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The white shark (Carcharodon carcharias) (Linnaeus, 1758), an iconic apex predator occurring in all oceans,1,2 is classified as Vulnerable globally3-with global abundance having dropped to 63% of 1970s estimates,4-and as Critically Endangered in Europe.5 Identification of evolutionary significant units and their management are crucial for conservation,6 especially as the white shark is facing various but often region-specific anthropogenic threats.7,8,9,10,11 Assessing connectivity in a cosmopolitan marine species requires worldwide sampling and high-resolution genetic markers.12 Both are lacking for the white shark, with studies to date typified by numerous but geographically limited sampling, and analyses relying largely on relatively small numbers of nuclear microsatellites,13,14,15,16,17,18,19 which can be plagued by various genotyping artefacts and thus require cautious interpretation.20 Sequencing and computational advances are finally allowing genomes21,22,23 to be leveraged into population studies,24,25,26,27 with datasets comprising thousands of single-nucleotide polymorphisms (SNPs). Here, combining target gene capture (TGC)28 sequencing (89 individuals, 4,000 SNPs) and whole-genome re-sequencing (17 individuals, 391,000 SNPs) with worldwide sampling across most of the distributional range, we identify three genetically distinct allopatric lineages (North Atlantic, Indo-Pacific, and North Pacific). These diverged 100,000-200,000 years ago during the Penultimate Glaciation, when low sea levels, different ocean currents, and water temperatures produced significant biogeographic barriers. Our results show that without high-resolution genomic analyses of samples representative of a species' range,12 the true extent of diversity, presence of past and contemporary barriers to gene flow, subsequent speciation, and local evolutionary events will remain enigmatic.
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Tubarões , Tubarões/genética , Tubarões/classificação , Animais , Genoma , Polimorfismo de Nucleotídeo Único , Filogenia , BrancosRESUMO
Sequenced shark nuclear genomes are underrepresented, with reference genomes available for only four out of nine orders so far. Here, we present the nuclear genome, with annotations, of the spiny dogfish (Squalus acanthias), a shark of interest to biomedical and conservation efforts, and the first representative of the second largest order of sharks (Squaliformes) with nuclear genome annotations available. Using Pacific Biosciences Continuous Long Read data in combination with Illumina paired-end and Hi-C sequencing, we assembled the genome de novo, followed by RNA-Seq-supported annotation. The final chromosome-level assembly is 3.7 Gb in size, has a BUSCO completeness score of 91.6%, and an error rate of less than 0.02%. Annotation predicted 33,283 gene models in the spiny dogfish's genome, of which 31,979 are functionally annotated.
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Tubarões , Squalus acanthias , Animais , Squalus acanthias/genética , Tubarões/genética , Sequência de BasesRESUMO
Estimating the demographic parameters of contemporary populations is essential to the success of elasmobranch conservation programmes, and to understanding their recent evolutionary history. For benthic elasmobranchs such as skates, traditional fisheries-independent approaches are often unsuitable as the data may be subject to various sources of bias, whilst low recapture rates can render mark-recapture programmes ineffectual. Close-kin mark-recapture (CKMR), a novel demographic modelling approach based on the genetic identification of close relatives within a sample, represents a promising alternative approach as it does not require physical recaptures. We evaluated the suitability of CKMR as a demographic modelling tool for the critically endangered blue skate (Dipturus batis) in the Celtic Sea using samples collected during fisheries-dependent trammel-net surveys that ran from 2011 to 2017. We identified three full-sibling and 16 half-sibling pairs among 662 skates, which were genotyped across 6291 genome-wide single nucleotide polymorphisms, 15 of which were cross-cohort half-sibling pairs that were included in a CKMR model. Despite limitations owing to a lack of validated life-history trait parameters for the species, we produced the first estimates of adult breeding abundance, population growth rate, and annual adult survival rate for D. batis in the Celtic Sea. The results were compared to estimates of genetic diversity, effective population size (N e ), and to catch per unit effort estimates from the trammel-net survey. Although each method was characterized by wide uncertainty bounds, together they suggested a stable population size across the time-series. Recommendations for the implementation of CKMR as a conservation tool for data-limited elasmobranchs are discussed. In addition, the spatio-temporal distribution of the 19 sibling pairs revealed a pattern of site fidelity in D. batis, and supported field observations suggesting an area of critical habitat that could qualify for protection might occur near the Isles of Scilly.
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The feeding ecology of broadbill swordfish (Xiphias gladius) in the California Current was described based on analysis of stomach contents collected by fishery observers aboard commercial drift gillnet boats from 2007 to 2014. Prey were identified to the lowest taxonomic level and diet composition was analyzed using univariate and multivariate methods. Of 299 swordfish sampled (74 to 245 cm eye-to-fork length), 292 non-empty stomachs contained remains from 60 prey taxa. Genetic analyses were used to identify prey that could not be identified visually. Diet consisted mainly of cephalopods but also included epipelagic and mesopelagic teleosts. Jumbo squid (Dosidicus gigas) and Gonatopsis borealis were the most important prey based on the geometric index of importance. Swordfish diet varied with body size, location and year. Jumbo squid, Gonatus spp. and Pacific hake (Merluccius productus) were more important for larger swordfish, reflecting the ability of larger specimens to catch large prey. Jumbo squid, Gonatus spp. and market squid (Doryteuthis opalescens) were more important in inshore waters, while G. borealis and Pacific hake predominated offshore. Jumbo squid was more important in 2007-2010 than in 2011-2014, with Pacific hake being the most important prey item in the latter period. Diet variation by area and year probably reflects differences in swordfish preference, prey availability, prey distribution, and prey abundance. The range expansion of jumbo squid that occurred during the first decade of this century may particularly explain their prominence in swordfish diet during 2007-2010. Some factors (swordfish size, area, time period, sea surface temperature) that may influence dietary variation in swordfish were identified. Standardizing methods could make future studies more comparable for conservation monitoring purposes.
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Gadiformes , Perciformes , Animais , Ecologia , Estômago , Dieta , DecapodiformesRESUMO
This study presents the results of analyses of data on infections of 2646 whiting Merlangius merlangus with the monogenean Diclidophora merlangi. All fish were caught in the North Sea and off the north coast of Scotland in 1990, 1993 and 1995. The aims were to analyse these data in relation to the locations of whiting sampling stations and oil installations active at that time, and to evaluate the results in terms of D. merlangi as an indicator of hydrocarbon pollution. Mean abundance of D. merlangi increased significantly with increasing proximity to the nearest oil field, with an accelerated rate of increase within approximately 2 km of the oil field. Age of oil field and whiting length showed no significant effect on parasite abundance, but there was a small difference between years. The results support those of previous studies in demonstrating the value of monogeneans as indicators of hydrocarbon pollution.
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Gadiformes , Trematódeos , Animais , Mar do Norte , Peixes/parasitologia , HidrocarbonetosRESUMO
Disruptions to reproductive health in wildlife species inhabiting polluted environments is often found to occur alongside compromised immunity. However, research on impacts of aquatic pollution on freshwater mollusc immune responses is limited despite their importance as vectors of disease (Schistosomiasis) in humans, cattle and wild mammals. We developed an in vitro 'tool-kit' of well-characterized quantitative immune tests using Biomphalaria glabrata hemocytes. We exposed hemocytes to environmentally-relevant concentrations of common aquatic pollutants (17ß-estradiol, Bisphenol-A and p,p'-DDE) and measured key innate immune responses including motility, phagocytosis and encapsulation. Additionally, we tested an extract of a typical domestic tertiary treated effluent as representative of a 'real-world' mixture of chemicals. Encapsulation responses were stimulated by p,p'-DDE at low doses but were suppressed at higher doses. Concentrations of BPA (above 200 ng/L) and p,p'-DDE (above 500 ng/L) significantly inhibited phagocytosis compared to controls, whilst hemocyte motility was reduced by all test chemicals and the effluent extract in a dose-dependent manner. All responses occurred at chemical concentrations considered to be below the cytotoxic thresholds of hemocytes. This is the first time a suite of in vitro tests has been developed specifically in B. glabrata with the purpose of investigating the impacts of chemical pollutants and an effluent extract on immunity. Our findings indicate that common aquatic pollutants alter innate immune responses in B. glabrata, suggesting that pollutants may be a critical, yet overlooked, factor impacting disease by modulating the dynamics of parasite transmission between molluscs and humans.
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Biomphalaria , Poluentes Ambientais , Animais , Biomphalaria/parasitologia , Bovinos , Diclorodifenil Dicloroetileno , Estradiol , Hemócitos , Humanos , Mamíferos , Fagocitose , Schistosoma mansoniRESUMO
We describe the complete mitochondrial genomes of the flapper skate Dipturus intermedius (Parnell 1837) and the longnose skate Dipturus oxyrinchus (Linnaeus 1758), which have been obtained by Sanger sequencing. We report the length of the sequences to be 16,906 and 16,911 bp, respectively. The length and structure of gene regions, containing 13 protein-coding regions, 22 tRNA genes, two rRNA genes, and two non-coding areas, resemble those of related skate species. Despite D. intermedius being considered a cryptic species with D. batis, the full mitogenomes confirm that D. intermedius and D. oxyrinchus are more genetically similar. In comparison to other Dipturus species, D. intermedius is missing a whole codon in its cytochrome oxidase subunit 2 gene. These mitogenomes will be a useful resource furthering investigation of the population genetic differences and evolutionary history of skate species.
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The blue skate (Dipturus batis) has a patchy distribution across the North-East Atlantic Ocean, largely restricted to occidental seas around the British Isles following fisheries-induced population declines and extirpations. The viability of remnant populations remains uncertain and could be impacted by continued fishing and by-catch pressure, and the projected impacts of climate change. We genotyped 503 samples of D. batis, obtained opportunistically from the widest available geographic range, across 6 350 single nucleotide polymorphisms (SNPs) using a reduced-representation sequencing approach. Genotypes were used to assess the species' contemporary population structure, estimate effective population sizes and identify putative signals of selection in relation to environmental variables using a seascape genomics approach. We identified genetic discontinuities between inshore (British Isles) and offshore (Rockall and Faroe Island) populations, with differentiation most pronounced across the deep waters of the Rockall Trough. Effective population sizes were largest in the Celtic Sea and Rockall, but low enough to be of potential conservation concern among Scottish and Faroese sites. Among the 21 candidate SNPs under positive selection was one significantly correlated with environmental variables predicted to be affected by climate change, including bottom temperature, salinity and pH. The paucity of well-annotated elasmobranch genomes precluded us from identifying a putative function for this SNP. Nevertheless, our findings suggest that climate change could inflict a strong selective force upon remnant populations of D. batis, further constraining its already-restricted habitat. Furthermore, the results provide fundamental insights on the distribution, behaviour and evolutionary biology of D. batis in the North-East Atlantic that will be useful for the establishment of conservation actions for this and other critically endangered elasmobranchs.
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This study documented the parasite faunas of the spiral valves of blue sharks Prionace glauca (L. 1758) and common thresher sharks Alopias vulpinus (Bonnaterre, 1788) caught in the California Current Large Marine Ecosystem (CCLME) north of the Mexican border. The spiral valves of 18 blue and 19 thresher sharks caught in the CCLME from 2009 to 2013 were examined for parasites. Seven parasite taxa were found in blue sharks and nine in threshers. The tetraphyllidean cestode Anthobothrium sp. (78% prevalence) was the most common parasite in blue sharks, and the phyllobothriid cestode Paraorygmatobothrium sp. (90% prevalence) was the most common in threshers. An adult nematode of the genus Piscicapillaria was found in threshers for the first time and may be a new species. Adult individuals of Hysterothylacium sp. were found in both shark species. The adult acanthocephalan Rhadinorhynchus cololabis and remains of the parasitic copepod Pennella sp. - both parasites of Pacific saury, Cololabis saira - were found in the intestines of threshers, indicating recent feeding on saury. This study paves the way for a more comprehensive examination, including more samples and a wider variety of shark species, to provide a greater understanding of shark feeding behaviour and possibly provide information on shark population biology.
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Comportamento Alimentar , Doenças dos Peixes/parasitologia , Doenças Parasitárias em Animais/parasitologia , Tubarões/fisiologia , Tubarões/parasitologia , Animais , Ecossistema , México , Parasitos/classificação , Parasitos/isolamento & purificaçãoRESUMO
Migratory movements in response to seasonal resources often influence population structure and dynamics. Yet in mobile marine predators, population genetic consequences of such repetitious behaviour remain inaccessible without comprehensive sampling strategies. Temporal genetic sampling of seasonally recurring aggregations of planktivorous basking sharks, Cetorhinus maximus, in the Northeast Atlantic (NEA) affords an opportunity to resolve individual re-encounters at key sites with population connectivity and patterns of relatedness. Genetic tagging (19 microsatellites) revealed 18% of re-sampled individuals in the NEA demonstrated inter/multi-annual site-specific re-encounters. High genetic connectivity and migration between aggregation sites indicate the Irish Sea as an important movement corridor, with a contemporary effective population estimate (Ne) of 382 (CI = 241-830). We contrast the prevailing view of high gene flow across oceanic regions with evidence of population structure within the NEA, with early-season sharks off southwest Ireland possibly representing genetically distinct migrants. Finally, we found basking sharks surfacing together in the NEA are on average more related than expected by chance, suggesting a genetic consequence of, or a potential mechanism maintaining, site-specific re-encounters. Long-term temporal genetic monitoring is paramount in determining future viability of cosmopolitan marine species, identifying genetic units for conservation management, and for understanding aggregation structure and dynamics.
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Tubarões/genética , Tubarões/fisiologia , Migração Animal , Animais , Oceano Atlântico , Conservação dos Recursos Naturais , Feminino , Fluxo Gênico , Variação Genética , Genética Populacional , Irlanda , Masculino , Repetições de Microssatélites , Densidade Demográfica , Estações do Ano , Análise Espaço-TemporalRESUMO
The complete mitochondrial genome of the blue skate Dipturus batis is described from shotgun sequencing on an Illumina next-generation sequencing platform. We report a 16,911 bp long sequence similar in size to other members of the genus, containing 13 protein-coding regions, 22 tRNA genes, 2 rRNA genes, and 2 non-coding areas. Phylogenetic analysis was performed using the complete mitochondrial genomes of 17 related species, placing D. batis within the Rajini tribe of the Rajidae family, consistent with current taxonomy. The new resource adds to a growing database of rajid mitogenomes which will help resolve phylogenetic relationships within the family.
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This corrects the article DOI: 10.1038/ncomms15451.
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Highly migratory, cosmopolitan oceanic sharks often exhibit complex movement patterns influenced by ontogeny, reproduction, and feeding. These elusive species are particularly challenging to population genetic studies, as representative samples suitable for inferring genetic structure are difficult to obtain. Our study provides insights into the genetic population structure one of the most abundant and wide-ranging oceanic shark species, the blue shark Prionace glauca, by sampling the least mobile component of the populations, i.e., young-of-year and small juveniles (<2 year; N = 348 individuals), at three reported nursery areas, namely, western Iberia, Azores, and South Africa. Samples were collected in two different time periods (2002-2008 and 2012-2015) and were screened at 12 nuclear microsatellites and at a 899-bp fragment of the mitochondrial control region. Our results show temporally stable genetic homogeneity among the three Atlantic nurseries at both nuclear and mitochondrial markers, suggesting basin-wide panmixia. In addition, comparison of mtDNA CR sequences from Atlantic and Indo-Pacific locations also indicated genetic homogeneity and unrestricted female-mediated gene flow between ocean basins. These results are discussed in light of the species' life history and ecology, but suggest that blue shark populations may be connected by gene flow at the global scale. The implications of the present findings to the management of this important fisheries resource are also discussed.
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Biomphalaria snails are instrumental in transmission of the human blood fluke Schistosoma mansoni. With the World Health Organization's goal to eliminate schistosomiasis as a global health problem by 2025, there is now renewed emphasis on snail control. Here, we characterize the genome of Biomphalaria glabrata, a lophotrochozoan protostome, and provide timely and important information on snail biology. We describe aspects of phero-perception, stress responses, immune function and regulation of gene expression that support the persistence of B. glabrata in the field and may define this species as a suitable snail host for S. mansoni. We identify several potential targets for developing novel control measures aimed at reducing snail-mediated transmission of schistosomiasis.
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Biomphalaria/genética , Biomphalaria/parasitologia , Genoma , Esquistossomose mansoni/transmissão , Comunicação Animal , Animais , Biomphalaria/imunologia , Elementos de DNA Transponíveis , Evolução Molecular , Água Doce , Regulação da Expressão Gênica , Interações Hospedeiro-Parasita , Feromônios , Proteoma , Schistosoma mansoni , Análise de Sequência de DNA , Estresse FisiológicoRESUMO
Despite 400-450 million years of independent evolution, a strong phenotypic convergence has occurred between two groups of fish: tunas and lamnid sharks. This convergence is characterized by centralization of red muscle, a distinctive swimming style (stiffened body powered through tail movements) and elevated body temperature (endothermy). Furthermore, both groups demonstrate elevated white muscle metabolic capacities. All these traits are unusual in fish and more likely evolved to support their fast-swimming, pelagic, predatory behavior. Here, we tested the hypothesis that their convergent evolution was driven by selection on a set of metabolic genes. We sequenced white muscle transcriptomes of six tuna, one mackerel, and three shark species, and supplemented this data set with previously published RNA-seq data. Using 26 species in total (including 7,032 tuna genes plus 1,719 shark genes), we constructed phylogenetic trees and carried out maximum-likelihood analyses of gene selection. We inferred several genes relating to metabolism to be under selection. We also found that the same one gene, glycogenin-1, evolved under positive selection independently in tunas and lamnid sharks, providing evidence of convergent selective pressures at gene level possibly underlying shared physiology.
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Temperatura Corporal/genética , Evolução Molecular , Proteínas de Peixes/genética , Glucosiltransferases/genética , Glicoproteínas/genética , Animais , Músculo Esquelético/metabolismo , Seleção Genética , Tubarões/genética , Tubarões/fisiologia , Transcriptoma , Atum/genética , Atum/fisiologiaRESUMO
Gastropod mollusks have been proposed as alternative models for male reproductive toxicity testing, due to similarities in their reproductive anatomy compared to mammals, together with evidence that endocrine disrupting chemicals can cause effects in some mollusks analogous to those seen in mammals. To test this hypothesis, we used the freshwater pulmonate snail, Biomphalaria glabrata, for which various genetic tools and a draft genome have recently become available, to investigate the effects of two steroid androgens on the development of mollusk secondary sexual organs. Here we present the results of exposures to two potent androgens, the vertebrate steroid; 5α-dihydrotestosterone (DHT) and the pharmaceutical anabolic steroid; 17α-methyltestosterone (MT), under continuous flow-through conditions throughout embryonic development and up to sexual maturity. Secondary sexual gland morphology, histopathology and differential gene expression analysis were used to determine whether steroid androgens stimulated or inhibited organ development. No significant differences between tissues from control and exposed snails were identified, suggesting that these androgens elicited no biologically detectable response normally associated with exposure to androgens in vertebrate model systems. Identifying no effect of androgens in this mollusk is significant, not only in the context of the suitability of mollusks as alternative model organisms for testing vertebrate androgen receptor agonists but also, if applicable to other similar mollusks, in terms of the likely impacts of androgens and anti-androgenic pollutants present in the aquatic environment.
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Androgênios/farmacologia , Biomphalaria/efeitos dos fármacos , Biomphalaria/fisiologia , Exposição Ambiental , Reprodução/efeitos dos fármacos , Androgênios/efeitos adversos , Animais , Di-Hidrotestosterona/farmacologia , Relação Dose-Resposta a Droga , Exposição Ambiental/efeitos adversos , Perfilação da Expressão Gênica , Regulação da Expressão Gênica , Metiltestosterona/farmacologiaRESUMO
BACKGROUND: All vertebrates initially feed their offspring using yolk reserves. In some live-bearing species these yolk reserves may be supplemented with extra nutrition via a placenta. Sharks belonging to the Carcharhinidae family are all live-bearing, and with the exception of the tiger shark (Galeocerdo cuvier), develop placental connections after exhausting yolk reserves. Phylogenetic relationships suggest the lack of placenta in tiger sharks is due to secondary loss. This represents a dramatic shift in reproductive strategy, and is likely to have left a molecular footprint of positive selection within the genome. RESULTS: We sequenced the transcriptome of the tiger shark and eight other live-bearing shark species. From this data we constructed a time-calibrated phylogenetic tree estimating the tiger shark lineage diverged from the placental carcharhinids approximately 94 million years ago. Along the tiger shark lineage, we identified five genes exhibiting a signature of positive selection. Four of these genes have functions likely associated with brain development (YWHAE and ARL6IP5) and sexual reproduction (VAMP4 and TCTEX1D2). CONCLUSIONS: Our results indicate the loss of placenta in tiger sharks may be associated with subsequent adaptive changes in brain development and sperm production.
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Placenta , Seleção Genética , Tubarões/fisiologia , Animais , Sequência de Bases , Feminino , Masculino , Filogenia , Gravidez , Reprodução , Tubarões/genética , TranscriptomaRESUMO
Chronic obstructive pulmonary disease (COPD) hospitalizations and readmissions adversely impact the health and quality of life of COPD patients. Under the Hospital Readmissions Reduction Program, the Centers for Medicare & Medicaid Services reduce payments to those hospitals exceeding expected rates of COPD readmissions within 30 days of hospital discharge. It was within this climate that the COPD Foundation held its 2nd COPD Readmissions Summit in March 2015. Experts in attendance: (1) categorized challenges to optimal COPD care, ( 2) analyzed the state of care delivery and readmissions reduction strategies and (3) identified the best available evidence-based approaches to improving care delivery across the continuum, including early diagnosis via spirometry, ongoing device, oxygen and medication reconciliation, treatment that addresses comorbidities and preventive care, robust patient education, prompt post-acute follow up, home health services and pulmonary rehabilitation. Results of this collaborative event formed the basis for PRAXIS, the COPD Foundation's initiative to improve COPD care across the health continuum and to reduce readmissions.
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Nuclear receptors (NRs) are transcription regulators involved in an array of diverse physiological functions including key roles in endocrine and metabolic function. The aim of this study was to identify nuclear receptors in the fully sequenced genome of the gastropod snail, Biomphalaria glabrata, intermediate host for Schistosoma mansoni and compare these to known vertebrate NRs, with a view to assessing the snail's potential as a invertebrate model organism for endocrine function, both as a prospective new test organism and to elucidate the fundamental genetic and mechanistic causes of disease. For comparative purposes, the genome of a second gastropod, the owl limpet, Lottia gigantea was also investigated for nuclear receptors. Thirty-nine and thirty-three putative NRs were identified from the B. glabrata and L. gigantea genomes respectively, based on the presence of a conserved DNA-binding domain and/or ligand-binding domain. Nuclear receptor transcript expression was confirmed and sequences were subjected to a comparative phylogenetic analysis, which demonstrated that these molluscs have representatives of all the major NR subfamilies (1-6). Many of the identified NRs are conserved between vertebrates and invertebrates, however differences exist, most notably, the absence of receptors of Group 3C, which includes some of the vertebrate endocrine hormone targets. The mollusc genomes also contain NR homologues that are present in insects and nematodes but not in vertebrates, such as Group 1J (HR48/DAF12/HR96). The identification of many shared receptors between humans and molluscs indicates the potential for molluscs as model organisms; however the absence of several steroid hormone receptors indicates snail endocrine systems are fundamentally different.
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Gastrópodes/genética , Genoma , Receptores Citoplasmáticos e Nucleares/genética , AnimaisRESUMO
During its life cycle, the helminth parasite Schistosoma mansoni uses the freshwater snail Biomphalaria glabrata as an intermediate host to reproduce asexually generating cercariae for infection of the human definitive host. Following invasion of the snail, the parasite develops from a miracidium to a mother sporocyst and releases excretory-secretory products (ESPs) that likely influence the outcome of host infection. To better understand molecular interactions between these ESPs and the host snail defence system, we determined gene expression profiles of haemocytes from S. mansoni-resistant or -susceptible strains of B. glabrata exposed in vitro to S. mansoni ESPs (20 µg/ml) for 1 h, using a 5K B. glabrata cDNA microarray. Ninety-eight genes were found differentially expressed between haemocytes from the two snail strains, 57 resistant specific and 41 susceptible specific, 60 of which had no known homologue in GenBank. Known differentially expressed resistant-snail genes included the nuclear factor kappa B subunit Relish, elongation factor 1α, 40S ribosomal protein S9, and matrilin; known susceptible-snail specific genes included cathepsins D and L, and theromacin. Comparative analysis with other gene expression studies revealed 38 of the 98 identified genes to be uniquely differentially expressed in haemocytes in the presence of ESPs, thus identifying for the first time schistosome ESPs as important molecules that influence global snail host-defence cell gene expression profiles. Such immunomodulation may benefit the schistosome, enabling its survival and successful development in the snail host.