National Electrofishing Programme for Scotland (NEPS) 2023: status of juvenile Atlantic salmon and brown trout populations
The National Electrofishing Programme for Scotland (NEPS) is a statistical survey of freshwater fish populations and the pressures affecting them in Scotland, particularly water quality and genetic introgression. This report presents the latest analysis including data from 2023.
References
Adams, C. E., H. M. Honkanen, E. Bryson, I. E. Moore, M. MacCormick, J. A. Dodd. (2022) A Comparison of Trends in Population Size and Life History Features of Atlantic Salmon (Salmo salar) and Anadromous and Non-Anadromous Brown Trout (Salmo trutta) in a Single Catchment Over 116 Years. Hydrobiologia 849: 1–21.
Alexandre, C.M., Berry, M., Magnusson K., Silva, S., Louhi P., Walker, A., Höjesjö, J., Malcolm I.A., (2024) Spatial Variability in Juvenile Sea Trout Data Collection and Assessment Methods Across Europe: Limitations and Opportunities for Standardising Analyses. Aquatic Conservation: Marine and Freshwater Ecosystems, 2025; 35:e70040 DOI: 10.1002/aqc.70040
Almeida, P.R., Mateus, C.S., Alexandre, C.M. Pedro, S., Boavida-Portugal J., Belo A.F., Pereira E., Silva S., Oliveira I., Quintella B.R. (2023) The decline of the ecosystem services generated by anadromous fish in the Iberian Peninsula. Hydrobiologia 850, 2927–2961. DOI: 10.1007/s10750-023-05179-6
Anon (2024) Implementation of UK Eel Management Plans (2020–2023) UK Department for Environment, Food and Rural Affairs. Progress Report.
Avgar, T., Betini, G.S., Fryxell, J.M. (2020) Habitat selection patterns are density dependent under the ideal free distribution. The Journal of Animal Ecology, 89, 2777–2787.
Burnett, K.M., Reeves, G.H., Miller, D.J., Clarke, S., Vance-Borland, K., Christiansen, K., 2007. Distribution of salmon-habitat potential relative to landscape characteristics and implications for conservation. Ecol. Appl. 17, 66–80.
Briand, C., Mateo, M., Drouineau, H., Korta, M., Diaz, E., Beaulaton, L. (2022) Eel Density Analysis (EDA 2.3) Escapement of Silver Eels (Anguilla anguilla) from French, Spanish and Portuguese Rivers. Technical Report (last accessed 07 April 2025).
Carver, S., Comber A., McMorran, R., Nutter, S., (2012) A GIS model for mapping spatial patterns and distribution of wild land in Scotland. Landscape and Urban Planning 104 (3–4) 15, 395-409. DOI: 10.1016/j.landurbplan.2011.11.016
Cauwelier, E., Gilbey, J., Mollahan, P., Sampayo, J. and Morris, D.J. (2024). Exploring the potential for genetic stock identification of Atlantic salmon from the large Scottish East Coast Rivers. Scottish Marine and Freshwater Science. ISBN 9781836013297
Cauwelier, E., Gilbey, J., Sampayo, J., Stradmeyer, L.E., Middlemas. S.J., (2018) Identification of a single genomic region associated with seasonal river return timing in adult Scottish Atlantic salmon (Salmo salar), using a genome-wide association study. Canadian Journal of Fisheries and Aquatic Sciences. 75(9): 1427-1435. DOI: 10.1139/cjfas-2017-0293
Cauwelier, E., Gilbey, J., Sampayo, J. Middlemas S.J. (2024a). Development of a genetic tool to determine run timing proportions in Scottish Atlantic salmon populations. Scottish Marine and Freshwater Science 15 (1) 15p. DOI: 10.7489/12518-1.
Cauwelier, E., MacDonald, A., Henry, J., Stewart, D., Stradmeyer, L. Wallace, S. and Middlemas, S.J. (2024b). Mapping the early running component of juvenile Atlantic salmon populations. Scottish Marine and Freshwater Science 15(2) 21p. DOI: 10.7489/12519-1
Chaput., (2012) Overview of the status of Atlantic salmon (Salmo salar) in the North Atlantic and trends in marine mortality. ICES Journal of Marine Science. 69, 9, 1538-1548.
Chaput. G., Prévost. E., Dempson, J.B., Dionne. M., Jones, R., Levy, A., Robertson, M., Veinott G. (2015) Hierarchical Bayesian modelling of Atlantic Salmon egg to smolt time series from monitored rivers of eastern Canada to define and transport reference points. DFO Can. Sci. Advis. Sec. Res. Doc. 2015/075. v + 84 p.
Dauphin, G.J.R., Chaput, G., Breau, C., Cunjak, R.A. (2019). Hierarchical model detects decadal changes in calibration relationships of single-pass electrofishing indices of abundance of Atlantic Salmon in two large Canadian catchments. Canadian Journal of Fisheries and Aquatic Sciences, 76, 523–542.
Dębowski, P. (2018) The Largest Baltic Population of Sea Trout (Salmo trutta L.): Its Decline, Restoration Attempts, and Current Status. Fisheries & Aquatic Life 26, no. 2: 81–100.
Douglas, S., Underhill, K., Horsman, M., Chaput. G. (2023) Information on Atlantic Salmon (Salmon salar) from Salmon fishing area 16 (Gulf New Brunswick) of relevance to the development of a 2nd COSEWIC report. DFO Can. Sci. Advis. Sec. Res. Doc. 2023/033. v + 75 p.
Dumelle M., Kincaid T., Olsen A.R., Weber M., (2023) spsurvey: Spatial Sampling Design and Analysis in R. Journal of Statistical Software, 105(3), 1-29. DOI:10.18637/jss.v105.i03
Firman, J.C., Steel, E.A., Jensen, D.W., Burnett, K.M., Christiansen, K., Feist, B.E., Larsen, D.P., and Anlauf, K.J. 2011. Landscape models of adult coho salmon density examined at four spatial extents. Trans. Am. Fish. Soc. 140(2): 440-455. DOI:10.1080/ 00028487.2011.567854.
Fiske, P., Forseth, T., Thorstad, E.B., Bakkestuen, V., Einum, S., Falkegård, M. et al. (2024). Novel large-scale mapping highlights poor state of sea trout populations. Aquatic Conservation: Marine and Freshwater Ecosystems, 34(1), e4067. DOI: 10.1002/aqc.4067
Free, G., Poikane, S., Lyche Solheim, A., Bussettini, M. Bradley C., Smith, J.,Rossana Caroni, R,.Bresciani, M.,Pinardi M., Giardino C., van de Bund a. W (2024) Climate change and ecological assessment in Europe under the WFD – Hitting moving targets with shifting baselines? Journal of Environmental Management Volume 370, 122884
Forseth T., Barlaup, B.T., Finstad, B., Fiske, P., Gjøsæter, H., Falkegård, M., Hindar, A., Mo A.T., Rikardsen, A.H., Thorstad, E.B., Vøllestad, L.A., Wennevik, V. (2017) The major threats to Atlantic salmon in Norway, ICES Journal of Marine Science, 74, 6, Pages 1496–1513, DOI:10.1093/icesjms/fsx020
Gaston, K.J., Blackburn, T.M., Greenwood, J.J.D., Gregory, R.D., Quinn, R.M. and Lawton, J.H. (2000), Abundance–occupancy relationships. Journal of Applied Ecology, 37: 39-59. DOI: 10.1046/j.1365-2664.2000.00485.x
Gilbey, J. et al. (in prep) Integration of a novel statistical survey design and juvenile sampling by electrofishing to assess regional variability in farm to wild introgression in Scotland’s wild Atlantic salmon populations.
Gilbey J, Sampayo J, Cauwelier E, Malcolm I.A., Millidine K.J., Jackson F.L., Morris D.J. (2021) A national assessment of the influence of farmed salmon escapes on the genetic integrity of wild Scottish Atlantic salmon populations. Scottish Marine and Freshwater Science Vol 12 No 12. Crown Copyright, DOI: 10.7489/12386-1
Gilbey, J., Sampayo, J., Cauwelier, E., Malcolm, I., Millidine, K., Jackson, F., Morris.D. (2021) A national assessment of the influence of farmed salmon escapes on the genetic integrity of wild Scottish Atlantic salmon populations. Scottish Marine and Freshwater Science 12 (12) 70pp. DOI: 10.7489/12386-1
Gibson, A.J.F., Bowlby, H.D., Amiro, P.G., (2008) Are wild populations ideally distributed? Variations in density-dependent habitat use by age class in juvenile Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 65(8) DOI: 10.1139/F08-087
Glover R.S., Fryer R.J., Soulsby C., Malcolm I.A. (2019) These are not the trends you are looking for: poorly calibrated single-pass electrofishing data can bias estimates of trends in fish abundance. J Fish Biol. 95: 1223–1235. DOI: 10.1111/jfb.14119
Glover R.S., Soulsby C., Fryer R.J., Birkel C., Malcolm I.A. (2020) Quantifying the relative importance of stock level, river temperature and discharge on the abundance of juvenile Atlantic salmon (Salmo salar). Ecohydrology. 13:e2231. DOI: 10.1002/eco.2231
Goodwin, J.C.A., Andrew King, R., Iwan Jones, J., Ibbotson, A. and Stevens, J.R. (2016), A small number of anadromous females drive reproduction in a brown trout (Salmo trutta) population in an English chalk stream. Freshw Biol, 61: 1075-1089. DOI: 10.1111/fwb.12768
Gregory, S.D., Gillson, J.P., Whitlock, K., Barry, J., Gough, P., Hillman, R.J., Mee, D., Peirson, G., Shields, B.A., Talks, L., Toms, S., Walker, A.M., Wilson, B., Davidson, I. (2023) Estimation of returning Atlantic salmon stock from rod exploitation rate for principal salmon rivers in England & Wales, ICES Journal of Marine Science, Volume 80, Issue 10, 2504–2519, DOI: 10.1093/icesjms/fsad161
Gurney W.S.C, Bacon P.J., Tyldesley G, Youngson A.F. (2008) Process-based modelling of decadal trends in growth, survival, and smolting of wild salmon (Salmo salar) parr in a Scottish upland stream. Can. J. Fish. Aquat. Sci. 65: 2606–2622
Gurney W.S.C, Bacon P.J., Malcolm I.A., MacLean J.C., Youngson A., (2015) The demography of a phenotypically mixed Atlantic salmon (Salmo salar) population as discerned for an eastern Scottish river. Scottish Marine and Freshwater Science Vol 6 No 12. pp 72. DOI: 10.7489/1662-1
Gurney, W.S.C. Bacon P.J., McKenzie, E.M., McGinnity P., Mclean, J., Smith, G., Youngson. A., (2010) Form and uncertainty in stock–recruitment relations: observations and implications for Atlantic salmon (Salmo salar) management. Canadian Journal of Fisheries and Aquatic Sciences. 67(6): 1040-1055. DOI: 10.1139/F10-038
HELCOM (2023) Abundance of sea trout spawners and parr. HELCOM core indicator report. ISSN 2343-254 Date Accessed 25/02/2025
Höhne, L., Freese, M., Pohlmann, J.D., Diekmann, M., Fladung, E., Huisman, J.B.J., Hanel, R., Marohn, L., (2023) Overestimating management progress—modelled vs. monitored silver eel escapement in a North Sea draining river, ICES Journal of Marine Science, 80(7) 1936-1948, DOI: 10.1093/icesjms/fsad122
ICES (2024a). Working Group on North Atlantic Salmon (WGNAS). ICES Scientific Reports. DOI: 10.17895/ices.pub.25730247.v1
ICES. (2024b) Baltic Salmon and Trout Assessment Working Group (WGBAST). ICES Scientific Reports. 6:42. 425 pp. DOI: 10.17895/ices.pub.25868665
Isaak, D.J., Ver Hoef, J.M., Peterson, E.E., Horan, D.L., Nagel, D.E. (2017) Scalable population estimates using spatial-stream-network (SSN) models, fish density surveys, and national geospatial database frameworks for streams. Canadian Journal of Fisheries and Aquatic Sciences. 74: 147–156 (2017) DOI: 10.1139/cjfas-2016-0247
Jutila, E., A. Saura, I. Kallio-Nyberg, A. Huhmarniemi, and A. Romakkaniemi. (2006) The Status and Exploitation of Sea Trout on the Finnish Coast of the Gulf of Bothnia in the Baltic Sea. In Sea Trout: Biology, Conservation and Management, edited by G. Harris and N. Milner, 520. New Jersey: Wiley-Blackwell
Kuikka, S., Vanhatalo, J., Pulkkinen, H., Mäntyniemi, s., Corander, J. (2014) Experiences in Bayesian Inference in Baltic Salmon Management. Statistical Science, 29, 1, pp. 42–49
Limburg, K.E., Waldman., J.R. (2009) Dramatic declines in North Atlantic diadromous fishes. BioScience. DOI: 10.1525/bio.2009.59.11.7
McCall, A. 1990. Dynamic geography of marine fish populations. University of Washington Press, Seattle, 153p.
Malcolm, I.A. et al. (in prep) Development of an assessment benchmark for juvenile brown trout (Salmo trutta) using juvenile electrofishing data.
Malcolm I.A., Jackson F.L., Millidine K.J., Bacon P.J., McCartney A.G, Fryer R.J. (2023). The National Electrofishing Programme for Scotland (NEPS) 2021. Scottish Marine and Freshwater Science Reports Vol 14, No 2, pp. 63 DOI: 10.7489/12435-1
Malcolm I.A., Millidine K.J., Glover R.S., Jackson F.L., Millar C.P., Fryer R.J. (2019a) Development of a large-scale juvenile density model to inform the assessment and management of Atlantic salmon (Salmo salar) populations in Scotland. Ecological Indicators 96: 303–316 DOI: 10.1016/J.ECOLIND.2018.09.005
Malcolm I.A., Millidine K.J, Jackson F.L, Glover R.S Fryer R.J. (2020). The National Electrofishing Programme for Scotland (NEPS) 2019. Scottish Marine and Freshwater Science Vol 11 No 9, 56pp. DOI: 10.7489/12321-1
Malcolm, I.A. Millidine, K.J. Jackson, F.L. Glover, R.S. and Fryer, R.J. (2019b) Assessing the status of Atlantic salmon (Salmo salar) from juvenile electrofishing data collected under the National Electrofishing Programme for Scotland (NEPS). Scottish Marine and Freshwater Science Vol. 10 No. 2.
Marine Directorate (2024) Scottish salmon and sea trout fishery statistics 2023. Official Statistics. ISBN 9781836012009 Date Accessed 06/12/2024
Marine Scotland and Fisheries Management Scotland (2023). Regional and national assessment of the pressures acting on Atlantic salmon in Scotland, 2021. Scottish Marine and Freshwater Science Vol 14 No 4, 22p. DOI:10.7489/12447
Millar C.P., Fryer R.J., Millidine K.J., Malcolm I.A., (2016) Modelling capture probability of Atlantic salmon (Salmo salar) from a diverse national electrofishing dataset: Implications for the estimation of abundance. Fisheries Research. 177, 1–12.
Mota, M., E. Rochard, and C. Antunes. (2016) Status of the Diadromous Fish of the Iberian Peninsula: Past, Present and Trends. Limnetica 35, no. 1: 1–18.
Nunn, A.D., Ainsworth A.F., Qu, Y., Keller, V.D.J. Bachiller-Jareno N., Antoniou, V., Eastman, M., Rizzo, C., Peirson, G., Eley, F., Johnson, A.C., Cowx, I.G. (2025) Responses of fish to nationwide improvements in the water quality of a densely populated and heavily modified country over four decades. Water Research. 274, 123163. DOI: 10.1016/j.watres.2025.123163
R Core Team, (2023) R: A language and environment for statistical computing. R Foundation for Statistical Computing, (Versions R version 4.3.1 and 4.2.0)
Reuchlin-Hugenholtz E., Shackell N.L., Hutchings J.A., (2015) The potential for spatial distributin indices to signal thresholds in marine fish biomass. PLoS ONE 10(3) DOI:10.137/journal.pone.0120500
Rivers and Fisheries Trusts of Scotland. 2014. Data Supporting Site Condition Monitoring of Atlantic salmon SACs. Scottish Natural Heritage Commissioned Report No. 755.
Rohtla M, Matetski L, Svirgsden R, et al. Do sea trout Salmo trutta parr surveys monitor the densities of anadromous or resident maternal origin parr, or both? Fish Manag Ecol. 2017; 24: 156–162. DOI:10.1111/fme.12214
Schmutz, S., Cowx, I.G., Haidvogl, G. Pont, D. (2007), Fish-based methods for assessing European running waters: a synthesis. Fisheries Management and Ecology, 14: 369-380. DOI:10.1111/j.1365-2400.2007.00585.x
Scottish Government (2023) Scottish wild salmon strategy: implementation plan 2023 to 2028 Date Accessed 06/12/2024
Scottish Government (2022) Scottish wild salmon strategy Date Accessed 06/12/2024
Scottish Government (2021) Salmon Interactions Working Group Report: Scottish Government Response. Date Accessed 06/12/2024
Soulsby, C., Malcolm, I. A., & Tetzlaff, D. (2024). JAMES BUTTLE REVIEW: Six decades of ecohydrological research connecting landscapes and riverscapes in the Girnock Burn, Scotland: Atlantic salmon population and habitat dynamics in a changing world. Hydrological Processes, 38(3), e15105. DOI:10.1002/hyp.15105
Strus, I. Carver S., (2024) Developing a Wilderness Quality Index for Continental Europe. Land 13(4), 428; DOI:10.3390/land13040428
Thin, A., Hope J., Francis M. (2014) Report of the Wild Fisheries Review Panel, October 2014
Thorley, J.L., Eatherley, D.M.R., Stephen, A.B., Simpson, I., MacLean, J.C., Youngson, A.F., (2005) Congruence between automatic fish counter data and rod catches of Atlantic salmon (Salmo salar) in Scottish rivers, ICES Journal of Marine Science, 62(4), 808–817, DOI:10.1016/j.icesjms.2005.01.016
Thorson, J.T. Rindof A., Gao J, Hanselman D.D., Winker H., (2016) Density-dependent changes in effective are occupied for sea-bottom-associated marine fishes. Proceedings Royal Society B., 283: 20161853
Thorstad, E.B., Bliss, D., Breau, C., Damon-Randall, K., Sundt-Hansen, L.E., Hatfield, E.M.C., Horsburgh, G., Hansen, H., Maoiléidigh, N.Ó., Sheehan, T., Sutton, S.G., (2021) Atlantic salmon in a rapidly changing environment—Facing the challenges of reduced marine survival and climate change. Aquatic Conservation: Marine and Freshwater Ecosystems, 31(9), 2654–2665. DOI:10.1002/aqc.3624
Van Leeuwen, T.E., Lehnert, S.J., Breau, C., Fitzsimmons, M., Kelly, N.I., Dempson, J.B., Neville V.M., Young, M., Keefe, D., Bird T.J., Cote, D. (2023). Considerations for Water Temperature-Related Fishery Closures in Recreational Atlantic Salmon (Salmo salar) Catch and Release Fisheries: A Case Study from Eastern Canada. Reviews in Fisheries Science & Aquaculture, 31(4), 598–619. DOI:10.1080/23308249.2023.2242959
White, J., Fitzgerald, C., Gargan, P., de Eyto, E., Millane, M., Chaput, G., Boylan, P., Crozier, W.W., Doherty, D., Kennedy, B., Lawler, I., Lyons, D., Marnell, F., McGinnity, P., O'Higgins, K., Roche, W.K., Maxwell, H., Ó Maoiléidigh, N. (2023) Incorporating conservation limit variability and stock risk assessment in precautionary salmon catch advice at the river scale, ICES Journal of Marine Science, 80(4) 803–822, DOI:10.1093/icesjms/fsad006
Wood and Schiepl, (2020) gamm4: Generalized Additive Mixed Models using 'mgcv' and 'lme4' version 0.2-6. DOI:10.32614/CRAN.package.gamm4
Contact
Email: neps@gov.scot