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Genetic diversity and population structure in Indian featherback fish, Chitala chitala (Hamilton, 1822) was investigated by combined analyses of two full mitochondrial genes, ATPase 6/8 and Cytochrome b. A total of 403 individuals, collected from 14 rivers yielded 61 haplotypes. Hierarchical partitioning analysis identified 19.01% variance 'among' and 80.99% variance 'within groups and populations'. The mean coefficient of genetic differentiation (F ST ) was observed to be significant 0.26 (p < 0.05). Mantel tests rejected the hypothesis that genetic and geographic distances were correlated. The patterns of genetic differentiation, AMOVA and principal coordinate analyses indicated that natural populations were sub-structured and comprised of four genetic stocks of C. chitala in Indian rivers. The results also supported the higher resolution potential of concatenated gene sequences. The knowledge of genetic variation and divergence, from this study, can be utilized for its scientific conservation and management in the wild.

Myriad environmental and biological traits have been investigated for their roles in influencing the rate of molecular evolution across various taxonomic groups. However, most studies have focused on a single trait, while controlling for additional factors in an informal way, generally by excluding taxa. This study utilized a dataset of cytochrome c oxidase subunit I (COI) barcode sequences from over 7000 ray-finned fish species to test the effects of 27 traits on molecular evolutionary rates. Environmental traits such as temperature were considered, as were traits associated with effective population size including body size and age at maturity. It was hypothesized that these traits would demonstrate significant correlations with substitution rate in a multivariable analysis due to their associations with mutation and fixation rates, respectively. A bioinformatics pipeline was developed to assemble and analyze sequence data retrieved from the Barcode of Life Data System (BOLD) and trait data obtained from FishBase. For use in phylogenetic regression analyses, a maximum likelihood tree was constructed from the COI sequence data using a multi-gene backbone constraint tree covering 71% of the species. A variable selection method that included both single- and multivariable analyses was used to identify traits that contribute to rate heterogeneity estimated from different codon positions. Our analyses revealed that molecular rates associated most significantly with latitude, body size, and habitat type. Overall, this study presents a novel and systematic approach for integrative data assembly and variable selection methodology in a phylogenetic framework.

Whereas the gill chambers of jawless vertebrates open directly into the environment, jawed vertebrates evolved skeletal appendages that drive oxygenated water unidirectionally over the gills. A major anatomical difference between the two jawed vertebrate lineages is the presence of a single large gill cover in bony fishes versus separate covers for each gill chamber in cartilaginous fishes. Here, we find that these divergent patterns correlate with the pharyngeal arch expression of Pou3f3 orthologs. We identify a deeply conserved Pou3f3 arch enhancer present in humans through sharks but undetectable in jawless fish. Minor differences between the bony and cartilaginous fish enhancers account for their restricted versus pan-arch expression patterns. In zebrafish, mutation of Pou3f3 or the conserved enhancer disrupts gill cover formation, whereas ectopic pan-arch Pou3f3b expression generates ectopic skeletal elements resembling the multimeric covers of cartilaginous fishes. Emergence of this Pou3f3 arch enhancer >430 Mya and subsequent modifications may thus have contributed to the acquisition and diversification of gill covers and respiratory strategies during gnathostome evolution., Competing Interests: The authors declare no competing interest.

Biodiversity is an important parameter for the evaluation of the extant environmental conditions. Here, we used environmental DNA (eDNA) metabarcoding to investigate fish biodiversity in five different estuaries in Japan. Water samples for eDNA were collected from river mouths and adjacent coastal areas of two estuaries with high degrees of development (the Tama and Miya Rivers) and three estuaries with relatively low degrees of development (the Aka, Takatsu, and Sendai Rivers). A total of 182 fish species across 67 families were detected. Among them, 11 species occurred in all the rivers studied. Rare fishes including endangered species were successfully detected in rich natural rivers. Biodiversity was the highest in the Sendai River and lowest in the Tama River, reflecting the degree of human development along each river. Even though nutrient concentration was low in both the Aka and Sendai Rivers, the latter exhibited greater diversity, including many tropical or subtropical species, owing to its more southern location. Species composition detected by eDNA varied among rivers, reflecting the distribution and migration of fishes. Our results are in accordance with the ecology of each fish species and environmental conditions of each river., Competing Interests: The authors have declared that no competing interest exist.

Estuarine dependency by certain fish species has been clearly demonstrated in a number of studies, but the term has also been used for those species and guilds that are not dependent on estuaries. The origins and development of the term are explored, and definitions for four types of estuarine fish association are provided which may be helpful in facilitating classification and comparisons between fish taxa using estuarine systems in different parts of the world. In addition, a diagrammatic representation of more recent estuary-associated guild categories is presented to provide context and clarity on the estuarine dependency issue, and the fact that a continuum in terms of dependency is perhaps most appropriate for describing fish species relationships with estuaries. ETHICAL STATEMENT: This brief communication is a philosophical discussion and did not involve the capture, use or care of any living or dead fish. Therefore, no permit or animal ethics clearance was required to undertake the literature review., (© 2020 Fisheries Society of the British Isles.)

The Japanese scad Decapterus maruadsi (Carangidae) is an economically important marine species in Asia but its exploitation shows signs of overfishing. To document its stock structure, a population genetic and phylogeographic study of several populations of this species from the central part of the Indo-West Pacific region was conducted using the mitochondrial cytochrome b gene. Genetic homogeneity within the Sundaland region's population, including Rosario (the Philippines) and Ranong (Andaman Sea) populations was revealed with low nucleotide diversity ( π  = 0.001-0.003) but high haplotype diversity ( h  = 0.503-0.822). In contrast, a clear genetic structure was observed between this group and the northern Vietnam populations as revealed by F ST , AMOVA and SAMOVA, while the central Vietnam population of Khanh Hoa is an admixed group between the two differentiated regional populations. The neutrality and mismatch distribution analyses supported a demographic expansion of D. maruadsi in between last Pleistocene to early Holocene period which influenced present day distribution pattern. Contemporary factors such as oceanic currents and different life history traits are also believed to play significant roles in the observed population structure and biogeographical pattern. Based on these results, recommendations on how stocks of the Japanese scad should be managed are offered.

The clupeid fishes are large filter-feeding organisms and have diverse groups of trophic guilds and habitats. They are known for their special body scale, which is unique among the other teleost fishes. Here, we examined microscopic characteristics of scales in 21 clupeid species from four marine resources, including the Caspian Sea, the Persian Gulf and the Gulf of Oman (Indian Ocean) and South China Sea (Haian Islands and Shanwei, Pacific Ocean) to evaluate if the scale features could properly contribute to understanding the taxonomic relationships in these fishes. Typically, the studied scales were morphologically categorized into two types; circular (i.e., true circular, cordate, discoidal) and pentagonal. Also, it was found that the number and the orientation of radii and continuous striae, the presence of pores at the posterior field, overall shape, striations on the posterior field, and scale sizes could be used as suitable features to classify the clupeids in species and genus levels. The result of morphological analysis based on the scale characteristics was largely consistent with the phylogenetic relationships of the studied species. This highlighted that morphological characteristics of the clupeid scale could adequately contribute to the understanding of taxonomic relationships in this large group., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

The taxonomy of Hysterothylacium genus in Mediterranean waters remains incomplete and unresolved. The aim of the current study was to investigate the morphological and molecular identification of selected species of Hysterothylacium larvae in marine fish from the Tunisian Mediterranean coasts. A total of 192 marine fish samples were examined. In total, thirty-seven third-stage larvae of Hysterothylacium were morphologically identified as Hysterothylacium type V. In the present study, representatives of this type from the Mediterranean Sea were genetically characterized for the first time by sequencing the rDNA ITS (ITS1-5.8S-ITS2) regions and mtDNA cox2 gene. This study represents the first report of Hysterothylacium type V from the Mediterranean Sea. We also report Mullus barbatus, M. surmuletus, and Pagellus erythrinus as new hosts for this larval type. Based upon molecular and phylogenetic analyses considering the rDNA ITS regions, the Hysterothylacium type V described here was classified as a new genotype, named Genotype B. The valid genetic data of the described Hysterothylacium type V in the present study can be used to establish the phylogenetic relationships among Hysterothylacium species from the Mediterranean Sea and worldwide for future research.

Saint Peter and Saint Paul's Archipelago (SPSPA), one of the smallest and most isolated island groups in the world, is situated on the Mid-Atlantic Ridge, between Brazil and the African continent. SPSPA has low species richness and high endemism; nonetheless, the diversity of fishes from deep habitats (>30 m depth) had not been previously studied in detail. Several expeditions conducted between 2009 and 2018 explored the shallow and deep reefs of SPSPA using scuba, closed-circuit rebreathers, manned submersibles, baited remote underwater stereo-videos (stereo-BRUV) and fishing between 0 and 1050 m depth. These expeditions yielded 41 new records of fishes for SPSPA: 9 in open waters, 9 in shallow waters (0-30 m), 8 in mesophotic ecosystems (30-150 m) and 15 in deeper reefs (>150 m). Combined with literature records of adult pelagic, shallow and deep-reef species, as well as larvae, the database of the fish biodiversity for SPSPA currently comprises 225 species (169 recorded as adult fishes and 79 as larvae, with 23 species found in both stages). Most of them (112) are pelagic, 86 are reef-associated species and 27 are deep-water specialists. Species accumulation curves show that the number of fish species has not yet reached an asymptote. Whereas the number of species recorded in SPSPA is similar to that in other oceanic islands in the Atlantic Ocean, the proportion of shorefishes is relatively lower, and the endemism level is the third highest in the Atlantic. Twenty-nine species are listed as threatened with extinction. Observations confirm the paucity of top predators on shallow rocky reefs of the island, despite the presence of several pelagic shark species around SPSPA. Because all of the endemic species are reef associated, it is argued that the new marine-protected areas created by the Brazilian government do not ensure the protection and recovery of SPSPA's biodiversity because they allow exploitation of the most vulnerable species around the archipelago itself. This study suggests a ban on reef fish exploitation inside an area delimited by the 1000 m isobath around the islands (where all known endemics are concentrated) as the main conservation strategy to be included in the SPSPA management plan being prepared by the Brazilian government., (© 2020 Fisheries Society of the British Isles.)

Fishes are commercially, recreationally and functionally important inhabitants of coral reefs. Accordingly, accurate assessments of fish abundance and diversity are necessary for effective reef management. While some reef fish monitoring programmes target all fishes, many survey a subset of common and visually obvious species. Changing to counts of all species, while desirable, risks new and unwelcome biases from altered observer swimming speeds and search patterns. Here we test whether substantially increasing the number of target species in an established fish monitoring programme biases counts of the original subset, so precluding ongoing comparisons with historical data. A subset of 141 fish species have been visually surveyed along 50 × 5 m transects over 27 years throughout Australia's Great Barrier Reef. We experimentally compared counts of the subset from standard subset-only surveys and from surveys of all species (excluding small site-attached fishes that are surveyed separately) at three diverse reefs. Subset species richness and abundance, in total and of major families, and assemblage structure did not differ due to survey method. The high-level experience of the one observer appeared to overcome new biases from counting more species and the extra 2 min/transect was not logistically excessive. Surveys of all fishes recorded almost 80% more species than subset-only surveys and >130% higher total abundance on average from >150% more genera that included abundant and functionally important taxa. Overall, fish counts by an experienced observer were not biased by the number of species surveyed and counts of all species markedly improved assessments of reef fish diversity and function., (© 2020 Commonwealth of Australia. Journal of Fish Biology © 2020 The Fisheries Society of the British Isles.)

Gobies, sleepers, and cardinalfishes represent major clades of a species rich radiation of small bodied, ecologically diverse percomorphs (Gobiaria). Molecular phylogenetics has been crucial to resolving broad relationships of sleepers and gobies (Gobioidei), but the phylogenetic placements of cardinalfishes and nurseryfishes, as reciprocal or sequential sister clades to Gobioidei, are uncertain. In order to evaluate relationships among and within families we used a phylogenetic data mining approach to generate densely sampled trees inclusive of all higher taxa. We utilized conspecific amino acid homology to improve alignment accuracy, included ambiguously identified taxa to increase taxon sampling density, and resampled individual gene alignments to filter rogue sequences before concatenation. This approach yielded the most comprehensive tree yet of Gobiaria, inferred from a sparse (17 percent-complete) supermatrix of one ribosomal and 22 protein coding loci (18,065 characters), comprised of 50 outgroup and 777 ingroup taxa, representing 32 percent of species and 68 percent of genera. Our analyses confirmed the lineage-based classification of gobies with strong support, identified sleeper clades with unforeseen levels of systematic uncertainty, and quantified competing phylogenetic signals that confound resolution of the root topology. We also discovered that multilocus data completeness was related to maximum likelihood branch support, and verified that the phylogenetic uncertainty of shallow relationships observed within goby lineages could largely be explained by supermatrix sparseness. These results demonstrate the potential and limits of publicly available sequence data for producing densely-sampled phylogenetic trees of exceptionally biodiverse groups., 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 © 2020. Published by Elsevier Inc.)

In the present study we evaluate the population structure and potential colonization routes of the silverside Chirostoma humboldtianum through approximate Bayesian computations. Six microsatellite loci were amplified in a total of 288 individuals from six different locations covering the complete geographic distribution of the species. Additionally, two mitochondrial DNA markers, a D loop control region and cytochrome b were amplified in a subset of 107 individuals. The results found with microsatellites allow recovering well-structured populations that have experienced a drastic reduction in the effective population size. On the other hand, mtDNA sequences showed a moderate phylogeographic structure with shared haplotypes between geographic localities and signalsof a slight increase in the effective population size. Finally, the approximate Bayesian computation analysis performed with both datasets suggested a west-to-east colonization route for the species in Central Mexico., (© 2020 Fisheries Society of the British Isles.)

Which biological groups (in the present study, periphyton, macroinvertebrates, and fishes) are surveyed is a fundamental question in environmental impact assessment programs in metal-contaminated rivers. We performed a systematic review of 202 studies that investigated the ecological impacts of metal contamination on aquatic populations and communities in streams and rivers to examine 1) which biological groups were surveyed, 2) whether their responses were correlated with each other, and 3) which biological group was most responsive to changes in metal contamination level. In these studies, published from 1991 to 2015, benthic macroinvertebrates were most frequently chosen throughout the period (59-76% in different 5-yr periods), followed by periphyton and fishes, and the number of studies that surveyed at least 2 or 3 biological groups was very limited (10%). Pearson's correlation coefficients calculated between the metrics of different biological groups were often low, emphasizing the importance of investigating multiple biological groups to better understand the responses of aquatic communities to metal contamination in running waters. Despite the limited data collected, our meta-analysis showed that, in most cases, biological metrics based on macroinvertebrates were more responsive to changes in metal contamination level than those based on periphyton or fishes. This finding suggests that benthic macroinvertebrates could be a reasonable choice to detect the ecological impacts of metal contamination on a local scale. Environ Toxicol Chem 2020;39:1964-1972. © 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC., (© 2020 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.)

Patterns of genetic structure and connectivity of the monotypic cigar wrasse Cheilio inermis within western Indian Ocean (WIO) are poorly understood. Whether the species exists as a single panmictic population across the WIO is unclear. Sequence data were generated from two mitochondrial genes (cytochrome b and ATPase 6) and one nuclear intron (S7 intron I). High levels of haplotype and allelic diversity ( h = 0.88-0.98; A = 0.95-0.98), along with low nucleotide diversities were observed across all markers. The pairwise Φ ST values indicated differentiation of Tanga from the four WIO localities (Inhaca, Nosy Bé, Gazi, and Shimoni), as well as differentiation between the northernmost WIO localities. AMOVAs indicated high differentiation among defined locality groups, whereas nuclear gene analysis found little differentiation among groups. The observed genetic differentiation in C. inermis could be caused by oceanic barriers, and by limited larval dispersal with the pelagic larvae possibly settling near their parental origin and promoting differentiation.

The Revillagigedo Archipelago National Park is the largest no-take Marine Protected Area in North America and it is essential for the conservation of globally endangered marine megafauna, including cetaceans, sea birds and cartilaginous fishes. The present paper reports the occurrence of 28 chondrichthyan species, including 19 sharks, seven batoids and two chimaeras in the Revillagigedo Archipelago, comprising eight new records and a brief revision of confirmed species to date., (© 2020 Fisheries Society of the British Isles.)

Deep-sea habitats may drive unique dispersal and demographic patterns for fishes, but population genetic analyses to address these questions have rarely been conducted for fishes in these environments. This study investigates the population structure of 3 tropical deepwater snappers of the genus Etelis that reside at 100-400 m depth, with broad and overlapping distributions in the Indo-Pacific. Previous studies showed little population structure within the Hawaiian Archipelago for 2 of these species: Etelis coruscans and E. carbunculus. Here we extend sampling to the entire geographic range of each species to resolve the population genetic architecture for these 2 species, as well as a recently exposed cryptic species (Etelis sp.). One goal was to determine whether deepwater snappers are more dispersive than shallow-water fishes. A second goal was to determine whether submesophotic fishes have older, more stable populations than shallow reef denizens that are subject to glacial sea-level fluctuations. Both goals are pertinent to the management of these valuable food fishes. A total of 1153 specimens of E. coruscans from 15 geographic regions were analyzed, along with 1064 specimens of E. carbunculus from 11 regions, and 590 specimens of E. sp. from 16 regions. The first 2 species were analyzed with mtDNA and 9-11 microsatellite loci, while E. sp. was analyzed with mtDNA only. Etelis coruscans had a non-significant microsatellite global FST, but significant global mtDNA Ф ST = 0.010 (P = 0.0007), with the isolation of Seychelles in the western Indian Ocean, and intermittent signals of isolation for the Hawaiian Archipelago. Etelis carbunculus had a non-significant microsatellite global FST, and significant global mtDNA Ф ST = 0.021 (P = 0.0001), with low but significant levels of isolation for Hawai'i, and divergence between Tonga and Fiji. Etelis sp. had mtDNA Ф ST = 0.018 (P = 0.0005), with a strong pattern of isolation for both Seychelles and Tonga. Overall, we observed low population structure, shallow mtDNA coalescence (similar to near-shore species), and isolation at the fringes of the Indo-Pacific basin in Hawai'i and the western Indian Ocean. While most shallow-water species have population structure on the scale of biogeographic provinces, deepwater snapper populations are structured on the wider scale of ocean basins, more similar to pelagic fishes than to shallow-water species. This population structure indicates the capacity for widespread dispersal throughout the Indo-Pacific region., (© The American Genetic Association 2020. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Pronounced organism-wide morphological stasis in evolution has resulted in taxa with unusually high numbers of primitive characters. These 'living fossils' hold a prominent role for our understanding of the diversification of the group in question. Here we provide the first detailed osteological analysis of Aenigmachanna gollum based on high-resolution nano-CT scans and one cleared and stained specimen of this recently described snakehead fish from subterranean waters of Kerala in South India. In addition to a number of derived and unique features, Aenigmachanna has several characters that exhibit putatively primitive conditions not encountered in the family Channidae. Our morphological analysis provides evidence for the phylogenetic position of Aenigmachanna as the sister group to Channidae. Molecular analyses further emphasize the uniqueness of Aenigmachanna and indicate that it is a separate lineage of snakeheads, estimated to have split from its sister group at least 34 or 109 million years ago depending on the fossil calibration employed. This may indicate that Aenigmachanna is a Gondwanan lineage, which has survived break-up of the supercontinent, with India separating from Africa at around 120 mya. The surprising morphological disparity of Aenigmachanna from members of the Channidae lead us to erect a new family of snakehead fishes, Aenigmachannidae, sister group to Channidae, to accommodate these unique snakehead fishes.

Sexual parasitism has evolved as a distinctive mode of reproduction among deep-sea anglerfishes. The permanent attachment of males to host females observed in these species represents a form of anatomical joining, which is otherwise unknown in nature. Pronounced modifications to immune facilities are associated with this reproductive trait. The genomes of species with temporarily attaching males lack functional aicda genes that underpin affinity maturation of antibodies. Permanent attachment is associated with additional alterations, culminating in the loss of functional rag genes in some species, abolishing somatic diversification of antigen receptor genes, the hallmark of canonical adaptive immunity. In anglerfishes, coevolution of innate and adaptive immunity has been disentangled, implying that an alternative form of immunity supported the emergence of this evolutionarily successful group of vertebrates., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

A 16S rRNA next-generation sequencing technique was applied to investigate the microbial diversity and liquid chromatography-tandem mass spectrometry was used to identify glutamyl peptide profiles of 10 Thai fermented freshwater fish (Pla-ra) samples. A total of 12 genera of bacteria were able to be detected, with Tetragenococcus spp., Staphylococcus spp., and Lactobacillus spp. dominating. Of the 18 glutamyl peptides analyzed, 17 were found, even though the amounts detected were lower than the taste threshold. Despite this, an increase in mouthfulness sensation, reflecting kokumi activity, was clearly identified in most of the samples, which might be because of a synergistic effect of different sub-threshold compounds present in the samples. In principle component analysis, the relationship between microorganisms and glutamyl peptide generation was observed, especially between Tetragenococcus spp. and Lentibacillus spp. and the generation of γ-Glu-Val-Gly. Correlations between microbial diversity and the generation of taste enhancers were identified in this study.

Industrial-scale harvest of species at risk of extinction is controversial and usually highly regulated on land and for charismatic marine animals (e.g. whales). In contrast, threatened marine fish species can be legally caught in industrial fisheries. To determine the magnitude and extent of this problem, we analyze global fisheries catch and import data and find reported catch records of 91 globally threatened species. Thirteen of the species are traded internationally and predominantly consumed in European nations. Targeted industrial fishing for 73 of the threatened species accounts for nearly all (99%) of the threatened species catch volume and value. Our results are a conservative estimate of threatened species catch and trade because we only consider species-level data, excluding group records such as 'sharks and rays.' Given the development of new fisheries monitoring technologies and the current push for stronger international mechanisms for biodiversity management, industrial fishing of threatened fish and invertebrates should no longer be neglected in conservation and sustainability commitments.

Sculpin fishes belonging to the family Cottidae represent a large and complex group, inhabiting a wide range of freshwater, brackish-water, and marine environments. Numerous studies based on analysis of their morphology and genetic makeup frequently provided controversial results. In the present work, we sequenced complete mitochondrial (mt) genomes and fragments of nuclear ribosomal DNA (rDNA) of the fourhorn sculpin Myoxocephalus quadricornis and some related cottids to increase the power of phylogenetic and taxonomic analyses of this complex fish group. A comparison of the My. quadricornis mt genomes obtained by us with other complete mt genomes available in GenBank has revealed a surprisingly low divergence (3.06 ± 0.12%) with Megalocottus platycephalus and, at the same time, a significantly higher divergence (7.89 ± 0.16%) with the species of the genus Myoxocephalus . Correspondingly, phylogenetic analyses have shown that My. quadricornis is clustered with Me. platycephalus but not with the Myoxocephalus species. Completely consistent patterns of divergence and tree topologies have been obtained based on nuclear rDNA. Thus, the multi-gene data in the present work indicates obvious contradictions in the relationships between the Myoxocephalus and Megalocottus species studied. An extensive phylogenetic analysis has provided evidence for a closer affinity of My. quadricornis with the species of the genus Megalocottus than with the species of the genus Myoxocephalus . A recombination analysis, along with the additional GenBank data, excludes introgression and/or incorrect taxonomic identification as the possible causative factors responsible for the observed closer affinity between the two species from different genera. The above facts necessitate realignment of the genera Myoxocephalus and Megalocottus . The genetic data supports the two recognized genera, Myoxocephalus and Megalocottus , but suggests changing their compositions through transferring My. quadricornis to the genus Megalocottus . The results of the present study resolve the relationships within a complex group of sculpin fishes and show a promising approach to phylogenetic systematics (as a key organizing principle in biodiversity research) for a better understanding of the taxonomy and evolution of fishes and for supplying relevant information to address various fish biodiversity conservation and management issues.

Aim: Exotic species' introductions together with extinction of native species represent the main mechanisms driving biotic homogenization of freshwater fish assemblages around the world. While generally ichtyofaunistic realms transit towards biotic homogenization, for conservation purposes it is essential to understand what specific mechanisms are promoting it on particular areas or regions. Here, we report the occurrence of biotic homogenization in 29 Chilean watersheds, analyzing its β-diversity (including turnover and nestedness) and predicting future trends., Location: Continental Chile (18o-56o S)., Methods: We determined fish composition per basin for historical and current assemblages; extant native, exotic, and extinct species were recorded as 1 (presence) or 0 (absence) in two matrices basins × species. For each matrix, we calculated the turnover (βsim), nestedness (βnes), and β-diversity (βsor); then, we obtained Δβsim, Δβnes, and Δβsor, as the arithmetical difference between basin pairs over time. In addition, we search for explanatory variables correlating Δβsim, Δβnes, and Δβsor with geographical and land use variables. Finally, simulating events of species introduction (i.e., invasion) and extinction, we generated 15 hypothetical assemblages, looking to establish future trends towards biotic change in Chilean basins., Results: Species turnover and β-diversity significantly decreased from historical to current assemblages (Δβsim = -0.084; Δβsor = -0.061, respectively), while the species nestedness did not show significant changes (Δβnes = 0.08). Biotic changes have been driven mainly by the introduction of 28 exotic species, with a minor role of extinctions (one species) and translocations (0 species) of native species. Changes in β-diversity were negatively correlated with area, elevation, and geographical distance between basins but not with land-use nor human population. Finally, the analysis of 15 future assemblages predicts a significant decrease of β-diversity and turnover, and an increase for species nestedness, this time promoted by an increase in the extinction of native species., Main Conclusion: Chilean basins show a significant decrease of the distributional β-diversity and species turnover of the freshwater fish fauna, evidencing a trend towards biotic homogenization. This trend is shared with other Neotropical basins; however, specific mechanisms driving it show different magnitude. Changes in the β-diversity components do not show correlation with variables associated to land use, thus suggesting that casual introductions of freshwater fishes in Chile follow an opportunistic mode related to commercial use. According to future scenarios simulated, biotic homogenization should increase further, mainly as consequence of increased native extinctions., Competing Interests: The authors have declared that no competing interests exist.

Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Fish diversity and species identification is utmost important for fisheries management. But, in some cases morphological characteristics based identification is difficult for a non-specialist to perform. In view of the above, the present study emphasized on the assessment of DNA barcoding, phylogenetics and genetic diversity of fish species in the Ranganadi River, Arunachal Pradesh, India. India. Arunachal Pradesh, the largest state of North-East India covers almost 60.93% of the Eastern Himalayan hotspot. Altogether 114 specimens, representing 22 species, belonging to 3 orders and 5 families were successfully barcoded and found to be 98-100% identical from both GenBank and BOLD databases. Out of these 22 fish species, it was found that one species assessed was Endangered, three species as Near Threatened and one species as Vulnerable. A Neighbour Joining (NJ) tree was constructed using Rstudio for the purpose of a phylogenetic analysis of the identified species. The barcoding gap analysis using K2P, P-distance and Jukes-Cantor was done to detect the presence of cryptic species and barcoding success. The nucleotide base composition and genetic distance analysis were also performed, using MEGA 6.0. DNA Sequence Polymorphism v6.12.03 analysis revealed the nucleotide diversity (p) and haplotype diversity (Hd). The Hd for the whole dataset was found to be 0.975, which showed high genetic diversity in the Ranganadi River. Both morphological key identifying characters and molecular data corroborated the phylogenetic analysis. This COI barcode library, generated in the present study, not only helped in species identification and molecular study, but also in cryptic species identification., 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 © 2020 Elsevier B.V. All rights reserved.)

Corals create complex reef structures that provide both habitat and food for many fish species. Because of numerous natural and anthropogenic threats, many coral reefs are currently being degraded, endangering the fish assemblages they support. Coral reef restoration, an active ecological management tool, may help reverse some of the current trends in reef degradation through the transplantation of stony corals. Although restoration techniques have been extensively reviewed in relation to coral survival, our understanding of the effects of adding live coral cover and complexity on fishes is in its infancy with a lack of scientifically validated research. This study reviews the limited data on reef restoration and fish assemblages, and complements this with the more extensive understanding of complex interactions between natural reefs and fishes and how this might inform restoration efforts. It also discusses which key fish species or functional groups may promote, facilitate or inhibit restoration efforts and, in turn, how restoration efforts can be optimised to enhance coral fish assemblages. By highlighting critical knowledge gaps in relation to fishes and restoration interactions, the study aims to stimulate research into the role of reef fishes in restoration projects. A greater understanding of the functional roles of reef fishes would also help inform whether restoration projects can return fish assemblages to their natural compositions or whether alternative species compositions develop, and over what timeframe. Although alleviation of local and global reef stressors remains a priority, reef restoration is an important tool; an increased understanding of the interactions between replanted corals and the fishes they support is critical for ensuring its success for people and nature., (© 2020 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of The Fisheries Society of the British Isles.)

The Acipenseriformes, as one of the earliest extant vertebrates, plays an important role in the evolution of fishes and even the whole vertebrates. Here we collected and analyzed all complete mitochondrial genomes of Acipenseriformes species. Phylogenetic analyses demonstrated that the polytomous branch included Acipenseridae and Polyodontidae formed five clades. The Polyodontidae clade and the Scaphirhynchus clade both were monophyletic group, whereas the Acipenser species and the Huso species both were polyphyletic group. The Bayesian divergence times showed that the origin time for Acipenseriformes was at 318.0 Mya, which was similar to the some previous results of 312.1 Mya, 346.9 Mya and 389.7 Mya. The result was in good consistent with the paleontological data available and the split time of the Pacific and Atlantic Oceans from the Jurassic to the Cretaceous (Laurasia splits in North America and Eurasia). The dN/dS ratios showed the evolutionary rates gradually slow down in five major Acipenseriformes clades from the Clade A (the Pacific sturgeons species) to Clade C (the genus Scaphirhynchus), which was related to the process of geographical formation., Competing Interests: Declaration of Competing Interest The authors declare that they have no conflict of interest., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The presence of the opal chimaera, Chimaera opalescens, is reported for the first time in the deep waters of the Azores, with the capture of four specimens by fishermen and the video recording of an additional five individuals. Species identification was supported by the 646 bp sequenced fragment of the mitochondrial gene cytochrome oxidase subunit I. Because C. opalescens is a recently recognised species that had been recurrently misidentified as rabbitfish, Chimaera monstrosa, the historical data of C. monstrosa in the Azores were reviewed to assess the possible presence of both Chimaera species in the region. Although several authors have reported the occurrence of C. monstrosa in the Azorean waters since the 1800s, the majority of these are based on only three specimens caught during the late 1800s. The investigation performed using literature and examination of the museum specimens still available concluded that the most likely scenario is that C. monstrosa is absent from the Azores and past records of that species in the region are most likely misidentifications of C. opalescens., (© 2020 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of The Fisheries Society of the British Isles.)

Background: Fish is a major food and allergen source, requiring safety declarations on packages. Enzyme-linked immunosorbent assays (ELISAs) are often used to ensure that the product meets the required standards with regard to the presence of allergens. Over 1000 different fish species are traded and consumed worldwide, and they are increasingly provided by aquaculture. Up to 3% of the general population is at risk of sometimes fatal allergic reactions to fish, requiring strict avoidance of this commodity. The aim of this study is to evaluate the capacity of three commercially available ELISA tests to detect a wide variety of bony and cartilaginous fish and their products, which is essential to ensure reliable and safe food labeling., Results: The detection rates for 57 bony fish ranged from 26% to 61%. Common European and North American species, including carp, cod, and salmon species, demonstrated a higher detection rate than those from the Asia-Pacific region, including pangasius and several mackerel and tuna species. Among the 17 canned bony fish products, only 65% to 86% were detected, with tuna showing the lowest rate. None of the cartilaginous fish (n = 9), other vertebrates (n = 8), or shellfish (n = 5) were detected., Conclusions: We demonstrated that three commercial fish ELISA kits had a limited capacity to detect fish and their products. The complexity of fish as a protein source that is increasingly utilized means that there is an urgent need for improved detection methods. This is crucial for the food industry to provide safe seafood products and comply with international legislation. © 2020 Society of Chemical Industry., (© 2020 Society of Chemical Industry.)

The use of environmental DNA (eDNA) for monitoring aquatic macrofauna allows the non-invasive species determination and measurement of their DNA abundance and typically involves the analysis of eDNA captured from water samples. In this proof-of-concept study, we focused on the novel use of eDNA extracted from archived suspended particulate matter (SPM) for identifying fish species using metabarcoding, which benefits from the prospect of retrospective monitoring and also analysis of fish communities through time. We used archived SPM samples of the German Environmental Specimen Bank (ESB), which were collected using sedimentation traps from different riverine points in Germany. Environmental DNA was extracted from nine SPM samples differing in location, organic content, and porosity (among other factors) using four different methods for the isolation of high-quality DNA. Application of the PowerSoil DNA Isolation Kit with an overnight incubation in lysis buffer, resulted in DNA extraction with the highest purity and eDNA metabarcoding of these eDNA fragments was used to detect a total of 29 fish taxa among the analyzed samples. Here we demonstrated for the first time that SPM is a promising source of eDNA for metabarcoding analysis, which could provide valuable retrospective information (when using archived SPM) for fish monitoring, complementing the currently used approaches.

Marine fish species checklists from six Chinese coastal waters were combined for the analysis of taxonomic diversity. The Genus-Family index (G-F index) ranged between 0.39 and 0.84, which generally indicated a decreasing trend with increasing latitude, with the exception of the southernmost area. Average taxonomic distinctness showed a slight increasing trend from northern to central study areas, but whether the taxonomic distinctness indices represent a latitudinal gradient of biodiversity requires further study. The multivariate analysis revealed a distinct latitudinal variation in fish assemblages. These results indicate that species checklist data are helpful in understanding the diversity distribution of fish species in the coastal zone. The potential of a species inventory should be exploited to fully understand biodiversity., (© 2020 The Fisheries Society of the British Isles.)

This study investigated the fauna of monogeneans on gills of 13 fish species from the Matapi River, Brazilian Amazon. A total 548 fish belonging to 13 species (1 Anostomidae, 3 Characidae, 1 Curimatidae, 1 Hemiodontidae, 2 Serrasalmidae, 3 Scianidae, 1 Ageneiosidae and 1 Tetradontidae) were examined. From these fish, 6 species were infected and with a total prevalence of 22.4%. Monogeneans collected are represented by the following taxa: Anacanthorus gravihamulatus, Notozothecium minor, Notozothecium penetrarum, Diplectanum piscinarius, Aetheolabes goeldiensis, Euryhaliotrema succedanus, Anacanthorus jegui, Urocleidoides astyanacis, Urocleidoides strombicirrus, Euryhaliotrema sp. and Urocleidoides spp. There was a variation in the prevalence, mean intensity and mean abundance of monogeneans among the host populations examined. Monogeneans of Metynnis lippincottianus, Plagioscion squamosissimus, Astyanax bimaculatus and Curimata incompta presented a highly aggregated dispersion pattern. Body weight of M. lippincottianus and C. incompta presented a weak positive correlation with abundance of parasites. Lastly, this is first study for 12 fish species from the Matapi River and the first report of E. succedanus for Plagioscion surinamensis and N. penetrarum for Serrasalmus rhombeus.

Declines in animal body sizes are widely reported and likely impact ecological interactions and ecosystem services. For harvested species subject to multiple stressors, limited understanding of the causes and consequences of size declines impedes prediction, prevention, and mitigation. We highlight widespread declines in Pacific salmon size based on 60 years of measurements from 12.5 million fish across Alaska, the last largely pristine North American salmon-producing region. Declines in salmon size, primarily resulting from shifting age structure, are associated with climate and competition at sea. Compared to salmon maturing before 1990, the reduced size of adult salmon after 2010 has potentially resulted in substantial losses to ecosystems and people; for Chinook salmon we estimated average per-fish reductions in egg production (-16%), nutrient transport (-28%), fisheries value (-21%), and meals for rural people (-26%). Downsizing of organisms is a global concern, and current trends may pose substantial risks for nature and people.

The biodiversity and composition of endoparasites in fish obtained from the Antarctic and subantarctic zones are compared in this study. Several fish were collected in the summer from Antarctica (King George Island) and the Southern Pacific coast (Strait of Magellan and Almirante Montt Gulf). This database was complemented with published information on fish endoparasite communities from both zones, with specimens of fish sample size n ≥ 15. Thus, 31 fish species were analysed in this study, which altogether had 79 parasite species. Diversity indices were calculated for the parasite community of each fish species. Then they were compared between the Antarctic and subantarctic zones. Parasite species composition and host specificity (as the number of fish species used by a parasite species) were also analysed and compared between zones. The diversity indices and the abundance of parasites were significantly higher in the Antarctic than the subantarctic fish. Few parasite species (7.6%) were shared between fish from both zones, showing significant differences in parasite composition. Antarctic parasites were less host-specific than subantarctic parasites, which allowed the coexistence of several parasite species in the fish. The high parasite abundance in Antarctic fish could trigger sympatric speciation in certain parasitic lineages or the exploitation of new resources, resulting in more parasite species than those in subantarctic environments. The high abundance of Antarctic parasites implies different methods and rates of transmission than those of subantarctic parasites. In addition, more alternative fish hosts were used by the Antarctic than subantarctic parasites. This altogether indicates that host-parasite interaction dynamics significantly differ between the Antarctic and subantarctic systems.

Taxonomic research plays an important role in the classification of organisms. Molecular techniques provide useful tools for the determination of the taxonomic status of species, although often time-consuming and not cost-efficient. Herein, we developed a strategy to analyze fish samples in a rapid mode. Experimentally, fish fillet samples were pretreated with trifluoroacetic acid aqueous solution, and the obtained protein fraction was analyzed by matrix-assisted laser desorption/ionization mass spectrometry. Principal component analysis of mass spectrometric datasets was used to visualize the taxonomical distance among the analyzed 13 seafood species. The results were illustrated using treemaps where the fish relationship distance can be visualized. The obtained mass spectral results can be taken as reference and successfully used for the identification of unknown fish fillet samples. It is promising to utilize the present strategy to provide clues for the taxonomy study among ambiguous species and identify fish species.

The current study represents the first molecular characterization of freshwater fish species in Egypt from two major fish resources; the River Nile and Lake Nasser. A total of 160 DNA barcodes using a 655-bp-long fragment of the mitochondrial cytochrome oxidase subunit I (COI) gene were generated from 37 species belonging to 32 genera that represent 15 families from nine orders. The studied species were identified using different molecular-based identification approaches, in addition to the morphological identification, including neighbor-joining (NJ) trees, Barcode Index Number, and Automatic Barcode Gap Discovery (ABGD). The average genetic divergence based on the Kimura two-parameter model (K2P) within orders, families, genera, and species were 0.175, 0.067, 0.02, and 0.008, respectively. The minimum and maximum K2P distance-based genetic divergences were 0.0 and 0.154, respectively. Nucleotide diversity (π) varied among families and ranged between 0.0% for families Malapteruridae, Auchenoglanididae, Schilbeidae, Anguillidae, Centropomidae and Tetraodontidae and 17% for family Cyprinidae. The current study cautions against the lack of species coverage at public databases which limits the accurate identification of newly surveyed species and recommends that multiple methods are encouraged for accurate species identification. The findings of the current study also support that COI barcode enabled effective fish species identification in River Nile and Lake Nasser. Moreover, the results of the current study will establish a comprehensive DNA barcode library for freshwater fishes along the River Nile in Egypt. Egyptian freshwater fish DNA barcodes will contribute substantially to future efforts in monitoring, conservation, and management of fisheries in Egypt.

Haemulon steindachneri (Jordan and Gilbert) (Haemulidae), popularly known as "cocoroca-de-boca-larga", "latin-grunt" or "latin-burro", represents a species complex found on the Atlantic western coast and on the Pacific eastern coast, condition confirmed recently by molecular phylogenies. In the present study, DNA barcoding analysis recognizes two distinct clusters; the first includes Brazil and Caribbean, and the second is composed of Pacific specimens, with genetic distance of 7.4%, differentiated by 35 base pairs. In addition to the molecular evidence, our results show morphological differences that distinguish the Atlantic lineage from that of the Pacific: anal fin, usually, with eight rays (vs. generally nine rays in Pacific); 13-15 scales below the lateral line, rarely 12 (vs. 12 scales below the lateral line, rarely 13 in Pacific), posterior margin of the maxilla robust with a slightly angled end (vs. smaller maxilla with moderately convex extremity), and presence of a spot on the pre-operculum, broad and robust, with no definite shape (vs. narrow spot, with anterior extremity tuned and posterior straight, resembling a triangle in Pacific). Therefore, based on both molecular and morphological evidences, H. steindachneri is redescribed for the Pacific coast while a new species is described for the Atlantic coast., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

Modern taxonomy requires the preservation of biospecimens for both morphological and molecular applications. The utility of a previously identified preservative, dimethyldimethylhydantoin hydantoin (Dekafald ® ), to retain both physical diagnostic traits and the DNA integrity of biological specimens remains unknown. Using 439 eggs and 414 larvae from two North American fish species, we compared three hydantoin solutions at different concentrations (5%, 10%, and 20%) with gold standard preservatives (10% buffered formalin, 95% ethanol) to evaluate morphological trait retention up to 90 days, and DNA barcoding success up to 56 days. While the 5% hydantoin solution had the most sequencing success by 56 days, the 10% hydantoin solution was the best multipurpose preservative. Future work should assess the performance of ∼10% hydantoin solution over longer time periods, and its applicability to other taxa such as Arthropoda.

Animal pigmentation primarily depends on the presence and mixing ratio of chromatophores, functioning in animal survival and communication. For the benthic and carnivorous Siniperca chuatsi, pigmentation pattern is key to concealment and predation. In this study, the formation, distribution, and main pattern of chromatophores were observed in the embryos, larvae, skins, and visceral tissues from S. chuatsi. Melanophores were firstly visualized in the yolk sac at segmentation stage, and then they were migrated to the whole body and further clustered into the black stripes, bands, and patches. In adult S. chuatsi, the head, black band, and body side skins mainly contained melanophores, showing as deep or light black. The abdomen skin mainly contained iridophores, showing as silvery. In the eye, the pigment layers were located in the epithelial layers of iris and retina and shown as black. Then, the pigmentation-related gene, tyrosinase gene from S. chuatsi (Sc-tyr) was analyzed by bioinformatics and quantitative methods. The Sc-tyr gene encoded a protein with 540 amino acids (Sc-TYR). The Sc-TYR contained two copper ion binding sites, which were coordinated by six conserved histidines (H182, H205, H214, H366, H370, H393) and necessary for catalytic activity. The Sc-TYR was well conserved compared with TYR of various species with higher degree of sequence similarity with other fishes (77.6-98.3%). The qRT-PCR test showed that the Sc-tyr mRNA reached the peak value at segmentation stage in the embryo development, the black skins displayed a higher expression level than that in silvery skin, and the eye had the highest expression level compared with other tissues. Further research on enzyme activity showed that the expression patterns of tyrosinase activity were similar to that of the Sc-tyr mRNA. Comparing with the results of molecular and phenotype, it was found that the temporal and spatial distributions of tyrosinase corresponded well with changes in pigmentation patterns and the intensity of skin melanization. This study initially explored the pigmentation formation and tyrosinase expression, which served as a foundation for further insight into the genetics mechanism of body color formation in S. chuatsi.

Monitoring freshwater fish communities in a large human-impacted river is a challenging task. The structure of fish assemblages has been monitored yearly in the Marne and the Seine Rivers, across the Paris conurbation, France, using traditional electrofishing (EF) surveys since 1990, in accordance with the European Water Framework Directive. In addition, metabarcoding of DNA extracted from environmental samples (eDNA) was concomitantly conducted in nine sampling sites in 2017 and in 2018 to compare the estimates of species richness and relative abundance among three methods: annual, long-term EF monitoring and eDNA. The present study confirms better detection of fish species using eDNA compared to annual EF. eDNA metabarcoding was also more efficient for species detection than a 3-6-year EF survey but was similar or less efficient than a long-term EF survey of 14 years of monitoring. In addition, the numbers of reads per species relative to the total number of reads significantly increased with (a) increasing relative abundance (relative percentage of individuals caught per species) and (b) increasing number of years that a fish species was detected during the 2000-2018 period. These results suggest that eDNA could reflect local population persistence., (© 2020 The Fisheries Society of the British Isles.)

Mixed-species animal groups (MSGs) are widely acknowledged to increase predator avoidance and foraging efficiency, among other benefits, and thereby increase participants' fitness. Diversity in MSG composition ranges from two to 70 species of very similar or completely different phenotypes. Yet consistency in organization is also observable in that one or a few species usually have disproportionate importance for MSG formation and/or maintenance. We propose a two-dimensional framework for understanding this diversity and consistency, concentrating on the types of interactions possible between two individuals, usually of different species. One axis represents the similarity of benefit types traded between the individuals, while the second axis expresses asymmetry in the relative amount of benefits/costs accrued. Considering benefit types, one extreme represents the case of single-species groups wherein all individuals obtain the same supplementary, group-size-related benefits, and the other extreme comprises associations of very different, but complementary species (e.g. one partner creates access to food while the other provides vigilance). The relevance of social information and the matching of activities (e.g. speed of movement) are highest for relationships on the supplementary side of this axis, but so is competition; relationships between species will occur at points along this gradient where the benefits outweigh the costs. Considering benefit amounts given or received, extreme asymmetry occurs when one species is exclusively a benefit provider and the other a benefit user. Within this parameter space, some MSG systems are constrained to one kind of interaction, such as shoals of fish of similar species or leader-follower interactions in fish and other taxa. Other MSGs, such as terrestrial bird flocks, can simultaneously include a variety of supplementary and complementary interactions. We review the benefits that species obtain across the diversity of MSG types, and argue that the degree and nature of asymmetry between benefit providers and users should be measured and not just assumed. We then discuss evolutionary shifts in MSG types, focusing on drivers towards similarity in group composition, and selection on benefit providers to enhance the benefits they can receive from other species. Finally, we conclude by considering how individual and collective behaviour in MSGs may influence both the structure and processes of communities., (© 2020 The Authors. Biological Reviews published by John Wiley & Sons Ltd on behalf of Cambridge Philosophical Society.)

Tropical ectotherms are hypothesized to be vulnerable to environmental changes, but cascading effects of organismal tolerances on the assembly and functioning of reef fish communities are largely unknown. Here, we examine differences in organismal traits, assemblage structure, and productivity of cryptobenthic reef fishes between the world's hottest, most extreme coral reefs in the southern Arabian Gulf and the nearby, but more environmentally benign, Gulf of Oman. We show that assemblages in the Arabian Gulf are half as diverse and less than 25% as abundant as in the Gulf of Oman, despite comparable benthic composition and live coral cover. This pattern appears to be driven by energetic deficiencies caused by responses to environmental extremes and distinct prey resource availability rather than absolute thermal tolerances. As a consequence, production, transfer, and replenishment of biomass through cryptobenthic fish assemblages is greatly reduced on Earth's hottest coral reefs. Extreme environmental conditions, as predicted for the end of the 21st century, could thus disrupt the community structure and productivity of a critical functional group, independent of live coral loss.

Connectivity and local adaptation are two contrasting evolutionary forces highly influencing population structure. To evaluate the impact of early-life traits and environmental conditions on genetic structuring and adaptation, we studied two sympatric fish species in the Western Mediterranean Sea: Symphodus tinca and S. ocellatus. We followed an individual-based approach and measured early-life history traits from otolith readings, gathered information on environmental variables and obtained genome-wide markers from genotyping-by-sequencing (GBS). The two species presented contrasting population structure across the same geographic gradient, with high and significant population differentiation in S. ocellatus, mostly determined by oceanographic fronts, and low differentiation and no front effect in S. tinca. Despite their different levels of genetic differentiation, we identified in both species candidate regions for local adaptation by combining outlier analysis with environmental and phenotypic association analyses. Most candidate loci were associated to temperature and productivity in S. ocellatus and to temperature and turbulence in S. tinca suggesting that different drivers may determine genomic diversity and differentiation in each species. Globally, our study highlights that individual-based approach combining genomic, environmental and phenotypic information is key to identify signals of selection and the processes mediating them.

Diadromous fishes have drastically declined over the last century, especially in Europe. Several authors have highlighted the role of large dams in this decline, but in fact, its causes are potentially multiple and cumulative, including degradation of local environmental conditions and widespread fragmentation of hydrographic networks associated with the pervasive establishment of smaller barriers. Consequently, there is a need to improve the identification and prioritization of the drivers of diadromous species loss in order to identify and apply the most appropriate conservation and restoration measures. In this study, we used both historical sources (from mid-18th to early 20th century) and current data to quantify the long-term loss of diadromous taxa over 555 sites throughout the French river network. Then, we modeled the effects of several anthropogenic pressures (e.g. barriers, water quality, hydrological and river morphological alterations) on diadromous taxon loss. Lastly, we assessed the potential consequences of four different scenarios of anthropogenic pressure reduction. Due to uncertainties in historical sources, some species were grouped into taxa leading to a potential underestimation of actual species extinctions. Despite this limitation, our results showed that the decline in diadromous assemblages is widespread but with contrasting magnitudes depending on site locations. The maximum height and density of barriers appeared as the major factors of taxon loss. Over the scenarios tested, we observed that exclusively improving local conditions have much more limited effects than restoring river continuity. Focusing actions on large dam removal did not show the strongest responses compared to removing medium and small-sized barriers. For effective and sustainable restoration of diadromous fish assemblage, (1) historical occurrences of diadromous fishes should be used as an indicator for assessing recovery, and (2) undertaken measures must be adapted to each basin to target and limit the number of barriers to remove while allowing diadromous fish recovery., Competing Interests: The authors have declared that no competing interests exist.

The arrangement and composition of habitats within landscapes and fine-scale habitat characteristics influence community structure and ecological processes. These aspects can be altered by anthropogenic activities, thus influencing associated assemblages. Farming of macroalgae is a common practice in tropical settings and alters the natural composition of seascapes by introducing monoculture patches. The farmed macroalgae may also differ in palatability compared to naturally-occurring macroalgae, influencing herbivory. This study assessed how these farms may differ from natural macroalgal beds in terms of habitat heterogeneity, fish assemblages, and herbivory. We surveyed fish assemblages and deployed macroalgal assays within macroalgal beds, farms and at varying distances from these habitats near Mafia Island, Tanzania. Fish composition and herbivory differed between the habitats likely due to different macrophyte species richness, underlying hard substrate in natural macroalgal beds, and high abundance of browsers nearby the farms. Additionally, fish assemblage patterns and herbivory were not consistent across the seascapes and varied with distance from the focal habitats possibly due to the presence of other habitats. The results suggest alterations of seascapes by farming practices may have consequences on fish assemblages and the ecological functions performed, thus positioning of farms should be carefully considered in management and conservation plans.

Background: Infectious hematopoietic necrosis virus (IHNV) and viral hemorrhagic septicemia virus (VHSV) are highly contagious, pathogenic Novirhabdoviruses affecting fish and are thusly notifiable diseases with the World Organization for Animal Health. This study assessed the relative capacities of IHNV and VHSV genes to modulate host general transcription and explores the abilities of specific IHNV genes to interfere with the interferon pathway in heterogenous teleost cell-lines., Methods: Optimized protocols allowed for efficient transient transfections in EPC, BF-2, RTG-2 and RTgill-W1 cell lines of plasmids encoding IHNV (M genogroup) and VHSV (-IVb genotype) genes, including N, P, M, G and NV. Their impact on general cellular transcription was measured 48 hours post transfection (hpt) with luciferase constructs driven by a modified β-Actin promoter (pCAG). Their modulation of the innate antiviral immune response was characterized 72 hpt, using luciferase constructs measuring rainbow trout Type I IFN or MX-1 promoter augmentation, upon MAVS co-transfection., Results: M was generally confirmed as the strongest constitutive transcriptional suppressor while IHNV P, but not VHSV P, augmented constitutive transcription in fibroblastic cell types. Cell-specific effects were observed for viral G gene, with VHSV G exhibiting suppression of basal transcription in EPC and BF-2 but not in trout cells; while IHNV G was stimulatory in RTG-2, but inhibitory in RTgill-W1. NV consistently stimulated constitutive transcription, with higher augmentation patterns seen in fibroblastic compared to epithelial cells, and for IHNV NV compared to VHSV NV. The innate antiviral immune response, focusing on the IFN pathway, was silenced by IHNV M in all cell lines tested. IHNV N showed a dose-dependent suppression of type I IFN, but with minor effects on MX-1. IHNV P and G played minor IFN-inhibitory roles, consistent and dose-dependent only for G in rainbow trout cells. IHNV NV mediated a consistent stimulatory effect on either Type I IFN or MX-1, but much less pronounced in RTgill-W1., Conclusions: This study extends our understanding of Novirhabdoviruses-host interaction, showing differential innate immune responses in heterogenous cell types. Viral regulators of innate immune signaling are identified, either as dose-dependent suppressors (such as M and N) or stimulators (mainly NV), indicating novel targets for the design of more efficient vaccination strategies.

Rainbowfishes (Melanotaeniidae) are the largest monophyletic group of freshwater fishes occurring in Australia and New Guinea, with 112 species currently recognised. Despite their high taxonomic diversity, rainbowfishes remain poorly studied from a cytogenetic perspective. Using conventional (Giemsa staining, C banding, chromomycin A 3 staining) and molecular (fluorescence in situ hybridisation with ribosomal DNA (rDNA) and telomeric probes) cytogenetic protocols, karyotypes and associated chromosomal characteristics of five species were examined. We covered all major lineages of this group, namely, Running River rainbowfish Melanotaenia sp., red rainbowfish Glossolepis incisus , threadfin rainbowfish Iriatherina werneri , ornate rainbowfish Rhadinocentrus ornatus , and Cairns rainbowfish Cairnsichthys rhombosomoides . All species had conserved diploid chromosome numbers 2n = 48, but karyotypes differed among species; while Melanotaenia sp., G. incisus , and I. werneri possessed karyotypes composed of exclusively subtelo/acrocentric chromosomes, the karyotype of R. ornatus displayed six pairs of submetacentric and 18 pairs of subtelo/acrocentric chromosomes, while C. rhombosomoides possessed a karyotype composed of four pairs of submetacentric and 20 pairs of subtelo/acrocentric chromosomes. No heteromorphic sex chromosomes were detected using conventional cytogenetic techniques. Our data indicate a conserved 2n in Melanotaeniidae, but morphologically variable karyotypes, rDNA sites, and heterochromatin distributions. Differences were observed especially in taxonomically divergent species, suggesting interspecies chromosome rearrangements.

Knowledge of intraspecific variability of a certain species is essential for their long-term survival and for the development of conservation plans. Nowadays, molecular/genetic methods are the most frequently used for this purpose. Although, the Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) technique has become a promising alternative tool to specify intraspecific variability, there is a lack of information about the limitations of this method, and some methodological issues need to be resolved. Towards this goal, we tested the sensitivity of this method on an intraspecific level, using genetically identified individuals of a cryptic fish species complex collected from five distinct populations. Additionally, some methodologic issues, such as the effect of (1) delayed sample preparation, (2) clove oil anaesthetization, and (3) different tissue types (muscle, and brain) were investigated using the MS analysis results. Our results show that the delayed sample preparation has a fundamental effect on the result of MS analysis, while at the same time the clove oil did not affect the results considerably. Both the brain and muscle samples were usable for cryptic species identification, but in our opinion this method has limited applicability for population-level segregation. The application of MALDI-TOF MS to the exploitable toolkit of phylogenetic and taxonomic researches could be used to broaden conclusions.

Estuaries are crucial ecosystems where human activities deeply affect numerous ecological functions. Here we present a survey dataset based on the monitoring of fish nursery grounds of the Seine estuary and eastern bay of Seine collected once a year using a beam trawl during three distinct periods (1995-2002, 2008-2010 and 2017-2019). The surveys happen at the start of autumn in order to maximize the catchability of juvenile fish. The beam trawl mainly targets benthic and demersal species on a study area that extends over 600 square kilometers. The dataset includes abundance and densities of 161 species for 634 hauls performed around 40 stations each year. These data can be used by fishery scientists and ecologists motivated by early life stages of commercial species or by the impact of human disturbances, such as harbor developments, on estuarine communities.

This study contributes to the knowledge of continental fishes recovered from sedimentary successions corresponding to the Bonaerean Stage/Age (late mid-Pleistocene) in the locality of Centinela del Mar, General Alvarado County, Buenos Aires province, Argentina. At this site we describe fossil fishes from a palaeolagoon, including Corydoras sp., Pimelodella sp., Rhamdia sp., Oligosarcus sp., small undetermined characids, Jenynsia sp. and Odontesthes sp. The recovered ichthyofaunal assemblage comprises at least seven taxa of Paranaean lineage. The taxonomic composition of the palaeoichthyofauna is quite comparable to that presently found in Bonaerean Watercourses of the Atlantic Drainage ecoregion. This suggests that local ichthyofaunal communities have remained relatively stable since the late mid-Pleistocene., Competing Interests: The authors have declared that no competing interests exist.

Species' vulnerability to climate change depends on the most temperature-sensitive life stages, but for major animal groups such as fish, life cycle bottlenecks are often not clearly defined. We used observational, experimental, and phylogenetic data to assess stage-specific thermal tolerance metrics for 694 marine and freshwater fish species from all climate zones. Our analysis shows that spawning adults and embryos consistently have narrower tolerance ranges than larvae and nonreproductive adults and are most vulnerable to climate warming. The sequence of stage-specific thermal tolerance corresponds with the oxygen-limitation hypothesis, suggesting a mechanistic link between ontogenetic changes in cardiorespiratory (aerobic) capacity and tolerance to temperature extremes. A logarithmic inverse correlation between the temperature dependence of physiological rates (development and oxygen consumption) and thermal tolerance range is proposed to reflect a fundamental, energetic trade-off in thermal adaptation. Scenario-based climate projections considering the most critical life stages (spawners and embryos) clearly identify the temperature requirements for reproduction as a critical bottleneck in the life cycle of fish. By 2100, depending on the Shared Socioeconomic Pathway (SSP) scenario followed, the percentages of species potentially affected by water temperatures exceeding their tolerance limit for reproduction range from ~10% (SSP 1-1.9) to ~60% (SSP 5-8.5). Efforts to meet ambitious climate targets (SSP 1-1.9) could therefore benefit many fish species and people who depend on healthy fish stocks., (Copyright © 2020, American Association for the Advancement of Science.)

Social living of animals is a broadly occurring phenomenon, although poorly studied in freshwater systems, fish schooling behaviour is an excellent example. The composition of fish schools, species-specific schooling tendencies and preferences of adult fish were studied in the pelagic habitat of the Římov Reservoir, Czech Republic. Video recordings captured over a total of 34 days (16 h per day) in the clear water period of three seasons were analysed. From four species identified as school-forming species - bream, bleak, roach and perch, 40% of the individuals observed formed schools of 3-36 individuals. Although conspecific schools prevailed, 20% of individuals formed heterospecific schools, except bleak that schooled strictly with conspecifics. Schools were composed of individuals of similar body size and life strategy. Heterospecific schools were significantly larger than conspecific schools and showed uneven proportion among species, that is, one species being more abundant when the school dimension increased. Probability of encounter in bleak was lowest and proved highest inclination for schooling. Gregarianism levels depended on species morphology and body size, with larger and morphologically advanced fish tending less to sociability. This indicates that the antipredator function of schooling behaviour is intensified with increasing vulnerability of the species., (© 2020 The Fisheries Society of the British Isles.)