ICES Journal of Marine Science: Journal du Conseil, 2016
It is recommended that demersal elasmobranchs be managed using spatial proxies for Maximum Sustai... more It is recommended that demersal elasmobranchs be managed using spatial proxies for Maximum Sustainable Yield. Here we combine escapement biomass -the percentage of the stock which must be retained each year to conserve it -with maps of predicted CPUE of four ray species (cuckoo (Leucoraja naevus), thornback (Raja clavata), blonde (R. brachyura), and spotted (R. montagui)), created using Boosted Regression Tree modelling. We then use a Decision Support Tool to generate location and size options for Marine Protected Areas to protect these stocks, based on the priorities of the various stakeholders, notably the minimisation of fishing effort displacement. Variations of conservation/fishing priorities are simulated, as well as differential priorities for individual species, with a focus on protecting nursery grounds and spawning areas. Prioritising high CPUE cells results in a smaller closed area that displaces the most fishing effort, whereas prioritising low fishing effort results in a larger closed area that displaces the least fishing effort. The final result is a complete software package that produces maps of predicted species CPUE from limited survey data, allowing disparate stakeholders and policymakers to discuss management options within a mapping interface.
Relative indices of abundance of albacore tuna (Thunnus alalunga) from the Irish mid water pair t... more Relative indices of abundance of albacore tuna (Thunnus alalunga) from the Irish mid water pair trawl fishery are presented for the years 2003-2012 in the format requested by the Working Group on Stock Assessment Methods. National landings log book data were used to estimate nominal catch rates in biomass. A standardised catch per unit effort index was produced using a Delta-lognormal model. RÉSUMÉ Des indices d'abondance relative du germon (Thunnus alalunga) capturé dans la pêcherie irlandaise de chaluts pélagiques en paire sont présentés pour les années 2003-2012 dans le format requis par le Groupe de travail sur les méthodes d'évaluation des stocks. Les données des débarquements nationaux des carnets de pêche ont été utilisées pour estimer les taux de capture nominale en biomasse. Un indice standardisé de prise par unité d'effort a été créé au moyen d'un modèle delta log normal. RESUMEN Se presentan índices de abundancia relativa de atún blanco (Thunnus alalunga) procedentes de la pesquería irlandesa de arrastre epipelágico por parejas para los años 2003-2012 en el formato solicitado por el Grupo de trabajo sobre métodos de evaluación de stock. Los datos de desembarques nacionales de los cuadernos de pesca se utilizaron para estimar las tasas de captura nominal en biomasa. Se obtuvo un índice estandarizado de captura por unidad de esfuerzo utilizando un modelo Delta-lognormal.
Tissues from a range of fish were examined for the presence of parathyroid hormone-related protei... more Tissues from a range of fish were examined for the presence of parathyroid hormone-related protein (PTHrP) to investigate PTHrP protein distribution and PTHrP gene expression in jawless fish, cartilaginous fish, and bony fish. Immunoreactive PTHrP was localized using antisera to N-terminal and mid-molecule regions of human PTHrP and PTHrP gene expression examined using a digoxigenin labeled riboprobe to a conserved region of the mammalian PTHrP gene. In all of the fish studied, PTHrP protein and messenger RNA (mRNA) were localized to the skin, kidney, and skeletal muscle, following the pattern seen in higher vertebrates. Additional sites of localization for both protein and mRNA included gill, nerve cord, and pituitary, as well as developing dermal denticles and rectal gland in the elasmobranch species. The sites of PTHrP distribution indicate that PTHrP may have roles in ionoregulation as well as growth and differentiation in fish, as has been suggested in higher vertebrates. The results imply that the distribution of PTHrP is widespread in fish and that there is homology between the PTHrP molecules found in humans and fish. The conservation of localization and possible similarity of the PTHrP molecules between tetrapods and fish suggests that PTHrP has a number of fundamental roles in vertebrates.
Catch-per-unit-effort (CPUE) data are routinely standardized to account for factors that influenc... more Catch-per-unit-effort (CPUE) data are routinely standardized to account for factors that influence catch rates that are not related to resource abundance. Despite improvement in the methods applied to CPUE standardization, for many datasets model diagnostics can still indicate poor conformity to modeling assumptions, imprecision and unexplained fishing behaviors. In this study we examine catch rate data of an Irish mid-water pair trawl fleet targeting albacore tuna (Thunnus alalunga) in the North East Atlantic. A fleet strategy of searching and congregating on fish aggregations combined with negative skew in model residuals suggest that multiple components exist within the dataset. Assuming up to five components, finite mixture models are applied and compared using the Bayesian information criterion. The two component model most consistently explained observed distributions in fishing behaviors and catch rates. Finite mixture modeling markedly improved conformity to modeling assumptions, resulting in substantial improvement in the precision of specific components used in CPUE standardization and reduced inter-annual variability of the catch rate trend. These methods may facilitate investigations of technological creep but also raise questions on how best to use the results in assessment.
Page 1. Irish Fisheries Bulletin No. 30 / 2007 VALIDATION OF STANDARD WEIGHTS AND RAISING COEFFIC... more Page 1. Irish Fisheries Bulletin No. 30 / 2007 VALIDATION OF STANDARD WEIGHTS AND RAISING COEFFICIENTS FOR DISCARD ESTIMATION: REPORT OF A SURVEY ABOARD MFV ROISIN BAIRBRE Turloch Smith1, Stephen Comerford2 and Rick Officer3 ...
Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe fr... more Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe from surface waters to deep-sea sediments. Identifying patterns of microplastic distribution will benefit an understanding of the scale of their potential effect on the environment and organisms. As sea ice extent is reducing in the Arctic, heightened shipping and fishing activity may increase marine pollution in the area. Microplastics may enter the region following ocean transport and local input, although baseline contamination measurements are still required. Here we present the first study of microplastics in Arctic waters, south and southwest of Svalbard, Norway. Microplastics were found in surface (top 16 cm) and sub-surface (6 m depth) samples using two independent techniques. Origins and pathways bringing microplastic to the Arctic remain unclear. Particle composition (95% fibres) suggests they may either result from the breakdown of larger items (transported over large distances ...
Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe fr... more Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe from surface waters to deep-sea sediments. Identifying patterns of microplastic distribution will benefit an understanding of the scale of their potential effect on the environment and organisms. As sea ice extent is reducing in the Arctic, heightened shipping and fishing activity may increase marine pollution in the area. Microplastics may enter the region following ocean transport and local input, although baseline contamination measurements are still required. Here we present the first study of microplastics in Arctic waters, south and southwest of Svalbard, Norway. Microplastics were found in surface (top 16 cm) and sub-surface (6 m depth) samples using two independent techniques. Origins and pathways bringing microplastic to the Arctic remain unclear. Particle composition (95% fibres) suggests they may either result from the breakdown of larger items (transported over large distances by prevailing currents, or derived from local vessel activity), or input in sewage and wastewater from coastal areas. Concurrent observations of high zooplankton abundance suggest a high probability for marine biota to encounter microplastics and a potential for trophic interactions. Further research is required to understand the effects of microplastic-biota interaction within this productive environment.
Deepwater sharks are caught in several fisheries in the northeast Atlantic. Among the most import... more Deepwater sharks are caught in several fisheries in the northeast Atlantic. Among the most important are the Spanish longline fishery, the Norwegian autoline longline fishery and the mixed-species trawl fishery, mainly prosecuted by French vessels. The main species exploited are Centrophorus squamosus and Centroscymnus coelolepis. These fisheries are difficult to assess because accurate time series of catch and effort are collected only by France, and in that instance only for both commercial species combined. Two approaches have been taken to stock assessment of these commercial deepwater shark species: Schaefer production model and Leslie depletion model. The deficiencies in the knowledge base are highlighted and future data and model requirements are discussed.
Until recently, it was thought impossible to directly and accurately age crustacean species. Perm... more Until recently, it was thought impossible to directly and accurately age crustacean species. Permanent growth structures were thought to be lost during the biological process of moulting. However recent research has shown that calcified parts of the eyestalk and gastric mill are retained through moults and appear to preserve annual growth bands in some species of shrimp, crab and lobster (Kilada et al., 2012).
Contamination of marine habitats by plastic debris is recognised as an environmental problem and ... more Contamination of marine habitats by plastic debris is recognised as an environmental problem and has been identified on a global scale. A standardised protocol for monitoring the distribution and abundance of small plastic debris in the marine environment is lacking. We present our novel sampling method for easy, fast and continuous extraction of particles from water samples. This method was used during surveys on the RV Celtic Explorer in the North East Atlantic to identify the presence and characteristics of non–biological synthetic particles. Analysis of 164 samples collected between January and March 2013 found synthetic particles in 100% of the samples. Particles were assigned to four product type categories: fibres, fragments, raw plastic pellets and abrasive bead scrubbers, and five size categories: <1 mm, 1–2.5 mm, 2.5–5 mm, 5–10 mm, and >10 mm. Fibres made up the majority of particles collected and the most prevalent colours were black and blue. The most common size c...
It has recently been confirmed that some species of decapod crustacean retain their gastric mill ... more It has recently been confirmed that some species of decapod crustacean retain their gastric mill and calcified region of the eyestalks throughout their moults. It had previously been assumed that crustacea lost all growth structures that could potentially record age information, such as the bones and otoliths in fish, through moulting. In this study, a novel preparation method was used for observing growth increments within these calcified structures of Nephrops norvegicus and Cancer pagurus . This method involved: boiling, drying, resin embedding, sectioning, and polishing the gastric mill and eyestalks. Clear and readable growth increments were observed in longitudinal sections of the mesocardiac ossicle of the gastric mill for N. norvegicus, and longitudinal sections of the zygocardiac ossicle of the gastric mill for C. pagurus. Growth increments were also observed in longitudinal sections of the calcified region of the eyestalk for N. norvegicus. Validation is needed to confirm the periodicity of these growth increments.
Value achieved from time spent at sea is a central driver of fishing decisions and fishing behavi... more Value achieved from time spent at sea is a central driver of fishing decisions and fishing behaviors. Value per unit effort (VPUE) is an important indicator of economic performance in itself and a useful metric within integrated mixed fisheries models. A time series of Irish first sale prices and total per trip landings values (VPT) highlight heterogeneity in fish prices and VPTs achieved by the Irish fleet spatially and temporally, as well as variability with species targeting. This investigation compared models to standardize fishing trip VPUE accounting for species targeting (métier groupings), engine power (a kW proxy for vessel size), seasonal and annual variability, fishing effort, and individual vessels (encompassing variability in vessel characteristics and skipper effects). Linear mixed effects models incorporating random vessel effects and within-group variance between métier groupings performed best at describing the variability in the dataset. All investigated factors were important in explaining variability, and thus important in standardizing VPUE. Models incorporating fishing days (days with reported fishing activity) and engine power as separate 2 variables resulted in improved AIC values. Therefore, fishing days were considered to be the most appropriate effort measure to generate VPUE. The effort unit traditionally applied in measures of per unit effort, fishing hours, performed comparatively poorly in relation to VPT.
The Japanese development of mass culture techniques for Ulvella lens during the 1980s for aquacul... more The Japanese development of mass culture techniques for Ulvella lens during the 1980s for aquaculture has stimulated the development of rearing techniques for abalone and sea urchins in producing countries. However, since the late 1980s, there has not been any in-depth evaluation of culture methods for U. lens, nor the development of a new robust method for aquaculture operators. The use of this known inducer for settlement of veliger larvae has not been employed on a commercial scale in Ireland or in European aquaculture systems. The new methodology described here has produced a threefold increase in the settlement of sea urchins (Paracentrotus lividus) and is recommended for adoption by the European aquaculture industry.
Fuel costs are an important element in models used to analyse and predict fisher behaviour for ap... more 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 generalised 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.
Levels of marine debris, including microplastics, are largely un-documented in the Northeast Atla... more Levels of marine debris, including microplastics, are largely un-documented in the Northeast Atlantic Ocean. Broad scale monitoring efforts are required to understand the distribution, abundance and ecological implications of microplastic pollution. A method of continuous sampling was developed to be conducted in conjunction with a wide range of vessel operations to maximise vessel time. Transects covering a total of 12,700 km were sampled through continuous monitoring of open ocean sub-surface water resulting in 470 samples. Items classified as potential plastics were identified in 94% of samples. A total of 2315 particles were identified, 89% were less than 5mm in length classifying them as microplastics. Average plastic abundance in the Northeast Atlantic was calculated as 2.46 particles m(-3). This is the first report to demonstrate the ubiquitous nature of microplastic pollution in the Northeast Atlantic Ocean and to present a potential method for standardised monitoring of mic...
Tissues from a range of fish were examined for the presence of parathyroid hormone-related protei... more Tissues from a range of fish were examined for the presence of parathyroid hormone-related protein (PTHrP) to investigate PTHrP protein distribution and PTHrP gene expression in jawless fish, cartilaginous fish, and bony fish. Immunoreactive PTHrP was localized using antisera to N-terminal and mid-molecule regions of human PTHrP and PTHrP gene expression examined using a digoxigenin labeled riboprobe to a conserved region of the mammalian PTHrP gene. In all of the fish studied, PTHrP protein and messenger RNA (mRNA) were localized to the skin, kidney, and skeletal muscle, following the pattern seen in higher vertebrates. Additional sites of localization for both protein and mRNA included gill, nerve cord, and pituitary, as well as developing dermal denticles and rectal gland in the elasmobranch species. The sites of PTHrP distribution indicate that PTHrP may have roles in ionoregulation as well as growth and differentiation in fish, as has been suggested in higher vertebrates. The results imply that the distribution of PTHrP is widespread in fish and that there is homology between the PTHrP molecules found in humans and fish. The conservation of localization and possible similarity of the PTHrP molecules between tetrapods and fish suggests that PTHrP has a number of fundamental roles in vertebrates.
ICES Journal of Marine Science: Journal du Conseil, 2016
It is recommended that demersal elasmobranchs be managed using spatial proxies for Maximum Sustai... more It is recommended that demersal elasmobranchs be managed using spatial proxies for Maximum Sustainable Yield. Here we combine escapement biomass -the percentage of the stock which must be retained each year to conserve it -with maps of predicted CPUE of four ray species (cuckoo (Leucoraja naevus), thornback (Raja clavata), blonde (R. brachyura), and spotted (R. montagui)), created using Boosted Regression Tree modelling. We then use a Decision Support Tool to generate location and size options for Marine Protected Areas to protect these stocks, based on the priorities of the various stakeholders, notably the minimisation of fishing effort displacement. Variations of conservation/fishing priorities are simulated, as well as differential priorities for individual species, with a focus on protecting nursery grounds and spawning areas. Prioritising high CPUE cells results in a smaller closed area that displaces the most fishing effort, whereas prioritising low fishing effort results in a larger closed area that displaces the least fishing effort. The final result is a complete software package that produces maps of predicted species CPUE from limited survey data, allowing disparate stakeholders and policymakers to discuss management options within a mapping interface.
Relative indices of abundance of albacore tuna (Thunnus alalunga) from the Irish mid water pair t... more Relative indices of abundance of albacore tuna (Thunnus alalunga) from the Irish mid water pair trawl fishery are presented for the years 2003-2012 in the format requested by the Working Group on Stock Assessment Methods. National landings log book data were used to estimate nominal catch rates in biomass. A standardised catch per unit effort index was produced using a Delta-lognormal model. RÉSUMÉ Des indices d'abondance relative du germon (Thunnus alalunga) capturé dans la pêcherie irlandaise de chaluts pélagiques en paire sont présentés pour les années 2003-2012 dans le format requis par le Groupe de travail sur les méthodes d'évaluation des stocks. Les données des débarquements nationaux des carnets de pêche ont été utilisées pour estimer les taux de capture nominale en biomasse. Un indice standardisé de prise par unité d'effort a été créé au moyen d'un modèle delta log normal. RESUMEN Se presentan índices de abundancia relativa de atún blanco (Thunnus alalunga) procedentes de la pesquería irlandesa de arrastre epipelágico por parejas para los años 2003-2012 en el formato solicitado por el Grupo de trabajo sobre métodos de evaluación de stock. Los datos de desembarques nacionales de los cuadernos de pesca se utilizaron para estimar las tasas de captura nominal en biomasa. Se obtuvo un índice estandarizado de captura por unidad de esfuerzo utilizando un modelo Delta-lognormal.
Tissues from a range of fish were examined for the presence of parathyroid hormone-related protei... more Tissues from a range of fish were examined for the presence of parathyroid hormone-related protein (PTHrP) to investigate PTHrP protein distribution and PTHrP gene expression in jawless fish, cartilaginous fish, and bony fish. Immunoreactive PTHrP was localized using antisera to N-terminal and mid-molecule regions of human PTHrP and PTHrP gene expression examined using a digoxigenin labeled riboprobe to a conserved region of the mammalian PTHrP gene. In all of the fish studied, PTHrP protein and messenger RNA (mRNA) were localized to the skin, kidney, and skeletal muscle, following the pattern seen in higher vertebrates. Additional sites of localization for both protein and mRNA included gill, nerve cord, and pituitary, as well as developing dermal denticles and rectal gland in the elasmobranch species. The sites of PTHrP distribution indicate that PTHrP may have roles in ionoregulation as well as growth and differentiation in fish, as has been suggested in higher vertebrates. The results imply that the distribution of PTHrP is widespread in fish and that there is homology between the PTHrP molecules found in humans and fish. The conservation of localization and possible similarity of the PTHrP molecules between tetrapods and fish suggests that PTHrP has a number of fundamental roles in vertebrates.
Catch-per-unit-effort (CPUE) data are routinely standardized to account for factors that influenc... more Catch-per-unit-effort (CPUE) data are routinely standardized to account for factors that influence catch rates that are not related to resource abundance. Despite improvement in the methods applied to CPUE standardization, for many datasets model diagnostics can still indicate poor conformity to modeling assumptions, imprecision and unexplained fishing behaviors. In this study we examine catch rate data of an Irish mid-water pair trawl fleet targeting albacore tuna (Thunnus alalunga) in the North East Atlantic. A fleet strategy of searching and congregating on fish aggregations combined with negative skew in model residuals suggest that multiple components exist within the dataset. Assuming up to five components, finite mixture models are applied and compared using the Bayesian information criterion. The two component model most consistently explained observed distributions in fishing behaviors and catch rates. Finite mixture modeling markedly improved conformity to modeling assumptions, resulting in substantial improvement in the precision of specific components used in CPUE standardization and reduced inter-annual variability of the catch rate trend. These methods may facilitate investigations of technological creep but also raise questions on how best to use the results in assessment.
Page 1. Irish Fisheries Bulletin No. 30 / 2007 VALIDATION OF STANDARD WEIGHTS AND RAISING COEFFIC... more Page 1. Irish Fisheries Bulletin No. 30 / 2007 VALIDATION OF STANDARD WEIGHTS AND RAISING COEFFICIENTS FOR DISCARD ESTIMATION: REPORT OF A SURVEY ABOARD MFV ROISIN BAIRBRE Turloch Smith1, Stephen Comerford2 and Rick Officer3 ...
Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe fr... more Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe from surface waters to deep-sea sediments. Identifying patterns of microplastic distribution will benefit an understanding of the scale of their potential effect on the environment and organisms. As sea ice extent is reducing in the Arctic, heightened shipping and fishing activity may increase marine pollution in the area. Microplastics may enter the region following ocean transport and local input, although baseline contamination measurements are still required. Here we present the first study of microplastics in Arctic waters, south and southwest of Svalbard, Norway. Microplastics were found in surface (top 16 cm) and sub-surface (6 m depth) samples using two independent techniques. Origins and pathways bringing microplastic to the Arctic remain unclear. Particle composition (95% fibres) suggests they may either result from the breakdown of larger items (transported over large distances ...
Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe fr... more Plastic, as a form of marine litter, is found in varying quantities and sizes around the globe from surface waters to deep-sea sediments. Identifying patterns of microplastic distribution will benefit an understanding of the scale of their potential effect on the environment and organisms. As sea ice extent is reducing in the Arctic, heightened shipping and fishing activity may increase marine pollution in the area. Microplastics may enter the region following ocean transport and local input, although baseline contamination measurements are still required. Here we present the first study of microplastics in Arctic waters, south and southwest of Svalbard, Norway. Microplastics were found in surface (top 16 cm) and sub-surface (6 m depth) samples using two independent techniques. Origins and pathways bringing microplastic to the Arctic remain unclear. Particle composition (95% fibres) suggests they may either result from the breakdown of larger items (transported over large distances by prevailing currents, or derived from local vessel activity), or input in sewage and wastewater from coastal areas. Concurrent observations of high zooplankton abundance suggest a high probability for marine biota to encounter microplastics and a potential for trophic interactions. Further research is required to understand the effects of microplastic-biota interaction within this productive environment.
Deepwater sharks are caught in several fisheries in the northeast Atlantic. Among the most import... more Deepwater sharks are caught in several fisheries in the northeast Atlantic. Among the most important are the Spanish longline fishery, the Norwegian autoline longline fishery and the mixed-species trawl fishery, mainly prosecuted by French vessels. The main species exploited are Centrophorus squamosus and Centroscymnus coelolepis. These fisheries are difficult to assess because accurate time series of catch and effort are collected only by France, and in that instance only for both commercial species combined. Two approaches have been taken to stock assessment of these commercial deepwater shark species: Schaefer production model and Leslie depletion model. The deficiencies in the knowledge base are highlighted and future data and model requirements are discussed.
Until recently, it was thought impossible to directly and accurately age crustacean species. Perm... more Until recently, it was thought impossible to directly and accurately age crustacean species. Permanent growth structures were thought to be lost during the biological process of moulting. However recent research has shown that calcified parts of the eyestalk and gastric mill are retained through moults and appear to preserve annual growth bands in some species of shrimp, crab and lobster (Kilada et al., 2012).
Contamination of marine habitats by plastic debris is recognised as an environmental problem and ... more Contamination of marine habitats by plastic debris is recognised as an environmental problem and has been identified on a global scale. A standardised protocol for monitoring the distribution and abundance of small plastic debris in the marine environment is lacking. We present our novel sampling method for easy, fast and continuous extraction of particles from water samples. This method was used during surveys on the RV Celtic Explorer in the North East Atlantic to identify the presence and characteristics of non–biological synthetic particles. Analysis of 164 samples collected between January and March 2013 found synthetic particles in 100% of the samples. Particles were assigned to four product type categories: fibres, fragments, raw plastic pellets and abrasive bead scrubbers, and five size categories: <1 mm, 1–2.5 mm, 2.5–5 mm, 5–10 mm, and >10 mm. Fibres made up the majority of particles collected and the most prevalent colours were black and blue. The most common size c...
It has recently been confirmed that some species of decapod crustacean retain their gastric mill ... more It has recently been confirmed that some species of decapod crustacean retain their gastric mill and calcified region of the eyestalks throughout their moults. It had previously been assumed that crustacea lost all growth structures that could potentially record age information, such as the bones and otoliths in fish, through moulting. In this study, a novel preparation method was used for observing growth increments within these calcified structures of Nephrops norvegicus and Cancer pagurus . This method involved: boiling, drying, resin embedding, sectioning, and polishing the gastric mill and eyestalks. Clear and readable growth increments were observed in longitudinal sections of the mesocardiac ossicle of the gastric mill for N. norvegicus, and longitudinal sections of the zygocardiac ossicle of the gastric mill for C. pagurus. Growth increments were also observed in longitudinal sections of the calcified region of the eyestalk for N. norvegicus. Validation is needed to confirm the periodicity of these growth increments.
Value achieved from time spent at sea is a central driver of fishing decisions and fishing behavi... more Value achieved from time spent at sea is a central driver of fishing decisions and fishing behaviors. Value per unit effort (VPUE) is an important indicator of economic performance in itself and a useful metric within integrated mixed fisheries models. A time series of Irish first sale prices and total per trip landings values (VPT) highlight heterogeneity in fish prices and VPTs achieved by the Irish fleet spatially and temporally, as well as variability with species targeting. This investigation compared models to standardize fishing trip VPUE accounting for species targeting (métier groupings), engine power (a kW proxy for vessel size), seasonal and annual variability, fishing effort, and individual vessels (encompassing variability in vessel characteristics and skipper effects). Linear mixed effects models incorporating random vessel effects and within-group variance between métier groupings performed best at describing the variability in the dataset. All investigated factors were important in explaining variability, and thus important in standardizing VPUE. Models incorporating fishing days (days with reported fishing activity) and engine power as separate 2 variables resulted in improved AIC values. Therefore, fishing days were considered to be the most appropriate effort measure to generate VPUE. The effort unit traditionally applied in measures of per unit effort, fishing hours, performed comparatively poorly in relation to VPT.
The Japanese development of mass culture techniques for Ulvella lens during the 1980s for aquacul... more The Japanese development of mass culture techniques for Ulvella lens during the 1980s for aquaculture has stimulated the development of rearing techniques for abalone and sea urchins in producing countries. However, since the late 1980s, there has not been any in-depth evaluation of culture methods for U. lens, nor the development of a new robust method for aquaculture operators. The use of this known inducer for settlement of veliger larvae has not been employed on a commercial scale in Ireland or in European aquaculture systems. The new methodology described here has produced a threefold increase in the settlement of sea urchins (Paracentrotus lividus) and is recommended for adoption by the European aquaculture industry.
Fuel costs are an important element in models used to analyse and predict fisher behaviour for ap... more 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 generalised 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.
Levels of marine debris, including microplastics, are largely un-documented in the Northeast Atla... more Levels of marine debris, including microplastics, are largely un-documented in the Northeast Atlantic Ocean. Broad scale monitoring efforts are required to understand the distribution, abundance and ecological implications of microplastic pollution. A method of continuous sampling was developed to be conducted in conjunction with a wide range of vessel operations to maximise vessel time. Transects covering a total of 12,700 km were sampled through continuous monitoring of open ocean sub-surface water resulting in 470 samples. Items classified as potential plastics were identified in 94% of samples. A total of 2315 particles were identified, 89% were less than 5mm in length classifying them as microplastics. Average plastic abundance in the Northeast Atlantic was calculated as 2.46 particles m(-3). This is the first report to demonstrate the ubiquitous nature of microplastic pollution in the Northeast Atlantic Ocean and to present a potential method for standardised monitoring of mic...
Tissues from a range of fish were examined for the presence of parathyroid hormone-related protei... more Tissues from a range of fish were examined for the presence of parathyroid hormone-related protein (PTHrP) to investigate PTHrP protein distribution and PTHrP gene expression in jawless fish, cartilaginous fish, and bony fish. Immunoreactive PTHrP was localized using antisera to N-terminal and mid-molecule regions of human PTHrP and PTHrP gene expression examined using a digoxigenin labeled riboprobe to a conserved region of the mammalian PTHrP gene. In all of the fish studied, PTHrP protein and messenger RNA (mRNA) were localized to the skin, kidney, and skeletal muscle, following the pattern seen in higher vertebrates. Additional sites of localization for both protein and mRNA included gill, nerve cord, and pituitary, as well as developing dermal denticles and rectal gland in the elasmobranch species. The sites of PTHrP distribution indicate that PTHrP may have roles in ionoregulation as well as growth and differentiation in fish, as has been suggested in higher vertebrates. The results imply that the distribution of PTHrP is widespread in fish and that there is homology between the PTHrP molecules found in humans and fish. The conservation of localization and possible similarity of the PTHrP molecules between tetrapods and fish suggests that PTHrP has a number of fundamental roles in vertebrates.
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