Deep Sea – Close Kin: A Genetic Approach for Improved Fisheries Management

Deep-sea fish stocks consist of species that live at depths of greater than 400 metres. While being important for EU fisheries, this natural renewable resource is particularly vulnerable to over-fishing, as many deep sea species are slow-growing and commonly of low fecundity. Generally little is known about the biology of deep sea species, and there prevails a substantial lack of scientific data on deep-sea stocks. This constitutes a major impediment to management strategies underpinning sustainable and profitable deep sea fisheries. Europe’s deep-sea fisheries began in the 1970’s and were entirely unregulated. The fleet grew as rewards were high, but many species were rapidly depleted. It was only in 2003 that a management plan was brought into action. While some measures to better protect commercially exploited deep sea fish have been adopted, such as the limitation of fishing effort or total allowable catches, these have been insufficient to allow stocks to recover and there is a general consensus that most deep-water stocks remain below safe biological limits for exploitation. In a recent communication to the Council and the European Parliament, the European Commission has emphasized the need to improve our knowledge on deep sea fish species to move away from the current prevailing unsustainable exploitation. Ideally, this would be the development of a robust and practical approach to estimate the abundance of deep sea species to support stock assessments and reduce the uncertainty about the state and rebuilding rates of commercially exploited deep sea stocks. The current rapid technology development and concurrent steep drop in costs of large-scale genotyping offers major opportunities for fisheries management. This report explores whether the concept of genetic close-kin abundance estimation, recently applied to establish biomass estimates of Southern Bluefin Tuna, can be applied to fisheries management of deep sea fish species.JRC.G.3-Maritime affair

Population genetic structure of the European lobster (Homarus gammarus) in the Irish Sea and implications for the effectiveness of the first British marine protected area

Levels of self-recruitment within and connectivity among populations are key factors influencing marine population persistence and stock sustainability, as well as the effectiveness of spatially explicit management strategies such as Marine Protected Areas (MPAs). In the United Kingdom (UK), Lundy Island in the Bristol Channel was designated a No-Take Zone (NTZ) in 2003 and became the UK’s first Marine Conservation Zone (MCZ) in 2009. This NTZ is expected to represent an additional resource for the sustainable management of the European lobster (Homarus gammarus) fishery. As the first step in a genetic monitoring program, this study aimed to investigate population genetic structure of lobster within and between the Irish Sea and Bristol Channel and in doing so to assess the functioning of the Lundy NTZ in the context of connectivity and other genetic parameters. Analysis of microsatellite data indicated that lobsters within the study area are genetically homogeneous and supports the view of a single panmictic population wherein the Lundy NTZ is highly connected. Levels of genetic variability were universally high with no evidence of differences for the NTZ. Furthermore, there was no evidence of recent genetic bottlenecks, and estimates of effective population sizes were infinitely large. The results suggest that if current management and breeding stock sizes are maintained genetic drift will not be strong enough to reduce neutral genetic diversity

Ancient Divergence in the Trans-Oceanic Deep-Sea Shark Centroscymnus crepidater

Unravelling the genetic structure and phylogeographic patterns of deep-sea sharks is particularly challenging given the inherent difficulty in obtaining samples. The deep-sea shark Centroscymnus crepidater is a medium-sized benthopelagic species that exhibits a circumglobal distribution occurring both in the Atlantic and Indo-Pacific Oceans. Contrary to the wealth of phylogeographic studies focused on coastal sharks, the genetic structure of bathyal species remains largely unexplored. We used a fragment of the mitochondrial DNA control region, and microsatellite data, to examine genetic structure in C. crepidater collected from the Atlantic Ocean, Tasman Sea, and southern Pacific Ocean (Chatham Rise). Two deeply divergent (3.1%) mtDNA clades were recovered, with one clade including both Atlantic and Pacific specimens, and the other composed of Atlantic samples with a single specimen from the Pacific (Chatham Rise). Bayesian analyses estimated this splitting in the Miocene at about 15 million years ago. The ancestral C. crepidater lineage was probably widely distributed in the Atlantic and Indo-Pacific Oceans. The oceanic cooling observed during the Miocene due to an Antarctic glaciation and the Tethys closure caused changes in environmental conditions that presumably restricted gene flow between basins. Fluctuations in food resources in the Southern Ocean might have promoted the dispersal of C. crepidater throughout the northern Atlantic where habitat conditions were more suitable during the Miocene. The significant genetic structure revealed by microsatellite data suggests the existence of present-day barriers to gene flow between the Atlantic and Pacific populations most likely due to the influence of the Agulhas Current retroflection on prey movements

Fine‐scale seascape genomics of an exploited marine species, the common cockle Cerastoderma edule, using a multimodelling approach

Population dynamics of marine species that are sessile as adults are driven by oceanographic dispersal of larvae from spawning to nursery grounds. This is mediated by life-history traits such as the timing and frequency of spawning, larval behaviour and duration, and settlement success. Here, we use 1725 single nucleotide polymorphisms (SNPs) to study the fine scale spatial genetic structure in the commercially important cockle species Cerastoderma edule and compare it to environmental variables and current-mediated larval dispersal within a modelling framework. Hydrodynamic modelling employing the NEMO Atlantic Margin Model (AMM15) was used to simulate larval transport and estimate connectivity between populations during spawning months (April - September), factoring in larval duration and inter-annual variability of ocean currents. Results at neutral loci reveal the existence of three separate genetic clusters (mean FST=0.021) within a relatively fine spatial scale in the northwest Atlantic. Environmental Association analysis indicates that oceanographic currents and geographical proximity explain over 20% of the variance observed at neutral loci, while genetic variance (71%) at outlier loci was explained by sea surface temperatures extremes. These results fill an important knowledge gap in the management of a commercially important and overexploited species, bringing us closer to understanding the role of larval dispersal in connecting populations at a fine geographical scale

Simvastatin and downstream inhibitors circumvent constitutive and stromal cell-induced resistance to doxorubicin in IGHV unmutated CLL cells

The immunoglobulin heavy-chain variable region (IGHV) mutational status is a strong determinant of remission duration in chronic lymphocytic leukemia (CLL). The aim of this work was to compare the multidrug resistance (MDR) signature of IGHV mutated and unmutated CLL cells, identifying biochemical and molecular targets potentially amenable to therapeutic intervention.We found that the mevalonate pathway-dependent Ras/ERK1-2 and RhoA/RhoA kinase signaling cascades, and the downstream HIF-1\u3b1/P-glycoprotein axis were more active in IGHV unmutated than in mutated cells, leading to a constitutive protection from doxorubicin-induced cytotoxicity. The constitutive MDR phenotype of IGHV unmutated cells was partially dependent on B cell receptor signaling, as shown by the inhibitory effect exerted by ibrutinib. Stromal cells further protected IGHV unmutated cells from doxorubicin by upregulating Ras/ERK1-2, RhoA/RhoA kinase, Akt, HIF-1\u3b1 and P-glycoprotein activities. Mevalonate pathway inhibition with simvastatin abrogated these signaling pathways and reversed the resistance of IGHV unmutated cells to doxorubicin, also counteracting the protective effect exerted by stromal cells. Similar results were obtained via the targeted inhibition of the downstream molecules ERK1-2, RhoA kinase and HIF-1\u3b1.Therefore, targeting the mevalonate pathway and its downstream signaling cascades is a promising strategy to circumvent the MDR signature of IGHV unmutated CLL cells

Genetic connectivity and hybridization with its siter species challenge the current management paradigm of white anglerfish (Lophius piscatorius)

Understanding the inter and intraspecific dynamics of fish populations is essential to promote effective management and conservation actions and to predict adaptation to changing conditions. This is possible through the analysis of thousands of genetic markers, which has proven useful to resolve connectivity among populations. Here, we have tackled this issue in the white anglerfish (Lophius piscatorius), which inhabits the Northeast Atlantic and Mediterranean Sea and coexists with its morphologically almost identical sister species, the black anglerfish (L. budegassa). Our genetic analyses based on 16,000 SNP markers and 700 samples reveal that i) the white anglerfish from the Mediterranean Sea and the Atlantic Ocean are genetically isolated, but that no differentiation can be observed within the later, and that ii) black and white anglerfish naturally hybridize, resulting in a population of about 20% of, most likely sterile, hybrids in some areas. These findings challenge the current paradigm of white anglerfish management, which considers three independent management units within the North East Atlantic and assumes that all mature fish have reproductive potential. Additionally, the northwards distribution of both species, likely due to temperature raises, calls for further monitoring of the abundance and distribution of hybrids to anticipate the effects of climate change in the interactions between both species and their potential resilience

Epidemiological and virological investigation of a Norovirus outbreak in a resort in Puglia, Italy

<p>Abstract</p> <p>Background</p> <p>This paper describes the third large outbreak of Norovirus (NoV) gastroenteritis reported in the Southern Italy region of Puglia.</p> <p>Methods</p> <p>A matched case control study was conducted, on 19 July 2005, for investigating risk factors, using a structured questionnaire on food consumption. A multivariate analysis was conducted to estimate the adjusted Odds Ratios. Laboratory and environmental investigation were also performed.</p> <p>Results</p> <p>On the day of the study 41 cases were identified and 41 controls were enrolled. Controls were matched for age and gender. The mean age of the cases was 26 years old, and 58% were female. The clinical pattern of the disease was characterised by the presence of diarrhoea (95%), vomiting (70%), abdominal pain (51%) and fever (32%). Of the 41 cases included in the study, the majority (65%) were residents of Northern Italian regions. No food samples were available for testing. The matched univariate analysis revealed that cases were more likely to have consumed raw mussels, eggs or ice cubes made of tap water than controls. In the multivariate conditional logistic regression analysis, having eaten raw mussels or ice became more strongly associated with illness.</p> <p>All of the 20 faecal samples collected were tested for NoVs. Eighteen stools (90% of total examined) were positive by RT-PCR, and sequence analysis performed onto 3 samples confirmed the presence of a GGII NoV. No test specific for NoV was performed on water or food samples.</p> <p>Conclusion</p> <p>The most likely hypothesis supported by the findings of the epidemiological investigation was that illness was associated with raw mussels and ice, made with tap water. These hypothesis could not be confirmed by specific microbiologic testing for NoV in food or ice. The lack of clear knowledge of NoV as a major causative agent of epidemic outbreaks of gastroenteritis in Italy is due to the absence of timely reporting of the cases to the local public health offices and the uncommon practice of saving clinical samples for virological analysis after bacteriological testing.</p

Workshop to scope and preselect indicators for criterion D3C3 under MSFD decision (EU) 2017/848 (WKD3C3SCOPE)

The workshop to scope and preselect indicators for Descriptor 3 criterion 3 under MSFD Commission Decision (EU) 2017/848 (WKD3C3SCOPE) provided a platform for experts from the EU member states and relevant regional bodies to meet and support development and progress the assessment methodology, based on a request by the EC (DGENV). WKD3C3SCOPE is the first of a series of three workshops (WKD3C3THRESHOLDS and WKSIMULD3) to provide guidance in relation to operational indicators for MSFD D3C3. The workshop was organized as a series of presentations with intermittent group discussions. On the first day of the workshop the participants discussed what defines a ‘healthy population structure’ for species with different life history traits (ToR a). During the following days, the group discussed and identified relevant D3C3 indicators (ToR b) and developed criteria to select among the identified D3C3 indicators to allow further testing and setting of thresholds at WKD3C3THRESHOLDS (ToR c). The participants found that overall, healthy fish stocks are characterized by high productivity, wide age and size structuring in the population, and the ability to quickly recover from disturbances. The groups noted that environmental factors, along with stock biomass and fishing pressure, influence the productivity and health of a stock, with environment playing a particularly large role in the recruitment of short-lived stocks. It was suggested that the age structure of a stock might be more relevant for evaluating the health of long-lived stocks. However, it was acknowledged that not all stocks have sufficient data to evaluate all proposed indicators, and a single indicator is unlikely to suffice for all stocks. Data availability, species- specific factors and regional or sub-regional variation are thus also important considerations. In relation to ToR b, the participants presented their work on potential indicators including: recruitment time-series, proportion of fish larger than the mean size of first sexual maturation, F rec/Fbar, length distribution L 90, relative proportion of old fish above A 90, indicators of spawner quality, and SSB/R. A discussion on pros/cons, benefits to the population of high or low indicator values, benefits supported by empirical evidence, applicability to data-poor stocks and benefits supported by simulation/theoretical considerations followed the presentations. Finally, in relation to ToR c, the difficulty emerged in ranking the indicators alone without considering the data used to estimate them and a new set of evaluation criteria for use in WKD3C3THRESHOLDS were defined. Based on the outputs of the meeting a list of indicators to be further evaluated has been drafted, which also emphasizes the stocks for which studies have empirically demonstrated effects on productivity. In addition to the listed indicators, indicators of genetic diversity and proportion of fish with parasite infestation were mentioned but to the knowledge of the participants, widespread data for these are currently not publicly available.info:eu-repo/semantics/publishedVersio