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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.)

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 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.

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.)

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).)

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.)

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.)

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.)

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.

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.)

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.

Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL:  http://210.22.121.250:8888/CoSFISH/home/indexPage., (© The Author(s) 2024. Published by Oxford University Press.)

The Cosmonaut Sea is one of the least accessed regions in the Southern Ocean, and our knowledge about the fish biodiversity in the region is sparse. In this study, we provided a description of demersal fish diversity in the Cosmonaut Sea by analysing cytochrome oxidase I ( COI ) barcodes of 98 fish samples that were hauled by trawling during the 37th and 38th Chinese National Antarctic Research Expedition (CHINARE) cruises. Twenty-four species representing 19 genera and 11 families, namely, Artedidraconidae, Bathydraconidae, Bathylagidae, Channichthyidae, Liparidae, Macrouridae, Muraenolepididae, Myctophidae, Nototheniidae, Paralepididae and Zoarcidae, were discriminated and identified, which were largely identical to local fish occurrence records and the general pattern of demersal fish communities at high Antarctic shelf areas. The validity of a barcoding gap failed to be detected and confirmed across all species due to the indicative signals of two potential cryptic species. Nevertheless, DNA barcoding still demonstrated to be a very efficient and sound method for the discrimination and classification of Antarctic fishes. In the future, various sampling strategies that cover all geographic sections and depth strata of the Cosmonaut Sea are encouraged to enhance our understanding of local fish communities, within which DNA barcoding can play an important role in either molecular taxonomy or the establishment of a dedicated local reference database for eDNA metabarcoding analyses.

Anthropogenically forced changes in global freshwater biodiversity demand more efficient monitoring approaches. Consequently, environmental DNA (eDNA) analysis is enabling ecosystem-scale biodiversity assessment, yet the appropriate spatio-temporal resolution of robust biodiversity assessment remains ambiguous. Here, using intensive, spatio-temporal eDNA sampling across space (five rivers in Europe and North America, with an upper range of 20-35 km between samples), time (19 timepoints between 2017 and 2018) and environmental conditions (river flow, pH, conductivity, temperature and rainfall), we characterise the resolution at which information on diversity across the animal kingdom can be gathered from rivers using eDNA. In space, beta diversity was mainly dictated by turnover, on a scale of tens of kilometres, highlighting that diversity measures are not confounded by eDNA from upstream. Fish communities showed nested assemblages along some rivers, coinciding with habitat use. Across time, seasonal life history events, including salmon and eel migration, were detected. Finally, effects of environmental conditions were taxon-specific, reflecting habitat filtering of communities rather than effects on DNA molecules. We conclude that riverine eDNA metabarcoding can measure biodiversity at spatio-temporal scales relevant to species and community ecology, demonstrating its utility in delivering insights into river community ecology during a time of environmental change., (© 2024. The Author(s).)

In the face of global ecosystem changes driven by anthropogenic activities, effective biomonitoring strategies are crucial for mitigating impacts on vulnerable aquatic habitats. Time series analysis underscores a great significance in understanding the dynamic nature of marine ecosystems, especially amidst climate change disrupting established seasonal patterns. Focusing on Norway's Oslo fjord, our research utilises eDNA-based monitoring for temporal analysis of aquatic biodiversity during a one year period, with bi-monthly sampling along a transect. To increase the robustness of the study, a taxonomic assignment comparing BLAST+ and SINTAX approaches was done. Utilising MiFish and Elas02 primer sets, our study detected 63 unique fish species, including several commercially important species. Our findings reveal a substantial increase in read abundance during specific migratory cycles, highlighting the efficacy of eDNA metabarcoding for fish composition characterization. Seasonal dynamics for certain species exhibit clear patterns, emphasising the method's utility in unravelling ecological complexities. eDNA metabarcoding emerges as a cost-effective tool with considerable potential for fish community monitoring for conservation purposes in dynamic marine environments like the Oslo fjord, contributing valuable insights for informed management strategies., (© 2024. The Author(s).)

Sebastes schlegelii is one of the most commercially important marine fish in the northwestern Pacific. However, little information about the genome-wide genetic characteristics is available for S. schlegelii individuals from the Bohai and Yellow Seas. In this study, a total of 157,778, 174,480, and 188,756 single-nucleotide polymorphisms from Dalian (DL), Yantai (YT), and Qingdao (QD) coastal waters of China were, respectively, identified. Sixty samples (twenty samples per population) were clustered together, indicating shallow structures and close relationships with each other. The observed heterozygosity, expected heterozygosity, polymorphism information content, and nucleotide diversity ranged from 0.14316 to 0.17684, from 0.14035 to 0.17145, from 0.20672 to 0.24678, and from 7.63 × 10 -6 to 8.77 × 10 -6 , respectively, indicating the slight difference in genetic diversity among S. schlegelii populations, and their general genetic diversity was lower compared to other marine fishes. The population divergence showed relatively low levels (from 0.01356 to 0.01678) between S. schlegelii populations. Dispersing along drifting seaweeds, as well as the ocean current that flows along the western and northern coasts of the Yellow Sea and southward along the eastern coast of China might be the major reasons for the weak genetic differentiation. These results form the basis of the population genetic characteristics of S. schlegelii based on GBS (Genotyping by Sequencing). In addition to basic population genetic information, our results provid a theoretical basis for further studies aimed at protecting and utilizing S. schlegelii resources.

Over recent years, fish parasites of the genus Cymothoa Fabricius, 1793, have received increased attention due to both their ecological and their economic importance to aquaculture and fishery. As the studies about Cymothoa have increased this improve our understanding on the host specificity and distribution of these parasites. The aim of this paper was to review the current global geographic distribution, distribution patterns and parasite-host interactions patterns of Cymothoa spp. associated with fish from marine and brackish water bodies around the world. A total of 144 samples were analyzed, from which 23 species of Cymothoa were found parasitizing 84 teleost fish species of 35 families and 20 orders. Most of these parasites were found in the mouth of the host fish, including in wild fish. The highest occurrence of parasites was found in host species belonging to the families Carangidae and Lutjanidae. Host specificity was an important factor in the geographic distribution of Cymothoa species as also environmental temperature. Cymothoa indica, Cymothoa exigua and Cymothoa excisa were the species with lowest specificity for host family and widest geographic distribution.

The evolution of reproductive barriers is the first step in the formation of new species and can help us understand the diversification of life on Earth. These reproductive barriers often take the form of hybrid incompatibilities, in which alleles derived from two different species no longer interact properly in hybrids 1-3 . Theory predicts that hybrid incompatibilities may be more likely to arise at rapidly evolving genes 4-6 and that incompatibilities involving multiple genes should be common 7,8 , but there has been sparse empirical data to evaluate these predictions. Here we describe a mitonuclear incompatibility involving three genes whose protein products are in physical contact within respiratory complex I of naturally hybridizing swordtail fish species. Individuals homozygous for mismatched protein combinations do not complete embryonic development or die as juveniles, whereas those heterozygous for the incompatibility have reduced complex I function and unbalanced representation of parental alleles in the mitochondrial proteome. We find that the effects of different genetic interactions on survival are non-additive, highlighting subtle complexity in the genetic architecture of hybrid incompatibilities. Finally, we document the evolutionary history of the genes involved, showing signals of accelerated evolution and evidence that an incompatibility has been transferred between species via hybridization., (© 2024. The Author(s).)

FastFish-ID for rapid and accurate identification of fish species was conceived at Brandeis University based on pioneering work on Closed-Tube Barcoding (Rice et al., Mitochondrial DNA Part A 27(2):1358-1363, 2016; Sirianni et al., Genome 59:1049-1061, 2016). FastFish-ID was subsequently validated and commercialized at Thermagenix, Inc. using a portable device and high-precision PCR (Naaum et al., Food Res Int 141:110035, 2021). The motivation for these efforts was the pressing need for a technology that could be widely used throughout the seafood supply chain to combat IUU Fishing (Helyar et al., PLOS ONE 9, 2014) and overfishing (FAO, State of the World Fisheries and Aquaculture 2018. http://www.fao.org/documents/card/en/c/I9540EN/ , 2018), along with seafood fraud and mislabeling (Watson et al., Fish Fish 17:585-595, 2015). These destructive practices are wasting fish stocks, frustrating attempts to achieve seafood sustainability, endangering oceanic ecosystems, and causing consumers billions of dollars each year (Porterfield et al., Oceana: February, 2022). During the past three Covid19 pandemic years, EcologeniX, LLC has taken over further development and optimization of FastFish-ID. The present chapter provides an overview of the improvements introduced throughout the FastFish-ID process., (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

We evaluated the influence of flooding and receding comparison and spatial variation on the composition and structure of fish assemblages in blackwater and clearwater rivers of the Aracá-Demeni sub-basin in the middle Negro River, Amazonas state, Brazil. The collections were carried out during the falling-water period (November 2018) and the rising-water period (April 2019) using gillnets with meshes ranging from 30 to 120mm stretched mesh size. Ecological estimates of richness, equitability, the Shannon-Wiener diversity index, and the Berger-Parker index showed no significant differences between the periods. The composition of the ichthyofauna showed variations between the falling-water and rising-water periods. Beta diversity in the Aracá-Demeni sub-basin is almost completely caused by species substitution, with spatial turnover accounting for most of the estimate. The identification of these patterns and of the responsible factors are fundamental for the definition of conservation strategies, especially in an ecosystem whose dynamics can be influenced by climate change through changes in the intensity of the flood pulse and connectivity.

Marine heatwaves have been linked to negative ecological effects in recent decades 1,2 . If marine heatwaves regularly induce community reorganization and biomass collapses in fishes, the consequences could be catastrophic for ecosystems, fisheries and human communities 3,4 . However, the extent to which marine heatwaves have negative impacts on fish biomass or community composition, or even whether their effects can be distinguished from natural and sampling variability, remains unclear. We investigated the effects of 248 sea-bottom heatwaves from 1993 to 2019 on marine fishes by analysing 82,322 hauls (samples) from long-term scientific surveys of continental shelf ecosystems in North America and Europe spanning the subtropics to the Arctic. Here we show that the effects of marine heatwaves on fish biomass were often minimal and could not be distinguished from natural and sampling variability. Furthermore, marine heatwaves were not consistently associated with tropicalization (gain of warm-affiliated species) or deborealization (loss of cold-affiliated species) in these ecosystems. Although steep declines in biomass occasionally occurred after marine heatwaves, these were the exception, not the rule. Against the highly variable backdrop of ocean ecosystems, marine heatwaves have not driven biomass change or community turnover in fish communities that support many of the world's largest and most productive fisheries., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Holocephalans exhibit auxiliary appendages called pre-pelvic claspers (PPCs) that are located anterior to the pelvic fins, while pelvic claspers are pelvic fin modifications located posteriorly as modified metapterygia. Articulation points of the PPCs have not previously been imaged or evaluated in a comparative context, therefore, they may represent modified pelvic fin structures if they articulate with the propterygium. Alternatively, they could represent the only example of an independent third set of paired appendages in an extant taxon, if they articulate independently from any pelvic fin basal cartilages, challenging the current paradigm that extant jawed vertebrates are constrained to two sets of paired appendages. Two extinct groups, including Placoderms and Acanthodians, exhibit variation in the number of paired appendages, suggesting this may be a plesiomorphic trait. We evaluated PPC developmental growth rates, morphology, and articulation points in spotted ratfish (Hydrolagus Colliei, Holocephali). We also compared variation in PPC morphology among representatives of the three extant holocephalan families. Both, the pre-pelvic and pelvic claspers exhibit a dramatic surge in growth at sexual maturity, and then level off, suggesting synchronous development via shared hormonal regulation. While mature females are larger than males, pelvic fin growth and development is faster in males, suggesting a selective advantage to larger fins with faster development. Finally, microcomputed tomography scans revealed that PPCs are not modified propterygia, nor do they articulate with the propterygium. They articulate with the anterior pre-pelvic process on the anterior puboischiadic bar (or pelvic girdle), suggesting that while they are associated with the pelvic girdle, they may indeed represent a third, independent set of paired appendages in extant holocephalans., (© 2023 Wiley Periodicals LLC.)

Among ray-finned fishes that provide parental care, many spawn in constructed nests, ranging from bowls, burrows and ridges to nests made of algae or bubbles. Because a nest by definition is a construction that enhances the nest-builder's fitness by helping it meet the needs of the developing offspring, nest-building behaviour is naturally selected, as is a preference for spawning with mates that provide well-built nests. However, nest-building behaviour can also be sexually selected, when nest traits increase mating success, protect against sperm competition or nest take-overs by conspecifics. Here, we offer a systematic review, with examples of how competition for sites and location of fish nests relates to sexual selection. We examine direct and indirect benefits of mate choice linked to nest traits, and different types of nests, from a sexual selection perspective. Nest-related behaviours are often under both natural and sexual selection, and we disentangle examples where that is the case, with special attention to females. We highlight some taxa in which nest building is likely to be sexually selected, but lack of research has left them uninvestigated. Some of them are established aquarium species, making them particularly amenable for future research. Finally, we compare with arthropods, amphibians and birds. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.

Individual growth is a fundamental life history trait 1-4 , yet its macroevolutionary trajectories have rarely been investigated for entire animal assemblages. Here we analyse the evolution of growth in a highly diverse vertebrate assemblage-coral reef fishes. We combine state-of-the-art extreme gradient boosted regression trees with phylogenetic comparative methods to detect the timing, number, location and magnitude of shifts in the adaptive regime of somatic growth. We also explored the evolution of the allometric relationship between body size and growth. Our results show that the evolution of fast growth trajectories in reef fishes has been considerably more common than the evolution of slow growth trajectories. Many reef fish lineages shifted towards faster growth and smaller body size evolutionary optima in the Eocene (56-33.9 million years ago), pointing to a major expansion of life history strategies in this Epoch. Of all lineages examined, the small-bodied, high-turnover cryptobenthic fishes shifted most towards extremely high growth optima, even after accounting for body size allometry. These results suggest that the high global temperatures of the Eocene 5 and subsequent habitat reconfigurations 6 might have been critical for the rise and retention of the highly productive, high-turnover fish faunas that characterize modern coral reef ecosystems., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Human society is dependent on nature 1,2 , but whether our ecological foundations are at risk remains unknown in the absence of systematic monitoring of species' populations 3 . Knowledge of species fluctuations is particularly inadequate in the marine realm 4 . Here we assess the population trends of 1,057 common shallow reef species from multiple phyla at 1,636 sites around Australia over the past decade. Most populations decreased over this period, including many tropical fishes, temperate invertebrates (particularly echinoderms) and southwestern Australian macroalgae, whereas coral populations remained relatively stable. Population declines typically followed heatwave years, when local water temperatures were more than 0.5 °C above temperatures in 2008. Following heatwaves 5,6 , species abundances generally tended to decline near warm range edges, and increase near cool range edges. More than 30% of shallow invertebrate species in cool latitudes exhibited high extinction risk, with rapidly declining populations trapped by deep ocean barriers, preventing poleward retreat as temperatures rise. Greater conservation effort is needed to safeguard temperate marine ecosystems, which are disproportionately threatened and include species with deep evolutionary roots. Fundamental among such efforts, and broader societal needs to efficiently adapt to interacting anthropogenic and natural pressures, is greatly expanded monitoring of species' population trends 7,8 ., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Accurate species phylogenies are a prerequisite for all evolutionary research. Teleosts are the largest and most diversified group of extant vertebrates, but relationships among their three oldest extant lineages remain unresolved. On the basis of seven high-quality new genome assemblies in Elopomorpha (tarpons, eels), we revisited the topology of the deepest branches of the teleost phylogeny using independent gene sequence and chromosomal rearrangement phylogenomic approaches. These analyses converged to a single scenario that unambiguously places the Elopomorpha and Osteoglossomorpha (arapaima, elephantnose fish) in a monophyletic sister group to all other teleosts, i.e., the Clupeocephala lineage (zebrafish, medaka). This finding resolves more than 50 years of controversy on the evolutionary relationships of these lineages and highlights the power of combining different levels of genome-wide information to solve complex phylogenies.

Although there have been many studies on the taxonomy of lanternfishes, morphological similarities during larval and juvenile stages make it difficult to identify species and understand their early life histories. During an ichthyoplankton survey in the Northwest Pacific (East Sea, East China Sea) between 2017 and 2020, a research vessel from the National Institute of Fisheries Science collected larvae and juveniles that belonged to the family Myctophidae using a bongo net. To accurately identify species, mtDNA sequences encoding cytochrome c oxidase subunit I and 16S ribosomal RNA were obtained and compared with those of adult voucher specimens. These comparisons led to the identification of four previously unknown larval lanternfish species (Diaphus chrysorhynchus, Diaphus suborbitalis, Diaphus watasei and Lampanyctus fernae), which are described here for the first time. The authors also describe the cryptic diversity of Benthosema pterotum and provide identification keys for 10 species of larval lanternfish, in accordance with their developmental stages., (© 2022 Fisheries Society of the British Isles.)

A study of the type series of Stylophthalmus paradoxus and Idiacanthus atlanticus (Stomiidae), and Cyclothone livida, C. obscura and C. pallida (Gonostomatidae), uncovered errors in the synonymy of Idiacanthus and inconsistencies regarding the number of type specimens of the three species of Cyclothone. The syntypes of S. paradoxus were matched with the illustrations of this species in Brauer (1906) and the specimen used in the description was identified and designated as a lectotype of this species. A comparison of these syntypes with specimens of Idiacanthus atlanticus, including its syntypes, and of I. fasciola indicated that S. paradoxus is most likely a junior synonym of I. fasciola. In addition, the research resulted in a reliable way to distinguish between I. fasciola and I. atlanticus and in the identification of the primary type of the latter species. Mismatches were found in the information Brauer (1906) provided about the material he had for the three species of Cyclothone as well as with published data about the type series of these species. It seems that the whereabouts of many of the type series specimens is unknown. We therefore propose that the individual specimens Brauer singled out for measurements in his original descriptions of C. livida, C. obscura and C. pallida be recognized as lectotypes.

Teleost fishes are ancient tetraploids descended from an ancestral whole-genome duplication that may have contributed to the impressive diversification of this clade. Whole-genome duplications can occur via self-doubling (autopolyploidy) or via hybridization between different species (allopolyploidy). The mode of tetraploidization conditions evolutionary processes by which duplicated genomes return to diploid meiotic pairing, and subsequent genetic divergence of duplicated genes (cytological and genetic rediploidization). How teleosts became tetraploid remains unresolved, leaving a fundamental gap in the interpretation of their functional evolution. As a result of the whole-genome duplication, identifying orthologous and paralogous genomic regions across teleosts is challenging, hindering genome-wide investigations into their polyploid history. Here, we combine tailored gene phylogeny methodology together with a state-of-the-art ancestral karyotype reconstruction to establish the first high-resolution comparative atlas of paleopolyploid regions across 74 teleost genomes. We then leverage this atlas to investigate how rediploidization occurred in teleosts at the genome-wide level. We uncover that some duplicated regions maintained tetraploidy for more than 60 million years, with three chromosome pairs diverging genetically only after the separation of major teleost families. This evidence suggests that the teleost ancestor was an autopolyploid. Further, we find evidence for biased gene retention along several duplicated chromosomes, contradicting current paradigms that asymmetrical evolution is specific to allopolyploids. Altogether, our results offer novel insights into genome evolutionary dynamics following ancient polyploidizations in vertebrates., (© 2022 Parey et al.; Published by Cold Spring Harbor Laboratory Press.)

Modern representatives of chondrichthyans (cartilaginous fishes) and osteichthyans (bony fishes and tetrapods) have contrasting skeletal anatomies and developmental trajectories 1-4 that underscore the distant evolutionary split 5-7 of the two clades. Recent work on upper Silurian and Devonian jawed vertebrates 7-10 has revealed similar skeletal conditions that blur the conventional distinctions between osteichthyans, chondrichthyans and their jawed gnathostome ancestors. Here we describe the remains (dermal plates, scales and fin spines) of a chondrichthyan, Fanjingshania renovata gen. et sp. nov., from the lower Silurian of China that pre-date the earliest articulated fossils of jawed vertebrates 10-12 . Fanjingshania possesses dermal shoulder girdle plates and a complement of fin spines that have a striking anatomical similarity to those recorded in a subset of stem chondrichthyans 5,7,13 (climatiid 'acanthodians' 14 ). Uniquely among chondrichthyans, however, it demonstrates osteichthyan-like resorptive shedding of scale odontodes (dermal teeth) and an absence of odontogenic tissues in its spines. Our results identify independent acquisition of these conditions in the chondrichthyan stem group, adding Fanjingshania to an increasing number of taxa 7,15 nested within conventionally defined acanthodians 16 . The discovery of Fanjingshania provides the strongest support yet for a proposed 7 early Silurian radiation of jawed vertebrates before their widespread appearance 5 in the fossil record in the Lower Devonian series., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

A fundamental gap in the study of the origin of limbed vertebrates lies in understanding the morphological and functional diversity of their closest relatives. Whereas analyses of the elpistostegalians Panderichthys rhombolepis, Tiktaalik roseae and Elpistostege watsoni have revealed a sequence of changes in locomotor, feeding and respiratory structures during the transition 1-9 , an isolated bone, a putative humerus, has controversially hinted at a wider range in form and function than now recognized 10-14 . Here we report the discovery of a new elpistostegalian from the Late Devonian period of the Canadian Arctic that shows surprising disparity in the group. The specimen includes partial upper and lower jaws, pharyngeal elements, a pectoral fin and scalation. This new genus is phylogenetically proximate to T. roseae and E. watsoni but evinces notable differences from both taxa and, indeed, other described tetrapodomorphs. Lacking processes, joint orientations and muscle scars indicative of appendage-based support on a hard substrate 13 , its pectoral fin shows specializations for swimming that are unlike those known from other sarcopterygians. This unexpected morphological and functional diversity represents a previously hidden ecological expansion, a secondary return to open water, near the origin of limbed vertebrates., (© 2022. The Author(s).)

The suborder Gobioidei is among the most diverse groups of vertebrates, comprising about 2310 species. In the fossil record gobioids date back to the early Eocene (c. 50 m.y. ago), and a considerable increase in numbers of described species is evident since the middle Miocene (c. 16 m.y. ago). About 40 skeleton-based gobioid species and > 100 otolith-based species have been described until to date. However, assignment of a fossil gobioid species to specific families has often remained tentative, even if well preserved complete specimens are available. The reasons are that synapomorphies that can be recognized in a fossil skeleton are rare (or absent) and that no phylogenetic framework applicable to gobioid fossils exists. Here we aim to overcome this problem by developing a phylogenetic total evidence framework that is suitable to place a fossil skeleton-based gobioid at family level. Using both literature and newly collected data we assembled a morphological character matrix (48 characters) for 29 extant species, representing all extant gobioid families, and ten fossil gobioid species, and we compiled a multi-gene concatenated alignment (supermatrix; 6271 bp) of published molecular sequence data for the extant species. Bayesian and Maximum Parsimony analyses revealed that our selection of extant species was sufficient to achieve a molecular 'backbone' that fully conforms to previous molecular work. Our data revealed that inclusion of all fossil species simultaneously produced very poorly resolved trees, even for some extant taxa. In contrast, addition of a single fossil species to the total evidence data set of the extant species provided new insight in its possible placement at family level, especially in a Bayesian framework. Five out of the ten fossil species were recovered in the same family as had been suggested in previous works based on comparative morphology. The remaining five fossil species had hitherto been left as family incertae sedis. Now, based on our phylogenetic framework, new and mostly well supported hypotheses to which clades they could belong can be presented. We conclude that the total evidence framework presented here will be beneficial for all future work dealing with the phylogenetic placement of a fossil skeleton-based gobioid and thus will help to improve our understanding of the evolutionary history of these fascinating fishes. Moreover, our data highlight that increased sampling of fossil taxa in a total-evidence context is not universally beneficial, as might be expected, but strongly depends on the study group and peculiarities of the morphological data., Competing Interests: The authors have declared that no competing interests exist.