• Herring larval surveys in the Celtic Sea and division VIIj in 1983/1984

      Cullen, A.; Barnwall, E.; Grainger, R. J. (International Council for the Exploration of the Sea, 1984)
      Surveys for herring larvae in the Celtic Sea were conducted for the sixth ~ successive season between October 1983 and February 1984. The modifications made to the survey grid in the previous season to take account of the amalgamation of the Celtic Sea and Division VIIj for assessment purposes and to ascertain if larvae drift into the Irish Sea were also adopted for the 1983/84 surveys. A drift of larvae towards the Irish Sea was apparent in 1983/84. The larval abundance index for 1983/84 based on a standard survey area was almost three times higher than any previous value. A continuous increase in larval indices since 1978/79 indicates a recovery of the spawning stock.
    • The age Distribution of the Herring Stocks around the Irish Coast during 1993

      Barnwall, E.; Molloy, J. (1994)
      The age distribution of stocks is usually considered as an indication of how healthy a stock may be. In general stocks which are lightly exploited will contain a much larger proportion of older fish than a stock which is heavily exploited. A stock which is heavily exploited will probably be dependent on one year class which will recruit to the fishery and which will immediately be subjected to fishing effort. Obviously in such a fishery failure of recruitment or poor recruitment will have drastic effect on the catches. Herrings can be aged accurately until are about 10 years old and generally recruit to the adult stocks during their third year. During this year, the majority of fish will spawn for the first time.
    • Mean weights at age in Celtic Sea Herrings

      Molloy, J. (Marine Institute, 2000)
      Stock recruitment analysis for Celtic sea herring suggest that exploitation rates of F >0.4 carry a high probability of long term SSB decline. Fmed, which would carry a much lower risk of reducing the SSB, has been suggested as a candidate for Fpa and most recent analyses give this value at 0.29. However based on last years assessment only 4 of the 41 estimated fishing mortalaties were equal or less than 0.3 while 26 were higher or equal to 0.4 with the series average being F=0.50. This would indicate that F>0.4 does not seem carry a high probability of stock collapse. Thus there is an apparent discrepancy between the analyses and experience.
    • The Assessment of Irish Pelagic Species

      Molloy, J.; Mullins, E. (Marine Institute, 2001)
      The exploitation of pelagic species, particularly of herring and mackerel has for a long time been one of the most important components of the Irish fishing industry. Fisheries for both species have been responsible for the development of the very successful Irish pelagic fleet and also for the development of a very large processing industry in the Donegal area. The responsibility of assessing the stocks and providing management advice to the main Irish managing authority, The Department of the Marine and Natural Resources, lies with the Marine Fisheries Services Division (MFSD) of the Marine Institute. Both mackerel and herring have been continuously assessed since the 1960’s as a result of programmes carried out under the auspices of the International Council for the Exploration of the Sea (ICES) the international body that co-ordinates research and provides management advice to the EU. However, since the 1980’s both mackerel and herring stocks have been subjected to decreased total allowable catches (TACs) and decreased national quota and tighter management measures as a result of decreases in the stock sizes. This situation has forced the pelagic fleet, particularly that in the North west of Ireland to develop fisheries for alternative species so that it is not totally dependent on mackerel and herring. New fisheries have therefore developed for other pelagic species in recent years. Three species which are now exploited regularly are horse mackerel, (trachurus trachurus), also known as scad .or craig herring; blue whiting (Micromesistius poutassou) and Norwegian spring spawning herring (clupea harengus) also known as atlanto-scandian herring. When the fisheries for these species first developed there were no restrictions on catches for horse mackerel and blue whiting while catches on the Norwegian spring spawning herring were subject to an international agreement under which the EU was allowed a quota. None of these three species had previously been assessed by any Irish research project and the amount of scientific information was extremely limited. The international assessments carried out by ICES were based on poor data and had no input from Ireland. Ireland had for a number of years been taking significant catches of some species. The Processing Industry in Donegal were concerned that the lack of adequate biological sampling programmes could lead to inappropriate and inaccurate advice for the management of the stocks. This, it was felt, could have serious effects on the industry and would also demonstrate that Ireland had an irresponsible attitude to the development of these fisheries which was inconsistent with the Precautionary Approach to Fisheries Management. Therefore the Donegal Fish Merchants Association decided to co-operate with the Marine Institute to fund an initial biological sampling programmes on horse mackerel, blue whiting and Norwegian spring spawning herring and to make this data available to the relevant ICES Working Group. The objective of the sampling programme was to collect essential biological data necessary to expand the existing international programmes. In addition it was decided to provide an increased scientific input to existing MFSD assessment programmes such as the mackerel and horse mackerel tagging programmes, the international mackerel and horse mackerel egg surveys and the international blue whiting acoustic surveys. All the collected data has been submitted to the relevant ICES Assessment Working Groups from 1999 to 2001.
    • Reports from the FSS mini-symposia 2004-2005

      Codling, E.; Kelly, C.; (eds) (Marine Institute, 2006)
      The mini symposia documented in this publication were meetings organised in October 2004 and August 2005 by the 'Modelling and Simulation' team in Fisheries Science Services (FSS) of the Marine Institute, Ireland. Both symposia took place at the Harbour Hotel in Galway, Ireland. Each meeting consisted of a number of presentations (given as talks or posters) followed by a round-table informal discussion session. The two meetings were attended by participants from FSS and the Marine Institute, BIM (Bord Iascaigh Mara - Irish Sea Fisheries Board), FRS (Fisheries Research Services) Aberdeen, and universities in both Ireland and UK. The Appendix contains a full list of the participants at each meeting, while contact details for those who gave presentations are given at the start of each summary paper.
    • Certified Reference Materials for Marine Monitoring

      Pellizzato, Francesca; McGovern, Evin; Quevauviller, Philippe (J. Wiley & Sons, Chichester, West Sussex, 2011)

      Ryder, L; DeEyto, E; Gormally, M; Sheehy Skeffington, M; Dillane, M; Poole, R (The Royal Irish Academy, 2011)
      Plantation forests were established on western Irish peatlands before it became apparent that riparian buffer zones were essential for the health of important salmonid habitats and aquatic ecosystems. The option to retrofit a riparian buffer zone several years before the clearfelling of the main plantation may lessen the possible effect of the clearfelling on receiving waters and provide some protection against sediment and nutrient runoff. The option to create a riparian buffer zone can only be considered if it can be shown that clearfelling this zone of coniferous forestry along the stream does not pose a significant risk to the water bodies in the short term. To assess this risk, the hydrology, water chemistry and biota at three locations in western peatland catchments within mature, harvestable-age forestry plantations were studied before, during and immediately after riparian buffer zones were created. Results indicate that water discharge and suspended sediment increased significantly at two experimental sites post-felling. Maximum and minimum daily temperature and pH also increased significantly at two of the sites. The biological results from macroinvertebrate analysis indicated some significant changes in richness and abundance of species post-felling. The juvenile trout (Salmo trutta L.) densities remained stable over the sampling period and appeared unaffected by the clearfelling operations.
    • Varying disease-mediated selection at different life-history stages of Atlantic salmon in fresh water

      DeEyto, Elvira; McGinnity, Philip; Huisman, Jisca; Coughlan, Jamie; Consuegra, Sofia; Farrell, Killian; O'Toole, Ciar; Tufto, Jarle; Megens, Hendrik-Jan; Jordan, William; et al. (Blackwell Publisher, 2011)
      Laboratory studies on associations between disease resistance and susceptibility and major histocompatibility (MH) genes in Atlantic salmon Salmo salar have shown the importance of immunogenetics in understanding the capacity of populations to fight specific diseases. However, the occurrence and virulence of pathogens may vary spatially and temporally in the wild, making it more complicated to predict the overall effect that MH genes exert on fitness of natural populations and over several life-history stages. Here we show that MH variability is a significant determinant of salmon survival in fresh water, by comparing observed and expected genotype frequencies at MH and control microsatellite loci at parr and migrant stages in the wild. We found that additive allelic effects at immunogenetic loci were more likely to determine survival than dominance deviation, and that selection on certain MH alleles varied with life stage, possibly owing to varying pathogen prevalence and/or virulence over time. Our results highlight the importance of preserving genetic diversity (particularly at MH loci) in wild populations, so that they have the best chance of adapting to new and increased disease challenges as a result of projected climate warming and increasing aquaculture.
    • Contrasting responses to selection in class I and class IIα major histocompatibility-linked markers in salmon

      Consuegra, S; De Eyto, E; McGinnity, P; Stet, R.J.M.; Jordan, W.C. (Nature Publishing Group, 2011-08)
      Comparison of levels and patterns of genetic variation in natural populations either across loci or against neutral expectation can yield insight into locus-specific differences in the strength and direction of evolutionary forces. We used both approaches to test the hypotheses on patterns of selection on major histocompatibility (MH)-linked markers. We performed temporal analyses of class I and class IIα MH-linked markers and eight microsatellite loci in two Atlantic salmon populations in Ireland on two temporal scales: over six decades and 9 years in the rivers Burrishoole and Delphi, respectively. We also compared contemporary Burrishoole and Delphi samples with nearby populations for the same loci. On comparing patterns of temporal and spatial differentiation among classes of loci, the class IIα MH-linked marker was consistently identified as an outlier compared with patterns at the other microsatellite loci or neutral expectation. We found higher levels of temporal and spatial heterogeneity in heterozygosity (but not in allelic richness) for the class IIα MH-linked marker compared with microsatellites. Tests on both within- and among-population differentiation are consistent with directional selection acting on the class IIα-linked marker in both temporal and spatial comparisons, but only in temporal comparisons for the class I-linked marker. Our results indicate a complex pattern of selection on MH-linked markers in natural populations of Atlantic salmon. These findings highlight the importance of considering selection on MH-linked markers when using these markers for management and conservation purposes.
    • MHC-mediated spatial distribution in brown trout (Salmo trutta) fry

      O'Farrell, Brian; Benzie, John A. H.; McGinnity, Philip; Carlsson, Jens; De Eyto, Elvira; Dillane, Eileen; Graham, Conor; Coughlan, James; Cross, Tom (Nature Publishing Group, 2011-09)
      Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited dispersal from the nest (redd effect) would predict that all such pairs would have a similar distribution. However, this study demonstrates a strong, significant trend for reduced distance between pairs of full-sibling fry sharing more MHC class I alleles reflecting their closer aggregation (no alleles shared, 311.5±(s.e.)21.03m; one allele shared, 222.2±14.49m; two alleles shared, 124.9±23.88m; P<0.0001). A significant trend for closer aggregation among fry sharing more MHC class I alleles was also observed in fry pairs, which were known to have different mothers and were otherwise unrelated (ML-r=0) (no alleles: 457.6±3.58m; one allele (422.4±3.86 m); two alleles (381.7±10.72 m); P<0.0001). These pairs are expected to have emerged from different redds and a passive association would then be unlikely. These data suggest that sharing MHC class I alleles has a role in maintaining kin association among full-siblings after emergence. This study demonstrates a pattern consistent with MHC-mediated kin association in the wild for the first time.
    • Temperature quenching of CDOM fluorescence sensors: temporal and spatial variability in the temperature response and a recommended temperature correction equation

      Ryder, Elizabeth; Jennings, Eleanor; DeEyto, Elvira; Dillane, Mary; NicAonghusa, Caitriona; Pierson, Donald C.; Moore, Karen; Rouen, Martin; Poole, Russell (ASLO, 2012)
      Field-based instruments measuring chromophoric dissolved organic matter (CDOM) fluorescence are often used as a proxy for dissolved organic carbon concentrations in lakes and streams. CDOM fluorescence yield is, however, affected by water temperature at the time of measurement, a factor which varies on both diel and seasonal timescales. A temperature correction must therefore be applied to these data. We present data on temporal and site-specific variability in temperature quenching of CDOM fluorescence for water from a humic lake and one of its main inflows in the west of Ireland. In addition, we present a temperature compensation equation and show that this equation is an improvement on methods previously proposed.
    • Balancing selection on MHC class I in wild brown trout Salmo trutta

      O'Farrell, B; Dennis, C; Benzie, JA; McGinnity, P; Carlsson, J; De Eyto, E; Coughlan, J; Igoe, F; Meehan, R; Cross, T (Wiley, 2012-09)
      Evidence is reported for balancing selection acting on variation at major histocompatibility complex (MHC) in wild populations of brown trout Salmo trutta. First, variation at an MHC class I (satr-uba)–linked microsatellite locus (mhc1) is retained in small S. trutta populations isolated above waterfalls although variation is lost at neutral microsatellite markers. Second, populations across several catchments are less differentiated at mhc1 than at neutral markers, as predicted by theory. The population structure of these fish was also elucidated.
    • Nutrient dynamics in a peatland forest riparian buffer zone and implications for the establishment of planted saplings

      Finnegan, J.; Regan, J.T.; De Eyto, E.; Ryder, E.; Tiernan, D.; Healy, M.G. (Elsevier, 2012-10)
      Forestry on peatland throughout the world is now focused on minimising destructive effects to the surrounding environment, especially during harvesting. These effects may be mitigated through the use of well-developed riparian buffers zones (RBZs). However, much of the commercial forestry planted in Ireland and the UK in the mid-20th century was planted without adequate RBZs. The creation of new RBZs prior to clearfelling may be a possible mitigation measure in these circumstances. The aim of this paper was to assess the nutrient content and phosphorus (P) adsorption capacity of the soil, and survival of planted saplings in a RBZ, positioned downslope from a standing forest and partly covered with brash mats, five years after its establishment. Dissolved reactive phosphorus (DRP) concentrations were significantly higher under the brash mats in the RBZ when compared to all other areas. The standing forest had the highest concentrations of ammonium nitrogen (NH4-N), while total oxidised nitrogen (TON) was similar for all areas. Water extractable phosphorus and desorption–adsorption testing also confirmed the high concentrations of P under the brash mats, but P did not leach through the peat to the stream. The overall survival rate of the saplings was relatively high, with over half of Quercus robur (oak) (57%), Sorbus aucuparia (rowan) (57%) and Betula pendula (birch) (51%) surviving. Salix cinerea (willow) (22%), Alnus glutinosa (alder) (25%) and Ilex aquifolium (holly) (44%) did not survive as successfully. The RBZ was capable of providing nutrients for the survival of planted saplings, fertilizing the peat with degrading brash material and preventing elevated levels of nutrients entering the adjacent aquatic ecosystem.
    • The palaeolimnology of Lough Murree, a brackish lake in the Burren, Ireland.

      Cassina, Filippo; Dalton, Catherine; De Eyto, Elvira; Sparber, Karin (The Royal Irish Academy, 2013)
      Lough Murree, a rock/karst barrier lagoon, is superficially isolated from the sea and seasonal variations in lake water level reflect precipitation and groundwater variation. Lake salinity is influenced by subsurface saline intrusions, occasional barrier overwash together with precipitation and groundwater inflow, leading to poikilohaline conditions. Palaeolimnological reconstructions in Murree support the supposition that the lagoon was once superficially connected to the sea around the mid-nineteenth century. Physical, chemical and biological proxies suggest an evolution to more freshwater conditions. Uncertainties about the timing of the transition persist because of an unresolved sediment chronology. The isolation of Murree from the Atlantic Ocean has promoted the formation of dense charophyte beds composed of lagoonal specialist species, which are able to tolerate large variations in salinity.
    • Biotic response to forest harvesting in acidic blanket peat fed streams: a case study from Ireland

      O'Driscoll, Connie; de Eyto, Elvira; Rodgers, Michael; O'Connor, Mark; Asam, Zaki-ul-Zaman; Xiao, Liwen (Elsevier, 2013)
      Blanket peat catchments are important biodiversity refugia and are increasingly recognised for their role in regional carbon and water balances. A key pressure on these catchments is forest clearfelling which increases stream phosphorus potentially leading to eutrophication. However, these unique systems are underrepresented in the development of bioassessment monitoring programmes and so are at risk to impacts. In this study, a multiple before-after-control-impact (MBACI) study was designed in three neighbouring peatland catchments and provided a unique opportunity to assess the impact of forest clearfelling events on macroinvertebrate and phytobenthic assemblages. Statistical analysis revealed substantial differences in the macroinvertebrate assemblages after clearfelling with higher abundances of chironomids. Macroinvertebrate derived indices EPT, diversity and species richness were significantly reduced. This was accompanied by a shift in functional feeding group representation away from shredders and collector–filterers to a dominance of collector–gatherers after clearfelling. In contrast, forest clearfelling did not significantly impact the diatom assemblages and diatom derived indices remained static for the duration of the study period.
    • Boarfish (Capros aper) target strength modelled from magnetic resonance imaging (MRI) scans of its swimbladder

      Fassler, S.; O'Donnell, C.; Jech, J. (International Council for the Exploration of the Sea (ICES), 2013)
      Boarfish (Capros aper) abundance has increased dramatically in the Northeast Atlantic from the early 1970s after successive years of good recruitment attributed to an increase in sea surface temperature. Due to increased commercial fishing over recent years, an acoustic boarfish survey funded by the Killybegs Fishermen's Organisation was initiated by the Marine Institute to establish a baseline for the future management of this stock. In the absence of any species-specific boarfish target strength (TS), acoustic backscatter was estimated by a Kirchhoff-ray mode model using reconstructed three-dimensional swimbladder shapes which were computed from magnetic resonance imaging scans of whole fish. The model predicted TS as a function of size, fish tilt angle, and operating frequency. Standardized directivity patterns revealed the increasing importance of changes in the inclination of the dorsal swimbladder surface at higher frequencies (120 and 200 kHz) and a less directive response at lower frequencies (18 and 38 kHz). The model predicted a TS-to-total fish length relationship of TS = 20 log10(L) − 66.2. The intercept is ∼1 dB higher than in the general physoclist relationship, potentially reflecting the bulky nature of the boarfish swimbladder with its relatively large circumference.
    • A genetic marker for the maternal identification of Atlantic salmon × brown trout hybrids

      Karlsson, S.; Hagen, M.; Eriksen, L.; Hindar, K.; Jensen, A.; De Leaniz, C.; Cotter, D.; Guobergsson, G.; Kahilainen, K.; Guojonsson, S.; et al. (Springer Netherlands, 2013)
      Interspecific hybridization between Atlantic salmon and brown trout is well documented, but why it should vary so much among populations is not clear. Determining the maternal origin of hybrids can provide insights into the mechanisms underlying interspecific hybridization, but this information is lacking in many studies. Here we present a species-specific mitochondrial DNA marker for the identification of the maternal origin of hybrids. This marker involves only one PCR step followed by fragment analysis, can be integrated within PCR multiplexing for existing nuclear markers for hybrid identification, and is therefore faster and more cost-effective than previous methods.
    • Improving abundance estimates from electrofishing removal sampling

      Hedger, Richard D; De Eyto, Elvira; Dillane, Mary; Diserud, Ola; Hindar, Kjetil; McGinnity, Philip; Poole, Russell; Rogan, Ger (Elsevier, 2013-01)
      Estimates of fish abundance from electrofishing surveys depend on accurate estimation of capture probability. We examine in this paper how estimates of capture probability and abundance of Atlantic salmon from multi-pass removal sampling can be improved by comparing the results of an experimental programme of closed electrofishing sites within selected rivers in west-central Norway, and those obtained from open electrofishing sites established for monitoring long-term juvenile Atlantic salmon population abundance within the Burrishoole catchment, western Ireland. We first establish that the Carle & Strub method provides a more robust estimate of population abundance than the Zippin and Seber methods. We then show how prior information on capture probability may be used to improve the accuracy of the abundance estimate in open sites. We also show that the use of prior information with single-pass electrofishing may improve the accuracy of the abundance estimate so that it is comparable with that of multi-pass electrofishing in terms of stock prediction while requiring less sampling effort
    • Creation and functioning of a buffer zone in an upland peat forested catchment

      O'Driscoll, Connie; O'Connor, Mark; Asam, Zaki-ul-Zaman; de Eyto, Elvira; Rodgers, Michael; Xiao, Liwen (Elsevier, 2014)
      Buffer zones can be used to reduce nutrient and suspended sediment export following forest clearfelling by directing runoff over a vegetated area. This study demonstrates the achievability of constructing a buffer zone by initially clearfelling the standing forest, seeding with two native grass species and directing the water from a semi-natural stream draining an upstream 10 ha forested peatland site through it. Following the clearfelling of the upstream study site this study tested the efficacy of this management practice in reducing nutrient and suspended sediment concentration in the receiving water. The buffer zone reduced total reactive phosphorus (TRP) and suspended sediment (SS) loads by 18% and 33%, respectively. Phosphorus (P) retention efficiency was dependent on inlet concentrations, loading and hydraulic loading rates. In storm events with a loading rate of >28 g P ha-1, a flow rate higher than 88.5 L s-1 and an inlet concentration of <17 µg L-1 the buffer zone became a TRP release source. The maximum P concentration in the buffer zone did not exceed 40 µg L-1 during this study demonstrating that the buffer zone method could be used efficiently in peatland forestry to moderate the high P concentrations and assist in protecting salmonids and freshwater pearl mussels.
    • Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

      Aykanat, T.; Johnston, S.; Cotter, D.; Cross, T.; Poole, R.; Prodohl, P.; Reed, T.; Rogan, G.; McGinnity, P.; Primmer, C. (BioMed Central, 2014)
      Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.