• The occurrence of persistent chlorinated and brominated organic contaminants in the European eel (Anguilla anguilla) in Irish waters

      McHugh, B; Poole, R; Corcoran, J; Pinelopi, A; Boyle, B (Elsevier, 2010)
      The European eel (Anguilla anguilla) is a relatively high lipid, long lived species capable of living in a variety of brackish, fresh and marine habitats. As such, eels can accumulate organic pollutants and have been incorporated into environmental monitoring programs as a suitable “bioindicator” species for the determination of the levels of organic contaminants within different water bodies. The global eel stock is now in decline and while the cause of the collapse remains unidentified, it is likely to include a combination of anthropogenic mortality in addition to environmental degradation. This study provides valuable data on a range of contaminants (PCDD/Fs, PCBs, OCPs, PBDEs, HBCD, TBBPA and PBBs) and extractable lipid levels in eel muscle tissue collected from five Irish catchments. Extractable lipid levels were lower in the yellow eels compared to those in the silver eels. These levels were similar to those reported elsewhere and it has been posited that a decline in the lipid content in yellow eels may have consequences for the future viability of the stock. With the exception of higher substituted dioxins (especially OCDD), in three samples collected from one catchment (Burrishoole) in the West of Ireland, POP levels in general were determined to be low in eels from Irish waters compared to those in other countries.
    • The occurrence of persistent chlorinated and brominated organic contaminants in the European eel (Anguilla anguilla) in Irish waters

      McHugh, B; Poole, R; Corcoran, J; Anninou, P; Boyle, B; Joyce, E; Foley, M B; McGovern, E (Elsevier, 2010)
      The European eel (Anguilla anguilla) is a relatively high lipid, long lived species capable of living in a variety of brackish, fresh and marine habitats. As such, eels can accumulate organic pollutants and have been incorporated into environmental monitoring programs as a suitable “bioindicator” species for the determination of the levels of organic contaminants within different water bodies. The global eel stock is now in decline and while the cause of the collapse remains unidentified, it is likely to include a combination of anthropogenic mortality in addition to environmental degradation. This study provides valuable data on a range of contaminants (PCDD/Fs, PCBs, OCPs, PBDEs, HBCD, TBBPA and PBBs) and extractable lipid levels in eel muscle tissue collected from five Irish catchments. Extractable lipid levels were lower in the yellow eels compared to those in the silver eels. These levels were similar to those reported elsewhere and it has been posited that a decline in the lipid content in yellow eels may have consequences for the future viability of the stock. With the exception of higher substituted dioxins (especially OCDD), in 3 samples collected from one catchment (Burrishoole) in the West of Ireland, POP levels in general were determined to be low in eels from Irish waters compared to those in other countries.
    • The oil spill model OILTRANS and its application to the Celtic Sea

      Berry, Alan; Dabrowski, Tomasz; Lyons, Kieran (Elsevier, 2012)
      This paper describes details of an oil spill model, OILTRANS, developed by the authors. The model is an off-line particle-transport model coupled to the most up to date operational met-ocean model forecasts. Formulations for the dominant oil fate processes of spreading, advection, diffusion, evaporation, emulsification and dispersion have been encoded, providing the model with the ability to accurately predict the horizontal movement of surface oil slick, the vertical entrainment of oil into the water column and the mass balance of spilled oil. The application of the OILTRANS model to an accidental release during a ship-to-ship fuel transfer in the Celtic Sea in February 2009 is presented to validate the system. Comparisons with aerial observations of the oil slick at the time of the incident, and subsequent model simulations, indicate that the OILTRANS model is capable of accurately predicting the transport and fate of the oil slick.
    • An operational biogeochemical model of the North-East Atlantic: model description and skill assessment

      Dabrowski, T.; Lyons, K.; Berry, A.; Cusack, C.; Nolan, G. (Elsevier, 2013)
      This paper presents a high resolution operational biogeochemical model of the North-East Atlantic that encompasses part of the continental shelf and adjacent deep sea and includes all of Ireland's territorial waters. The setup of the model is described, followed by its skill assessment in reproducing chlorophyll and nitrate spatio-temporal variability. Part of the model skill assessment concerns the evaluation of its usefulness in a decision-making process and is based on the application of a binary discrimination analysis. The model is one-way nested within a 1/12° Mercator Ocean PSY2V4R2 operational model that provides physical forcing at the lateral open boundaries. Nitrate fields are also proscribed at the open boundaries; the World Ocean Atlas 2009 monthly climatologies are used in the upper 500 m and at greater depths a formula that relates nitrate concentration to temperature and latitude is applied in the model. The model represents the intra-annual variability of surface chlorophyll and nitrate concentrations at monthly time scales across key oceanographic regions reasonably well; deficiencies are identified in some regions along with possible causes. The model can reproduce important characteristic bio-physicochemical features e.g. the frontal dynamics and upwelling off southwest Ireland and the properties of different water masses in the Rockall Trough. The model is deemed suitable for operational purposes, with a high probability to make correct positive and negative decisions. Operational since 2011, the output is publicly available via a dedicated THREDDS server.
    • Overcoming the “tragedy of the commons” in fishery management

      Kraak, S. B. M. (International Council for the Exploration of the Sea (ICES), 2011)
      In situations of declining or depleted fish stocks, fishers seem to have fallen prey to the “tragedy of the commons”. This occurs because fishers face the dilemma that, although they understand that limiting their catches would pay off in the form of sustainable future catches, they can never be sure that the catch which they have just sacrificed will not be immediately snapped up by competing fishers. Standard economic theory predicts that, in such dilemmas, individuals are not willing to cooperate and sacrifice catches in the short term, and that, consequently, the resource is overharvested. However, over past decades, a multitude of research endeavours have shown that humans often achieve outcomes that are “better than rational” by building conditions where reciprocity, reputation, and trust help to overcome the temptations of short-term self-interest.
    • Phosphorus release from forest harvesting on an upland blanket peat catchment

      Rodgers, Michael; O’Connor, Mark; Healy, Mark Gerard; O’Driscoll, Connie; Asam, Zaki-ul-Zaman; Nieminen, Mika; Poole, Russell; Müller, Markus; Xiao, Liwen (Elsevier, 2010)
      The aim of this study was to investigate the release of phosphorus (P) to receiving waters resulting from harvesting 34-year-old lodgepole pine trees in an upland peat catchment. The study site was within a 25.3-hectare (ha) area, and was drained by a stream that received flows from ploughed furrows, mainly, via collector drains, and discharged directly to the salmonid Shrahrevagh River, Burrishoole, Co. Mayo, Ireland. The study site was divided in two parts: the upstream part was left intact and the downstream part was harvested in early Autumn 2005 following implementation of forest guidelines. Good management practices such as proper use of brash mats and harvesting only in dry weather were implemented. Two instrumented stations were established – one just upstream (US) and the other just downstream (DS) of the clearfelled area. The measurement of P concentrations at the two stations commenced in May 2005, two months before the harvesting started. The daily mean P concentration at the DS station increased from about 6 μg L-1 of total reactive phosphorus (TRP) during pre-clearfelling to 429μg L-1 in August 2006. By October 2009, four years after clearfelling, the P concentrations at the DS station had returned to pre-clearfelling levels. In the first three years after harvesting, up to 5.15 kg ha-1 of TRP were released from the harvested catchment to the receiving water; in the second year alone, 2.3 kg ha-1 of TRP were released. Linear regression can be used to describe the relationship between TRP load and water discharge. About 80 % of the total phosphorus (TP) in the study stream was soluble and more than 70 % of the P release occurred in storm events, indicating that traditional buffer strips with widths of 15-20 m might not be efficient for P immobilization. The P concentrations were affected by antecedent weather conditions and highest concentrations occurred during storm events following prolonged drought periods. The water extractable phosphorus (WEP) contents in the soil were significantly higher below windrow/brash material than in brash-free areas, and whole-tree harvesting should be studied as one of the means to decrease P export from blanket peats.
    • 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.
    • A potential solution to mitigate phosphorus release following clearfelling in peatland forest catchments

      O’Driscoll, Connie; Rodgers, Michael; O’Connor, Mark; Asam, Zaki-ul-Zaman; de Eyto, Elvira; Poole, Russell; Xiao, Liwen (Springer, 2011)
      Since the 1950s, large areas of upland peat have been afforested in northern European countries. Due to the poor phosphorus (P) adsorption capacity and low hydraulic permeability in blanket peat soil and increased labile P sources, harvesting these blanket peat forests can significantly increase P concentrations in the receiving aquatic systems. This paper briefly reviews the current management practices on the control of P releases from forestry in Ireland and the UK, and proposes a possible novel practice—grass seeding clearfelled areas immediately after harvesting, which should reduce P release from blanket peat forest harvesting. The study was conducted in the Burrishoole Catchment in the west of Ireland. A field trial was carried out to identify the successful native grass species that could grow quickly in the blanket peat forest. The two successful grass species—Holcus lanatus and Agrostis capillaris—were sown in three blanket peat forest study plots with areas of 100, 360, and 660 m2 immediately after harvesting. Areas without grass seeding were used as controls. One year later, the P content in the aboveground vegetation biomass of the three study plots were 2.83, 0.65, and 3.07 kg P ha−1, respectively, which were significantly higher than the value of 0.02 kg P ha−1 in the control areas. The water extractable phosphorus in the three study plots were 8.44, 9.83, and 6.04 mg (kg dry soil)−1, respectively, which were lower than the value of 25.72 mg (kg dry soil)−1 in the control sites. The results indicate that grass seeding of the peatland immediately after harvesting can quickly immobilize significant amounts of P and warrants additional research as a new Best Management Practice following harvesting in the blanket peatland forest to mitigate P release.
    • A predictive model for estimating river habitat area using GIS-derived catchment and river variables

      McGinnity, P; de Eyto, E; Gilbey, J; Gargan, P; Roche, W; Stafford, T; McGarrigle, M; Ó Maoiléidigh, N; Mills, P (Blackwell Publishing Ltd., 2012)
      The implementation of many fisheries management-related activities in fresh water depends on habitat area inventories over extensive geographical scales. While river lengths are readily available, representative widths, necessary for area calculations, are difficult to obtain. As field surveys to collect this information are resource intensive, a predictive model was developed to enable the calculation of river wetted width using GIS-derived values for catchment and river descriptors. A model containing upstream catchment area and the Shreve river drainage network index accounted for 88% of the variation in field measured river wetted width. Comparisons in Irish and Scottish rivers between modelled and measured widths were highly correlated and suggest that the model may be transferable to neighbouring geographic areas. As an example, the model is applied to provide an estimate of the usable fluvial habitat available to Atlantic salmon in Ireland.
    • The preparation of certified calibration solutions for azaspiracid-1, -2, and -3, potent marine biotoxins found in shellfish

      Perez, R; Rehmann, N; Crain, S; LeBlanc, P; Craft, C; MacKinnon, S; Reeves, K; Burton, I W; Walter, J A; Hess, P; et al. (Springer Verlag, 2010)
      The production and certification of a series of azaspiracid (AZA) calibration solution reference materials is described. Azaspiracids were isolated from contaminated mussels, purified by preparative liquid chromatography and dried under vacuum to the anhydrous form. Purity was assessed by liquid chromatography–mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy. Final concentration of each AZA in a CD3OH stock solution was determined accurately by quantitative NMR spectroscopy. This solution was then diluted very accurately in degassed, high purity methanol to a concentration of 1.47 ± 0.08 μmol/L for AZA1, 1.52 ± 0.05 μmol/L for AZA2, and 1.37 ± 0.13 μmol/L for AZA3. Aliquots were dispensed into argon-filled glass ampoules, which were immediately flame-sealed. The calibration solutions are suitable for method development, method validation, calibration of liquid chromatography or mass spectrometry instrumentation and quality control of shellfish monitoring programs.
    • Production and Isolation of Azaspiracid-1 and -2 from Azadinium spinosum Culture in Pilot Scale Photobioreactors

      Jauffrais, Thierry; Kilcoyne, Jane; Séchet, Véronique; Herrenknecht, Christine; Truquet, Philippe; Hervé, Fabienne; Bérard, Jean Baptiste; Nulty, Cíara; Taylor, Sarah; Tillmann, Urban; et al. (MPDI Publishing, 2012)
      Azaspiracid (AZA) poisoning has been reported following consumption of contaminated shellfish, and is of human health concern. Hence, it is important to have sustainable amounts of the causative toxins available for toxicological studies and for instrument calibration in monitoring programs, without having to rely on natural toxin events. Continuous pilot scale culturing was carried out to evaluate the feasibility of AZA production using Azadinium spinosum cultures. Algae were harvested using tangential flow filtration or continuous centrifugation. AZAs were extracted using solid phase extraction (SPE) procedures, and subsequently purified. When coupling two stirred photobioreactors in series, cell concentrations reached 190,000 and 210,000 cell•mL−1 at steady state in bioreactors 1 and 2, respectively. The AZA cell quota decreased as the dilution rate increased from 0.15 to 0.3 day−1, with optimum toxin production at 0.25 day−1. After optimization, SPE procedures allowed for the recovery of 79 ± 9% of AZAs. The preparative isolation procedure previously developed for shellfish was optimized for algal extracts, such that only four steps were necessary to obtain purified AZA1 and -2. A purification efficiency of more than 70% was achieved, and isolation from 1200 L of culture yielded 9.3 mg of AZA1 and 2.2 mg of AZA2 of >95% purity. This work demonstrated the feasibility of sustainably producing AZA1 and -2 from A. spinosum cultures.
    • Quantitative analysis of azaspiracids in Azadinium spinosum cultures

      Jauffrais, Thierry; Herrenknecht, Christine; Séchet, Véronique; Sibat, Manoella; Tillmann, Urban; Krock, Bernd; Kilcoyne, Jane; Miles, Christopher O.; McCarron, Pearse; Amzil, Zouher; et al. (Springer, 2012)
      Azaspiracids (AZAs) are secondary metabolites of Azadinium spinosum that can accumulate in shellfish and cause food poisoning when consumed. We describe here an analytical procedure for the determination of AZAs in cultures of A. spinosum with a focus on the formation of AZA methyl esters as artefacts during extraction and sample pre-treatment. A. spinosum cells were collected from bioreactor cultures using centrifugation or filtration. Different extraction procedures were evaluated for formation of methyl ester artefacts, yield, and matrix effects. Filtration of cultures using glass-fibre filters led to increased formation of methyl esters, and centrifugation is recommended for recovery of cells. The extraction solvent (methanol (MeOH), acetone, and acetonitrile (MeCN)) did not significantly affect the yield of AZAs as long as the organic content was 80% or higher. However, the use of MeOH as extraction solvent led to increased formation of methyl esters. AZA1 recovery over two successive extractions was 100% at the 95% confidence level for acetone and MeOH. In standard-addition experiments, no significant matrix effects were observed in extracts of A. spinosum or Azadinium obesum up to a sample size of 4.5 × 109 μm3. Moreover, experiments carried out to clarify the formation and structure of methylated AZA analogues led to the description of two AZA methyl esters and to the correction of the chemical structures of AZAs29–32.
    • Rapid and highly variable warming of lake surface waters around the globe

      O'Reilly, C.M.; Sharma, S.; Gray, D.K.; Hampton, S.E.; Read, J.S.; Rowley, R.J.; Schneider, P.; Lenters, J.D.; McIntyre, P.B.; Kraemer, B.J.; et al. (American Geophysical Union, 2015)
      In this first worldwide synthesis of in situ and satellite-derived lake data, we find that lake summer surface water temperatures rose rapidly (global mean = 0.34°C decade 1) between 1985 and 2009. Our analyses show that surface water warming rates are dependent on combinations of climate and local characteristics, rather than just lake location, leading to the counterintuitive result that regional consistency in lake warming is the exception, rather than the rule. The most rapidly warming lakes are widely geographically distributed, and their warming is associated with interactions among different climatic factors —from seasonally ice-covered lakes in areas where temperature and solar radiation are increasing while cloud cover is diminishing (0.72°C decade 1) to ice-free lakes experiencing increases in air temperature and solar radiation (0.53°C decade 1). The pervasive and rapid warming observed here signals the urgent need to incorporate climate impacts into vulnerability assessments and adaptation efforts for lakes.
    • Recent data suggest no further recovery in North Sea Large Fish Indicator

      Fung, Tak; Farnsworth, Keith D.; Reid, David G.; Rossberg, Axel G. (Oxford Journals, 2012)
      We detail the calculations of North Sea Large Fish Indicator values for 2009–2011, demonstrating an apparent stall in recovery. Therefore, recovery to the Marine Strategy Framework Directive's good environmental status of 0.3 by the 2020 deadline now looks less certain and may take longer than was expected using data from 2006 to 2008.
    • The recent population expansion of boarfish, Capros aper (Linnaeus, 1758): interactions of climate, growth and recruitment

      Coad, J.O.; Hüssy, K.; Farrell, E.D.; Clarke, M.W. (John Wiley & Sons, Inc, 2014)
      The objectives of this study were to evaluate whether temperature changes in the Northeast Atlantic influence the growth and recruitment dynamics of boarfish, Capros aper. Two geographically separate areas were examined, ‘north’ at the northern distribution range west of Ireland and ‘south’ on the main fishing grounds south of Ireland. No significant differences in length-at-age were observed between the two areas. Interannual otolith growth patterns were similar between the two areas with distinct years of faster and slower growth. In the ‘north’, no significant relationship between adult growth and temperature was observed, while growth in the ‘south’ was positively related to temperature up to approximately 16°C growth rates were suppressed in the years with temperatures above that. Recruitment showed a positive correlation with adult growth the previous year for the Spanish recruitment index only, suggesting spatial connectivity between the Celtic Sea and the Bay of Biscay. The age distributions were similar in both areas and despite the boarfish's longevity of >30 years, are dominated by the age classes corresponding to the years with high recruitment, suggesting that increased recruitment is responsible for the observed stock expansion.
    • Report of the Study Group on Nephrops Surveys (SGNEPS)

      Doyle, J.; Lordan, C. (International Council for the Exploration of the Sea (ICES), 2013)
      The Study Group on Nephrops Surveys (SGNEPS) met in Ancona, Italy from 6–8 March 2012. The group consisted of 12 scientists from Ireland, Scotland, England, Northern Ireland, Spain, Denmark, Portugal and Italy under the chairmanship of Colm Lordan, Ireland. SGNEPS has an important role as the international coordina-tion group for Nephrops UWTV surveys in the North Atlantic and Mediterranean. Heretofore SGNEPS has focused on planning, protocols, quality control, design and survey development issues. At the 2012 meeting group compiled a table summarizing the station densities and precision levels of most annual Nephrops UWTV surveys. Large variations in survey station densities occur across the grounds currently sur-veyed. Station density, accuracy and precision trade-offs were investigated and dis-cussed in detail for the two main survey design types (random stratifies and grids). The main outcome of these deliberation was that a minimum precision level of <20% CV (also known as Relative Standard Error) should be attained for these types of surveys. There may be operational reasons why individual surveys should aim for higher precision than that (e.g. to ensure good coverage and accurate burrow surfac-es). In some areas station densities could be reduce to allow for improved coverage to previously unsurveyed Nephrops grounds. Progress towards integrated stock assess-ments for Nephrops which make use of all sources of fisheries dependent and inde-pendent information was reported to the group. There was consensus that the current ICES framework for assessing and providing catch options based on the UWTV sur-veys remains the most appropriate methodology for the moment. There has been significant progress since WKNEPH (ICES, 2007) in addressing many of the per-ceived uncertainties in the methodology. The remaining assumptions on burrow occupancy, burrow size, growth, discard survival can only be addressed through dedicated research projects of which there have been few. Several video enhancement and technological developments were presented to the group and these look very promising in terms of improving certainty of burrow identification and facilitating validation counts. The group also discussed the various Nephrops trawl surveys and biological sampling requirements under the DCF and concluded that the role of the group should be expanded to cover these in future.
    • Reproductive biology of the starry smooth-hound shark (Mustelus asterias): geographic variation and implications for sustainable exploitation

      Farrell, E D; Mariani, S; Clarke, M W (Wiley-Blackwell, 2010)
      Examination of the reproductive biology of Mustelus asterias in the north-east Atlantic Ocean highlighted apparent geographical variation in maturity, fecundity and ovarian cycle between Atlantic and Mediterranean populations. The stretch total length (LST) and age at 50% maturity for Atlantic males and females were estimated at 78 cm LST and 4–5 years and 87 cm LST and 6 years, respectively. Size at maturity of females was considerably smaller than in Mediterranean specimens (96 cm LST). Ovarian fecundity ranged from eight to 27 oocytes and uterine fecundity from six to 18 embryos. The gestation period was c. 12 months, followed by a resting period of c. 12 months, resulting in a biennial cycle. Females stored sperm in the oviducal gland and, unlike Mediterranean specimens, no uterine compartments were observed in Atlantic specimens. This study reveals the existence of strong, possibly adaptive, divergence in life-history traits in an elasmobranch, whose northern populations may be more susceptible to overexploitation than previously believed.
    • The response of North Atlantic diadromous fish to multiple stressors including land use change: a multidecadal study

      de Eyto, E.; Dalton, C.; Dillane, M.; Jennings, E.; McGinnity, P.; O'Dwyer, B.; Poole, R.; Rogan, G.; Taylor, D. (NRC Research Press, 2016)
      Reduction of freshwater habitat quality due to land use change can have significant impacts on diadromous fish. Partitioning this impact from other potential drivers, such as changing marine conditions and climate, is hampered by a lack of long term datasets. Here, four decades of data were used to assess the impact of land use change on <i>Salmo salar</i> L. and anadromous <i>Salmo trutta</i> L. in the Burrishoole catchment, Ireland, one of the few index sites for diadromous fish in the North Atlantic. Land use change was found to have no significant impact on the freshwater survival of either salmon or trout. However, climate impacted significantly on the survival of salmon and trout in freshwater, with poor survival in years with wetter warmer winters, coinciding with positive North Atlantic Oscillation values. Additionally, cold springs were associated with higher survival in trout. The addition of hatchery salmon into the salmon spawning cohort coincided with low freshwater survival. Our results highlight the necessity for a broad ecosystem approach in any conservation effort of these species.
    • The rise and fall of autumn-spawning herring (Clupea harengus L.) in the Celtic Sea between 1959 and 2009: Temporal trends in spawning component diversity

      Harma, Clémentine; Brophy, Deirdre; Minto, Cóilín; Clarke, Maurice (Elsevier, 2012)
      Sub-stock components of highly exploited migratory fish species exhibit different life-history traits and can thus show variation in productivity and vulnerability to fishing pressure. Celtic Sea herring comprises both autumn and winter-spawners that are targeted by the same fishery. The current study investigated if the relative abundances of the two components in the Celtic Sea have changed over time, and whether this could explain marked long-term trends in size-at-age. The study utilized a remarkably long time-series of biological data from commercial landings (1959–2009). Based on the maturity state of the gonads at the time of sampling, herring were assigned to seasonal spawning components. Significant temporal variations in spawning component dominance were found, even after potential bias due to fishing history patterns were accounted for. Strong directional changes in the relative proportion of spawning components consisted of autumn spawning herring proportions reaching a peak in the 1990s before drastically declining. Winter spawning herring had lower mean lengths- and weights-at-age than autumn spawning herring. The recent decline in the autumn spawning component did not fully explain the observed decline in size-at-age in the catches, with both spawning components showing similar decreases in mean-size parameters over time. Response of spawning components to environmental changes may have consequences for the fishery, especially in light of the observed influence of temperature on spawning components. Life-cycle diversity in herring stocks may confer resilience to potential climate-induced changes. Therefore, it is suggested that the relative proportions of spawning components should be monitored and diversity should be preserved as part of the management of fisheries for this species, which is characterized by stock complexity.
    • Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon

      Vasemägi, Anti; Nilsson, Jan; McGinnity, Philip; Cross, Tom; O'Reilly, Patrick; Glebe, Brian; Peng, Bo; Berg, Paul Ragnar; Primmer, Craig Robert (Hindawi Publishing Corporation, 2012)
      Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.