School of Biological, Earth & Environmental Sciences ...

Aquaculture & Fisheries Development Centre

School of Biological, Earth & Environmental Sciences

University College Cork

Annual Report 2013

Aquaculture & Fisheries Development Centre Annual Report 2013

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AFDC Strategic Vision “To support, stimulate and promote the development of aquaculture and

fisheries, thereby enabling these sectors to achieve their full socio-economic potential by utilising sustainable natural resources”


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CONTENTS

Page

Executive Summary 5

Facilities & Specifications 7

Focus on 8

Postgraduate Students Graduated in 2013 16

Research Funding 16

On-going and New Research Grants During 2013 17

Publications 18

Conference Presentations 20

AFDC Personnel 21


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2013 was another research active year at The Aquaculture & Fisheries Development Centre in the School of

Biological, Earth & Environmental Sciences at University College Cork. The personnel profile of the centre in

2013 included a Director, Dr Sarah Culloty, a Manager, Dr Maria O’Mahoney, five Principal Investigators in

each of the four thematic areas; Prof. Tom Cross/ Dr Phil McGinnity (Molecular Genetics of Aquatic Animals),

Dr Sarah Culloty (Shellfish Health), Prof. Gavin Burnell (Aquaculture) and Dr Emer Rogan (Marine Mammals

& Fisheries), 2 Senior Researchers, 5 Post-doctoral Researchers, 13 PhD students, 1 MSc student and 3 Re-

search Assistants. During 2013, MSc’s were awarded to 1 AFDC/School of BEES student. A total of 29 pub-

lications in peer-reviewed journals were produced including articles in high impact journals such as Molecular

Ecology, PLoS One and the Journal of Experimental Biology. Two oral presentations were given at interna-

tional conferences.

Two new research projects with a combined funding value of over €223,360 started in 2013. This brings the

tally of research funding at the AFDC to €8.9m for 18 research projects. The profile of research funding at

the AFDC is an amalgamation of Exchequer and EU funding. The research capacity, diversity and strengths

continue to grow through both national and international collaborations. One of the main priorities of the

AFDC is to provide continued support to industry and to enhance industry. The AFDC also continues to play

an important role in the education of undergraduate and postgraduate students within the School of BEES.

Dr Sarah Culloty

Director,


Dr Maria O’Mahoney

Manager,


EXECUTIVE SUMMARY


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The Aquaculture & Fisheries Development Centre (AFDC) is a 1200m2 research facility embedded within the

School of Biological, Earth & Environmental Sciences (BEES). The facility includes recirculating fish and

shellfish systems, laboratories (Wet and Dry) and offices. The tank rooms are equipped with marine and

freshwater tropical marine system recirculation units, broodstock conditioning units, shellfish on-growing

units, filter-feeder broodstock conditioning units, a larval culture system and live food culture facilities.

Seawater (Grade A) is delivered to on-site and stored. The AFDC has facilities seawater filtration and UV

treatment if required.

The AFDC is authorised to operate under the European Communities Health of Aquaculture Animals and

Products Regulations 2008 (Authorisation number: 006 / FHA).

FACILITIES & SPECIFICATIONS

The indoor recirculation units consist of mechanical and biological water filtration, water treatment

systems involving UV sterilisation and ozonation, and temperature control conditioning units to

enable full control of environmental parameters/variables. Light intensity and photoperiod are

available in some areas and may be locally controlled on a number of discrete systems. A range of

tank designs and sizes are incorporated which allow fish to be held at each life cycle stage, and

also for the production of research specific systems/units to suit almost any form of aquatic

research with experimental-scale trial replication. The infrastructure at the AFDC also allows for the

Algal culture and live feed production areas are available to support the culture of many species

through their larval stages. A recirculating shellfish nursery system, broodstock holding/

conditioning unit, thermally controlled hatchery and live feed production units are custom designed

to provide a series of systems suitable to the needs of a number of shellfish species. The two tank

rooms of the AFDC are fully backed-up with a 50KVa Generator fitted with an Automatic transfer

Switch (ATS) and Digi-dialler. The dedicated AFDC Laboratory houses water quality analysis

equipment, a Beckman Z2 coulter counter (particle size analyser) and drying oven as well as the

standard laboratory equipment. On site laboratories provide dedicated research facilities and

technical support essential to research at the AFDC.

Additional laboratory facilities available at the AFDC include:

Molecular genetics laboratory

Water quality testing

Wet lab/post mortem room

Tissue culture laboratory

Histology and Immunology laboratory


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Focus On Aquaculture Research

Sea Urchin Immunology (PI Prof. Gavin Burnell, PhD Student Ashlie Cipriano)

The sea urchin immunology project is investigating several

aspects of the physiology and anatomy of the purple sea

urchin, Paracentrotus lividus, in aquaculture. P. lividus is a

Lusitanian species, valued commercially for its gonads, which

are a delicacy in European and Pacific/Asian countries. Wild

sea urchin populations worldwide are overfished.

During 2013, the project investigated different tagging

techniques which would identify individuals whether in

laboratory or field settings. Passive Integrated Transponder

(PIT) tagging was the most successful technique. The

technology involved in PIT tagging is the same at that used by

Veterinarians when micro-chipping cats and dogs and is

programmed with a unique 12-digit identification number that,

when scanned with a handheld scanner and linked to a

database, can provide information about the individual (e.g.

Owner’s information). The use of PIT tags permits repeated

non-destructive identification of individuals, has an indefinite

life span, involves little to no tagging mortality, has a high tag

retention, and no apparent long-term effects on growth and

survival of tagged individuals.

As part of this project, Ashlie is also working on the use of

immunostimulatory agents – immunostimulants, prebiotics,

probiotics, and the synergy between them – to boost the sea

urchins immune system naturally. This application is especially

important in aquaculture due to the ban on antibiotics in fish

farming (Regulations, EC No.1831) and may provide for a

more holistic approach to sea urchin health in culture.

Attaching various tags to the sea urchin, P.

lividus

Using the handheld scanner to retrieve

identification data from the PIT tag

PhD Student Ashlie Cipriano retrieving PIT

tags from P. lividus


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As an Irish Research Council Industry-based PhD

Candidate working on the Integrated Multi-trophic

Aquaculture project, Daryl Gunning has been based part-

time in Bantry, Co. Cork at the Daithi O’ Murchu Research

Station (DOMMRS), who are the industry partners in the

project. Whilst based in industry, Daryl has been heavily

involved in the EU FP7 funded IDREEM (Increasing

Industrial Resource Efficiency in European Mariculture)

project (http://www.idreem.eu/cms/about-project/) which

aims to protect the long-term sustainability of European

aquaculture by developing and demonstrating a new

innovative production technology, Integrated Multi-Trophic

Aquaculture (IMTA), and is therefore closely aligned with

his own research.

In addition to the considerable experience gained whilst

based at Industry, Daryl has had an active year

conducting research as part of his own IMTA research

project. During 2013, Daryl conducted sea cucumber

anaesthesia trials using MgCl2, MgSO4 and KCl. The

project also investigated the use of PIT tags attached to

various body locations as a mechanism to physically tag

sea cucumbers.

Three experimental IMTA land-based units were

constructed from recycled Intermediate Bulk Containers

(IBCs). A medium to long term (3-6 month) experiment will

be run from July 2014, monitoring water quality and

growth rates of seaweeds, mussels, sea-cucumbers, and rainbow-trout growing in these recirculation units.

As an alternative to seaweed, Salicornia europaea (a halophytic annual dicot) will be used.

Integrated Multi-Trophic Aquaculture (PI Prof. Gavin Burnell, PhD student Daryl Gunning)

PhD student Daryl Gunning deploying seaweed

longlines as part of the IDREEM project

http://www.idreem.eu/cms/about-project/

http://en.wikipedia.org/wiki/Halophyte

http://en.wikipedia.org/wiki/Dicot


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Focus On Shellfish Health Research

HERPISH (PI Dr Sarah Culloty, Marie Curie Intra-European Fellow Dr Maria Prado-Alvarez)

The project Herpes virus in Irish oysters and identification of

resistant stocks (HERPISH) commenced in June 2013. During

summer time several hatcheries located in areas with different

susceptibility to the ostreid herpes virus were selected and 1 year

old Crassostrea gigas were sampled twice per month to monitor

disease progress and susceptibility to infection. Mortality was

determined in 200 oysters and a total of 60 oysters per sampling

and location were collected and processed for DNA extraction and

histology. In another set of survey, spat from a virus free hatchery

were transferred to two affected areas and were sampled as

described before for 1 year old oysters. Ostreid herpes virus was detected by PCR on gill tissues or total

body tissue depending on the size of the organism. These results were used to determine the prevalence of

infection per site over a 2.5 month period. At the end of the sampling, spat survivors were transferred to the

facilities of the AFDC and keep in a close circuit to carry out an experimental trial. After anesthesia with

Magnesium Chloride, a suspension of purified virus from heavy infected oysters was injected in the adductor

muscle and the mortality rate and the prevalence of infection was determined over a 7 days period. Genomic

material was also kept in order to carry out the genetic analyses proposed for the second year of the project.

Both field and laboratory trials were carried out in 2013

as part of the BIVALIFE project to investigate (a) how

ostreid herpesvirus 1 microVar (OsHV-1 μVar) is

sustaining itself in the environment outside its natural

host the Pacific oyster Crassostrea gigas and (b) the

environmental parameters which might be making

oysters more susceptible to infection with this virus.

Nine samples consisting of 605 individual samples of

invertebrates, sediment, biofilm and water were

collected at Carlingford Lough every two weeks from

July to October. A single sample of invertebrates was

Processing oysters for histology and

the material used

BIVALIFE (PI Dr Sarah Culloty, Research Fellow Dr Sharon Lynch, PhD Student Ms Amy O’Reilly,

Research Assistant Dr Steve Hutton)

Dr Steven Hutton and PhD student Amy O’Reilly

during fieldwork at Carlingford Lough


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collected from two non-culture sites at Ardmore and Bullen’s Bay. In 2013, mortalities were minimal (<0.5%)

to absent in Carlingford during the field trial period even though OsHV-1 μVar was detected by polymerase

chain reaction (PCR) in C. gigas (45-100% prevalence) and grouped macroinvertebrates (3-69%). All

invertebrate samples screened at the two control sites, Ardmore and Bullen’s Bay, were negative for OsHV-1

μVar. OsHV-1 μVar was most frequently observed in bivalves followed by gastropods, tunicates,

crustaceans, polychaetes and the chordate. The high prevalence of OsHV-1 μVar in other filter feeding

bivalves, the blue mussel Mytilus edulis and the common cockle Cerastoderma edule, may be due to the

intake of the virus during suspension feeding, while the high prevalence in the shore crab Carcinus maenas

may be due to the ingestion of the virus by feeding on dead or dying infected C. gigas. Grazing gastropods,

including the periwinkle Littorina littorea, may have ingested the virus by feeding on the biofilm. Further

studies are required to indicate if the virus is replicating in these other macroinvertebrate species.

Several laboratory trials were carried out in 2013 to (a) determine the effects of different salinities (20, 35 and

38‰) and (b) different nutrient concentrations (‘Low’, ‘Med’ and ‘High’) on C. gigas spat (4 months old) held

at an elevated temperature (22°C) and exposed to OsHV-1 μVar over a 29 day period. Higher mortalities

were observed in oysters held at the higher salinities (35 and 38 ‰) while minimal mortality was observed in

oysters held at a reduced salinity (20‰), even when oysters were exposed to OsHV-1 μVar. In the nutrient

trial (22°C and 20‰) mortalities were also minimal and although more oysters were becoming infected with

OsHV-1 μVar after week 3, mortalities were not occurring. Reduced salinity may control C. gigas mortality

and reduce the impact of OsHV-1 μVar and its virulence, even when seawater temperatures and nutrients

are elevated.

Dr Steven Hutton processing samples in the Aquaculture laboratory at the

AFDC


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Focus On Marine Mammals & Fisheries Research

Beaufort Ecosystem Approach to Fisheries Management (PI Prof Gavin Burnell/ Dr

Emer Rogan, Postdoctoral Researcher Dr Susie Brown)

Funded under the Irish Beaufort Marine

Research Awards, the Ecosystem

Approach to Fisheries Management

(EAFM) is a 7 year €3.9m project involving

a consortium comprising research groups

from University College Cork, Queens

University Belfast, and the Marine Institute.

The EAFM is a move away from traditional

single stock fisheries management and

includes links between fish species and

wider fisheries-ecosystem interactions. In

particular the ecological focus has

broadened from concerns about target

species and resources to concerns about

non target species, including protected species, habitats, ecological communities and socio economics. For

example, if sand-eel stocks are depleted what impacts does this have on both commercial species like cod

and other animals such as dolphins and seabirds.

The School of BEES is conducting Ecological Risk Assessments for the Effects of Fishing (ERAEF) within the

EAFM project, under the work package “Fishing Impacts and Approaches to Management”. These

assessments identify the activities within fisheries with the potential to impact aspects of the ecosystem,

including target and non-target species, habitats and communities. In addition to examining the impact of

fishing activities on the ecosystem as a whole, the school is looking in detail at the interactions between

fisheries and cetacean species. The specific risks posed to cetaceans are being examined with a view to

identifying fisheries and gears with the greatest potential for bycatch of whales and dolphins. Key to this aim

has been the development of an ERAEF procedure which enables the screening of risk to cetacean species

from fishing activities (Brown et al. 2013). A spatially and temporally explicit extension of this ERAEF

procedure is currently being developed to facilitate the mapping of risk to cetacean species from different

fisheries and enable the identification of areas of high bycatch risk. Further to this, investigations into the

feeding ecology of two coastal species (bottlenose dolphins and harbour porpoises) and four pelagic species

(white-sided dolphins, white beaked dolphins, common dolphins and striped dolphins) are contributing to our

understanding of the interactions between fisheries and cetaceans. Dietary information is being collected

Bottlenose dolphins, Tursiops truncatus, in Connemara


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from stranded and bycatch animals and is being used to identify dietary preferences; estimate annual food

consumption; assess their role as top predators; and the impacts of overfishing/stock collapse on these

species. In a broader fisheries context ERAEF is being applied to a number of fisheries operating in Irish

waters. Focussing initially on fisheries operating within the Biologically Sensitive Area, these assessments

will examine the impact of fisheries on target species, non-target species, protected species and habitats.

The outputs from these assessments will be used to contribute to management plans for fisheries and the

species and habitats they impact. Further details on the Beaufort EAFM project can be found on the project

website http://www.beaufort-eafm.eu.

The early part of the 2013 (January – May) was spent on

planning and preparing for the summer field season,

including taking training courses for advanced power boat

driving, getting practice in handling and shooting a 0.22

calibre rifle (for bottlenose dolphin biopsies), biopsy

training, attending courses on Personal Survival

Techniques, marine VHF radio and Marine Elementary 1st

Aid. I also attended and presented a poster at the annual

conference of the European Cetacean Society in April

2013. The title of the presentation was “Social structure of

coastal bottlenose dolphins (Tursiops truncatus) in

western Ireland”.

May-August was spent doing fieldwork. I conducted boat-based surveys of bottlenose dolphins in Connemara

(Co. Galway), Mayo and south Donegal with the purpose of gathering photo-identification and biopsy data

during dolphin encounters. I also gave a public talk in Connemara National Park in July 2013. The field

season was funded by the National Parks and Wildlife Service.

After the field season I analysed the identification photographs collected during the surveys and submitted a

progress report and a biopsy report on the 2013 field season to the NPWS. I also started working on an

abundance estimate for bottlenose dolphins occurring in the waters in Connemara, Co. Galway, and on an

abundance estimate for a wider area covering Connemara, Mayo and south Donegal. In addition, I deployed

a passive acoustic monitoring device, a C-POD, in Saint John’s point, Co. Donegal. The purpose of the

deployment is to give an indication of habitat use and occupancy rates of bottlenose dolphins in this area.

West Coast of Ireland Bottlenose Dolphin Project (PI Dr Emer Rogan, PhD Student Milaja

Nykanen)

PhD student Milaja Nykanen conducting a boat

survey during her fieldwork season 2013


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The focus of activities in 2013 and beyond was divided in two elements; the first was orientated towards the

completion of ongoing work programmes and the fulfilment of the contractual commitments associated with

the various contracted research projects acquired during the lifetime of Beaufort Fish Population Genetics

Award and the second element was focused on the continued acquisition of new research grants. The project

achieved a significant milestone in 2013 by surpassing €2.5m in external funding since the projects

commencement in June 2008.

The Beaufort Marine Research Award in Fish Population Genetics is a joint project with Queen’s University

Belfast and the Marine Institute and is funded by the Irish Government under the Sea Change Programme. In

keeping with the priorities of the Beaufort genetics research programme, the majority of new grants are

focused on the key species (i.e. Atlantic salmon, Atlantic cod, brown trout and lobsters). However, additional

research projects in collaboration with our Beaufort project partners in Queen’s University Belfast, focusing

on other species of strategic value from economic and/or conservation perspectives (e.g. sea bass, marine

and river lampreys, eels, European perch, oysters) are also been undertaken by the group. Dr Tom Reed,

supported by the Beaufort, has being preparing an application for funding through the prestigious European

Research Councils starter grants. ERC Starting Grants aim to support up-and-coming research leaders who

are about to establish a proper research team and to start conducting independent research in Europe. The

scheme targets promising researchers who have the proven potential of becoming independent research

leaders. In 2013, seven scientific papers have been published by the group at UCC with numerous additional

papers published in press or in review for 2014.

In respect of personnel matters, in Cork, Dr Jens Carlsson was appointed as Lecturer in Zoology at the

School of Biological and Environment Science in University College Dublin. The vacant position has now

been filled by Dr Tom Reed (http://www.ucc.ie/en/afdc/peopleandcontacts/tomreed/). Dr Eileen Dillane

continues in her role as laboratory supervisor in UCC. Mr Brian Clarke and Mr Trevor Stafford were

employed as research assistants funded by the Atlantic Area Inter-Reg programme as part of the AARC

project. Mr Ross O’Neill commenced a study for MSc on the biology and genetics of sea bass

(Dincentrarchus labrax) in 2013. Dr Ciar O’Toole, funded and supervised as part of the Beaufort Award,

successfully completed her PhD research for a thesis entitled the ‘Biological significance of molecular

variation in salmonid fish’.

During 2013, progress continued on previously established projects which were acquired under the Beaufort

Fish Population Genetics Award. These included the CSTP, Lobster (NELCO V-notching), Lobster (Kilkeel

Focus On Molecular Genetics of Aquatic Animals Research

Beaufort Fish Population Genetics (Prof Tom Cross - Grantee/ Dr Phil McGinnity - Principal

Investigator, Senior Researcher Dr Jamie Coughlan, Senior Researcher Dr Tom Reed, Research Sup-

port Officer Dr Eileen Dillane, PhD Student Ciar O’Toole)


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Development Association), Reciprocal transfer experiment, Burrishoole pedigree, Girnock Burn pedigree,

West Greenland GSI, Jamie Magee’s trout studies in the Burrishoole, Cathy Johnson’s studies in Donegal

and the Bush, Ciar O’Toole’s studies in the Burrishoole, Newfoundland and Lough Currane, Update NGSI,

EirCOD, Galloway brown trout population genetics studies and IFI brown trout studies. New research

initiatives started in 2013 include an additional ranching element to the common garden experiment

undertaken in the Bunowen River as part of the Atlantic ARC project extension. The objective here is to

obtain some estimate of the relative marine performance of the some of the candidate populations assessed

in freshwater. The ESB have generously sponsored an assessment of the provenance of the contemporary

wild salmon population returning to the upper river. The key management question here is whether these

fish originate from natural spawning or are the product of the stocking programme. The outcome of the

investigation will inform the best strategy for stock rebuilding. As part of an MSc research project Mr Ross

O’Neill has undertaken an investigation into the distribution of European sea bass (Dicentrarchus labrax) in

Irish waters.

Polymorphic microsatellite DNA loci were used

here in three studies during this PhD, one on

Salmo salar and two on S. trutta. In 2013, all

laboratory work was completed, data analysis was

carried out and the thesis was written and

submitted on the 4th January 2014. Final results

showed, in the case of S. salar, that the survival of

native fish and non-natives from a nearby

catchment, and their hybrids, differed significantly

during a common-garden experiment. Overall

survival of non-natives was 35% of natives. These

results imply a genetic basis and suggest local

adaptation can occur in salmonids across

relatively small geographic distances. In the first case study with S. trutta, the species was investigated as an

invasive in Newfoundland, eastern Canada. Genetic investigation provided a clear example of the structure

of two expanding waves of spread along coasts. Finally, the genetics of anadromous S. trutta from the

Waterville catchment in south western Ireland were studied and used to assign very large rod caught sea

trout individuals (so called “specimen” sea trout) back to region of origin. All these studies provide results

which will contribute to future management of the species. It might be concluded that the overarching

message from this thesis is to highlight the importance of maintaining genetic diversity in salmonid

populations as vital for their long-term productivity and resilience.

Biological Significance of Molecular Variation in Salmonid Fish (Supervisors Prof. Tom Cross &

Dr Phil McGinnity, PhD Student Ciar O’Toole)

The Atlantic Salmon Salmo salar


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Allocation of research funding (%) on-going during

2013 from different funding bodies.

MSc Theses

O’Grady, E. 2013. Modelling thresholds in parasite life-cycles

using delayed exchange of stability - with particular reference to

the Unikaryon legeri problem. Supervisors: Dr Sarah Culloty, Dr

Tom Kelly, Dr Dmitri Rachinskii (School of Mathematics).

PhD Theses

McCarthy, M. 2013. Ecotoxicology of marine biotoxins in bivalve

shellfish. Supervisors: Prof. John O’Halloran (School of BEES),

Prof. Frank Van Pelt (School of Pharmacy), Prof. Kevin James

(UCC/CIT).

Morgan, E. 2013. Synecology in soft sediment bivalves: the influence of parasites, physiological processes,

and environmental stressors on health and disease. Supervisors: Dr Sarah Culloty, Dr Ruth Ramsay (School

of BEES).

Ribeiro Santos, A.M.A. 2013. The life history and ecology of black scabbardfish (Alphanopus carbo Lowe

1839) in the north-east Atlantic. Supervisor: Dr Emer Rogan.

POSTGRADUATE STUDENTS GRADUATED IN 2013

RESEARCH FUNDING

During 2013, eighteen research projects to the value of €8.9m were on-going at the AFDC. New projects to

the value of €223,360 started in 2013. National funding sources, through the Marine Institute, Inland Fisheries

Ireland, Irish Research Council, National Parks and Wildlife Service and the School of Biological, Earth and

Environmental Sciences, University College Cork, account for 69% of the total research funding for 2013.

The proportion of funding for research through European Union funding (Framework 7 and the European Re-

gional Development Fund) at the AFDC has increased from 29% in 2012 to 31% in 2013.

School of BEES/AFDC PhD Graduates 2013


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2013 Funding

Burnell, G.B. The ecological and economic contribution of the detritivore component to novel marine

Integrated Multi-tophic Aquaculture (IMTA) systems. Irish Research Council, 2013-2017. €32,000.

Culloty, S.C. Herpes virus in Irish oysters and identification of resistant stocks (HERPISH). FP7 Marie Curie

Intra-European Fellowship, 2013-2015. €191,360.

2012 Funding

Culloty, S.C. Bridging the gap between science and producers to support the European marine mollusc

production sector (EUROSHELL). EU FP7 Funding, 2012-2014. €18,168.

Burnell, G.B. & Culloty, S.C. The effect of pre- and probiotics on marine invertebrates in aquaculture.

School of BEES Crawford Hayes Scholarship, 2012-2015. €72,000.

2011 Funding

Culloty, S.C. Bioengineered micro-encapsulation of active agents delivered to shellfish (BEADS). EU FP7

Capacities Support for SME’s Funding Programme, 2011-2013. €303,899.

Culloty, S.C. Management of infectious diseases in oysters and mussels in Europe (BIVALIFE). EU FP7

Funding, 2011-2014. €256,410.

Rogan, E. The genetic structure, foraging ecology, movement patterns and habitat choices of bottlenose

dolphins (Tursiops truncatus) along the west coast of Ireland. National Parks and Wildlife Service, 2011-

2015. €45,000.

Rogan, E. The genetic structure, foraging ecology, movement patterns and habitat choices of bottlenose

dolphins (Tursiops truncatus) along the west coast of Ireland. School of BEES Crawford Hayes Scholarship,

2011-2015. €72,000.

2010 Funding

Culloty, S.C. Establishing the scientific bases and technical procedures and standards to recover the

European flat oyster production through strategies to tackle the main constraint bonamiosis

(OYSTERECOVER). EU FP7 Funding, 2010-2013, €730,894.

McGinnity, P., Cross, T.F. & Coughlan, J. Atlantic aquatic resource conservation (AARC). European

Regional Development Fund (ERDF): INTERREG 4 Atlantic Area Programme, 2010-2013, €255,429.

McGinnity, P. & Cross, T.F. IFI Strategic Partnership Project – Setting Conservation Limits. National

Salmon Conservation Stamp. IFI Research Partnership Project, Inland Fisheries Ireland. €80,000.

2009 Funding

Culloty, S.C. Shellfish productivity in the Irish Sea: working towards a sustainable future (SUSFISH). ERDF

INTERREG 4A, 2009-2013, €618,399.

McGinnity, P. & Cross, T.F. Celtic Sea Trout project: Genetic Stock Identification of sea trout stocks. EU

INTERREG, 2009-2013, €359,830.

McGinnity, P., Cross, T.F. & Coughlan, J. IFI Strategic Partnership Project. Inland Fisheries Ireland.

(Research grant award to Beaufort consortium. 2009-2013, €320,000.

2008 Funding

Burnell, G. & Cummins, V. Beaufort Marine Research Award: Ecosystem Approach to Fisheries

Management. Irish Government NDP administered by the Marine Institute, 2008-2015, €1,860,004.

Cross, T.F. & McGinnity, P. Irish cod breeding programme. Marine Institute, 2008-2015, €213,088.

Cross, T.F. & McGinnity, P. Beaufort Marine Research Award: Fish population genetics. Irish Government

ON-GOING & NEW RESEARCH GRANTS DURING 2013


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NDP administered by the Marine Institute, 2008-2015. €2,710,236.

Rogan E. & Codling, E. Develop and test through simulation a suite of measures that will contribute to

rebuilding depleted fish stocks in waters around Ireland. Marine Institute, 2008-2014. €627,633.

1. Bourret V., Kent M.P., Hayes B.J., Primmer C.R., Vasemagi A., Karlsson S., Hindar K., McGinnity P.,

Verspoor E., Bernatchez L. & Lien S. 2013. SNP-array reveals genome wide patterns associated with

geographical and potential adaptive divergence across the natural range of Atlantic salmon (Salmo

salar). Molecular Ecology, 22, 532–551.

2. Brown S.L., Reid D. & Rogan E. 2013. A risk-based approach to rapidly screen vulnerability of

cetaceans to impacts from fisheries bycatch. Biological Conservation, 168: 78-87.

3. Cronin M., Zuur A.F. & Rogan E. 2013. A modelling framework to optimize timing of haulout counts for

estimating harbour seal (Phoca vitulina) abundance. NAMMCO Scientific Publications, doi: http://

dx.doi.org/10.7557/3.2686.

4. Carlsson J., Gauthier D., Carlsson J.E.L., Coughlan J.P., Dillane E., Fitzgerald R.D., Keating F.U.,

McGinnity P., Mirimin L. & Cross T.F. 2013. Rapid, economical single nucleotide polymorphism and

microsatellite discovery based on de novo assembly of a reduced representation genome in a non-

model organism: a case study of Atlantic cod. Journal of Fish Biology, 82: 944–958.

5. Davenport J., Cotter E., Rogan E., Kelliher D. & Murphy C. 2013. Structure, material characteristics

and function of the upper respiratory tract of the pygmy sperm whale. Journal of Experimental Biology,

doi: 10.1242/jeb.083782.

6. Ensing D., Crozier W.W., Boylan P., O’Maoiléidigh N. & McGinnity P. 2013. An analysis of Genetic

Stock Identification on a small geographical scale using microsatellite makers, and its application in the

management of a Mixed-Stock fishery for Atlantic salmon (Salmo salar L.) in Ireland. Journal of Fish

Biology, 82 (6): 2080-2094.

7. Friedland K.D., Shank B.V., Todd C.D., McGinnity P. & Nyee, J. 2013. Differential response of

continental stock complexes of Atlantic salmon (Salmo salar) to the Atlantic Multi-decadal Oscillation.

Journal of Marine Systems, 133: 77-78.

8. Gauthier D., Audemard C.A., Carlsson J.E., Darden T.L., Denson M.R., Reece K.S. & Carlsson J.

2013. Genetic Population Structure of US Atlantic Coastal Striped Bass (Morone saxatilis). Journal of

Heredity, 104 (4): 510-520.

9. Greco G., Svaldo Lanero T., Torrassa S., Young R., Vassali M., Cavaliere A., Rolandi R., Pelucchi El,

Faimali M. & Davenport J. 2013. Microtopography of the eye surface of the crab Carcinus maenas : an

atomic force microscope study suggesting a possible antifouling potential. Journal of the Royal Society

Interface 2013 10, 20130122. doi: 10.1098/rsif.2013.0122.

10. Hammond P.S., Macleod K., Berggren P., Borchers D.L., Burt L., Cañadas A., Desportes, G., Donovan,

G.P., Gilles A., Gillespie D., Gordon J., Hiby L., Kuklik I., Leaper R., Lehnert K., Leopold M., Lovell P.,

Oien N., Paxton C.G.M., Ridoux V., Rogan E., Samarra F., Schieidat M., Sequeira M., Siebert U., Skov

H., Swift R., Tasker M.L., Teilmann J.M., Van Canneyt O., Vazquez J.A. 2013. Cetacean abundance

and distribution in European Atlantic shelf waters to inform conservation and management. Biological

Conservation, 164: 107-122.

11. Hedger R.D., de Eyto E., Dillane M., Diserud O., Hindar K., McGinnity P., Poole R. & Rogan G. 2013.

Improving abundance estimates from electrofishing removal sampling. Fisheries Research, 137: 104–

115.

12. Keenan K., Bradley C.R., Magee J.J., Hynes R.A., Kennedy R.J., Crozier W.W., Poole R., Cross T.F.,

McGinnity P. & Prodöhl P. A. 2013. Beaufort Trout MicroPlex: A high throughput multiplex platform

comprising 38 informative microsatellite loci for use in brown trout and sea trout (Salmo trutta L.)

PUBLICATIONS


19

population genetics studies. Journal of Fish Biology, 82 (6):1789-804.

13. Keenan K., McGinnity P., Cross T., Crozier W.W. & Prodohl P. 2013. diveRsity: An R package for the

estimation and exploration of population genetics parameters and their associated errors. Methods in

Ecology and Evolution, 4 (8): 782-788.

14. Lynch S.A., Dillane E., Carlsson J. & Culloty S.C. 2013. Development and Assessment of a

Sensitive and Cost-Effective Polymerase Chain Reaction to Detect Ostreid Herpes virus 1 and Variants.

Journal of Shellfish Research, 32 (3), 657-664.

15. Lynch, S.A., Villalba, A., Abollo, E., Engelsma, M., Stokes, N. & Culloty, S.C. 2013. The occurrence of

haplosporidian parasites, Haplosporidium nelsoni and Haplosporidium sp., in oysters in Ireland.

Journal of Invertebrate Pathology, 112: 208-212.

16. Luque, P. L., Pierce, G. J., Learmonth, J. A., Rogan, E., Boon, J. & Lockyer, C.H. (2013). Are

Mineralization Anomalies in Common Dolphin Teeth Associated with Life-History Events And/Or The

Exposure to Anthropogenic Pollutants?Journal of Zoology, 291 (3): 194-204

17. Mackenzie C.L., Bell M.C., Birchenough S.N.R., Culloty S.C., Sanderson W.G., Whiteley N.M. &

Malham, S.K. 2013. Future socio-economic and environmental sustainability of the Irish Sea requires a

multi-disciplinary approach with industry and research collaboration, and cross-border partnership.

Ocean & Coastal Management, 8: 1-6.

18. Maloy A.P., Culloty S.C. & Slater J.W. 2013. Dietary analysis of small planktonic consumers: a case

study with marine bivalve larvae. Journal of Plankton Research. doi: 10.1093/plankt/fbt027.

19. Maloy A.P., Nelle P., Culloty S.C., Slater J.W. & Harrod, C. 2013. Identifying trophic variation in a

marine suspension feeder: DNA-and stable isotope-based dietary analysis in Mytilus spp. Marine

biology, 160 (2), 479-490.

20. Morgan E., O'Riordan R.M. & Culloty S.C. (2013). Climate change impacts on potential recruitment in

an ecosystem engineer. Ecology and Evolution, 393, 581-594.

21. Moura, A.E., Natoli, A., Rogan, E. & Rus Hoelzel, A. (2013). Evolution of Functional Genes in

Cetaceans Driven by Natural Selection on a Phylogenetic and Population Level. Evolutionary Biology,

40 (3): 341-354.

22. Moura, A. E., Natoli, A., Rogan E. & Hoelzel, A. (2013). Atypical Panmixia In A European Dolphin

Species (Delphinus delphis): Implications For The Evolution Of Diversity Across Oceanic Boundaries,

Journal of Evolutionary Biology, 26 (1): 63-75.

23. O'Farrell B., Benzie J.A.H., McGinnity P., de Eyto, E., Dillane E., Coughlan J. & Cross T. 2013.

Selection and Phylogenetics of Salmonid MHC Class I: Wild Brown Trout (Salmo trutta) Differ from a

Non-Native Introduced Strain. PLoS ONE, 8 (5): e63035.

24. Outerbridge M. & Davenport J. 2013. Malaclemys terrapin (Diamondback Terrapin). Dredging foraging

behavior. Herpetological Review, 44: 307-308.

25. Pazhayamadom D.G., Kelly C.J., Rogan E. & Codling E. 2013. Self-starting CUSUM approach for

monitoring data poor fisheries. Fisheries Research, 145: 114-127.

26. Santos A.R., Minto C., Connolly P. & Rogan E. 2013. Oocyte dynamics and reproductive strategy of

Aphanopus carbo in the NE Atlantic—Implications for fisheries management. Fisheries Research, 143:

161-173.

27. Santos A.R., Trueman C., Connolly P. & Rogan E. 2013. Trophic ecology of black scabbardfish,

Aphanopus carbo in the NE Atlantic—Assessment through stomach content and stable isotope

analyses. Deep Sea Research Part I: Oceanographic Research Papers, 77: 1-10.

28. Sullivan T., Broszeit S., O’Sullivan K.P.A., McAllen R., Davenport J. & Regan F. 2013. High resolution

monitoring of episodic stratification events in an enclosed marine system. Estuarine, Coastal and Shelf

Science 123: 26-33.


20

29. Thrupp T.J., Lynch S.A., Wootton E.C., Malham S.K., Vogan C.L., Culloty S.C. & Rowley A.F. 2013.

Infection of juvenile edible crabs, Cancer pagurus by a haplosporidian-like parasite. Journal of

Invertebrate Pathology, 114 (1): 92–99.

Published Abstracts

1. Prado-Alvarez M., Darmody G., Lynch S., Maloy A., Cotterill J., Wontner-Smith T. & Culloty S.C.

2013. In vivo immunostimulation of the flat oyster Ostrea edulis and tissue targeting by microspheres

uptake. Fish & Shellfish Immunology, 34 (6): 1731.

Non-Peer Reviewed Publications

1. Robert R., Sanchez J.L., Perez-Paralle L., Ponis E., Kamermans P. & O’Mahoney M. 2013. A glimpse

of the mollusc industry in Europe. Aquaculture Europe, 38 (1): 5-11.

Books

1. Allan G. & Burnell G. (Ed.s) 2013. Advances in aquaculture hatchery technology. Woodhead

Publishing Series in Food Science, Technology and Nutrition No. 242.

Oral Presentations

1. Cipriano A., Culloty S.C., Burnell G. & Ryan P. 2013. External and internal tagging methods for

Paracentrotus lividus. Asian-Pacific Aquaculture 2013, 11th-13th December, Ho Chi Minh City,

Vietnam.

2. Cipriano A., Culloty S.C., Burnell G. & Ryan P. 2013. Effects of immunostimulants on the purple sea

urchin Paracentrotus lividus. Asian-Pacific Aquaculture 2013, 11th-13th December, Ho Chi Minh City,

Vietnam.

3. Lynch S.A., Villalba A., Engelsma M., Stokes N.A., Burreson E. & Culloty S.C. 2013. A parasite can

have a significant impact on the ecology of the cockle Cerastoderma edule. SUSFISH 4Sea

Conference, 12th - 13th March 2013, Welsh Government Buildings, Llandudno Junction, Wales, UK.

Poster Presentations

1. Prado-Alvarez M., Darmody G., Lynch S., Maloy A., Cotterill J., Wontner-Smith T. & Culloty

S.C. 2013. In vivo immunostimulation of the flat oyster Ostrea edulis and tissue targeting by

microspheres uptake. 1st International Conference of Fish and Shellfish Immunology, 25th-28th June

2013, Vigo, Spain.

2. Flannery G., Lynch S. & Culloty S.C. 2013. Investigating the existence of a vector or reservoir of

Bonamia ostreae. 16th European Association of Fish Pathologists (EAFP) Conference, 4th September

2013, Tampere, Finland.

3. Lynch S.A. & Culloty S.C. 2013. Haplosporidium nelsoni and Haplosporidium amoricanum detected in

Irish oysters. SUSFISH 4Sea Conference, 12th - 13th March 2013, Welsh Government Buildings

Llandudno Junction, Wales, UK.

4. Lynch S.A., Morgan E. & Culloty S.C. 2013. Investigation into the prevalence and distribution of

pathogens in cultured and wild populations of mussels Mytilus spp. in Ireland. SUSFISH 4Sea

Conference, 12th - 13th March 2013, , Welsh Government Buildings Llandudno Junction, Wales, UK.

5. Lynch S.A., Cross M., O’ Grady, E., Morgan E., O’ Riordan R. & Culloty S. 2013. Shellfish

productivity in the Irish Sea: working towards a sustainable future (SUSFISH). SUSFISH 4Sea

Conference,12th - 13th March 2013, Welsh Government Buildings Llandudno Junction, Wales, UK.

CONFERENCE PRESENTATIONS


21

AFDC PERSONNEL

Dr Sarah Culloty, Director of the AFDC is PI with

the Shellfish Health research group and Senior

Lecturer with the School of BEES.

Professor Tom Cross, is PI with the Molecular

Genetics research group and Professor Emeritus

with the School of BEES.

Prof. Gavin Burnell is PI with the Aquaculture

Research Group. Gavin is also Vice Head of the

School of BEES and Acting Head of Zoology.

Dr Emer Rogan is PI with the Marine Mammals

and Fisheries Research Group and Senior

Lecturer with the School of BEES.

Dr Phil McGinnity is the Beaufort Marine

Research Award Principal Investigator with the

Molecular Genetics research group.

Prof. John Davenport is Professor Emeritus with

the School of BEES and has a particular interest

in aquaculture and the environment.

Dr Eileen Dillane is Postdoctoral Researcher with

the Molecular Genetics of Aquatic Animals Re-

search Group.

Dr Sharon Lynch is Postdoctoral Researcher with

the Shellfish Health Research Group working on a

range of projects within the group.

Dr Sarah Kraak, Postdoctoral Researcher with the

Marine Mammals and Fisheries Research Group,

working on the SeaChange project.

Dr Susie Brown is Postdoctoral Researcher with

the Marine Mammals and Fisheries Research

Group working on the Beaufort EAFM project.

Dr Maria Prado Alvarez, is Postdoctoral

Researcher with the Shellfish Health Research

Group working on oyster herpes virus.

Anneli Englund is a PhD student with the Marine

Mammals and Fisheries Research Group working

on vocalisations in marine mammals.

Deepak George Pazhayamadom is a PhD

student with the Marine Mammals and Fisheries

Research Group working on the application of

Signal Detection Methods to the Fisheries

Management.

Dr Jens Carlsson is Senior Researcher with the

Beaufort Fish Population Genetics project with

the Molecular Genetics of Aquatic Animals (until

July 2013)

Dr Jamie Coughlan is Senior Researcher with the

Beaufort Fish Population Genetics project with the

Molecular Genetics of Aquatic Animals.

Principal Investigators

Manager

Dr Maria O’Mahoney is Manager of the AFDC. Maria‘s

research background is in the application of novel

technologies to the aquaculture of sea urchins and abalone.

Researchers

Dr Thomas Reed is Senior Researcher with the

Beaufort Fish Population Genetics project with

the Molecular Genetics of Aquatic Animals (latter

half of 2013)


22

Emer Morgan is a PhD student with the Shellfish

Health Research Group working on the ERDF

funded SUSFISH project.

Grace Flannery is a PhD student with the

Shellfish Health Research Group. Grace’s

research is part of the EU FP7

OYSTERECOVER project.

Maud Cross is a PhD student with the Shellfish

Health Research Group. Maud’s research is part

of the EU FP7 SUSFISH project.

Moira McCarthy is a PhD student with the EU

FP7 Environment and Climate Change: Impacts

& Responses project. This project is supervised

by Prof. John O’Halloran (School of BEES), Dr

Frank van Pelt and Prof. Kevin James.

Ashlie Cipriano is a PhD student with the

Aquaculture Research Group. Ashlie’s research

investigates the effect of prebiotics and probiotics

on marine invertebrates in aquaculture.

Milaja Nykanen is a PhD student with the Marine

Mammals and Fisheries Research Group.

Milaja’s research investigates coastal bottlenose

dolphins in Western Ireland.

Elaine Brennan is conducting an MSc by research

with the Shellfish Health Research Group.

Grainne Darmody is Research Assistant with the

Shellfish Health Research Group. Grainne is

working on the EU FP7 funded project, BEADS

project.

Jeanette (Nettan) Carlsson is Research

Assistant with the Shellfish Health Research

Group. Jeanette is working on the EU FP7

funded OYSTERECOVER project.

Gema Hernandez-Milian is the Beaufort EAFM

PhD student with the Marine Mammals and

Fisheries Research Group.

Amy O’Reilly is a PhD student with the Shellfish

Health Research Group. Amy ‘s research is part

of the EU FP7 funded BIVALIFE project.

Ana Santos is a PhD student with the Marine

Mammals and Fisheries Research Group working

on the ecology of Black Scabbardfish

(Aphanopus carbo).

Daryl Gunning is a PhD student with the

Aquaculture Research Group. Daryl’s research is

based on IMTA.

Amy Geraghty is a PhD student with the Shellfish

Health Research Group. Amy is researching the

health status of Irish waters in marine reserve and

non-marine reserve areas.


23

CONTACT:

The Aquaculture & Fisheries Development Centre

School of Biological, Earth & Environmental Sciences

Distillery Fields, North Mall

Cork, Ireland

Director: Dr Sarah Culloty

Manager: Dr Maria O’Mahoney

Email: [email protected]; [email protected]

http://afdc.ucc.ie

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