Find below our list of publications

Last update (01/01/2021)


(in progress)

  • AMBER report – D4.3 Trans-European, river by river assessment of the status of Atlantic salmon (EU salmon Atlas)
  • Kirubakaran, T. G., Andersen, Ø., Moser, M., Arnyasi, M., McGinnity, P., Lien, S., & Kent, M. (2020). A Nanopore Based Chromosome-Level Assembly Representing Atlantic Cod from the Celtic Sea. G3: Genes|Genomes|Genetics.
  • Archer, L. C., Hutton, S. A., Harman, L., McCormick, S. D., O’Grady, M. N., Kerry, J. P., … Reed, T. E. (2020). Food and temperature stressors have opposing effects in determining flexible migration decisions in brown trout (Salmo trutta). Global Change Biology.
  • Heys, C., Cheaib, B., Busetti, A., Kazlauskaite, R., Maier, L., Sloan, W. T., … Llewellyn, M. S. (2020). Neutral processes dominate microbial community assembly in Atlantic Salmon, Salmo salar. Applied and Environmental Microbiology.
  • Egerton, S., Wan, A., Murphy, K., Collins, F., Ahern, G., Sugrue, I., … Stanton, C. (2020). Replacing fishmeal with plant protein in Atlantic salmon (Salmo salar) diets by supplementation with fish protein hydrolysate. Scientific Reports.
  • Dauwalter, D. C., Duchi, A., Epifanio, J., Gandolfi, A., Gresswell, R., Juanes, F., … Williams, J. E. (2020). A call for global action to conserve native trout in the 21st century and beyond. Ecology of Freshwater Fish.
  • Finlay, R., Poole, R., Coughlan, J., Phillips, K. P., Prodöhl, P., Cotter, D., … Reed, T. E. (2020). Telemetry and genetics reveal asymmetric dispersal of a lake-feeding salmonid between inflow and outflow spawning streams at a microgeographic scale. Ecology and Evolution.
  • De Noia, Michele; Poole, Russell; Kaufmann, Joshka; Waters, Catherine; Adams, Colin; McGinnity, Philip; Llewellyn, Martin;  In-situ non-lethal rapid test to accurately detect the presence of the nematode parasite, Anguillicoloides crassus, in European eel, Anguilla anguilla. bioRxiv    2020
  • Husby, A., Reed, T. E., Visser, M. E. (2020) Demonstrating temperature induced phenological mismatch does not require negative effects on fitness or population growth: A comment on Samplonius et al. EcoEvoRxiv
  • Finlay, R., Poole, R., & Reed, T. E. (2020). Development of a Double-Breakaway Pass-Through PIT Tag Antenna System for Flood-Prone Rivers. North American Journal of Fisheries Management.
  • Konczal, M., Przesmycka, K. J., Mohammed, R. S., Phillips, K. P., Camara, F., Chmielewski, S., … Radwan, J. (2020). Gene duplications, divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis. Molecular Ecology.
  • Sagonas, K., Meyer, B. S., Kaufmann, J., Lenz, T. L., Häsler, R., & Eizaguirre, C. (2020). Experimental Parasite Infection Causes Genome-Wide Changes in DNA Methylation. Molecular Biology and Evolution.
  • Moran, P. A., Hunt, J., Mitchell, C., Ritchie, M. G., & Bailey, N. W. (2020). Sexual selection and population divergence III: Interspecific and intraspecific variation in mating signals. Journal of Evolutionary Biology.
  • Colgan, T. J., Carolan, J. C., Sumner, S., Blaxter, M. L., & Brown, M. J. F. (2020). Infection by the castrating parasitic nematode Sphaerularia bombi changes gene expression in Bombus terrestris bumblebee queens. Insect Molecular Biology.
  •  Herdegen-Radwan, M., Phillips, K.P., Babik, W. et al.  (2020) Balancing selection versus allele and supertype turnover in MHC class II genes in guppies. Heredity.


  • Muhlfeld, Clint & Dauwalter, Daniel & D’angelo, Vincent & Ferguson, Andrew & Giersch, Joe & Impson, Neville & Koizumi, Itsuro & Kovach, Ryan &
    Mcginnity, Phil & Schöffmann, Johannes & Vøllestad, Leif & Epifanio, J. (2019). Global Status of Trout and Char: Conservation Challenges
    in the Twenty-First Century. Global Status of Trout and Char: Conservation Challenges in the Twenty-First Century.
  • Colgan, T. J., Finlay, S., Brown, M. J. F., & Carolan, J. C. (2019). Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause. BMC Genomics.
  • Deslyper, G., Holland, C. V., Colgan, T. J., & Carolan, J. C. (2019). The liver proteome in a mouse model for Ascaris suum resistance and susceptibility: Evidence for an altered innate immune response. Parasites and Vectors.
  • Colgan, T. J., Fletcher, I. K., Arce, A. N., Gill, R. J., Ramos Rodrigues, A., Stolle, E., … Wurm, Y. (2019). Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees. Molecular Ecology.
  • Green, D. S., Colgan, T. J., Thompson, R. C., & Carolan, J. C. (2019). Exposure to microplastics reduces attachment strength and alters the haemolymph proteome of blue mussels (Mytilus edulis). Environmental Pollution.
  • Moran, P. A., Hunt, J., Mitchell, C., Ritchie, M. G., & Bailey, N. W. (2019). Behavioural mechanisms of sexual isolation involving multiple modalities and their
    inheritance. Journal of Evolutionary Biology.
  • Masó, G., Kaufmann, J., Clavero, H., & Fitze, P. S. (2019). Age-dependent effects of moderate differences in environmental predictability forecasted by climate change, experimental evidence from a short-lived lizard (Zootoca vivipara). Scientific Reports.
  • Reed, T. E. (2019). Can Arctic seabirds adapt to climate change? Functional Ecology.
  •  Pinfield, R., Dillane, E., Runge, A. K. W.,Evans, A., Mirimin, L., Niemann, J., … Foote, A. D. (2019). False‐negative detections from environmental DNA collected in the presence of large numbers of
    killer whales ( Orcinus orca ) . Environmental DNA.
  • Radchuk, V., Reed, T.,Teplitsky, C., van de Pol, M., Charmantier, A., Hassall, C., … Kramer-Schadt,S. (2019). Adaptive responses of animals to climate change are most likely insufficient. Nature Communications.
  • Archer, L.C., ,Hutton, S., Harman, L., O’Grady, M. N., Kerry, J.P., Poole, R., Gargan, P., McGinnity, P., Reed, T.E. (2019) The interplay between extrinsic and intrinsic factors in determining migration decisions in brown trout (Salmo trutta): an experimental study. Frontiers in Ecology and Evolution, 7
  • Ferguson, A., Reed, T.E., Cross, T.F., Mcginnity, P., Prodöhl, P.A. (2019).  Anadromy, potamodromy and residency in brown trout Salmo trutta: the role of genes and the environment. Journal of Fish Biology,
  • Hughes, M. R., Hooker, O. E., Van Leeuwen, T. E., Kettle‐White, A., Thorne, A., Prodöhl, P., & Adams, C. E. (2019). Alternative routes to piscivory: Contrasting growth trajectories in brown trout (Salmo trutta) ecotypes exhibiting contrasting life history strategies. Ecology of freshwater fish28(1), 4-10.
  • O’Sullivan, R.j., Aykanat, T., Johnston, S.E., Kane, A., Poole, R., Rogan, G., Prodöhl, P.A., Primmer, C.R., McGinnity, P., Reed. T.E. (2019).  Evolutionary stasis of a heritable morphological trait in a wild fish population despite apparent directional selection.  Ecology & Evolution 00:1-16.
  • Perry, W.B., Solberg, M.F., Besnier, F., Dyrhovden, L., Matre, I.H., Fjelldal, P.G., Ayllon, F., Creer, S., Llewellyn, M., Taylor, M.I. and Carvalho, G., 2019. Evolutionary drivers of kype size in Atlantic salmon (Salmo salar): domestication, age and genetics. Royal Society Open Science6(4), p.190021.
  • Prodöhl, P. A., Ferguson, A., Bradley, C. R., Ade, R., Roberts, C., Keay, E. J., … & Hynes, R. (2019). Impacts of acidification on brown trout Salmo trutta populations and the contribution of stocking to population recovery and genetic diversity. Journal of fish biology.
  • Williams, M.A., O’Grady, J., Ball, B., Carlsson, J., de Eyto, E., McGinnity, P., Jennings, E., Regan, F., Parel-McDermott, A. (2019).  The application of CRISPR-Cas for single species identification from environmental DNA.  Molecular Ecology Resources.


  • Gerry F. Killeen, Prosper P. Chaki, Thomas E. Reed, Catherine L. Moyes and Nicodem J. Govella (2018). Entomological Surveillance as a Cornerstone of Malaria Elimination: A Critical Appraisal
  • Entomological Surveillance as a Cornerstone of Malaria Elimination: A Critical Appraisal In: Towards Malaria Elimination – A Leap Forward
  • Killeen, GF;Reed, TE (2018) ‘The portfolio effect cushions mosquito populations and malaria transmission against vector control interventions’
  • O’Neill, R., Ó Maoiléidigh, N., McGinnity, P., Bond, N., & Culloty, S. (2018). The novel use of pop‐off satellite tags (PSATs) to investigate the migratory behaviour of European sea bass Dicentrarchus labrax. Journal of fish biology92(5), 1404-1421.
  • Reed, Thomas E.; Prodöhl, Paulo A.; Bradley, Caroline; Gilbey, John; McGinnity, Philip; Primmer, Craig R.; Bacon, Phil J. (2018) ‘Heritability estimation via molecular pedigree reconstruction in a wild fish population reveals substantial evolutionary potential for sea-age at maturity, but not size within age-classes’. Canadian Journal of Fisheries and Aquatic Sciences, 76 (5):790-805
  • Scott, David Daniel, Emma SM Boston, Mathieu G. Lundy, Daniel J. Buckley, Yann Gager, Callum J. Chaplain, Emma C. Teeling, William Ian Montgomery, and Paulo A. Prodöhl. “Relatedness, parentage, and philopatry within a Natterer’s bat (Myotis nattereri) maternity colony.” Population ecology 60, no. 4 (2018): 361-370.


  • 2017
  • Ferguson, A., Reed, T., McGinnity, P., Prodöhl, P. (2017). Anadromy in brown trout (Salmo trutta): A review of the relative roles of genes and environmental factors and the implications for management and conservation. In Sea Trout: from Science Management (Proceedings of the 2nd Sea trout Symposium, Dundalk, Ireland, 2017.
  • Gilbey, John, Jamie Coughlan, Vidar Wennevik, Paulo Prodöhl, Jamie R. Stevens, Carlos Garcia de Leaniz, Dennis Ensing et al. “A microsatellite baseline for genetic stock identification of European Atlantic salmon (Salmo salar L.).” ICES Journal of Marine Science 75, no. 2 (2017): 662-674.
  • Glover, K., Solberg, M., McGinnity, P., Hindar, K., Verspoor, E., Coulson, M. W., Hansen, M. M., Araki H. Skaala1, Ø. Svåsand, T. (2017). Wild Atlantic salmon, farmed escapees and genetic interactions: status of knowledge and unanswered questions after 40 years of research. Fish & Fisheries 2017, 1-38.DOI: 10.1111/faf.12214.
  • Prodöhl, P. A., Antoniacomi, A.Bradley, C., Carlsson J., Carvalho, G. R., Coughlan, J., Coyne, J., Cross, M. C., Cross, M. E., Davies, C. A., Dillane, E., Gargan, P., Hynes, R., McGinnity, P. , Milner, N., Reed, T. , Roche, W., Taylor, M. Tyskind, N., Cross, T. F. (2017). Population genetics and Genetic Stock Identification of anadromous Salmo trutta from the Irish Sea and adjacent areas, using microsatellite DNA loci.  In Sea Trout: from Science Management (Proceedings of the 2nd Sea trout Symposium, Dundalk, Ireland, 2017).
  • McLennan, D., Armstrong, J.D., Stewart, D.C., Mckelvey, S., Boner, W., Monaghan, P. & Metcalfe, N.B. 2017. Shorter juvenile telomere length is associated with higher survival to spawning in migratory Atlantic salmon. Funct. Ecol. In press.
  • Reed, T.E., de Eyto, E., O’Higgins, K., Gargan, P., Roche, W., White, J., O’Maoileidigh, N., Quinn, T.P. and McGinnity, P., 2017. Availability of holding habitat in lakes and rivers affects the incidence of spring (premature) upriver migration by Atlantic salmon. Canadian Journal of Fisheries and Aquatic Sciences74(5), pp.668-679.
  • Van Leeuwen, T.E., Killen, S.S., Metcalfe, N.B. & Adams, C.E. 2017. Differential early development in offspring from alternative life history strategies. Ecol. Fresh. Fish. 26: 371-382.


  • Auer, S.K., Bassar, R.D., Salin, K. & Metcalfe, N.B. 2016. Repeatability of metabolic rate is lower for animals living under field versus laboratory conditions. J. Exp. Biol. 219: 631-634.
  • Auer, S.K., Salin, K., Anderson, G.J. & Metcalfe, N.B. 2016. Flexibility in metabolic rate and activity level determine individual variation in overwinter performance. Oecologia 182: 703-712.
  • Auer, S.K., Salin, K., Anderson, G.J., Rudolf, A.M. & Metcalfe, N.B. 2016. Differential effects of food availability on minimum and maximum rates of metabolism. Biol. Letts. 12: 20160586.
  • Burton, T., Robertsen, G., Stewart, D.C., McKelvey, S., Armstrong, J.D. & Metcalfe, N.B. 2016. Maternal age at maturation underpins contrasting behavior in offspring. Behav. Ecol. 27: 1280-1287.
  • Cross, M. E., Bradley, C. R., Cross, T. F., Culloty, S., Lynch, S., McGinnity, P., O’Riordan, R. M., Vartia S. and. Prodöhl. P. A. (2016). Genetic evidence supports post Pleistocene colonisation by Mya arenaria (L.) of western Europe from eastern North America’. Marine Ecology Progress Series, 549: 99-112.
  • de Eyto, E., Dalton, C., Dillane, M., Jennings, E., McGinnity, P., Barry O’Dwyer, B., Poole, R., Rogan, G and Taylor, D. (2016). The response of diadromous fish to land use change: a five-decade study of the Burrishoole river system in the Northwest of Ireland. Canadian Journal of Fisheries & Aquatic Science, 73 (12), 1759-1769.
  • Grant, B., Davie, A., Taggart, J.B, Selly, S.-L.C., Picchi, N., Bradley, C. Prodohl, P., Leclercq, E., Migauda H., (2016). Seasonal changes in broodstock spawning performance and egg quality in ballan wrasse (Labrus bergylta). Aquaculture 464, 505–514.
  • McLennan, D., Armstrong, J.D., Stewart, D.C., Mckelvey, S., Boner, W., Monaghan, P. & Metcalfe, N.B. 2016. Interactions between parental traits, environmental harshness and growth rate in determining rates of telomere loss in wild juvenile salmon. Mol. Ecol. 25: 5425-5438.
  • Metcalfe, N.B., Van Leeuwen, T.E. & Killen, S.S. 2016. Does individual variation in metabolic phenotype predict fish behaviour and performance? J. Fish Biol. 88: 298-321.
  • Quinn, J.L., Cole, E.F., Reed, T.E. and Morand-Ferron, J., 2016. Environmental and genetic determinants of innovativeness in a natural population of birds. Phil. Trans. R. Soc. B371(1690), p.20150184.
  • Quinn T, McGinnity P & Reed TE. 2016. The paradox of ‘premature migration’ by anadromous salmonid fishes: patterns and hypotheses. Canadian Journal of Fisheries & Aquatic Science, 73(7), 1015-1030.
  • Reed, T., Elvira de Eyto, E., O’Higgins, K., Gargan, P. Roche, W., White, J., O’Maoileidigh, N., Quinn, T.P., McGinnity, P. (2016). Availability of holding habitat in lakes and rivers affects the incidence of premature upriver migration by Atlantic salmon. Canadian Journal of Fisheries & Aquatic Science, 73 (7), 1015-1030.
  • Reed, T.E., Gienapp, P. and Visser, M.E., 2016. Testing for biases in selection on avian reproductive traits and partitioning direct and indirect selection using quantitative genetic models. Evolution70(10), pp.2211-2225.
  • Sundqvist, L., Keenan, K., Zackrisson, M., Prodöhl, P., & Kleinhans, D. (2016). Directional genetic differentiation and relative migration. Directional genetic differentiation and relative migration. Ecology and Evolution, 6(11), 3461-3475. DOI: 10.1002/ece3.2096.
  • Van Leeuwen, T.E., Hooker, O.E., Metcalfe, N.B. & Adams, C.E. 2016. Differences in diet-induced flexibility in morphology and growth in a partially migratory species. Can. J. Fish. Aquat. Sci. 73: 358-365.
  • Van Leeuwen, T.E., Hughes, M.R., Dodd, J.A., Adams, C.E. & Metcalfe, N.B. 2016. Resource availability and life history origin affect competitive ability in territorial disputes. Behav. Ecol. 27: 385-392.
  • Van Leeuwen, T.E., McLennan, D., McKelvey, S., Stewart, D.C., Adams, C.E. & Metcalfe, N.B. 2016. The association between parental rearing environment and offspring phenotype. J. exp. Biol. 219: 374-382.
  • Vartia, S., Villanueva, J.L., Collins, P.C., Farrell, E.D., John Finarelli, J., Hughes, G., Carlsson, J.E.L., Gauthier, D.T., McGinnity, P., Cross, T.F., FitzGerald, R.D., Mirimin, L., Cotter, P. and Carlsson, J. (2016). A novel method of microsatellite genotyping-by-sequencing using individual combinatorial barcoding. R. Soc. open sci.3: 150565.


  • Auer, S.K., Salin, K., Anderson, G.J, Rudolf, A.M. & Metcalfe, N.B. 2015. Greater flexibility in metabolic rate confers a growth advantage under changing food availability. J. Anim. Ecol. 84: 1405-1411.
  • Auer, S.K., Salin, K., Anderson, G.J & Metcalfe, N.B. 2015. Aerobic scope explains individual variation in feeding capacity. Biol. Letts. 11: 20150793.
  • Auer, S.K., Salin, K., Rudolf, A.M., Anderson, G.J. & Metcalfe, N.B. 2015. The optimal combination of standard metabolic rate and aerobic scope for somatic growth depends on food availability. Funct. Ecol. 29: 479-486.
  • 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, D.P., Carlsson, J. and Carlsson, J.E.L. Mind the Gap II: new insights into the Irish postglacial. Irish Naturalists’ Journal, Belfast
  • Clarke, C.R, Karl, S. A., Horn, R., Bernard, A., Lea, J., Hazin, F., Prodöhl, P. A., Shivji, M. (2015). Global mitochondrial DNA phylogeography and population structure of the silky shark, Carcharhinus falciformis. Marine Biology, 162: 945-955.
  • 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.
  • Llewellyn, M., McGinnity, P., Dionne, M., Letourneau, J.,  Thonier, F., Carvalho, G.R., Creer, S., Derome, N. (2015). The biogeography of the Atlantic salmon (Salmo salar) gut microbiome revealed by deep sequencing. ISJME doi:10.1038/ismej.2015.189.
  • Mantua NJ, Crozier LG, Reed TE, Schindler DE & Waples RS. 2015. Response of Chinook salmon to climate change. Nature Climate Change, 5(7), 613-615.
  • 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). The signature of fine scale local adaptation in Atlantic salmon revealed from common garden experiments in nature. Evolutionary Applications Vol 8 (9): 881-900.
  • Quéméré, E. Jean-Luc 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 43, 498–509,  DOI: 10.1111/jbi.12632.
  • 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 Science73: 1015–1030, 10.1139/cjfas-2015-0345.
  • 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).
  • 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.
  • 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 Evolution3, 1-13 (doi: 10.3389/fevo.2015.00001).
  • Reed, T.E., Prodöhl, P. A., Hynes, R., Cross, T., Ferguson, A., & McGinnity, P. (2015). Quantifying heritable variation in fitness-related traits of wild, farmed and hybrid Atlantic salmon families in a wild river environment. Heredity 115 (2), 173-184, doi:10.1038/hdy.2015.29.
  • Salin, K., Auer, S.K., Rey, B., Selman, C. & Metcalfe, N.B. 2015. Variation in the link between oxygen consumption and ATP production and its relevance for animal performance. Proc. R. Soc. B 282: 20151028.
  • Salin, K., Auer, S.K., Rudolf, A.M., Anderson, G.J., Cairns, A., Hartley, R.C., Selman, C. & Metcalfe, N.B. 2015. Individuals with higher metabolic rates have lower levels of reactive oxygen species in vivo. Biol. Letts. 11: 20150538.
  • Schindler, D.E., Armstrong, J.B., Reed, T.E. (2015). The portfolio concept in ecology and evolution. Frontiers Ecology and the Environment 2015; 13(5): 257–263.
  • Stevenson, T.J., Visser, M.E., Arnold, W., Barrett, P., Biello, S., Dawson, A., Denlinger, D.L., Dominoni, D., Ebling, F.J., Elton, S. and Evans, N… Reed, TE.,… Helm, B., 2015. Disrupted seasonal biology impacts health, food security and ecosystems. Proc. R. Soc. B (Vol. 282, No. 1817, p. 20151453).
  • Sydeman WJ, Poloczanska E, Reed TE & Thompson SA. 2015. Climate change and marine vertebrates. Science, 350, 772-777.
  • Verspoor, E., McGinnity, P., Bradbury, I., and 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.


  • Aykanat, T., Johnston, S.E., Cotter, D., Cross, T.F., Poole, R., Prodöhl, P.A., Reed, T., 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).
  • Bailie, D. A., Fitzpatrick, S., Connolly, M., Thiel, M., Hynes, R., Prodöhl, P. A. (2014). Genetic assessment of parentage in the caridean rock shrimp Rhynchocinetes typus based on microsatellite markers. Journal of Crustacean Biology, 34 (5), 658-662.
  • 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.
  • Daunt, F., Reed, T.E.,  Newell, M., Burthe, S., Phillips, R.A., Lewis, S., Wanless, S. (2014). Longitudinal bio-logging reveals interplay between extrinsic and intrinsic carry-over effects in a long-lived vertebrate. Ecology95 (8), 2077–2083.
  • 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.
  • 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: 573-585.
  • 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, 93-107.
  • O’Malley, K.G., Cross, T.F., Bailie, D., Carlsson, J., Coughlan, J.P., Dillane, E., Prodöhl, P.A., McGinnity, P. (2014). Circadian clock gene (OtsClock1b) variation and time of ocean return in Atlantic salmon Salmo salarFisheries Management and Ecology, 21: 82-87.
  • Ravinet, M., C. Eizaguirre, C. Harrod, and P. A. Prodöhl. (2014). Unique mitochondrial DNA lineages in Irish stickleback populations: cryptic refugium or rapid recolonization? Ecology and Evolution 4: 2488-2504. (doi:10.1002/ece3.853).
  • 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.


  • 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.
  • Burton, T., Armstrong, J.D., McKelvey, S., Stewart, D.C. & Metcalfe, N.B. 2013. Early maternal experience shapes offspring performance in the wild. Ecology 94: 618-626.
  • Burton, T., Hoogenboom, M.O., Beevers, N.D., Armstrong, J.D. & Metcalfe, N.B. 2013. Within-clutch differences in the phenotypes of juvenile fish depend on their location within the egg mass and maternal dominance rank. Proc. R. Soc. B 280: 20122441.
  • Burton, T., McKelvey, S., Stewart, D.C., Armstrong, J.D. & Metcalfe, N.B. 2013. Offspring investment in wild Atlantic salmon (Salmo salar): relationships with smolt age and spawning condition. Ecol. Fresh. Fish 22: 317-321.
  • Carlsson J, Gauthier D, Carlsson JEL, Coughlan JP, Dillane E, FitzGerald RD, Keating FU, McGinnity P, Mirimin L & Cross TF. (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.
  • 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.
  • Gauthier, D.T., Audemard, C.A., Carlsson, J.E.L., Darden, T.L., Denson, M.R., Reece, K.S., Carlsson, C. (2013) Genetic Population Structure of US Atlantic Coastal Striped Bass (Morone saxatilis). Journal of Heredity 2013:104(4):510–520
  • Havelka, M., Hulák, M,  Bailie, D. A., Prodöhl, P. A., Flajšhans, M.(2013). Extensive genome duplications in sturgeons: new evidence from microsatellite data. J. Appl. Ichthyol. 29 (2013), 704–708.
  • 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.
  • Hoogenboom, M.O., Armstrong, J.D., Groothuis, T.G.G. & Metcalfe, N.B. 2013. The growth benefits of aggressive behavior vary with individual metabolism and resource predictability. Behav. Ecol. 24: 253-261.
  • Keenan, K., McGinnity, P., Cross, T., Crozier, W.W. & Prodöhl, 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.
  • 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): 1789-1804.
  • Killen, S.S., Marras, S., Metcalfe, N.B., McKenzie, D.J. & Domenici, P. 2013. Environmental stressors alter relationships between physiology and behaviour. Trends Ecol. Evol. 28: 651-658.
  • O’Farrell, B; Benzie, JAH; McGinnity, P; de Eyto, E; Dillane, E; Coughlan, J. & Cross, T (2013) Major histocompatibility class I variation in wild Irish brown trout (Salmo trutta). PLoS ONE  8(5): e63035.
  • Ravinet, M., Prodöhl, P.A., Harrod, C., (2013). On Irish stickleback: morphological diversification in a secondary contact zone. Evolutionary Ecology Research, 2013, 15: 271–294.
  • Ravinet, M., Prodöhl, P.A., Harrod, C., (2013). Parallel and nonparallel ecological, morphological and genetic divergence in lake–stream stickleback from a single catchment J. Evol. Biol. 26: 186–204.


  • Drinan, T.J., McGinnity, P., Coughlan, J.P., Cross, T.F. & Harrison, S.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.
  • 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 of Mathematical Biology 74: 615-640.
  • 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):661–671
  • 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, inIreland. Parasitology, 139, 1526-1532).
  • 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.
  • McInerney, C.E., Allcock, A.L., Johnson, M.P., Prodöhl, P.A. (2012). Ecological coherence in marine reserve network design: An empirical evaluation of sequential site selection using genetic structure. Biological Conservation 152, 262–270.
  • 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. doi:10.1093/icesjms/fss108.
  • 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.
  • 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.
  • Reid, D., Armstrong, J.D. & Metcalfe, N.B. 2012. The performance advantage of a high resting metabolic rate in juvenile salmon is habitat dependent. J. Anim. Ecol. 81: 868-875.
  • 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, Volume 2012, Article ID 628204, 14 pagesdoi:10.1155/2012/628204.


  • Bailie, D.A., Hynes, R., Prodöhl, P.A. (2011). Genetic parentage in the squat lobsters Munida rugosa and M. sarsi (Crustacea, Anomura, Galatheidae). Mar. Ecol. Prog. Ser. Vol. 421: 173–182, 2011 doi: 10.3354/meps08895.
  • Burton, T., Killen, S.S., Armstrong, J.D. & Metcalfe, N.B. 2011. What causes intra-specific variation in resting metabolic rate and what are its ecological consequences? Proc. R. Soc. B 278: 3465-3473.
  • Carlsson, J., Shephard, S, Coughlan, J., Trueman, C., Rogan, E., Cross, T. (2011). Fine-scale population structure in a deep-sea teleost (orange roughy, Hoplostethus atlanticus). Deep-Sea Research I 58 (2011) 627–636.
  • Consuegra S, de Eyto E, McGinnity P, Stet RJM, Jordan WC. (2011). Contrasting responses to selection in class I and class II Major Histocompatibility linked markers in salmon. Heredity 107: 143-154.
  • 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.
  • 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.
  • Ensing, D., Prodöhl, P. A., McGinnity, P., Boylan, P., O’Maoileidigh, N. and Crozier, W.W. (2011) Complex pattern of genetic structuring in the Atlantic salmon (Salmo salar L.) of the River Foyle system in north-west Ireland: disentangling the evolutionary signal from population stochasticity. Ecology and Evolution 1:359-372.
  • Fitzpatrick, S., Shivji, M.S., Chapman, D.D., Prodöhl, P. (2011). Development and characterization of 10 polymorphic microsatellite loci for the blue shark, Prionace glauca, and their cross shark-species amplification. Conservation Genetic Resources, 3:523–527
  • McInerney, C.E., Allcock, A.L., Johnson, M.P., Bailie, D.A., Prodöhl, P.A. (2011). Comparative genomic analysis reveals speciesdependent complexities that explain difficulties with microsatellite marker development in molluscs. Heredity (2011) 106, 78–87.
  • 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.
  • Mirimin, L., Miller, R., Dillane, E., Berrow, S. D., Ingram, S., Cross, T. F.,  Rogan, E. (2011). Fine-scale population genetic structuring of bottlenose dolphins (Tursiops truncates) in Irish coastal waters. Animal Conservation 14: 342–353.
  • Reid, D., Armstrong, J.D. & Metcalfe, N.B. 2011. Estimated standard metabolic rate interacts with territory quality and density to determine growth rates of juvenile Atlantic salmon. Funct. Ecol. 25: 1360-1367.
  • Schultz, T.F., Hsing, P-Yuan, Eng, A., Zelnio, K.A., Thaler, A.D., Carlsson, J., Van Dover, C.L. (2011). Characterization of 18 polymorphic microsatellite loci from Bathymodiolus manusensis (Bivalvia, Mytilidae) from deep-sea hydrothermal vents. Conservation Genetic Resources 3:25–27.


  • Bailie, D.A., Fletcher, H., Prodöhl, P.A. (2010). High Incidence of Cryptic Repeated Elements in Microsatellite Flanking Regions of Galatheid Genomes and Its Practical Implications for Molecular Marker Development. Journal of Crustacean Biology, 30(4):664-672.
  • Feldheim, K.A., Chapman, D.D., Sweet, D., FitzPatrick, S., Prodöhl, P.A. (2010). Shark virgin birth produces multiple viable offspring. Journal of Heredity 2010:101(3):374–377.
  • 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, R. (2010)  Genetic stock identification of Atlantic salmon (Salmo salar) populations in the southern part of the European range. BMC Genetics, Vol. 11, 31, doi:10.1186/1471-2156-11-31.
  • Gurney, W.S.C., Bacon, P.J., McKenzie, E., McGinnity, P., Mclean, J., Smith, G. and Youngson, A. (2010). Form and uncertainty in stock-recruitment relations: observations and implications for Atlantic salmon management. Can. J. Fish. Aquat. Sci. 67: 1040-1055.
  • McKeown, N. J., Hynes, R. A., Duguid, R. A., Ferguson, A., Prodöhl, P. A. (2010). Phylogeographic structure of brown trout Salmo trutta in Britain and Ireland: glacial refugia, postglacial colonization and origins of sympatric populations. Journal of Fish Biology. 76, 319–347.
  • 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 Genetic Resources 2:101–103.


  • Anderson, C., Aparicio, G., J. et al. and the Molecular Ecology Resources Primer Development Consortium (2010). Permanent Genetic Resources added to Molecular Ecology Resources Database 1 December 2009–31 January 2010. Molecular Ecology Resources 10, 576–579.
  • Jørstad , K.E., Kristiansen, T. S.,  Farestveit , E., Agnalt , A.‐L.,  Prodöhl , P.A., Hughes,  M. Ferguson,  A., Taggert , J.B. (2009). Survival of laboratory‐reared juvenile European lobster (Homarus gammarus) from three brood sources in southwestern Norway. New Zealand Journal of Marine and Freshwater Research, 43:1, 59-68.
  • Kenchington, E.L., Harding, G.C., Jones, M.W., Prodöhl, P.A. (2009). Pleistocene glaciation events shape genetic structure across the range of the American lobster, Homarus americanusMolecular Ecology 18, 1654–1667.
  • McGinnity, P., Jennings, E., deEyto, E., Allott, N., Samuelsson, P., Rogan, G., Whelan, K., and Cross, T. (2009). Impact of naturally spawning captive-bred Atlantic salmon on wild populations: depressed recruitment and increased risk of climate-mediated extinction. Proc. R. Soc. B Vol. 276 No. 1673 3601-3610.
  • McInerney, C.E., Allcock, A.L., Johnson, M.P., Prodöhl, P.A. (2009a). Understanding marine reserve function in a seascape genetics context: Nucella lapillus in Strangford Lough (Northern Ireland) as an example. Aquatic Biology Vol. 7: 45–58.
  • McInerney, C.E., Allcock, A.L., Johnson, M.P., Prodöhl, P.A. (2009b). Characterization of polymorphic microsatellites for the periwinkle gastropod, Littorina littorea (Linnaeus, 1758) and their cross-amplification in four congeners. Conservation Genetics 10:1417–1420.
  • 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.
  • Sagarin, R., Carlsson, J., Duval, M., Freshwater, W., Godfrey, M.H., Litaker, W., Muñoz, R., Noble, R., Schultz, T., Wynne, B. (2009). Bringing molecular tools into environmental resource management: Untangling the molecules to policy pathway. PLoS Biology, March 2009 | Volume 7 | Issue 3 | e1000069.
  • 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.


  • Cross, T.F., Burnell, G., Coughlan, J., Culloty, S., Dillane, E., McGinnity P. and 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 Ecosystem Ed. M. Holmer, Springer Press, p 117- 154.
  • Dillane E, McGinnity P.*, Coughlan J, Cross M, de Eyto, E., Prodohl, P., Kenchington, E., and Cross T. (2008). Landscape features influence intra-river population genetic structure in Atlantic salmon (Salmo salar L.). Molecular Ecology 17: 4786-4800.
  • Strugnell, J.M., Rogersd, A.D., Prodöhl, P.A., Collins, M., A., Allcock, L. (2008). The thermohaline expressway: the Southern Ocean as a centre of origin for deep-sea octopuses. Cladistics, 24 (2008) 853–860.
  • 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.


  • McGinnity, P., de Eyto, E., Cross, T., Coughlan J. and Ferguson, A. (2008). Population specific smolt development, migration and maturity schedules in Atlantic salmon in a natural river environment. Aquaculture. DOI: 10.1016/j.aquaculture.2007.10.008. Volume 273, Issues 2–3, 18:  257-268.

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