Falsificações por troca de espécies de peixes: uma revisão sistemática das espécies mais comumente substituídas / Fish mislabeling: a systematic review of the most commonly mislabeled species

O objetivo deste artigo é determinar quais são as espécies de peixes mais comumente substituídas, relatadas em revisões sobre falsificações por troca de espécies, em artigos científicos publicados entre 2002 e 2022, assim como expor quais são os fatores que levam à ocorrência de casos de falsificação, quais os danos sociais que tal prática ilegal pode gerar e em que tipo de estabelecimentos as falsificações normalmente são detectadas. Assim, por meio de uma revisão sistemática de literatura, foi verificado que as espécies de peixes mais comumente falsificadas foram Anoplopoma fimbria, Gadus morhua, Solea solea, Thunnus albacares, Scomberomorus commerson, Lates calcarifer e Rastrelliger brachysoma. As motivações por trás das falsificações intencionais foram predominantemente econômicas, tendo sido observados impactos negativos das falsificações na economia, na saúde pública e no meio ambiente. A maioria das falsificações foi encontrada no final da cadeia produtiva, em locais como varejos, restaurantes e peixarias. Dessa forma, ao saber como as falsificações acontecem e suas razões, torna-se possível saber como minimizar a sua ocorrência.

The aim of this article is to identify the most frequently mislabeled fish species, based on reports and reviews of species mislabeling-related falsifications, in scientific articles published between 2002 and 2022. It also aims to explore the factors contributing these counterfeiting incidents, the social harms associated with this illegal practice and the types of establishments where counterfeits are typically detected. Through a systematic literature review, it was verified that the most commonly mislabeled fish species were Anoplopoma fimbria, Gadus morhua, Solea solea, Thunnus albacares, Scomberomorus commerson, Lates calcarifer and Rastrelliger brachysoma. The primary motivations behind intentional counterfeiting were economic in nature, and negative impacts of counterfeiting on the economy, public health and the environment were widely recognized. Most counterfeits were found at the end of the production chain, in places such as retail stores, restaurants and fishmongers' businesses. By understanding the mechanisms and motivations behind counterfeiting, we can effectively minimize its prevalence.

Influence of urbanization on stream fish assemblages in three microbasins in the Upper Paraná River Basin / Influência da urbanização em assembleias de peixes de riachos em três microbacias na bacia do Alto Rio Paraná

The colonization pattern of fish assemblages in streams is often studied in the context of environmental filters. On the other hand, when fish assemblages are subjected to anthropogenic effects, variables associated with environmental quality assume more importance. Therefore, this work evaluated the richness and composition of fish from streams sampled at different urbanization levels, aiming to determine any direct effects on the structure of fish assemblages. To accomplish this, samples were collected from 2003 to 2011 at 31 sites distributed among 3 microbasins in the Rio Ivinhema Basin, Alto Rio Paraná. Based on environmental variables, physicochemical of the water and analysis of the use and occupation of the soil, the microbasins were classified into different urbanization levels (low, medium and high). A total of 4,320 individuals were sampled, out of which 57 fish species were recorded. Sampled sites with medium urbanization level presented higher richness compared to sampled sites with high urbanization level which presented lower richness. Species richness in these sites was explained mainly by water temperature and water velocity. Results confirmed that urbanization does directly affect environmental integrity, which, in turn, can lead to the homogenization of stream assemblages.

Estudos sobre assembleias de peixes em riachos enfatizam o papel dos filtros ambientais associados ao padrão de colonização das assembleias, por outro lado, quando a assembleia está sujeita aos efeitos antropogênicos, as variáveis ambientais associadas à qualidade ambiental assumem maior importância. Dessa forma, o objetivo deste estudo foi analisar a riqueza e a composição de peixes de riachos amostrados em diferentes níveis de urbanização, buscando evidenciar se o efeito reflete diretamente na estrutura das assembleias. As amostragens foram realizadas em 31 locais distribuídos em três microbacias na bacia Rio Ivinhema, Alto Rio Paraná, no período de 2003 a 2011. Com base nas variáveis ambientais, físico-químicos da água e análise do uso e ocupação do solo as microbacias foram classificadas em diferentes níveis de urbanização (baixo, médio e alto). Foram amostrados um total 4.320 indivíduos, dos quais foram registradas 57 espécies de peixes. Os locais amostrados com influência média da urbanização apresentaram maior riqueza de espécies, entretanto, os locais amostrados com alta influência da urbanização apresentaram menor riqueza de espécies. Dessa forma, constatamos que a urbanização influencia diretamente na integridade ambiental, que pode levar a homogeneização das assembleias de riachos.

Biodiversity of commercially important finfish species caught by mid-water and bottom trawls from two different coasts of Arabian Sea: threats and conservation strategies / Biodiversidade de espécies de peixes comercialmente importantes capturadas por redes de arrasto de médio e fundo do Baluchistão e costas de Sindh do mar da Arábia no Paquistão: ameaças e estratégias de conservação

This study was conducted to estimate the diversity and the occurrence of commercially important finfish species collected by twenty fish sampling site of Sindh and Baluchistan coasts of the Arabian Sea in Pakistan from January to December 2019. Additionally, physicochemical characteristics of seawater were analyzed from these selected sites and found to be within suitable ranges required for fish growth and survive. A total of 81287 fish individuals were collected and identified as 49 species belonging to 26 families in our study. The most diversified family was Sparidae (13 species) followed by Carangidae and Lutjanidae (4 species), Mullidae, Serranidae, Ariidae (3 species), and Sciaenidae (2 species). The remaining 20 families were represented by only one species. The values of Shannon diversity index calculated for the four selected habitats revealed that high fish diversity was reported at Sonmiani Coast (H’=1.81), while less at Ormara Coast (H’=0.23). Likewise, Evenness index (E) was high at Sonmiani Coast (E=0.50) and less fish diversity was reported at Ormara Coast (E=0.06). Reducing risks to threatened marine species in coastal habitats also requires conservation actions at multiple scales. Thus, it was concluded that our study could be valuable in providing the more information’s regarding to the diversity of finfish species and their occurrence along the Pakistan Coast. Further, to better understand the effects, regular monitoring and conservation measures should be taken to mitigate the influence of anthropogenic activities and protect finfish diversity from further decline.

Este estudo foi conduzido para estimar a diversidade e a ocorrência de espécies de peixes comercialmente importantes coletadas por vinte locais de amostragem de peixes nas costas de Sindh e Baluchistão do mar da Arábia, no Paquistão, de janeiro a dezembro de 2019. Além disso, as características físico-químicas da água do mar foram analisadas a partir desses peixes locais selecionados e considerados dentro dos intervalos adequados necessários para o crescimento e sobrevivência dos peixes. Um total de 8.1287 indivíduos de peixes foi coletado e identificado como 49 espécies pertencentes a 26 famílias em nosso estudo. A família mais diversificada foi Sparidae (13 espécies), seguida por Carangidae e Lutjanidae (4 espécies), Mullidae, Serranidae, Ariidae (3 espécies) e Sciaenidae (2 espécies). As 20 famílias restantes foram representadas por apenas uma espécie. Os valores do índice de diversidade de Shannon calculados para os quatro habitats selecionados revelaram que uma alta diversidade de peixes foi relatada na costa Sonmiani (H’ = 1,81), enquanto menos na costa Ormara (H’ = 0,23). Da mesma forma, o índice de regularidade (E) foi alto na costa de Sonmiani (E = 0,50) e menos diversidade de peixes foi relatada na costa de Ormara (E = 0,06). A redução dos riscos para as espécies marinhas ameaçadas em habitats costeiros também requer ações de conservação em várias escalas. Assim, concluiu-se que nosso estudo pode ser valioso para fornecer mais informações sobre a diversidade de espécies de peixes finos e sua ocorrência ao longo da costa do Paquistão. Além disso, para compreender melhor os efeitos, medidas regulares de monitoramento e conservação devem ser tomadas para mitigar a influência das atividades antropogênicas e proteger a diversidade de peixes finos de um declínio maior.

Geographic range, distribution patterns and interactions of Monogenea Van Beneden 1858, with species of native host freshwater fishes from Brazil / Distribuição geográfica, padrões de distribuição e interações de Monogenea Van Beneden 1858, com espécies de peixes hospedeiros nativos de água doce do Brasil

Abstract This paper investigated information on monogenean species using 312 scientific papers, to search for infection and geographic distribution patterns in native freshwater fish from Brazil. We used 1,698 samples of 296 fish species of 28 families distributed into Characiformes, Siluriformes, Cichliformes, Gymnotiformes, Perciformes, Mugiliformes, Osteoglossiformes and Clupeiformes, in addition to four hybrid fish. Among the hosts of the different orders and families, the greatest numbers of parasite-host associations were found for species of the families Serrasalmidae, Characidae, Loricariidae, Curimatidae and Anostomidae. The 578 species of monogeneans used in parasite-host interactions were distributed in 86 genera of six five families (Dactylogyridae, Gyrodactylidae, Diplectanidae, Microcotylidae, Ancylodiscoididae and Ancyrocephalidae), but with great predominance of Dactylogyridae species. There was variation in prevalence, intensity and abundance levels of monogeneans species among host fish species, as well as in infection sites that occurred predominantly in external organs. Positive correlations of prevalence, intensity and abundance with body length of hosts were observed. There was geographic distribution pattern of monogeneans limited mostly to two hydrographic basins those being the Amazon River and Paraná River. Just approximately 6% of potential monogeneans have been explored thus far, showing a clear need for further studies on this interesting group of parasites.

Resumo Este estudo investigou informações sobre espécies de monogenéticos, usando 312 artigos científicos para buscar padrões de infecção e distribuição geográfica em peixes nativos de água doce do Brasil. Foram utilizadas 1.698 amostras de 296 espécies de peixes de 28 famílias, distribuídas em Characiformes, Siluriformes, Cichliformes, Gymnotiformes, Perciformes, Mugiliformes, Osteoglossiformes e Clupeiformes, além de quatro peixes híbridos. Entre os hospedeiros das diferentes ordens e famílias, os maiores números de associações parasito-hospedeiro foram encontrados para espécies das famílias Serrasalmidae, Characidae, Loricariidae, Curimatidae e Anostomidae. As 578 espécies de monogenéticos, utilizadas nas interações parasito-hospedeiro, foram distribuídas em 86 gêneros de seis famílias (Dactylogyridae, Gyrodactylidae, Diplectanidae, Microcotylidae, Ancylodiscoididae e Ancyrocephalidae), mas com grande predominância de espécie de Dactylogyridae. Houve variação nos níveis de prevalência, intensidade e abundância das espécies de monogenéticos entre as espécies de peixes hospedeiros, bem como nos locais de infecção que ocorreram predominantemente em órgãos externos. Correlações positivas de prevalência, intensidade e abundância com o comprimento corporal dos hospedeiros foram observadas. Houve padrão de distribuição geográfica dos monogenéticos limitados principalmente a duas bacias hidrográficas, sendo elas o Rio Amazonas e Rio Paraná. Apenas aproximadamente 6% dos potenciais monogenéticos são conhecidos até agora, mostrando uma clara necessidade de mais estudos sobre esse interessante grupo de parasitos.

Correlation between acoustic divergence and phylogenetic distance in soniferous European gobiids (Gobiidae; Gobius lineage).

In fish, species identity can be encoded by sounds, which have been thoroughly investigated in European gobiids (Gobiidae, Gobius lineage). Recent evolutionary studies suggest that deterministic and/or stochastic forces could generate acoustic differences among related animal species, though this has not been investigated in any teleost group to date. In the present comparative study, we analysed the sounds from nine soniferous gobiids and quantitatively assessed their acoustic variability. Our interspecific acoustic study, incorporating for the first time the representative acoustic signals from the majority of soniferous gobiids, suggested that their sounds are truly species-specific (92% of sounds correctly classified into exact species) and each taxon possesses a unique set of spectro-temporal variables. In addition, we reconstructed phylogenetic relationships from a concatenated molecular dataset consisting of multiple molecular markers to track the evolution of acoustic signals in soniferous gobiids. The results of this study indicated that the genus Padogobius is polyphyletic, since P. nigricans was nested within the Ponto-Caspian clade, while the congeneric P. bonelli turned out to be a sister taxon to the remaining investigated soniferous species. Lastly, by extracting the acoustic and genetic distance matrices, sound variability and genetic distance were correlated for the first time to assess whether sound evolution follows a similar phylogenetic pattern. The positive correlation between the sound variability and genetic distance obtained here emphasizes that certain acoustic features from representative sounds could carry the phylogenetic signal in soniferous gobiids. Our study was the first attempt to evaluate the mutual relationship between acoustic variation and genetic divergence in any teleost fish.

Emerging Viral Pathogens in Sturgeon Aquaculture in Poland: Focus on Herpesviruses and Mimivirus Detection.

Recently, Poland has become a leading producer of sturgeon meat and caviar in Europe and is one of the largest in the world. The growing importance of this branch of aquaculture means that diseases of these fish, especially viral ones, are becoming the object of interest for ichthyopathologists. In recent years, there have been increasing reports of health problems in the dynamically developing sturgeon farming. The greatest risk appears to be emerging infectious diseases that are caused by viruses and that can become a serious threat to the development of the aquaculture industry and the success of sturgeon restitution programs undertaken in many European countries, including Poland. In this paper, an attempt was made to determine the spread of the two most important groups of viruses in Polish sturgeon farming: These include the herpesviruses and sturgeon nucleocytoplasmic large DNA viruses (sNCLDV), in particular, mimiviruses. In the years 2016-2020, 136 samples from nine farms were collected and tested by using the WSSK-1 cell line, PCR and Real Time PCR methods. All results were negative for herpesviruses. Out of the samples, 26% of the samples have been tested positive for mimiviruses. Sanger sequencing of mimiviruses demonstrated their affiliation with AciV-E. The sequence characterization confirmed the presence of both V1 and V2 lineages in Polish fish facilities, but variant V2 seems to be more widespread, as is observed in other European countries.

Phylogenomic Species Delimitation Dramatically Reduces Species Diversity in an Antarctic Adaptive Radiation.

Application of genetic data to species delimitation often builds confidence in delimitations previously hypothesized using morphological, ecological, and geographic data and frequently yields recognition of previously undescribed cryptic diversity. However, a recent critique of genomic data-based species delimitation approaches is that they have the potential to conflate population structure with species diversity, resulting in taxonomic oversplitting. The need for an integrative approach to species delimitation, in which molecular, morphological, ecological, and geographic lines of evidence are evaluated together, is becoming increasingly apparent. Here, we integrate phylogenetic, population genetic, and coalescent analyses of genome-wide sequence data with investigation of variation in multiple morphological traits to delimit species within the Antarctic barbeled plunderfishes (Artedidraconidae: Pogonophryne). Pogonophryne currently comprises 29 valid species, most of which are distinguished solely by variation in the ornamentation of the mental barbel that projects from the lower jaw, a structure previously shown to vary widely within a single species. However, our genomic and phenotypic analyses result in a dramatic reduction in the number of distinct species recognized within the clade, providing evidence to support the recognition of no more than six species. We propose to synonymize 24 of the currently recognized species with five species of Pogonophryne. We find genomic and phenotypic evidence for a new species of Pogonophryne from specimens collected in the Ross Sea. Our findings represent a rare example in which the application of molecular data provides evidence of taxonomic oversplitting on the basis of morphology, clearly demonstrating the utility of an integrative species delimitation framework.[ddRADseq; multispecies coalescent; Notothenioidei; SNPs; Southern Ocean.].

Unravelling the taxonomy of an interstitial fish radiation: Three new species of Gouania (Teleostei: Gobiesocidae) from the Mediterranean Sea and redescriptions of G. willdenowi and G. pigra.

The clingfish (Gobiesocidae) genus Gouania Nardo, 1833 is endemic to the Mediterranean Sea and inhabits, unlike any other vertebrate species in Europe, the harsh intertidal environment of gravel beaches. Following up on a previous phylogenetic study, we revise the diversity and taxonomy of this genus by analysing a comprehensive set of morphological (meristics, morphometrics, microcomputed tomography imaging), geographical and genetic (DNA-barcoding) data. We provide descriptions of three new species, G. adriatica sp. nov., G. orientalis sp. nov. and G. hofrichteri sp. nov., as well as redescriptions of G. willdenowi (Risso, 1810) and G. pigra (Nardo, 1827) and assign neotypes for the latter two species. In addition to elucidating the complex taxonomic situation of Gouania, we discuss the potential of this enigmatic clingfish genus for further ecological, evolutionary and biodiversity studies that might unravel even more diversity in this unique Mediterranean fish radiation.

Fish TNF and TNF receptors.

Tumor necrosis factors (TNFs) are a group of cytokines that play critical roles in regulating a diverse range of physiological processes in vertebrates. TNFs function by activating a large number of structurally related receptors, leading to TNF mediated biological processes which are evolutionarily conserved. Fish have a much diversified TNF family, partly due to the whole genome duplication events which have occurred in this lineage, providing an excellent model to investigate the neo- and sub-functionalised properties of TNF superfamily. Fish possess most of the TNFs and receptors found in mammals and also some homologues exclusively present in fish. It seems that TNFSF4 (OX40), TNFSF7 (CD27) and TNFSF8 (CD30) and their cognate receptors are absent in teleosts. It has been shown that fish viruses are able to produce TNFR homologues to establish infection by manipulating the host immune system. Understanding the roles of TNFSFs in fish immune defence and the pathogenesis of fish diseases will provide insights into the functions of TNFSFs from an evolutionary perspective and better strategies for improving fish health and welfare in aquaculture. This review summarises recent advances in the study offish TNF biology and focuses on the molecular properties and immunological functions of the TNF and TNFR superfamily.

The repertoire of vertebrate STAT transcription factors: Origin and variations in fish.

The stat gene family diversified during early vertebrate evolution thanks to two rounds of whole genome duplication (WGD) to produce a typical repertoire composed of 6 STAT factors (named 1-6). In contrast, only one or two stat genes have been reported in C. elegans and in D. melanogaster. The main types of STAT found from bony fish to mammals are present in Agnathan genomes, but a typical STAT1-6 repertoire is only observed in jawed vertebrates. Comparative syntenies showed that STAT6 was the closest to the ancestor of the family. An extensive survey of stat genes across fish including polyploid species showed that whole genome duplications did not lead to a uniform expansion of stat genes. While 2 to 5 stat1 are present in salmonids, whose genome duplicated about 35My ago, only one copy of stat2 and stat6 is retained. In contrast, common carp, with a recent whole genome duplication (5-10My), possesses a doubled stat repertoire indicating that the elimination of stat2 and stat6 additional copies is not immediate. Altogether our data shed light on the multiplicity of evolutionary pathways followed by key components of the canonical cytokine receptor signalling pathway, and point to differential selective constraints exerted on these factors.

Taxonomic loss and functional reduction over time in the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River, Southern Brazil

We evaluated the fish composition and ecological attributes of the ichthyofauna collected in a limnological zone of the Taquaruçu Reservoir, lower Paranapanema River. Information about the fish community was updated when compared to the previous study (2006). Non-metric multidimensional scaling (NMDS) showed differences in species composition between periods and community weighted means (CWMs) exhibited changes in functional composition over time. Four functional indices were used in the principal coordinate analysis (PcoA) to measure changes in the functional space of species, whereas functional β-diversity inspected differences in the traits composition between the periods. 1,203 individuals were sampled of 43 species, being 16 non-native and 14 new records. Compared to 2006, 27 species were absent, most of them native to Loricariidae and Anostomidae, while Curimatidae and Pimelodidae decreased in abundance. Functional indexes showed a reduction in functional diversity, whereas new species records exhibited functional redundancy. It might have occurred a simplification of the fish community over time, excluding the migratory and specialists species such as the herbivores and detritivores. Accordingly, we concluded that the ichthyofauna of the Taquaruçu Reservoir might have been undergoing a process towards biotic homogenization.(AU)

Avaliamos a composição de peixes e atributos ecológicos da ictiofauna coletada em uma zona limnológica do reservatório de Taquaruçu, baixo rio Paranapanema. As informações sobre a comunidade de peixes foram atualizadas quando comparadas ao estudo anterior (2006). O escalonamento multidimensional não métrico (NMDS) mostrou diferenças na composição de espécies entre os períodos, e as médias ponderadas da comunidade (CWMs) exibiram mudanças na composição funcional ao longo do tempo. Quatro índices funcionais foram utilizados na análise de coordenadas principais (PcoA) para medir as mudanças no espaço funcional das espécies, enquanto a β-diversidade funcional inspecionou diferenças na composição de traços entre os períodos. Foram amostrados 1,203 indivíduos de 43 espécies, sendo 16 não-nativas e 14 novos registros. Em comparação com 2006, 27 espécies estavam ausentes, a maioria nativa de Loricariidae e Anostomidae, enquanto Curimatidae e Pimelodidae diminuíram em abundância. Os índices funcionais mostraram redução na diversidade funcional, enquanto novos registros de espécies exibiram redundância funcional. Pode ter ocorrido uma simplificação da comunidade de peixes ao longo do tempo, excluindo as espécies migradoras e especialistas como os herbívoros e detritívoros. Dessa forma, concluímos que a ictiofauna do reservatório de Taquaruçu pode estar sofrendo um processo de homogeneização biótica.(AU)

Taxonomic and functional turnover of Amazonian stream fish assemblages is determined by deforestation history and environmental variables at multiple scales

High rates of deforestation, either in the past or the present, affect many of the ecological processes in streams. Integrating deforestation history and the current landscape structure enhances the evaluation of ecological effects of land-use change. This is especially true when contemporary landscape conditions are similar but the temporal path to those conditions differs. One approach that has shown promise for evaluating biodiversity responses over time and space is the β-diversity partitioning, which combines taxonomic and functional trait-based approaches. We tested hypotheses related to stream fish assemblages' turnover in watersheds with different environmental conditions and deforestation histories. We sampled fish from 75 watersheds in the Machado River basin, Brazil, and environmental factors were quantified at multiple scales. Taxonomic turnover was higher than expected by chance, whereas functional turnover was lower than expected by the observed taxonomic turnover, indicating that deterministic processes are structuring these assemblages. The turnover, and the environmental factors differed among watersheds with different deforestation histories. Besides being scale-dependent, turnover patterns are also likely dependent on land use dynamics and involve time-lags.(AU)

Altas taxas de desmatamento, seja no passado ou no presente, afetam muitos processos ecológicos em riachos. Integrar o histórico do desmatamento à estrutura atual da paisagem melhora a avaliação dos efeitos ecológicos da mudança do uso do solo. Isto é especialmente verdadeiro quando as condições da paisagem contemporânea são semelhantes, mas seguiram trajetórias distintas. Uma abordagem promissora para avaliar as respostas da biodiversidade ao longo do tempo e espaço é a partição da diversidade-β, que combina abordagens taxonômica e funcional. Testamos hipóteses relacionadas à substituição das assembleias de peixes de riachos em microbacias com diferentes condições ambientais e histórias de desmatamento. Amostramos 75 microbacias na bacia do rio Machado, fatores ambientais foram quantificados em múltiplas escalas. A substituição taxonômica foi maior do que esperada pelo acaso, enquanto a substituição funcional foi menor do que o esperado pela substituição taxonômica, indicando que as assembleias são estruturadas por processos determinísticos. As substituições e fatores ambientais diferiram entre microbacias com históricos de desmatamento distintos. Além de serem escala-dependentes, os padrões de substituição provavelmente são dependentes da dinâmica do uso do solo, envolvendo defasagem temporal.(AU)

Evolution of MicroRNA Biogenesis Genes in the Sterlet (Acipenser ruthenus) and Other Polyploid Vertebrates.

MicroRNAs play a crucial role in eukaryotic gene regulation. For a long time, only little was known about microRNA-based gene regulatory mechanisms in polyploid animal genomes due to difficulties of polyploid genome assembly. However, in recent years, several polyploid genomes of fish, amphibian, and even invertebrate species have been sequenced and assembled. Here we investigated several key microRNA-associated genes in the recently sequenced sterlet (Acipenser ruthenus) genome, whose lineage has undergone a whole genome duplication around 180 MYA. We show that two paralogs of drosha, dgcr8, xpo1, and xpo5 as well as most ago genes have been retained after the acipenserid-specific whole genome duplication, while ago1 and ago3 genes have lost one paralog. While most diploid vertebrates possess only a single copy of dicer1, we strikingly found four paralogs of this gene in the sterlet genome, derived from a tandem segmental duplication that occurred prior to the last whole genome duplication. ago1,3,4 and exportins1,5 look to be prone to additional segment duplications producing up to four-five paralog copies in ray-finned fishes. We demonstrate for the first time exon microsatellite amplification in the acipenserid drosha2 gene, resulting in a highly variable protein product, which may indicate sub- or neofunctionalization. Paralogous copies of most microRNA metabolism genes exhibit different expression profiles in various tissues and remain functional despite the rediploidization process. Subfunctionalization of microRNA processing gene paralogs may be beneficial for different pathways of microRNA metabolism. Genetic variability of microRNA processing genes may represent a substrate for natural selection, and, by increasing genetic plasticity, could facilitate adaptations to changing environments.

Artificial whole genome duplication in paleopolyploid sturgeons yields highest documented chromosome number in vertebrates.

Critically endangered sturgeons, having undergone three whole genome duplication events, represent an exceptional example of ploidy plasticity in vertebrates. Three extant ploidy groups, combined with autopolyploidization, interspecific hybridization and the fertility of hybrids are important issues in sturgeon conservation and aquaculture. Here we demonstrate that the sturgeon genome can undergo numerous alterations of ploidy without severe physiological consequences, producing progeny with a range of ploidy levels and extremely high chromosome numbers. Artificial suppression of the first mitotic division alone, or in combination with suppression of the second meiotic division of functionally tetraploid zygotes (4n, C-value = 4.15) of Siberian sturgeon Acipenser baerii and Russian sturgeon A. gueldenstaedtii resulted in progeny of various ploidy levels-diploid/hexaploid (2n/6n) mosaics, hexaploid, octoploid juveniles (8n), and dodecaploid (12n) larvae. Counts between 477 to 520 chromosomes in octoploid juveniles of both sturgeons confirmed the modal chromosome numbers of parental species had been doubled. This exceeds the highest previously documented chromosome count among vertebrates 2n ~ 446 in the cyprinid fish Ptychobarbus dipogon.

A comparison of two remotely operated vehicle (ROV) survey methods used to estimate fish assemblages and densities around a California oil platform.

Offshore oil and gas platforms have a finite life of production operations. Once production ceases, decommissioning options for the platform are assessed. The role that a platform's jacket plays as fish habitat can inform the decommissioning decision. In this study, conducted along the crossbeams of a California platform jacket and using an ROV, we compared estimates of fish diversity and densities determined from a targeted "biological" survey with those from a replicated "structural" survey. We found that the water column fish species assemblages characterized by the two methods were similar. By contrast, the two survey methods yielded different species assemblages inhabiting the crossbeam at the platform jacket base. This difference occurred because, at least off California, the platform jacket base species diversity tends to be highest where the bottom crossbeam is undercut, creating sheltering sites for many species. Because the structural method inadequately imaged the seafloor-crossbeam interface, particularly where a gap occurred between crossbeam and seafloor, substantial numbers of fishes were not visible. While we cannot extrapolate from this study to all platforms' worldwide, it is clear that routine platform structural integrity surveys may be a valuable source for opportunistic marine community surveys. Intentional planning of the structural survey to incorporate relatively minor variations (e.g., maintaining fixed ROV distance from the infrastructure and consistent 90° camera angle) coupled with a deliberate consideration of the platform ecology (e.g., positioning the ROV to capture the seafloor-crossbeam interface) can substantially improve the effects on fish assemblage assessments from routine structural surveys without compromising the integrity assessment. We suggest that these biases should be both acknowledged and, understood when using routine structural surveys to inform platform ecology assessment. Additional consideration may be given to structural surveys that incorporate incremental adjustments to provide better data applicability to biological assessments.

Comparative effects of Novirhabdovirus genes on modulating constitutive transcription and innate antiviral responses, in different teleost host cell types.

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 ß-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.

The lasting after-effects of an ancient polyploidy on the genomes of teleosts.

The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.

Functional Analysis of IRF1 Reveals its Role in the Activation of the Type I IFN Pathway in Golden Pompano, Trachinotus ovatus (Linnaeus 1758).

Interferon (IFN) regulatory factor 1 (IRF1), a transcription factor with a novel helix-turn-helix DNA-binding domain, plays a crucial role in innate immunity by regulating the type I IFN signaling pathway. However, the regulatory mechanism through which IRF1 regulates type I IFN in fish is not yet elucidated. In the present study, IRF1 was characterized from golden pompano, Trachinotus ovatus (designated ToIRF1), and its immune function was identified to elucidate the transcriptional regulatory mechanism of ToIFNa3. The full-length complementary DNA (cDNA) of IRF1 is 1763 bp, including a 900-bp open reading frame (ORF) encoding a 299-amino-acid polypeptide. The putative protein sequence has 42.7-71.7% identity to fish IRF1 and possesses a representative conserved domain (a DNA-binding domain (DBD) at the N-terminus). The genomic DNA sequence of ToIRF1 consists of eight exons and seven introns. Moreover, ToIRF1 is constitutively expressed in all examined tissues, with higher levels being observed in immune-relevant tissues (whole blood, gill, and skin). Additionally, Cryptocaryon irritans challenge in vivo increases ToIRF1 expression in the skin as determined by Western blotting (WB); however, protein levels of ToIRF1 in the gill did not change significantly. The subcellular localization indicates that ToIRF1 is localized in the nucleus and cytoplasm with or without polyinosinic/polycytidylic acid (poly (I:C)) induction. Furthermore, overexpression of ToIRF1 or ToIFNa3 shows that ToIRF1 can notably activate ToIFNa3 and interferon signaling molecule expression. Promoter sequence analysis finds that several interferon stimulating response element (ISRE) binding sites are present in the promoter of ToIFNa3. Additionally, truncation, point mutation, and electrophoretic mobile shift (EMSA) assays confirmed that ToIRF1 M5 ISRE binding sites are functionally important for ToIFNa3 transcription. These results may help to illuminate the roles of teleost IRF1 in the transcriptional mechanisms of type I IFN in the immune process.

Comparative anatomy of the fin muscles of non-sarcopterygian fishes, with notes on homology and evolution.

Limited gross anatomical information about the muscles of fins, in particular those of the median fins, creates substantial gaps in the comparative anatomy, homologies, and evolution of these muscles across fishes. The scarcity of data also makes it difficult to interpret results obtained in developmental studies done in model organisms, such as zebrafish. To overcome these gaps, we provide descriptions of the configuration of all appendicular muscles of Amia, median fins of Polypterus, and the dorsal and anal fins of Lepisosteus and Chondrostei. The musculature of other species, including sharks and sturgeons, is also revised. We describe muscles that were previously overlooked, report sexual dimorphism in the muscles of the anal fin of Polypterus, and reveal muscle variations within Polypterus males. Species dissected for the present study thus represent all major non-sarcopterygian extant clades of gnathostomes, i.e. Chondrichthyes, Polypteriformes, Chondrostei, Lepisosteiformes, Amiiformes and Teleostei. Moreover, we compare our observations with the relatively few works that have provided information about muscles of at least some fins of these taxa in order to provide a broad discussion on - and detailed schemes showing - the major evolutionary patterns within the appendicular musculature of these fishes. Such discussion provides an opportunity for a more comprehensive understanding of appendicular evolution and fish evolution in particular and of gnathostome and morphological evolution in general.