• Second report on the fishes of the Irish Atlantic Slope

      Holt, E. W. L.; Byrne, L. W. (His Majesty's Stationary Office, Dublin, 1909)
      Many of the fishes which inhabit the deeper water of the Atlantic coast are unfamiliar to fishermen, and were not described in the books to which the general reader had ready access in the early 1900s. It was therefore the intention of the authors to give an account and figure; or sketch, of all except the well-known kinds. This is the second report in an occasional series on the fishes of the Irish Atlantic Slope.
    • The deep water fisheries of the Rockall trough: some insights gleaned from Irish survey data

      Kelly, C.J.; Connolly, P.L.; Clarke, M.W. (International Council for the Exploration of the Sea (ICES), 1998)
      The Fisheries Research Centre (FRC) has conducted trawl and longline surveys in the Rockall Trough since 1993, fishing a total of 223 stations over the depth range 201 to 4,945m. Trawls produced greater species diversity and higher discard rates than longlines, which selected larger squalifurm sharks. In 1997, limited selectivity work, based on ten comparative tows, showed that the size range of roundnose grenadier (Coryphaenoides rupestris) caught using a commercial trawl (llOmm), with and without a small mesh end liner (30mm), were similar. This indicates that mesh size, because of poor selectivity and perceived low survival rates of escapees, may not be a useful management tool in the regulation of the trawl fishery.
    • 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.
    • Comparison of the effects of exploitation on theoretical long-lived fish species with different life-history strategies and the implications for management

      Codling, E.A.; Kelly, C.J.; Clarke, M. (International Council for the Exploration of the Sea (ICES), 2005)
      A stage-based simulation model is used to investigate the effect of exploitation on theoretical populations representing long-lived elasmobranch and teleost species with different life-history strategies. A comparison is made between the effect of exploitation on the elasmobranch ‘k-strategists’ and other teleost species that are ‘r-strategists’. We demonstrate the effects of stage-based exploitation on a typical long-lived elasmobranch population and discuss the implications of this when designing a management plan to ensure survival of the stock.
    • Variability in the assignment of maturity stages of plaice (Pleuronectes platessa L.) and whiting (Merlangius merlangus L.) using macroscopic maturity criteria

      McGrath, D; Gerritsen, H.D. (Elsevier, 2006)
      This study investigates if a macroscopic scale can be applied consistently, by examining the variablity between and within ten people who repeatedly assessed the sex and maturity stages of 80 plaice (Pleuronectes platessa L.) and 79 whiting (Merlangius merlangus L.) gonads. In most cases, agreement within assessors was not significantly higher than agreement between assessors, suggesting that variability was random and not due to differences in interpretation. This finding was supported by the fact that a significant bias was only found for one assessor. Some maturity stages were assigned quite consistently, while other stages were not defined objectively enough to be assigned reliably, even when fish were assessed repeatedly by the same person. For both species, well-defined maturity scales with fewer stages would be prefereable over scales that distinguish a larger number of maturity stages. As maturity staging will always contain a form of subjective judgement, it should be subject to continuous quality control measures.
    • A simple method for comparing age–length keys reveals significant regional differences within a single stock of haddock (Melanogrammus aeglefinus)

      McGrath, D; Lordan, C; Gerritsen, H.D. (Oxford University Press, 2006)
      A multinomial logistic model is presented as a tool for comparing two or more age–length keys. The model provides an objective way to fill in missing values and can be used for estimating uncertainty and visualizing age–length keys (ALKs). An example of haddock (Melanogrammus aeglefinus L.) in ICES Division VIa (West of Scotland) is used to illustrate that significant regional differences in the proportions of age classes-at-length can exist on a small spatial scale. These differences are caused by regional variation in both length-at-age and relative abundance at age. As the length-at-age data are normally not weighted by the local catch rate (abundance), the ALK of the combined age data can result in strongly biased estimates of numbers-at-age. In the present case, the use of unweighted age data would have resulted in an overestimate of recruitment of nearly 200% and an underestimate of spawning stock biomass of 15%. Comparing ALKs using this method has several practical applications in fisheries science.
    • 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.
    • Population specific smolt development, migration and maturity schedules in Atlantic salmon in a natural river environment

      McGinnity, P; deEyto, E; Cross, T F; Coughlan, J; Whelan, K; Ferguson, A (Elsevier, 2007)
      Identifying differences in quantitative life history traits between cultured and native or non-native wild populations is important in assessing the impact of accidental and deliberate introductions of hatchery-reared fish into the wild. As the ability to exploit the marine environment is the defining life history characteristic of anadromous salmonids, knowledge of variation in smoltification characteristics among populations is crucial in determining how these introductions affect fitness in recipient populations. Data are presented here describing the timing and extent of the autumn migration; the propensity for male parr maturation; the timing of the spring migration; and the size of autumn and spring migrants from Atlantic salmon (Salmo salar) populations from various genetic backgrounds. These experiments were carried out under common garden conditions over a decade in the Srahrevagh River in the west of Ireland. Population specific genetically determined differences in quantitative life history traits associated with smoltification were apparent. These differences may reflect smolt quality and therefore impact on marine survival and ultimately lifetime fitness. Both hatchery domestication and geography (different selective environments) were found to be important factors determining smolt phenotypes, although it was difficult to measure the relative contribution of each. These results indicate that farm, native hatchery, non-native wild salmon (even from a neighbouring catchment) and their hybrids with native wild fish, are likely to produce less well adapted and thus poorer quality smolts than native wild populations and, where wild populations are extant, such stocks should not be used for enhancement purposes.
    • Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

      de Eyto, E.; McGinnity, P.; Consuegra, S.; Coughlan, J.; Tufto, J.; Farrell, K.; Megens, H.J.; Jordan, W.; Cross, T.; Stet, R.J.M. (Royal Society Publishing, 2007)
      Pathogen-driven balancing selection is thought to maintain polymorphism in major histocompatibility (MH) genes. However, there have been few empirical demonstrations of selection acting on MH loci in natural populations. To determine whether natural selection on MH genes has fitness consequences for wild Atlantic salmon in natural conditions, we compared observed genotype frequencies of Atlantic salmon (Salmo salar) surviving in a river six months after their introduction as eggs with frequencies expected from parental crosses. We found significant differences between expected and observed genotype frequencies at the MH class II alpha locus, but not at a MH class I-linked microsatellite or at seven non-MH-linked microsatellite loci. We therefore conclude that selection at the MH class II alpha locus was a result of disease-mediated natural selection, rather than any demographic event. We also show that survival was associated with additive allelic effects at the MH class II alpha locus. Our results have implications for both the conservation of wild salmon stocks and the management of disease in hatchery fish. We conclude that natural or hatchery populations have the best chance of dealing with episodic and variable disease challenges if MH genetic variation is preserved both within and among populations.
    • A new scientific initiative with the Pelagic RAC to develop a management plan for western horse mackerel

      Clarke, M.; van Balsfoort, G.; Coers, A.; Campbell, A.; Dickey-Collas, M.; Egan, A.; Ghiglia, M.; Harkes, I.; Kelly, C.; O' Donoghue, S.; Olesen, C.; Roel, B.; Tait, A.; Uriarte, A. (International Council for the Exploration of the Sea (ICES), 2007)
      The western horse mackerel stock is currently managed by annual TACs covering only part of its distribution area. No stock assessment has been accepted and recent ICES advice has consistently been for status quo catches. In 2006, the Pelagic Regional Advisory Committee asked scientists to help with developing a harvest control rule for the stock that would both meet conservation and stability objectives. An initial questionnaire was circulated to the industry, to elicit feedback on possible management options. A series of Harvest Control Rules were developed. These were tested by simulation and presented to the RAC at a number of meetings. Results will be presented within the ICES advisory process and elsewhere in the scientific literature. This is a developing approach involving scientists and stakeholders in an iterative process. The problems encountered and lessons learned, are discussed.
    • 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.
    • Significant differences in the length–weight relationships of neighbouring stocks can result in biased biomass estimates: examples of haddock (Melanogrammus aeglefinus, L.) and whiting (Merlangius merlangus, L.)

      McGrath, D; Gerritsen, H.D. (Elsevier, 2007)
      Length–weight relationships of fish are often used to estimate the biomass of length distributions or to obtain indices of condition. Although large-scale spatial trends are known to exist, it is often assumed that length–weight relationships do not vary significantly within stocks or between neighbouring stocks. The present study examined length–weight relationships of 1334 haddock (Melanogrammus aeglefinus) and 1186 whiting (Merlangius merlangus) collected on a groundfish survey in the waters around Ireland in 2004. Additionally, condition indices were estimated for individual fish and for length frequency samples. The length–weight regression showed a significant area effect and no differences between the sexes. The condition indices showed a moderate spatial structure for both species: around 25% of the variability could be explained by the location of the samples, the rest of the variability was due to other sources. Length–weight relationships did not appear to vary significantly within stocks, however differences between stocks were significant. In the present case, a bias of up to 10% could occur in biomass estimates as a result of applying length–weight relationships of one stock to length data of a neighbouring stock.
    • 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.
    • A Model Compound Study: The ecotoxicological evaluation of five organic contaminants with a battery of marine bioassays

      Macken, A; Giltrap, M; Foley, B; McGovern, E; McHugh, B; Davoren, M (Elsevier, 2008)
      This paper describes the ecotoxicological evaluation of five organic contaminants frequently detected in marine sediments (tributyltin, triphenyltin, benzo[a]pyrene, fluoranthene, and PCB 153) using three marine species (Vibrio fischeri, Tetraselmis suecica, and Tisbe battagliai). The sensitivity of each species varied for all compounds. The triorganotins were consistently the most toxic to all species. The applicability of each test system to assess the acute toxicity of environmental contaminants and their use in Toxicity Identification Evaluation (TIE) is discussed. Suitability of the Microtox and T. battagliai tests for employment in TIE studies were further assessed through spiking experiments with tributyltin. Results demonstrated that the most effective treatment to remove organotin toxicity from the sample was the C18 resin. The results of this study have important implications for risk assessment in estuarine and coastal waters in Ireland, where, at present the monitoring of sediment and water quality is predominantly reliant on chemical analysis alone. Ecotoxicological evaluation of five organic marine sediment contaminants was conducted and the suitability of the test species for marine porewater TIE discussed.
    • 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.
    • 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.
    • Effects of cooking and heat treatment on concentration and tissue distribution of okadaic acid and dinophysistoxin-2 in mussels (Mytilus edulis)

      McCarron, P; Kilcoyne, J; Hess, P (Elsevier, 2008)
      Using high performance liquid chromatography with mass spectrometry the influence of conventional steaming and other heat treatments on the level of azaspiracids, okadaic acid and dinophysistoxin-2 in mussels (Mytilus edulis) was investigated. A prior study looking at the influence of steaming on the concentration and distribution of azaspiracids showed significant increases in concentration as a result. Described is a follow-up study using two separate mussel samples, where the contribution of water loss during steaming to increases of toxin levels was examined. In addition to water loss it was demonstrated that heating of fresh azaspiracid contaminated mussels resulted in significant increases in the quantity of the desmethyl analogue (azaspiracid-3) measured. A systematic heat treatment experiment confirmed these findings and showed that azaspiracid-3 was the most thermally instable of the three regulated azaspiracid analogues. In parallel, the same studies were carried out for okadaic acid and dinophysistoxin-2 also naturally present in the samples used. Concentration increases correlated with water loss during steaming. More so than for azaspiracids, increased distribution of okadaic acid and dinophysistoxin-2 from the digestive glands to the remainder tissues was observed as a result of the processes examined. This suggests that analysis of whole flesh tissues, as opposed to dissected digestive glands, is more appropriate for regulatory purposes, particularly if cooked samples are being analysed. The findings of the studies reported here have importance in terms of the methodology applied in regulatory phycotoxin monitoring programmes. Therefore, options for sample pre-treatment are discussed.
    • Distribution patterns of ichthyoplankton communities in different ecosystems of the Northeast Atlantic.

      Dransfeld, L; Dwane, O; Zuur, A F (Wiley-Blackwell, 2009)
      Results are presented of an extensive ichthyoplankton survey that covered the continental slope, the offshore banks and oceanic regions west of Ireland. Oceanographic measurements revealed domes of cold, less saline water over the Porcupine, Rockall and Faroese Banks, constituting Taylor columns. The most species-rich stations were those found on and close to the offshore banks and the shelf edge. Larvae found in these areas were mainly from demersal fish species, including some commercial species such as haddock Melanogrammus aeglefinus, lemon sole Microstomus kitt (Walbaum, 1792), ling Molva molva (L.) and witch Glyptocephalus cynoglossus (L.). The deep water stations of the Rockall Trough and the north and west stations off the Rockall and Hatton Banks were characterized by a low number of species and high numbers of individuals of mesopelagic species such as Maurolicus muelleri and Benthosema glaciale. Results from multivariate statistical analysis confirmed that species compositions varied significantly at different sites and were related to environmental conditions, whereby sites of similar temperature, salinity and bottom depth harboured similar species assemblages. Generalized additive mixed modelling was used to model the relationship between species richness and environmental variables and confirmed that there was a significant negative relationship between species richness and bottom depth indicating that the offshore banks and the slope stations present favourable habitats for a large number of species.
    • 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.
    • Vulnerability of male spider crab Maja brachydactyla (Brachyura: Majidae) to a pot fishery in south-west Ireland

      Fahy, E; Carroll, J (Cambridge University Press, 2009)
      The Magharees fishery (Brandon and Tralee Bays in south-west Ireland) is 495 sq.km in extent, the majority of this area ≤20 m in depth. Since 1981 it has been occupied by a directed spider crab fishery yielding in some years all of the national catch of Maja brachydactyla. Maximum recorded landings were 336 t in 1999 and effort has numbered up to 10,000 pots annually. Increasing fishing capacity and declining opportunities have accentuated fishing effort on spider crab. This paper describes a catch census undertaken in the fishing season of March to August inclusive, 2000–2007 and a mark–recapture experiment, 2005–2007. A method of ageing the adult moult by attributing a chronology to the rate of erosion of the claw on the dactyl is introduced. Males migrated longer distances, moved into the fishery on a wider trajectory and demonstrated greater wear on the claw than females. Recapture rate of males was twice that of females. The conduct of the fishery changed in its 26 years in existence. Landings became more concentrated in the earlier months of the year and the recent summer fishery was characterized by fewer male captures. Larger males were quickly removed and none >140 mm carapace length survived in the fishery longer than one year.