Spring salmon on the River South Esk, Scotland: Scottish Marine and Freshwater Science Vol 7 No 10

References

Anon. (2015 a). Status of Scottish Salmon and Sea Trout Stocks 2014. Marine Scotland Science Report 01/15. 27 pp.

Anon. (2015 b). The application of conservation limits for Atlantic salmon in Scotland. 33 pp. Available online at http://www.gov.scot/Resource/0048/00486109.pdf. Accessed on 21/10/15.

Anderson, E.C. (2010). Assessing the power of informative subsets of loci for population assignment, standard methods are upwardly biased. Molecular Ecology Resources, 10, 701-710.

Armstrong, J.D., Kemp, P.S., Kennedy, G.J.A., Ladle, M. & Milner, N.J. (2003). Habitat requirements of Atlantic salmon and brown trout in rivers and streams. Fisheries Research, 62, 143-170.

Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Wheeler, D.L. (2005). GenBank. Nucleic Acids Research, 33, D34-D38.

Bourret, V., Kent, M.P., Primmer, C.R., Vasemägi, A., Karlsson, S., Hindar, K., McGinnity, P., Verspoor, E., Bernatchez, L. & Lien, S. (2013). SNP-array reveals genome-wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar). Molecular Ecology, 22, 532-551.

Campbell, R. (1998). A fisheries management plan for the River Tweed in the Scottish borders. Freshwater Forum, 10, 2-19.

Dempsey, K.A. (2009). The ecology of bottlenose dolphins " Tursiops truncatus " in Montrose Bay, North East Scotland. Summary based on a Wildlife Management BSc Hons Dissertation 2008/9: School of Biological Sciences, University of Aberdeen. Tay Estuary Forum, Occasional Paper Series, Report No. 3.

Gidskehaug, L., Kent, M., Hayes, B.J. & Lien, S. (2011). Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array. Bioinformatics, 27, 303-310.

Godfrey, J.D. (2005). Site condition monitoring of Atlantic salmon SACs. Report by the SFCC to Scottish Natural Heritage, Contract F02AC608.

Goudet, J. (2005). hierfstat, a package for r to compute and test hierarchical F-statistics. Molecular Ecology Notes, 5, 184-186.

Grey, & Tosh, J.R. (1894). 14 ^th annual report of the Fishery Board for Scotland, Part II, Note 2.

Gilbey, J., Stradmeyer, L., Cauwelier, E. & Middlemas, S. (2012). Genetic investigation of the north east English net fisheries. Marine Scotland Science Report 04/12. 83 pp.

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, Volume 6, No. 12.

Hawkins, A.D. & Smith, G.W. (1986). Radio-tracking observations on Atlantic salmon ascending the Aberdeenshire Dee. Scottish Fisheries Research Report, 36, 24pp.

ICES. (2014). Report of the Working Group on North Atlantic Salmon ( WGNAS), 19-28 March 2014, Copenhagen, Denmark. ICES CM 2014/ACOM:09. 433 pp.

ICES. (2015). Report of the Working Group on North Atlantic Salmon ( WGNAS), 17-26 March 2015, Moncton, Canada. ICES CM 2015/ACOM:09. 332pp.

Ikediashi, C., Billington, S. & Stevens, J.R. (2012). The origins of Atlantic salmon ( Salmo salar L.) recolonizing the River Mersey in northwest England. Ecology and Evolution, 2, 2537-2548.

Johnston, S., Lindqvist, M., Niemelä, E., Orell, P., Erkinaro, J., Kent, M., Lien, S., et al. (2013). Fish scales and SNP chips, SNP genotyping and allele frequency estimation in individual and pooled DNA from historical samples of Atlantic salmon ( Salmo salar). BMC Genomics, 14, 1-13.

Jones, O.R. & Wang, J. (2010). COLONY, a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources, 10, 551-555.

Karlsson, S., Moen, T., Lien, S., Glover, K.A. & Hindar, K. (2011). Generic genetic differences between farmed and wild Atlantic salmon identified from a 7K SNP-chip. Molecular Ecology Resources, 11 (Suppl. 1), 247-253.

Laughton, R. (1989). The movements of adult salmon within the River Spey. Scottish Fisheries Research Report, 41, 19pp.

Laughton, R. (1991). The movements of adult Atlantic salmon ( Salmo salar L.) in the River Spey as determined by radio telemetry during 1988 and 1989. Scottish Fisheries Research Report, 50, 35pp.

Laughton, R. & Smith, G.W. (1992). The relationship between the date of river entry and the estimated spawning position of adult Atlantic salmon ( Salmo salar L.) in two major Scottish east coast rivers. In: Wildlife telemetry: remote monitoring and tracking of animals. Ed: Priede, I.G. & Smith, S.M. pp. 423-433. Ellis Horwood Ltd., Chichester, England.

Lien, S., Gidskehaug, L., Moen, T., Hayes, B., Berg, P., Davidson, W., Omholt, S., et al. (2011). A dense SNP-based linkage map for Atlantic salmon ( Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. BMC Genomics, 12, 615.

Marine Life Angus. (2013). Marine Life Angus: Species. Available online at http://www.marinelifeangus.co.uk/species. Accessed on 26/08/13.

Malcolm, I.A., Godfrey, J. & Youngson, A.F. (2010). Review of migratory routes and behaviour of Atlantic salmon, sea trout and European eel in Scotland's coastal environment: Implications for the development of marine renewables. Scottish Marine and Freshwater Science, Volume 1, No. 14.

Middlemas, S.J., Armstrong, J.D. & Thompson, P.M. (2003). The significance of marine mammal predation on salmon and sea trout. In: Salmon at the edge. Edited by D. Mills. Blackwell Science Ltd., Oxford.

Millar, C.P., Millidine, K.J., Middlemas, S.J. & Malcolm, I.A. (2015). Development of a model for predicting large scale spatio-temporal variability in juvenile fish abundance from electrofishing data. Scottish Marine and Freshwater Science, Volume 6, No. 6.

Mills, D. (1989). Ecology and management of Atlantic salmon. Chapman and Hall, London.

River South Esk Catchment Partnership. (2009). The South Esk Catchment Management Plan. 68 pp. Available online at http://theriversouthesk.org/assets/Docs/river-south-esk-plan-dec09.pdf Accessed on 12/03/15.

Nei, M. (1972). Genetic distance between populations. American Naturalist, 106, 283.

Peakall, R. & Smouse, P. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research - an update. Bioinformatics, 28, 2537-2539.

Piry, S., Alapetite, A., Cornuet, J.M., Paetkau, D., Baudouin, L. & Estoup, A. (2004). GENECLASS2, A software for genetic assignment and first-generation migrant detection. Journal of Heredity, 95, 536-539.

R Core Team. (2013). R, a language and environment for statistical computing. http://www.R-project.org

Rannala, B. & Mountain, J.L. (1997). Detecting immigration by using multilocus genotypes. Proceedings of the National Academy of Science, USA, 94, 9197-9201.

Scottish Government. (2013). Provisional salmon fishery statistics - 2012 season. Marine Scotland Topic Sheet No. 94 v3 2013. Available online at http://www.scotland.gov.uk/Resource/0041/00418360.pdf

Scottish Wildlife Trust. (2011). Species profile - Common seal (Phoca vitulina) Montrose Basin Blog 24 ^th June 2011. Available online at http://blogs.scottishwildlifetrust.org.uk/montrosebasin/2011/06/14/species-profile-common-seal-phoca-vitulina. Accessed on 26/08/13.

Shearer, W.M. (1972). A study of the North Esk population of the North Esk 1961 - 1970. MSc Thesis, University Of Edinburgh, 230pp.

Shearer, W.M. (1986). The exploitation of Atlantic salmon in Scottish home water fisheries in 1952-83. In: The status of the Atlantic salmon in Scotland. Edited by D. Jenkins & W.M. Shearer. Institute of Terrestrial Ecology symposium no. 15, Banchory.

Shearer, W.M. (1992). The Atlantic salmon. Natural history, exploitation and future management. Halsted Press, John Wiley and Sons, Inc., New York.

Smith, I.P. & Johnstone, A.D.F. (1996). Migration of adult Atlantic salmon ( Salmo salar L.) in the Aberdeenshire Dee, 1995. Fisheries Research Services Report No 5/96. Scottish Office Agriculture, Environment and Fisheries Department, Aberdeen.

Smith, G.W., Smith, I.P. & Armstrong, S.M. (1994). The relationship between river flow and entry to the Aberdeenshire Dee by returning adult Atlantic salmon. Journal of Fish Biology, 45, 953-960.

Smith, G.W., Laughton, R. & Dora, S. (1996). Interpreting trends in adult Atlantic salmon ( Salmo salar L.) populations from angling records: an analysis of catch and effort data from the River Spey. In: Cowx, I.G. (ed.) Stock Assessment in Inland Fisheries, pp. 141-153. Fishing News Books, Oxford.

Smith, G.W., Campbell, R.N.B. & MacLaine, J.S. (1998). Regurgitation rates of intragastric transmitters by adult Atlantic salmon ( Salmo salar L.) during riverine migration. Hydrobiologia, 371/372, 117-121.

SNIFFER. (2011 a). Physical restoration options for priority catchments - phase 1. River South Esk catchment restoration scoping study. Project RR01, Final Report. 128 pp.

SNIFFER. (2011 b). River fish classification tool: science work phase 3 report. Project WFD68c, Final Report. Available to download at http://www.sniffer.org.uk/files/4413/4183/7993/Fisheries_Classification_Phase3v4.0.pdf Accessed 08 April 2015. 93 pp.

Stewart, D.C., Smith, G.W. & Youngson, A.F. (2002). Tributary-specific variation in timing of return of adult Atlantic salmon ( Salmo salar) to fresh water has a genetic component. Canadian Journal of Fisheries and Aquatic Sciences, 59, 276-281.

Stewart, D.C., Middlemas, S.J. & Youngson, A.F. (2006). Population structuring in Atlantic salmon ( Salmo salar): evidence of genetic influence on the timing of smolt migration in sub-catchment stocks. Ecology of Freshwater Fish, 15, 552-558.

Stewart, D.C, Middlemas, S.J., Mackay, S. & Armstrong, J.D. (2009). Over-summering behaviour of Atlantic salmon Salmo salar returning to rivers in the Cromarty Firth, north-east Scotland. Journal of Fish Biology, 74, 1347-1352.

Tamura, K., Stecher, G., Peterson, D., Filipski, A. & Kumar, S. (2013). MEGA6, Molecular Evolutionary Genetics Analysis Version 6.0. Molecular Biology and Evolution , 30, 2725-2729.

Waples, R.S. (2010). High-grading bias, subtle problems with assessing power of selected subsets of loci for population assignment. Molecular Ecology, 19, 2599-2601.

Webb, J. (1989). The movements of Adult Atlantic salmon in the River Tay. Scottish Fisheries Research Report, 44, 32pp.

Webb, J. & Hawkins, A.D. (1989). The movements and spawning behaviour of Adult salmon in the Girnock Birn, a tributary of the Aberdeenshire Dee, 1986. Scottish Fisheries Research Report, 40, 42pp.

Youngson, A.F., Jordan, W.C. & Hay D.W. (1994). Homing of Atlantic salmon ( Salmo salar L.) to a tributary stream in a major river catchment. Aquaculture, 121, 259-267.