Generic reassignment of Centropristis fuscula Poey, 1861 (Teleostei: Serranidae), with re-description of the species and comments on its geographical range and sexual system.

Centropristes fusculus Poey, 1861 historically has variously and somewhat perplexingly been assigned to Centropristis Cuvier, 1829, Prionodes Jenyns, 1840, and Serranus Cuvier, 1816. Here, we provide evidence from comparisons of morphology, ecology, and sexual systems for its inclusion in Serranus and redescribe the species based on the holotype and 60 specimens from Brazil, the Caribbean, the United States, and Uruguay. Serranus fusculus is a simultaneous hermaphrodite, a sexual system that is relevant to its generic placement. The inclusion of Serranus fusculus in the genus Serranus increases to 33 the number of currently valid Serranus species, of which two are found in the Western Indian Ocean, six in the eastern Pacific and 25 in the Atlantic Ocean (15 restricted to the western Atlantic and 10 to the eastern and Central Atlantic). An identification key to western Atlantic species of the genus is provided.

Additions and emendations to the annotated checklist of anthiadine fishes (Percoidei: Serranidae).

Anderson (2018) published an annotated checklist of anthiadine fishes with information on the 29 genera and 226 species then considered valid. Since then there have been a number of publications on the systematics of anthiadines, including descriptions of 23 new species and one new genus. Herein, data on those new taxa and emended accounts of others are presented.

Phylogeny and time scale of diversification in the fossil-rich sunfishes and black basses (Teleostei: Percomorpha: Centrarchidae).

Species of the North American freshwater fish lineage Centrarchidae are apex predators in their habitats and are among the world's most popular sport fishes. Centrarchids boast a rich fossil record that extends from the latest Eocene to the Pleistocene. To investigate the phylogeny and timing of diversification of Centrarchidae, we deploy a dataset of DNA sequences of 16 nuclear genes sampled from nearly all of the recognized and undescribed species. We also utilize previously published morphological datasets to assess the phylogenetic placement of one of the oldest known centrarchid fossils, †Plioplarchus whitei. A Bayesian multispecies coalescent species tree analysis provides insight on relationships that evaded resolution in earlier studies, such as the relationships of Acantharchus pomotis, the resolution of a clade consisting of species previously synonymized under the Spotted Bass, Micropterus punctulatus, and a clade of recently described species previously considered populations of the Redeye Bass, Micropterus coosae. This new molecular phylogeny and the inclusion of †P. whitei and other centrarchid fossils in the tip-dated fossilized birth-death analysis results in a new hypothesis of the timing of diversification in Centrarchidae that contextualizes the ages of centrarchid fossils to the timing of speciation among the extant species. In addition to providing new temporal perspectives on the diversification of freshwater fishes in North America, this study may close of the chapter of centrarchid phylogeny inferred using Sanger-sequenced genes, as the use of genomic-scale datasets becomes mainstream in the phylogenetics of fishes.

Comparative demography of commercially important species of coral grouper, Plectropomus leopardus and P. laevis, from Australia's great barrier reef and Coral Sea marine parks.

Understanding the spatial and environmental variation in demographic processes of fisheries target species, such as coral grouper (Genus: Plectropomus), is important for establishing effective management and conservation strategies. Herein we compare the demography of Plectropomus leopardus and P. laevis between Australia's Great Barrier Reef Marine Park (GBRMP), which has been subject to sustained and extensive fishing pressure, and the oceanic atolls of Australia's Coral Sea Marine Park (CSMP), where there is very limited fishing for reef fishes. Coral grouper length-at-age data from contemporary and historical otolith collections across 9.4 degrees of latitude showed little difference in lifetime growth between GBRMP and CSMP regions. Plectropomus laevis populations in GBRMP reefs had significantly higher rates of total mortality than populations in the CSMP. Mean maximum lengths and mean maximum ages of P. laevis were also smaller in the GBRMP than in the CSMP, even when considering populations sampled within GBRMP no-take marine reserves (NTMRs). Plectropomus leopardus, individuals were on average smaller on fished reefs than NTMRs in the GBRMP, but all other aspects of demography were broadly similar between regions despite the negligible levels of fishing pressure in the CSMP. Similarities between regions in growth profiles and length-at-age comparisons of P. laevis and P. leopardus suggest that the environmental differences between the CSMP and the GBRMP may not have significant impacts on lifetime growth. Our results show that fishing may have influenced the demography of coral grouper on the GBR, particularly for the slower growing and longer lived species, P. laevis.

The HIF1αn gene and its association with hypoxia tolerance in the Asian seabass.

Hypoxia is one of the major challenges in aquaculture industry. Breeding of fish tolerant to hypoxia is an important task in genetic improvement of aquaculture species. The Asian seabass, Lates calcarifer, is an important foodfish species. We identified and characterized the hypoxia-inducible factor inhibitor (HIF1αn) gene in the Asian seabass. The full-length cDNA sequence of the HIF1αn was 3425 bp, with an ORF of 1065 bp, encoding 354 amino acids. The genomic sequence of the gene was 8667 bp in length, and contained eight exons and seven introns. Phylogenetic analysis of the gene in fish and tetrapods revealed that the HIF1αn in the Asian seabass was closely related to that of tilapia (Oreochromis niloticus). The HIF1αn was highly up-regulated in the gill, spleen and heart after 3.5-hours hypoxia treatment. We identified three SNPs in the third and fourth introns of the HIF1αn gene. The SNP (i.e. SNP 9332241 (C/T)) in the fourth intron was significantly (P < 0.01) associated with hypoxia tolerance. This SNP might be useful in selecting Asian seabass for improved tolerance to hypoxia. Our data also provide useful information for further detailed analysis of the function of the HIF1αn gene in hypoxia tolerance.

Global diversity and genetic landscape of natural populations and hatchery stocks of largemouth bass micropterus salmoides across American and Asian regions.

Although largemouth bass Micropterus salmoides has shown its extremely economic, ecological, and aquacultural significances throughout the North American and Asian continents, systematic evaluation of genetic variation and structure of wild and cultured populations of the species is yet to be documented. In this study, we investigated the genetic structure of M. salmoides from 20 wild populations and five cultured stocks across the United States and China using eight microsatellite loci, which are standard genetic markers for population genetic analysis. Our major findings are as follows: (1) the result of Fst showed largemouth bass had high genetic differentiation, and the gene flow indicated the genetic exchange among wild populations is difficult; (2) AMOVA showed that 14.05% of the variation was among populations, and 85.95% of the variation was within populations; (3) The majority of largemouth bass populations had a significant heterozygosity excess, which is likely to indicate a previous population bottleneck; (4) Allelic richness was lower among cultured populations than among wild populations; (5) Effective population size in hatcheries could promote high levels of genetic variation among individuals and minimize loss of genetic diversity; China's largemouth bass originated from northern largemouth bass of USA. The information provides valuable basis for development of appropriate conservation policies for fisheries and aquaculture genetic breeding programs in largemouth bass.

The European sea bass: a key marine fish model in the wild and in aquaculture.

The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10-15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype-by-environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large-scale aquaculture productions.

Translocation of promoter-conserved hatching enzyme genes with intron-loss provides a new insight in the role of retrocopy during teleostean evolution.

The hatcing enzyme gene (HE) encodes a protease that is indispensable for the hatching process and is conserved during vertebrate evolution. During teleostean evolution, it is known that HE experienced a drastic transfiguration of gene structure, namely, losing all of its introns. However, these facts are contradiction with each other, since intron-less genes typically lose their original promoter because of duplication via mature mRNA, called retrocopy. Here, using a comparative genomic assay, we showed that HEs have changed their genomic location several times, with the evolutionary timings of these translocations being identical to those of intron-loss. We further showed that HEs maintain the promoter sequence upstream of them after translocation. Therefore, teleostean HEs are unique genes which have changed intra- (exon-intron) and extra-genomic structure (genomic loci) several times, although their indispensability for the reproductive process of hatching implies that HE genes are translocated by retrocopy with their promoter sequence.

Mitochondrial genetic markers for authentication of major Red Sea grouper species (Perciformes: Serranidae) in Egypt: A tool for enhancing fisheries management and species conservation.

Groupers are coral fish species of prime ecological and economic significance. The interactions among them and other coral reefs organisms aid the healthiness and species balance in this fundamental marine niches. Also, groupers are among the top priced fisheries species. The Egyptian habitats of the Red Sea are lacking genetic studies that assess species diversity for the final goal of conservation and fisheries management. Moreover, morphological similarities among these organisms sometimes hinder a proper species identification. Hence, more accurate groupers authentication methods are crucially required. Sixteen grouper species belonging to the genera Epinephelus, Anyperodon, Cephaolopholes, Aethaloperca, Variola, and Plectropomus, present in the Red Sea in Egypt, were investigated for species authentication through mitochondrial DNA variations, applying cytochrome oxidase subunit I (COI) and 12srRNA genes sequencing. GenBank comparisons, phylogenetic analyses and comparisons of pairwise distances were carried out. All these analyses aimed to species authentication and identifying their relations at the international scale. The results exhibited >98% identity with E. fasciatus, A. rogaa, C. oligosticta, E. areolatus, V. louti, P. areolatus, E. malabaricus, C. sexmaculata, E. summana, E. chlorostigma, E. polyphekadion, C. miniataus, A. leucogrammicus, E. tauvina, C. argus, C. hemistiktos. Pairwise distances showed a clear increase upon raising comparison level from among species to among-genera. Combined 12srRNA and COI genes sequencing resulted in an accurate tool for Egyptian Red Sea grouper species unambiguous discrimination. This can provide vital aid to the active efforts for these species conservation and fisheries management in Egypt and the world.

Toward the Authentication of European Sea Bass Origin through a Combination of Biometric Measurements and Multiple Analytical Techniques.

The authenticity of fish products has become an imperative issue for authorities involved in the protection of consumers against fraudulent practices and market stabilization. The present study aimed to provide a method for authentication of European sea bass ( Dicentrarchus labrax) according to the requirements for seafood labels (Regulation 1379/2013/EU). Data on biometric traits, fatty acid profile, elemental composition, and isotopic abundance of wild and reared (intensively, semi-intensively, and extensively) specimens from 18 southern European sources ( n = 160) were collected, clustered in six sets of parameters, and then subjected to multivariate analysis. Correct allocations of subjects according to their production method, origin, and stocking density were demonstrated with good approximation rates (94, 92, and 92%, respectively) using fatty acid profiles. Less satisfying results were obtained using isotopic abundance, biometric traits, and elemental composition. The multivariate analysis also revealed that extensively reared subjects cannot be analytically discriminated from wild subjects.

The origin and remolding of genomic islands of differentiation in the European sea bass.

Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unrelated to speciation can interfere. Here we use haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. Local ancestry patterns show that genomic islands first emerged in allopatry through linked selection acting on a heterogeneous recombination landscape. Then, upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we find that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression.

Temporal changes in hamlet communities (Hypoplectrus spp., Serranidae) over 17 years.

Transect surveys of hamlet communities (Hypoplectrus spp., Serranidae) covering 14 000 m2 across 16 reefs off La Parguera, Puerto Rico, are presented and compared with a previous survey conducted in the year 2000. The hamlet community has noticeably changed over 17 years, with a > 30% increase in relative abundance of the yellowtail hamlet Hypoplectrus chlorurus on the inner reefs at the expense of the other hamlet species. The data also suggest that the density of H. chlorurus has declined and that its distribution has shifted towards shallower depths. Considering that H. chlorurus has been previously identified as one of the few fish showing a positive association with seawater turbidity on the inner reefs of La Parguera and that sedimentation of terrestrial origin has increased over recent decades on these reefs, it is proposed that turbidity may constitute an important but so far overlooked ecological driver of hamlet communities.

Characterization and expression analysis of grouper (Epinephelus coioides) co-stimulatory molecules CD83 and CD80/86 post Cryptocaryon irritans infection.

Co-stimulatory molecules (CD83, CD80 and CD86), belong to immunoglobulin superfamily, are type I membrane glycoprotein, which express on antigen presenting cells and provide the second signal for the activation of T lymphocytes. In the present study, we cloned the grouper's CD83 (675 bp) and CD80/86 (876 bp). Homology analysis showed that both EcCD83 and EcCD80/86 shares the highest amino acid similarity (51% and 47%) for the overall sequence with puffer fish (Takifugu rubripes). Some conserved features and important functional residues in mammalian CD83, CD80 and CD86 were also identified from these molecules of teleosts including grouper, suggesting the function of both molecules may be conserved among vertebrates. In transfected HEK293T cells, both molecules localized on the membrane surface. Tissue distribution analysis showed both EcCD83 and EcCD80/86 mRNAs were mainly expressed in immune organs, and EcCD80/86 was extremely higher expressed in mucosal immune tissues including skin and gill than systematic immune organs, which indicates these co-stimulatory molecules may prime T cell activation in local mucosal tissues. In Cryptocaryon irritans infected groupers, the expression level of EcCD83 and EcCD80/86 were both seen significant up-regulation in the skin at most tested time points.

Molecular cloning and expression analysis of CCL25 and its receptor CCR9s from Epinephelus coioides post Cryptocaryon irritans infection.

Among other functions, CCL25/CCR9 has an important role in regulating the trafficking of developing T cells in the thymus, and in homing memory T cells to the small intestine. The function of this chemokine-receptor complex is not well studied in fish. We identified a CCL25-like (EcCCL25, 108 aa) and two CCR9-like sequences (EcCCR9aa 373 aa; and EcCCR9b, 375 aa) from a transcriptome database of orange-spotted grouper (Epinephelus coioides). EcCCL25, EcCCR9a, and EcCCR9b shared conserved structural features with homologs from mammals and from other fish, and a consistent relationship with phylogenetic trees and sequence identities. In healthy grouper, EcCCL25, EcCCR9a, and EcCCR9b were highly expressed in the thymus, and the gills, were expressed at lower levels in the stomach, and had different expression levels in other tissues. After infection with Cryptocaryon irritans, EcCCL25 expression was up-regulated at early time points in the spleen and head kidney, and in the skin, and gills at later time points; EcCCR9a expression was increased in the gill, spleen, and head kidney. After infection with C. irritans, EcCCR9b expression was reduced in all tissues tested. These results suggested that grouper CCL25/CCR9a complex may be involved in host defense against C. irritans infection.

Three new piscidins from orange-spotted grouper (Epinephelus coioides): Phylogeny, expression and functional characterization.

The present study reports the identification, and characterization of three new putative piscidin paralogues, ecPis-2, ecPis-3 and ecPis-4, from orange-spotted grouper (Epinephelus coioides). The cDNA of the three piscidins with the 207, 216, and 231 nt open reading frame encoded respectively a 68-, 71-, and 76-amino acid preprotein consisting of the predicted signal peptide, and putative mature peptide and prodomain. The phylogenetic analysis indicated that multiple piscidin paralogues in one fish species are highly diversified, the analysis suggested that the piscidins should be a family belonging to the superfamily of ancient cationic, linear, and amphipathic host defence peptides widespread across invertebrate and vertebrate taxa comprising insect cecropins and ceratotoxins, and the amphibian dermaseptins. The synthetic putative mature peptides, ecPis-2S, ecPis-3S and ecPis-4S, had strong activities against bacterial and fungal species. EcPis-3S exhibited powerful activity against the infective stage of Cryptocaryon irritans, theronts. The full length ecPis-2 and ecPis-4 by removal of signal peptide, ecPis-2L and ecPis-4L respectively, had potency against bacterial, fungal and parasitic species. The peptide ecPis-2S was proved to exist in spleen of orange-spotted grouper by HPLC followed by ESI-LCMS analysis. Basal transcriptions of ecPis-2, ecPis-3 and ecPis-4 were detected not only in the potential sites of pathogen entry such as gills, skin and intestine, but also in tissues such as head kidney, trunk kidney, blood cells, and spleen with highly abundant immune cells, however different paralogues expressed constitutively with different levels in the tissues. In addition, the expression of ecPis-2, ecPis-3 and ecPis-4 was upregulated in orange-spotted grouper challenged by Vibrio Parahaemolyticus, in different tissues at different time point after bacteria injection. These results support ecPis-2, ecPis-3 and ecPis-4 being the important immune-related genes in orange-spotted grouper innate immune system and playing multifunctional and complementary roles following their structural and functional diversification, and expression pattern difference. Finally, this study facilitates the evaluation of ecPis-2S, 2L, ecPis-3S, and ecPis-4S, -4L as potential templates of therapeutic agents against pathogens.

Molecular identification and expression analysis of TLR5M and TLR5S from orange-spotted grouper (Epinepheluscoioides).

Toll-like receptor 5 (TLR5) is an important receptor that interacts with bacterial flagellin and regulates host immune response in mammal. Recent studies demonstrate that piscine contains two types of TLR5, namely membrane form of TLR5 (TLR5M) and soluble form of TLR5 (TLR5S), and both of which perform crucial role in flagellin response. In the present study, a TLR5M and a TLR5S sequence was cloned from orange-spotted grouper (Epinepheluscoioides), and their ORFs are respectively 2466 bp (821 aas) and 1935 bp (644 aas). EcTLR5M has the typical TLR structure of a LRR domain, a transmembrane region and a TIR domain, while EcTLR5S only contains a LRR domain like other species' TLR5S. Both molecules have 23 LRR motifs, a LRR-NT and a LRR-CT in the LRR domain, similar to those of other species. Phylogenetic and sequence alignment indicated that both EcTLR5s respectively displayed closer relationship and higher sequence identity with those in other fish species. In healthy grouper, EcTLR5M was highly expressed in the skin, head kidney and spleen, while EcTLR5S was mainly detected in the liver. Ciliate Cryptocaryon irritans infection could significantly up-regulate the expression level of EcTLR5s in the gill and spleen from day 1 to day 3, and higher expression fold change was observed in the spleen. Taken together, the present studies contributed to understanding the function of piscine TLR5M/S and clarify their possible role in fish immune response against ciliate infection.

Evolution of lymphocytes. Immunoglobulin T of the teleost sea bass (Dicentrarchus labrax): Quantitation of gene expressing and immunoreactive cells.

Immunoglobulin T (IgT) is one of the key effector molecules of jawed vertebrate's adaptive immune system, and in this work we describe the quantitative distribution of IgT-expressing and IgT-producing cells in tissues of the European seabass Dicentrarchus labrax by using mRNA riboprobes and a specific anti-IgT antibody. A polyclonal antiserum (pAb) was prepared by immunizing rabbits with three synthetic peptides deduced from the full length IgT cDNA sequence and located in a surface-exposed CH3 domain of IgT constant region. The obtained antiserum, named RAIgT1, was able to recognize by ELISA immunization antigens and IgT from intestinal mucus and serum. In western blots of head kidney leukocytes lysates the antiserum recognized a 180 kDa polypeptide in non-reducing, and a 75 kDa peptide in reducing conditions. Interestingly, the RAIgT1 pAb crossreacted intensely in western blots with rainbow trout IgT purified from mucus and serum. Antisense mRNA IgT oligonucleotide sequences were employed in in situ hybridization to detect IgT-expressing cells in sections from lymphoid tissues, and positive cells were observed in head kidney, spleen, intestine and gills. By employing RAIgT1 in quantitative immunohistochemistry, the highest number of IgT-producing cells was observed in the gills (9.5 ± 0.7%), followed by intestine (8.4 ± 1.2%), head kidney (6.2 ± 1.4%), and spleen (4.1 ± 0.7%). Interestingly, the number of IgT-B cells showed a regionalization in the intestine, increasing from the proximal to the terminal part. By immunofluorescence and flow cytometry of live leukocytes, the percentages of RAIgT1 stained cells were 34 ± 11% in the intestine, 22 ± 5% in head kidney, 16 ± 7% in spleen, and 9 ± 5% in gills. At the fluorescence microscope, live cells from these tissues showed a typical membrane-associated positivity and a lymphocytic morphology, and no IgT/IgM double positive cells were detected. Immunoreactive cells have been purified from head kidney using magnetic beads, and IgT-enriched cells showed by RT-PCR an enhanced expression of the IgT gene, whereas IgT-depleted cells had an highest expression of IgM and TRß genes. These data describe for the first time a quantitative panel of IgT-expressing and IgT-immunoreactive cells in tissues of a teleost fish species.

Mitochondrial signatures for identification of grouper species from Indian waters.

Groupers are important commercial fish in many parts of the world. Accurate identification is critical for effective conservation assessment and fisheries management. Genetic barcodes provide a simple and reproducible method for the identification of species even in the absence of taxonomic expertise. The generation of reference barcodes from properly identified specimens is an important first step in this direction. Here, 36 species belonging to the subfamily Epinephelinae (Family: Serranidae) were collected from landings on the west coast of India and Port Blair, Andaman, and partial nucleotide sequence data of the mitochondrial cytochrome C oxidase subunit I (COI) gene was generated. Barcodes for 13 species were developed from Indian waters for the first time. Analysis using the COI gene produced phylogenetic trees in concurrence with other multi-gene studies. Epinephelus fasciatus and E. areolatus were found to be a species complex, as hypothesized in other studies. The DNA barcodes developed in the study can be used for identifying species within Epinehelinae, where taxonomic ambiguity still exists.

Cartilage acidic protein 1, a new member of the beta-propeller protein family with amyloid propensity.

Cartilage acidic protein1 (CRTAC1) is an extracellular matrix protein of chondrogenic tissue in humans and its presence in bacteria indicate it is of ancient origin. Structural modeling of piscine CRTAC1 reveals it belongs to the large family of beta-propeller proteins that in mammals have been associated with diseases, including amyloid diseases such as Alzheimer's. In order to characterize the structure/function evolution of this new member of the beta-propeller family we exploited the unique characteristics of piscine duplicate genes Crtac1a and Crtac1b and compared their structural and biochemical modifications with human recombinant CRTAC1. We demonstrate that CRTAC1 has a beta-propeller structure that has been conserved during evolution and easily forms high molecular weight thermo-stable aggregates. We reveal for the first time the propensity of CRTAC1 to form amyloid-like structures, and hypothesize that the aggregating property of CRTAC1 may be related to its disease-association. We further contribute to the general understating of CRTAC1's and beta-propeller family evolution and function. Proteins 2017; 85:242-255. © 2016 Wiley Periodicals, Inc.

The complete mitochondrial genome and phylogenetic analysis of Lateolabrax maculatus (Perciformes, Moronidae).

The complete mitogenome of Lateolabrax maculatus was determined through high-throughput DNA sequencing technology. The circular mtDNA molecule was 16 723 bp in size and comprised 37 genes and two non-coding regions, with the gene arrangement and content identical to other typical vertebrate mitogenomes. The identity analysis revealed that the mitogenome sequence of L. maculatus shared the highest identity with that of L. japonicus (91.3%) among 12 species. The neighbor-joining tree indicated that 13 species clustered into three distinct clades strongly supported. Within Moronidae clade, L. maculatus first clustered together with L. japonicus, and then gathered with two Dicentrarchus species and Morone saxatilis. Finally, Moronidae clade grouped with Percichthyidae clade and Serranidae clade. This finding agreed with the opinion classifying Lateolabrax into the family Moronidae but not Serranidae or its own family, Lateolabracidae. These results provided useful molecular information for phylogenetic relationships and further studies on the population genetic of L. maculatus.