• A test battery approach to the ecotoxicological evaluation of cadmium and copper employing a battery of marine bioassays

      Macken, A; Giltrap, M; Ryall, K; Foley, B; McGovern, E; McHugh, B; Davoren, M (Springer, 2009)
      Heavy metals are ubiquitous contaminants of the marine environment and can accumulate and persist in sediments. The toxicity of metal contaminants in sediments to organisms is dependent on the bioavailability of the metals in both the water and sediment phases and the sensitivity of the organism to the metal exposure. This study investigated the effects of two metal contaminants of concern (CdCl2 and CuCl2) on a battery of marine bioassays employed for sediment assessment. Cadmium, a known carcinogen and widespread marine pollutant, was found to be the least toxic of the two assayed metals in all in vivo tests. However CdCl2 was found to be more toxic to the fish cell lines PLHC-1 and RTG-2 than CuCl2. Tisbe battagliai was the most sensitive species to both metals and the Microtox® and cell lines were the least sensitive (cadmium was found to be three orders of magnitude less toxic to Vibrio fischeri than to T. battagliai). The sensitivity of Tetraselmis suecica to the two metals varied greatly. Marine microalgae are among the organisms that can tolerate higher levels of cadmium. This hypothesis is demonstrated in this study where it was not possible to derive an EC50 value for CdCl2 and the marine prasinophyte, T. suecica. Conversely, CuCl2 was observed to be highly toxic to the marine alga, EC50 of 1.19 mg l-1. The genotoxic effect of Cu on the marine phytoplankton was evaluated using the Comet assay. Copper concentrations ranging from 0.25 to 2.50 mg l-1 were used to evaluate the effects. DNA damage was measured as percent number of comets and normal cells. There was no significant DNA damage observed at any concentration of CuCl2 tested and no correlation with growth inhibition and genetic damage was found.
    • Testes and brain gene expression in precocious male and adult maturing Atlantic salmon (Salmo salar)

      Guiry, A; Flynn, D; Hubert, S; O'Keeffe, A; LeProvost, O; White, S L; Forde, P F; Davoren, P; Houeix, B; Smith, T J; Cotter, D; Wilkins, N P; Cairns, M T (Biomed Central, 2010)
      Background: The male Atlantic salmon generally matures in fresh water upon returning after one or several years at sea. Some fast-growing male parr develop an alternative life strategy where they sexually mature before migrating to the oceans. These so called ‘precocious’ parr or ‘sneakers’ can successfully fertilise adult female eggs and so perpetuate their line. We have used a custom-built cDNA microarray to investigate gene expression changes occurring in the salmon gonad and brain associated with precocious maturation. The microarray has been populated with genes selected specifically for involvement in sexual maturation (precocious and adult) and in the parr-smolt transformation. Results: Immature and mature parr collected from a hatchery-reared stock in January were significantly different in weight, length and condition factor. Changes in brain expression were small - never more than 2-fold on the microarray, and down-regulation of genes was much more pronounced than up-regulation. Significantly changing genes included isotocin, vasotocin, cathepsin D, anamorsin and apolipoprotein E. Much greater changes in expression were seen in the testes. Among those genes in the testis with the most significant changes in expression were anti-Mullerian hormone, collagen 1A, and zinc finger protein (Zic1), which were down-regulated inprecocity and apolipoproteins E and C-1, lipoprotein lipase and anti-leukoproteinase precursor which were upregulated in precocity. Expression changes of several genes were confirmed in individual fish by quantitative PCR and several genes (anti-Mullerian hormone, collagen 1A, beta-globin and guanine nucleotide binding protein (G protein) beta polypeptide 2-like 1 (GNB2L1) were also examined in adult maturing testes. Down-regulation of anti-Mullerian hormone was judged to be greater than 160-fold for precocious males and greater than 230-fold for November adult testes in comparison to July testes by this method. For anti-Mullerian hormone and guanine nucleotide binding protein beta polypeptide 2-like 1 expression changes in precocious males mirrored mature adults (November) but for collagen 1A and beta-globin the pattern was more complex. Conclusions: Expression changes in the fish brain during the process of precocious sexual maturation were small compared to those in the testes. Microarray analysis suggested down-regulation of housekeeping functions and up-regulation of a small number of specific processes. Transcriptional changes in the testes were much more pronounced with anti-Mullerian hormone playing a major role. Expression profiles for mature parr and maturing adult testes indicate subtle differences in gene expression between these two related groups.
    • An unintended experiment in fisheries science: a war mediated protected area in the North Sea results in Mexican waves in fish numbers-at-age

      Beare, D; Hölker, F; Engelhard, G H; McKenzie, E; Reid, D (Springer, 2010)
      Marine protected areas (MPAs) are attaining increasing importance in the management of marine ecosystems. They are effective for conservation in tropical and subtropical areas (mainly coral and rocky reefs), but it is debated whether they are useful in the management of migratory fish stocks in open temperate regions. World War II created a large marine area within which commercial fishing was prevented for 6 years. Here we analyse scientific trawl data for three important North Sea gadoids, collected between 1928 and 1958. Using statistical models to summarise the data, we demonstrate the potential of MPAs for expediting the recovery of over-exploited fisheries in open temperate regions. Our age-structured data and population models suggest that wild fish stocks will respond rapidly and positively to reductions in harvesting rates and that the numbers of older fish in a population will react before, and in much greater proportion, than their younger counterparts in a kind of Mexican wave. Our analyses demonstrate both the overall increase in survival due to the lack of harvesting in the War and the form of the age-dependent wave in numbers. We conclude that large closed areas can be very useful in the conservation of migratory species from temperate areas and that older fish benefit fastest and in greater proportion. Importantly, any rise in spawning stock biomass may also not immediately result in better recruitment, which can respond more slowly and hence take longer to contribute to higher future harvestable biomass levels.
    • The ups and downs of working with industry to collect fishery-dependent data: the Irish experience

      Lordan, Colm; Ó Cuaig, Macdara; Graham, Norman; Rihan, Dominic (Oxford University Press, 2011)
      Working with the fishing industry to collect fishery-dependent data for scientific and advisory purposes is essential in most countries, but despite the many advantages of working with fishers, it is not without challenges. The objectives and the ups and downs of 16 recent projects in Ireland are described, and four case studies are discussed in detail. Some common themes that characterize both successful and unsuccessful experiences are identified. One critical aspect is industry’s sometimes unrealistic time-horizons and expectations when engaging in scientific data collection. Detailed communication of objectives, procedures, results, and relevance not only to industry representatives, but also to vessel owners and crew, is required throughout the life cycle of a project. For some projects, there is a clear need to include incentives in the design, but for others this is less critical. The critical needs for ongoing quality control and assurance, validation of data, and appropriate project design are discussed, along with the link between successful management systems and participatory research. Finally, comment is provided on how the expected reforms of the EU’s Common Fisheries Policy will place new demands on joint research.
    • 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.
    • 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.
    • When good neighbours become good friends: observing small scale structures in fish aggregations using multibeam sonar

      Gerlotto, F; Jones, E; Bez, N; Reid, D G (EDP Sciences, 2010)
      Converging results in different scientific fields (behavioural ecology, fisheries biology, acoustic tagging, fisheries acoustics, behavioural modelling) suggest the existence of “micro-groups” inside fish schools. These would comprise a few (5–10) fish maintaining contact during a period long enough to allow individuals to recognise each other. It is hypothesised that they would prefer to share the space with familiar rather than anonymous conspecifics. To evaluate whether acoustic methods could be used to recognise “micro-structures” inside fish schools and help test the “micro-group” hypothesis we analysed acoustic data from anchovy schools off Peru, and gadoids in the North Sea. Data collection used a multibeam sonar (Reson SeaBat 6012). In the Peruvian case study, the sonar was mounted set horizontally on a drifting research vessel and the internal structure of the schools of anchovies was analysed, although individual fish could not be discriminated. In the North Sea case study, the sonar was orientated vertically above a demersal trawl to allow observation of individual fish entering the trawl. Geostatistical analyses were used to evaluate the existence of small spatial structures in anchovy schools. In these schools, “micro-structures” with a scale as small as 0.5 m were observed acoustically. For the gadoids nearest neighbour distance (NDD) measurements were carried out, suggesting that the fish aggregated in small groups (2 to 25 individuals, with an average of 3.7 fish per group) in the trawl catches. The perspectives and limitations of these results are discussed.
    • Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks

      Ravinet, M.; Hynes, R.; Poole, R.; Cross, T.F.; McGinnity, P.; Harrod, C.; Prodöhl, P.A. (PLoS ONE, 2015)
      Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback (Gasterosteus aculeatus L.) forms are numerous and common throughout the species distribution, offering an opportunity to examine these contrasting hypotheses in greater detail. This study reports on an interesting new contact zone located in a tidally influenced lake catchment in western Ireland, characterised by high polymorphism for lateral plate phenotypes. Using neutral and QTL-linked microsatellite markers, we tested whether the high diversity observed in this contact zone arose as a result of introgression or reproductive isolation between divergent forms: we found strong support for the latter hypothesis. Three phenotypic and genetic clusters were identified, consistent with two divergent resident forms and a distinct anadromous completely plated population that migrates in and out of the system. Given the strong neutral differentiation detected between all three morphotypes (mean FST = 0.12), we hypothesised that divergent selection between forms maintains reproductive isolation. We found a correlation between neutral genetic and adaptive genetic differentiation that support this. While strong associations between QTL linked markers and phenotypes were also observed in this wild population, our results support the suggestion that such associations may be more complex in some Atlantic populations compared to those in the Pacific. These findings provide an important foundation for future work investigating the dynamics of gene flow and adaptive divergence in this newly discovered stickleback contact zone.
    • Whole-tree harvesting and grass seeding as potential mitigation methods for phosphorus export in peatland catchments

      O'Driscoll, Connie; O'Connor, Mark; Asam, Zaki-ul-Zaman; DeEyto, Elvira; Poole, Russell; Rodgers, Michael; Zhan, Xinmin; Nieminen, Mika; Xiao, Liwen (Elsevier, 2014)
      Forest clearfelling is potentially a major environmental problem with respect to the degradation of water quality in receiving water courses due to phosphorus (P) release from soil and clearfelling residue stocks. Recent studies have highlighted the need to investigate the performance and benefits of potential mitigation methods such as whole tree harvesting (WTH) and grass seeding. In this study, fifteen plots (0.014 ha each) were constructed in a standing coniferous forest and P concentrations in plot runoff were monitored for one year prior to clearfelling. Following clearfelling three replicates of five forest harvesting management practices/treatments were applied to the plots: brash with grass seeding (Treatment 1), brash (Treatment 2), brash mat/ tree extraction route (Treatment 3), WTH (Treatment 4) and WTH with grass seeding (Treatment 5). These treatments were designed to comparatively assess the benefits of WTH and grass seeding practices on mitigating P released from forested peatlands following clearfelling and to determine the sources and sinks of P following clearfelling operations. Annual average total reactive phosphorus (TRP) concentrations in the plot runoff were < 20 µg L-1 in all treatments before clearfelling, and increased to 79 µg L-1, 160 µg L-1, 335 µg L-1, 50 µg L-1 and 38 µg L-1 in Treatments 1, 2, 3, 4 and 5, respectively, after clearfelling. These results highlight that WTH and grass seeding can be used efficiently as methods to improve water quality, aiding in the protection of the biota residing in the aquatic systems draining peatland catchments.
    • Winter measurements of biogeochemical parameters in the Rockall Trough (2009–2012)

      McGrath, T.; Kivimäe, C.; McGovern, E.; Cave, R.R.; Joyce, E. (Copernicus publications, 2013)
      This paper describes the sampling and analysis of biogeochemical parameters collected in the Rockall Trough in January/February of 2009, 2010, 2011 and 2012. Sampling was carried out across two transects, one southern and one northern transect each year. Samples for dissolved inorganic carbon (DIC) and total alkalinity (TA) were taken alongside salinity, dissolved oxygen and dissolved inorganic nutrients (total-oxidised nitrogen, nitrite, phosphate and silicate) to describe the chemical signatures of the various water masses in the region. These were taken at regular intervals through the water column. The 2009 and 2010 data are available on the CDIAC database.