Minto C.,Dalhousie University |
Minto C.,Mayo Institute of Technology, Galway |
Worm B.,Dalhousie University
Ecology | Year: 2012
Species interactions that play out over large spatial scales are difficult to observe, particularly in the oceans. The current lack of empirical evidence for biologically meaningful interaction parameters likely delays the application of holistic management procedures. Here we estimate interactions during the early life history of fish across regions. We present separate and hierarchical Bayesian models that estimate the direction and strength of interactions between Atlantic cod and dominant pelagic fishes across much of their range in the North Atlantic. We test the hypothesis that small pelagic fish may reduce survival of cod at early life stages, and thereby contribute to the delayed recovery of depleted cod populations. Significant regional variation exists between cod recruitment and Atlantic herring abundance with eight of 14 regions displaying a negative relationship, four regions displaying no relationship, and a positive relationship observed in two regions. In contrast, most regions where Atlantic mackerel co-occurs showed no relationship with cod recruitment, with the possible exception of Gulf of St. Lawrence and Celtic Sea regions. Regions with sprat or capelin as dominant pelagics also displayed weak or no relationship, although the probability of a negative interaction with sprat increased when time series autocorrelation was accounted for. Overall, the interaction between herring and young cod was found to be negative with 94% probability, while the probability of negative interactions with mackerel was only 68%. Our findings suggest that the strength of predation or competition effects on young cod varies among small pelagic species but appears consistently for Atlantic herring; this effect may need to be considered in recovery trajectories for depleted cod populations. The methods introduced here are applicable in the investigation of species interactions from time series data collected across different study systems. © 2012 by the Ecological Society of America.
Aguera A.,Mayo Institute of Technology, Galway |
Brophy D.,Mayo Institute of Technology, Galway
Fisheries Research | Year: 2011
The aim of this study was to test the hypothesis that Atlantic saury stocks from the Mediterranean Sea and northeastern Atlantic could be identified by means of saggital otolith shape. Saury is a pelagic fish inhabiting the north Atlantic that undertakes long migrations for feeding and reproduction. A combination of otolith shape indices and elliptic Fourier descriptors are analysed by multivariate statistical procedures. The results obtained show that saury from the Mediterranean Sea and northeastern Atlantic can be distinguished using otolith shape analysis. Whether or not those differences are due to genetic isolation is not tested here but possible drivers of the observed shape variation are explored. © 2011 Elsevier B.V.
Quinn B.,Mayo Institute of Technology, Galway |
Schmidt W.,Mayo Institute of Technology, Galway |
O'Rourke K.,Enterprise Ireland |
Hernan R.,Enterprise Ireland
Chemosphere | Year: 2011
Pharmaceuticals, including the lipid regulator gemfibrozil and the non-steroidal anti-inflammatory drug diclofenac have been identified in waste water treatment plant effluents and receiving waters throughout the western world. The acute and chronic toxicity of these compounds was assessed for three freshwater species (Daphnia magna, Pseudokirchneriella subcapitata, Lemna minor) using standardised toxicity tests with toxicity found in the non-environmentally relevant mid mgL-1 concentration range. For the acute endpoints (IC50 and EC50) gemfibrozil showed higher toxicity ranging from 29 to 59mgL-1 (diclofenac 47-67mgL-1), while diclofenac was more toxic for the chronic D. magna 21d endpoints ranging from 10 to 56mgL-1 (gemfibrozil 32-100mgL-1). These results were compared with the expression of several biomarkers in the zebra mussel (Dreissena polymorpha) 24 and 96h after exposure by injection to concentrations of 21 and 21,000μgL-1 corresponding to nominal concentrations of 1 and 1000μgL-1. Exposure to gemfibrozil and diclofenac at both concentrations significantly increased the level of lipid peroxidation, a biomarker of damage. At the elevated nominal concentration of 1000μgL-1 the biomarkers of defence glutathione transferase and metallothionein were significantly elevated for gemfibrozil and diclofenac respectively, as was DNA damage after 96h exposure to gemfibrozil. No evidence of endocrine disruption was observed using the alkali-labile phosphate technique. Results from this suite of biomarkers indicate these compounds can cause significant stress at environmentally relevant concentrations acting primarily through oxidation pathways with significant destabilization of the lysosomal membrane and that biomarker expression is a more sensitive endpoint than standardised toxicity tests. © 2011 Elsevier Ltd.
Shephard S.,Mayo Institute of Technology, Galway |
Reid D.G.,Marine Institute of Ireland |
Greenstreet S.P.R.,Marine Scotland - Marine Laboratory
ICES Journal of Marine Science | Year: 2011
The large fish indicator (LFI) was developed in the North Sea as a size-based indicator of fish community state. It is now established as OSPAR's fish community Ecological Quality Objective (EcoQO) metric and will be applied across all OSPAR regions. To produce a protocol for use when developing regional LFIs, the North Sea experience is interpreted using data from the Celtic Sea. Differences in fish community species composition and size distribution were reflected in a different species complex and large fish threshold (50 cm) for the Celtic Sea LFI. However, a lag of 12-14 years in the relationship between assemblage-averaged fishing mortality F com,y and the LFI suggested similar underlying ecological mechanisms to the North Sea. The indicator responded to changes in small fish biomass that follow fishing-induced changes in the level of predation by large demersal piscivores. The Celtic Sea LFI showed maximum observed values >0.40 before 1990, and 0.40 is here proposed as an EcoQO. Development of regional LFIs demands a flexible process rather than a strictly prescriptive protocol. © 2011 International Council for the Exploration of the Sea.
Ni Chualain C.,Mayo Institute of Technology, Galway |
Robinson M.,Marine Center
ICES Journal of Marine Science | Year: 2011
Endoparasitic dinoflagellates of the genus Hematodinium have recently gained attention as significant pathogens of the brown crab Cancer pagurus in Ireland. Patent infections, which are characterized by a hyperpigmented carapace and moribund condition, are limited to the discrete periods when macroscopic identification is possible. Three methods are assessed for diagnosing Hematodinium sp. infections in brown crab at the times when macroscopic identification is not always possible. Haemolymph smears, histological sections of gill, heart, midgut, hepatopancreas, muscle, and gonad, and a polymerase chain reaction (PCR) assay provided virtually equivalent accuracy in gauging infection prevalence, regardless of season. Sequences of PCR amplicons from the 18S ribosomal RNA gene confirmed the identity of the parasite as belonging to the genus Hematodinium. Infection intensity values (<1-87%) obtained from haemolymph smears underscored infection levels within tissues, 90% of which contained advanced levels of infection. Alterations to tissues of infected crabs included haemocytopoenia, oedema, which caused dilation of the haemal sinuses resulting in pressure necrosis to the connective tissues around the oocytes, myocardial bundles, and hepatopancreatic tubules. The claw muscle of infected animals contained the fewest parasites. © 2011 International Council for the Exploration of the Sea.
Healy J.,Mayo Institute of Technology, Galway
Advances in Intelligent Systems and Computing | Year: 2016
The advent of high throughput DNA sequencing has lead to the availability of a rapidly growing number of genomes of complete or draft quality. Whole genome alignment has consequently become an increasingly important field in bioinformatics. This paper describes a novel approach for comparing two whole genomes based on fuzzy logic. Benchmarks against pre-eminent whole genome alignment systems have demonstrated that the fuzzy approach outperforms existing systems in the context of alignment times and enables analyses that are not possible with other approaches. © Springer International Publishing Switzerland 2016.
Costello G.J.,Mayo Institute of Technology, Galway
European Journal of Engineering Education | Year: 2016
The purpose of this work is to contribute to the debate on the best pedagogical approach to developing undergraduate mechanical engineering skills to meet the requirements of contemporary complex working environments. The paper provides an example of using student–entrepreneur collaboration in the teaching of modules to Mechanical Engineering final-year students. Problem-based learning (PBL) is one of the most significant recent innovations in the area of education for the professions. This work proposes to make an original contribution by simulating a real-life entrepreneur interaction for the students. The current literature largely confines simulation-based learning to computer applications such as games. However, this paper argues that role playing by students interfacing with technology start-ups can also be regarded as ‘simulation’ in a wider sense. Consequently, the paper proposes the concept of simulation-action learning as an enhancement of PBL and to distinguish it from computer simulation. © 2016 SEFI
Gerritsen H.D.,Marine Institute of Ireland |
Minto C.,Mayo Institute of Technology, Galway |
Lordan C.,Marine Institute of Ireland
ICES Journal of Marine Science | Year: 2013
Demersal trawling impacts extensively on the seabed, and the extent and frequency of this impact can be assessed using Vessel Monitoring System (VMS) data (positional data of fishing vessels). Existing approaches interpolate fishing tracks from consecutive VMS locations (track interpolation) and/or aggregate VMS point data in a spatial grid (point summation). Track interpolation can be quite inaccurate with the current 2-hour time interval between VMS records, leading to biased estimates. Point summation approaches currently only produce relative estimates of impact and are highly sensitive to the grid size chosen. We propose an approach that provides absolute estimates of trawling impact from point data and is not sensitive to an arbitrary choice of grid-cell size. The method involves applying a nested grid and estimating the swept area (area covered by fishing gear) for each VMS point. We show that the ratio of the swept area to the surface area of a cell can be related to the proportion of the seabed that was impacted by the gear a given number of times. We validate the accuracy of this swept-area ratio approach using known vessel tracks and apply the method to international VMS data in the Celtic Sea. © 2013 © 2013 International Council for the Exploration of the Sea. Published by Oxford University Press. All rights reserved.
Jennings D.J.,Newcastle University |
Hayden T.J.,University College Dublin |
Gammell M.P.,Mayo Institute of Technology, Galway
Animal Behaviour | Year: 2013
Individuals often differ from each other in how they respond to environmental events: a feature of behaviour often termed animal personality. Furthermore, animals often show unpredictability in how much they respond to these events over time leading to the suggestion that personality and intraindividual variability (IIV) might have important fitness consequences. We investigated this hypothesis by focusing on the tendency for individually identifiable male fallow deer, Dama dama, to escalate low-level (noncontact) agonistic interactions to fighting during the rut. Males differed in their tendency to escalate noncontact interactions to fighting; however, repeatability in escalation rates was unstable over the rut suggesting that escalation rate is a poor measure of personality. There was no difference in the level of IIV in escalation rate shown by males. A comparison of IIV recorded over two consecutive annual ruts showed that IIV was highly correlated between years; therefore, over an extended time period individuals were consistent in their willingness to engage in fighting. There was a nonlinear relationship between IIV and mating success; specifically, individuals that showed either low or high IIV in escalation rate had lower mating success than individuals that showed intermediate levels of IIV. Aggression and the willingness to commit to fighting are important fitness correlates; nevertheless, our understanding of how personality and IIV are related to aggression is poorly understood. This study shows that although escalation rate appears to be a poor measure of personality in the fallow deer, IIV is related to increased fitness in individuals that show intermediate levels of predictability in their willingness to fight over therut. © 2013 The Association for the Study of Animal Behaviour.
Agency: European Commission | Branch: FP7 | Program: CP-IP | Phase: NMP-2007-3.1-1 | Award Amount: 8.02M | Year: 2009
The primary concept of this project is to research, develop, validate and valorise an architecture and set of tools, methodologies and structures which will assist European companies attain a competitive position in world markets in the mid to long term horizon. The target group is SMEs and specifically those from the 50 150 employee level. Within this target group, those organisations with high growth potential will be prioritised. The primary development focus will be on operation models which reflect the High Mix Low Volume (HMLV) manufacturing environment which companies must migrate towards in order to survive and compete. The project will address competitiveness issues relating to European SMEs, the lack of take up of productivity methodologies such as Lean and Six Sigma and the changing nature of the business environment in which SMEs operate. A comprehensive response will be generated which will deliver and demonstrate solutions for SMEs in relation to strategic planning, cultural and structural issues preventing adoption of best practices, modified lean and six sigma tools tailored for SME businesses, virtual manufacturing and collaboration methods, value chain enhancement methods, process modelling and simulation tools, implementation methodologies within SME organisations, design for environment support tools and workflow process development tools for SMEs. In addition, a special task will pilot and test how lean, six sigma and environmental philosophies can be integrated into school curricula in order to influence the mindset of future employees towards best practice business philosophies. The manufacturing model will be thoroughly tested through application in SMEs and other companies across a number of manufacturing sectors and also within several countries. Results will be disseminated widely across the EU and the outputs will be exploited for the benefit of SMEs across Europe.