Predicting juvenile-to-adult survival in Chinook salmon using non-lethal scale-derived growth and regeneration indices

References

• Achord S, Zabel RW, Sandford BP. 2007. Migration timing, growth, and estimated parr-to-smolt survival rates of wild Snake River spring–summer Chinook salmon from the Salmon River basin, Idaho, to the lower Snake River. T Am Fish Soc. 136(1):142–154. doi: 10.1577/T05-308.1.
   Web of Science ®Google Scholar
• Barton BA. 2002. Stress in fishes: a diversity of responses with particular reference to changes in circulating corticosteroids. Integr Comp Biol. 42(3):517–525. doi: 10.1093/icb/42.3.517.
   PubMed Web of Science ®Google Scholar
• Beacham TD, Araujo HA, Tucker S, Trudel M, Fujiwara M. 2018. Validity of inferring size-selective mortality and a critical size limit in Pacific salmon from scale circulus spacing. PLoS One. 13(6):e0199418. doi: 10.1371/journal.pone.0199418.
   PubMed Web of Science ®Google Scholar
• Beakes MP, Sharron S, Charish R, Moore JW, Satterthwaite WH, Sturm E, Wells BK, Sogard SM, Mangel M. 2014. Using scale characteristics and water temperature to reconstruct growth rates of juvenile steelhead Oncorhynchus mykiss. J Fish Biol. 84(1):58–72. doi: 10.1111/jfb.12254.
   PubMed Web of Science ®Google Scholar
• Beckman BR, Dickhoff WW, Zaugg WS, Sharpe C, Hirtzel S, Schrock R, Larsen DA, Ewing RD, Palmisano A, Schreck CB, et al. 1999. Growth, smoltification, and smolt-to-adult return of spring chinook salmon from hatcheries on the Deschutes River, Oregon. T Am Fish Soc. 128(6):1125–1150. doi: 10.1577/1548-8659(1999)128<1125:GSASTA>2.0.CO;2.
   Web of Science ®Google Scholar
• Biro PA, Post JR, Abrahams MV. 2005. Ontogeny of energy allocation reveals selective pressure promoting risk-taking behaviour in young fish cohorts. Proc R Soc B. 272(1571):1443–1448. doi: 10.1098/rspb.2005.3096.
   PubMed Web of Science ®Google Scholar
• Budy P, Thiede GP, Bouwes N, Petrosky CE, Schaller HA. 2002. Evidence linking delayed mortality of Snake River salmon to their earlier hydrosystem experience. T Am Fish Soc. 22(1):35–51. doi: 10.1577/1548-8675(2002)022<0035:ELDMOS>2.0.CO;2.
   Google Scholar
• Burke BJ, Peterson WT, Beckman BR, Morgan C, Daly EA, Litz M, MacKenzie BR. 2013. Multivariate models of adult Pacific salmon returns. PLOS ONE. 8(1):e54134. doi: 10.1371/journal.pone.0054134.
   PubMed Web of Science ®Google Scholar
• Bürkner P-C. 2017. brms: an R package for Bayesian multilevel models using Stan. J Stat Softw. 80(1):1–28. doi: 10.18637/jss.v080.i01.
   Web of Science ®Google Scholar
• Bürkner P-C, Gabry J, Wever S, Johnson A, Modrak M, Badr HS, Weber F, Ben-Shachar MS, Rabel H, Mills SC, et al. 2023. Bayesian regression models using ‘Stan’, brms package, version 2.20.4, date published 2023-09-25.
   Google Scholar
• Campbell M. 2012. Obtaining scales from juvenile steelhead and Chinook salmon v1.0. Method ID 1360. https://www.monitoringresources.org/Document/Method/Details/1360.
   Google Scholar
• Claiborne AM, Fisher JP, Hayes SA, Emmett RL. 2011. Size at release, size-selective mortality, and age of maturity of Willamette River hatchery yearling Chinook salmon. T Am Fish Soc. 140(4):1135–1144. doi: 10.1080/00028487.2011.607050.
   Web of Science ®Google Scholar
• Denny SK, Fanning LM. 2016. A Mi’kmaw perspective on advancing salmon governance in Nova Scotia, Canada: setting the stage for collaborative co-existence. Int Indigenous Pol J. 7:4. doi: 10.18584/iipj.2016.7.3.4.
   Google Scholar
• Enberg K, Jorgensen C, Dunlop ES, Varpe O, Boukal DS, Baulier L, Eliassen S, Heino M. 2012. Fishing-induced evolution of growth: concepts, mechanisms and the empirical evidence. Mar Ecol-Evol Persp. 33(1):1–25. doi: 10.1111/j.1439-0485.2011.00460.x.
   Web of Science ®Google Scholar
• Faulkner JR, Bellerud BL, Widener DL, Zabel RW. 2019. Associations among fish length, dam passage history, and survival to adulthood in two at-risk species of Pacific salmon. T Am Fish Soc. 148(6):1069–1087. doi: 10.1002/tafs.10200.
   Web of Science ®Google Scholar
• Fisher JP, Pearcy WG. 1990. Spacing of scale circuli versus growth rate in young Coho salmon. Fish Bull. 88:637–643.
   Google Scholar
• Fisher JP, Pearcy WG. 2005. Seasonal changes in growth of Coho salmon (Oncorhynchus kisutch) off Oregon and Washington and concurrent changes in the spacing of scale circuli. Fish Bull. 103:34–51.
   Google Scholar
• Ford MJ, editor. 2022. Biological viability assessment update for pacific salmon and steelhead listed under the Endangered Species Act: Pacific Northwest. In: U.S. Department of Commerce, NOAA Technical Memorandum NMFS-NWFSC-171. doi: 10.25923/kq2n-ke70.
   Google Scholar
• Fukuwaka MA. 1998. Scale and otolith patterns prove growth history of Pacific salmon. N Pac Anadromous Fish Commission Bull. 1:190–198.
   Google Scholar
• Gamble MM, Connelly KA, Gardner JR, Chamberlin JW, Warheit KI, Beauchamp DA. 2018. Size, growth, and size-selective mortality of subyearling Chinook salmon during early marine residence in Puget Sound. T Am Fish Soc. 147(2):370–389. doi: 10.1002/tafs.10032.
   Web of Science ®Google Scholar
• Gao SY, Sun P, Zhao XY, Chang K, Chen WJ. 2023. Waterborne copper exposure decreases fish growth and survival by promoting gills and liver impairments in largemouth bass (Micropterus salmoides). Environ Sci Pollut Res. 30(56):119204–119216. doi: 10.1007/s11356-023-30755-7.
   PubMed Web of Science ®Google Scholar
• Garrido S, Ben-Hamadou R, Santos AMP, Ferreira S, Teodósio MA, Cotano U, Irigoien X, Peck MA, Saiz E, Ré P. 2015. Born small, die young: Intrinsic, size-selective mortality in marine larval fish. Sci Rep. 5(1):17065. doi: 10.1038/srep17065.
   PubMedGoogle Scholar
• Gelman A, Carlin JB, Stern HS, Dunson DB, Vehtari A, Rubin DB. 2014. Bayesian Data Analysis. 3rd ed. Boca Raton, Florida: Chapman & Hall Book, CRC Press.
   Google Scholar
• Ghods S, Waddell S, Weller E, Renteria C, Jiang HY, Janak JM, Mao SS, Linley TJ, Arola D. 2020. On the regeneration of fish scales: structure and mechanical behavior. J Exp Biol. 223:jeb211144. doi: 10.1242/jeb.211144.
   PubMed Web of Science ®Google Scholar
• Goertler PAL, Scheuerell MD, Simenstad CA, Bottom DL, Castonguay M. 2016. Estimating common growth patterns in juvenile Chinook salmon (Oncorhynchus tshawytscha) from diverse genetic stocks and a large spatial extent. PLOS ONE. 11(10):e0162121. doi: 10.1371/journal.pone.0162121.
   PubMed Web of Science ®Google Scholar
• Gosselin JL, Anderson JJ, Sanderson BL, Middleton MA, Sandford BP, Weitkamp LA. 2022. Assessing seasonal and biological indices of juvenile Chinook salmon for freshwater decision triggers that increase ocean survival. Freshw Sci. 41(2):253–269. doi: 10.1086/720007.
   Web of Science ®Google Scholar
• Gosselin JL, Buhle ER, Van Holmes C, Beer WN, Iltis S, Anderson JJ. 2021. Role of carryover effects in conservation of wild Pacific salmon migrating regulated rivers. Ecosphere. 12(7):e03618. doi: 10.1002/ecs2.3618.
   Web of Science ®Google Scholar
• Gregory SD, Ibbotson AT, Riley WD, Nevoux N, Lauridsen RB, Russell IC, Britton JR, Gillingham PK, Simmons OM, Rivot E, et al. 2019. Atlantic salmon return rate increases with smolt length. ICES J Mar Sci. 76(6):1702–1712. doi: 10.1093/icesjms/fsz066.
   Web of Science ®Google Scholar
• Hernandez K, Copeland T, Wright K. 2014. Quantitative assessment of scale resorption in migrating and spawning steelhead of the Snake River Basin. T Am Fish Soc. 143(6):1562–1568. doi: 10.1080/00028487.2014.954054.
   Web of Science ®Google Scholar
• Hinrichsen RA, Paulsen CM. 2020. Low carrying capacity a risk for threatened Chinook salmon. Ecol Model. 432:109223. doi: 10.1016/j.ecolmodel.2020.109223.
   Web of Science ®Google Scholar
• Hostetter NJ, Evans AF, Loge FJ, Rr O, Cramer BM, Fryer D, Collis K. 2015. The influence of individual fish characteristics on survival and detection: similarities across two salmonid species. N Am J Fish Manage. 35(5):1034–1045. doi: 10.1080/02755947.2015.1077176.
   Web of Science ®Google Scholar
• Houde ALS, Akbarzadeh A, Güntherd OP, Li S, Pattersone DA, Farrell AP, Hinch SG, Miller KM. 2019. Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity, temperature, but not dissolved oxygen. J Exp Biol. 222:jeb198036. doi: 10.1242/jeb.198036.
   PubMed Web of Science ®Google Scholar
• Izzo LK, Zydlewski J. 2017. Retrospective analysis of seasonal ocean growth rates of two sea winter Atlantic salmon in eastern Maine using historic scales. Mar Coast Fish. 9(1):357–372. doi: 10.1080/19425120.2017.1334723.
   Web of Science ®Google Scholar
• Jensen AJ, Maoileidigh NO, Thomas K, Einarsson SM, Haugland M, Erkinaro J, Fiske P, Friedland KD, Gudmundsdottir AK, Haantie J, et al. 2012. Age and fine-scale marine growth of Atlantic salmon post-smolts in the Northeast Atlantic. ICES J Mar Sci. 69(9):1668–1677. doi: 10.1093/icesjms/fss086.
   Web of Science ®Google Scholar
• Johnson J, Johnson T, Copeland T. 2012. Defining life histories of precocious male parr, minijack, and jack Chinook salmon using scale patterns. T Am Fish Soc. 141(6):1545–1556. doi: 10.1080/00028487.2012.705256.
   Web of Science ®Google Scholar
• Killen SS, Humphries M. 2014. Growth trajectory influences temperature preference in fish through an effect on metabolic rate. J Anim Ecol. 83(6):1513–1522. doi: 10.1111/1365-2656.12244.
   PubMed Web of Science ®Google Scholar
• Kovach M. 2021. Indigenous methodologies: characteristics, conversations, and contexts. 2nd ed. Toronto: University of Toronto Press.
   Google Scholar
• Lamb JJ, Sandford BP, Axel GA, Nesbit MG, Sanderson BL. 2019. Monitoring the migrations of wild Snake River spring/summer Chinook salmon juveniles: fish collection and tagging, 2019. Report of research by the Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, for the Division of Fish and Wildlife, Bonneville Power Administration, U.S. Department of Energy, Portland, Oregon.Contract No.: 46273 REL 163.
   Google Scholar
• Lamb JJ, Sandford BP, Axel GA, Smith SG, Nesbit MG, Sanderson BL. 2020. Monitoring the migrations of wild Snake River spring/summer Chinook salmon juveniles: survival and timing, 2019. Report of research by the Fish Ecology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington, for the Division of Fish and Wildlife, Bonneville Power Administration, U.S. Department of Energy, Portland, Oregon. Contract No.: 46273 REL 163.
   Google Scholar
• Lee Q, Punt AE. 2018. Extracting a time-varying climate-driven growth index from otoliths for use in stock assessment models. Fish Res. 200:93–103. doi: 10.1016/j.fishres.2017.12.014.
   Web of Science ®Google Scholar
• Mantua NJ, Hare SR, Zhang Y, Wallace JM, Francis RC. 1997. A Pacific interdecadal climate oscillation with impacts on salmon production. Bull Amer Meteor Soc. 78(6):1069–1079. doi: 10.1175/1520-0477(1997)078<1069:APICOW>2.0.CO;2.
   Web of Science ®Google Scholar
• Morrongiello JR, Thresher RE, Smith DC. 2012. Aquatic biochronologies and climate change. Nat Clim Change. 2(12):849–857. doi: 10.1038/nclimate1616.
   Web of Science ®Google Scholar
• [NWFSC] Northwest Fisheries Science Center. 2022. Seasonal transport – a study to determine the seasonal effects of transporting fish from the Snake River to optimize a transportation strategy. Seattle (WA): Northwest Fisheries Science Center. https://www.fisheries.noaa.gov/inport/item/20563.
   Google Scholar
• Peyronnet A, Friedland KD, Maoileidigh NO, Manning M, Poole WR. 2007. Links between patterns of marine growth and survival of Atlantic salmon Salmo salar L. J Fish Biol. 71(3):684–700. doi: 10.1111/j.1095-8649.2007.01538.x.
   Web of Science ®Google Scholar
• Portz DE, Woodley CM, Cech JJ. 2006. Stress-associated impacts of short-term holding on fishes. Rev Fish Biol Fisher. 16(2):125–170. doi: 10.1007/s11160-006-9012-z.
   Web of Science ®Google Scholar
• Quist MC, Isermann DA. 2017. Age and growth of fishes: principles and techniques. Bethesda (MD): American Fisheries Society.
   Google Scholar
• R Core Team. 2023. R: a language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing. https://www.R-project.org/.
   Google Scholar
• Reid AJ, Eckert LE, Lane JF, Young N, Hinch SG, Darimont CT, Cooke SJ, Ban NC, Marshall A. 2021. “Two-eyed seeing”: an indigenous framework to transform fisheries research and management. Fish Fisher. 22(2):243–261. doi: 10.1111/faf.12516.
   Web of Science ®Google Scholar
• Sogard SM. 1997. Size-selective mortality in the juvenile stage of teleost fishes: a review. Bull Mar Sci. 60:1129–1157.
   Web of Science ®Google Scholar
• Stan Development Team. 2022. Stan modeling language users guide and reference manual, version 2.34. https://mc-stan.org.
   Google Scholar
• Stan Development Team. 2024. RStan: the R interface to Stan. R package version 2.32.5. https://mc-stan.org/.
   Google Scholar
• Thorstensen MJ, Vandervelde CA, Bugg WS, Michaleski S, Vo L, Mackey TE, Lawrence MJ, Jeffries KM. 2022. Non-lethal sampling supports integrative movement research in freshwater fish. Front Genet. 13:19. doi: 10.3389/fgene.2022.795355.
   Web of Science ®Google Scholar
• Todd CD, Hanson NN, Boehme L, Revie CW, Marques AR. 2021. Variation in the post-smolt growth pattern of wild one sea-winter salmon (Salmo salar L.), and its linkage to surface warming in the eastern North Atlantic Ocean. J Fish Biol. 98(1):6–16. doi: 10.1111/jfb.14552.
   PubMed Web of Science ®Google Scholar
• Todd CD, Whyte BDM, Jc M, Revie CW, Lonergan ME, Hanson NN, Gillanders BM. 2014. A simple method of dating marine growth circuli on scales of wild one sea-winter and two sea-winter Atlantic salmon (Salmo salar). Can J Fish Aquat Sci. 71(5):645–655. doi: 10.1139/cjfas-2013-0359.
   Web of Science ®Google Scholar
• Ulaski ME, Finkle H, Westley PAH. 2020. Direction and magnitude of natural selection on body size differ among age-classes of seaward-migrating Pacific salmon. Evol Appl. 13(8):2000–2013. doi: 10.1111/eva.12957.
   PubMed Web of Science ®Google Scholar
• Vehtari A, Gabry J, Magnusson M, Yao Y, Bürkner P, Paananen T, Gelman A. 2024. loo: efficient leave-one-out cross-validation and WAIC for Bayesian models. R package version 2.7.0. https://mc-stan.org/loo/.
   Google Scholar
• Vehtari A, Gelman A, Gabry J. 2017. Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC. Stat Comput. 27(5):1413–1432. doi: 10.1007/s11222-016-9696-4.
   Web of Science ®Google Scholar
• Walker BM, Sutton TM. 2016. Growth-increment formation using otoliths and scales for age-0 Chinook salmon. N Am J Fish Manage. 36(5):995–999. doi: 10.1080/02755947.2016.1184202.
   Web of Science ®Google Scholar
• Woodson LE, Wells BK, Weber PK, MacFarlane RB, Whitman GE, Johnson RC. 2013. Size, growth, and origin-dependent mortality of juvenile Chinook salmon Oncorhynchus tshawytscha during early ocean residence. Mar Ecol Prog Ser. 487:163–175. doi: 10.3354/meps10353.
   Web of Science ®Google Scholar
• Yasumiishi EM, Farley EV, Ruggerone GT, Agler BA, Wilson LI. 2016. Trends and factors influencing the length, compensatory growth, and size-selective mortality of juvenile Bristol Bay, Alaska, Sockeye salmon at sea. Mar Coast Fish. 8:315–333. doi: 10.1080/19425120.2016.1167793.
   Web of Science ®Google Scholar