Marine Institute Open Access Repository

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The Marine Institute Open Access Repository facilitates full text access to the publications of the Marine Institute in accordance with copyright permissions. The aim of the Repository is to collect, preserve and provide open access to the publications of the Marine Institute, including the research publications supported by National and European funded marine research programmes.



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  • Reproductive Failure of Landlocked Atlantic Salmon from New York's Finger Lakes: Investigations into the Etiology and Epidemiology of the “Cayuga Syndrome”

    Fisher, J.P.; Spitsbergen, J.M.; Rodman, G.; symula, j. (American Fisheries Society, 1995)
    We describe a disease syndrome that afflicts larval, landlocked Atlantic salmon Salmo salar from Cayuga Lake, one of central New York's Finger Lakes. Mortality associated with the “Cayuga syndrome” is 98–100%. Death usually occurs between 650 and 850 centigrade degreedays after fertilization, approximately 2–4 weeks before yolk resorption is complete. Although there is minor temporal variation in the onset of the Cayuga syndrome in progeny from individual females, all sac fry eventually succumb. Incubation of embryos and sac fry under constant, ambient, or reduced temperature regimens slightly alters the degree-day timing of syndrome onset, but does not improve survival. Based on mortality rate, manifestation of the Cayuga syndrome has not changed in the past 10 years, even though incubation waters of varying chemistry and temperature have been used. Mortality of the negative control stocks used for these studies never exceeded 10% from hatching to first feeding. Findings from reciprocal crossbreeding experiments indicate the problem is associated with ova only. A noninfectious etiology is indicated by the lack of consistently identifiable fish pathogens from syndrome-afflicted sac fry and by the failure to transmit the condition horizontally. Suspect contaminants were eliminated as potential causative factors. Epidemiological studies on the viability of other Finger Lakes stocks indicate that Atlantic salmon from Keuka and Seneca lakes are also afflicted (100% mortality). yet those from Skaneateles Lake are not. The cause of this syndrome appears to be nutritional.
  • Atlantic Herring and Horse Mackerel in 6aS/7b; Industry Acoustic Survey Cruise Report

    O’Malley, M.; Clarke, M.; Smith, T.; Mullins, E. (Marine Institute, 2018)
    An acoustic survey of Atlantic herring Clupea harengus and horse mackerel Trachurus trachurus was conducted in ICES areas 6aS/7b in Nov 2017 using the pair trawl vessels MFV Eilean Croine S238 and MFV Sparkling Star D437. This survey is the second in a time series that is hoped will be developed into a long-term index of spawning/pre-spawning herring and horse mackerel in 6aS/7b, for use in stock assessments in the future. The survey design was based on the predicted distribution of herring and horse mackerel in this area during this time. In total 1,482nmi of cruise track was completed using 27 transects and related to a total area coverage of approximately 2,200 nmi². Parallel transect spacing was set at 7.5nmi for the wider area, and 3.5nmi for Donegal Bay. Coverage extended from inshore coastal areas to the 200 m contour in the west and north. A mini survey was carried out in Lough Swilly using a zig-zag design. A Simrad ES-38B (38 kHz) split-beam transducer mounted on a towed body was calibrated before the survey near Rathmullan Pier in Lough Swilly, Co. Donegal. Very strong herring marks (e.g. > 2nmi long, 200m wide and ~18m deep) were evident in Lough Swilly, an area where boats in the monitoring fishery were concentrating effort. There was also a series of strong herring marks in Bruckless Bay and Inver Bay in discreet areas. There were very few herring marks offshore. A total of four hauls were taken for biological analysis. Biological samples from the monitoring fishery were used to augment the samples from the survey. Samples were taken from boats fishing in Lough Swilly, Bruckless Bay and Inver Bay as close spatially and temporally as possible to the survey in these areas. Herring were dominated by 3-wr fish in all hauls. The 3-wr age class constituted 32% of the overall numbers. Horse mackerel were distributed throughout the survey area, but particularly throughout the area to the north and west of Tory Island. Horse mackerel length distribution was dominated by a mode at 24cm, with a smaller mode at 30cm. This corresponded to a dominance of 3-wr fish (~67%) in all of the samples. The total stock biomass (TSB) estimate of herring for the combined 6aS/7b area was 40,646 tonnes (Lough Swilly = 12,098 tonnes, Donegal Bay = 23,157 tonnes, and the remaining NW area = 5,391 tonnes). This is considered to be a minimum estimate of herring in the 6aS/7b survey area at the time of the survey. The TSB estimate of horse mackerel for the total surveyed area in 6aS/7b area was 68,079 tonnes, considered to be a minimum estimate of horse mackerel in the 6aS/7b survey area at the time of the survey. The CV estimates on biomass and abundance are high (~0.50 for herring and ~ 0.62 for horse mackerel) for the survey in 2017. For herring, this is mostly caused by the over-reliance on a few acoustic marks of herring in Lough Swilly and Bruckless/Inver Bays in particular. For horse mackerel, this is most likely caused by and over-reliance of two transects in particular. Horse mackerel are a widely distributed stock, therefore the stock was not contained by this survey.
  • The Irish Maritime Transport Economist Volume 14

    Irish Maritime Development Office (Marine Institute, 2017)
  • Sensitive Ecosystem Assessment and ROV Exploration of Reef Survey Report 2017

    O’Sullivan, D.; Leahy, Y.; Guinan, J.; Shipboard Scientific Party (Marine Institute, 2018)
    A requirement exists to quantify the abundance and distribution of offshore biogenic and geogenic reef habitats in Irish waters to fulfil Ireland’s legal mandate and to generate baseline data from which appropriate monitoring systems can be established. To address this an extensive offshore reef survey of Ireland’s Northwest Continental margin was commissioned by the National Parks and Wildlife Service (NPWS), funded by the European Maritime and Fisheries Fund (EMFF), and coordinated and led by INFOMAR (Integrated Mapping for the Sustainable Development of Ireland’s Marine Resources) and Ireland’s Marine Institute. The objectives of the survey were to implement the EMFF’s Marine Biodiversity Scheme - Natura Fisheries by mapping offshore reef habitats with a view to protecting them from deterioration due to fishing pressures. The reef project aligns with sub-article 6.2 of the Habitats Directive (EC 92/43/EEC) which requires member states to take measures to avoid deterioration of protected habitats. A survey, Sensitive Ecosystem Assessment and ROV Exploration of Reef (SeaRover), took place in July 2017 aboard the ILV Granuaile equipped with the Marine Institute’s remotely operated vehicle (ROV) Holland 1 and a multidisciplinary team of scientists to observe seabed features and biological associations along the northwest continental shelf. The Holland 1 employs high-definition (HD) camera, various composite video feeds and a robotic arm to facilitate sample collection. The primary scientific objective was to map the distribution and abundance of geogenic and biogenic reef habitat along the northwest shelf edge of Ireland’s continental slope with HD video. Secondary objectives included the collection of biological samples for genetic and population analysis and the collection of sediment cores for ground-truthing seabed mapping data and analysis of micro-plastics within deep-water sediment.
  • Celtic Sea Herring Acoustic Survey Cruise Report 2017, 15-04 November 2017

    O'Donnell, C.; O'Malley, M.; Lynch, D.; Lyons, K.; Keogh, N.; O’Driscoll, D. (Marine Institute, 2017)
    In the southwest of Ireland and the Celtic Sea (ICES Divisions VIIaS, g & j), herring are an important commercial species to the pelagic and polyvalent fleet. For a period in the 1970s and1980s, larval surveys were conducted for herring in this area. However, since 1989, acoustic surveys have been carried out, and currently are the only tuning indices available for this stock. In the Celtic Sea and VIIj, herring acoustic surveys have been carried out since 1989. Since 2004 the survey has been fixed in October and carried out onboard the RV Celtic Explorer. The geographical confines of the annual 21 day survey have been modified in recent years to include areas to the south of the main winter spawning grounds in an effort to identify the whereabouts of winter spawning fish before the annual inshore spawning migration. Spatial resolution of acoustic transects has been increased over the entire south coast survey area. The acoustic component of the survey has been further complemented since 2004 by detailed hydrographic, marine mammal and seabird surveys.

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