findings. A score (WelfareScore) is calculated from these ratings, serving as a reference to identify knowledge gaps, assess welfare, and suggest ways to improve it. Here, we performed an in-depth analysis of the species with WelfareChecks already published in the fair-fish database based on their respective WelfareScores. In general, although just a small percentage of farmed aquatic species (~5%) have at least a 20% chance of experiencing a good level of welfare under minimal aquaculture conditions, 60% of them have at least some potential to achieve good welfare under high-standard conditions, with more than a third of the species (~37%) having at least a 20% potential. Despite that, several species exhibit a very high frequency of low chances and potential for experiencing good welfare levels under aquaculture conditions, besides a low degree of certainty based on literature reviews. Furthermore, many others show a very frequent occurrence of unclear or nonexistent knowledge in their profiles. The current welfare state is therefore poor for the majority of farmed aquatic species; yet, there is considerable potential for improvement. However, many species are very unlikely to achieve good welfare, even under high-standard conditions. Importantly, large knowledge gaps remain for an accurate assessment of the welfare of several farmed species., (© 2024 Fisheries Society of the British Isles.)

China has experienced substantial coastal reclamation and damming of rivers. These changes have the potential to impact migrations of diadromous fishes between the sea and fresh waters, but the composition of these fishes and the impacts of barriers to their movement in China have received little attention. We inventoried the species composition and distribution of diadromous fishes, and the impacts of barriers on them, in the Hong Kong Special Administrative Region (HKSAR), southern China. Fish assemblages were surveyed using hand-nets, supplemented by cast-netting and single-pass snorkel surveys, in 24 small coastal streams across three regions. Surveys were undertaken on multiple occasions during the wet and dry seasons to account for the monsoonal tropical climate. Twenty-eight diadromous fishes were collected, mostly gobies, amounting to over half (53%) of the total richness of primary freshwater fishes; four additional species are known from literature records. Diadromous richness was 48% greater during the wet season, when all species were encountered. Richness varied substantially among streams, from a maximum of 17 (2 streams that were diversity hot spots) to none (3 streams). The most widespread diadromous fish was Glossogobius giuris (71% frequency of occurrence), followed by Mugil cephalus (58% occurrence) and Eleotris oxycephala (50% occurrence). The remaining 25 diadromous fishes occurred in fewer than half of the streams; 12 species were confined to a single stream and may be locally threatened. There were conspicuous spatial differences in diadromous assemblages across HKSAR, despite its limited extent (1114 km 2 ), the proximity of the surveyed streams, and the broad geographic distribution of most species. Regional species assemblages were influenced by localized habitat characteristics, with a noticeable distinction between areas with and without large, fast-flowing, and highly oxygenated streams. The presence of in-stream barriers (weirs: 0.3-8.7 m high) did not affect spatial patterns in species assemblages, although, on average, diadromous richness was lower in weir-obstructed streams (4.0 vs. 6.9 species in unobstructed streams). In total, 18 species were confined to unobstructed streams or sections below weirs, whereas the remaining 10 species were recorded both above and below weirs. Only the mottled eel (Anguilla marmorata) and a goby (Stiphodon multisquamus) were able to ascend weirs over 2 m. Although at least 400 m of the lower course of each stream was sampled, diadromous fishes were confined to the first 300 m in 12 of the 13 weir-obstructed streams. Remarkably, the tally of 32 diadromous species in HKSAR exceeds the 19 known from mainland China, highlighting the need for further research on composition and conservation status of diadromous fishes., (© 2024 The Author(s). Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Ichthyoplankton monitoring is crucial for stock assessments, offering insights into spawning grounds, stock size, seasons, recruitment, and changes in regional ichthyofauna. This study evaluates the efficiency of multi-marker DNA metabarcoding using mitochondrial cytochrome c oxidase subunit I (COI), 12S rRNA and 16S rRNA gene markers, in comparison to morphology-based methods for fish species identification in ichthyoplankton samples. Two transects with four coastal distance categories were sampled along the southern coast of Portugal, being each sample divided for molecular and morphological analyses. A total of 76 fish species were identified by both approaches, with DNA metabarcoding overperforming morphology-75 versus 11 species-level identifications. Linking species-level DNA identifications with higher taxonomic morphological identifications resolved several uncertainties associated with traditional methods. Multi-marker DNA metabarcoding improved fish species detection by 20-36% compared to using a single marker/amplicon, and identified 38 species in common, reinforcing the validity of our results. PERMANOVA analysis revealed significant differences in species communities based on the primer set employed, transect location, and distance from the coast. Our findings underscore the potential of DNA metabarcoding to assess ichthyoplankton diversity and suggest that its integration into routine surveys could enhance the accuracy and comprehensiveness of fish stock assessments., (© 2024. The Author(s).)

While recent technical breakthroughs have enabled advances in the description of reefs down to 150 m, the structure and depth zonation of deep-reef communities below 150 m remains largely unknown. Here, we present results from over 10 years of deep-reef fish surveys using human-occupied submersibles at four locations across the Caribbean Sea, constituting one of the only continuous reef-fish surveys from 10 to 480 m (1 site) and 40 to 300 m (3 sites). We identify four vertically stratified deep-reef fish communities between 40 and 300 m bordered by an altiphotic (0-10 m) and a deep-sea (300-480 m) community. We found a strong faunal break around 150 m that separates mesophotic and rariphotic zones and secondary breaks at ~ 70 to 90 m and ~ 180 to 200 m subdividing these zones into upper and lower communities. From 300 to 480 m in Roatán, we found a single fish community dominated by deep-sea families, indicating that the lower boundary of the reef-fish realm occurs at 300 m. No differences were found between communities ranging from 20 to 60 m, suggesting that fishes from the lower altiphotic and upper mesophotic form an ecological continuum. While some variability was observed across sites, the overall depth zonation and key species characterizing depth zones were consistent. Most deep-reef species observed were depth specialists restricted to a single depth zone, but many shallow-reef species extended down to mesophotic depths. Depth segregation among species of a genus was found across ten reef-fish genera and likely constitutes one of the mechanisms driving community distinctiveness and thereby fish diversity across depths., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Population growth combined with the need for electrical energy resulted in the construction of hundreds of hydroelectric plants in the state of São Paulo, Brazil. The consequence of these interventions was the fragmentation of rivers, forming barriers, that hinder the mobility of migratory fish species, generating an impact on the life cycle of these species, especially about movement between breeding and feeding areas. For this reason, this article aimed to evaluate the state-of-the-art knowledge regarding dams, free stretches, and migratory species in the three main river basins of the state of São Paulo and its tributaries. Through a systematic review from 2003 to 2023, 89 articles were obtained, 48 of which were about dams, 5 which addressed fish transposition systems, and 36 portraying migratory species. In the first half, research focused more on the impacts of dams on fish fauna, while in the second half of the period studied, studies of migratory fish were dominant. Most research was conducted in the main rivers, with few in the tributaries. Finally, 16 migratory species, considered long-distance, were studied, the most studied being P. lineatus, P. maculatus, L. friderici, M. obtusidens and S. hilarri and the ones that occurred most frequently in rivers are Prochilodus lineatus, Pimelodus maculatus, Megaleporinus obtusidens and Salminus hilarii. Therefore, we recommend maintaining the natural flow regime that still exists in the main rivers and tributaries of the state of São Paulo, to maintain healthy populations of the inventoried species.

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex ("ciscoes") radiated rapidly prior to the Last Glacial Maximum (80-90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation., (© 2024. The Authors. Parts of this work were authored by US Federal Government authors and are not under copyright protection in the US; foreign copyright protection may apply.)

The Amazon floodplain is home to an extremely high diversity of fish, with lakes playing an important role in the establishment of this biological richness. These lacustrine environments are subject to constant fluctuations caused by the annual flood pulse, with local factors and other regional patterns also contributing to the variation in fish community structure. The present study verified how local (depth and transparency of the water, the size and species composition of the macrophyte stands) and regional factors (spatial distribution of the stands and the hydrological phase) influence the structure of the fish community of the floodplain lakes of the Môa River, in northern Brazil. Fish species richness was influenced by the depth of the water and the spatial distribution of the macrophyte stands. Fish species composition was influenced by local environmental variables, spatial structure, and the hydrological phase. However, variation partitioning indicated that only the hydrological phase explained the variation in fish composition. These findings indicate that the local environment, the spatial structure, and the hydrological phase drive changes in the structure of the fish communities associated with aquatic macrophytes in the floodplain lakes of the Amazon basin.

Abyssal (3501-6500 m) and hadal (>6500 m) fauna evolve under harsh abiotic stresses, characterized by high hydrostatic pressure, darkness and food shortage, providing unique opportunities to investigate mechanisms underlying environmental adaptation. Genomes of several hadal species have recently been reported. However, the genetic adaptation of deep sea species across a broad spectrum of ocean depths has yet to be thoroughly investigated, due to the challenges imposed by collecting the deep sea species. To elucidate the correlation between genetic innovation and vertical distribution, we generated a chromosome-level genome assembly of the macrourids Coryphaenoides yaquinae, which is widely distributed in the abyssal/hadal zone ranging from 3655 to 7259 m in depth. Genomic comparisons among shallow, abyssal and hadal-living species identified idiosyncratic and convergent genetic alterations underlying the extraordinary adaptations of deep-sea species including light perception, circadian regulation, hydrostatic pressure and hunger tolerance. The deep-sea fishes (Coryphaenoides Sp. and Pseudoliparis swirei) venturing into various ocean depths independently have undergone convergent amino acid substitutions in multiple proteins such as rhodopsin 1, pancreatic and duodenal homeobox 1 and melanocortin 4 receptor which are known or verified in zebrafish to be related with vision adaptation and energy expenditure. Convergent evolution events were also identified in heat shock protein 90 beta family member 1 and valosin-containing protein genes known to be related to hydrostatic pressure adaptation specifically in fishes found around the hadal range. The uncovering of the molecular convergence among the deep-sea species shed new light on the common genetic innovations required for deep-sea adaptation by the fishes., (© 2024 John Wiley & Sons Ltd.)

The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation., (© 2024. The Author(s).)

Plateau river ecosystems are often highly vulnerable and responsive to environmental change. The driving mechanism of fish diversity and community assembly in plateau rivers under changing environments presents a significant complexity to the interdisciplinary study of ecology and environment. This study integrated molecular biological techniques and mathematical models to identify the mechanisms influencing spatial heterogeneity of freshwater fish diversity and driving fish community assembly in plateau rivers. By utilizing environmental-DNA metabarcoding and the null model, this study revealed the impact of the stochastic process on fish diversity variations and community assembly in the Huangshui Plateau River of the Yellow River Basin (YRB) in China. This research identified 30 operational taxonomic units (OTUs), which correspond to 20 different fish species. The findings of this study revealed that the fish α-diversity in the upstream region of Xining is significantly higher than in the middle-lower reach (Shannon index: P = 0.017 and Simpson: P = 0.035). This pattern was not found to be related to any other environmental factors besides altitude (P = 0.023) that we measured. Further, the study indicated that the assembly of fish communities in the Huangshui River primarily depends on stochastic ecological processes. These findings suggested that elevation was not the primary factor impacting the biodiversity patterns of fish in plateau rivers. In plateau rivers, spatial heterogeneity of fish community on elevation is mainly determined by stochastic processes under habitat fragmentation, rather than any other physicochemical environmental factors. The limitations of connectivity in the downstream channel of the river could be taken the mainly responsibility for stochastic processes of fish community in Huangshui River. Incorporating ecological processes in the eDNA approach holds great potential for future monitoring and evaluation of fish biodiversity and community assembly in plateau rivers., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

The Abrau sprat (tyulka or sardelka) Clupeonella abrau (Maliatsky, 1930) is an endemic fish of the Lake Abrau (Krasnodar Krai, Russia). The full C. abrau mitochondrial genome (16 650 bp) showed a gene arrangement conserved in Clupeidae and 98.8% similarity with the mitochondrial genome of the related species Black and Caspian Sea sprat C. cultriventris from the Black Sea. The COX1 gene sequence was additionally studied in a museum specimen collected in the Lake Abrau in 1938. Variability in modern Abrau sprat COX1 gene locus was estimated at approximately 0.15%, the difference between C. abrau and C. cultriventris was 1.2%, and the difference between the museum and modern C. abrau specimens from the Lake Abrau was 0.92%. The study confirmed that the Abrau sprat is present in the fish community and is capable of reproducing in the lake. Various scenarios were proposed to explain colonization of the Lake Abrau by C. abrau., (© 2024. Pleiades Publishing, Ltd.)

Backgroud: The Northeast India, being part of two global biodiversity hotspot namely the Indo-Burma and Eastern Himalayan Hotspots supports a wide variety of rich aquatic biodiversity including fishes. The family Danionidae is a widely diverse group inhabiting the upper colder stretches of river although few are abundant in the lower stretches. The persisting similarity in the morphological appearance and body colouration within the members of this family seeks an integrated method to identify the species correctly., Methods and Results: In the present study, the mt-DNA barcode was generated for correct identification and confirmation of the species. A total of nine mitochondrial cytochrome c oxidase subunit I gene sequences were generated for each species under the study. The pairwise distance values ranged from 0.09 to 9.11% within species and 9.06-32.71% between species. A neighbour-joining tree was constructed based on the Kimura 2 parameter model. Two major groups were observed where Danioninae formed a sister group to the Chedrinae and Rasborinae., Conclusion: The present study is a preliminary work to document and identify the species under the family Danionidae from Brahmaputra basin, Assam, using molecular tools and establish the phylogenetic relationship., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

This study investigated the spatial distribution, parasite interactions, and affinities of Branchiura parasites according to macrohabitat and surface type on fish from the Araguari River, Amapá State, in the Brazilian Amazon. This study presents novel information on the interactions of branchiuran species with host fish, and how the morphology of their attachment structures is associated with different host surface morphologies, with and without scales. A total of 558 fish specimens of 26 species were collected, of which 109 fish (10 species) were parasitized by at least one branchiuran parasite; these were selected for further study. The parasites were collected from the buccal cavity, gills, fins, and integument of the host fish. Parasites with suction discs (Argulus) were mainly associated to hosts with small scales and no scales, while parasites with hooks (Dolops) were mainly associated to hosts with large scales. Overall, parasites with suction discs were more specialized per site than those with hooks.

Fish parasites are an important part of aquatic biodiversity and knowing these species and their interactions with their hosts helps in monitoring the aquatic biota. The present study investigated the ectoparasite crustacean fauna of ten fish species from the upper Araguari River, in the state of Amapá, northern Brazil. A total of 508 fish were collected and analyzed from July to November 2014, of which 82.6% (109) were parasitized by one or more crustacean ectoparasite species. In the ten host fish species, a total of 308 ectoparasite specimens were collected, from 12 taxa, such as Argulus multicolor Stekhoven, 1937, Argulus spinulosus Silva, 1980, Argulus sp.1, Argulus sp.2, Argulus sp.3, Dipteropeltis sp., Dipteropeltis hirundo Calman, 1912, Dolops bidentata Bouvier, 1899, Dolops striata Bouvier, 1899 (Argulidae), Braga fluviatilis Richardson, 1911, Braga amapaensis Thatcher, 1996 (Cymothoidae) and Excorallana berbicensis Boone, 1918 (Corallanidae). Higher levels of prevalence and abundance were recorded for Hoplias aimara (Valenciennes, 1847) and Tometes trilobatus Valenciennes, 1850, respectively. These ectoparasites were found in the fins, integument, mouth, and anus of the host fish. Argulus sp.2 and D. bidentata were the most abundant parasites (65.1%), and had the highest species richness. This study registered 36 novel host-parasite interactions, and thus represents a new record for all host species here examined.

The integration of eDNA metabarcoding into monitoring programs provides valuable information about fish community structures. Despite the growing body of evidence supporting the method's effectiveness in distinguishing fine-scale eDNA signals, there is a limited understanding of eDNA distribution in shallow, well-mixed environments, especially related to sampling depth. We analyzed 167 samples collected from the surface and bottom water at 17 locations of the Belgian Part of the North Sea (BPNS), where the deepest sampling point was 31 m, and compared this to beam trawl catch data collected simultaneously at the same locations. eDNA metabarcoding identified an additional 22 species compared to beam trawl catch data. Diversity measures and patterns were very similar between surface and bottom samples and revealed community patterns that were previously described by long-term beam trawl catch data. Surface and bottom samples had 39 fish species in common, while six and eight rare species were uniquely detected, respectively. Our results demonstrate that eDNA metabarcoding effectively identifies spatial community patterns of fishes in the highly dynamic environment of the BPNS regardless of sampling depth. Out of the six most common species tested, eDNA metabarcoding read abundances correlated strongly with catch-based abundance data for one species, but moderately for two others, indicating that inferring fish abundance and biomass via eDNA metabarcoding remains challenging., (© 2024. The Author(s).)

This paper presents the conclusions of a comparative analysis of six osteological features: the Structure of the vertebral column, the morphology of the predorsal bones, the vertebral column regionalization, the pterygiophore interdigitation with neural spines of dorsal fin, the pterygiophores interdigitation of with the haemal spines of the anal fin, and the intermuscular bones (IMB) and hypomerals (HM) of 12 clupeid species of the families Alosidae, Dorosomatidae, Dussumieridae and Ehiravidae. Conceivable taxonomically beneficial osteological features are nominated and utilized to discrete the clupeid species explored. Formulae for the structure of the vertebral column, the dorsal- and anal-fin pterygiophores' interdigitation with the neural and haemal spines of the vertebrae are established. These morphological descriptive traits disclose a morphotype that may be related to the mode of swimming of the species searched. The morphological study of the vertebral column of the species in question permits the division of this bony structure into six morphologically different regions. This regionalization is more intricate than the classical division in abdominal and caudal parts only., (© 2024 Wiley‐VCH GmbH. Published by John Wiley & Sons Ltd.)

Climate change has had a significant impact on many marine organisms. To investigate the effects of environmental changes on deep-water benthic fishes, we selected the genus Oplegnathus and applied species distribution modeling and ecological niche modeling. From the last glacial maximum to the present, the three Oplegnathus species (O. conwayi, O. robinsoni, and O. peaolopesi) distributed in the Cape of Good Hope region of southern Africa experienced fitness zone fluctuations of 39.9%, 13%, and 5.7%, respectively. In contrast, O. fasciatus and O. punctatus, which were primarily distributed in the western Pacific Ocean, had fitness zone fluctuations of -6.5% and 11.7%, respectively. Neither the O. insignis nor the O. woodward varied by more than 5% over the period. Under future environmental conditions, the range of variation in fitness zones for the three southern African Oplegnathus species was expected to be between -30.8% and -26.5%, while the range of variation in fitness zones for the two western Pacific stonefish species was expected to remain below 13%. In addition, the range of variation in the fitness zones of the O. insignis was projected to be between -2.3% and 7.1%, and the range of variation in the fitness zones of the O. woodward is projected to be between -5.7% and -2%. The results indicated that O. fasciatus and O. punctatus had a wide distribution and high expansion potential, while Oplegnathus species might have originated in western Pacific waters. Our results showed that benthic fishes were highly adaptable to extreme environments, such as the last glacial maximum. The high ecological niche overlap between Oplegnathus species in the same region suggested that they competed with each other. Future research could explore the impacts of environmental change on marine organisms and make conservation and management recommendations., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

If similar evolutionary forces maintain intra- and interspecific diversity, patterns of diversity at both levels of biological organization can be expected to covary across space. Although this prediction of a positive species-genetic diversity correlation (SGDC) has been tested for several taxa in natural landscapes, no study has yet evaluated the influence of the community delineation on these SGDCs. In this study, we focused on tropical fishes of the Indo-Pacific Ocean, using range-wide single nucleotide polymorphism data for a deep-sea fish (Etelis coruscans) and species presence data of 4878 Teleostei species. We investigated whether a diversity continuum occurred, for different community delineations (subfamily, family, order and class) and spatial extents, and which processes explained these diversity patterns. We found no association between genetic diversity and species richness (α-SGDC), regardless of the community and spatial extent. In contrast, we evidenced a positive relationship between genetic and species dissimilarities (β-SGDC) when the community was defined at the subfamily or family level of the species of interest, and when the Western Indian Ocean was excluded. This relationship was related to the imprint of dispersal processes across levels of biological organization in Lutjanidae. However, this positive β-SGDC was lost when considering higher taxonomic communities and at the scale of the entire Indo-Pacific, suggesting different responses of populations and communities to evolutionary processes at these scales. This study provides evidence that the taxonomic scale at which communities are defined and the spatial extent are pivotal to better understand the processes shaping diversity across levels of biological organization., (© 2024 The Author(s). Molecular Ecology published by John Wiley & Sons Ltd.)

Many actinopterygian fish groups, including fossil and extant polypteriforms and lepisosteiforms, fossil halecomorphs, and some basal teleosts, have stout bony scales covered by layers of ganoin-an enamel layer ornamented with minute tubercles. Ganoid scales preserve well as disarticulated remains and notably constitute most of the fossil record for polypteriform in both South America and Africa. Based on two variables (tubercle size and distance between tubercles), some authors reported that the ganoin tubercle ornamentation in these scales is constant within a species and differs between species and allows distinguishing species or at least groups of species. However, despite its promising potential for assessing polypteriform paleodiversity, this tool has remained unused, probably because the variables are not well defined, and intraspecific variation does not seem to have been considered. To address this gap, we aimed to test the intraspecific and intra-individual variation in the ornamentation of ganoid scales in the type species Polypterus bichir. We propose three different parameters to describe the tubercle ornamentation: the distance between contiguous tubercles centers, their density, and their relative spatial organization. With these parameters, we investigate the variation in ganoin ornamentation among four specimens and across different regions of the body. Our results show that the distribution of the tubercles is highly variable within a same species, regardless of the body region, and sometimes even between different sectors of a same scale. Moreover, the variation observed in P. bichir overlaps with the distribution described in the literature for several extant and fossil species. Thus far, the ornamentation of ganoid scales is not a reliable diagnostical feature for polypterids., (© 2024 Fisheries Society of the British Isles.)

Objective: Channidae family, are major freshwater fish species amongst the local aquatic fauna of Pakistan, while, there is limited availability of local data on their molecular identification and phylogenetic analysis., Methods: Channa species were collected from four different geographical sites in the tertiary of Punjab province on the Indus and Chenab rivers of Pakistan. Morphometric records and molecular techniques were used to determine the intraspecific variations among populations of Channa marulius. Mitochondrial DNA was extracted from the flesh of C. marulius, while, COI gene was used for molecular identification and variation levels were estimated by using Principal Component Analysis., Results: Data recorded on the basis of morphometric parameters clearly divided the C. marulius of different locations into two distinct categories, which accounted for a cumulative variability of 97.6%. Non-significance (P < 0.05) among the C. marulius showed that it contains a unique control haplotype localized within the sub-population. The intra-species distance ranged from 0.000 to 0.001 for four different populations, in contrast, the sequences retrieved from the NCBI database exhibited a range span of 0.000-0.003, while, sequence diversity ranged from 0.000 to 0.006 for this intra-specific comparison. The cladogram was also constructed for C. marulius of different geographical locations for observation of phylogenetic relationship. The conclusion drawn from the phylogenetic analysis of C. marulius populations used in this study, contributes significantly to the understanding of genetic variations within populations of this species. The findings provide valuable insight to devise conservation strategies in fisheries management programs in Pakistan., (© 2024. The Author(s), under exclusive licence to Springer Nature B.V.)

Arapaima gigas, an emblematic species of the Amazon region and a longstanding primary fishing resource, currently holds a "Data Deficient" status on the International Union for Conservation of Nature Red List, and is listed as an endangered species in Brazil. The Tocantins River is the most extensively modified large tributary of the Amazon Basin, and thus can affect the dynamics of ichthyofaunal populations. Over a period of 1 year, representatives of the fishing communities and fishermen from 25 fishing communities from four municipalities in the lower Tocantins River region were interviewed, and the obtained information was evaluated based on the literature to survey the population abundance status of A. gigas in the region and its impact on local communities. Among the fishermen interviewed, only one reported still encountering and fishing A. gigas on Jaracuera Island. The disappearance of A. gigas in the region are viewed as having economically disastrous consequences for the residents. Additionally, other endemic fish species are no longer observed in this locality either. If fishery management officials do not work together with local communities, A. gigas could disappear from the northern region of Brazil, where information on the dynamics of A. gigas fishing is lacking.

The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission., Competing Interests: The authors declare no conflict of interest.

Marine species are widely shifting their distributions in response to global changes and it is commonly expected they will move northward and to greater depths to reach cooler, less disturbed habitats. However, local manifestations of global changes, anthropogenic pressures, and species characteristics may lead to unanticipated and varied responses by individual species. In this regard, the Celtic-Biscay Shelf is a particularly interesting study system because it has historically been heavily fished and occurs at the interface between two distinct biogeographic provinces, its community thus comprised of species with diverse thermal preferenda. In the context of rapidly warming temperatures and intense fishery exploitation, we investigated the distribution shifts of 93 taxa (65 Actinopteri, 10 Elasmobranchii, 11 Cephalopoda, 5 Malacostraca, and 2 Bivalvia), which were sampled annually from 1997 to 2020 during a scientific bottom trawl survey. We used a set of 11 complementary spatial indices to quantify taxon distribution shifts over time. Then, we explored the relative effect of taxon abundance, fishing pressure, and climatic conditions on taxon's distribution shift when a significant shift was detected. We observed that 56% of the taxa significantly shifted. Not all taxa will necessarily shift northward and to deeper areas, as it is often expected. Two opposite patterns were identified: taxa either moving deeper and to the southeast, or moving closer to the surface and to the northwest. The main explanatory factors were climate change (short- and long-term temperatures) and taxon abundance. Fishing pressure was the third, but still significant, explanatory factor of taxa of greater commercial importance. Our research highlights that taxa are displaying complex distribution shifts in response to the combined anthropogenic disturbances and underscores the need to conduct regional studies to better understand these responses at the ecosystem scale to develop more suitable management plans and policies., (© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)

In biogeography, vicariance and long-distance dispersal are often characterised as competing scenarios. However, they are related concepts, both relying on collective geological, ecological, and phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when freshwater connections are temporarily present and later severed (vicariance), or by unusual means when ocean gaps are crossed (long-distance dispersal). Marine barriers have a strong filtering effect on freshwater fishes, limiting immigrants to those most capable of oceanic dispersal. The roles of vicariance and dispersal are debated for freshwater fishes of the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Greater Antilles-Aves Ridge (GAARlandia), long-distance dispersal] and propose long-distance dispersal to be an appropriate model due to limited support for freshwater fish use of landspans. Greater Antillean freshwater fishes have six potential source bioregions (defined from faunal similarity): Northern Gulf of México, Western Gulf of México, Maya Terrane, Chortís Block, Eastern Panamá, and Northern South America. Faunas of the Greater Antilles are composed of taxa immigrating from many of these bioregions, but there is strong compositional disharmony between island and mainland fish faunas (>90% of Antillean species are cyprinodontiforms, compared to <10% in Northern Gulf of México and Northern South America, and ≤50% elsewhere), consistent with a hypothesis of long-distance dispersal. Ancestral-area reconstruction analysis indicates there were 16 or 17 immigration events over the last 51 million years, 14 or 15 of these by cyprinodontiforms. Published divergence estimates and evidence available for each immigration event suggests they occurred at different times and by different pathways, possibly with rafts of vegetation discharged from rivers or washed to sea during storms. If so, ocean currents likely provide critical pathways for immigration when flowing from one landmass to another. On the other hand, currents create dispersal barriers when flowing perpendicularly between landmasses. In addition to high salinity tolerance, cyprinodontiforms collectively display a variety of adaptations that could enhance their ability to live with rafts (small body size, viviparity, low metabolism, amphibiousness, diapause, self-fertilisation). These adaptations likely also helped immigrants establish island populations after arrival and to persist long term thereafter. Cichlids may have used a pseudo bridge (Nicaragua Rise) to reach the Greater Antilles. Gars (Lepisosteidae) may have crossed the Straits of Florida to Cuba, a relatively short crossing that is not a barrier to gene flow for several cyprinodontiform immigrants. Indeed, widespread distributions of Quaternary migrants (Cyprinodon, Gambusia, Kryptolebias), within the Greater Antilles and among neighbouring bioregions, imply that long-distance dispersal is not necessarily inhibitory for well-adapted species, even though it appears to be virtually impossible for all other freshwater fishes., (© 2024 Cambridge Philosophical Society.)

Notacanthid fishes constitute a common part of benthopelagic deep-sea fish communities on seamounts and continental slopes around the world. However, their highly conserved morphology and the usual lack of information on deep-water organisms make it difficult to appropriately address their biodiversity. A multidisciplinary approach combining morphological data with a DNA-based species delimitation analyses was used to explore the taxonomy of Notacanthus species. For this purpose, morphological and molecular data were obtained from 43 individuals, and the resulting information was combined with the available data. The results showed the occurrence of Notacanthus arrontei n. sp. from the Iberian Peninsula and highlighted several taxonomic conundrums regarding the Notacanthus genus. For instance, no significant differences were found between Notacanthus indicus and the recently described Notacanthus laccadiviensis, questioning its taxonomic status. Similarly, the result of the species delimitation molecular analysis coincided with previous DNA barcoding studies supporting the snubnosed spiny eel Notacanthus chemnitzii as a species complex that requires further research. Moreover, two unidentified records from the Indian Ocean were confirmed to belong to an unknown species pending formal description, and barcoding data show for the first time the occurrence of the shortfin spiny eel Notacanthus bonaparte in the Australia-New Zealand area. This research confirms the existence of important gaps in the knowledge of notacanthid fishes and represents a step forward toward a better understanding of their biological diversity., (© 2024 Fisheries Society of the British Isles.)

Coastal areas host a major part of marine biodiversity but are seriously threatened by ever-increasing human pressures. Transforming natural coastlines into urban seascapes through habitat artificialization may result in loss of biodiversity and key ecosystem functions. Yet, the extent to which seaports differ from nearby natural habitats and marine reserves across the whole Tree of Life is still unknown. This study aimed to assess the level of α and β-diversity between seaports and reserves, and whether these biodiversity patterns are conserved across taxa and evolutionary lineages. For that, we used environmental DNA (eDNA) metabarcoding to survey six seaports on the French Mediterranean coast and four strictly no-take marine reserves nearby. By targeting four different groups-prokaryotes, eukaryotes, metazoans and fish-with appropriate markers, we provide a holistic view of biodiversity on contrasted habitats. In the absence of comprehensive reference databases, we used bioinformatic pipelines to gather similar sequences into molecular operational taxonomic units (MOTUs). In contrast to our expectations, we obtained no difference in MOTU richness (α-diversity) between habitats except for prokaryotes and threatened fishes with higher diversity in reserves than in seaports. However, we observed a marked dissimilarity (β-diversity) between seaports and reserves for all taxa. Surprisingly, this biodiversity signature of seaports was preserved across the Tree of Life, up to the order. This result reveals that seaports and nearby marine reserves share few taxa and evolutionary lineages along urbanized coasts and suggests major differences in terms of ecosystem functioning between both habitats., (© 2024 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

The fish fauna of the Tocantins River possesses many endemic species; however, it is little studied in molecular terms and is quite threatened by the construction of several hydroelectric dams. Therefore, the objective of this study was to identify the ichthyofauna of the Tocantins River using DNA barcoding. For this, collections were carried out in five points of this river, which resulted in the capture of 725 individuals from which partial sequences of the cytochrome oxidase subunit I (COI) gene were obtained for genetic analysis. A total of 443 haplotypes were recovered with the mean intraspecific K2P genetic distance of 1.82%. Altogether, 138 species were identified based on morphological criteria, which was a quantity that was much lower than that indicated by the four molecular methods (assemble species by automatic partitioning [ASAP], barcode index number [BIN], generalized mixed Yule coalescent (GMYC), and Bayesian Poisson tree processes [bPTP]) through which 152-157 molecular entities were identified. In all, 41 unique BINs were obtained based on the data generated in the BOLDSystems platform. According to the result indicated by ASAP (species delimitation approach considered the most appropriate in the present study), there was an increase of 17 molecular entities (12.32%), when compared to the number of species identified through their morphological criteria, as it can show cryptic diversity, candidates for new species, and misidentifications. There were 21 incongruities indicated between the different identification approaches for species. Therefore, it is suggested that these taxonomic problems be cautiously evaluated by experts to solve such taxonomic issues., (© 2024 Fisheries Society of the British Isles.)

This study was designed to assess the ichthyofaunal diversity of River Panjkora, Khyber Pakhtunkhwa, Pakistan. For this purpose, a total of 1189 fish from six different sites were collected along the river and identified using standard keys. The fish collected and identified were representing 38 species, belonging to 7 families. The investigation spanned a year, from July 2021 to May 2022. The most dominant family was Cyprinidae 76% (n=906/1189), followed by Nemacheilidae 5.8% (n=69/1189), Channidae 5.2% (n=62/1189), Sisoridae 5.1% (n=61/1189), Mastacembelidae 4.9% (n=58/1189), Salmonidae 2.6% (n=31/1189) and least was Bagridae 0.17 (n=2/1189). The most abundant speices was Schizothorax plagiostomus with relative density of 16.8. Family Cyprinidae was represented by 21 species, Sisoridae by 7 species, Nemacheilidae by 5 species, Channidae by 2 species, while Bagridae, Salmonidae and Mastacembelidae, were each represented by a single species. PAST 3, XLSTAT and EXCEL 2019 were used for principal component analysis to study correlation of fish diversity and richness. Eigenvalue obtained from Kumrat to Busaq were 3.32, 1.01, 0.80, 0.44, 0.31 and 0.10 respectively. The higher value at Kumrat shows higher diversity. The water quality assessment showed average value of water temperature 10.4 ͦC, pH 7.0, electrical conductivity 184 mg/L, dissolved oxygen 7.9 mg/L, turbidity 43.73 mg/L, total dissolved solids 101 mg/L, total suspended solids 34.72 mg/L, total solids 135.53 mg/L, total alkalinity 75.77 mg/L, total hardness 58.37 mg/L, ammonia 0.46 mg/L, sulphate 26.03 mg/L, chloride 14.67 mg/L, calcium 69.11 mg/L, chromium 0.18 mg/L, copper 0.03, cobalt mg/L 0.04, nickel 0.039 mg/L, lead 0.02 mg/L and Zinc 0.35 mg/L. The findings of this study indicated that most of the physicochemical parameters remained within the acceptable limits throughout the study period. Analysis of fish gut contents included; nymphs, insect larvae, the presence of algae, protozoans and macroinvertebrates in the river ecosystem.