• 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.
    • 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.
    • Certified Reference Materials for Marine Monitoring

      Pellizzato, Francesca; McGovern, Evin; Quevauviller, Philippe (J. Wiley & Sons, Chichester, West Sussex, 2011)
    • 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.
    • 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.
    • 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.; Romakkaniemi, A.; Ryman, N. (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.
    • Identifying the role of environmental drivers in organic carbon export from a forested peat catchment

      Ryder, Elizabeth; DeEyto, Elvira; Dillane, Mary; Poole, Russell; Jennings, Eleanor (Elsevier, 2014)
      Carbon export in streams draining peat catchments represents a potential loss of carbon from long-term stores to downstream aquatic systems and ultimately, through mineralisation, to the atmosphere. There is now a large body of evidence that dissolved organic carbon (DOC) export has increased significantly in recent decades at many sites, although there is still debate about the drivers of this increase. In this study, DOC export and particulate organic carbon (POC) export were quantified from a forested peatland catchment in the west of Ireland over two years at a fine temporal resolution. The principle drivers of change in stream DOC and POC concentrations were investigated using a general additive modelling (GAM) approach. The study period included drought conditions in the early summer of 2010 and clearfelling of some commercial forestry in early 2011. The results indicated that annual loads of 9.5 t DOC km2 year− 1 and 6.2 t POC km2 year− 1 were exported from the catchment in 2010. This combined annual load of 15.7 t C km2 year− 1 would represent between 0.01% and 0.02% of typical estimates for peat soil carbon storage in the region. Soil temperature, river discharge and drought explained 59.7% the deviance in DOC concentrations, while soil temperature, river discharge, and rainfall were the significant drivers of variation in POC concentrations, explaining 58.3% of deviance. Although clearfelling was not a significant factor in either model, large spikes in POC export occurred in 2011 after the first forestry clearance. The results illustrate the complexity of the interactions between climate and land management in driving stream water carbon export. They also highlight the sensitivity of peatland carbon stores to changes in temperature and precipitation, which are projected to be more extreme and variable under future climate scenarios.
    • 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
    • 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.
    • Modelling fuel consumption of fishing vessels for predictive use

      Davie, S.; Minto, C.; Officer, R.; Lordan, C.; Jackson, E. (ICES, 2015)
      Fuel costs are an important element in models used to analyse and predict fisher behaviour for application within the wider mixed fisheries and ecosystem approaches to management. This investigation explored the predictive capability of linear and generalized additive models (GAMs) in providing daily fuel consumption estimates for fishing vessels given knowledge of their length, engine power, fleet segment (annual dominant gear type), and fuel prices. Models were fitted to half of the Irish fishing vessel economic data collected between 2003 and 2011. The predictive capabilities of the seven best models were validated against the remaining, previously un-modelled, data. The type of gear used by a fleet segment had an important influence on fuel consumption as did the price of fuel. The passive pot gear and Scottish seine gear segments indicated consistently lower consumptions, whereas dredge and pelagic gears showed consistently higher fuel consumptions. Furthermore, increasing fuel price negatively affected fuel consumption, especially for more powerful, larger vessels. Of the formulated models, the best fit to training data were a GAM with a gear main effect and two smooth functions; standardized vessel length and engine power interacting with fuel price. For prediction, overall, this model showed the closest predictions with the least bias, followed by three linear models. However, all seven models compared for predictive capability performed well for the most sampled segments (demersal and pelagic trawlers).
    • 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.
    • Numerical modelling of blue mussel (Mytilus edulis) bacterial contamination

      Dabrowski, T.; Dore, W.; Lyons, K.; Nolan, G. (Elsevier, 2014)
      Bivalve shellfish such as oysters and mussels can concentrate human pathogens when grown in areas impacted by municipal wastewater. Under EU regulation this risk to consumers is controlled by determining the sanitary quality of bivalve shellfish production areas based on the concentration of Escherichia coli present in shellfish flesh. The authors present a modelling approach to simulate an uptake of E. coli from seawater and subsequent depuration by Mytilus edulis. The model that dynamically predicts E. coli concentration in the mussel tissue is embedded within a 3-D numerical modelling system comprising hydrodynamic, biogeochemical, shellfish ecophysiological and the newly proposed microbial modules. The microbial module has two state variables, namely, the concentrations of E. coli in water and in the mussel tissue. Novel formulations to calculate the filtration rates by mussels and the resulting uptake of bacteria are proposed; these rates are updated at every computational time step. Concentrations of E. coli in seawater are also updated accordingly taking into account the amounts ingested by mussels. The model has been applied to Bantry Bay in the south-west of Ireland. The results indicate that the model is capable of reproducing the official classification of shellfish waters in the bay based on monthly sampling at several stations. The predicted filtration rates and ratios of E. coli in water and mussels also compare well with the literature. The model thus forms a tool that may be used to assist in the classification of shellfish waters at much greater spatial and temporal detail than that offered by a field monitoring programme. Moreover, it can also aid in designing an efficient monitoring programme. The model can also be utilised to determine the contribution of individual point sources of pollution on the microbial loading in mussels and, when incorporated into an operational framework, it can provide a short-term forecasting of microbial contamination in a shellfishery. Also, the model can be easily extended to include other shellfish and pathogen species.
    • 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.
    • Prey preferences of sympatric fin (Balaenoptera physalus) and humpback (Megaptera novaeangliae) whales revealed by stable isotope mixing models

      Ryan, C; Berrow, S; McHugh, B; O'Donnell, C; Trueman, C; O'Connor, I (Wiley, 2014-01)
      Over-exploitation of top predators and fish stocks has altered ecosystems towards less productive systems with fewer trophic levels. In the Celtic Sea (CS), discards and bycatch levels have prompted concern about some fisheries, while fin and humpback whales are recovering from centuries of over-exploitation. A lack of empirical evidence on the preferred diet of some predators such as whales in the CS has hindered the implementation of effective conservation measures using an ecosystem-based approach to fisheries management. Using a Bayesian framework (SIAR), stable carbon (δ13C) and nitrogen (δ15N) isotope mixing models were used to assign proportionate diet solutions to fin and humpback whales (skin biopsies) and putative prey items: herring (Clupea harengus), sprat (Sprattus sprattus), and krill (Meganyctiphanes norvegica and Nyctiphanes couchii) in the CS. Krill was the single most important prey item in the diet of fin whales, but one of the least important for humpback whales (albeit based on a small sample of humpback whale samples). Age 0 sprat and herring comprised a large proportion of the diet of both species, followed by older sprat (age 1–2) and older herring (age 2–4). An ecosystem based approach to fisheries management will be required in the CS if we seek effective conservation of both fin and humpback whales, and sustainable fisheries.
    • RIPARIAN ZONE CREATION IN ESTABLISHED CONIFEROUS FORESTS IN IRISH UPLAND PEAT CATCHMENTS: PHYSICAL, CHEMICAL AND BIOLOGICAL IMPLICATIONS

      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.
    • 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.
    • 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.
    • 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; Cross, Tom; Stet, Rene J. M. (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.