Publications and Technical Reports

Technical Reports

Beauchamp et al. (2020) Trophic relationships of resident Chinook and coho salmon and the influence of artificial light at night (ALAN) on predation risk during early marine life stages of juvenile salmon and forage fishes in Puget Sound. SSMSP Technical Report.

Greene et al. (2020) Linking environmental and biotic variation to growth and survival of juvenile Chinook salmon in Puget Sound. SSMSP Technical Report.

Banas et al. (2019) Climate impacts on patterns of phytoplankton production in Puget Sound, USA: A model synthesis and narrowing of hypotheses. SSMSP Technical Report.

Hiltunen et al. (2019) Fatty acid composition of zooplankton prey for juvenile salmonids in Puget Sound. SSMSP Technical Report.

Beauchamp et al. (2018) Effects of seasonal availability and energy content of key prey on growth performance during critical periods for juvenile Chinook salmon. SSMSP Technical Report.

Connelly et al. (2018) Marine survival of Puget Sound Chinook: size-selective mortality growth limitation and bioenergetics of sub-yearling Chinook salmon in Puget Sound, Washington. SSMSP Technical Report.

Voelker (2018) Cross-sectional scat sampling reveals intrapopulation feeding diversity in a marine predator. M.S. thesis, Western Washington University.

Campbell et al. (2017) Successful juvenile life history strategies in returning adult Chinook from five Puget Sound populations; Age and growth of Chinook salmon in selected Puget Sound and coastal Washington watersheds. SSMSP Technical Report.

Chamberlin et al. (2017) Assessing early marine growth in juvenile Chinook salmon: factors affecting variability in individual growth in Northern Puget Sound. SSMSP Technical Report.

Esenkulova et al. (2017) Ecology of Alexandrium spp. in the Strait of Georgia, British Columbia, Canada 2015. Harmful Algae News No. 56 March 2017, p 7-8.

Keister et al. (2017) Zooplankton Monitoring Program 2014-2015. SSMSP Technical Report.

Stonecipher (2017) Participation in ecosystem-scale research: A case study of the Salish Sea Marine Survival Project. Senior Thesis, Yale University.

Gamble (2016) Size-selective mortality and environmental factors affecting early marine growth during early marine life stages of sub-yearling Chinook salmon in Puget Sound, Washington. M.S. thesis, University of Washington.

MacCready & Banas (2016) Linking Puget Sound primary production to stratification and atmospheric drivers on seasonal to inter-decadal scales. SSMSP Technical Report.

Kemp & Keister (2015) Zooplankton community patterns in Puget Sound: description of a 20-year qualitative dataset. SSMSP Technical Report.

O’Neill et al. (2015) Toxic contaminants in juvenile Chinook salmon (Oncorhynchus tshawytscha) migrating through estuary, nearshore and offshore habitats of Puget Sound. SSMSP Technical Report.

Pearson et al. (2015) Identifying potential juvenile steelhead predators in the marine waters of the Salish Sea. SSMSP Technical Report.

Wade, J. (2014)  Citizen science bird survey in the Cowichan Valley in support of the Pacific Salmon Foundation’s Salish Sea Program 2014. Can. Manuscr. Rep. Fish. Aquat. Sci. 3044: iv + 30 p.

Pellett, Craig, Wightman (2013) Preliminary Investigation of Habitat Preferences and Abundance of Juvenile Chinook Salmon in the Lower Cowichan River Floodplain (Spring, 2013), with Reference to Habitat Compensation Options BCCF Technical Report

Craig (2015) Early Life History and Critical Rearing Habitat Requirements of Cowichan River Chinook Salmon BCCF Technical Report (2014)

Kintama Research Services Ltd (2019) Mortality, Movements, and Migration Timing of Age-0 Cowichan Chinook Salmon Tagged in the Southern Gulf Islands in Fall 2017. Technical Report to PSF

Kintama Research Services Ltd. (2016) The Use of Telemetry to Investigate Residence Time and Survival of Fraser River Chinook Salmon in the Strait of Georgia, 2016. Technical Report to PSF

Kintama Research Services Ltd. (2016) Final Report on the Comparative Marine Survival of Seymour River Steelhead and Testing the Performance of 180 kHz Small Acoustic Tags in the Salish Sea, 2015. Technical Report to PSF

Publications Associated with Strategic Salmon Health Initiative (SSHI)

Outputs of SSHI to date (asterisk indicates graduate student/PDF in SSHI program):


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;

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:

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: /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.

*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):

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

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:

*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:

*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


Suchy et al. (2022). Match/mismatch between phytoplankton and crustacean zooplankton phenology in the Strait of Georgia, Canada.

Keister et al. (2022). Zooplankton composition links to climate and salmon survival in a northern temperate fjord.

Cheng et al. (2022). Acoustic imaging observes predator-prey interactions between bull trout and migrating sockeye salmon smolts.


Hiltunen et al. (2021) Taxonomic, temporal, and spatial variation in zooplankton fatty acid composition in Puget Sound, WA, USA.

Furey et al. (2021) Infected juvenile salmon can experience increased predation during freshwater migration. DOI: 10.1098/rsos.201522

Moore et al. (2021) Environmental fluctuation and shifting predation pressure contribute to substantial variation in early marine survival of steelhead. DOI: 10.3354/meps13606

Nelson et al. (2021) Variation in predator diet and prey size affects perceived impacts to salmon species of high conservation concern. DOI: 10.1139/cjfas-2020-0300

Rechisky et al. (2021) Exposure time of wild, juvenile Sockeye salmon to open-net-pen Atlantic salmon farms in British Columbia, Canada. DOI: 10.1002/nafm.10574

Sobocinski et al. (2021) A hypothesis-driven statistical approach for identifying ecosystem indicators of coho & Chinook salmon marine survival


Allegue et al. (2020) Harbour seals responded differently to pulses of out-migrating coho and Chinook smolts. DOI: 10.3354/meps13389

Chalifour et al. (2020) Chinook salmon exhibit long-term rearing and early marine growth in the Fraser River, British Columbia, a large urban estuary. 

Claiborne et al. (2020) Correspondence between scale growth, feeding conditions, and survival of adult Chinook salmon returning to the southern Salish Sea: implications for forecasting

Davis et al. (2020) Variable prey consumption leads to distinct regional differences in Chinook salmon growth during the early marine critical period. DOI: 10.3354/meps13279

Furey et al. (2020) Migratory salmon smolts exhibit consistent interannual depensatory predator swamping: Effects on telemetry‐based survival estimates. DOI: 10.1111/eff.12556

Kendall et al. (2020) Density-dependent marine survival of hatchery-origin Chinook salmon may be associated with pink salmon. DOI: 10.1002/ecs2.3061

Nahirnick et al. (2020) Long-term eelgrass habitat change and associated human impacts on the west coast of Canada. DOI:10.2112/JCOASTRES-D-18-00112.1

Rechisky et al. (2020) Performance of a high-frequency (180 kHz) acoustic array for tracking juvenile Pacific salmon in the coastal ocean. DOI: 10.1186/s40317-020-00205-z

Schroeder et al. (2020) Spatial and temporal persistence of nearshore kelp beds on the west coast of British Columbia, Canada using satellite remote sensing. DOI: 10.1002/rse2.142

Sobocinski et al. (2020) Ecosystem indicators of marine survival in Puget Sound steelhead trout. DOI: 10.1016/j.pocean.2020.102419

Voelker et al. (2020) Large-scale molecular barcoding of prey DNA reveals predictors of intrapopulation feeding diversity in a marine predator. DOI: 10.1002/ece3.6638


Chalifour et al. (2019) Habitat use by juvenile salmon, other migratory fish, and resident fish species underscores the importance of estuarine habitat mosaics. DOI: 10.3354/meps13064

Duguid et al. (2019) Historical fluctuations and recent observations of Northern Anchovy Engraulis mordax in the Salish Sea. DOI: 10.1016/j.dsr2.2018.05.018

Hershberger et al. (2019) Intra-annual changes in waterborne Nanophyetus salmincola. DOI: 10.1002/aah.10074

Hershberger et al. (2019) Susceptibility of Nanophyetus salmincola cercaria to formalin, hydrogen peroxide, and seawater. DOI: 10.1002/aah.10050

O’Neill et al. (2019) Chemical tracers guide identification of the location and source of persistent organic pollutants in juvenile Chinook salmon (Oncorhynchus tshawytscha), migrating seaward through an estuary with multiple contaminant inputs. DOI: 10.1016/j.scitotenv.2019.135516

Schroeder et al. (2019) Passive remote sensing technology for mapping bull kelp (Nereocystis luetkeana): A review of techniques and regional case study. DOI: 10.1016/j.gecco.2019.e00683

Suchy et al. (2019) Influence of environmental drivers on spatio-temporal dynamics of satellite-derived chlorophyll a in the Strait of Georgia. DOI: 10.1016/j.pocean.2019.102134

Weil et al. (2019) A hyperiid amphipod acts as a tropic link between a scyphozoan medusa and juvenile Chinook Salmon. DOI: 10.1016/j.ecss.2019.01.025

Weil et al. (2019) Percent ash-free dry weight as a robust method to estimate energy density across taxa. DOI: 10.1002/ece3.5775 


Boldt et al. (2018) Bottom-up and top-down control of small pelagic forage fish: factors affecting age-0 herring in the Strait of Georgia, British Columbia. DOI: 10.3354/meps12485

Chen et al. (2018) Infection by Nanophyetus salmincola and toxic contaminant exposure in out-migrating steelhead from Puget Sound, Washington: implications for early marine survival. DOI: 10.1002/aah.10017

Chittenden et al. (2018) Estuarine and marine diets of outmigrating Chinook salmon smolts in relation to local zooplankton populations, including harmful blooms. DOI: 10.1016/j.ecss.2017.11.021

Duguid et al. (2018) Assessing indices of growth for field studies of juvenile salmon: an experiment and synthesis. DOI: 10.1002/mcf2.10020

Furey et al. (2018) Migratory coupling between predators and prey. DOI: 10.1038/s41559-018-0711-3

Gamble et al. (2018) Size, growth, and size-selective mortality of subyearling Chinook salmon during early marine residence in Puget Sound. DOI: 10.1002/tafs.10032

Healy et al. (2018) Transcriptome profiles relate to migration fate in hatchery Steelhead (Oncorhynchus mykiss) smolts. DOI: 10.1139/cjfas-2017-0424

Iacarella et al. (2018) Anthropogenic disturbance homogenizes seagrass fish communities. DOI: 10.1111/gcb.14090

Kennedy et al. (2018) Eelgrass as valuable nearshore foraging habitat for juvenile Pacific salmon in the early marine period. DOI: 10.1002/mcf2.10018

Rechisky et al. (2018) Quantifying survival of age two Chilko Lake sockeye salmon during the first 50 days of migration. DOI: 10.1139/cjfas-2017-0425

Schwarz et al. (2018) Large-scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern. DOI: 10.1002/ece3.4474

Sobocinski et al. (2018) Using a qualitative model to explore the impacts of ecosystem and anthropogenic drivers upon declining marine survival in Pacific salmon. DOI: 10.1017/S0376892917000509


Duguid & Juanes (2017) Microtrolling: an economical method to nonlethally sample and tag juvenile Pacific salmon at sea. DOI: 10.1080/00028487.2016.1256835

Furey & Hinch (2017) Bull trout movements match the life history of sockeye salmon: consumers can exploit seasonally distinct resource pulses. DOI: 10.1080/00028487.2017.1285353

Healy et al. (2017) Route-specific movements and survival during early marine migration of hatchery steelhead Oncorhynchus mykiss smolts in coastal British Columbia. DOI: 10.3354/meps12238 

Kendall et al. (2017) Declining patterns of Pacific Northwest steelhead trout (Oncorhynchus mykiss) adult abundance and smolt survival in the ocean. DOI: 10.1139/cjfas-2016-0486

Moore & Berejikian (2017) Population, habitat, and marine location effects on early marine survival and behavior of Puget Sound steelhead smolts. DOI: 10.1002/ecs2.1834

Purcell et al. (2017) Detection of Nanophyetus salmincola in water, snails and fish tissues by quantitative PCR. DOI: 10.1080/08997659.2017.1365780

Ruff et al. (2017) Salish Sea Chinook salmon exhibit weaker coherence in early marine survival trends than coastal populations. DOI: 10.111/fog.12222

Thomas et al. (2017) Harbour seals target juvenile salmon of conservation concern. DOI: 10.1139/cjfas-2015-0558


Berejikian et al. (2016) Predator-prey interactions between harbor seals and migrating steelhead trout smolts revealed by acoustic telemetry. DOI: 10.3354/meps11579

Furey et al. (2016) Predator swamping reduces predation risk during nocturnal migration of juvenile salmon in a high‐mortality landscape. 


Moore et al. (2015) Multi-population analysis of Puget Sound steelhead survival and migration behavior. DOI: 10.3354/meps11460

Zimmerman et al. (2015) Spatial and temporal patterns in smolt survival of wild and hatchery coho salmon in the Salish Sea. DOI: 10.1080/19425120.2015.1012246

Furey et al. (2015) Variability in migration routes influences early marine survival of juvenile salmon smolts. DOI: 10.1371/journal.pone.0139269

Affiliated Publications

Nelson et al. (2019) Ecological implications of changing hatchery practices for Chinook salmon in the Salish Sea. DOI: 10.1002/ecs2.2922

Hobbs et al. (2019) Toxic burdens of freshwater biofilms and use as a source tracking tool in rivers and streams. DOI: 10.1021/acs.est9b02865

Nelson et al. (2018) Wild Chinook salmon productivity is negatively related to seal density and not related to hatchery releases in the Pacific Northwest. DOI: 10.1139/cjfas-2017-0481

Carswell et al. (2017) Evaluation of MODIS-Aqua atmospheric correction and chlorophyll products of western North American coastal waters based on 13 years of data. DOI: 10.3390/rs9101063

Chasco et al. (2017) Competing tradeoffs between increasing marine mammal predation and fisheries harvest of Chinook salmon. DOI: 10.1038/s41598-017-14984-8

Chasco et al. (2017) Estimates of Chinook salmon consumption in Washington State inland waters by four marine mammal predators from 1970 to 2015. DOI: 10.1139/cjfas-2016-0203

Phillips & Costa (2017) Spatial-temporal bio-optical classification of dynamic semi-estuarine waters in western North America. DOI: 10.1016/j.ecss.2017.09.029