Technical Reports
Keister et al. (2017) Zooplankton Monitoring Program 2014-2015. SSMSP Technical Report.
Publications Associated with Strategic Salmon Health Initiative (SSHI)
Outputs of SSHI to date (asterisk indicates graduate student/PDF in SSHI program):
Published:
Miller, K.M., I.A. Gardner, R. Vanderstichel, T. Burnley, A.D. Schulze, S. Li, K.H. Kaukinen, T.J. Ming, and N.G. Ginther. 2014. Report on the performance evaluation of the Fluidigm BioMarkTM platform for high-throughput microbe monitoring in salmon. CSAS Working Paper 2014/15 NHQ12.
*Jeffries, K. M., S. G. Hinch, M. K. Gale, T. D. Clark, A. G. Lotto, M. T. Casselman, and K. M. Miller. 2014. Immune response genes and pathogen presence predict migration survival in wild salmon smolts. Molecular ecology, 23(23), 5803-5815.
Miller, K.M., A. *Teffer, S. Tucker, S. Li, A.D. Schulze, M. Trudel, F. Juanes, A. *Tabata, K.H. Kaukinen, N.G. Ginther, T.J. *Ming, S.J. Cooke, J.M. Hipfner, D.A. Patterson, and S.G. Hinch. 2014. Infectious disease, shifting climates and opportunistic predators: cumulative factors potentially impacting wild salmon declines. Evolutionary Applications 7.7: 812-855.
Raby, G. D., M.R. *Donaldson, S.G. Hinch, T.D. Clark, E.J. Eliason, K.M. *Jeffries, K.V. Cook., A. *Teffer, A.L. *Bass, A, K.M. Miller, D.A. Patterson, A.P. Farrell, and S.J. Cooke. 2015. Fishing for Effective Conservation: Context and Biotic Variation are Keys to Understanding the Survival of Pacific Salmon after Catch-and-Release. Integrative and comparative biology, icv088.
DFO. 2015. Science advice to guide a research study using the Fluidigm BioMarkTM platform for microbe detection in wild and farmed salmon. Canadian Science Advisory Secretariat National Capital Region Science Advisory Report 2015/039.
Patterson, D.A., S.J. Cooke, S,G. Hinch, K.A. Robinson, N. Young, A.P. Farrell, and K.M. Miller. 2016. A perspective on physiological studies supporting the provision of scientific advice for the management of Fraser River sockeye salmon (Oncorhynchus nerka). Conservation Physiology. 4: cow026; https://doi.org/10.1093/conphys/cow026
Garner, B.A., Hand, B.K., Amish, S.J., Bernatchez, L., Foster, J.T., Miller, K.M., Morin, P.A., Narum, S.R., O’Brien, S.J., Roffler, G. and Templin, W.D. 2016. Genomics in conservation: case studies and bridging the gap between data and application. Trends in ecology & evolution 31(2): 81-3.
*Tucker, S., KM Miller, S Li, K Kaukinen, A Tabata, A Schulze, N Ginther, T Ming. 2017. Broad based genomic screening for microbes in Salish Sea juvenile Chinook salmon. Salish Sea Ecosystem Conference: https://cedar.wwu.edu/ssec/2016ssec/species_food_webs/86/
Miller, KM, S Li, T Ming, K Kaukinen, N Ginther, DA Patterson, M Trudel. 2017. Survey of infectious agents detected in juvenile Chinook and Sockeye salmon from British Columbia and Washington. NPAFC 1718: http://www.npafc.org/new/publications/Documents /PDF%202017/1718(Canada).pdf
Bernatchez L, Wellenreuther M, Araneda C, Ashton DT, Barth JM, Beacham TD, Maes GE, Martinsohn JT, Miller KM, Naish KA, Ovenden JR. 2017. Harnessing the Power of Genomics to Secure the Future of Seafood. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2017.06.010
*Bass, A.L., S.G. Hinch, A.K. *Teffer, D.A. Patterson, K.M. Miller. 2017. A survey of microparasites present in adult migrating Chinook salmon (Oncorhynchus tshawytscha) in southwestern British Columbia determined by high-throughput quantitative polymerase chain reaction. Journal of Fish Diseases 40(4): 453-477; doi:10.1111/jfd.12607.
*Di Cicco, E., H.W. Ferguson, A.D. Schulze, K.H. Kaukinen, S. Li, R. Vanderstichel, Ø. Wessel, E. Rimstad, I.A. Gardner, K.L. Hammell, and K.M. Miller. 2017. Heart and skeletal muscle inflammation (HSMI) disease diagnosed on a British Columbia salmon farm through a longitudinal farm study. PLOS ONE 12 (2017) e0171471.
*Teffer A.K., S.G. Hinch, K.M. Miller, D.A. Patterson, A.P. Farrell, S.J. Cooke, A.L. *Bass, P. Szekeres, and F .Juanes. 2017. Capture severity, infectious disease processes, and sex influence post-release mortality of sockeye salmon bycatch. Conservation Physiology 5(1): doi.org/10.1093/conphys/cox017
Miller, K.M., O.P. Günther, S. Li, K.H. Kaukinen, T.J. Ming. 2017. Molecular indices of viral disease development in wild migrating salmon. Conservation Physiology Conservation Physiology 5(1); doi 10.1093/conphys/cox036.
*Drenner, S.M., Hinch, S.G.,* Furey, N.B., Clark, T.D., Li, S., Ming, T., *Jeffries, K.M., Patterson, D.A., Cooke, S.J., Robichaud, D. and Welch, D.W., Farrell, A.P., and Miller, K.M. 2017. Transcriptome patterns and blood physiology associated with homing success of sockeye salmon during their final stage of marine migration. Can. J. Fish. Aquat. Sci https://doi.org/10.1139/cjfas-2017-0391
Miller, K.M., S. Li, T. Ming, K. Kaukinen, N. Ginther, D.A. Patterson, and M. Trudel. 2017. Survey of infectious agents detected in juvenile chinook and sockeye salmon from British Columbia and Washington. NPAFC doc1718.
*Healy, S, Hinch SG, *Bass, AL, Porter, AD, Rechisky, EL, Welch, DW, Lotto, AG, *Furey, NB, Miller, KM. 2018. Transcriptome profiles relate to migration fate in hatchery Steelhead (Oncorhynchus mykiss) smolts. CJFAS: Online: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2017-0424#.WsPoMaplLnM
*Teffer AK, Bass AL, Miller KM, Patterson DA, Juanes F, Hinch SG . 2018. Infections, fisheries capture, temperature and host responses: multi-stressor influences on survival and behaviour of adult Chinook salmon. CJFAS: Online: http://www.nrcresearchpress.com/doi/abs/10.1139/cjfas-2017-0491#.WsPnzqplLnM
*Tucker S, *Li S, Kaukinen KH, Patterson, DA, Miller KM. 2018. Distinct seasonal infectious agent profiles in life-history variants of juvenile Fraser River Chinook salmon; an application of high-throughput genomic screening. PLOS ONE 13(4), e0195472.
*Di Cicco, E, HW Ferguson, KH Kaukinen, AD Schulze, S Li, A Tabata, O Gunther, G Mordecai, CA Suttle, KM Miller. The same strain of Piscine orthoreovirus (PRV) is involved with the development of different, but related, diseases in Atlantic and Pacific Salmon in British Columbia. FACETS: In Press; arXiv preprint arXiv:1805.01530 (2018).
*Thakur KK, R Vanderstichel, S Li, E *Laurin, S *Tucker, C Neville, A Tabata, KM Miller. 2018. A comparison of infectious agents between hatchery-enhanced and wild out-migrating juvenile Chinook salmon (Oncorhynchus tshawytscha) from Cowichan River, British Columbia. Facets 3: 695-721. doi:10.1139/facts-2017-0013
In Press
*Laurin, E, D *Jarmillo, R Vanderstichel, H Ferguson, KH Kaukinen, AD Schulze, IR Keith, IA Gardner, KM Miller. Histopathological and novel high-throughput molecular monitoring data from farmed salmon (Salmo salar and Oncorhynchus spp.) in British Columbia, Canada, from 2011-2013. Aquaculture: In Press.
*Bass, AL, SG Hinch, AK *Teffer, DA Patterson, KM Miller. Fisheries capture and infectious agents were associated with travel rate and survival of Chinook salmon during spawning migration through a natal river. Fisheries Research: In Press.
In Review
*Teffer AK, S Hinch, KM Miller, KM *Jeffries, DA Patterson, SJ Cooke, AP Farrell, KH Kaukinen, S Li, and F Juanes. Cumulative effects of thermal and fisheries stressors reveal sex-specific effects on pathogen development and early mortality of adult coho salmon (Oncorhynchus kisutch). Journal of Experimental Biology: In Review.
*Nekouei O, R. Vanderstichel, T Ming, KH Kaukinen, K *Thakur, A Tabata, E *Laurin, S *Tucker, KM Miller. Spatio-temporal burden of infectious agents in juvenile Fraser River Sockeye salmon (two years of average and poor productivity). Diseases of Aquatic Organisms: In Review.
*Thakur KK, R Vanderstichel, K Kaukinen, O *Nekouei, E *Laurin, KM Miller. Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia (1985-1994). FACETS: In Review.
Project Publications
2023
2022
Beamish, R. 2022. The need to see a bigger picture to understand the ups and downs of Pacific salmon abundances. ICES Journal of Marine Science 79:1005-1014. Doi: 10:1093/icesjms/fsac036
Jarnikova T, et al. (2022). Anthropogenic Carbon Increase has Caused Critical Shifts in Aragonite Saturation Across a Sensitive Coastal System. Global Biogeochemical Cycles. 36
Jarnikova T, et al. (2022). A clustering approach to determine biophysical provinces and physical drivers of productivity dynamics in a complex coastal sea. Ocean Science. 18: 1451-1475.
Moore-Maley B, Allen S. (2022). Wind driven upwelling and surface nutrient delivery in a semi-enclosed coastal sea. Ocean Sciences. 18: 143-167.
Morzaria-Luna, etal. (2022). Design and Parameterization of a Spatially Explicit Atlantis Ecosystem Model for Puget Sound. NOAA Technical Memorandum NMFS-NWFSC-177.
2021
Bass, et al. (2021). Aquaculture mediates global transmission of a viral pathogen to wild salmon
2020
2019
2018
Furey et al. (2018) Migratory coupling between predators and prey. DOI: 10.1038/s41559-018-0711-3