Resources

 

Plans and Groundwork

These reports are the plans and foundation for the Salish Sea Marine Survival research effort:

  1. Salish Sea- Strait of Georgia Marine Survival Research Plan 2017-2018
  2. Canadian SSMSP Status and Findings to Date 2016
  3. Salish Sea – Strait of Georgia Marine Survival Research Plan 2015-2016
  4. PSF Strait of Georgia SSMSP Backgrounder 2015
  5. Canadian SSMSP Status and Findings to Date 2015
  6. US-Canada Operating and Alignment Summary (2015)
  7. Puget Sound Steelhead Marine Survival: 2017-2019 Research Plan (2018)
  8. Puget Sound Steelhead Marine Survival: 2015-2017 Research Plan (2015)
  9. Puget Sound Marine Survival Research Plan Version 1: 2014-2015 Research Details (2014)
  10. Research Work Plan: Marine Survival of Puget Sound Steelhead (2014)
  11. Marine Survival of Salmon & Steelhead in the Salish Sea: Hypotheses and Preliminary Research Recommendations for Puget Sound (2012)
  12. Strait of Georgia Chinook and Coho Proposal (2009)
  13. Comprehensive list of hypotheses

 Meeting Summaries

  1. 2017 US – Canada Science Retreat Report (2018)
  2. 2016 US – Canada Science Retreat Report (2017)
  3. 2015 US – Canada Science Retreat Report (2016)
  4. 2014 US – Canada Planning and Coordination Retreat (2015)
  5. 2013 US – Canada Planning and Coordination Retreat (2014)
  6. 2012 Research Planning and Ecosystem Indicators Workshop Series Results & Recommendations Report (2013)

Summaries of Findings

Puget Sound Steelhead Marine Survival: 2013-2017 research findings summary (2018)

Puget Sound Steelhead Marine Survival: 2013-2015 research findings summary (2015)

Technical Reports

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.

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.

Affiliated Publications

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

Project Publications

2018

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

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

Duguid et al. (2018) Historical fluctuations and recent observations of Northern Anchovy Engraulis mordax in the Salish Sea. DOI: 10.1016/j.dsr2.2018.05.018

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

2017

Chittenden et al. (2017) 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 & 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

Sobocinski et al. (2017) Using a qualitative model to explore the impacts of ecosystem and anthropogenic drivers upon declining marine survival in Pacific salmon. DOI: 10.1017/S0376892917000509

2016

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

Thomas et al. (2016) Harbour seals target juvenile salmon of conservation concern. DOI: 10.1139/cjfas-2015-0558

2015

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

 

 

 

 

 

 

Publications Associated with Strategic Salmon Health Initiative (SSHI)

Outputs of SSHI to date (asterix 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.