• National Survey of Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongatus Nordmann) on Fish Farms in Ireland – 2019

      O’Donohoe, P.; Kane, F.; Kelly, Suzanne; D'Arcy, J.; Casserly, Joanne; Downes, Jamie K.; McLoughlin, S.; Ruane, N.M.; Jackson, D. (Marine Institute, 2020)
      Farmed stocks of Atlantic salmon in Ireland are inspected on 14 occasions throughout the year to monitor sea lice levels as part of a national programme. Sea lice are a naturally occurring parasite found on marine fish, including salmonids. They are small ecto-parasitic copepod crustaceans and there are approximately 559 species. The objectives of the National Sea Lice Monitoring Programme are:  To provide an objective measurement of infestation levels on farms.  To investigate the nature of infestations.  To provide management information to drive the implementation of control and management strategies.  To facilitate further development and refinement of this strategy. The sea lice control and management strategy has five principal components:  Separation of generations.  Annual fallowing of sites.  Early harvest of two-sea-winter fish.  Targeted treatment regimes, including synchronous treatments.  Agreed husbandry practices.
    • National Survey of Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongatus Nordmann) on Fish Farms in Ireland – 2020

      O’Donohoe, P.; Kane, F.; Kelly, Suzanne; McDermott, Tom; D'Arcy, J.; Casserly, Joanne; Downes, Jamie K.; Thomas, K.; McLoughlin, S.; Ruane, N. M. (Marine Institute, 2021)
      Farmed stocks of Atlantic salmon in Ireland are inspected on 14 occasions throughout the year to monitor sea lice levels as part of a national programme. Sea lice are a naturally occurring parasite found on marine fish, including salmonids. They are small ecto-parasitic copepod crustaceans and there are approximately 559 species. The objectives of the National Sea Lice Monitoring Programme are: *To provide an objective measurement of infestation levels on farms. * To investigate the nature of infestations. * To provide management information to drive the implementation of control and management strategies. * To facilitate further development and refinement of this strategy. The sea lice control and management strategy has five principal components: * Separation of generations. * Annual fallowing of sites. * Early harvest of two-sea-winter fish. * Targeted treatment regimes, including synchronous treatments. * Agreed husbandry practices.
    • National Survey of the Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongates Nordmann) on Fish Farms in Ireland - 2000

      McCarney, P; Copley, L; Jackson, D; Nulty, C; Kennedy, S (Marine Institute, 2001-09)
      Fanned fish can be divided into three distinct groups, rainbow trout and two year classes (or generations) of salmon. In terms of husbandry and lice management, salmon which are at sea for a year or longer in April (growers/one-sea winter) are treated separately from younger salmon (smolts) and rainbow trout. Those salmon that were put to sea in winter 1999/spring 2000 are referred to as smolts, or 2000 year class fish. The farms were inspected twice a month in March, April and May and once a month thereafter, with one exception, December/January where sites were visited only once. Two species of lice are commonly found on cultured salmonids, Caligus elongates Nordmann, a species of parasite that infests over fifty different species of marine fish, and Lepeophtheirus salmonis Krøyer, which infests only salmon and closely related species such as rainbow trout. Lepeophtheirus salmonis, the Salmon Louse, is regarded as the more serious of the two species and occurs most frequently on Irish cultivated salmon (Jackson and Minchin, 1992). Results for both species are given for each sampling period. These sea-lice inflict damage to their hosts through their feeding activity on the host's body (Jones et al., 1990; Jonsdottir et al., 1992; Kabata, 1974) and significant economic losses were attributed to these copepod ectoparasites by Roth et al. (1993). Lepeophtheirus salmonis is a member of the Family Caligidae and has a direct lifecycle (i.e. a single host). This life-cycle comprises ten stages. Following hatching from paired egg strings, two free-living nauplius stages are dispersed into the plankton. These stages are followed by a copepodid stage where contact with the host takes place. The copepodid then moults through four chalimus stages before becoming a pre-adult male or female. This pre-adult phase comprises two stages and is followed by the fully mature adult phase. The adult female can produce a number of batches of paired egg-strings which in turn hatch into the water column to give rise to the next generation (Kabata, 1979; Schram, 1993).
    • National Survey of the Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongates Nordmann) on Fish Farms in Ireland - 2001

      McCarney, P; Copley, L; Kennedy, S; Nulty, C; Jackson, D (Marine Institute, 2002-02)
      Two species of lice are found on cultured salmonids, Caligus elongatus Nordmann, a species of parasite that infests over fifty different types of marine fishes, and Lepeophtheirus salmonis Krøyer, which infests only salmon and other salmonids. The Salmon Louse (L. salmonis) is regarded as the more serious parasite of the two species and has been found to occur most frequently on Irish farmed salmon (Jackson and Minchin, 1992). Most of the damage caused by these parasites is thought to be mechanical, carried out during the course of attachment and feeding (Kabata, 1974; Brandal et al., 1976; Jones et al., 1990). Inflammation and hyperplasia (enlargement caused by an abnormal increase in the number of cells in an organ or tissue) have been recorded in Atlantic salmon in response to infections with L. salmonis (Jones et al., 1990; Jonsdottir et al., 1992; Nolan et al., 2000). Increases in stress hormones caused by sea lice infestations have been suggested to increase the susceptibility of fish to infectious diseases (MacKinnon, 1998). Severe erosion around the head caused by heavy infestations of L. salmonis has been recorded previously (Pike, 1989; Berland, 1993). This is thought to occur because of the rich supply of mucus secreted by mucous cell-lined ducts in that region (Nolan et al., 1999). In experimental and field investigations carried out in Norway heavy infestation was found to cause fish mortalities (Finstad et al., 2000). Lepeophtheirus salmonis (Caligidae) has a direct life cycle, meaning it uses a single host. After hatching from the egg (which is extruded from the adult female louse in paired egg strings) two free-living nauplii stages are dispersed into the water column. A copepodid stage then follows during which a host must be located before the parasite can develop further. After finding a host the copepodid moults through four chalimus stages, which all occur while the parasite is attached to the host, before developing into a mobile pre-adult male or female. A moult then separates two pre-adult stages after which the fully mature adult develops. The adult female is capable of producing a number of batches of paired egg-strings during her life-span, which in turn hatch into the water column giving rise to the next generation. This gives a total of ten stages through which the parasite must develop to reach adulthood (Kabata, 1979; Schram, 1993). Caligus elongatus is a non-host specific parasite and can be found on many different fish species (Kabata, 1979). It has a similar life cycle to that of L. salmonis (Hogans and Trudeau, 1989). Four groups of farmed fish were examined during sea-lice inspections in 2001. These include rainbow trout, salmon smolts (200 I generation), one sea-winter salmon (2000 generation) and two sea-winter salmon (1999 generation). S1/2's or half year smolts are fish which are transferred to sea in Autumn/Winter of the same year that they are hatched, they smoltify early due to a photoperiod manipulation (Willoughby, 1999). Their S1 siblings smoltify and are put to sea in early spring. S1/2's are included in each year class of fish for the purpose of analyses.
    • National Survey of the Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongates Nordmann) on Fish Farms in Ireland - 2002

      O'Donohoe, P; Kennedy, S; Copley, L; Kane, F; Naughton, O; Jackson, D (Marine Institute, 2003)
      Salmonids farmed in Ireland in 2002 can be divided into the following groups: one year class of rainbow trout Oncorhynchus mykiss and three year classes of Atlantic salmon Salmo safar. The year classes of salmon include, smolts (2002 generation), one sea-winter salmon (2001 generation) and two sea-winter salmon (2000 generation). S1/2' s are fish which are transferred to sea in Autumn/Winter of the same year that they are hatched. Their S1 siblings smoltify and are put to sea in early spring, some three to four months later. Salmon which are at sea for a year or longer in April are known as growers/one sea-winter and are treated separately from younger salmon (smolts) and rainbow trout. Those salmon that were put to sea in winter 200 I /spring 2002 are referred to as smolts, or 2002 year class fish. During the 2002 sampling period all four groups of farmed fish were examined. Two species of sea lice are found on cultured salmonids in Ireland, Caligus elongates Nordmann, a species of parasite that infests over eighty different types of marine fish, and Lepeophtheirus salmonis Krøyer, which infests only salmon and other salmonids. Sea lice are regarded as having the most commercially damaging effect on cultured salmon in the world with major economic losses to the fish farming community resulting per annum (Bristow and Berland, 1991; Jackson and Costello, 1991). They affect salmon in a variety of ways: mainIy by reducing fish growth, loss of scales which leaves the fish open to secondary infections (Wootten et aI., 1982) and damaging of fish which reduces marketability.
    • National Survey of the Sea Lice (Lepeophtheirus salmonis Krøyer and Caligus elongates Nordmann) on Fish Farms in Ireland - 2003

      O'Donohoe, P; Kennedy, S; Kane, F; Naughton, O; Tierney, D; Copley, L; Jackson, D (Marine Institute, 2004)
      Sea lice are regarded as having the most commercially damaging effect on cultured salmon in the world with major economic losses to the fish farming community resulting per annum (Bristow and Berland, 1991; Jackson and Costello, 1991). They affect salmon in a variety of ways; by reducing fish growth; by causing loss of scales, which leaves the fish open to secondary infections (Wootten et al., 1982); and by damaging the fish, which reduces its marketability. The two species of sea lice found on cultured salmonids in Ireland are Caligus elongatus Nordmann, a species of parasite that infests over 80 different types of marine fish, and Lepeophtheirus salmanis Kroyer, which infests only salmon and other salmonids. L. salmonis is regarded as the more serious parasite of the two species and has been found to occur most frequently on farmed salmon (Jackson and Minchin, 1992). Most of the damage caused by these parasites is thought to be mechanical, carried out during the course of attachment and feeding (Kabata, 1974; Brandal et al., 1976; Jones et al., 1990). Inflammation and hyperplasia (enlargement caused by an abnormal increase in the number of cells in an organ or tissue) have been recorded in Atlantic salmon in response to infections with L. salmonis (Jones et al., 1990; Jonsdottir et al., 1992; Nolan et al., 2000). Increases in stress hormones caused by sea lice infestations have been suggested to increase the susceptibility of fish to infectious diseases (MacKinnon, 1998). Severe erosion around the head caused by heavy infestations of L. salmonis has been recorded previously (Pike, 1989; Berland, 1993). This is thought to occur because of the rich supply of mucus secreted by mucous cell-lined ducts in that region (Nolan et al., 1999). In experimental and field investigations carried out in Norway heavy infestation was found to cause fish mortalities (Finstad et al., 2000).
    • A National Survey of Water-Based Leisure Activities in Ireland 2003

      Marine Institute (Marine Institute, 2004)
      This survey profiles the domestic market for water-based tourism, sport and leisure in Ireland. The data provides up-to-date statistical information on 18 water-based leisure activities broadly grouped under the following categories: Seaside/Resort trips; Angling; Coastal and Inland Boating; and Watersports. The objective of the survey is to demonstrate the significant contribution of marine leisure activity to the national economy, and to highlight emerging trends and the potential for development of our water-based leisure resources. A key finding of the survey, conducted by the ESRI in 2003, is that marine leisure activity based on Ireland’s marine and freshwater resources generates €434 million in expenditure by Irish residents, and approximately 5,100 jobs are supported by this level of expenditure. A comparison of the domestic tourism market and the water-based tourism domestic market further highlights the value of the sector. In 2003, water-based tourism accounted for 22 per cent of the domestic tourism market and generated 45 per cent of domestic tourism revenue.Our seaside resorts, beaches, inland waterways and rivers provide the resource for a wide range of water-based tourism recreation, sport and leisure activities. The survey results show that 1.48 million persons, representing 49 per cent of the adult population participated in some form of water-based activity during the survey period. Although overall satisfaction with facilities was high, a further 10 per cent of the adult population (294,100) said they would take up some marine leisure activity if facilities were better. This demonstrates the potential and scope for development in the sector.
    • A National Survey of Water-Based Leisure Activities in Ireland 2003

      Williams, J [ESRI]; Ryan, B [ESRI] (Marine Institute, 2004)
      This survey profiles the domestic market for water-based tourism, sport and leisure in Ireland. The data provides up-to-date statistical information on 18 water-based leisure activities broadly grouped under the following categories: Seaside/Resort trips; Angling; Coastal and Inland Boating; and Watersports. The objective of the survey is to demonstrate the significant contribution of marine leisure activity to the national economy, and to highlight emerging trends and the potential for development of our water-based leisure resources. A key finding of the survey, conducted by the ESRI in 2003, is that marine leisure activity based on Ireland’s marine and freshwater resources generates €434 million in expenditure by Irish residents, and approximately 5,100 jobs are supported by this level of expenditure. A comparison of the domestic tourism market and the water-based tourism domestic market further highlights the value of the sector. In 2003, water-based tourism accounted for 22 per cent of the domestic tourism market and generated 45 per cent of domestic tourism revenue. Our seaside resorts, beaches, inland waterways and rivers provide the resource for a wide range of water-based tourism recreation, sport and leisure activities. The survey results show that 1.48 million persons, representing 49 per cent of the adult population participated in some form of water-based activity during the survey period. Although overall satisfaction with facilities was high, a further 10 per cent of the adult population (294,100) said they would take up some marine leisure activity if facilities were better. This demonstrates the potential and scope for development in the sector.
    • Natural selection acts on Atlantic salmon major histocompatibility (MH) variability in the wild

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

      Cross, T F; Galvin, P T (Marine Institute, 1997)
      This study was commissioned by the Irish Marine Institute in response to a Ministerial request from the Department of the Marine. The definition of Genetically Modified fish (GMO) that we use throughout this report is of fish that have a gene added from the same or another species, i.e. transgenics. This is a narrow definition, in that it excludes products of sex manipulation or ploidy manipulation, but is the one accepted by, for example, the European Union (Council Directive 90/220/EEC, Anon. 1990). We were asked to address a number of questions, viz. 1. Current "state of the art" in salmon genetic engineering. 2. What is available commercially and what commercial strains would be attractive to Irish interests? 3. What is the potential impact of transgenic Atlantic salmon (Salmo salar) in general? 4. What particular concerns would there be if a strain currently being reared in Scotland, were to be introduced to Ireland? 5. Are current ED Directives sufficient to protect Irish interests. If not what changes should be proposed? 6. What research is required to clarify the issues? This report was produced within twenty days of the initial request and thus we were confined largely to the literature that was available locally, though we were able to talk to some people who have various areas of expertise in the field and these people, who are listed in the acknowledgements, provided useful discussion and additional literature. One other point that should be made is that this is a very rapidly expanding field and the material described here will rapidly become dated.
    • Negotiations for the establishment of a pilchard fishery at Bantry in 1875

      Went, A. E. J. (Cork Historical and Archaeological Society, 1875)
    • New Connections II: A Review of Irish Participation in EU Marine Research Projects 2011-2013.

      O’Reilly, Elizabeth; Molloy, Eoin; O’Sullivan, Geoffrey (Marine Institute, 2014)
      New Connections II (2011-2013) complements its predecessor New Connections (2007-2010) published in 2011, and together they record the success of the Irish marine research community in competitive EU funded programmes such as FP7, INTERREG-IV, LIFE+, COST and the Lifelong Learning Programme. Over the period 2007-2013, 111 Irish marine research groups (including SMEs) participated in 210 marine related EU funded marine projects winning grant aid of over €70m.
    • New Connections: Exploring Ireland’s International Marine Research Partnerships

      O’Sullivan, Geoffrey; Nic Aonghusa, Caitriona; Kenny, Aine (Marine Institute, 2011)
      New Connections is a directory of Irish participation in EU funded marine research projects over the period 2007-2010. It contains a profile of each of the 98 co-operative and competitive projects that involve Irish partners under the FP7 Programme (64 projects), the INTERREG-IV Programme (32 projects), the Life+ Programme (1 project) and the Erasmus Mundus Programme (1 project). Each profile outlines the aims and objectives of the project, the project partnership and the Irish participants. New Connections (2011) is a companion publication to Oceans of Opportunity II (April 2007) which described Irish participation in the EU 6th Framework Programme (FP6) over the period 2002-2006.
    • New insights into the causes of human illness due to consumption of azaspiracid contaminated shellfish

      Chevallier, O.P.; Graham, S.F.; Alonso, E.; Duffy, C.; Silke, J.; Campbell, K.; Botana, L.M.; Elliott, C.T. (Nature Publishing Group, 2015)
      Azaspiracid (AZA) poisoning was unknown until 1995 when shellfish harvested in Ireland caused illness manifesting by vomiting and diarrhoea. Further in vivo/vitro studies showed neurotoxicity linked with AZA exposure. However, the biological target of the toxin which will help explain such potent neurological activity is still unknown. A region of Irish coastline was selected and shellfish were sampled and tested for AZA using mass spectrometry. An outbreak was identified in 2010 and samples collected before and after the contamination episode were compared for their metabolite profile using high resolution mass spectrometry. Twenty eight ions were identified at higher concentration in the contaminated samples. Stringent bioinformatic analysis revealed putative identifications for seven compounds including, glutarylcarnitine, a glutaric acid metabolite. Glutaric acid, the parent compound linked with human neurological manifestations was subjected to toxicological investigations but was found to have no specific effect on the sodium channel (as was the case with AZA). However in combination, glutaric acid (1mM) and azaspiracid (50nM) inhibited the activity of the sodium channel by over 50%. Glutaric acid was subsequently detected in all shellfish employed in the study. For the first time a viable mechanism for how AZA manifests itself as a toxin is presented.
    • A new scientific initiative with the Pelagic RAC to develop a management plan for western horse mackerel

      Clarke, M.; van Balsfoort, G.; Coers, A.; Campbell, A.; Dickey-Collas, M.; Egan, A.; Ghiglia, M.; Harkes, I.; Kelly, C.; O' Donoghue, S.; et al. (International Council for the Exploration of the Sea (ICES), 2007)
      The western horse mackerel stock is currently managed by annual TACs covering only part of its distribution area. No stock assessment has been accepted and recent ICES advice has consistently been for status quo catches. In 2006, the Pelagic Regional Advisory Committee asked scientists to help with developing a harvest control rule for the stock that would both meet conservation and stability objectives. An initial questionnaire was circulated to the industry, to elicit feedback on possible management options. A series of Harvest Control Rules were developed. These were tested by simulation and presented to the RAC at a number of meetings. Results will be presented within the ICES advisory process and elsewhere in the scientific literature. This is a developing approach involving scientists and stakeholders in an iterative process. The problems encountered and lessons learned, are discussed.
    • Newport Research Facility, Annual Report No. 59, 2014

      Marine Institute (Marine Institute, 2015)
      This report represents a continuation of the Annual Reports published by the Salmon Research Agency of Ireland, now integrated them into the Fisheries Ecosystem Advisory Services Group (FEAS)of the Marine Institute.The data presented creates a unique record of fish rearing and wild fish census data for the past 43 years. This data is an essential component in the local, regional and national management of salmon, sea trout and eel and is becoming ever more valuable in the light of increasing pressures on natural stocks, such as exploitation, habitat degradation and global climate change scenarios. The fish monitoring facilities in Newport, along with the reared and ranched salmon stocks held in Burrishoole, are also essential for the evaluation of novel enhancement techniques, alternative stocks and ranching and evaluation of interactions between farmed, ranched and wild strains.
    • Newport Research Facility, Annual Report No. 60, 2015

      Marine Institute (Marine Institute, 2017)
      This report represents a continuation of the Annual Reports published by the Salmon Research Agency of Ireland, now integrated them into the Fisheries Ecosystem Advisory Services Group (FEAS)of the Marine Institute. The data presented creates a unique record of fish rearing and wild fish census data for the past 44 years. This data is an essential component in the local, regional and national management of salmon, sea trout and eel and is becoming ever more valuable in the light of increasing pressures on natural stocks, such as exploitation, habitat degradation and global climate change scenarios. The fish monitoring facilities in Newport, along with the reared and ranched salmon stocks held in Burrishoole, are also essential for the evaluation of novel enhancement techniques, alternative stocks and ranching and evaluation of interactions between farmed, ranched and wild strains.
    • Newport Research Facility, Annual Report No. 63, 2018

      Marine Institute (Marine Institute, 2019)
    • Newport Research Facility, Annual Report No. 64, 2019

      Marine Institute (Marine Institute, 2020)
    • Newport Research Facility, Annual Report No. 65, 2020

      Marine Institute (Marine Institute, 2021)
      This report represents a continuation of the scientific aspects of the Annual Reports published by the Salmon Research Agency of Ireland, now integrated into the Fisheries Ecosystem Advisory Services Group (FEAS) of the Marine Institute. The data presented creates a unique record of fish rearing and wild fish census data for the past 49 years. This data is an essential component in the local, regional and national management of salmon, sea trout and eel and is becoming ever more valuable in the light of increasing pressures on natural stocks, such as exploitation, habitat degradation and global climate change scenarios. The fish monitoring facilities in Newport, along with the reared and ranched salmon stocks held in Burrishoole, are also essential for supporting projects such as development of novel enhancement techniques, alternative stocks and ranching and evaluation of interactions between farmed, ranched and wild strains. An expanding programme in the Burrishoole system is including ecological and genetics research into eel, sticklebacks and stock dynamics of juvenile salmonids and eels.