Peer-Reviewed Publications

1. Cross M.E., Bradley C.R., Cross T.F., Culloty S., Lynch S., McGinnity P., O’Riordan R.M., Vartia S. & Prodohl P.A. 2016. Genetic evidence supports recolonisation by Mya arenaria (L.) of Western Europe from North America. Marine Ecology Progress Series, doi: 10.3354/meps11672.

2. Flannery G., Lynch S.A. & Culloty S.C. 2016. Investigating the significance of the role of Ostrea edulis larvae in the transmission and transfer of Bonamia ostreae.  Journal of Invertebrate Pathology, 136: 7-9.  



Peer-Reviewed Publications

  1. Brown S.L., Reid D. & Rogan E. 2015. Spatial and temporal assessment of potential risk to cetaceans from static fishing gears. Marine Policy, 51, 267-280.
  2. Carlsson J., Cross T.F., McGinnity P., Prodöhl P. & McDevitt, A. 2015. The use of genetics to infer the origins of the terrestrial and freshwater elements of the Irish fauna. In: Sleeman DP, Carlsson J & Carlsson, JEL (eds). Mind the Gap II: new insights into the Irish postglacial. Belfast: Irish Naturalists' Journal.
  3. Darmody G., Maloy A.P., Lynch S. A.Prado-Alvarez M., Cotterill J., Wontner-Smith T. & Culloty S.C. 2015.  Tissue targeting of the European flat oyster, Ostrea edulis, using microencapsulated microbeads as a biological proxy. Aquaculture International, 23: 647-659. DOI 10.1007/s10499-014-9842-y
  4. De Castro, F., Shephard S., Kraak S.B.M., Reid D. & Farnsworth K.D. 2015.  Footprints in the sand: a persistent spatial impression of fishing in a mobile groundfish assemblageMarine Biology, 162 (6), 1239-1249.
  5. de Eyto  E., White  J., Boylan P., Clarke B., Cotter D., Doherty D., Gargan P., Kennedy R., McGinnity P., O'Maoiléidigh N. & O’Higgins K. 2015. The fecundity of wild Irish Atlantic salmon Salmo salar L. and its application for stock assessment purposes. Fisheries Research, 164: 159-169.
  6. Feis M.E., Thieltges D.W., Olsen J.L., de Montaudouin X., Jensen K.T., Bazaïri H., Culloty S.C. & Luttikhuizen P.C. 2015. The most vagile host as the main determinant of population connectivity in marine macroparasites. Marine Ecology Progress Series 520: 85-99. doi: 10.3354/meps11096.
  7. Fernández R., Schubert M., Vargas A.M., Brownlow A., Vikingsson G.A., Siebert U., Jensen L.F., Øien N., Wall D., Rogan E., Mikkelsen B., Dabin W., Alfarhan A.H., Alquraishi S.A., Al-Rasheid K.A.S., Guillot G. & Orlando L. 2015. A genome-wide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins. Molecular Ecology Resources.  doi: 10.1111/1755-0998.12427.
  8. Hernandez-Milian G., Berrow S., Begoña Santos M., Reid D.G. & Rogan E. 2015. Insights into the trophic ecology of bottlenose dolphins (Tursiops truncatus) in Irish waters. Aquatic Mammals 41(2): 226-239. doi: 10.1578/AM.41.2.2015.226
  9. Hernandez-Milian G., Begoña Santos M., Reid D. & Rogan E. 2015. Insights into the diet of Atlantic white-sided dolphins (Lagenorhynchus acutus) in the Northeast Atlantic. Marine Mammal Science, 2015 Oct 1, DOI: 10.1111/mms.12272.
  10. Hu W., Culloty S., Darmody G., Lynch S., Davenport J., Ramirez-Garcia S., Dawson K., Lynch I., Doyle H. & Sheehan D. (2015) Neutral red retention time assay in determination of toxicity of nanoparticles. Marine Environmental Research doi:10.1016/j.marenvres.2015.05.007.
  11. Jacob A., Xia A., Gunning D., Burnell G. & Murphy J.D. 2015.  Seaweed biofuel derived from Integrated Multi-trophic Aquaculture.
  12. Juhel G., Ramsay R.M., O'Halloran J., Culloty S.C. & Davenport J. 2015.  Effect of the microcystin producing cyanbacterium, Microcystis aeruginosa, on immune functions of the zebra mussel Dreissena polymorpha.  Journal of Shellfish Research 34(2): 433-442.
  13. Jones A.C., Mead A., Kaiser M.J., Austen M.C.V., Adrian A.W., Auchterlonie N.A., Black K.D., Blow L.R., Bury C., Brown J.H., Burnell G.M., Connolly E., Dingwall A., Derrick S., Eno N.C., Gautier D.J.H., Green K.A., Gubbins M., Hart P.R., Holmyard J.M., Immink A.J., Jarrad D.L., Katoh E., Langley J.C.R., O'C Lee D., Le Vay L., Leftwich C.P., Mitchell M., Moore A., Murray, A.G., McLaren E.M.R., Norbury H., Parker D., Parry S.O., Purchase D., Rahman A., Sanver F., Siggs M., Simpson S.D., Slaski R.J., Smith K., Le Q Syvret M., Tibbott C., Thomas P.C., Turnbull J., Whiteley R., Whittles M., Wilcockson M.J., Wilson J., Dicks L.V. & Sutherland W.J. 2015. Prioritization of knowledge needs for sustainable aquaculture: a national and global perspective.  Fish and Fisheries 16 ( 4), 668–683.
  14. Kraak S.B.M., Reid D.G., Bal G., Barkai A., Codling E.A., Kelly C.J. & Rogan E. 2015. RTI (“real-time incentives”) outperforms traditional management in a simulated mixed fishery and cases incorporating protection of vulnerable species and areas. Fisheries Research, 172:209-224 doi:10.1016/j.fishres.2015.07.014
  15. Duggan D.E., Farnsworth K.D., Kraak S.B.M. & Reid F.G. 2015.  Integration of Indicator Alarm Signals for Ecosystem-Based Fishery ManagementConservation Letters,8 (6), 414-423.
  16. Llewellyn, M., McGinnity, P., Dionne, M., Letourneau, J., Thonier, F., Carvalho, G.R., Creer, S. & Derome, N. (in press). The biogeography of the Atlantic salmon (Salmo salar) gut microbiome revealed by deep sequencing. The ISME Journal, 30 Oct 2015, doi: 10.1038/ismej.2015.189.
  17. Lynch S.A., Darmody G., Laide C., Walsh D. & Culloty S.C. 2015. A preliminary health survey of the hermit crab, Pagurus bernhardus, on the southwest coast of Ireland. Journal of Invertebrate Pathology. doi: 10.1016/j.jip.2015.03.006.
  18. Mäkinen H.  Vasemägi A., McGinnity P., Cross T.F. & Primmer C. 2015. Population genomic analyses of early phase Atlantic salmon (Salmo salar) domestication/captive breeding'. Evolutionary Applications 8: (1), 93-107.
  19. Mantua N.J., Crozier L.G., Reed T.E., Schindler D.E. & Waples R.S. 2015. Response of Chinook salmon to climate change. Nature Climate Change. 5(7): 613-615.
  20. O’Grady E.A., Culloty S.C., Kelly T.C., O’Callaghan M.J.A. & Rachinskii D. 2015. A preliminary threshold model of parasitism in the cockle Cerastoderma edule using delayed exchange of stability. Journal of Physics: Conference Series 585:012013. doi:10.1088/1742-6596/585/1/012013.
  21. O’Toole C., Reed T.E., Bailie D., Bradley C., Cotter D., Coughlan J., Cross T., Dillane E., McEvoy S., O’Maoileidigh N., Prodöhl P., Rogan G. & McGinnity P. 2015. The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature. Evolutionary Applications. doi: 10.1111/eva.12299
  22. O’Toole C., Reed T., Bailie D., Bradley C., Cotter D., Coughlan J., Cross T., Dillane E., McEvoy S., Prodohl P., Rogan G. & McGinnity P. 2015. Local adaptation in Atlantic salmon between neighbouring catchments: evidence from a common garden field-experiment with hybrids.  Evolutionary Applications Vol 8 (9): 881-900.
  23. Oudejans M.G., Visser F., Englund A., Rogan E. & Ingram S.N. 2015. Evidence for distinct coastal and offshore communities of bottlenose dolphins in the north east Atlantic. PLoS ONE 10(4): e0122668. doi:10.1371/journal.pone.0122668.
  24. Pazhayamadom, D.G., Kelly C.J., Rogan E. & Codling E.A. 2015.  Self-Starting Cumulative Sum Harvest Control Rule (SS-CUSUM-HCR) for status-quo management of data limited fisheries.  Canadian Journal of Fisheries and Aquatic Sciences, 10.1139/cjfas-2015-0039.
  25. Pazhayamadom D.G., Kelly C.J., Rogan E. & Codling E.A. 2015. Decision Interval Cumulative Sum Harvest Control Rules (DI-CUSUM-HCR) for managing fisheries with limited historical information.  Fisheries Research, 171: 154-169.
  26. Prado-Alvarez M., Carlsson J. & Culloty S.C. 2015. Experimental Infection Of Crassostrea Gigas Spat And Larvae With Different Susceptibility To OsHV-1 μVar. Journal of Shellfish Research, 34 (2), 671-672. (Abstract)
  27. Prado-Alvarez M., Darmody G., Hutton S., O’Reilly A., Lynch S. & Culloty S.C. 2015. Ostreid Herpes Virus (OsHV-1 μVar) Detection In The Irish Coast During A Very Warm Summer. Journal of Shellfish Research, 34 (2), 671-671. (Abstract)
  28. Prado-Alvarez M., Lynch S.A., Kane A., Darmody G., Pardo B.G., Martínez P., Cotterill J., Wontner-Smith T. & Culloty S.C. 2015. Oral immunostimulation of the oyster Ostrea edulis: Impacts on the parasite Bonomia ostreae. Fish and Shellfish Immunology doi: 10.1016/j.fsi.2015.01.019
  29. Ravinet M., Hynes R., Poole R., Cross T.F., McGinnity P., Harrod C. & Prodöhl P.A. 2015. Where the lake meets the sea: strong reproductive isolation is associated with adaptive divergence between lake resident and anadromous three-spined sticklebacks.  PLoS ONE. 10(4): e0122825. doi:10.1371/journal.pone.0122825.
  30. Reed T.E., Gienapp P. & Visser M.E. 2015. Density dependence and microevolution interactively determine effects of phenology mismatch on population dynamics. Oikos 124(1):81-91.
  31. Reed T.E., Harris M.P. & Wanless S. 2015. Skipped breeding in common guillemots in a changing climate: restraint or constraint? Frontiers in Ecology and Evolution, doi: 10.3389/fevo.2015.00001
  32. Reed T.E., Prodöhl, P. A., Hynes, R., Cross, T., Ferguson, A. & McGinnity, P. (in press). Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment. Heredity . doi: 10.1038/hdy.2015.29
  33. Reed T.E., Prodöhl P. A., Hynes R., Cross T., Ferguson A. & McGinnity P. (2015). Partitioning sources of variation in freshwater survival and size-at-age of wild, farmed and hybrid Atlantic salmon families in the wild. Heredity  115, 173-184 doi:10.1038/hdy.2015.29
  34. Schindler D.E., Armstrong J.B., and Reed T.E. 2015. The portfolio concept in ecology and evolution. Frontiers in Ecology and the Environment 13: 257–263.
  35. Sydeman W.J., Poloczanska E., Reed T.E. & Thompson S.A. 2015. Climate change and marine vertebrates. Science, 350, 772-777.
  36. Verspoor E., McGinnity P., Bradbury I. & Glebe B. 2015. The potential direct and indirect genetic consequences for native Newfoundland Atlantic Salmon from interbreeding with European-origin farm escapes. DFO Can. Sci. Advis. Sec. Res. Doc. 2015/030. viii + 36 p.
  37. Quéméré E. Baglinière J.L., Roussel J.M.,  Evanno G., McGinnity P. &  Launey S. 2015. Seascape and its effect on migratory life-history strategy influences gene flow among coastal brown trout populations (Salmo trutta) in the English Channel.  Journal of Biogeography, 1 November 2015, doi:10.1111/jbi.12632.
  38. Quinn T., McGinnity P. & Reed T.E. 2015. The paradox of ‘premature migration’ by anadromous salmonid fishes: Patterns and hypotheses. Canadian Journal of Fisheries & Aquatic Science. 10.1139/cjfas-2015-0345.

Peer-Reviewed Publications

1. Aykanat T., Johnston S.E., Cotter D., Cross T.F., Poole W.R., Prodöhl P.A., Reed T.E., Rogan G., McGinnity P. & Primmer C.R. 2014. Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis. BMC Evolutionary Biology, 14: 68, doi:10.1186/1471-2148-14-68.

2. Banguera-Hinestroza E., Evans P.G.H., Mirimin L., Reid R.J., Mikkelsen B., Couperus A.S., Deaville R., Rogan  E., Hoelzel A.R. 2014. Phylogeography and population dynamics of the white-sided dolphin (Lagenorhynchus acutus) in the North Atlantic. Conservation Genetics, 15 :789-802.

3. Brown S., Reid D. & Rogan E. 2014.  Characteristics of Fishing Operations, Environment and Life History Contributing to Small Cetacean Bycatch in the Northeast Atlantic.  Plos One, 9(8) e104486. DOI: 10.1371/journal.pone.0104468.

4. Carlsson J., Cross T.F., McGinnity P. Prodhöhl P., McDevitt A. 2014. The use of genetics to infer the origins of the terrestrial and freshwater elements of the Irish fauna. In 'Mind the gap II: new insights into the Irish postglacial' ed. Sleeman D.P., Carlsson J., Carlsson J.E.L. The Irish Naturalist's Journal, Belfast

4. Cross M., Lynch S.A., O' Riordan R.M. & Culloty S.C. 2014. A health status of clams, Mya arenaria and Ensis siliqua, in the Irish Sea. Journal of Invertebrate Pathology,  doi: 10.1016/j.jip.2014.11.001.

5. Cross M.E., O’Riordan R.M., & Culloty S.C. 2014. The reproductive biology of the exploited razor clam, Ensis siliqua, in the Irish Sea. Fisheries Research, 150, 11-17.

6. Cronin M., Gregory S. & Rogan E. 2014. Moulting phenology of the harbour seal in south-west Ireland.  Journal of The Marine Biological Association of The United Kingdom, 94 :1079-1086.

7. Dalton C.,  O’Dwyer B., Taylor D., de Eyto E., Jennings E., Chen G., Poole R., Dillane M. & McGinnity P. 2014. Anthropocene environmental change in an internationally important oligotrophic catchment on the Atlantic seaboard of western Europe. Anthropocene, 5: 9-21.

8. Engelsma M.Y., Culloty S.C., Lynch S.A., Arzul I. Carnegie R.B. 2014. Bonamia parasites: a rapidly changing perspective on a genus of important mollusc pathogens. Diseases of Aquatic Organisms, 110 (1-2): 5-23.

9. Fernández R., Pierce G.J. MacLeoda C.D. Brownlow A., Reid R.J., Rogan E., Addinka M., Robert Deaville R., Jepson P.D. &  Begoña Santos M.  2014.  Strandings of northern bottlenose whales, Hyperoodon ampullatus, in the north-east Atlantic: seasonality and diet. Journal of the Marine Biological Association of the United Kingdom, 94 (06): 1109-1116.

10. Flannery G., Lynch S.A., Carlsson J., Cross T.F. & Culloty S.C. 2014. Assessment of the impact of a pathogen, Bonamia ostreae, on Ostrea edulis oyster stocks with different histories of exposure to the parasite in Ireland. Aquaculture, 432 :243-251.

11. Flannery G., Lynch S.A., Longshaw M., Stone D., Martin P., Ramilo A., Villalba A. & Culloty S.C. 2014. Interlaboratory variability in screening for Bonamia ostreae, protistan parasite of the European flat oyster Ostrea edulis. Diseases of Aquatic Organisms, 110 (1-2): 93-99.

12. Friedland K.D., Shank B.V., Todd C.D., McGinnity P. & Nye J.A. 2014. Differential response of continental stock complexes of Atlantic salmon (Salmo salar) to the Atlantic Multidecadal Oscillation. Journal of Marine Systems, 133: 77-87.

13. Fontaine M.C., Roland K., Calves I., Austerlitz F., Palstra F.P., Tolley K.A., Ryan S., Ferreira M., Jauniaux T., Llavona A., Öztürk B., Öztürk A.A., Ridoux V., Rogan E., Sequeira M., Siebert U., Vikingsson G.A., Borrell A., Michaux J.R. & Aguilar A. 2014.  Postglacial climate changes and rise of three ecotypes of harbour porpoises, Phocoena phocoena, in western Palearctic waters.  Molecular Ecology, 23 (13): 3306-3321.

14. Gosch M., Hernandez-Milian G., Rogan, E., Jessopp M., Cronin M. 2014. Grey seal diet analysis in Ireland highlights the importance of using multiple diagnostic features. Aquatic Biology, 20:155-167.

15. Gurney W.S.C., Brennan L.O., Bacon P.J., Whelan K.F., O'Grady M., Dillane E. & McGinnity P. 2014.  Objectively assigning species and ages to salmonid length data from dual-frequency identification sonar.  Transactions of the American Fisheries Society, 143 (3), 573-585.

16. Hammond P.S., Gillespie D., Lovell P., Samarra F., Swift R., Macleod K., Tasker  M.L., Berggren P., Borchers D.L., Burt L., Paxton C.G.M., Cañadas A., Desportes G., Donovan G.P.,   Gilles A., Lehnert K., Siebert U., Gordon J., Leaper R., Leopold M., Scheidat M., Øien N., Ridoux V., Rogan E., Skov H., Teilmann J.,Van Canneyt O., Vázquez J.A. 2014.  Large scale surveys for cetaceans: Line transect assumptions, reliability of abundance estimates and improving survey efficiency – A response to MacLeod.  Biological Conservation, 170: 338-339.

17. Hu W., Culloty S., Darmody G., Lynch S., Davenport J., Ramirez-Garcia S., Dawson K.A., Lynch I., Blasco J. & Sheehan D. 2014. Toxicity of copper oxide nanoparticles in the blue mussel, Mytilus edulis. Chemosphere, 108: 289-299.

18. Lynch S.A., Flannery G., Hugh-Jones T., Hugh-Jones D. & Culloty S.C. 2014. Thirty-year history of Irish (Rossmore) Ostrea edulis selectively bred for disease resistance to Bonamia ostreae. Diseases of Aquatic Organisms. 110: 113-121 DOI 10.3324/dao02734

19. Lynch S.A., Morgan E., Carlsson J., Mackenzie C., Wooton E.C., Rowley A.F., Malham S. & Culloty S.C. 2014.  The health status of mussels, Mytilus spp., in Ireland and Wales with the molecular identification of a previously undescribed haplosporidian.  Journal of Invertebrate Pathology, 118, 59-65.

20. Mackenzie C.L., Lynch S.A.Culloty S.C. & Malham S.K 2014. Future oceanic warming and acidification alter immune response and disease status in a commercial shellfish species, Mytilus edulis L. Plos One, 9(6): e99712. DOI: 10.1371/journal.pone.0099712.

21. Mäkinen H., Vasemägi A., McGinnity P.Cross T.F. & Primmer C. 2014. Population genomic analyses of early phase Atlantic salmon (Salmo salar) domestication/captive breeding. Evolutionary Applications, 8(1): 93-107. DOI: 10.1111/eva.12230.

22. McAllen R., Hernandez-Milan G., Rogan E., Geaney C., Kelly A. & Kearney, T. 2014.  First record of a cetacean (Common Dolphin Delphinus delphis) within the marine nature reserve at Lough Hyne, Co. Cork. The Irish Naturalists' Journal, 33 (2):100-101.

23. O'Mahoney M., Rice O., Mouzakitis G. & Burnell G. 2014.  Towards sustainable feeds for abalone culture: Evaluating the use of mixed species seaweed meal in formulated feeds for the Japanese abalone, Haliotis discus hannai.  Aquaculture, 430, 9-16.

24. O'Malley K.G., Cross T.F., Bailie D., Carlsson J.Coughlan J.P., Dillane E., Prodohl P.A. & McGinnity P. 2014. Circadian clock gene (OtsClock1b) variation and time of ocean return in Atlantic salmon Salmo salar.  Fisheries Management and Ecology, 21 (1): 82–87.

25. Pazhayamadon D.G., Kelly C.J., Rogan E. & Codling E.A. 2014.  Decision Interval Cumulative Sum Harvest Control Rules (DI-CUSUM-HCR) for managing fisheries with limited historical information.  Fisheries Research, doi:10.1016/j.fishres.2014.09.009.

26. Rowley A.F., Cross M.E.Culloty S.C.Lynch S.A., Mackenzie C.L., Morgan E.O'Riordan R.M., Robins P.E., Smith A.L., Thrupp T.J., Vogan C.L., Wootton E.C. & Malham S.K. 2014.  The potential impact of climate change on the infectious diseases of commercially important shellfish populations in the Irish Sea - a review. ICES Journal of Marine Science, 71(4): 741-759. doi:10.1093/icesjms/fst234.

27. Vartia, S., Collins P.C., Cross T.F., Fitzgerald R.D., Gauthier D.T., McGinnity P., Mirimin L. & Carlsson J. 2014. Multiplexing with three-primer PCR for rapid and economical microsatellite validation. Hereditas, 151: 43-54.

Book Chapters

1. Carlsson J., Cross T.F., McGinnity P., Prodöhl P. & McDevitt A. 2014. The use of genetics to infer the origins of the terrestrial and freshwater elements of the Irish fauna. In: Sleeman P., Carlsson J. & Carlsson J.E.L. (eds). Mind the Gap II: new insights into the Irish postglacial. Irish Naturalists’ Journal, Belfast, 150 pp.

Non-Peer Reviewed Publications

Published Reports

1. Cronin M., Gosch M., Jessopp M., Luck C., Rogan E. & Reid D. 2014. A pilot study of seal predation on salmon in selected Irish rivers and estuaries. IFI/2014/1-4178. Inland Fisheries Ireland, Dublin.



Peer-Review Publications

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:

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 SNP 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.

8. 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. 

9. 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.

10. 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.

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

12. 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.

13. 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.

14. 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.

15. 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.

16. 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.

17.  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.

18.  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.

19.  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, DOI: 10.1371/journal.pone.0063035.

20. Outerbridge M. & Davenport J. 2013.  Malaclemys terrapin (Diamondback Terrapin). Dredging foraging behavior. Herpetological Review, 44: 307-308.

21.  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.

22.  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.

23.  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.

24.  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.

25.  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.

26.  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.


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.


1. Allan G. & Burnell G. (Ed.s) 2013.  Advances in aquaculture hatchery technology.  Woodhead Publishing Series in Food Science, Technology and Nutrition No. 242. 




Peer-Review Publications

1. Callaway, R., Shill, A.P., Grenfell, S.E., Bron, J.E., Burnell, G., Cook, E.J., Crumlish, M., Culloty, S., Davidson, K., Ellis, R.P., Flynn, K.J., Fox, C., Green, D.M., Hays, G.C., Hughes, A.D., Johnston, E., Lowe, C.D., Lupatsch, I., Malham, S., Mendzil, A.F., Nickell, T., Pickerell, T., Rowley, A.F., Stanley, M.S., Tocher, D.R., Turnbull, J.F., Webb, G., Wootton, E., Shields, R.J. 2012. Review of climate change impacts on marine aquaculture in the UK and Ireland. Aquatic Conservation-Marine and Freshwater Ecosystems, 22: 389-421.

2. Cross, M.E., Lynch, S., Whitaker, A., O'Riordan, R.M. & Culloty, S.C. 2012. The reproductive biology of the soft shell clam Mya arenaria in Ireland and the possible impacts of climate variability. Journal of Marine Biology, 2012 (Article ID 908163).

3. de Montaudouin, X., Bazairi, H. & Culloty, S. 2012. Effect of trematode parasites on cockle Cerastoderma edule growth and condition index: a transplant experiment. Marine Ecology Progress Series, 471: 111-121.

4. Drinan, T.J., McGinnity, P., Coughlan, J.P., Cross, T.F. & Harrison, S.C. 2012. Morphological variability of Atlantic salmon Salmo salar and brown trout Salmo trutta in different river environments. Ecology of Freshwater Fish, 21: 420–432.

5. Ezgeta-Balic, D., Peharda, M., Davenport, J., Vidjak, O. & Boban, J. 2012.  Size structure of Size structure of zooplankton ingested by four commercially important bivalves. Acta Adriatica 53: 275-288.

6. Finn J., Carlsson, J., Kelly, T. & Davenport, J. 2012. Avoidance of headwinds or exploitation of ground effect – why do birds fly low? Journal of Field Ornithology, 89: 192-202.

7. Gerritsen, H.D., Lordan, C., Minto, C., Kraak, S.B.M. 2012. Spatial patterns in the retained catch composition of Irish demersal otter trawlers: high-resolution fisheries data as a management tool. Fisheries Research, 129–130: 127–136.

8. Gurney, W.S.C., Bacon, P.J., Speirs, D.C., McGinnity, P. & Verspoor, E. 2012. Sea-age variation in maiden Atlantic salmon spawners: phenotypic plasticity or genetic polymorphism? Bulletin Mathematical Biology 74:615–640.

9. Jafaar, Z., Yeo, D.C.J., Tan, H.H., O'Riordan, R. 2012. Status of estuarine and marine non-indigenous species in Singapore. The Raffles Bulletin of Zoology Supplement, 25: 79–92.

10. Kraak, S.B.M., Reid, D.G., Gerritsen, H.D., Kelly, C.J., Fitzpatrick, M., Codling, E.A., & Rogan, E. 2012. 21st century fisheries management: a spatio-temporally explicit tariff-based approach combining multiple drivers and incentivising responsible fishing. ICES Journal of Marine Science, 69(4): 590–601.

11. Kochmann, J., Carlsson, J., Crowe, T.P. & Mariani, S. 2012. Genetic evidence for the uncoupling of local aquaculture activities and a population of an invasive species – a case study of Pacific oysters (Crassostrea gigas). Journal of Heredity, 103(5): 661-71.

12. Lynch, S.A., Carlsson, J., Reilly, A.O., Cotter, E.  & Culloty, S.C. 2012. A previously undescribed ostreid herpes virus 1 (OsHV-1) genotype detected in the Pacific oyster Crassostrea gigas, in Ireland. Parasitology, 139: 1-7.

13. Lyons, L.J., O'Riordan, R.M., Cross, T.F. & Culloty, S.C. 2012. Reproductive biology of the shore crab Carcinus maenas (Decapoda, Portunidae): a macroscopic and histological view. Invertebrate Reproduction & Development, 56: 144-156.

14. Lynch, S.A., Villalba, A., Abollo, E., Engelsma, M., Stokes, N. & Culloty, S.C. 2012. The occurrence of haplosporidian parasites, Haplosporidium nelsoni and Haplosporidium sp., in oysters in Ireland. Journal of Invertebrate Pathology, 112(3): 208-12.

15. Maloy, A.P., Nelle, P., Culloty, S.C., Slater, J.W. & Harrod, C. 2012. Identifying trophic variation in a marine suspension feeder: DNA- and stable isotope-based dietary analysis in Mytilus spp. Marine Biology, 160(2): 479-490.

16. McGinnity, P., de Eyto, E., Gilbey, J., Gargan, P., Roche, W., Stafford, T., McGarrigle, M., Ó Maoiléidigh, N. & Mills, P. 2012. A predictive model for estimating river habitat area using GIS derived catchment and river variables. Fisheries Management and Ecology, 19: 69–77.

17. Morgan, E., Kelly, T., O'Riordan, R.M. & Culloty, S.C. 2012. The influence of disseminated neoplasia, trematode infections and gametogenesis on surfacing and mortality in the cockle, Cerastoderma edule. Diseases of Aquatic Organisms, 98: 73-84.

18.  Mork, K.-A., Gilbey, J., Hansen L.-P., Jensen, A.J., Jacobsen, J.-A., Holm, M., Holst, J.-C., Ó Maoiléidigh, N., McGinnity, P., Melle, W., Thomas, K., Verspoor, E., Vikebø, F. & Wennevik, V. 2012. Modelling the migration of post-smolt Atlantic salmon (Salmo salar) in the North East Atlantic. ICES Journal of Marine Science, 69(9): 1616–1624.

19. O’Farrell, B., Dennis, C., Benzie, J., McGinnity, P., Carlsson, J., de Eyto, E., Coughlan, J., Igoe, F., Meehan, R. & Cross, T. 2012. Balancing selection on MHC class I in wild brown trout (Salmo trutta). Journal of Fish Biology, 81: 1357–1374.

20.  O’Farrell, B., Benzie, J., McGinnity, P., Carlsson, J., de Eyto, E., Dillane, E., Graham, C., Coughlan, J. & Cross, T. 2012. MHC-mediated spatial distribution in brown trout (Salmo trutta) fry. Heredity, 108: 403-409.

21.  Peharda, M., Ezgeta-Balic, D., Davenport, J., Bojanic, N. Vidjak, O. & Nincevic-Gladan, Z. 2012.  Differential ingestion of zooplankton by four species of bivalve molluscs in Mali Ston Bay, Croatia. Marine Biology 159: 881-895.

22. O’Meara, D.B., Edwards, C.J., Sleeman D.P., Cross, T.F., Statham, M.J., McDowell, J.R., Dillane, E., Coughlan, J.P., O’Leary, D., O’Reilly, C., Bradley, D.G. & Carlsson, J. 2012. Genetic relationships between Eurasian badgers Meles meles (Carnivora: Mustelidae) in Europe and implications for the colonisation history of Ireland. Biological Journal of the Linnean Society, 106: 893-909.

23. Vasemägi, A., Nilsson, J., McGinnity, P., Cross, T., O’Reilly, P., Glebe, B., Peng, B., Berg, P., & Primmer C.R. 2012. Footprints of selection on standing variation during domestication/captive breeding of Atlantic salmon. Comparative and Functional Genomics, Article ID 628204.


Non-Peer Reviewed Publications

1. Becker, P., Burnell, G.  & Ron, T.B. 2012. Using GIS to improve Coastal Marine Spatial Planning. Sea Technology, 53(8): 29-35.



Peer-Review Publications

1. Carlsson, J.,Shephard, S., Coughlan, J.,Trueman, C.N., Rogan, E. & Cross, T.F. (2011). Fine-scale population structure in a deep-sea teleost (Orange Roughy, Hoplostethus atlanticus). Deep-Sea Research Part I-Oceanographic Research Papers, 58:627-636.

2. de Eyto, E., McGinnity, P., Huisman, J., Coughlan, J., Consuegra, S., Farrell, K., Tufto, J., Megens, H.J., Jordan, W., Cross, T., Stet, R.J.M. 2011. Varying disease-mediated selection at different life history stages of Atlantic salmon in freshwater. Evolutionary Applications. 4: 6: 749-762.

3. Ellis, J., Gilbey, J. Armstrong, A., Balstad, T., Cauweiler, E., Cherbonnel, C., Consuegra, S., Coughlan, J., Cross, T., Crozier, W., Dillane, E., Ensing, D., Garcia de Leaniz, C., Garcia-Vasquez, E., Griffiths, A., Hindar, K., Hjorleifsdottir, S., Knox, D., Machado-Schiaffino, G., McGinnity, P., Meldrop, D., Neilsen, E., Olafsson, K., Primmer, C., Prodöhl, P., Stradmeyer, L., Vaha, J-P., Verspoor, E., Wennevik, V. and Stevens, J. 2011. Microsatellite standardisation and evaluation of genotyping error in a large multi-partner research programme for conservation of Atlantic salmon (Salmo salar L.).  Genetica 139: 353-367.

4. Fermer, J., Culloty, S.C., Kelly, T.C. & O'Riordan, R.M. (2011). Manipulation of Cerastoderma edule burrowing ability by Meiogymnophallus minutus metacercariae. Journal of The Marine Biological Association of The United Kingdom, 91 (4):907-911.

5. Fermer, J., Culloty, S.C., Kelly, T.C. & O'Riordan, R.M. (2011). Parasitological survey of the edible cockle Cerastoderma edule (Bivalvia) on the south coast of Ireland. Journal of the Marine Biological Association of the United Kingdom, 91 (4):923-928.

6. Foote, A.D., Vilstrup, J.T., De Stephanis, R., Verborgh, P., Abel Nielsen, S.C., Deaville, R., Kleivane, L., Martin, V., Miller, P.J.O., Øien, N., Pérez-Gil, M., Rasmussen, M., Reid, R.J., Robertson, K.M., Rogan, E.,Similä, T., Tejedor, M.L., Vester, H., Víkingsson, G.A., Willerslev, E., Gilbert, M.T.P., Piertney, S.B.; (2011) Genetic differentiation among North Atlantic killer whale populations. Molecular Ecology, 20 (3): 629-641.

7. Kraak, S.B.M.,and Hart, P.J.B. 2011. Modelling sympatric speciation by means of biologically plausible mechanistic processes as exemplified by threespine stickleback species pairs. Organisms Diversity & Evolution, 11: 287-306.

8. Kraak, S.B.M. (2011).  Exploring the 'public goods game' model to overcome the Tragedy of the Commons in fisheries management. Fish And Fisheries, 12: 18-33.

9. Lyons, L.J., O'Riordan, R.M., Cross, T.F. & Culloty, S.C. (2011). Reproductive biology of the shore crab Carcinus maenas (decapoda: Portunidae): a macroscopic and histological view. Invertebrate Reproduction and Development.

10. Maloy, A.P., Culloty, S.C., Bolton-Warberg, M., Fitzgerald, R. & Slater, J.W. (2011). Molecular identification of laser dissected gut contents from hatchery reared larval cod, Gadus morhua: a new approach to diet analysis. Aquaculture Nutrition, 17:536-541.

11. McCarthy, M., Culloty, S.C. (2011). Optomisation of two immunofluorescent antibodies for the detection of Escherichia coli using immunofluorescent microscopy and flow cytometry. Current Microbiology, 62 (2):402-408.

12. Mirimin, L., Banguera-Hinestroza, E., Dillane, E.,Hoelzel, A.R., Cross, T.F., Rogan, E. (2011).  Insights into genetic diversity, parentage, and group composition of Atlantic white-sided dolphins (Lagenorhynchus acutus) off the west of Ireland based on nuclear and mitochondrial genetic markers. Journal of Heredity, 102(1): 79-87.

13. Mirimin, L. , Miller, R., Dillane, E. , Berrow, S.D. , Ingram, S.,  Cross, T.F. & Rogan, E.  (2011). Fine-scale population genetic structuring of bottlenose. Animal Conservation, 14 (4): 342-353.

14.  O'Mahoney, M.,Mouzakitis, G., Doyle, J., & Burnell, G. (2011) A novel konjac glucomannan-xanthan gum binder for aquaculture feeds: the effect of binder configuration on formulated feed stability, feed palatability and growth performance of the Japanese abalone, Haliotis discus hannai'. Aquaculture Nutrition, 17: 395-407.

15.  Prinz, K., Kelly, T.C., O'Riordan, R.M. & Culloty, S.C. (2011). Factors influencing cercarial emergence and settlement in the digenean trematode Parorchis acanthus (Philophthalmidae). Journal of The Marine Biological Association of The United Kingdom, 91 (8):1673-1679.

16. Thaler, A.D, Zelnio, K., Saleu, W., Schultz, T.F., Carlsson, J.SCunningham, C., Vrijenhoek, R. & Van Dover, C.L. 2011. The effects of spatial scale on the population dynamics of Ifremeria nautilei, a hydrothermal vent endemic gastropod from the southwest Pacific. BMC Evolutionary Biology, 11: 372.


Non Peer-Reviewed Articles

1. Caurant F., Chouvelon T., Lahaye V., Mendez-Fernandez P., Rogan E., Spitz J. and Ridoux V. (2011). The use of ecological tracers for discriminating dolphin population structure: the case of the short-beaked common dolphin Delphinus delphis in European Atlantic waters.  PaperAC18/Doc.5-02 (P) to the 18th ASCOBANS Advisory Committee Meeting.

2. Kraak, S. B. M., Reid, D. G., Gerritsen, H. D., Fitzpatrick, M., Kelly, C. J., Codling, E. A., & Rogan, E.  (2011).  21st century fisheries management: A spatio-temporally explicit tariff-based approach combining multiple drivers and incentivising responsible fishing. ICES CM 2011/P:11.

3. Kraak, S. B. M. (2011).  Overcoming the "tragedy of the commons" in fishery management. ICES Insight September 2011.



1. Rogan, E. & Hernandez-Milian, G. (2011). Preliminary analysis of beaked whale strandings in Ireland: 1800 – 2009 SC/63/SM 19 Report of the International Whaling Commission.

2. STECF (Scientific, Technical & Economic Committee for Fisheries) (2011). Evaluation of multi-annual plans for cod in Irish Sea, Kattegat, North Sea, and West of Scotland (STECF-11-07), reviewed by the STECF during its 37th plenary meeting held from 11 to 25 July, 2011 in Copenhagen, Denmark. Edited by John Simmonds and Sarah Kraak.



Peer-Review Publications

  1. Anderson, C.M., Aparicio, G.J., Atangana, A.R., Beaulieu, J., Bruford, M.W., Cain, F., Campos, T., Cariani, A., Carvalho, M.A., Chen, N, Chen, P.P., Clamens, A.L., Clark, A.M., Coeur D'Acier, A., Connolly, P., Cordero-Rivera, A., Coughlan, J.P., Cross, T.S., David, B., De Bruyn, C., De Meyer, M., De Ridder, C., Delatte, H., Dettori, M.T., Downer, S.J., Dubreuil, C., Evans, K.J., Fan, B., Ferrara, G., Gagne, A., Gaillard, M., Gigliarelli, L., Giovinazzi, J., Gomez, D.R., Grunwald, N.J., Hansson, B., Huotari, T., Jank, L., Jousselin, E., Jungmann, L., Kaczmarek, M.E., Khasa, D.P., Kneebone, J., Korpelainen, H., Kostamo, K., Lanfaloni, L., Lin, H.R., Liu, X.C., Lucentini, L., Maes, G.E., Mahaffee, W.F., Meng, Z.N., Micali, S., Milano, I., Mok, H.F., Morin, L., Neill, T.M., Newton, C.H., Ostrow, D.G., Palomba, A., Panara, F., Puletti, M.E., Quarta, R., Quilici, S., Ramos, A.K.B., Rigaud, T., Risterucci, A.M., Salomon, M.P., Sanchez-Guillen, R.A., Sarver, S.K. (2010). 'Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009-31 January 2010'. Molecular Ecology, 10 :576-579.
  2. Culloty, S.C., Favier, E., Ní Ríada, M., Ramsay, N.F. & O'Riordan, R.M. (2010).  Reproduction of the biogenic reef-forming honeycomb worm Sabellaria alveolata in Ireland.  Journal of the Marine Biological Association of the United Kingdom, 90 (3):503-507.
  3. Drummond, L., Mulcahy, M.F., Culloty, S.C. (2010).  A survey of the health status of the Manila clam Ruditapes philippinarum in Ireland with specific reference to brown ring disease.  Aquaculture International, 18 (5):787-800.   
  4. Fermer, J., Culloty, S.C., Kelly, T.C., O'Riordan, R.M. (2010).  Temporal variation of Meiogymnophallus minutus infections in the first and second intermediate host. Journal of Helminthology, 84 (4):362-368.
  5. Fontaine, M.C., Tolley, K.A., Michaux, J.R., Birkun, A., Ferreira, M., Jauniaux, T., Llavona, A., Öztürk, B., Ayaka A Öztürk, A. A., Ridoux, V., Rogan, E., Sequeira, M., Bouquegneau, J-M, & Baird, S.J.E. (2010). 'Genetic And Historic Evidence For Climate-Driven Population Fragmentation In A Top Cetacean Predator: The Harbour Porpoises In European Water'. Proceedings of the Royal Society, B, doi: 10.1098/rspb.2010.0412.
  6. Griffiths, A.M., Machado-Schiaffino, G., Dillane, E., Coughlan, J., Horreo, J.L., Bowkett, A.E, Minting, P., Toms, S., Roche, W., Gargan, P., McGinnity, P., Cross, T., Bright, D., Garcia-Vazquez, E., Stevens, J.R. (2010). 'Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range'. BMC Genetics, 11:31 doi:10.1186/1471-2156-11-31  .
  7. Kavanagh, A., Cronin, M., Walton, M., Rogan, E. (2010). 'Diet of the harbour seal (Phoca vitulina vitulina) on the west and south west of Ireland'. Journal of the Marine Biological Association of the United Kingdom, 90 (8):1517-1527.
  8. Kraak, S.B.M., Kelly, C.J., Codling, E.A. & Rogan, E. (2010).  On scientists’ discomfort in fisheries advisory science: the example of simulation-based fisheries management-strategy evaluations.  Fish and Fisheries, 11, 119-132.
  9. Lynch, S.A., Abollo, E., Ramilo, A. Cao, A, Culloty, S.C. & Villalba, A. (2010). Observations raise the question if the Pacific oyster Crassostrea gigas can act as either a carrier or a reservoir for Bonamia ostreae or Bonamia exitiosa.  Parasitology, 137 (10):1515-1526.
  10. Maloy, A.P., Culloty, S.C., Bolton-Warberg, M., Fitzgerald, R. & Slater, J.W. (2010) Molecular identification of laser dissected gut contents from hatchery realred larval cod, Gadus morhua: a new approach to diet analysis.  Aquaculture Nutrition, doi: 10.1111/j.1365-2095.2010.00836.x
  11. McCarron, E., Burnell, G., Kerry, J., Mouzakitis, G. (2010).  An experimental assessment on the effects of photoperiod treatments on the somatic and gonadal growth of the juvenile European purple sea urchin Paracentrotus lividus. Aquaculture Research, 41:1072-1081.
  12. Murphy, S. Pierce, G.J. Law, R.J. Bersuder, P. Jepson, P.D. Learmonth, J.A. Addink, M. Dabin, W. Santos, M.B.. Deaville R, Zegers B.N., Mets A., Rogan E., Ridoux V., Reid R.J., Smeenk C., Jauniaux T., López A., Alonso Farré J.M., González A.F., Guerra (2010) 'Assessing the effect of persistent organic pollutants on reproductive activity in small cetaceans in the eastern North Atlantic'. Journal of Northwest Atlantic Fishery Science, 42, 153-173.
  13. Prinz, K., Kelly, T.C., O’Riordan, R.M., Culloty, S.C. (2010).  Factors influencing cercarial emergence and settlement in the digenean termatode Parorchis acanthus (Philophthalmidae).  Journal of Marine Biological Association of the United Kingdom,
  14. Prinz, K., Kelly, T.C., O'Riordan, R.M. & Culloty, S.C. (2010).  Occurrence of macroparasites in four common intertidal molluscs on the south coast of Ireland. Marine Biodiversity Records, 3 (e89); doi:10.1017/S1755267210000035.
  15. Prinz, K., Kelly, T.C., O'Riordan, R.M. & Culloty, S.C. (2010).  Infection of Mytilus edulis by the trematode Echinostephilla patellae (Digenea: Philophthalmidae). Journal of Helminthology, 84 (2):193-198.
  16. Prinz, K., Kelly, T.C., O'Riordan, R.M. & Culloty, S.C. (2010).  Temporal variation in prevalence and vcercarial development of Echinstephilla patellae (Digenea, Philophythalmidae) in the intertidal gastropod Patella vulgata.  Acta Parasitologica, 55 (1): 39-44.
  17. Thaler, A.D., Zelnio, K., Jones, R., Carlsson, J., Van Dover, C.L. & Schultz T.F. (2010).  Characterization of 12 polymorphic microsatellite loci in Ifremeria nautilei, a chemoautotrophic gastropod from deep-sea hydrothermal vents. Conservation Genetics Resources. DOI 10.1007/s12686-010-9174-9.
  18. Zlenio, K.A., Thaler, A.D., Jones, R.E., Saleu, W., Schultz, T.H., Van Dover, C.L. & Carlsson, J. (2010).  Characterization of nine polymorphic microsatellite loci in Chorocaris sp. (Crustacea, Caridea, Alvinocarididae) from deep-sea hydrothermal vents. Conservation Genetics Resources. DOI: 10.1007/s12686-010-9243-0.


  1. Juhel, G., Moroney, G., O'Riordan, R. & Culloty, S. (2010).  Dynamics of endoparasitic infection in zebra mussels, Dreissena polymorpha, in Lough Derg, Ireland. In: The Zebra Mussel in Europe. Leiden, The Netherlands: Backhuys Publishers. 


  1. Rogan, E. (2010).  Ireland. Progress on cetacean research, June 2009 to May 2010, with statistical data for the calendar year 2009.  Department of Zoology, Ecology and Plant Science, University College Cork, Ireland.



Peer-Review Publications

1. Bogaards, J.A., Kraak, S.B.M. & Rijnsdorp, A.D. (2009).  Bayesian survey-based assessment of North Sea plaice (Pleuronectes platessa): extracting integrated signals from multiple surveys.  ICES Journal of Marine Science, 66, 665-679.

2. Cronin, M., Zuur, A.F., Rogan, E. &McConnell, B.J. (2009).  Using mobile phone telemetry to investigate the haul-out behaviour of harbour seals Phoca vitulina vitulinaEndangered Species Research, 10, 255-267.

3. Cronin, M.A., Zuur, A.F., Ingram, S. and Rogan, E. (2009).  A modeling framework to optimize timing of haul-out counts for estimating harbour seal abundance , NAMMCO Scientific Publications (In press).

4. Fermer, J., Culloty, S.C., Kelly, T.C. & O’Riordan, R.M. (2009).  Intrapopulational distribution of Meiogymnophallus minutus (Digenea, Gymnophallidae) infections in its first and second intermediate host.  Parasitology Research, 105, 1231-1238.

5. Kraak, S.B.M., Daan, N. & Pastoors, M.A. (2009).  Biased stock assessment when using multiple, hardly overlapping, tuning series if fishing trends vary spatially.  ICES Journal of Marine Science, 66, 000-000.

6. Luque, P.L., Pierce G.J., Learmonth J.A., Santos M.B., Ieno E., López A., Reid R.J., Rogan, E., González, A.F., Boon, J., Law, R.J.  & Lockyer, C.H. (2009).  Dentinal anomalies in teeth of harbour porpoises (Phocoena phocoena) from Scottish waters: are they linked to sexual maturation and environmental events? Journal of the Marine Biological Association, 89 (5), 893-902.

7. Malham, S.K., Cotter, E., O’Keeffe, S., Lynch, S., Culloty, S.C., Latchford, J.W. & Beaumont, A.R. (2009).  Summer mortality of the Pacific oyster Crassostrea gigas in the Irish Sea: The influence of temperature and nutrients on health and survival.  Aquaculture, 287, 128-139.

8. Maloy, A.P., Culloty, S.C. & Slater J.W. (2009).  Use of PCR DGGE to investigate the trophic ecology of marine suspension feeding bivalves.  Marine Ecology Progress Series,381, 109-118.

9. McCarron, E., Burnell, G. & Mouzakitis G. (2009).  Growth assessment on three size classes of the purple sea urchin Paracentrotus lividus using continuous and intermittent feeding regimes.  Aquaculture, 288, 83-91.

10. McGinnity, P., Jennings, E., deEyto, E., Allott, N., Samuelsson, P., Rogan, G., Whelan, K. & Cross, T. (2009).  Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction.  Proceedings of the Royal Society B, 276, 3601-3610.

11. Mirimin, L., Westgate, A., Rogan, E., Rosel, P., Read, A., Coughlan, J. & Cross, T. (2009).  Population structure of short-beaked common dolphins (Delphinus delphis) in the North Atlantic ocean as revealed by mitochondrial and nuclear genetic markers.  Marine Biology, 156, 821-834.

12. Murphy, S., Winship, A., Dabin,W., Jepson, P.D., Deaville, R., Reid, RJ, Spurrier, C., Rogan,E., López,A., González, A., Read, F., Addink, M., Silva, M., RidouxV., PierceG.J. & Northridge, P.S. (2009).  Assessing life history parameters of female common dolphins Delphinus delphis in the eastern North Atlantic, and investigating density dependent compensatory responses.  Marine Ecology Progress Series, 388, 273-291.

13. O’Riordan, R.M. Culloty, S. Davenport J & McAllen R (2009).  Increases in the abundance of the invasive barnacle Austrominius modestus on the Isle of Cumbrae.  Scotland Biodiversity Records, 2, 1-4.

14. Prinz, K.,Kelly, T.C., O'Riordan R.M & Culloty S.C. (2009).  Infection of Mytilus edulis by the trematode Echinostephilla patellae (Digenea: Philophthalmidae).  Journal of Helminthology, 84, 193-198.

15. Prinz, K., Kelly, T.C., O’Riordan, R.M. & Culloty, S.C. (2009).  Non-host organisms affect transmission processes in two common trematode parasites of rocky shores.  Marine Biology, 156, 2303-2311.

16. Sagarin, R., Carlsson, J., Duval, M., Freshwater, W., Godfrey, M., Litaker, W., Munoz, R., Noble, R., Schultz, T. & Wynne, B. (2009).  Bringing molecular tools into environmental resource management: Untangling the molecules to policy pathway.  PLoS Biology, 7, 426-430.

17. Stefánsson, M.Ö., Sigurdsson, T., Pampoulie, C., Daníelsdóttir, A. K., Thorgilsson, B., Ragnarsdóttir, A., Gíslason, D., Coughlan, J., Cross, T.F. & Bernatchez, L. (2009).  Pleistocene genetic legacy suggests incipient species of Sebastes mentella in the Irminger Sea.  Heredity, 102, 514-524.


1. Burnell, G. & Allan, G (Eds). (2009). New technologies in aquaculture: Improving production efficiency, quality and environmental management.  Woodhead Publishing Ltd. pp 1162.


1. Carvalho, G., Helyar, S., Bekkevold, D., Volkert, F., Hanel, R., McPhee, D., Ford, M., Carlsson, J., Trautner, J., Ogden, R. and Martinsohn, J. (2009).  Review the current status of traceability methods in the fisheries sector based on genetics.  ICES WGAGFM Report.

2. Coughlan, J., McGinnity, P. & Cross, T. (2009).  Genetic Stock Identification of southeast Ireland rivers and prioritising small rivers for conservation. Final report to the Southern Regional Fisheries Board, December 2009.

3. CODA 2009.  Cetacean Offshore Distribution and Abundance in the European Atlantic (CODA).  Report available from SMRU, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife KY16 8LB, UK.  (with Dr E. Rogan, AFDC)

4. Cross, T.F., McGinnity, P., Carlsson, J., Coughlan, J., Dillane, E., deEyto, E., Ferguson, A., Fitzgerald, R. & Prodöhl, P.A. (2009).  Possible genetic interactions between reared strains and wild populations of cod (Gadus morhua):  lessons from salmon (Salmo salar) common garden field experiments.  ICES CM 2009/Q:10, ASC Berlin, September, 2009.

5. Fogarty B., McCarthy, M., Duignan, L., Culloty, S., Davenport , J. & Alderman, J. (2009).  Demonstration of a miniaturised multichannel cytometry system and its suitability for autonomous deployment. STRIVE Programme 2007-2013 (AT/04/01/07).

6. Ingram, S., Kavanagh, A., Englund, A., & Rogan, E. (2009).  Site assessment of the water of northwest Connemara.  A survey of bottlenose dolphins (Tursiops truncatus).  Report to National Parks and Wildlife Service.  University College Cork, 34 pp.


1. Cross, T.F., McGinnity, P. Carlsson, J., Coughlan, J. Dillane, E. deEyto, E., Ferguson, A., FitzGerald, R. and Prodöhl, P.  (2009).  Possible genetic interactions between reared strains and wild populations of cod (Gadus morhua): relevance of findings from salmon (Salmo salar) common-or-garden field experiments. Conseils Internationale pour l'Exploration de la Mer C.M. Doc.  2009/Q:10, 15p.

2. Dillane, E., McGinnity, Cross, T. & Coughlan, J. (2009).  Wild or farmed? Using DNA to identify the origin of Atlantic salmon.  Newsletter item, April 2009. 




Peer-Review Publications

1. deEyto, E., McGinnity, P., Consuegra, S., Coughlan, J., Tufto, J., Farrell, K., Megens, H.-J., Jordan, W., Cross T. & Stet, R.J.M. (2007).  Natural selection acts on Atlantic salmon MHC variability in the wild. Proceedings of the Royal Society B, 274, 861-869.

2. Dillane, E.Cross, M., McGinnity, P., Coughlan, J.P., Galvin, P., Wilkins, N.P. & T.F. Cross (2007).  Spatial and temporal patterns in microsatellite DNA variation of wild Atlantic salmon (Salmo salar) in Irish Rivers.  Fisheries Management and Ecology, 14, 209-220.

3. Dillane, E., McGinnity, P., Coughlan, J.P., Cross, M.C., de Eyto, E, Kenchington ,E, Prodöhl, P, Cross, T.F. (2008). Demographics and landscape features determine intra-river population structure in Atlantic salmon (Salmo salar L.): the case of the River Moy in Ireland.  Molecular Ecology.17, 4786-4800.

4. Drummond, L., Beaz, R., Balboa, S., Mulcahy, M.F., Romalde, J & S.C. Culloty (2007). The susceptibility of Irish- and Spanish- manila clams Ruditapes philippinarum to Vibrio tapetis and Brown Ring disease.  Journal of Invertebrate Pathology.  95, 1-8.

5. Fontaine, M.C., Baird, St. J. E., Piry, S., Ray, N., Duke, S., Birkun, A. Jr., Bloch, D., Ferreira, M., Sequeira, M., Jauniaux, T., Llavona, A., Oien, N.L., Ozturk, B., Ozturk, A.A., Ridoux, V., Rogan, E., Siebert, U., Vikingsson, G.A., Bouquegneau, J-M., & Michaux, J.R. (2007). Rise in Oceanographic barriers in continuous populations of a cetacean: the harbour porpoise in old world waters.  BMC Evolutionary Biology.

6. Ingram, S.N., Walsh, L., Johnson, D. & Rogan, E. (2007). The distribution of fin whales (Balaenoptera physalus) and minke whales (Balaenoptera acutorostrata) in the Bay of Fundy, Canada: using a tour-boat as a platform of opportunity.  Journal of the Marine Biological Association 87, 149–156.

7. Lahaye V., Bustamante P., Law R.J., Learmonth J.A., Santos M.B., Boon J.P., Rogan E., Dabin W., Addink M.J., López A., Zuur A.F., Pierce G.J. & Caurant F. (2007). Biological and ecological factors related to trace element levels in harbour porpoises (Phocoena phocoena) from European waters. Marine Environmental Research 64(3), 247 – 266

8. Lynch, S., Mulcahy, M.F. & Culloty, S.C. (2008). Efficiency of diagnostic techniques for the parasite Bonamia ostreae. Aquaculture, 281, 17-21.

9. Lynch, S.A.,  Armitage, D.V., Coughlan, J.,  Mulcahy M.F. & Culloty, S.C.(2007). Investigating the  possible role of benthic macroinvertebrates and zooplankton in the life cycle of the haplosporidian Bonamia ostreae.  Experimental Parasitology, 115, 359-368.

10. Malham., S. Cotter, E., O’Keeffe, S. Lynch, S. A.,. Latchford, J.W King, J.W. Culloty, S.C., & A.R. Beaumont. (2008). Summer mortality of the Pacific oyster Crassostrea gigas in the Irish seas: the influence of environmental factors.  Aquaculture 287, 128-138.

11. McHugh, B., Law, R.J., Allchin,  C., Rogan, E., Murphy, S., Foley, M.B., Glynn,D.& McGovern, E. (2007).  Bioaccumulation and enantiomeric profiling of organochlorine pesticides and persistent organic pollutants in the Killer Whale (Orcinus orca) from British and Irish waters.  Marine Pollution Bulletin 54(11), 1724 – 1731.

12. McGinnity, P., de Eyto, E., Cross, T., Coughlan, J. and Ferguson, A. (2007).  Population specific smolt development, migration and maturity schedules in Atlantic salmon in a natural river environment. Aquaculture, 273, 257-268.

13. O’Leary, D.B., Coughlan, J., McCarthy, T.V. and Cross, T.F. (2007).  Microsatellite variation in cod (Gadus morhua) throughout its geographic range.  Journal of Fish Biology, 70, Supplement C, 310-335.

14. Philpott, E., Englund, A., Ingram, S., and Rogan, E.  (2007).  Using T-Pods to investigate detection range and echolocation behaviour of coastal bottlenose dolphins.  Journal of the Marine Biological Association 87, 11–17.

15. Pierce, G.J., Santos, M.B ., Murphy, S.,  Learmonth, J.A., Zuur, A.F., Rogan, E.,  Bustamante, P., Caurant, F., Lahaye, V., Ridoux, V., Zegers, B.N., Mets, A., Addink, M., Smeenk, C., Jauniaux, T., Law, R.J., Dabin W., Lopez A., Alonso Farre, J.M., Gonzalez A.F., Guerra, A., Garcıa-Hartmann, M., Reid, R.J., Moffat, C.F., Lockyer, C., Boon, J.P.  (2008).  Bioaccumulation of persistent organic pollutants in female common dolphins (Delphinus delphis) and harbour porpoises (Phocoena phocoena) from western European seas: Geographical trends, causal factors and effects on reproduction and mortality.  Environmental Pollution 153,401 – 415.

16. Rogan, E. & Mackey, M.  (2007)  Bycatch and discarding in the Irish tuna driftnet fishery.  Fisheries Research, 86(1), 6 – 14.                                                                

17. Shephard, S., Connolly, P.,Nils-Roar Hareide&. Rogan. E. (2007).  Establishing stake holder linkages for management of the Irish Orange Rough fishery.  ICES J. Marine Science 64(4), 841 – 84.

18. Shephard, S., Trueman, C., Rickaby, R. & Rogan, E.  (2007).  Juvenile life history of NE Atlantic orange roughy from otolith stable isotopes.  Deep Sea Research 54(8) 1221 – 1230.   

19. Watts, P.C., O’Leary, D., Cross,M.C., Coughlan, J., Dillane, E., Kay, S.M., Wylde,S., Stet,R., Nash,R.D.M., Hatfield,E.M.C. & Cross, T.F.  (2008).Contrasting levels of genetic differentiation among putative neutral microsatellite loci in Atlantic herring Clupea harengus populations and the implications for assessing stock structure.  Hydrobiologia, 606, 27-33


1. Philpott, E., Wall, D. & Rogan, E. (2007).  Records from the Irish Whale and Dolphin Group for 2004.  Irish Naturalists’ Journal 28 (9) 379 – 385.

2. Philpott, E. & Rogan, E. (2007).  Records from the Irish Whale and Dolphin Group for 2005.  Irish Naturalists’ Journal 28 (10) 414 – 418.


Conference Proceedings (editorship)

1. Davenport, J., Burnell, G.M., Cross, T.F., Emmerson, M., McAllen, R., Ramsay, R., & Rogan, E.(2008). Challenges to Marine Ecosystems. Proceedings of the 41st European Marine Biology Symposium. Developments in Hydrobiology, Vol. 202, 211pp./Hydrobiologia Vol. 606. Kluwer Academic Press, Netherlands.

Chapter/Article in a book

1. Cross, T.F., McGinnity, P., Coughlan, J.,Dillane, E., Ferguson, A., Koljonen, M-L., Milner, N., O’Reilly, P. & Vasemagi, A. (2007).  Genetic considerations for Stocking and Ranching of Atlantic salmon. In Verspoor, E., Stradmeyer, L. and Nielsen, J.L. (eds.) The genetic nature of Atlantic salmon: implications for management and conservation.  The Atlantic Salmon Trust, 325-356.

2. Ferguson, A., Fleming, I.A., Hindar, K., Skaala, Ø., McGinnity, P., Cross, T. & Prodöhl, P. (2007).  Farm Escapes. In Verspoor, E., Stradmeyer, L. and Nielsen, J.L. (eds.) The genetic nature of Atlantic salmon: implications for management and conservation.  The Atlantic Salmon Trust, 357-398.

3. Cross, T.F., Burnell, G., Coughlan, J., Culloty, S., Dillane, E., McGinnity, P. & Rogan, E.(2008). Detrimental genetic effects of interactions between reared strains and wild populations of marine and anadromous fish and invertebrate species: are all species at risk? In M. Holmer (Ed) Aquaculture and the Ecosystem, Springer, pps.117-154. ISBN: 978-1-4020-6809-6.


1. Culloty, S.C. & Mulcahy, M.F. (2007) Bonamia ostreae: a Review. Marine Environment and Health Series, Marine Institute, Galway.  No. 29, 36pp.

2. Culloty, S.C. (2008). Recent research on Bonamia ostreae: an investigation into the role of Molluscs other than Ostrea edulis as possible carriers of this parasite.  In Report of the annual meeting of the National Reference Laboratories for Mollusc Diseases. IFREMER, Nantes France, 18-19 March 2008. 

3. Cross T. F. Coughlan, J., Dillane, E., McGinnity, P. (2008). Genetic stock identification of Irish commercially caught salmon.  Marine Institute Report.

4. Dillane, E., Cross, T.F. (2008). Genetic identification of farmed salmon in smoked product.  Food Safety Authority of Ireland.

5. Little, D., Collins, K., Cross, J., Cooke, D and McGinnity, P. (2008). Native riparian woodlands – a guide to identification, design, establishment and management.  Native woodland scheme information note No. 4 – published by Forest Service and Woodlands of Ireland.

6. Thorstad, E.B., Fleming, I.A., McGinnity, P., Soto, D., Wennevik, V. & Whoriskey, F. (2008). Incidence and impacts of escaped farmed Atlantic salmon Salmo salar in nature. NINA Special Report 36. 110 pp.

7. Verspoor, E., Kenchington, E., McGinnity, P., Tysklind, N., Cauwelier,  E. and Vasin, O. (2008) To evaluate prospects for the use of genetic monitoring for evaluating conservation status, intraspecific biodiversity, and stock “health” in fishes. ToR e): ICES WGAGFM Report 2008, ICES Mariculture Committee ICES CM 2008/MCC:04 REF. ACOM.

8. McGinnity P. (2008). Genetic interactions between hatchery and wild Atlantic salmon. Proceedings of IFM Annual Study course 2007. pp9

Informal or Non-refereed publications

1. Hatfield, E.M.C., Nash, R.D.M., Zimmerman, C., Schon, P-J., Kelly, C. Dickey-Collins, M., McKenzie, K., Cross, T. F. (2007).  The scientific implications of the EU Project WESTHER (Q5RS-2002-01056) to the assessment and management of the herring stocks to the west of the British Isles. Conseils Internationale pour l'Exploration de la Mer C.M. Doc. 2007/L:11, 23p.



Close X