Peer Reviewed Papers 2012/13
Adams, C E; Godfrey J D; Dodd, J A and Maitland, P S (2013). Is proximity to the North Atlantic Drift and the Continental Shelf Current sustaining freshwater European eel populations in western Scotland? Freshwater Biology 58 (1):1-9.
Armstrong, J D and Nislow K H (2012). Modelling approaches for relating effects of change in river flow to populations of Atlantic salmon and brown trout. Fisheries Management and Ecology 19:527-536.
Bacon, P J; Malcolm, I A; Maclean, J C; McLaren, I and Thorne, A (2012). Female length and Mass Quantify the Difference between Atlantic Salmon Ova Fecundity and Ova Deposition. North American Journal of Fisheries Managment 32:491- 498.
Bland, F; Snow, M; Garver, K A and Matejusova, I (2013). Genotype-specific Taqman (R) assays for the detection and rapid characterisation of European strains of viral haemorrhagic septicaemia virus. Journal of Virological Methods 187 (2):209-214.
Bresnan, E; Davidson, K; Edwards, M; Fernand, L; Gowen, R; Hall, A; Kennington, K; McKinney, A; Milligan, S; Raine, R and Silke, J (In press). Harmful Algal Bloom Report Card. Marine Climate Change Impacts Partnership (MCCIP).
Brookes, K L; Bailey, H and Thompson, P M (2013). Predictions from harbour porpoise habitat association models are confirmed by long-term passive acoustic monitoring. Journal of the Acoustical Society of America, 134: 2523-2533.
Brown, L; Bresnan, E; Summerbell, K and O'Neill, F G (2013). The influence of demersal trawl fishing gears on the resuspension of dinoflagellate cysts. Marine Pollution Bulletin 66 (1-2):17-24.
Burton, T; Hoogenboom, M O; Beevers, N D; Armstrong, J D and Metcalfe, N B (2013). Among-sibling differences in the phenotypes of juvenile fish depend on their location within the egg mass and maternal dominance rank. Proceedings of the Royal Society B-Biological Sciences 280 (1751).
Burton, T; Killen, S S; Armstrong, J D and Metcalfe, N B (2011). What causes intra-specific variation in resting metabolic rate and what are its ecological consequesnces? Proceedings of the Royal Society Series B 278 (1724): 3465-3473.
Burton, T; McKelvey, S; Stewart, D C; Armstrong, J D and Metcalfe, N B (2012). Offspring investment in wild Atlantic salmon (Salmo salar): relationships with smolt age and spawning condition. Ecology of Freshwater Fish 22 (2):317-321.
Burton, T; McKelvey, S; Stewart, D C; Armstrong, J D and Metcalfe, N B (2013). Early maternal experience shapes offspring performance in the wild. Ecology 94:618-626.
Castro, C; Wright, P J; Millar, C P and Holmes, S J (2013). Evidence for sub-stock dynamics within whiting (Merlangius merlangus) management regions. ICES Journal of Marine Science 70 (6):1118-1127.
Cauwelier, E; Gilbey, J; Jones, C; Noble, L and Verspoor, E (2012). Asymmetrical viability in backcrosses between highly divergent populations of Atlantic salmon (Salmo salar): implications for conservation. Conservation Genetics 13 (6):1665-1669.
Collet, B; Urquhart, K; Noguera, P; Larsen, K; Lester, K; Smail, D and Bruno, D (2013). A method to measure an indicator of viraemia in Atlantic salmon using a reporter cell line. Journal of Virological Methods 191 (2):113-117.
Cook, R M; Needle, C L and Fernandes, P G (2012). Comment on "Fisheries mismanagement". Marine Pollution Bulletin 64 (10):2265-2266.
Davidson, K; Gowen, R J; Tett, P; Bresnan, E; Harrison, P J; McKinney, A; Milligan, S; Mills, D K; Silke, J and Crooks, A-M (2012). Harmful algal blooms: how strong is the evidence that nutrient ratios and forms influence their occurrence? Estuarine, Coastal and Shelf Science 115:399-413.
Devine, J. A; Wright, P J; Pardoe, H E and Heino, M (2012). Comparing rates of contemporary evolution in life-history traits for exploited fish stocks. Canadian Journal of Fisheries and Aquatic Sciences 69 (6):1105-1120.
Embling, C B; Illian, J; Armstrong, E; van der Kooij, J; Sharples, J; Camphuysen, K C J and Scott, B E (2012). Investigating fine-scale spatio-temporal predator-prey patterns in dynamic marine ecosystems: a functional data analysis approach. Journal of Applied Ecology 49 (2):481-492.
Emelogu, E S; Pollard, P; Robinson, C D; Smedes, F; Webster, L; Oliver, I W; McKenzie, C; Seiler, T B; Hollert, H and Moffat, C F (2013). Investigating the significance of dissolved organic contaminants in aquatic environments: Coupling passive sampling with in vitro bioassays. Chemosphere 90 (2):210-219.
Emelogu, E S; Pollard, P; Robinson, C D; Webster, L; McKenzie, C; Napier, F; Steven, L and Moffat, C F (2013). Identification of selected organic contaminants in streams associated with agricultural activities and comparison between autosampling and silicone rubber passive sampling. Science of the Total Environment 445-446:261-272.
Garduno-Paz, M V; Adams, C E; Verspoor, E; Knox, D and Harrod, C (2012). Convergent evolutionary processes driven by foraging opportunity in two sympatric morph pairs of Arctic charr with contrasting post-glacial origins. Biological Journal of the Linnean Society 106 (4):794-806.
Greenstreet, S P R; Rogers, S I; Rice, J C; Piet, G J; Guirey, E J; Fraser, H M and Fryer, R J (2012). A reassessment of trends in the North Sea large fish indicator and a re-evaluation of earlier conclusions. ICES Journal of Marine Science 69 (2):343-345.
Greenstreet, S P R; Rossberg, A G; Fox C J; Le Quesne, W J F; Blasdale, T; Boulcott, P; Mitchell, I; Millar, C and Moffat, C F (2012). Demersal fish biodiversity: species-level indicators and trends-based targets for the Marine Strategy Framework Directive. ICES Journal of Marine Science 69 (10):1789-1801.
Grutjen, F; Lang, T; Feist, S; Bruno, D; Noguera, P and Wosniok, W (2013). Hyperpigmentation in North Sea dab Limanda limanda. I. Spatial and temporal patterns and host effects. Diseases of Aquatic Organisms 103 (1):9-24.
Hall, M; Wallace, I S; Munro, L A; Munro, E S; McIntosh, R; Cook, P; Allan, C E T and Murray, A G (2013). Reliability of individual and pooled test procedures for detecting the pathogenic agent for clinical infectious salmon anaemia. Journal of Fish Diseases 36 (8):741-746.
Heath, M R; Neat, F C; Pinnegar, J K; Reid, D G; Sims, D W and Wright, P J (2012). Review of climate change impacts on marine fish and shellfish around the UK and Ireland. Aquatic Conservation-Marine and Freshwater Ecosystems 22 (3):337-367.
Holt, J; Hughes, S; Hopkins, J; Wakelin, S L; Holliday, N P; Dye, S; Gonzalez-Pola, C; Hjollo, S S; Mork, K A; Nolan, G; Proctor, R; Read, J; Shammon, T; Sherwin, T; Smyth, T; Tattersall, G; Ward, B and Wiltshire, K H (2012). Multi-decadal variability and trends in the temperature of the northwest European continental shelf: A model-data synthesis. Progress in Oceanography 106:96-117.
Hoogenboom, M O; Armstrong, J D; Groothuis, T G G and Metcalfe, N B (2013). The growth benefits of aggressive behavior vary with individual metabolism and resource predictability. Behavioral Ecology 24 (1):253-261.
Hughes, S L; Holliday, N P and ICES Working Group on Oceanic Hydrography (2012). Variability in the ICES/NAFO region between 1950 and 2009: observations from the ICES Report on Ocean Climate. ICES Journal of Marine Science 69 (5):706-719.
Imholt, C; Soulsby, C; Malcolm, I A and Gibbins, C N (2012). Influence of contrasting riparian forest cover on stream temperature dynamics in salmonid spawning and nursery streams. River Research and Applications Online first.
Jacobsen, J A; Hansen, L P; Bakkestuen, V; Halvorsen, R; Reddin, D G; White, J; Maoileidigh, N O; Russell, I; Potter, E C E; Fowler, M; Smith, G; Mork, K A; Isaksson, A; Oskarsson, S; Karlsson L and Pedersen, S (2012). Distribution by origin and sea age of Atlantic salmon (Salmo salar) in the sea around the Faroe Islands based on analysis of historical tag recoveries. ICES Journal of Marine Science 69 (9):1598 - 1608.
Kalavati, C; Mackenzie, K; Collins, C; Hemmingsen, W and Brickle, P (2013). Two new species of myxosporean parasites (Myxosporea: Bivalvulida) from gall bladders of Macruronus magellanicus Lonnberg, 1907 (Teleostei: Merlucciidae). Zootaxa 3647 (4):541-554.
Kilburn, R; Gregory, A and Murray, A G (2012). Using Markov-chain Monte-Carlo modelling approach to identify the relative risk to farmed Scottish rainbow trout (Oncorhynchus mykiss) in a multisector industry of viral haemorrhagic septicaemia from introduction and emergent sources. Ecological Modelling 237-238:34-42.
Kilburn, R; Murray, A G; Hall, M; Bruno, D W; Cockerill, D and Raynard, R S (2012). Analysis of a company's production data to describe the epidemiology and persistence of pancreas disease in Scottish Atlantic salmon (Salmo salar L.) farms off western Scotland. Aquaculture 368-369:89-94.
Kraak, S B M; Bailey, N; Cardinale, M; Darby, C; De Oliveira, J A A; Eero, M; Graham, N; Holmes, S; Jakobsen, T; Kempf, A; Kirkegaard, E; Powell, J; Scott, R D; Simmonds, E J; Ulrich, C; Vanhee, W and Vinther, M (2013). Lessons for fisheries management from the EU cod recovery plan. Marine Policy 37:200-213.
Lynam, C P; Halliday, N C; Höffle, H; Wright, P J; van Damme, C J G; Edwards, M and Pitois, S G (2013). Spatial patterns and trends in abundance of larval sandeels in the North Sea: 1950-2005. ICES Journal of Marine Science 70 (3):540-553.
Malcolm, I A; Gibbins, C N; Soulsby, C; Tetzlaff, D and Moir, H J (2012). The influence of hydrology and hydraulics between spawning and emergence: implications for the management of flows in regulated rivers. Fisheries Management and Ecology 19:464-474.
Malcolm, I A; Bacon, P J; Middlemas, S J; Fryer, R J; Shilland, E M and Collen, P (2012). Relationships between hydrochemistry and the presence of juvenile brown trout (Salmo trutta) in headwater streams recovering from acidification. Ecological Indicators, 37 (Part B): 351-364.
Malcolm, I A; Gibbins, C N; Fryer, R J; Keay, J; Tetzlaff, D and Soulsby, C (2012). The influence of forestry on acidification and recovery: Insights from long-term hydrochemical and invertebrate data. Ecological Indicators, 37 (Part B): 317-329.
Marcos-Lopez, M; Waltzek, T B; Hedrick, R P; Baxa, D V; Garber, A F; Liston, R; Johnsen, E; Forward, B S; Backman, S and Ferguson, H W (2012). Characterization of a novel alloherpesvirus from Atlantic cod (Gadus morhua). Journal of Veterinary Diagnostic Investigation 24 (1):65-73.
Matejusova, I; Doig, F; Hall, A J; Harris, R; Douglas, A; Snow, M and Middlemas, S J (2013). Real time PCR assays for the identification of harbor and gray seal species and sex: a new tool for ecology and management. Marine Mammal Science 29:186-194.
Matějusová, I; Lester, K; Li, Z; Bravo, J; Bland, F and Collet, B (2013). Comparative genotypic and phenotypic analysis of two salmon alphavirus isolates in salmon cell lines. Archives of Virology 158:2143-2146.
Mayor, D J; Thornton, B; Hay, S; Zuur, A F; Nicol, G W; McWilliam, J M and Witte, U F M (2012). Resource quality affects carbon cycling in deep-sea sediments. Isme Journal 6 (9):1740-1748.
McBeath, A; Bain, N; Fourrier, M; Collet, B and Snow, M (2013). A strand specific real-time RT-PCR method for the targeted detection of the three species (vRNA, cRNA and mRNA) of infectious salmon anaemia virus (ISAV) replicative RNA. Journal of Virological Methods 187 (1):65-71.
McCarthy, Ú; Casadei, E; Wang, T and Secombes, C J (2013). Red mark syndrome in rainbow trout Oncorhynchus mykiss: investigation of immune responses in lesions using histology, immunohistochemistry and analysis of immune gene expression. Fish and Shellfish Immunology 34 (5):1119-1130.
McCarthy, U; Stagg, H; Donald, K; Garden, A and Weir, S J (2013). Psychrobacter sp. isolated from Atlantic salmon (Salmo salar) kidney at a number of aquaculture sites in Scotland. Bulletin of the European Association of Fish Pathologists 33 (2):67.
Middlemas, S J; Fryer, R; Tulett, D and Armstrong, J D (2013). Relationship between sea lice levels on sea trout and fish farm activity in western Scotland. Fisheries Management and Ecology 20:67-74.
Millidine, K J; Malcolm, I A; Gibbins, C N; Fryer, R J and Youngson, A F (2012). The influence of canalisation on juvenile salmonid habitat. Ecological Indicators 23:262-273.
Milner, N J; Solomon, D J and Smith, G W (2012). The role of river flow in the migration of adult Atlantic salmon, Salmo salar, through estuaries and rivers. Fisheries Management and Ecology 19:537-547.
Monteith, D T; Evans, C D; Henrys, P; Simpson, G L and Malcolm, I A (2012). Trends in the hydro-chemistry of acid-sensitive surface waters in the UK 1988 - 2008. Eological Indicators 37(Part B): 287-303.
Morgan, M J; Wright, P J and Rideout, R M (2013). Effect of age and temperature on spawning time in two gadoid species. Fisheries Research 138:42-51.
Mork, K A; Gilbey, J; Hansen, L P; Jensen, A J; Jacobsen, J A; Holm, M; Holst, J C; Maoileidigh, N O; Vikebo, F; McGinnity, P; Melle, W; Thomas, K; Verspoor, E and Wennevik, V (2012). Modelling the migration of post-smolt Atlantic salon (Salmo salar) in the Northeast Atlantic. ICES Journal of Marine Science 69 (9):1616 - 1624.
Murray, A G; Hall, M; Munro, L A and Wallace, I S (2012). Modelling management strategies for a disease including undetected sub-clinical infection: Bacterial kidney disease in Scottish salmon and trout farms (vol 3, pg 171, 2012). Epidemics 4 (4):227-227.
Murray, A G (2013). Epidemiology of the spread of viral diseases under aquaculture. Current Opinions in Virology 3 (1):74-78.
———. (2013). Implications of Leaky Boundaries for Compartmentalised Control of Pathogens: A Modeling Case Study for Bacterial Kidney Disease in Scottish Salmon Aquaculture. Ecological Modelling 250 (February 2013):6.
Murray, A G and Soje, J (2012). Epidemiology and economics of bacterial kidney disease to inform control policy. Fish Veterinary Journal 13:30-34.
Murray, R B O; Hodgson, D M and Thorne, P D (2012). Wave groups and sediment resuspension processes over evolving sandy bedforms. Continental Shelf Research 46:16-30.
Nash, R D M; Wright, P J; Matejusova, I; Dimetrov, S P; O'Sullivan, M; Augley, J and Hoffle, H (2012). Spawning location of Norway pout (Trisopterus esmarkii Nilsson) in the North Sea. ICES Journal of Marine Science 69:1338-1346.
Neuenfeldt, S; Righton, D; Neat, F; Wright, P J; Svedang, H; Michalsen, K; Subbey, S; Steingrund, P; Thorsteinsson, V; Pampoulie, C; Andersen, K H; Pedersen, M W and Metcalfe, J (2013). Analysing migrations of Atlantic cod Gadus morhua in the north-east Atlantic Ocean: then, now and the future. Journal of Fish Biology 82 (3):741-763.
Nislow, K H and Armstrong, J D (2012). Towards a life-history based management framework for the effects of flow on juvenile salmonids in streams and rivers. Fisheries Management and Ecology 19:451-463.
Noguera, P A; Feist, S W; Bateman, K S; Lang, T; Gruetjen, F and Bruno, D W (2013). Hyperpigmentation in North Sea dab Limanda limanda. II. Macroscopic and microscopic characteristics and pathogen screening. Diseases of Aquatic Organisms 103 (1):25-34.
Oidtmann, B; Verner-Jeffreys, D; Pond, M; Peeler, E J; Noguera, P A; Bruno, D W; LaPatra, S E; St-Hilaire, S; Schubiger, C B; Snekvik, K; Crumlish, M; Green, D M; Metselaar, M; Rodger, H; Schmidt-Posthaus, H; Galeotti, M and Feist, S W (2013). Differential characterisation of emerging skin diseases of rainbow trout – a standardised approach to capturing disease characteristics and development of case definitions. Journal of Fish Diseases 36(11): 921-937.
Owen, E; Daunt, F; Moffat, C; Elson, D; Wanless, S and Thompson, P (2013). Analysis of fatty acids and fatty alcohols reveals seasonal and sex specific changes in the diets of seabirds. Marine Biology 160 (4):987-999.
Pan, M; Pierce, G J; Cunningham, C O and Hay, S J (2012). Seasonal and interannual variation of decapod larval abundance from two coastal locations in Scotland, UK (vol 91, pg 1443, 2011). Journal of the Marine Biological Association of the United Kingdom 92 (7):1637-1637.
Queiros, A M; Weetman, A; McLay, H A and Dobby, H (2013). Geographical variation in size at the onset of maturity of male and female Norway lobster Nephrops norvegicus (L., Homarida: Decapoda) in Scottish waters. Fisheries Research 139:132-144.
Rabe, B; Johnson, H L; Muenchow, A and Melling, H (2012). Geostrophic ocean currents and freshwater fluxes across the Canadian Polar Shelf via Nares Strait. Journal of Marine Research 70:603-640.
Reddin, D G; Hansen, L P; Bakkestuen, V; Russell, I; White, J; Potter, E C E; Dempson, B; Sheehan, T F; Maoileidigh, N O; Smith, G; Isaksson, A; Jacobsen, J A; Fowler, M and Amiro, P (2012). Distribution and biological characteristics of Atlantic salmon (Salmo salar) at Greenland based on the analysis of historical tag recoveries. ICES Journal of Marine Science 69 (9):1589 - 1597.
Reid, D; Armstrong, J D and Metcalfe, N B (2012). The performance advantage of a high resting metabolic rate in juvenile salmon is habitat dependent. Journal of Animal Ecology 81 (4):868-875.
Reilly, T O M; Fraser, H M; Fryer, R; Clarke, J and Greenstreet, S P R (2014). Interpreting variation in fish-based food web indicators: the importance of 'bottom-up limitation' and 'top-down control' processes. ICES Journal of Marine Science, 71(2): 406-416.
Rombouts, I; Beaugrand, G; Fizzala, X; Gaill, F; Greenstreet, S P R; Lamare, S; Le Loc'h, F; McQuattors-Gollop, A; Mialet, B; Niquil, N; Percelay, J; Renaud, F; Rossberg, A G and Féral, J P (2013). Food web indicators under the Marine Strategy Framework Directive: from complexity to simplicity? Ecology Letters 29:246-254.
Rose, N L; Munthe, J and McCartney, A (2013). Winter peaks of methylmercury in deposition to a remote Scottish mountain lake. Chemosphere 90 (2):805-811.
Russell, I; Aprahamian, M W; Barry, J; Davidson, I C; Fiske, P; Ibbotson, A T; Kennedy, R J; Maclean, J C; Moore, A; Otero, J; Potter, E C E and Todd, C D (2012). The influence of the freshwater environment and the biological characteristics of Atlantic salmon smolts on their subseqent marine survival. ICES Journal of Marine Science 69 (9):1563 - 1573.
Salama, N K G; Collins, C M; Fraser, J G; Dunn, J; Pert, C C; Murray, A G and Rabe, B (2013). Development and assessment of a biophysical dispersal model for sea lice. Journal of Fish Diseases 36 (3):323-337.
Saunders, R A; Rasmussen, J; Tarling, G A and Brierly, A S (2013). Distribution, population dynamics and growth rates of Thysanopoda acutifrons, Thysanoessa inermis and Nematobrachion boöpsis in the Irminger Sea, North Atlantic. Journal of the Marine Biological Association 93 (5):1287-1301.
Shepherd, S; Fung, T; Rossberg, A G; Farnsworth, K; Reid, D G; Greenstreet, S P R and Warnes, S (2013). Modelling recovery of Celtic Sea demersal fish community size structure. Fisheries Research 140:91-95.
Smail, D A; and Grant, R (2012). The stability of infectious salmon anaemia virus infectivity at -80 C in tissue homogenate and dry-stored tissue from clinically diseased Atlantic salmon, Salmo salar L. Journal of Fish Diseases 35:789-792.
Smith, J M; Macleod, C D; Valavanis, V; Hastie, L C; Valinassab, T; Bailey, N and Pierce, G J (2013). Habitat and distribution of post-recruit life stages of the squid Loligo forbesii. Deep-Sea Research II, 95: 145-159.
Soares, S; Murray, A G; Crumlish, M; Turnbull, J F and Green, D M (2012). Evaluating abnormal mortality as an indicator of disease presence in the Atlantic salmon industry using the receiver operating characteristic (ROC). Aquaculture 370-371:136-143.
Soares, S; Murray, A G; Crumlish, M; Turnbull, J F and Green, D M (2013). Factors affecting variation in mortality of marine Atlantic salmon Salmo salar in Scotland. Diseases of Aquatic Organisms 103:101-109.
Soulsby, C; Grant, J; Gibbins, C and Malcolm, I A (2012). Spatial and temporal variability of Atlantic salmon (Salmo salar L.) spawning activity in braided river channels: a preliminary assessment. Aquatic Sciences 74 (3):571-586.
Todd, C D; Friedland, K D; Maclean, J C; Whyte, B D; Russell, I C; Lonergan, M E and Morrissey, M B (2012). Phenological and phenotypic changes in Atlantic salmon populations in response to a changing climate. ICES Journal of Marine Science 69 (9):1686 - 1698.
Vasilakopoulos, P; O'Neill, F G and Marshall, C T (2012). Differential impacts of exploitation rate and juvenile exploitation on NE Atlantic fish stock dynamics over the past half century. Fisheries Research 134:21-28.
Verspoor, E; Consuegra, S; Fridjonsson, O; Hjorleifsdottir, S; Knox, D; Olafsson, K; Tompsett, S; Wennevik, V and Garcia de Leaniz, C (2012). Regional mtDNA SNP differentiation in European Atlantic salmon (Salmo salar): an assessment of potential utility for determination of natal origin. ICES Journal of Marine Science 69 (9):1625 - 1636.
Wright, P J and Tobin, D (2013). Maturation differences between sub-stocks of haddock, Melanogrammus aeglefinus. Marine Biology 160 (1):231-239.
Zettler, M L; Proffitt, C E; Darr, A; Degraer, S; Devriese, L; Greathead, C; Kotta, J; Magni, P; Martin, G; Reiss, H; Speybroeck, J; Tagliapietra, D; Van Hoey, G and Ysebaert, T (2013). On the myths of indicator species. PLoS One.