24 Works

Image annotation R Shiny app

Mikel Aristegui
This R Shiny application was built to annotate footage (HD-stills) from Nephrops norvegicus UWTV surveys carried out by the Marine Institute.

Data from: Identification and characterization of Cyprinid Herpesvirus-3 (CyHV-3) encoded microRNAs

Owen H. Donohoe, Kathy Henshilwood, Keith Way, Roya Hakimjavadi, David M. Stone & Dermot Walls
MicroRNAs (miRNAs) are a class of small non-coding RNAs involved in post-transcriptional gene regulation. Some viruses encode their own miRNAs and these are increasingly being recognized as important modulators of viral and host gene expression. Cyprinid herpesvirus 3 (CyHV-3) is a highly pathogenic agent that causes acute mass mortalities in carp (Cyprinus carpio carpio) and koi (Cyprinus carpio koi) worldwide. Here, bioinformatic analyses of the CyHV-3 genome suggested the presence of non-conserved precursor miRNA (pre-miRNA)...

A general swimming response in exhausted obligate swimming fish

Gil Iosilevskii, Jacinta Kong, Carl Meyer, Yuuki Watanabe, Yannis Papastamatiou, Mark Royer, Itsumi Nakamura, Katsufumi Sato, Thomas Doyle, Luke Harman, Jonathan Houghton, Adam Barnett, Jayson Semmens, Niall Ó Maoléidigh, Alan Drumm, Ross O'Neill, Daniel Coffey & Nicholas Payne
Marine organisms normally swim at elevated speeds relative to cruising speeds only during strenuous activity, such as predation or escape. We measured swimming speeds of 29 ram ventilating sharks from 10 species and of three Atlantic bluefin tunas immediately after exhaustive exercise (fighting a capture by hook-and-line), and unexpectedly found all individuals exhibited a uniform mechanical response, with swimming speed initially 2 times higher than the cruising speeds reached approximately 6 hours later. We hypothesised...

Data from: Evaluating adaptive divergence between migratory and non-migratory ecotypes of a salmonid fish, Oncorhynchus mykiss

Matthew C. Hale, Frank P. Thrower, Ewann A. Berntson, Michael R. Miller & Krista M. Nichols
Next generation sequencing and the application of population genomic and association approaches have made it possible to detect selection and unravel the genetic basis to variable phenotypic traits. Using the two approaches in parallel is an especially attractive approach in non-models organisms that lack a sequenced and annotated genome, but only works well when population structure is not confounded with the phenotype of interest. Herein, we use population genomics in a non-model fish species, rainbow...

Age of European silver eels during a period of declining abundance in Norway

Caroline Durif, Ola Diserud, Leif Asbjørn Vøllestad, Odd Terje Sandlund, Eva Thorstad, Knut Bergesen, Russell Poole, Steven Shema & Rosa Escobar-Lux
The European eel (Anguilla anguilla) is critically endangered throughout its range. Knowledge about age distribution of future spawners (silver eels) is essential to monitor the status and contribute to the recovery of this species. Determination of age in anguillid eels is challenging, especially in eels from the northern part of the distribution area where growth is slow and age at maturation can be up to 30 years or more. Eels from the river Imsa in...

Atlas of Commercial Fisheries around Ireland, third edition

Hans Gerritsen & Eoghan Kelly

Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

Ian R. Bradbury, Brendan F. Wringe, Beth Watson, Ian Paterson, John Horne, Robert Beiko, Sarah J. Lehnert, Marie Clément, Eric C. Anderson, Nicholas W. Jeffery, Steven Duffy, Emma Sylvester, Martha Robertson & Paul Bentzen
Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next-generation sequencing, in conjunction with novel bioinformatic tools allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here we scanned the published Atlantic salmon genome to identify 706 microsatellite loci,...

Data from: MHC-mediated spatial distribution in brown trout (Salmo trutta) fry

Brian O'Farrell, E De Eyto, J A H Benzie, P McGinnity, J Carlsson, E Dillane, C Graham, J Coughlan & T Cross
Major histocompatibility complex (MHC) class I-linked microsatellite data and parental assignment data for a group of wild brown trout (Salmo trutta L.) provide evidence of closer spatial aggregation among fry sharing greater numbers of MHC class I alleles under natural conditions. This result confirms predictions from laboratory experiments demonstrating a hierarchical preference for association of fry sharing MHC alleles. Full-siblings emerge from the same nest (redd), and a passive kin association pattern arising from limited...

Data from: A genome-wide approach to the phylogeography of the mussel Mytilus galloprovincialis in the Adriatic and the Black Seas

Marta Paterno, Levent Bat, Jamila B Souissi, Elisa Boscari, Aurore Chassanite, Leonardo Congiu, Giuseppe Guarnieri, Claudia Kruschel, Vesna Macic, Ilaria A Marino, Dragos Micu, Nataliya Milchakova, Marina Panayotova, Chiara Papetti, Stefan Strungaru, Valentina R Todorova, Emanuela Voutsinas & Lorenzo Zane
Connectivity between populations shapes the genetic structure of species being crucial for an effective management of environmental resources. Genetic approaches can provide indirect measures of connectivity, allowing the identification of genetically differentiated - unconnected - populations. In this study, we applied a 2b-RAD approach based on hundreds of polymorphic loci to provide the first detailed insight into the population genomics of the Mediterranean mussel Mytilus galloprovincialis in part of its native geographical range. We sampled...

Data from: Can biosecurity and local network properties predict pathogen species richness in the salmonid industry?

Tadaishi Yatabe, Simon J. More, Fiona Geoghegan, Catherine McManus, Ashley E. Hill & Beatriz Martinez-Lopez
Salmonid farming in Ireland is mostly organic, which implies limited disease treatment options. This highlights the importance of biosecurity for preventing the introduction and spread of infectious agents. Similarly, the effect of local network properties on infection spread processes has rarely been evaluated. In this paper, we characterized the biosecurity of salmonid farms in Ireland using a survey, and then developed a score for benchmarking the disease risk of salmonid farms. The usefulness and validity...

Image annotation R Shiny app - Release 2.0

Mikel Aristegui

Data from: Growth potential can affect timing of maturity in a long-lived semelparous fish

Kazuki Yokouchi, Francoise Daverat, Michael J. Miller, Nobuto Fukuda, Ryusuke Sudo, Katsumi Tsukamoto, Pierre Elie & W. Russell Poole
Many diadromous fishes such as salmon and eels that move between freshwater and the ocean have evolved semelparous reproductive strategies, but both groups display considerable plasticity in characteristics. Factors such as population density and growth, predation risk or reproduction cost have been found to influence timing of maturation. We investigated the relationship between female size at maturity and individual growth trajectories of the long-lived semelparous European eel, Anguilla anguilla. A Bayesian model was applied to...

Carbon Budget dataset for Lough Feeagh, Burrishoole, Co Mayo, Ireland

Brian Doyle, Elvira De Eyto, Eleanor Jennings, Mary Dillane & Valerie McCarthy
Lakes play a key role in the global carbon cycle, transporting, processing and storing organic carbon (OC) along the land-ocean aquatic continuum. An OC budget for Lough Feeagh (Ireland), an oligotrophic, peatland lake in a temperate oceanic location, was estimated for one year using both direct measurements and elements calculated from literature. The raw data needed to construct this budget are included in this datatset, comprising dissolved organic carbon (DOC), water discharge, water temperature, particulate...

Data from: Environmental monitoring through protist NGS metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

Jan Pawlowski, Philippe Esling, Franck Lejzerowicz, Tomas Cedhagen, Tom Wilding & Thomas A. Wilding
The measurement of species diversity represents a powerful tool for assessing the impacts of human activities on marine ecosystems. Traditionally, the impact of fish farming on the coastal environment is evaluated by monitoring the dynamics of macrobenthic infaunal populations. However, taxonomic sorting and morphology-based identification of the macrobenthos demands highly trained specialists and is extremely time-consuming and costly, what makes it unsuitable for large-scale biomonitoring efforts involving numerous samples. Here, we propose to alleviate this...

Data from: Trophic interactions of fish communities at midwater depths enhance long-term carbon storage and benthic production on continental slopes

Clive N. Trueman, Graham Johnston, Brendan O'Hea & Kirsteen M. MacKenzie
Biological transfer of nutrients and materials between linked ecosystems influences global carbon budgets and ecosystem structure and function. Identifying the organisms or functional groups that are responsible for nutrient transfer, and quantifying their influence on ecosystem structure and carbon capture is an essential step for informed management of ecosystems in physically distant, but ecologically linked areas. Here, we combine natural abundance stable isotope tracers and survey data to show that mid-water and bentho-pelagic-feeding demersal fishes...

Data from: Effects of seal predation on a modelled marine fish community and consequences for a commercial fishery

Jennifer E. Houle, Francisco De Castro, Michelle A. Cronin, Keith D. Farnsworth, Martha Gosch & David G. Reid
We constructed a size- and trait-based dynamic marine community model of the Celtic Sea/Biologically Sensitive Area, including grey seals Halichoerus grypus (Fabricius 1791) and harbour seals Phoca vitulina vitulina (Linnaeus 1758) to examine potential resource conflict between seals and commercial trawl fisheries. The model incorporates seal diet preference, population size and commercial fishery catch, with survey data to quantify ecological interactions between seals and fisheries. Total annual consumption by seals was an order of magnitude...

Data from: Population genomic analyses of early phase Atlantic salmon (Salmo salar) domestication/captive breeding.

Hannu Mäkinen, Anti Vasemägi, Philip McGinnity, Tom F. Cross, Craig Primmer & Craig R. Primmer
Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild Atlantic salmon (Salmo salar L.) populations are threatened by anthropogenic influences and they are supplemented with captively bred fish. The Atlantic salmon is also widely used in selective breeding programs to increase the mean trait values for desired phenotypic traits. We analyzed a genome-wide set of SNPs in three domesticated Atlantic salmon strains and...

Data from: An experimental comparison of three Towed Underwater Video Systems using species metrics, benthic impact and performance

Emma V. Sheehan, Sandrine Vaz, Erin Pettifer, Nicola L. Foster, Sarah J. Nancollas, Sophie Cousens, Luke Holmes, Jean-Valery Facq, Gregory Germain & Martin J. Attrill
1. Managing ecological systems, which operate over large spatial scales is inherently difficult and often requires sourcing data from different countries and organizations. The assumption might be made that data collected using similar methodologies are comparable but this is rarely tested. Here, benthic video data recorded using different towed underwater video systems (TUVSs) were experimentally compared. 2. Three technically different TUVSs were compared on different seabed types (rocky, mixed ground and sandy) in Kingmere Marine...

Data from: The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature

Ciar L O'Toole, Thomas E. Reed, Deborah Bailie, Caroline Bradley, Deirdre Cotter, Jamie Coughlan, Tom Cross, Eileen Dillane, Sarah McEvoy, Niall O'Maoileidigh, Paulo Prodöhl, Ger Rogan & Philip McGinnity
Understanding the extent, scale and genetic basis of local adaptation (LA) is important for conservation and management. Its relevance in salmonids at microgeographic scales, where dispersal (and hence potential gene flow) can be substantial, has however been questioned. Here, we compare the fitness of communally reared offspring of local and foreign Atlantic salmon Salmo salar from adjacent Irish rivers and reciprocal F1 hybrid crosses between them, in the wild ‘home’ environment of the local population....

Data from: Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks

Mark Ravinet, Rosaleen Hynes, Russell Poole, Tom F. Cross, Phil McGinnity, Harrod Harrod & Paulo A. Prodöhl
Contact zones between divergent forms of the same species are often characterised by high levels of phenotypic diversity over small geographic distances. What processes are involved in generating such high phenotypic diversity? One possibility is that introgression and recombination between divergent forms in contact zones results in greater phenotypic and genetic polymorphism. Alternatively, strong reproductive isolation between forms may maintain distinct phenotypes, preventing homogenisation by gene flow. Contact zones between divergent freshwater-resident and anadromous stickleback...

Data from: Harbour seals avoid tidal turbine noise: implications for collision risk

Gordon D. Hastie, Debbie J. F. Russell, Paul Lepper, Jim Elliott, Ben Wilson, Steven Benjamins & Dave Thompson
1. Tidal stream energy converters (turbines) are currently being installed in tidally energetic coastal sites. However, there is currently a high level of uncertainty surrounding the potential environmental impacts on marine mammals. This is a key consenting risk to commercial introduction of tidal energy technology. Concerns derive primarily from the potential for injury to marine mammals through collisions with moving components of turbines. To understand the nature of this risk, information on how animals respond...

Drivers of spatiotemporal variability in bycatch of a top marine predator: First evidence for the role of water turbidity in protected species bycatch

Cian Luck, Michelle Cronin, Martha Gosch, Kieran Healy, Ronan Cosgrove, Oliver Tully, Emer Rogan & Mark Jessopp
1. Bycatch of protected species in static net fisheries is a global conservation concern and is currently considered the dominant anthropogenic threat to many marine mammal species worldwide. Effective bycatch mitigation remains challenging, contingent on an understanding of the underlying mechanisms that cause individuals to become entangled. 2. We combined data collected by scientific observers and fishers to identify predictors of seal bycatch in static net fisheries along the west, southwest, and south coasts of...

Nephrops Underwater TV Survey FU16 Porcupine Bank

Jennifer Doyle
Nephrops norvegicus are common around the Irish coast, occurring in geographically distinct sandy or muddy areas where the sediment is suitable for construction of their burrow dwellings. This dataset provides quality assured estimates of Nephrops burrow densities from a randomised isometric grid of underwater television (UWTV) stations at six nautical mile spacing over the known spatial and bathymetric distribution of the FU (functional unit) 16: Porcupine Bank (illustrative shapefile provided with data). This dataset covers...

A baseline for the genetic stock identification of Atlantic herring, Clupea harengus, in ICES Divisions 6.a, 7.b-c

Edward Farrell, Leif Andersson, Dorte Bekkevold, Neil Campbell, Jens Carlsson, Maurice Clarke, Afra Egan, Arild Folkvord, Michael Gras, Susan Mærsk Lusseau, Steven Mackinson, Cormac Nolan, Steven O'Connell, Michael O'Malley, Martin Pastoors, Mats Pettersson & Emma White
Atlantic herring in ICES Divisions 6.a, 7.b-c comprises at least three populations, distinguished by temporal and spatial differences in spawning, which have until recently been managed as two stocks defined by geographic delineators. Outside of spawning the populations form mixed aggregations, which are the subject of acoustic surveys. The inability to distinguish the populations has prevented the development of separate survey indices and separate stock assessments. A panel of 45 SNPs, derived from whole genome...

Registration Year

  • 2022
  • 2020
  • 2019
  • 2018
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  • 2011

Resource Types

  • Dataset
  • Software


  • Marine Institute
  • University College Cork
  • Queen's University Belfast
  • University College Dublin
  • University of California, Davis
  • University of Padua
  • Sinop University
  • Plymouth University
  • Estonian University of Life Sciences
  • Irish Sea Fisheries Board