• 21st century fisheries management: a spatio-temporally explicit tariff-based approach combining multiple drivers and incentivising responsible fishing

      Kraak, Sarah B. M.; Reid, David G.; Gerritsen, H.D.; Kelly, Ciarán J.; Fitzpatrick, Mike; Codling, Edward A.; Rogan, Emer (Oxford University Press, 2012)
      Traditionally fisheries management has focused on biomass and mortality, expressed annually and across large management units. However, because fish abundance varies at much smaller spatio-temporal scales, fishing mortality can potentially be controlled more effectively if managed at finer scale. The ecosystem approach requires more indicators at finer scales as well. Incorporating ecosystem targets would need additional management tools with potentially conflicting results. We present a simple, integrated, management approach that provides incentives for “good behaviour”. Fishers would be given a number of fishing-impact credits, called real-time incentives (RTIs), to spend according to spatio-temporally varying tariffs per fishing day. RTI quotas and tariffs could be based on commercial stocks and ecosystem targets. Fishers could choose how to spend their RTIs, e.g. by limited fishing in high-catch or sensitive areas or by fishing longer in lower-catch or less sensitive areas. The RTI system does not prescribe and forbid, but instead allows fishers to fish wherever and whenever they want; ecosystem costs are internalized and fishers have to take them into account in their business decisions. We envisage no need for traditional landings or catch quotas for the fleets while operating under the scheme. The approach could facilitate further devolution of responsibility to industry.
    • Age and growth estimates for the starry smoothhound (Mustelus asterias) in the Northeast Atlantic Ocean

      Farrell, E D; Mariani, S; Clarke, M W (Oxford University Press, 2010)
      This study is the first to estimate age, growth and longevity of M. asterias based on interpretation of band pairs in sectioned vertebrae. Age and growth of 106 male and 114 female starry smooth-hound sharks (Mustelus asterias) were estimated by counting band pairs on unstained sectioned vertebrae. Growth curves were fitted to the length-at-age data using the von Bertalanffy and Gompertz models. The 1-parameter von Bertalanffy-L0 provided the best fit for males (L∞ = 104 cm TL, L0 = 30 cm TL and estimated K = 16 0.224) and females (L∞ = 133 cm TL, L0 = 30 cm TL and estimated K = 0.136). Longevity was estimated to be 11.8 and 20.2 years for males and females respectively. The length weight relationship is also presented for 304 male and 424 female M. asterias. The von Bertalanffy model was fitted to weight-at-age data. These estimates can form the basis of future work on the assessment and management of this species.
    • Anthropocene environmental change in an internationally important oligotrophic catchment on the Atlantic seaboard of western Europe

      Dalton, C; O'Dwyer, B; Taylor, D; DeEyto, E; Jennings, E; Chen, G; Poole, R; Dillane, M; McGinnity, P (Elsevier, 2014)
      Oligotrophic catchments with short spatey streams, upland lakes and peaty soils characterise northwest European Atlantic coastal regions. These catchments are important biodiversity refuges, particularly for sensitive diadromous fish populations but are subject to changes in land use and land management practices associated with afforestation, agriculture and rural development. Quantification of the degree of catchment degradation resulting from such anthropogenic impacts is often limited by a lack of long-term baseline data in what are generally relatively isolated, poorly studied catchments. This research uses a combination of palaeolimnological (radiometrically-dated variations in sedimentary geochemical elements, pollen, diatoms and remains of cladocera), census, and instrumental data, along with hindcast estimates to quantify environmental changes and their aquatic impacts since the late 19th century. The most likely drivers of any change are also identified. Results confirm an aquatic biotic response (phyto- and zooplankton) to soil erosion and nutrient enrichment associated with the onset of commercial conifer afforestation, effects that were subsequently enhanced as a result of increased overgrazing in the catchment and, possibly, climate warming. The implications for the health of aquatic resources in the catchment are discussed
    • Assessing the risk of vulnerable species exposure to deepwater trawl fisheries: the case of orange roughy Hoplostethus atlanticus to the west of Ireland and Britain

      Dransfeld, L.; Gerritsen, H.D.; Hareide, N.R.; Lorance, P. (Cambridge University Press, 2013)
      With slow growth rates, late maturity and a high maximum age of 100 years or more, orange roughy can be classified as a vulnerable deepwater fish species that can only sustain low rates of exploitation. Historical patterns of exploitation associated with this species suggest that it is currently not possible to manage its fisheries in the Northeast Atlantic sustainably, and the total allowable catch for orange roughy has been gradually reduced to zero for European fisheries since 2010. Orange roughy to the west of Ireland and Britain occurs on distinct bathymetric features (seamounts, hills and canyons) as well as on flat ground along the continental slope. Productivity-susceptibility analysis (PSA) was performed to evaluate the biological vulnerability of orange roughy in relation to other deepwater species and the risk that recent and current fisheries pose to its populations in the study area. Time-dependant PSA, based on the spatial overlap between orange roughy distribution and recent and current deepwater fisheries demonstrated a strong reduction in risk over time when fisheries stopped directed targeting practices and continued with mixed deepwater trawl fisheries. Some spatial overlap between the species and current fisheries remains, and while the method can show relative risk reduction, it cannot provide information on whether the risk is low enough to allow the recovery of depleted populations.
    • Assessing the status of shallow lakes using an additive model of biomass size spectra

      deEyto, E; Irvine, K (Wiley-Blackwell, 2007)
      1. Planktonic biomass size spectra were used to summarise the ecological quality of six shallow lakes sampled in spring, early summer and late summer. 2. A simple additive model fitted to the data was used to assess the applicability of the size spectrum theory to shallow lake ecosystems. 3. The additive model replicated the hierarchical pattern of biomass predicted by the predator-prey theory of aquatic production, and was a more appropriate model for predicting biomass size spectra than the frequently used linear regression. 4. Lakes with varying ecological quality were a significant source of variation in the additive model, and further research into using size spectra to monitor ecological quality in shallow lakes is warranted. Specifically, the production of size spectra from a wider range of sites is needed to provide greater statistical validation. 5. The use of size spectra can provide an attractive and cost-effective way for classifying lake ecosystems because it circumvents the need for difficult taxonomic description.
    • Assessment of biomarkers in Mytilus edulis to determine Good Environmental Status for implementation of MSFD in Ireland

      Giltrap, M.; Ronan, J.; Hardenberg, S.; Parkes, G.; McHugh, B.; McGovern, E.; Wilson, J.G. (Elsevier, 2013)
      Candidate OSPAR/ICES recommended biomarkers at the level of the individual in Mytilus edulis for determination of good environmental status for MSFD were evaluated against contaminant levels at sites around Ireland. The sites chosen ranged from moderate to low pollution levels, but the actual ranking of the sites varied according to the contaminant levels present. At the most contaminated site, Cork, 4 out of 16 contaminants exceeded the EAC, while at Shannon, no EACs were exceeded. The SOS assay suggested that Cork was the healthiest site with a LT50 of 17.6 days, while SOS for Shannon was 15.6 days. Likewise, condition factors varied among sites and did not always correspond to contaminant-based status. There may be uncertainty in assigning status around the not good:good boundary. This raises potential difficulties not only in the biomarker/contaminant load relationship but also in the reliability of the biomarkers themselves and hence barriers meeting compliance levels.
    • Azaspiracid Shellfish Poisoning: A Review on the Chemistry, Ecology, and Toxicology with an Emphasis on Human Health Impacts

      Twiner, M J; Rehmann, N; Hess, P; Doucette, G J (MDPI AG, 2008)
      Azaspiracids (AZA) are polyether marine toxins that accumulate in various shellfish species and have been associated with severe gastrointestinal human intoxications since 1995. This toxin class has since been reported from several countries, including Morocco and much of western Europe. A regulatory limit of 160 μg AZA/kg whole shellfish flesh was established by the EU in order to protect human health; however, in some cases, AZA concentrations far exceed the action level. Herein we discuss recent advances on the chemistry of various AZA analogs, review the ecology of AZAs, including the putative progenitor algal species, collectively interpret the in vitro and in vivo data on the toxicology of AZAs relating to human health issues, and outline the European legislature associated with AZAs.
    • Bayesian survey-based assessment of North Sea plaice (Pleuronectes platessa): extracting integrated signals from multiple surveys

      Bogaards, J A; Kraak, S B M; Rijnsdorp, A D (Oxford University Press, 2009)
      Dependence on a relatively small sample size is generally viewed as a big disadvantage for survey-based assessments. We propose an integrated catch-at-age model for research vessel data derived from multiple surveys, and illustrate its utility in estimating trends in North Sea plaice abundance and fishing mortality. Parameter estimates were obtained by Bayesian analysis, which allows for estimation of uncertainty in model parameters attributable to measurement error. Model results indicated constant fishing selectivity over the distribution area of the North Sea plaice stock, with decreased selectivity at older age. Whereas separate analyses of survey datasets suggested different biomass trends in the southeast than in the western and central North Sea, a combined analysis demonstrated that the observations in both subareas were compatible and that SSB has been increasing over the period 1996- 2005. The annual proportion of fish that dispersed in a northwesterly direction was estimated to increase from about 10% at age 2 to 33% at age 5 and older. We also found higher fishing mortality rates than reported in ICES assessments, which could be the consequence of inadequate specification of catchability-at-age in this study or underestimated fishing mortality by the conventional ICES assessment, which relies on official landings figures.
    • Biased stock assessment when using multiple, hardly overlapping, tuning series if fishing trends vary spatially

      Kraak, S B M; Daan, N; Pastoors, M A (Oxford University Press, 2009)
      Fishing-effort distributions are subject to change, for autonomous reasons and in response to management regulations. Ignoring such changes in a stock-assessment procedure may lead to a biased perception. We simulated a stock distributed over two regions with inter-regional migration and different trends in exploitation, and tested the performance of Extended Survivors Analysis (XSA) and a statistical catch-at-age model in terms of bias, when spatially restricted tuning series were applied. If we used a single tuning index that covered only the more heavily fished region, estimates of fishing mortality and spawning-stock biomass were seriously biased. If two tuning series each exclusively covering one region were used (without overlap but together covering the whole area), estimates were also biased. Surprisingly, a moderate degree of overlap of spatial coverage of the two tuning indices was sufficient to reduce bias of the XSA assessment substantially. However, performance was best when one tuning series covered the entire stock area.
    • Bioactive agents from marine mussels and their effects on human health

      Grienke, U.; Silke, J.; Tasdemir, D. (Elsevier, 2014)
      The consumption of marine mussels as popular seafood has increased steadily over the past decades. Awareness of mussel derived molecules, that promote health, has contributed to extensive research efforts in that field. This review highlights the bioactive potential of mussel components from species of the genus Mytilus (e.g. M. edulis) and Perna (e.g. P. canaliculus). In particular, the bioactivity related to three major chemical classes of mussel primary metabolites, i.e. proteins, lipids, and carbohydrates, is evaluated. Within the group of proteins the focus is mainly on mussel peptides e.g. those obtained by bio-transformation processes, such as fermentation. In addition, mussel lipids, comprising polyunsaturated fatty acids (PUFAs), are discussed as compounds that are well known for prevention and treatment of rheumatoid arthritis (RA). Within the third group of carbohydrates, mussel polysaccharides are investigated. Furthermore, the importance of monitoring the mussel as food material in respect to contaminations with natural toxins produced by microalgae is discussed
    • Chemical aspects of ocean acidification monitoring in the ICES marine area.

      Hydes, D.J.; McGovern, E.; Walsham, P. (International Council for the Exploration of the Sea, 2013)
      It is estimated that oceans absorb approximately a quarter of the total anthropogenic releases of carbon dioxide to the atmosphere each year. This is leading to acidification of the oceans, which has already been observed through direct measurements. These changes in the ocean carbon system are a cause for concern for the future health of marine ecosystems. A coordinated ocean acidification (OA) monitoring programme is needed that integrates physical, biogeochemical, and biological measurements to concurrently observe the variability and trends in ocean carbon chemistry and evaluate species and ecosystems response to these changes. This report arises from an OSPAR request to ICES for advice on this matter. It considers the approach and tools available to achieve coordinated monitoring of changes in the carbon system in the ICES marine area, i.e. the Northeast Atlantic and Baltic Sea.
    • Chemical characteristics of water masses in the Rockall Trough

      McGrath, Triona; Nolan, Glenn; McGovern, Evin (Elsevier, 2011)
      Direct observations of physical and chemical data in the Rockall Trough during February of 2008, 2009 and 2010 are presented. Results are compared to a similar WOCE transect, AR24, completed in November/December 1996. Temperature and salinity data have been used to identify the water masses present in the Trough, and have been combined with nutrient (nitrate, nitrite, phosphate, silicate) and oxygen data to produce a table outlining the chemical characteristics of each of the water masses. Eastern North Atlantic Water (ENAW) moving north through the Trough gains nutrients from a branch of the North Atlantic Current (NAC). Mediterranean Water (MW) was identified as a warm saline core, with characteristically low oxygen and low preformed nutrients along the Irish continental shelf break near 53°N. Found at a similar density level at the southern entrance to the Trough, Sub Arctic Intermediate Water (SAIW) has relatively high oxygen and preformed nutrients, likely entrained from the subpolar gyre when it was formed. LSW was identified as a prominent water mass between 1500–2000 m deep, with characteristically high oxygen content. Lower silicate, and to a lesser extent preformed nitrate, in 2009 coincide with a freshening of Labrador Sea Water (LSW) relative to other years, and could indicate a stronger influence from the Labrador Current when it was formed. Finally, traces of Antarctic Bottom Water (AABW) were found as far north as 53°N, indicated by a sharp increase in nutrient concentrations, particularly silicate in the deepest parts of the Trough.
    • Combined oral toxicity of azaspiracid-1 and yessotoxin in female NMRI mice

      Aasen, J A B; Espenes, A; Miles, C O; Samdal, I A; Hess, P; Aune, T (Elsevier, 2011)
      For many years, the presence of yessotoxins (YTXs) in shellfish has contributed to the outcome of the traditional mouse bioassay and has on many occasions caused closure of shellfisheries. Since YTXs do not appear to cause diarrhoea in man and exert low oral toxicity in animal experiments, it has been suggested that they should be removed from regulation. Before doing so, it is important to determine whether the oral toxicity of YTXs is enhanced when present together with shellfish toxins known to cause damage to the gastrointestinal tract. Consequently, mice were given high doses of YTX, at 1 or 5 mg/kg body weight, either alone or together with azaspiracid-1 (AZA1) at 200 μg/kg. The latter has been shown to induce damage to the small intestine at this level. The combined exposure caused no clinical effects, and no pathological changes were observed in internal organs. These results correspond well with the very low levels of YTX detected in internal organs by means of LCMS/MS and ELISA after dosing. Indeed, the very low absorption of YTX when given alone remained largely unchanged when YTX was administered in combination with AZA1. Thus, the oral toxicity of YTX is not enhanced in the presence of sub-lethal levels of AZA1.
    • Comparative effects of the marine algal toxins azaspiracid-1, -2, and -3 on Jurkat T lymphocyte cells

      Twiner, M.; El-Ladki, R.; Kilcoyne, J.; Doucette, G.J. (ACS Publications, 2012)
      Azaspiracids (AZA) are polyether marine toxins of dinoflagellate origin that accumulate in shellfish and represent an emerging human health risk. Although monitored and regulated in many European and Asian countries, there are no monitoring programs or regulatory requirements in the United States for this toxin group. This did not prove to be a problem until June 2009 when AZAs were identified in US seafood for the first time resulting in human intoxications and further expanding their global distribution. Efforts are now underway in several laboratories to better define the effects and mechanism(s) of action for the AZAs. Our investigations have employed Jurkat T lymphocyte cells as an in vitro model to characterize the toxicological effects of AZA1, AZA2, and AZA3. Cytotoxicity experiments employing a metabolically based dye (i.e., MTS) indicated that AZA1, AZA2, and AZA3 each elicited a lethal response that was both concentration- and time-dependent, with EC50 values in the sub- to low nanomolar range. On the basis of EC50 comparisons, the order of potency was as follows: AZA2 > AZA3 > AZA1, with toxic equivalence factors (TEFs) relative to AZA1 of 8.3-fold and 4.5-fold greater for AZA2 and AZA3, respectively. Image analysis of exposed cells using Nomarski differential interference contrast (DIC) imaging and fluorescent imaging of cellular actin indicated that the morphological effects of AZA1 on this cell type are unique relative to the effects of AZA2 and AZA3. Collectively, our data support the growing body of evidence suggesting that natural analogues of AZA are highly potent and that they may have multiple molecular targets.
    • Complex pattern of genetic structuring in the Atlantic salmon (Salmo salar L.) of the River Foyle system in northwest Ireland: disentangling the evolutionary signal from population stochasticity

      Ensing, Dennis; Prodöhl, Paulo A.; McGinnity, Philip; Boylan, Patrick; O’Maoiléidigh, Niall; Crozier, Walter W. (Blackwell Publishing Ltd., 2011)
      Little is known about the microevolutionary processes shaping within river population genetic structure of aquatic organisms characterized by high levels of homing and spawning site fidelity. Using a microsatellite panel, we observed complex and highly significant levels of intrariver population genetic substructure and Isolation-by-Distance, in the Atlantic salmon stock of a large river system. Two evolutionary models have been considered explaining mechanisms promoting genetic substructuring in Atlantic salmon, the member-vagrant and metapopulation models. We show that both models can be simultaneously used to explain patterns and levels of population structuring within the Foyle system. We show that anthropogenic factors have had a large influence on contemporary population structure observed. In an analytical development, we found that the frequently used estimator of genetic differentiation, FST, routinely underestimated genetic differentiation by a factor three to four compared to the equivalent statistic Jost's Dest (Jost 2008). These statistics also showed a near-perfect correlation. Despite ongoing discussions regarding the usefulness of “adjusted” FST statistics, we argue that these could be useful to identify and quantify qualitative differences between populations, which are important from management and conservation perspectives as an indicator of existence of biologically significant variation among tributary populations or a warning of critical environmental damage.
    • Critical Role of the Matricellular Protein SPARC in Mediating Erythroid Progenitor Cell Development in Zebrafish

      Ceinos, Rosa M.; Torres, Eva; Chamorro, Ruben; Novoa, Beatriz; Figueras, Antonio; Ruane, N. M.; Rotllant, Josep (Karger, 2012)
      Sparc (Osteonectin) is a multifunctional matricellular glycoprotein expressed by many differentiated cells. Members of this family mediate cell-matrix interactions rather than acting as structural components of the extracellular matrix and therefore can influence many remodelling events, including haematopoiesis. We have investigated the role of sparc in embryonic haematopoiesis, using a morpholino antisense oligonucleotidebased knockdown approach. Knockdown of sparc function resulted in specific erythroid progenitor cell differentiation defects that were highlighted by changes in gene expression and morphology, which could be rescued by injection of sparc mRNA. Furthermore, a comparison of blood phenotypes of sparc and fgfs knockdowns with similar defects and the sparc rescue of fgf21 blood phenotype places sparc downstream of fgf21 in the genetic network regulating haematopoiesis in zebrafish. These results establish a role for an extracellular matrix protein (Sparc) as an important regulator of embryonic haematopoiesis during early development in zebrafish.
    • Defining value per unit effort in mixed métier fisheries

      Davies, S.; Minto, C.; Officer, R.; Lordan, C. (Elsevier, 2015)
      Value achieved from time spent at sea is a central driver of fishing decisions and fishing behaviors. Value per unit effort (VPUE) is an important indicator of economic performance in itself and a useful metric within integrated mixed fisheries models. A time series of Irish first sale prices and total per trip landings values (VPT) highlight heterogeneity in fish prices and VPTs achieved by the Irish fleet spatially and temporally, as well as variability with species targeting. This investigation compared models to standardize fishing trip VPUE accounting for species targeting (métier groupings), engine power (a kW proxy for vessel size), seasonal and annual variability, fishing effort, and individual vessels (encompassing variability in vessel characteristics and skipper effects). Linear mixed effects models incorporating random vessel effects and within-group variance between métier groupings performed best at describing the variability in the dataset. All investigated factors were important in explaining variability, and thus important in standardizing VPUE. Models incorporating fishing days (days with reported fishing activity) and engine power as separate variables resulted in improved AIC values. Therefore, fishing days were considered to be the most appropriate effort measure to generate VPUE. The effort unit traditionally applied in measures of per unit effort, fishing hours, performed comparatively poorly in relation to VPT.
    • Definition, dynamics and stability of métiers in the Irish otter trawl fleet

      Davie, Sarah; Lordan, Colm (Elsevier, 2011)
      The Irish otter trawl fleet operates in a complex multi-species multi-gear fishery, spanning a wide geographic area, and involving around 275 trawlers. Factorial and clustering methods were applied to 2003 fishing trip data to define thirty-three métiers. Definitions were based on six trip characteristics taken from logbooks, namely: fishing gear, mesh size, vessel length, species composition, area, and month. Métiers exploiting demersal species or species groups are characterised by single vessel bottom otter trawls, typically with mesh sizes of 70 mm or more, operating year round. This includes nine Nephrops dominated métiers highlighting the importance of this species to the fleet. Many demersal métiers are characterised by groups of species, such as mixed whitefish or slope species. Métiers exploiting pelagic species are often focussed on single species, and are typically seasonal, mid-water trawling (often paired) with mesh sizes less than 70 mm. Pelagic métiers account for the majority of landings by over an order of magnitude in several cases. Demersal métiers account for the majority of fishing trips and effort, (primarily Nephrops métiers), and vessels (primarily mixed species métiers). The new métier definitions were found to be appropriate remained relevant despite declining fleet landings and effort between 2003 and 2006. Species compositions within these métiers have generally remained similar to the proportions defined in 2003. These robust métier definitions present opportunities to improve fisheries sampling, assessment and management. Although métiers pose complexity challenge for such applications they can be used the building blocks for appropriate management units.
    • Demographics and landscape features determine intrariver population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland

      Dillane, E; McGinnity, P; Coughlan, J P; Cross, M C; deEyto, E; Kenchington, E; Prodöhl, P; Cross, T F (Wiley-Blackwell, 2008)
      Contemporary genetic structure of Atlantic salmon (Salmo salar L.) in the River Moy in Ireland is shown here to be strongly related to landscape features and population demographics, with populations being defined largely by their degree of physical isolation and their size. Samples of juvenile salmon were collected from the 17 major spawning areas on the river Moy and from one spawning area in each of five smaller nearby rivers. No temporal allele frequency differences were observed within locations for 12 microsatellite loci, whereas nearly all spatial samples differed significantly suggesting that each was a separate population. Bayesian clustering and landscape genetic analyses suggest that these populations can be combined hierarchically into five genetically informative larger groupings. Lakes were found to be the single most important determinant of the observed population structure. Spawning area size was also an important factor. The salmon population of the closest nearby river resembled genetically the largest Moy population grouping. In addition we showed that anthropogenic influences on spawning habitats, in this case arterial drainage, can affect relationships between populations. Our results show that Atlantic salmon biodiversity can be largely defined by geography and thus knowledge of landscape features (for example, as characterised within Geographical Information Systems) has the potential, to predict population structure in other rivers without an intensive genetic survey, or at least to help direct sampling. This approach of combining genetics and geography, for sampling and in subsequent statistical analyses, has wider application to the investigation of population structure in other freshwater/anadromous fish species and possibly in marine fish and other organisms.
    • Diatom assemblages and their associated environmental factors in upland peat forest rivers

      O'Driscoll, Connie; de Eyto, Elvira; Rodgers, Michael; O'Connor, Mark; Asam, Zaki-ul-Zaman; Xiao, Liwen (Elsevier, 2012)
      The acid-sensitive upland blanket peat catchments are important habitats for diatom assemblages. In this study, the distribution patterns of epilithic diatom assemblages in the streams of upland forested blanket peat in north-west of Ireland are presented and the associated environmental factors are discussed. A total of 43 sites in 16 rivers were sampled. Multivariate analysis highlighted alkalinity and conductivity as the main physicochemical drivers of riverine diatom assemblages. Contrary to expectations nutrients were not found to have a major influence on the diatoms. A major flood event had a significant impact on the diatom assemblage, and one year after the event, long stalked diatom taxa were still largely absent from the river, indicating that floods could be one of the important factors affecting diatom assemblages. However, the ecological status of the affected sites, as determined by the EQR, did not alter from before to after the flood. The results of this study could be applied to similar acid-sensitive upland peat forest catchments and used as the benchmark to assess the impact of forest operations and peat degradation on ecological status.