Salmon Ecological Health

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2014

*Jeffries, KM, SG Hinch, T Sierocinski, P Pavlidis, and KM Miller. 2014. Transcriptomic responses to high water temperature in two species of Pacific salmon.  Evol App 7(2): 286-300. doi:10.1111/eva.12119
*Jeffries, KM, SG Hinch, MK 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. Mol ecol 23: 5803-5815.  doi: 10.1111/mec.12980
Miller, KM, 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.  Evol App 7.7: 812-855. doi:10.1111/eva.12164

2015

Raby, GD, Donaldson, MR, Hinch, SG, Clark, TD, Eliason, EJ, *Jeffries, KM, Cook, KV, *Teffer, A, *Bass, A.L, Miller, K.M, Patterson, D.A, Farrell, A.P, & Cooke, S. J. 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.  

2016

Miller, KM, IA Gardner, R Vanderstichel, T Burnley, AD *Schulze, S *Li, KH *Kaukinen, TJ. *Ming, and NG *Ginther.  2016. Report on the performance evaluation of the Fluidigm BioMarkTM platform for high-throughput microbe monitoring in salmon.  CSAS Working Paper 2014/15 NHQ12.  https://www.researchgate.net/profile/Kristi-Miller-2/publication/306281417_Report_on_the_Performance_Evaluation_of_the_Fluidigm_BioMark_Platform_for_High-Throughput_Microbe_Monitoring_in_Salmon/links/57b6565e08aede8a665bc0e5/Report-on-the-Performance-Evaluation-of-the-Fluidigm-BioMark-Platform-for-High-Throughput-Microbe-Monitoring-in-Salmon.pdf
Groner, M. L, Maynard, J, Breyta, R, Carnegie, R. B, Dobson, A, Friedman, C. S, ... & Noble, R. T. (2016). Managing marine disease emergencies in an era of rapid change. Phil. Trans. R. Soc. B, 371(1689), 20150364.
Garner, BA, Hand, BK, Amish, SJ, Bernatchez, L, Foster, JT, Miller, KM, 4 authors. 2016. Genomics in conservation: case studies and bridging the gap between data and application. Trends in ecol evol 31(2): 81-3.
Patterson, D.A, 5 authors, 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). Cons Physiol. 4: doi.org/10.1093/conphys/cow026.

2017

*Drenner, SM, Hinch, SG,* Furey, NB, Clark, TD, *Li, S,*Ming, T, *Jeffries, KM, Patterson, DA, Cooke, SJ, Robichaud, D, Welch, DW, Farrell, AP, and Miller, KM. 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.
*Di Cicco, E, HW Ferguson, AD  *Schulze, KH  *Kaukinen, S *Li, R Vanderstichel, Ø Wessel, E Rimstad, IA Gardner, KL Hammell, and KM 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. https://doi.org/10.1371/journal.pone.0171471.
*Teffer AK, SG Hinch, KM Miller, 6 authors. 2017. Capture severity, infectious disease processes, and sex influence post-release mortality of sockeye salmon bycatch. Cons Physiol 5(1): doi.org/10.1093/conphys/cox017
Miller, KM, OP *Günther, S* Li, KH * Kaukinen, TJ *Ming. 2017. Molecular indices of viral disease development in wild migrating salmon. Conservation Physiology Conservation Physiology 5(1); https://doi.org/10.1093/conphys/cox036. 
Jones, SJM, 7 authors, Suttle, C, *Mordecai, GD,  Miller, KM et al. 2017.  The genome of the beluga whale (Delphinapterus leucas). Genes 8, 378; doi:10.3390/genes8120378.
Miller, KM, S *Li, T *Ming, K *Kaukinen, N *Ginther, DA Patterson, and M Trudel. 2017. Survey of infectious agents detected in juvenile chinook and sockeye salmon from British Columbia and Washington. NPAFC doc1718.  
*Bass, A, SG Hinch, AK  *Teffer, DA Patterson, KM 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.
Bernatchez 7 authors, Miller KM, Naish KA, Ovenden JR. 2017. Harnessing the Power of Genomics to Secure the Future of Seafood. Trends in Ecology & Evolution 32, no. 9 (2017): 665-680. https://doi.org/10.1016/j.tree.2017.06.010

2018

Welch, DW, Futia, MH, Rinchard, J, *Teffer, AK, Miller, KM, Hinch, SG and Honeyfield, DC, 2018. Thiamine Levels in Muscle and Eggs of Adult Pacific Salmon from the Fraser River, British Columbia. Journal of Aquatic Animal Health, 30(3), pp.191-200.
*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: https://doi.org/10.1371/journal.pone.0195472 
*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:  doi.org/10.1139/cjfas-2017-0424
*Teffer AK, *Bass AL, Miller KM, Patterson, DM, Juanes, F, Hinch, SG. 2018. Infections, fisheries capture, temperature and host responses: multi-stressor influences on survival and behaviour of adult Chinook salmon. Can J Fish Aquat Sci  doi.org/10.1139/cjfas-2017-0491 
*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/facets-2017-0113
*Di Cicco, E, 8 authors, KM Miller.  2018. 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 3(1): https://doi.org/10.1139/facets-2018-0008.
*Nekouei, O, Vanderstichel, R, 7 authors, Miller, KM, 2018. Detection and assessment of the distribution of infectious agents in juvenile Fraser River Sockeye salmon, Canada, in 2012 and 2013. Front Microbiol 9: 3221. https://www.frontiersin.org/articles/10.3389/fmicb.2018.03221/full.
*Akbarzadeh, 6 authors, Miller, KM, 2018. Developing specific molecular biomarkers for thermal stress in salmonids. BMC genomics, 19(1): 749. https://doi.org/10.1186/s12864-018-5108-9.

2019

*Laurin, E, 7 authors, KM Miller. 2019.  Histopathological and novel high-throughput molecular monitoring data from farmed salmon (Salmo salar and Oncorhynchus spp.) in British Columbia, Canada, from 2011-2013. Aquaculture 499: 220-224. https://www.researchgate.net/publication/327315079.
*Bass, AL, SG Hinch, AK *Teffer, DA Patterson, KM Miller. 2019. Fisheries capture and infectious agents were associated with travel rate and survival of Chinook salmon during spawning migration through a natal river.  Fish Res 209: 156-166. https://doi.org/10.1016/j.fishres.2018.09.009
*Thakur KK, 4 authors KM Miller. 2019. Infectious agent detections in archived Sockeye salmon (Oncorhynchus nerka) samples from British Columbia (1985-1994).  J Fish Dis 2019: 1-15. https://onlinelibrary.wiley.com/doi/pdf/10.1111/jfd.12951
*Pagowski V, *Mordecai G, Miller, KM, *Schulze A, *Kaukinen K, *Ming T, *Li T, *Teffer A, *Tabata A, Suttle C. 2019. Distribution and phylogeny of erythrocytic necrosis virus (ENV) in salmon suggests marine origin. Viruses 11(4), p.358.  file:///C:/Users/pbs-ubc/Downloads/viruses-11-00358-v2.pdf
*Stevenson, CF, AL*Bass, NB *Furey, KM Miller, S Li, EL Rechisky, AS Porter, DW Welch, SG Hinch. 2019. Infectious agents and gene expression differ between sockeye salmon (Oncorhynchus nerka) smolt age classes but do not predict migration survival . Canadian Journal of Fisheries and Aquatic Sciences: https://doi.org/10.1139/cjfas-2019-0113.  EDITORS CHOICE AWARD
*Houde, ALS, 8 authors, Miller, KM, 2019. Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments. Comp Biochem Physiol D: Genomics and Proteomics 29:.32-42. https://www.sciencedirect.com/science/article/pii/S1744117X18301035
*Houde, ALS, 7 authors, Miller, KM. 2019. Discovery and validation of candidate smoltification gene expression biomarkers across multiple species and ecotypes of Pacific salmonids. Cons Physiol: 7(1), p.coz051. https://doi.org/10.1093/conphys/coz051
*Houde, ALS, 6 authors Miller, KM, 2019. Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity, temperature, but not dissolved oxygen. J. Exp. Biol, pp.jeb-198036. doi: 10.1242/jeb.198036
*Twardek WM, *Chapman JM, Miller KM, Beere MC, *Li S, *Kaukinen KH, Danylchuk AJ, Cooke SJ. 2019 Biotic and abiotic factors influencing microbial loads and physiology of migrating adult wild steelhead trout (Oncorhynchus mykiss).  Conservation Physiology 7(1); coz023, https://doi.org/10.1093/conphys/coz023
*Mordecai GJ, Miller KM, *Di Cicco E, *Schulze AD, *Kaukinen KH,*Ming TJ,*Li S, *Tabata A, *Teffer A, Patterson DA, Ferguson H, Suttle CA. 2019 Endangered wild salmon infected by newly discovered viruses. eLife, 8. doi: 10.7554/eLife.47615
Ferguson HW, *Di Cicco E, Sandoval C, MacPhee DD, Miller KM. 2019. Haemorrhagic kidney syndrome may not be a variation of Infectious salmon anaemia.  Aquaculture: 734498.  https://doi.org/10.1016/j.aquaculture.2019.734498
*Nekouei, O, Vanderstichel, R, *Kaukinen, KH, *Thakur, K, *Ming, T, Patterson, D.A, Trudel, M, Neville, C and Miller, KM. 2019. Comparison of infectious agents detected from hatchery and wild juvenile Coho salmon in British Columbia, 2008-2018. PloS one, 14(9). doi: 10.1371/journal.pone.0221956
*Teffer, A.K, Hinch, S, Miller, K,* Jeffries, K, Patterson, D, Cooke, S, Farrell, A, *Kaukinen, KH, *Li, S and Juanes, F. 2019. Cumulative Effects of Thermal and Fisheries Stressors Reveal Sex-Specific Effects on Infection Development and Early Mortality of Adult Coho Salmon (Oncorhynchus kisutch). Physiological and Biochemical Zoology, 92(5), pp.505-529.  DOI: 10.1086/705125

2020

Teffer, A.K. and Miller, K.M., 2019. A Comparison of Nonlethal and Destructive Methods for Broad‐Based Infectious Agent Screening of Chinook Salmon Using High‐Throughput qPCR. Journal of aquatic animal health, 31(3), pp.274-289.  DOI: 10.1002/aah.10079
*Teffer AK, Carr, J, *Tabata, A,* Schulze, A, Bradbury, I, Deschamps, D, Gillis, C-A, Brunsdon, EB, *Mordecai, G, Miller, KM.  2020. A molecular assessment of infectious agents carried by Atlantic salmon at sea and in three eastern Canadian rivers, including aquaculture escapees and North American and European origin wild stocks. Facets 5(1), 234-263; https://www.facetsjournal.com/doi/pdf/10.1139/facets-2019-0048
*Chapman, JM, *Teffer, AK, *Bass, AL, Patterson, DA, Hinch, SG, Miller, KM, Cooke, SJ. 2020. Handling, infectious agents, and physiological condition influence survival and post-release behaviour in migratory adult coho salmon after experimental displacement. Conserv Physiol 8(1): coaa033; doi:10.1093/conphys/coaa033.
Lennox, RJ, SH Eldøy, KW Vollset, KM Miller, S Li, KH *Kaukinen, TE Isaksen, and JG Davidsen. 2020. How pathogens affect the marine habitat use and migration of sea trout (Salmo trutta) in two Norwegian fjord systems. Journal of Fish Diseases 43: 729-746. DOI: 10.1111/jfd.13170 
Vollset, KW, Lennox, RJ, Barlaup, BT, Davidsen, J, Eldøy, SH, Isaksen, TE, Madhun, A, Karlsson, S, Garseth, Å, Miller, KM.   2020. Wild salmonids are running the gauntlet of pathogens and climate as fish farms expand northwards. ICES Journal of Marine Science: doi:10.1093/icesjms/fsaa138
Akbarzadeh, A., Houde, A.L.S., Sutherland, B.J., Günther, O.P. and Miller, K.M., 2020. Identification of hypoxia-specific biomarkers in salmonids using RNA-sequencing and validation using high-throughput qPCR. G3: Genes, Genomes, Genetics, 10(9), pp.3321-3336.  https://doi.org/10.1534/g3.120.401487
*Mordecai, GJ, *Di Cicco, Gunther, OP, *Schulze, AD, *Kaukinen, KH, *Li, S, *Tabata, A, *Ming, TJ, Ferguson, HW, Suttle, CA, Miller, KM. 2020. Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR.  Virus Evolution 7(1); https://doi.org/10.1093/ve/veaa069
Shea, D., Bateman, A., Li, S., Tabata, A., Schulze, A., Mordecai, G., Ogston, L., Volpe, J.P., Neil Frazer, L., Connors, B. and Miller, K.M., 2020. Environmental DNA from multiple pathogens is elevated near active Atlantic salmon farms. Proceedings of the Royal Society B, 287(1937), p.20202010.  https://doi.org/10.1098/rspb.2020.2010
*Bateman, AW, *Schulze, AD, *Kaukinen, KH, *Tabata, A, *Mordecai, G,* Flynn, K, *Di Cicco, E, Miller, KM. 2020. Descriptive multi-agent epidemiology via molecular screening on Atlantic salmon farms in the northeast Pacific Ocean. Sci Rep 11, 3466 (2021). https://doi.org/10.1038/s41598-020-78978-9.
Lehman, B, Johnson, R, Foott, S, Som, NA, Burgess, O, Adkison, M, Miller, K, Hallet, S, Purcell, M, Martínez-López, B, Valdes-Donoso, P, Connon, R, Fangu, N, Collins, AL. 2020. Disease in Central Valley salmon: Status and lessons from other systems. San Francisco Estuary and Watershed Science 18(3);  DOI: 10.15447//sfews.2020v18iss3art2

2021

Cooke, S.J., Raby, G.D., Bett, N.N., *Teffer, A.K., Burnett, N.J., Jeffries, K.M., Eliason, E.J., Martins, E.G., Miller, K.M., Patterson, D.A. and Nguyen, V.M., 2021. On conducting management-relevant mechanistic science for upriver migrating adult Pacific salmon. Conservation Physiology: Applications for Wildlife Conservation and Management. Oxford University Press, UK. DOI: 10.1093/oso/9780198843610.003.0003
Furey, N.B., Bass, A.L., Miller, K.M., Li, S., Lotto, A.G., Healy, S.J., Drenner, S.M. and Hinch, S.G., 2021. Infected juvenile salmon can experience increased predation during freshwater migration. Royal Society open science, 8(3), p.201522. DOI: 10.1098/rsos.201522
*Chapman, JM, Kelly, L, *Teffer, AK, Miller, KM, Cooke, SJ. 2021. Disease ecology of wild fish: Opportunities and challenges for linking infection metrics with behaviour, condition, and survival.  Canadian Journal of Fisheries and Aquatic Sciences, (ja). DOI: 10.1139/cjfas-2020-0315
Mordecai, G.J., Miller, K.M., Bass, A.L., Bateman, A.W., Teffer, A.K., Caleta, J.M., Di Cicco, E., Schulze, A.D., Kaukinen, K.H., Li, S. and Tabata, A., 2021. Aquaculture mediates global transmission of a viral pathogen to wild salmon. Science Advances, 7(22), p.eabe2592. DOI: 10.1126/sciadv.abe2592
Jeffries, K.M., Teffer, A., Michaleski, S., Bernier, N.J., Heath, D.D. and Miller, K.M., 2021. The use of non-lethal sampling for transcriptomics to assess the physiological status of wild fishes. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology, p.110629. DOI: 10.1016/j.cbpb.2021.110629
He, X., Gilmore, S.R., Sutherland, T.F., Hajibabaei, M., Miller, K.M., Westfall, K.M., Pawlowski, J. and Abbott, C.L., 2021. Biotic signals associated with benthic impacts of salmon farms from eDNA metabarcoding of sediments. Molecular Ecology, 30(13), pp.3158-3174. DOI: 10.1111/mec.15814
*Teffer AK, Hinch SG, Miller KM, Patterson DA, Beacham, TD, Cooke SJ, Farrell AP, Juanes F. In Press. River-acquired infections affect the health and longevity of adult sockeye salmon (Oncorhynchus nerka) exposed to multiple stressors. Molecular ecology (August 2021)
*Chapman, JM,  Lennox, RJ , *Twardek, WM, *Teffer, AK,  Robertson, MJ, Miller, KM,  Cooke, SJ.  In Press. Changes in the condition, infectious agents, and transcription profiles of wild Atlantic salmon during up-river migrations. Canadian Journal of Fisheries and Aquatic Sciences: In Press Jan 2021
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