Assessing the interactions and effects of sea lice on wild salmon populations: final report of project FW0050

Published Project Outputs

During FW0050 and associated work a number of published outputs were created. These include peer review publications, conference presentations, book chapters, reports and web pages. A list of publications in which the MD’s staff contributed through their work in FW0050 follows.

Peer Reviewed Papers

Boerlage, A.S., Shrestha, S., Leinonen, I., Jansen, M.D., Revie, C.W., Reeves, A. and Toma, L., 2024. Sea lice management measures for farmed Atlantic salmon (Salmo salar) in Scotland: costs and effectiveness. Aquaculture, 580, p.740274

Garnier, S., Moriarty, M., Murray, R.O.H., Gallego, A. and Murray, A.G., 2024. Modelling assessment of how small-scale vertical movements of infectious sea lice larvae can affect their large-scale distribution in fjordic systems. Ecological Modelling, 488, p.110587.

Garnier S., O’Hara Murray R., Gillibrand P., Gallego A., Robins and Moriarty M., 2025. Particle tracking modelling in coastal marine environments: recommended practices and performance limitations. Ecological Modelling 501 110999 (joint special issue on good modelling practice)

Gimpel, A., Stelzenmüller, V., Töpsch, S., Galparsoro, I., Gubbins, M., Miller, D., Murillas, A., Murray, A.G., Pınarbaşı, K., Roca, G. and Watret, R., 2018. A GIS-based tool for an integrated assessment of spatial planning trade-offs with aquaculture. Science of the Total Environment, 627, pp.1644-1655.

Hall, L.M. and Murray, A.G., 2018. Describing temporal change in adult female Lepeophtheirus salmonis abundance on Scottish farmed Atlantic salmon at the national and regional levels. Aquaculture, 489, pp.148-153.

Harte, A.J., Bowman, A.S., Salama, N.K. and Pert, C.C., 2017. Factors influencing the long-term dynamics of larval sea lice density at east and west coast locations in Scotland. Diseases of Aquatic Organisms, 123(3), pp.181-192.

Ives, S.C., Armstrong, J.D., Collins, C., Moriarty, M. and Murray, A.G., 2023. Salmon lice loads on Atlantic salmon smolts associated with reduced welfare and increased population mortalities. Aquaculture Environment Interactions, 15, pp.73-83.

Ives, S.C., Murray, A.G. and Armstrong, J.D., 2024. Association of ectoparasite Lepeophtheirus salmonis counts on farmed Atlantic salmon and wild sea trout in Scotland. Diseases of Aquatic Organisms, 157, pp. 95-106.

Moriarty, M., Ives, S.C., Murphy, J.M. and Murray, A.G., 2023. Modelling parasite impacts of aquaculture on wild fish: The case of the salmon louse (Lepeophtheirus salmonis) on out-migrating wild Atlantic salmon (Salmo salar) smolt. Preventive Veterinary Medicine, 214, p.105888.

Moriarty, M., Murphy, J.M., Brooker, A.J., Waites, W., Revie, C.W., Adams, T.P., Lewis, M., Reinardy, H.C., Phelan, J.P., Coyle, J.P. and Rabe, B., 2024. A gap analysis on modelling of sea lice infection pressure from salmonid farms. I. A structured knowledge review. Aquaculture Environment Interactions, 16, pp.1-25.

Morris, D.J., Fryer, R.J., Raffell, J.A., Middlemas, S.J., Godfrey, J.D. and Armstrong, J.D. 2026. A twenty-year study examining the effects of salmon lice on the return rate, time at sea and marine growth of sea trout migrating from the river Shieldaig in Scotland. ICES Journal of Marine Science, 83(1), fsag001.

Murphy, J.M., Moriarty, M., Brooker, A.J., Waites, W., Revie, C.W., Adams, T.P., Lewis, M., Reinardy, H.C., Phelan, J.P., Coyle, J.P. and Rabe, B., 2024. A gap analysis on modelling of sea lice infection pressure from salmonid farms. II. Identifying and ranking knowledge gaps: output of an international workshop. Aquaculture Environment Interactions, 16, pp.27-42.

Murray, A.G., 2016a. Increased frequency and changed methods in the treatment of sea lice (Lepeophtheirus salmonis) in Scottish salmon farms 2005–2011. Pest management science, 72(2), pp.322-326.

Murray, A.G., 2016b. A note on sea lice abundance on farmed Atlantic salmon in Scotland 2011–2013: significant regional and seasonal variation. Aquaculture Research, 47(3), pp.961-968.

Murray, A.G., 2016c. A modelling framework for assessing the risk of emerging diseases associated with the use of cleaner fish to control parasitic sea lice on salmon farms. Transboundary and emerging diseases, 63(2), pp.e270-e277.

Murray, A.G. and Salama, N.K., 2016. A simple model of the role of area management in the control of sea lice. Ecological Modelling, 337, pp.39-47.

Murray, A.G. and Gubbins, M., 2016. Spatial management measures for disease mitigation as practiced in Scottish aquaculture. Marine Policy, 70, pp.93-100.

Murray, A.G., 2017. A model of the process of spillover and adaption leading to potential emergence of disease in salmon held with cleaner fish used to control lice. Aquaculture, 473, pp.283-290.

Murray, A.G. and Salama, N.K.G., 2017. Modelling disease in aquatic systems that are spread by processes operating at different temporal and spatial scales: examples from salmon aquaculture. CABI Reviews, (2017), pp.1-11.

Murray, A.G. and Moriarty, M., 2021. A simple modelling tool for assessing interaction with host and local infestation of sea lice from salmonid farms on wild salmonids based on processes operating at multiple scales in space and time. Ecological Modelling, 443, p.109459.

Murray, A.G., Ives, S.C., Smith, R.J. and Moriarty, M., 2021. A preliminary assessment of indirect impacts on aquaculture species health and welfare in Scotland during COVID-19 lockdown. Veterinary and Animal Science, 11, p.100167.

Murray A.G., Asplin L., á Norði G., Erenbjerg S., Gallego A., Ives S.C., King E., Kragesteen T., Murphy J.M., Rabe B., Sandvik A.D., Skardhamar J., Moriarty M. 2025. “Knowledge Strength”: maximising the reliability of evidence derived from environmental modelling in the face of uncertainty – the case of the salmon louse (Lepeophtheirus salmonis). Socio-Environmental Systems Modelling 7, 18750

Ounsley, J.P., Gallego, A., Morris, D.J. and Armstrong, J.D., 2020. Regional variation in directed swimming by Atlantic salmon smolts leaving Scottish waters for their oceanic feeding grounds—a modelling study. ICES Journal of Marine Science, 77(1), pp. 315-325.

Pert, C.C., Wallace, I.S., MacDonald, P., Ives, S.C., Murray, A.G. and Rabe, B., 2023. Infestation rates of lice Lepeophtheirus salmonis and Caligus elongatus on Atlantic salmon in fixed and towed sentinel cages. Diseases of Aquatic Organisms, 155, pp.165-174.

Rabe, B., Gallego, A., Wolf, J., Murray, R.O.H., Stuiver, C., Price, D. and Johnson, H., 2020. Applied connectivity modelling at local to regional scale: the potential for sea lice transmission between Scottish finfish aquaculture management areas. Estuarine, Coastal and Shelf Science, 238, p.106716.

Rabe B., Murray, A.G., Ives S.C., Moriarty M., Morris D.J. 2024. Searching for sea lice: a review of surveillance to assess environmental infection pressures for modelling and informing sea lice infestation management. Aquaculture Environment Interactions 16, 241-262.

Rodgers J.R., Lilly, J., Honkanen H.M., del Villar D., Kennedy R., Maoiléidigh N.Ó., et al. 2025. Inshore and offshore marine migration pathways of Atlantic salmon post-smolts from multiple rivers in Scotland, England, Northern Ireland and Ireland. Journal of Fish Biology, 106, 1422-1439.

Salama, N.K.G., Murray, A.G. and Rabe, B., 2016. Simulated environmental transport distances of Lepeophtheirus salmonis in Loch Linnhe, Scotland, for informing aquaculture area management structures. Journal of Fish Diseases, 39(4), pp. 419-428.

Salama, N.K.G., Dale, A.C., Ivanov, V.V., Cook, P.F., Pert, C.C., Collins, C.M. and Rabe, B., 2018. Using biological–physical modelling for informing sea lice dispersal in Loch Linnhe, Scotland. Journal of Fish Diseases, 41(6), pp.901-919.

Susdorf, R., Salama, N.K., Todd, C.D., Hillman, R.J., Elsmere, P. and Lusseau, D., 2018. Context-dependent reduction in somatic condition of wild Atlantic salmon infested with sea lice. Marine Ecology Progress Series, 606, pp.91-104.

Susdorf, R., Salama, N.K. and Lusseau, D., 2018. Influence of body condition on the population dynamics of Atlantic salmon with consideration of the potential impact of sea lice. Journal of Fish Diseases, 41(6), pp.941-951.

Waites, W., Gillibrand, P., Adams, T., Bell, R., Guthrie, D., Kragesteen, T., Revie, C. and Moriarty, M., 2024. Infection Pressure on Fish in Cages. arXiv preprint arXiv:2411.05502.

Book Chapters

Armstrong J.D., Branding, A., Main, R., Mitchell, A., Morris, D.J. and Ounsley J. 2019. Science for crafting policy: tracking smolts and post-smolts. Atlantic Salmon Trust Blue book. The SAMARCH project international salmonid coastal and marine telemetry workshop held in Southampton (pp 81-84)

Morris, D.J., Godfrey, J., Gauld, N., Raffell, J. and Armstrong J.D. 2019. Acoustic tracking of sea trout and salmon smolts using a grid arrangement of acoustic receivers in a Scottish sea loch system. Atlantic Salmon Trust Blue book. The SAMARCH project international salmonid coastal and marine telemetry workshop held in Southampton (pp 32-34)

Murray, A.G., Shephard, S., Asplin, L., Adams, T., Ådlandsvik, B., Gallego, A., Hartnett, M., Askeland, I., Pert, C.C., Rabe, B. and Gargan, P.G., 2022. A standardised generic framework of sea lice model components for application in coupled hydrodynamic-particle models. In Sea Lice Biology and Control. 5M Books (pp. 167-187). Chapter 9 (PDF, 1.5Mb)

Pert C.C., Harte A., Kent A.J., Dwyer T. and Llewellyn M. 2022. Sea lice – active monitoring methods for sea lice in the marine environment. In Sea Lice Biology and Control. 5M Books (pp. 394-417)

Trade Journals

Salama, N.K.G., 2016. Salmon Lice Dispersal in the Marine Environment. Fish Farmer.

Rabe, B., Gallego, A., Wolf, J. and Salama, N.K.G., 2016. Interpretation of connectivity patterns amongst farm management areas in Scotland. Fish Farmer

Reports

MASTS 2017 Coupling of hydrodynamic and particle models for simulating larval sea lice dispersal workshop report Final report (PDF, 224Kb)

Morris DJ, Raynard RS, Armstrong JD, Collins C. 2018. SARFSP010 Piloting a network for determining spatial and temporal variation in marine survival of Atlantic salmon and effects of anti-sea lice agents. A study commissioned by the Scottish Aquaculture research forum (SARF).

Morris DJ, Gauld NR, Raynard R, Armstrong JD. 2019. A Pilot Study To Determine The Effect Of An Anti-Sea Lice Agent On The Marine Survival Of Atlantic Salmon On The West Coast Of Scotland. Scottish Marine and Freshwater Science Vol 10 No 5, 15pp. Final report (PDF, 1.0Mb)

Rabe, B. and Gallego, A. 2020. Interpretation of sea lice connectivity patterns among Scottish Farm Management Areas. Scottish Marine and Freshwater Science. Final report (PDF, 1.5Mb)

Thesis

Wawer A. 2024. Immunogenomic status of salmonids in Scotland. PhD University of Aberdeen. 203pp

Phelan J. 2025. Dynamic Spatial Forecasting of Sea Lice Abundances. PhD University of Highlands and Islands. 219pp

Conference presentations

Armstrong J.D., Branding, A., Main, R., Mitchell, A., Morris, D.J. and Ounsley J. (2019). Science for crafting policy: tracking smolts and post-smolts. The SAMARCH project international salmonid coastal and marine telemetry workshop held in Southampton.

Gauld, N., Morris, D.J., Armstrong, J.D. (2017). The utility of acoustic telemetry to investigate the initial marine migration of salmon on the west coast of Scotland. From headwater to headland: Improving smolt survival in rivers and estuaries. Atlantic Salmon Trust. Berwick upon Tweed.

Ives S.C., Armstrong J.D., Collins C., Moriarty M., Murray A.G. (2022) Critical lice loadings to protect wild Atlantic salmon smolts. p76 13th Sea Lice Conference International Faroe Islands 9-13th May 2022

Ives S.C., Murphy J.M., Murray A.G. (2023) Risk factors for increased levels of sea lice during marine production cycles in Scotland. P89, 21^st EAFP Conference September 2023, Aberdeen

Moriarty M., Murray A., Rabe B. (2019) Evaluation of multiple coupled physical-biological models in Loch Linnhe. Presentation at Challenger Society for Marine Science Ocean Modelling Special Interest Group Meeting 9-10th September, University of Edinburgh

Moriarty M., Murray A., Rabe B. (2020) Evaluation of multiple coupled physical-biological models in Loch Linnhe. Presentation at MAST Seminar Series 29th April 2020.

Morris, D.J., Godfrey, J., Gauld, N., Raffell, J. and Armstrong J.D. (2019) Acoustic tracking of sea trout and salmon smolts using a grid arrangement of acoustic receivers in a Scottish sea loch system. The SAMARCH project international salmonid coastal and marine telemetry workshop held in Southampton.

Murray A.G., Ives S.C., Murphy J., Moriarty M. (2022) Modelling parasite driven impacts of parasites on wild fish: The case of the salmon louse (Lepeophtheirus salmonis). p103-114 in K.A Robinson and K.M. McIntyre (eds) Proceedings of the Society for Veterinary Epidemiology and Preventive Medicine annual meeting held in Belfast, March 2022

Murray A.G., Ives S.C., Murphy J., Moriarty M. (2022) Developing a framework for assessing spatial and temporal variability in parasite density in Scottish waters – implications for wild smolt migration. p37 13th Sea Lice Conference International Faroe Islands 9-13th May 2022

Murray A.G., Ives S.C., Moriarty M. (2023) Three lice population density variables that inform management of salmon lice impacts on wild salmonids. P91. 21^st EAFP Conference September 2023, Aberdeen

Murray A.G., Ives S., Moriarty M. and Murphy J. (2024) Optimizing policy advice from salmon lice dispersal models: the “Knowledge Strength” approach. MASTS Conference November, Glasgow

Moriarty M. (2022) Towards ensemble models for predicting sea lice distributions: Evaluation of multiple coupled biophysical models in Loch Linnhe, Scotland. p39 13th Sea Lice Conference International Faroe Islands 9-13th May 2022

Moriarty M (2022) (Marine Scotland Science) Salmon Parasite Interactions in Linnhe, Lorn, and Shuna: Sea lice dispersal model evaluation using an ensemble approach. MASTS Glasgow November 2022

Moriarty M. (2023) Ensemble models under uncertainty p90 21^st EAFP Conference September 2023, Aberdeen

Moriarty M, Gillibrand P.A., Adams T.P., Brain S., Szewczyk T. and Waites W (2024) Ensemble Modelling and Uncertainty in Sea Lice Dispersal Patterns. MASTS Conference November, Glasgow

Pert, C.C., Rabe, B., Dunn, J., Salama, N.K.G. and Collins, C.M., 2017, June. Developing a method to investigate infestation pressure from sea lice on migratory salmonids utilising towed & static sentinel cages. In OCEANS 2017-Aberdeen (pp. 1-8). IEEE.

Phelan J.P., Burrows, M.T., Davidson K., Murray A.G., Gillibrand P.A., Adams T. (2022) Combining population models and larval dispersal – a tool for sea lice management p41 13th Sea Lice Conference International Faroe Islands 9-13th May 2022

Phelan J.P., Burrows, M.T., Davidson K., Murray A.G., Gillibrand P.A., Adams T. (2022) Combining population models and larval dispersal – a tool for sea lice management. ICES ASC 2022, Dublin

Rabe B., Murray A.G., Ives S.C., Moriarty M. (2022) Surveillance of sea lice – assessing environmental infection pressures. p85 13th Sea Lice Conference International Faroe Islands 9-13th May

Rabe B., Murray A., Ives S., Moriarty M., Morris D. (2024) Searching for sea lice: Surveillance to assess environmental infection pressures for modelling and sea lice infestation management gaps. Challenger 2024 Conference Oban September

Salama, N., Rabe, B., Pert, C., Murray, S., Gallego, A., Fraser, J., Wallace, S., Dunn, J., Hindson, J., Harte, A. and Collins, C. (2015). Determining sea lice distributions in the marine environment. In MASTS Annual Science Meeting, Sustainable Aquaculture Workshop, Technology & Innovation Centre, Glasgow, 30 September-2 October 2015.

Waites W, Moriarty M (2024) The SAVED Project. Salmon Scotland Science Meeting, Oban

Waites, W., Gillibrand. P., Adams T., Guthrie D., Kragesteen, T., Revie C., Moriarty M. (2024) Infection Pressure on Fish in Cages. MASTS Conference November, Glasgow

Conference posters

Lipschutz D., O'Hare A., Sturm A., Murray A.G., Enright J. (2019) Impact of treatment threshold and co-operation on the evolution of resistance in sea lice L. salmonis. Epidemics Conference, Charleston, SC Poster

Morris D.J., Collins C., Armstrong J., Raynard R. 2016 Overview of Scottish Government Project on the Interactions and Effects of Sea Lice on Wild Salmon. P93 11^th International Sea Lice Conference, Westport Ireland

Murray A .2016 Analysis of sea lice using data collected for management and regulatory purposes p126 11^th International Sea Lice Conference, Westport Ireland

Murray A., Salama N. 2016 using dispersal modelling connectivity outputs to produce a meta-population model of salmon lice in Loch Linnhe. P143 11^th International Sea Lice Conference, Westport Ireland

Murray A.G. 2018 Cleaner fish used to control parasites in aquaculture: identifying and controlling a new host-shift route for disease emergence. Poster as Ecology & Evolution of Infectious Diseases Conference Glasgow University

Rabe B., Gallego A, Wolf J, Salama N, Murray A 2016 Interpretation of connectivity patterns among farm management areas in Scotland p116 11^th International Sea Lice Conference, Westport Ireland