Dr Jamie Coughlan

I have been working on the molecular genetics of a range of species (mostly marine or anadromous) for the past 15 years and was recently appointed as Senior Researcher for the Beaufort Marine Research Award in Fish Population Genetics.  My main areas of interest involve aspects of Atlantic salmon population genetics, using a wide range of different molecular techniques and data analysis methods, with special reference to population differentiation and discrimination (Genetic Stock Identification) in mixed fisheries.  Other species and projects of interest include marine species (e.g. Atlantic cod and orange roughy) population genetics; differentiation and assignment for migratory species (e.g. sea trout and brown trout); the genetic effects of aquaculture practices (especially salmon, turbot and cod).  I'm currently analysing the very large data set generated by the National Atlantic SALMON Genetic Stock Identification project (microsatellite genotypes from over 8000 individuals sampled from more than 80 Irish rivers).  This involves describing the genetic differentiation between rivers and populations (which can then be used as a BASELINE for the assignment of over 6000 fishery samples) but also investigating how the different populations are related or form parts of evolutionary lineages. I also act as a population genetics consultant to various National Agencies and is also involved with a number of International projects (e.g. SALSEA-merge).

Publications

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.

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.

Dillane, E., McGinnity, P., Coughlan, J., Cross, M. & Cross, T. (2008). Landscape features influence intra-river population genetic structure in Atlantic salmon (Salmo salar L.). Molecular Ecology, 17, 4786-4800.

Watts, P., O’Leary, D., Cross, M., Coughlan, J., Dillane, E., Kay, S., Wylde, S., Stet, R., Nash, R., Hatfield, E. & Cross, T. (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.

Cross, T.F., Burnell, G., Coughlan, J., Culloty, S., Dillane, E., McGinnityP.& 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 Aquaculture in the EcosystemEd. M. Holmer, Springer Press, p 117-154.

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

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.

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

Dillane, E. Cross, M., McGinnity, P., Coughlan, J.P., Galvin, P., Wilkins, N.P. & Cross, T.F. (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.

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.

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

Coughlan, J. , Seymour, J. & Cross, T.F. (2006).  Isolation and characterisation of microsatellite loci in the box jellyfish (Chironex fleckeri).  Molecular Ecology Notes, 6, 41-43. 

Coughlan, J. , Mirimin, L., Dillane, E., Rogan, E. & Cross, T.F. (2006). Isolation and characterisation of novel microsatellite loci for the short-beaked common dolphin (Delphinus delphis) and cross-amplification in other cetacean species.  Molecular Ecology Notes, 6: 490-492.

Mirimin, L., Coughlan, J., Rogan, E. & Cross, T.F. (2006). Tetranucleotide microsatellite loci from the striped dolphin (Stenella coeruleoalba Meyen, 1833).  Molecular Ecology Notes, 6: 493-495.

O’Leary D.B., Coughlan, J., McCarthy, T.V. & Cross, T.F. (2006). Application of a rapid method of SNP analysis (Glycosylase Mediated Polymorphism Detection) to mtDNA and nuclear DNA of cod (Gadus morhua): substantial allele frequency differences between Atlantic and Baltic samples.  Journal of Fish Biology, 69, Supplement A, 145-153.

Coughlan, J ., McGinnity, P., O’Farrell, B., Dillane, E., Diserud, O., de Eyto, E., O’Farrell, K., Whelan, K., Stet, R.J.M. & Cross, T.F. (2006). Temporal variation in an immune response gene (MHC I) in anadromous Salmo trutta in an Irish river before and during aquaculture activities.  ICES Journal of Marine Science, 63, 1248-1255.

Dillane, E., Galvin, P., Coughlan, J., Lipinski, M. & Cross, T.F.  (2005).  Genetic variation in the lesser flying squid, Todaropsis eblanae, (Cephalopoda, Ommastrephidae) in East Atlantic and Mediterranean waters.  Marine Ecology Progress Series, 292, 225-232.

Coughlan, J.P., Kitson, L., Dillane, E., Davenport, J. & Cross, T.F.  (2004).   Characterization of six microsatellite loci in the Bermuda skink (Eumeces longirostris).  Molecular Ecology Notes, 4, 678-679. 

Stefansson, M.O., Coughlan, J. & Cross, T.F. (2001).  Microsatellite DNA variation in reared strains of turbot (Scophthalmus maximus) and Atlantic halibut (Hippoglossus hippoglossus) compared with wild samples. Conseils Internationale pour l'Exploration de la Mer C.M. Doc. 2001/L:16, 29p.

Coughlan, J., Stefansson, M., Galvin, P., Dillane, E., Fitzgerald, R. & Cross, T.F. (2000). Isolation and characterization of 11 microsatellite loci in Atlantic halibut (Hippoglossus hippoglossus).  Molecular Ecology 9, 822-824.

Dillane, E., Galvin, P., Coughlan, J., Rodhouse, P.G.K. & Cross, T.F. (2000).   Polymorphic variable number of tandem repeat (VNTR) loci in the ommastrephid squid, Illex coindetii and Todaropsis eblanae.  Molecular Ecology, 9, 1002-1004.

Coughlan, J.P. , Imsland, A.K., Galvin, P.T., FitzGerald, R.D., Naevdal, G. & Cross, T.F. (1998). Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study.  Journal of Fish Biology 52, 916-922

Bourke, E.A., Coughlan, J., Jansson, H., Galvin, P. & Cross, T.F.  (1997). The extent of allozyme variation in populations of Atlantic salmon located throughout Europe: diversity that could be compromised by introductions of reared fish.  ICES Journal of Marine Sciences, 54, 974-985.

Coughlan, J. , McCarthy, E., McGregor, D., O’ Donoghue, P., Galvin, P., Fitzgerald, R., Daemen, E., Imsland, A., Stefansson, S. & Cross T. (1996). Four Polymorphic microsatellites in turbot (Scophthalmus maximus).  Animal Genetics   27, 441.

FitzGerald, R.D., Flannigan, M., Brennan, C., Haraldsson, H., Clarke, J., Coughlan, J., Irwin, S., Roby, F., Ni Charra, U., Cross, T.  (1996).  Research on farmed turbot (Scophthalmus maximus) in Ireland.  In: Keegan, B. and O’Connor, R. (Eds.) Irish Marine Science, 1995.   Galway Academic Press, Ireland, pp. 407-422.