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Small-scale shrimp trawling is crucial for the economy and culture of coastal communities worldwide, providing several ecosystem services. However, bottom trawling is well-known for its negative impacts on habitat structure and marine communities. Bycatch, or the accidental capture of non-target species during fishing, can offer valuable insights into the composition and variation of fish assemblages. This study was conducted between 2009 and 2010 and focuses on the Barra do Sul, Penha, and Porto Belo areas, which are traditionally used for artisanal shrimp fishing. We evaluated the variation in the composition of fish species caught as accompanying fauna, as well as the influence of environmental variables on the associated fish assemblages. The results indicate that differences in species composition were more pronounced spatially than temporally, suggesting that the structural characteristics and environmental filters of different study areas play a crucial role in shaping marine fish bycatch assemblages. Porto Belo showed higher abundance, biomass, and diversity, likely due to its greater substrate heterogeneity and habitat complexity, which promote higher environmental quality and species richness. The gam models used for abundance and diversity confirm the complexity of ecological interactions and highlight that depth, salinity, temperature, chlorophyll a and nutrient concentration (NO 2 and PO 4 3 -) were key environmental variables in determining the abundance and diversity of fish assemblages, indicating that the response of these communities to environmental variations is influenced by a specific combination of these factors. Additionally, species from the Sciaenidae and Paralichthyidae families were identified as significant contributors to the variation in fish communities. The presence of threatened species, such as Zapteryx brevirostris and Atlantoraja cyclophora , in the bycatch is particularly concerning for conservation efforts. Finally, our findings emphasize the importance of implementing management strategies tailored to local environmental conditions and protecting endangered species to promote sustainable management of marine resources and mitigate the impacts of trawling on a global scale.

Indel (insertion–deletion) events observed in the genome represent irreversible mutational processes, making indel regions crucial characteristics for discussing phylogenetic relationships. The tribe Hippoglossoidini is a recently proposed taxonomic group based on the molecular phylogenetic analyses of both mitochondrial (mt) and nuclear DNA sequences. However, no synapomorphic characteristics have been identified within this tribe, either morphologically or molecularly. In the present study, we sequenced the ND5 region of mtDNA in the righteye flounder species and conducted interspecific comparisons. We found a 12 bp indel immediately upstream of the stop codon in the ND5 region. A comparative analysis of this region with outgroup species from the Paralichthyidae revealed that the indel was a unique insertion shared by the common ancestor of the Hippoglossoidini species, providing irreversible evidence to support the monophyly of this taxonomic group (synapomorphic characters).

Background We assessed metrics of the metazoan parasite infracommunities of the dusky flounder ( Syacium papillosum ) as indicators of aquatic environmental health of the Yucatan Shelf (YS) prior to oil extraction. We sampled the dusky flounder and its parasites along the YS, mostly during the 2015 north wind season (November–April). Our aims were: (i) to determine whether the parasite infracommunity metrics of S. papillosum exhibit significant differences among YS subregions; (ii) to determine whether the probability of the occurrence of its parasite species and individuals were affected by environmental variables, nutrients, heavy metals and hydrocarbons at the seascape level; and (iii) to determine whether there were statistical differences between the parasite infracommunity metrics of S. papillosum from YS and those of Syacium gunteri from the Campeche Sound. Multivariate statistical analyses and generalised additive models (GAMs) were used to examine the potential statistical associations between the contaminants, environmental variables and parasite community metrics, and the maximum entropy algorithm (MaxEnt) was used to characterise the habitat’s suitability for the parasite’s probability of occurrence. Results We recovered 48 metazoan parasite species from 127 S. papillosum , with larval cestodes and digeneans being the most numerically-dominant. Multivariate analyses showed significant differences in parasite infracommunity metrics among Western YS, Mid YS and Caribbean subregions, with the latter being the richest in species but not in individuals. The GAM and MaxEnt results indicated a negative effect of top predators (e.g. sharks and rays) removal on parasite metrics. The parasite infracommunities of S. papillosum were twice as rich in the number of species and individuals as those reported for S. gunteri from the Campeche Sound. Conclusions The significant differences among subregions in parasite metrics were apparently due to the interruption of the Yucatan current during the north wind season. The fishing of top predators in combination with an influx of nutrients and hydrocarbons in low concentrations coincides with an increase in larval cestodes and digeneans in S. papillosum . The dusky flounder inhabits a region (YS) with a larger number of metazoan parasite species compared with those available for S. gunteri in the Campeche Sound, suggesting better environmental conditions for transmission in the YS.

The Isthmosacanthidae acanthocephalan species of the genus Serrasentis are parasites of marine teleosts and an elasmobranch. In this study, Serrasentis gibsoni n. sp. is described from the intestines of four flatfish species (Paralichthyidae), namely Ancyclopsetta quadrocellata, Cyclopsetta chittendeni, Syacium gunteri, and S. papillosum from 10 oceanic sites in the Gulf of Mexico (GoM). Twenty sequences of the ‘barcoding’ region of cytochrome C oxidase subunit I gene were obtained from 20 adults of Serrasentis gibsoni n. sp. Additionally, five sequences of the barcoding region were obtained from five adults of rhadinorhynchid Gorgorhynchus lepidus from C. chittendeni, S. papillosum and one species of Haemulidae, Haemulom aurolineatum, from five oceanic sites from the GoM. Two phylogenetic approaches were followed: Bayesian inference and maximum likelihood. In both phylogenetic reconstructions, the sequences of Serrasentis gibsoni n. sp. were recovered as a monophyletic group within the genus Serrasentis and placed as a sister group to G. lepidus. However, due to the lack of molecular data for species of the Isthmosacanthidae and Rhadinorhynchidea, these phylogenetic inferences must be taken with caution. Serrasentis gibsoni n. sp. is the first species of Serrasentis described from Paralichthyidae flatfish species from marine waters of the Americas and from the GoM. Based on the barcoding data set analyzed, Serrasentis gibsoni n. sp. appears to have high intraspecific genetic variation; thus, it is necessary to continue exploring the genetic diversity of this species to infer its intraspecific evolutionary patterns.

The Northwest Pacific marginal waters comprising the South China Sea, East China Sea, Yellow Sea, and the Sea of Japan have unique geomorphic features. The Japanese flounder Paralichthys olivaceus, which is endemic to the Northwest Pacific, has high nutritional, economic, and ecological value. To allow the examination of the demographic history and population structure of the most common P. olivaceus species range over the five marginal seas (East China Sea, Yellow Sea, Bohai Sea, Northwest Pacific Ocean, and the Sea of Japan), the mitochondrial DNA control region of 91 individuals from six populations in China was sequenced. These sequences were combined with 233 sequences from four populations distributed in the Northwestern Pacific Ocean for analysis. Higher levels of nucleotide diversity (0.032 ± 0.016) and haplotype diversity (0.996 ± 0.001) were observed. The peripheral Fuqing population in the East China Sea had the relatively lowest genetic diversity and highest differentiation. Furthermore, when the results of the isolation by distance test, spatial analysis of molecular variation and geographic barrier analysis are also considered, there is a clear need to prioritize resource conservation and enhancement measures in this area. The phylogenetic trees, structure assignment test, and haplotypes network revealed no significant differences in the genealogical structure among ten populations. Mismatch distribution analysis, Bayesian skyline plots, and neutrality tests suggested that P. olivaceus experienced population expansion during the Pleistocene. Ocean currents and climate change play important roles in shaping the geographical distribution and genetic population structure of P. olivaceus. The Northwest Pacific marginal waters comprising the South China Sea, East China Sea, Yellow Sea, and the Sea of Japan have unique geomorphic features. The Japanese flounder Paralichthys olivaceus, which is endemic to the Northwest Pacific, has high nutritional, economic, and ecological value. To allow the examination of the demographic history and population structure of the most common P. olivaceus species range over the five marginal seas (East China Sea, Yellow Sea, Bohai Sea, Northwest Pacific Ocean, and the Sea of Japan), the mitochondrial DNA control region of 91 individuals from six populations in China was sequenced. These sequences were combined with 233 sequences from four populations distributed in the Northwestern Pacific Ocean for analysis. Higher levels of nucleotide diversity (0.032 ± 0.016) and haplotype diversity (0.996 ± 0.001) were observed. The peripheral Fuqing population in the East China Sea had the relatively lowest genetic diversity and highest differentiation. Furthermore, when the results of the isolation by distance test, spatial analysis of molecular variation and geographic barrier analysis are also considered, there is a clear need to prioritize resource conservation and enhancement measures in this area. The phylogenetic trees, structure assignment test, and haplotypes network revealed no significant differences in the genealogical structure among ten populations. Mismatch distribution analysis, Bayesian skyline plots, and neutrality tests suggested that P. olivaceus experienced population expansion during the Pleistocene. Ocean currents and climate change play important roles in shaping the geographical distribution and genetic population structure of P. olivaceus.

The complete mitochondrial genome of the fine flounder Paralichthys adspersus, was determined for the first time through Next Generation Sequencing (NGS) approach. The mitogenome (GenBank accession no. MW288827) has 17,060 bp in length and consisted of the well-known 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and the control region. The overall nucleotide composition of the whole mitogenome was A: 27.5%, C: 29.5%, G: 17.1%, and T: 25.9%. Phylogenetic analyses based on 12 protein-coding genes clustered P. adspersus in the monophyletic Paralichthyidae clade, showing the closest phylogenetic relationship with its congeneric species P. olivaceus.

Pleuronectes chrysopterus Bloch and Schneider 1801 has previously been regarded as a putative junior synonym of Pseudorhombus arsius (Hamilton 1822) (Paralichthyidae). However, the holotype of the former was found to conform to the right-eye flounder genus Platichthys Girard 1854 (Pleuronectidae), and be most similar to the European flounder Platichthys flesus (Linnaeus 1758) and Baltic flounder Platichthys solemdali Momigliano, Denys, Jokinen and Merilä 2018 in having rough scales with bony tubercles distributed along the anterior portion of the body and along the dorsal- and anal-fin bases, exposed cycloid scales entirely covering the body, and 64 dorsal- and 44 anal-fin rays. Such a character combination set the holotype specimen apart from two northwestern Pacific congeners of Platichthys , which suggests that the originally stated type locality “Chinese sea” of Pleuronectes chrysopterus , may have been erroneous. Furthermore, the holotype has an unusually high number of pored lateral-line scales compared with all other species of Platichthys (123 vs. 60–90), possibly indicating that the holotype is a morphologically abnormal individual of a species of Platichthys or a hybrid individual of a species of Platichthys and another pleuronectid species in a different genus, with a high number of pored lateral-line scales.

Viral hemorrhagic septicemia virus (VHSV), one of the most important viral marine pathogens worldwide, has a broad range of hosts, such as members of the families Salmonidae and Paralichthyidae. In addition to being highly contagious, VHSV causes high lethality. The transmission of VHSV can be both vertical and horizontal. In fish, the resolution of VHSV infection is challenging. Thus, early diagnosis of VHSV infections is critical, especially in fish farms that have a high population of juvenile fish. Serological methods are commonly used to detect viral antigens. However, limited serological methods are available for marine viruses. In this study, a VHSV-specific single-chain variable fragment (scFv), E5, was selected using the yeast surface display and phage display systems. scFv, a type of recombinant antibody, comprises a variable heavy chain (VH) and a variable light chain (VL) connected by a polypeptide linker. An scFv clone was selected from the VHSV glycoprotein-expressing yeast cells using the bio-panning method. The scFv-encoding gene was subcloned and expressed in the Escherichia coli expression system. The binding affinity of the expressed and purified scFv protein was determined using an enzyme-linked immunosorbent assay and western blotting. Thus, this study reported a method to identify VHSV-specific scFv using bio-panning that can be utilized to develop a diagnostic system for other viruses.

, an endemic flatfish from China's coastal waters, has remained taxonomically contentious owing to its distinctive morphology and osteology. We sequenced and annotated the first complete mitochondrial genome of this species using Illumina HiSeq 2500. The circular mitogenome spans 17,366 bp, encoding 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a control region. A maximum-likelihood phylogeny places as a single-taxon lineage sister to the remaining Paralichthyidae. This matrilineal pattern is congruent with the long-standing morphological debate over its familial placement.The complete mitogenome provides a foundational genomic resource for resolving relationships within Pleuronectiformes.

The mitogenome is an important tool for researching the evolution of metazoan animals. However, until now, only few mitochondrial genes of Pseudorhombus pentophthalmus have been reported. Here, we report the complete mitogenome of P. pentophthalmus, assembled using the Illumina platform. The circular mitogenome of P. pentophthalmus is 16,684 bp in length, has a bias A+T content of 52.78%, encodes 37 genes (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes), and has a control region. The overall nucleotide composition was A: 26.56%, T: 26.22%, G: 17.97%, and C: 29.25%. The phylogenetic tree based on the complete mitogenome P. pentophthalmus was shown to be monophyletic with the other Pseudorhombus species and was shown to be on the same branch as P. dupliciocellatus. This research might be useful for future studies on population genetics and evolution analysis.