• Field and mesocosm trials on passive sampling for the study of adsorption and desorption behaviour of lipophilic toxins with a focus on OA and DTX1

      Fux, E; Marcaillou, C; Mondeguer, F; Bire, R; Hess, P (Elsevier, 2008)
      It has been demonstrated that polymeric resins can be used as receiving phase in passive samplers designed for the detection of lipophilic marine toxins at sea and was referred to as solid phase adsorption toxin tracking (SPATT). The present study describes the uptake and desorption behaviour of the lipophilic marine toxins okadaic acid (OA) and dinophysistoxin-1 (DTX1) from Prorocentrum lima cultures by five styrene—divinylbenzene based polymeric resins Sepabeads® SP850, Sepabeads® SP825L, Amberlite® XAD4, Dowex® Optipore® L-493 and Diaion® HP-20. All resins accumulated OA and DTX1 from the P. lima culture with differences in adsorption rate and equilibrium rate. Following statistical evaluation, HP-20, SP850 and SP825L demonstrated similar adsorption rates. However, possibly due to its larger pore size, the HP-20 did not seem to reach equilibrium within 72h exposure as opposed to the SP850 and SP825L. This was confirmed when the resins were immersed at sea for 1 week on the West Coast of Ireland. Furthermore, this work also presents a simple and efficient extraction method suitable to SPATT samplers exposed to artificial or natural culture media.
    • First Detection of Paralytic Shellfish Poisoning (PSP) Toxins in Icelandic Mussels (Mytilus edulis): Links to Causative Phytoplankton Species.

      Burrell, Stephen; Gunnarsson, Thor; Gunnarsson, Karl; Clarke, Dave; Turner, Andrew D. (Elsevier, 2013)
      Paralytic shellfish poisoning (PSP) toxins were detected in blue mussels (Mytilus edulis) from two harvesting areas, Eyjafjordur on the north coast and Breidafjordur on the west coast of Iceland in 2009. During a bloom of Alexandrium spp. at both locations in June of that year, blue mussels were found to be contaminated with paralytic shellfish toxins (PSTs), leading to extensive closures of these harvesting sites. Phytoplankton data taken during this time showed the presence of large numbers of A. tamarense, with smaller numbers of A. ostenfeldii also being detected. Mussel samples were analysed by mouse bioassay (MBA) and liquid chromatography with fluorescence detection (LC-FLD). Toxicity over 10 times the European Union (EU) regulatory limit was observed in samples from Eyjafjordur while levels over 4 times this limit were detected in samples from Breidafjordur. The toxin profile determined by LC-FLD was found to be composed primarily of the carbamate toxins gonyautoxin-2,3 (GTX-2,3). Saxitoxin (STX) was also detected in all samples analysed and was the second most abundant toxin present. Gonyautoxin-1,4 (GTX-1,4) was detected at lower concentrations in half the samples analysed from both locations. Comparison is made between predicted toxin profiles from these algal species and the toxin profiles determined through LC-FLD analysis. These results represent the first identification and PST profile determination in shellfish harvested from Icelandic waters.
    • First estimates of age, growth, and maturity of boarfish (Capros aper): a species newly exploited in the Northeast Atlantic

      White, Emma; Minto, Cóilín; Nolan, Conor P.; King, Erna; Mullins, Eugene; Clarke, Maurice (Oxford University Press, 2011)
      Boarfish in the Northeast Atlantic have recently been exploited commercially for fishmeal. It is a sexually dimorphic species with an estimated maximum age of 26 years, late age at maturity (A50 = 5.25 years), relatively fast rate of growth (K = 0.186 year−1), and a small asymptotic length (L∞ = 128.9 mm).
    • Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon

      McGinnity, Philip; Prodohl, Paulo; Ferguson, Andy; Hynes, Rosaleen; Ó Maoiléidigh, Niall; Baker, Natalie; Cotter, Deirdre; O'Hea, Brendan; Cooke, Declan; Rogan, Ger; Taggart, John; Cross, Tom (The Royal Society, 2003)
      The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a twogeneration experiment examining the estimated lifetime successes, relative to wild natives, of farm, F1 and F2 hybrids and BC1 backcrosses to wild and farm salmon. Offspring of farm and ‘hybrids’ (i.e. all F1, F2 and BC1 groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC1 wild) of that of wild salmon, indicating additive genetic variation for survival. Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and ‘hybrids’ produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations.
    • How much of the seabed is impacted by mobile fishing gear? Absolute estimates from Vessel Monitoring Systems (VMS) point data

      Gerritsen, H.D.; Minto, C.; Lordan, C. (Oxford University Press, 2013)
      Demersal trawling impacts extensively on the seabed and the extent and frequency of this impact can be assessed using Vessel Monitoring Systems (VMS) data (positional data of fishing vessels). Existing approaches interpolate fishing tracks from consecutive VMS locations (track interpolation) and/or aggregate VMS point data in a spatial grid (point summation). Track interpolation can be quite inaccurate at the current 2-hour time interval between VMS records, leading to biased estimates. Point summation approaches currently only produce relative estimates of impact and are highly sensitive to the grid size chosen We propose an approach that provides absolute estimates of trawling impact from point data and is not sensitive to an arbitrary choice of grid cell size. The method involves applying a nested grid and estimating the swept area (area covered by fishing gear) for each VMS point. We show that the ratio of the swept area to the surface area of a cell can be related to the proportion of the seabed that was impacted by the gear a given number of times. We validate the accuracy of this swept-area ratio approach using known vessel tracks and apply the method to international VMS data in the Celtic Sea.
    • Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs

      Donohoe, O. H.; Henshilwood, K.; Way, K.; Hakimjavadi, R.; Stone, D. M.; Walls, D. (PLoS ONE, 2015)
      MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA) genes. Deep sequencing of small RNA fractions prepared from in vitro CyHV-3 infections led to the identification of potential miRNAs and miRNA–offset RNAs (moRNAs) derived from some bioinformatically predicted pre-miRNAs. DNA microarray hybridization analysis, Northern blotting and stem-loop RT-qPCR were then used to definitively confirm that CyHV-3 expresses two pre-miRNAs during infection in vitro. The evidence also suggested the presence of an additional four high-probability and two putative viral pre-miRNAs. MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. Candidate homologues of some CyHV-3 pre-miRNAs were identified in CyHV-1 and CyHV-2. This is the first report of miRNA and moRNA genes encoded by members of the Alloherpesviridae family, a group distantly related to the Herpesviridae family. The discovery of these novel CyHV-3 genes may help further our understanding of the biology of this economically important virus and their encoded miRNAs may have potential as biomarkers for the diagnosis of latent CyHV-3.
    • Identifying functional stakeholder clusters to maximise communication for the Ecosystem Approach to Fisheries Management

      Duggan, Deirdre E.; Farnsworth, Keith D.; Kraak, Sarah B. M. (Elsevier, 2013)
      Interaction with ecological models can improve stakeholder participation in fisheries management. Problems exist in efficiently communicating outputs to stakeholders and an objective method of structuring stakeholder differences is lacking. This paper aims to inform the design of a multi-user communication interface for fisheries management by identifying functional stakeholder groups. Intuitive categorisation of stakeholders, derived from survey responses, is contrasted with an evidence-based method derived from analysis of stakeholder literature. Intuitive categorisation relies on interpretation and professional judgement when categorising stakeholders among conventional stakeholder groups. Evidence-Based categorisation quantitatively characterises each stakeholder with a vector of four management objective interest strength values (Yield, Employment, Profit and Ecosystem Preservation). Survey respondents agreed little in forming intuitive groups and the groups were poorly defined and heterogeneous in interests. In contrast the Evidence-Based clusters were well defined and largely homogeneous, so more useful for identifying functional relations with model outputs. The categorisations lead to two different clusterings of stakeholders and suggest unhelpful stereotyping of stakeholders may occur with the Intuitive categorisation method. Stakeholder clusters based on literature-evidence show a high degree of common interests among clusters and is encouraging for those seeking to maximise dialogue and consensus forming.
    • Impact of early infestation with the salmon louse Lepeophtheirus salmonis on the subsequent survival of outwardly migrating Atlantic salmon smolts from a number of rivers on Ireland's south and west coasts

      Jackson, D.; Cotter, D.; Ó Maoiléidigh, N.; O'Donohoe, P.; White, J.; Kane, F.; Kelly, S.; McDermott, T.; McEvoy, S.; Drumm, A.; Cullen, A. (Elsevier, 2011)
      The potential impact of sea lice infestation on outwardly migrating Atlantic salmon smolts has been investigated by treating populations of ranched salmon, prior to release, with a prophylactic sea lice treatment conferring protection from sea lice infestation, for up to 9 weeks. Established populations of ranched Atlantic salmon with well described rates of return were chosen to investigate the potential contribution of early infestation with the salmon louse, Lepeophtheirus salmonis to mortality in Atlantic salmon. Results of five releases from four locations are presented and compared with a time series of releases from Lough Furnace in Newport, County Mayo. The results of this study would suggest that infestation of outwardly migrating salmon smolts with the salmon louse (L. salmonis) was a minor component of the overall marine mortality in the stocks studied.
    • Impact of Lepeophtheirus salmonis infestations on migrating Atlantic salmon, Salmo salar L., smolts at eight locations in Ireland with an analysis of lice-induced marine mortality

      Jackson, D; Cotter, D; Newell, J; McEvoy, S; O'Donohoe, P; Kane, F; McDermott, T; Kelly, S; Drumm, A (John Wiley and Sons, 2013)
      Sea lice infestation as a source of marine mortality of outwardly migrating Atlantic salmon smolts has been investigated by treating groups of ranched salmon, prior to release, with a prophylactic sea lice treatment conferring protection from sea lice infestation. A number of studies have been carried out in Ireland using both established ranched populations and groups of hatchery reared fish imprinted for 5–8 weeks in the sites of experimental releases. In this study, data on 352 142 migrating salmon from twenty-eight releases, at eight locations along Ireland's South and West coasts covering a 9-year period (2001 to 2009) are reviewed. Both published and new data are presented including a previously unpublished time series. The results of a meta-analysis of the combined data suggest that while sea lice-induced mortality on outwardly migrating smolts can be significant, it is a minor and irregular component of marine mortality in the stocks studied and is unlikely to be a significant factor influencing conservation status of salmon stocks.
    • Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction

      McGinnity, P; Jennings, E; deEyto, E; Allott, N; Samuelsson, P; Rogan, G; Whelan, K; Cross, T (Royal Society Publishing, 2009)
      The assessment report of the 4th International Panel on Climate Change confirms that global warming is strongly affecting biological systems and that 20–30% of species risk extinction from projected future increases in temperature. It is essential that any measures taken to conserve individual species and their constituent populations against climate-mediated declines are appropriate. The release of captive bred animals to augment wild populations is a widespread management strategy for many species but has proven controversial. Using a regression model based on a 37-year study of wild and sea ranched Atlantic salmon (Salmo salar) spawning together in the wild, we show that the escape of captive bred animals into the wild can substantially depress recruitment and more specifically disrupt the capacity of natural populations to adapt to higher winter water temperatures associated with climate variability. We speculate the mechanisms underlying this seasonal response and suggest that an explanation based on bio-energetic processes with physiological responses synchronized by photoperiod is plausible. Furthermore, we predict, by running the model forward using projected future climate scenarios, that these cultured fish substantially increase the risk of extinction for the studied population within 20 generations. In contrast, we show that positive outcomes to climate change are possible if captive bred animals are prevented from breeding in the wild. Rather than imposing an additional genetic load on wild populations by releasing maladapted captive bred animals, we propose that conservation efforts should focus on optimizing conditions for adaptation to occur by reducing exploitation and protecting critical habitats. Our findings are likely to hold true for most poikilothermic species where captive breeding programmes are used in population management.
    • Improved Isolation Procedure for Azaspiracids from Shellfish, Structural Elucidation of Azaspiracid-6 and Stability studies

      Kilcoyne, Jane; Keogh, Adela; Clancy, Ger; Le Blanc, Pat; Burton, Ian; Quilliam, Michael A.; Hess, Philipp; Miles, Christopher O. (ACS Publications, 2012)
      Azaspiracids are a group of lipophilic polyether toxins produced by the small dinoflagellate Azadinium spinosum. They may accumulate in shellfish and can result in illnesses when consumed by humans. Research into analytical methods, chemistry, metabolism, and toxicology of azaspiracids has been severely constrained by the scarcity of high-purity azaspiracids. Consequently, since their discovery in 1995, considerable efforts have been made to develop methods for the isolation of azaspiracids in sufficient amounts and purities for toxicological studies, in addition to the preparation of standard reference materials. A seven-step procedure was improved for the isolation of azaspiracids-1–3 (1, 2, and 3) increasing recoveries 2-fold as compared to previous methods and leading to isolation of sufficiently purified azaspiracid-6 (6) for structural determination by NMR spectroscopy. The procedure, which involved a series of partitioning and column chromatography steps, was performed on 500 g of Mytilus edulis hepatopancreas tissue containing 14 mg of 1. Overall yields of 1 (52%), 2 (43%), 3 (43%), and 6 (38%) were good, and purities were confirmed by NMR spectroscopy. The structure of 6 was determined by one- and two-dimensional NMR spectroscopy and mass spectrometry. The stability of 6 relative to 1 was also assessed in three solvents in a short-term study that demonstrated the greatest stability in aqueous acetonitrile.
    • Inferring marine distribution of Canadian and Irish Atlantic salmon (Salmo salar L.) in the North Atlantic from tissue concentrations of bio-accumulated Caesium 137

      Spares, Aaron D.; Reader, Jeffery M.; Stokesbury, Michael J.W.; McDermott, Tom; Zikovsky, Lubomir; Dadswell, Michael J. (Oxford University Press, 2007)
      Atlantic salmon returning from marine migrations to eastern Canada and western Ireland during 2002 and 2003 were analysed for tissue concentrations of bio-accumulated caesium 137 (137Cs). Salmon from Canadian and Irish waters demonstrated concentrations (0.20 ± 0.14 Bq kg-1 and 0.19 ± 0.09 Bq kg-1, mean ± s.d., respectively) suggesting similar oceanic feeding distributions during migration. Canadian aquaculture escapees had a similar mean tissue concentration (0.28 ± 0.22 Bq kg-1), suggesting migration with wild salmon. However, significantly higher concentrations in 1-sea-winter (1SW) escapees (0.43 ± 0.25 Bq kg-1) may alternatively suggest feeding within local estuaries. High concentrations in some Canadian 1SW salmon indicated trans-Atlantic migration. Low concentrations of Canadian multi-sea-winter (MSW) salmon suggested a feeding distribution in the Labrador and Irminger Seas before homeward migration, because those regions have the lowest surface water 137Cs levels. Estimates of wild Canadian and Irish salmon feeding east of the Faroes (~8oW) were 14.2% and 10.0% (1SW, 24.7% and 11.5%; MSW, 2.9% and 0.0%), respectively. We propose that most anadromous North Atlantic salmon utilize the North Atlantic Gyre for marine migration and should be classified as a single trans-Atlantic straddling stock.
    • Inorganic carbon and pH levels in the Rockall Trough 1991-2010

      McGrath, Triona; Kivimäe, Caroline; Tanhua, Toste; Cave, Rachel R.; McGovern, Evin (Elsevier, 2012)
      The accumulation of anthropogenic CO2 in the oceans is altering seawater carbonate chemistry. Investigation and monitoring of the carbonate parameters is therefore necessary to understand potential impacts on ocean ecosystems. Total alkalinity (AT) and dissolved inorganic carbon (CT) were sampled across the Rockall Trough in Feb 2009 (CE0903) and Feb 2010 (CE10002) as part of a baseline study of inorganic carbon chemistry in Irish shelf waters. The results have been compared with data from WOCE surveys A01E (Sept 1991), A01 (Dec 1994), AR24 (Nov 1996) and A24 (June 1997). The 2009 and 2010 datasets provide a snapshot of the biogeochemical parameters which can act as a baseline of inorganic carbon and acidity levels in surface waters of the Rockall Trough in late winter for future comparison since previous surveys in the area have been affected by biological activity. The dataset also offers the possibility to compare decadal changes in subsurface waters. The temporal evolution of anthropogenic carbon (D Cant) between the 1990s and 2010 was evaluated using two separate methods; (i) a comparison of the concentrations of CT between surveys, after correcting it for remineralisation of organic material and formation and dissolution of calcium carbonate (D CT-abio) and (ii) an extended Multiple Linear Regression was used to calculate the D Cant (D Cant eMLR). There was an increase in D CT-abio and D Cant eMLR of 1874 umol kg1 and1974 umol kg1, respectively, in the subsurface waters between 1991 and 2010, equivalent to a decrease of 0.0407± 0.003 pH units over the 19 year period. There was an increasein both D CT-abio and D Cant eMLR of 874 umol kg1 in Labrador Sea Water (LSW) in the Trough between 1991 and 2010, and LSW has acidified by 0.0297±0.002 pH units over the same time period. A reduction in calcite and aragonite saturation states was observed, which may have implications for calcifying organisms in the region.
    • An integrated approach to the toxicity assessment of Irish marine sediments. Application of porewater Toxicity Identification Evaluation (TIE) to Irish marine sediments.

      Macken, A; Giltrap, M; Foley, B; McGovern, E; McHugh, B; Davoren, M (Elsevier, 2009)
      An integrated approach to the ecotoxicological assessment of Irish marine sediments was carried out between 2004 and 2007. Phase I Toxicity Identification Evaluation (TIE) of sediment porewaters from two sites on the east coast of Ireland were conducted. Initial Tier I screening of three Irish sites identified the need for TIE after significant toxicity was observed with Tisbe battagliai and the Microtox® assay at two of the assayed sites (Alexandra Basin and Dunmore East). Porewaters classified as toxic were characterised using four manipulations, ethylenediaminetetraacetic acid (EDTA) chelation, sodium thiosulphate addition, C18 Solid Phase Extraction (SPE) and Cation Exchange (CE) SPE. Prior to initial testing, and TIE manipulations, all porewater samples were frozen at -20 ºC for several months until required. After initial Tier I testing Alexandra Basin porewater was classified as highly toxic by both assays while Dunmore East porewater only warranted a TIE with T. battagliai. Results of TIE manipulations for Alexandra Basin porewater and the Microtox® Basic test were inconclusive. The toxicity of the porewater in this assay was significantly reduced after freezing. Three experimental episodes were conducted with one month between each for the Alexandra Basin porewater. After each month of freezing the baseline toxicity was further reduced in the Microtox® assay, therefore it was not possible to draw accurate conclusions on the nature of the active contaminants in the sample. However, toxicity to T. battalgiai did not change after storage of the porewater. The C18 and CE SPE decreased the toxicity of Alexandra Basin porewater to the copepod indicating that both organic and cationic compounds (e.g. metals) were active in the sample. Dunmore East porewater was assayed with T. battalgiai and again a combination of organic and inorganic compounds were found to be partly responsible for the observed toxicity (C18, CE SPE and EDTA reduced toxicity). Results from these TIEs provide insight into the complexity of interpreting marine TIE data from porewater studies where mixtures of unknown substances are present.
    • Integrating vessel monitoring systems (VMS) data with daily catch data from logbooks to explore the spatial distribution of catch and effort at high resolution.

      Lordan, C; Gerritsen, H.D. (Oxford University Press, 2011)
      Vessel monitoring systems (VMS) automatically collect positional data from fishing vessels. The VMS data can be linked to catch data from logbooks to provide a census of spatially resolved catch-and-effort data. We explore and validate the most appropriate and practical method for integrating Irish VMS and logbook data. A simple speed rule is applied to identify VMS records that correspond to fishing activity. These data are then integrated with the catch data from logbooks using date and vessel identifier. A number of assumptions were investigated, and the resulting distribution maps of catch and effort appear to be unbiased. The method is illustrated with an example of a time-series of spatially explicit catch-per-unit-effort (cpue) estimates. The proposed method is relatively simple and does not require specialist software or computationally intensive methods. It will be possible to generalize this approach to similar datasets that are available within the EU and many other regions. Analysis of integrated VMS and logbook data will allow fisheries data to be analysed on a considerably finer spatial scale than was possible in the past, which opens up a range of potential applications.
    • Lessons for fisheries management from the EU cod recovery plan

      Kraak, Sarah B. M.; Bailey, Nick; Cardinale, Massimiliano; Darby, Chris; De Oliveira, José A. A.; Eero, Margit; Graham, Norman; Holmes, Steven; Jakobsen, Tore; Kempf, Alexander; Kirkegaard, Eskild; Powell, John; Scott, Robert D.; Simmonds, E. John; Ulrich, Clara; Vanhee, Willy; Vinther, Morten (Elsevier, 2012)
      The performance of the EU long-term management plan for cod stocks, in force since 2009, is analysed focusing on the human and institutional factors. The plan operates through landings quotas (TACs) and effort restrictions following a Harvest Control Rule, and deploys a novel instrument allowing Member States to ‘buy back’ or increase fishing effort for fleet segments engaged in cod-avoidance measures. The stipulated fishing mortality reductions have not been achieved. On the positive side, the ‘buy-back’ instrument has led to increased uptake of selective gear and implementation of permanent and real-time temporary closures. On the negative side, ignoring the dimension of fishers as reactive agents in the design, the impact assessment, and the annual implementation of the measures has contributed to the failure to adequately implement the plan and achieve its objectives. The main problem is that the landings quotas taken in a mixed fishery did not limit catches because fishers were incentivised to continue fishing and discard overquota catch while quota for other species was available. The effort limitations intended to reduce this effect were insufficient to adequately limit fishing mortality in targeted fisheries, although fishers experienced them as prohibiting the full uptake of other quotas. Recommendations for future plans include (i) management through catch rather than landings quotas, (ii) the internalisation of the costs of exceeding quotas, (iii) use of more selective gear types, (iv) the development of appropriate metrics as a basis for regulatory measures and for evaluations, (v) participatory governance, (vi) fishery-based management, (vii) flexibility in fishing strategy at vessel level.
    • ‘Linking Herring’: do we really understand plasticity?

      Dickey‐Collas, M; Clarke, M; Slotte, A (Oxford University Press, 2009)
      The symposium was organized to link our understanding of herring biology, population dynamics, and exploitation in the context of ecosystem complexity. It is beyond argument that herring play a pivotal role in shaping the structure and dynamics of many boreal continental-shelf ecosystems. Therefore, in moving to an ecosystem approach to fishery management, the time seemed right for ICES to hold another herring symposium. Since the last ICES symposia on herring in the 1960s (“Herring Symposium”, 1961; “Biology of Early Stages and Recruitment Mechanisms of Herring”, 1968), many of the old paradigms have been rejected, and substantial progress has been made by striking out along new avenues. In addressing this particular topic, we were also able to follow on from the decadal herring symposia series held in North America, and thus cover new research from both the ICES and PICES communities. The symposium took place from 26 to 29 August 2008, at the National University of Ireland, Galway, Ireland.
    • A Low-Complexity Mosaicing Algorithm for Stock Assessment of Seabed-Burrowing Species

      Corrigan, D.; Sooknanan, K.; Doyle, J.; Lordan, C.; Kokaram, A. (IEEE Xplore, 2018)
      This paper proposes an algorithm for mosaicing videos generated during stock assessment of seabed-burrowing species. In these surveys, video transects of the seabed are captured and the population is estimated by counting the number of burrows in the video. The mosaicing algorithm is designed to process a large amount of video data and summarize the relevant features for the survey in a single image. Hence, the algorithm is designed to be computationally inexpensive while maintaining a high degree of robustness. We adopt a registration algorithm that employs a simple translational motion model and generates a mapping to the mosaic coordinate system using a concatenation of frame-by-frame homographies. A temporal smoothness prior is used in a maximum a posteriori homography estimation algorithm to reduce noise in the motion parameters in images with small amounts of texture detail. A multiband blending scheme renders the mosaic and is optimized for the application requirements. Tests on a large data set show that the algorithm is robust enough to allow the use of mosaics as a medium for burrow counting. This will increase the verifiability of the stock assessments as well as generate a ground truth data set for the learning of an automated burrow counting algorithm.
    • Managing a complex population structure: exploring the importance of information from fisheries-independent sources

      Hintzen, N.T.; Roel, B.; Benden, D.; Clarke, M.; Egan, A.; Nash, R.D.M.; Rohlf, N.; Hatfield, E.M.C. (Oxford University Press, 2014)
      Natural resource managers aim to manage fish stocks at sustainable levels. Often, management of these stocks is based on the results of analytical stock assessments. Accurate catch data, which can be attributed to a specific population unit and reflects the population structure, are needed for these approaches. Often though, the quality of the catch data is compromised when dealing with a complex population structure where fish of different population units mix in a fishery. The herring population units west of the British Isles are prone to mixing. Here, the inability to perfectly allocate the fish caught to the population unit they originate from, due to classification problems, poses problems for management. These mixing proportions are often unknown; therefore, we use simulation modelling combined with management strategy evaluation to evaluate the role fisheries-independent surveys can play in an assessment to provide unbiased results, irrespective of population unit mixing and classification success. We show that failure to account for mixing is one of the major drivers of biased estimates of population abundance, affecting biomass reference points and MSY targets. When mixing of population units occurs, the role a survey can play to provide unbiased assessment results is limited. Either different assessment models should be employed or stock status should be considered from the survey data alone. In addition, correctly classifying the origin of fish is especially important for those population units that are markedly smaller in size than other units in the population complex. Without high classification success rates, smaller population units are extremely vulnerable to overexploitation.
    • Migration and Fisheries of North East Atlantic Mackerel (Scomber scombrus) in Autumn and Winter

      Jansen, Teunis; Campbell, Andrew; Kelly, Ciarán; Hátún, Hjálmar; Payne, Mark R. (Public Library of Science (PLOS), 2012)
      It has been suggested that observed spatial variation in mackerel fisheries, extending over several hundreds of kilometers, is reflective of climate-driven changes in mackerel migration patterns. Previous studies have been unable to clearly demonstrate this link. In this paper we demonstrate correlation between temperature and mackerel migration/distribution as proxied by mackerel catch data from both scientific bottom trawl surveys and commercial fisheries. We show that mackerel aggregate and migrate distances of up to 500 km along the continental shelf edge from mid-November to early March. The path of this migration coincides with the location of the relatively warm shelf edge current and, as a consequence of this affinity, mackerel are guided towards the main spawning area in the south. Using a simulated time series of temperature of the shelf edge current we show that variations in the timing of the migration are significantly correlated to temperature fluctuations within the current. The proposed proxies for mackerel distribution were found to be significantly correlated. However, the correlations were weak and only significant during periods without substantial legislative or technical developments. Substantial caution should therefore be exercised when using such data as proxies for mackerel distribution. Our results include a new temperature record for the shelf edge current obtained by embedding the available hydrographic observations within a statistical model needed to understand the migration through large parts of the life of adult mackerel and for the management of this major international fishery.