Nathan R, Getz WM, Revilla E, Holyoak M, Kadmon R, Saltz D, et al. A movement ecology paradigm for unifying organismal movement research. Proc Nat Acad Sci. 2008;105(49):19052–9.
Ferguson SH, Taylor MK, Messier F. Influence of sea ice dynamics on habitat selection by polar bears. Ecology. 2000;81(3):761–72.
Hebblewhite M, Merrill E, McDermid G. A multi-scale test of the forage maturation hypothesis in a partially migratory ungulate population. Ecol Monogr. 2008;78(2):141–66.
Thomson RE. Oceanography of the British Columbia coast. Can Special Publ Fisheries Aquatic Sci 1981; 291.
Raymond JA, Hassel A. Some characteristics of freezing avoidance in two Osmerids, rainbow smelt and capelin. J Fish Biol. 2000;57(sa):1–7.
Sutton G, Pichegru L, Botha JA, Kouzani AZ, Adams S, Bost CA, et al. Multi-predator assemblages, dive type, bathymetry and sex influence foraging success and efficiency in African penguins. PeerJ. 2020;8: e9380.
Madigan DJ, Richardson AJ, Carlisle AB, Weber SB, Brown J, Hussey NE. Water column structure defines vertical habitat of twelve pelagic predators in the South Atlantic. ICES J Mar Sci. 2021;78(3):867–83.
Brown A, Thatje S. The effects of changing climate on faunal depth distributions determine winners and losers. Glob Change Biol. 2015;21(1):173–80.
Sallée JB, Pellichero V, Akhoudas C, Pauthenet E, Vignes L, Schmidtko S, et al. Summertime increases in upper-ocean stratification and mixed-layer depth. Nature. 2021;591(7851):592–8.
Brill RW, Lutcavage ME. Understanding environmental influences on movements and depth distributions of tunas and billfishes can significantly improve population assessments. Am Fish Soc Symp. 2001;25:179–98.
NMFS. Trawl rockfish conservation area (RCA) boundary modifications—final environmental assessment. NOAA National Marine Fisheries Service, Sustainable Fisheries Division, West Coast Region, 2014;200.
Bigelow KA, Maunder MN. Does habitat or depth influence catch rates of pelagic species? Can J Fish Aquat Sci. 2007;64(11):1581–94.
Wright BM, Ford JKB, Ellis GM, Deecke VB, Shapiro AD, Battaile BC, et al. Fine-scale foraging movements by fish-eating killer whales (Orcinus orca) relate to the vertical distributions and escape responses of salmonid prey (Oncorhynchus spp.). Mov Ecol. 2017;5(1):3.
Braun CD, Arostegui MC, Thorrold SR, Papastamatiou YP, Gaube P, Fontes J, et al. The functional and ecological significance of deep diving by large marine predators. Ann Rev Mar Sci. 2022;14:129–59.
Maravelias CD. Habitat selection and clustering of a pelagic fish: effects of topography and bathymetry on species dynamics. Can J Fish Aquatic Sci. 1999;56:437–50.
Genin A. Bio-physical coupling in the formation of zooplankton and fish aggregations over abrupt topographies. J Mar Syst. 2004;50:3–20.
Borland HP, Gilby BL, Henderson CJ, Leon JX, Schlacher TA, Connolly RM, et al. The influence of seafloor terrain on fish and fisheries: a global synthesis. Fish Fish. 2021;22(4):707–34.
Hays GC. A review of the adaptive significance and ecosystem consequences of zooplankton diel vertical migrations. Hydrobiologia. 2003;503:163–70.
Pothoven SA, Vanderploeg HA. Diet and prey selection of alewives in Lake Michigan: seasonal, depth, and interannual patterns. Trans Am Fish Soc. 2004;133(5):1068–77.
Kitagawa T, Kimura S, Nakata H, Yamada H. Diving behavior of immature, feeding Pacific bluefin tuna (Thunnus thynnus orientalis) in relation to season and area: the East China Sea and the Kuroshio–Oyashio transition region. Fish Oceanogr. 2004;13(3):161–80.
Gallagher CP, Guzzo MM, Dick TA. Seasonal depth and temperature use, and diel movements of lake trout (Salvelinus namaycush) in a subarctic lake. Arctic Sci. 2019;5(2):71–89.
Seitz AC, Norcross BL, Wilson D, Nielsen JL. Identifying spawning behavior in Pacific halibut, Hippoglossus stenolepis, using electronic tags. Environ Biol Fishes. 2005;73(4):445–51.
Teo SLH, Boustany A, Dewar H, Stokesbury MJW, Weng KC, Beemer S, et al. Annual migrations, diving behavior, and thermal biology of Atlantic bluefin tuna, Thunnus thynnus, on their Gulf of Mexico breeding grounds. Mar Biol. 2007;151(1):1–18.
Werner EE, Gilliam JF, Hall DJ, Mittelbach GG. An experimental test of the effects of predation risk on habitat use in fish. Ecology. 1983;64(6):1540–8.
Walters CJ, Juanes F. Recruitment limitation as a consequence of natural selection for use of restricted feeding habitats and predation risk taking by juvenile fish. Can J Fish Aquatic Sci. 1993;50:2058–70.
Braun CD, Gaube P, Sinclair-Taylor TH, Skomal GB, Thorrold SR. Mesoscale eddies release pelagic sharks from thermal constraints to foraging in the ocean twilight zone. Proc Natl Acad Sci USA. 2019;116(35):17187–92.
Døving KB, Westerberg H, Johnsen PB. Role of olfaction in the behavioral and neuronal responses of Atlantic salmon, Salmo salar, to hydrographic stratification. Can J Fish Aquat Sci. 1985;42(10):1658–67.
Dittman AH, Quinn TP. Homing in Pacific salmon: mechanisms and ecological basis. J Exp Biol. 1996;199(1):83–91.
Roscoe DW, Hinch SG, Cooke SJ, Patterson DA. Behaviour and thermal experience of adult sockeye salmon migrating through stratified lakes near spawning grounds: the roles of reproductive and energetic states. Ecol Freshw Fish. 2010;19(1):51–62.
Ford JK, Ellis GM, Barrett-Lennard LG, Morton AB, Palm RS, Balcomb KC III. Dietary specialization in two sympatric populations of killer whales (Orcinus orca) in coastal British Columbia and adjacent waters. Can J Zool. 1998;76(8):1456–71.
Shirk PL, Richerson K, Banks M, Tuttle V. Predicting bycatch of Chinook salmon in the Pacific hake fishery using spatiotemporal models. ICES J Mar Sci. 2023;80:133–44.
Sabal MC, Richerson K, Moran P, Levi T, Tuttle VJ, Banks M. Warm oceans exacerbate Chinook salmon bycatch in the Pacific hake fishery driven by thermal and diel depth-use behaviours. Fish Fish. 2023;24(6):910–23.
Orsi JA, Wertheimer AC. Marine vertical distribution of juvenile Chinook and coho salmon in southeastern Alaska. Trans Am Fish Soc. 1995;124(2):159–69.
Hinke JT, Watters GM, Boehlert GW, Zedonis P. Ocean habitat use in autumn by Chinook salmon in coastal waters of Oregon and California. Mar Ecol Prog Ser. 2005;285:181–92.
Walker RV, Myers KW. Behavior of Yukon River Chinook salmon in the Bering Sea as inferred from archival tag data. North Pacific Anadromous Fish Commission Bulletin. 2009;5:121–30.
Smith JM, Fresh KL, Kagley AN, Quinn TP. Ultrasonic telemetry reveals seasonal variation in depth distribution and diel vertical migrations of sub-adult Chinook and coho salmon in puget sound. Mar Ecol Prog Ser. 2015;532:227–42.
Arostegui MC, Essington TE, Quinn TP. Interpreting vertical movement behavior with holistic examination of depth distribution: a novel method reveals cryptic diel activity patterns of Chinook salmon in the Salish Sea. Anim Biotelemetry. 2017;5(1):2.
Courtney MB, Evans MD, Strøm JF, Rikardsen AH, Seitz AC. Behavior and thermal environment of Chinook salmon Oncorhynchus tshawytscha in the North Pacific Ocean, elucidated from pop-up satellite archival tags. Environ Biol Fishes. 2019;102(8):1039–55.
Healey MC. Life History of Chinook Salmon. In: Groot C, Margolis L, eds. Life histories of Pacific Salmon. UBC Press; 1991.
Brodeur RD, Daly EA, Sturdevant MV, Miller TW, Moss JH, Thiess ME, et al. Regional comparisons of juvenile salmon feeding in coastal marine waters off the west coast of North America. Am Fish Soc Symp. 2007;57:183–203.
Weitkamp LA. Marine distributions of Chinook salmon from the west coast of North America determined by coded wire tag recoveries. Trans Am Fish Soc. 2010;139(1):147–70.
Freshwater C, Anderson SC, Beacham TD, Luedke W, Wor C, King J. An integrated model of seasonal changes in stock composition and abundance with an application to Chinook salmon. Peer J. 2021;9: e11163.
Crossin GT, Hinch SG. A nonlethal, rapid method for assessing the somatic energy content of migrating adult Pacific salmon. Trans Am Fish Soc. 2005;134:184–91.
Beacham TD, Wallace C, MacConnachie C, Jonsen K, McIntosh B, Candy JR, et al. Population and individual identification of Chinook Salmon in British Columbia through parentage-based tagging and genetic stock identification with single nucleotide polymorphisms. Can J Fish Aquatic Sci. 2018;75(7):1096–105.
Center NNGD. British Columbia 3 arc-second bathymetric digital elevation model. NOAA Nat Centers Environ Inform 2007.
Center NNGD. La Push, Washington 1/3 arc-second MHW Coastal Digital Elevation Model. NOAA Nat Centers Environ Inform 2007.
Kelley D, Richards C. Oce: Analysis of oceanographic data; 2022.
Thieurmel B, Elmarhraouii A. Suncalc: Compute sun position, sunlight phases, moon position and lunar phase; 2019.
MacCready P, McCabe RM, Siedlecki SA, Lorenz M, Giddings SN, Bos J, et al. Estuarine circulation, mixing, and residence times in the Salish Sea. J Geophys Res Oceans. 2021;126(2): e2020JC016738.
Haidvogel DB, Arango HG, Hedstrom K, Beckmann A, Malanotte-Rizzoli P, Shchepetkin AF. Model evaluation experiments in the North Atlantic Basin: simulations in nonlinear terrain-following coordinates. Dyn Atmos Oceans. 2000;32(3–4):239–81.
Shchepetkin AF, McWilliams JC. The regional oceanic modeling system (ROMS): a split-explicit, free-surface, topography-following-coordinate oceanic model. Ocean Model. 2005;9(4):347–404.
Winslow L, Read J, Woolway R, Brentrup J, Leach T, Zwart J, et al. rLakeAnalyzer: Lake Phys Tools 2019.
Lerner JE, Hunt BPV. Seasonal variation in the lipid content of Fraser River Chinook Salmon (Oncorhynchus tshawytscha) and its implications for Southern Resident Killer Whale (Orcinus orca) prey quality. Sci Rep. 2023;13:2675.
Breiman L. Random forests. Mach Learn. 2001;45(1):5–32.
Friedman JH. Greedy function approximation: a gradient boosting machine. Ann Stat. 2001;29(5):1189–232.
Valavi R, Elith J, Lahoz-Monfort JJ, Guillera-Arroita G. blockCV: an r package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models. Methods Ecol Evol. 2019;10(2):225–32.
Kuhn M. Caret: Building predictive models in R using the caret package. J Stat Softw. 2008;28(5):1–26.
Wright MN, Ziegler A. Ranger: a fast implementation of random forests for high dimensional data in C++ and R. J Stat Softw. 2017;77(1):1–17.
Wager S, Hastie T, Efron B. Confidence intervals for random forests: the jackknife and the infinitesimal jackknife. J Mach Learn Res. 2015;15(1):1625–51.
R Core Team. R: A Language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing; 2021.
Geurts P, Ernst D, Wehenkel L. Extremely randomized trees. Mach Learn. 2006;63(1):3–42.
Bakun A. Vertical ambush corridors: intriguing multi-mechanism ecological structures embedded in the kinetic fluid architectures of ocean living resource production systems. Fish Fish. 2023;24(1):3–20.
Bakun A. Patterns in the Ocean: processes and marine population dynamics. La Jolla, California: California Sea Grant; 1996.
Pike GC. Age, growth and maturity studies on the pacific anchovy (Engraulis Mordax) from the coast of British Columbia [Master of Arts]. Univeristy of British Columbia; 1951.
Carlson HR. Seasonal distribution and environment of Pacific herring near Auke Bay, Lynn Canal, Southeastern Alaska. Trans Am Fish Soc. 1980;109:71–8.
Brown ED, Seitz J, Norcross BL, Huntington HP. Ecology of herring and other forage fish as recorded by resource users of Prince William Sound and the outer Kenai Peninsula, Alaska. Alaska Fish Res Bull. 2002;9(2):75–101.
Hanson MB, Baird RW, Ford JKB, Hempelmann-halos J, Doornik DMV, Candy JR, et al. Species and stock identification of prey consumed by endangered southern resident killer whales in their summer range. Endanger Species Res. 2010;11:69–82.
Hanson MB, Emmons CK, Ford MJ, Everett M, Parsons K, Park LK, et al. Endangered predators and endangered prey: seasonal diet of southern resident killer whales. PLoS ONE. 2021;16(3): e0247031.
Thornton SJ, Toews S, Stredulinsky EH, Gavrilchuk K, Burnham R, Noren DP, et al. Southern resident killer whale (Orcinus orca) summer distribution and habitat use in the southern Salish Sea and the Swiftsure Bank area (2009 to 2020). DFO Canadian Science Advisory Secretariat Research Document. 2022; 2022/037:56 p.
Gregr EJ, Trites AW. Predictions of critical habitat for five whale species in the waters of coastal British Columbia. Can J Fish Aquat Sci. 2001;58(7):1265–85.
Gregr E, Trites A. A novel presence-only validation technique for improved Steller sea lion Eumetopias jubatus critical habitat descriptions. Mar Ecol Prog Ser. 2008;365:247–61.
Carlisle AB, Perle CR, Goldman KJ, Block BA. Seasonal changes in depth distribution of salmon sharks (Lamna ditropis) in Alaskan waters: implications for foraging ecology. Can J Fish Aquat Sci. 2011;68(11):1905–21.
Logan RK, Vaudo JJ, Wetherbee BM, Shivji MS. Patrolling the border: billfish exploit the hypoxic boundary created by the world’s largest oxygen minimum zone. J Anim Ecol. 2023;92(8):1658–71.
Berman CH, Quinn TP. Behavioural thermoregulation and homing by spring Chinook salmon, Oncorhynchus tshawytscha (Walbaum), in the Yakima river. J Fish Biol. 1991;39(3):301–12.
Minke-Martin V, Hinch SG, Braun DC, Burnett NJ, Casselman MT, Eliason EJ, et al. Physiological condition and migdratory experience affect fitness-related outcomes in adult female sockeye salmon. Ecol Freshw Fish. 2018;27(1):296–309.
Hinke JT, Foley DG, Wilson C, Watters GM. Persistent habitat use by Chinook salmon Oncorhynchus tshawytscha in the coastal ocean. Mar Ecol Prog Ser. 2005;304:207–20.
Winant CD, Bratkovich AW. Temperature and currents on the southern California shelf: a description of the variability. J Phys Oceanogr. 1981;11(1):71–86.
Hay DE, McCarter PB. Continental shelf area and distribution, abundance, and habitat of herring in the North Pacific. In: Forage fishes in marine ecosystems: proceedings of the international symposium on the role of forage fishes in Marine ecosystems. vol. 97–01. Anchorage, Alaska, USA: University of Alaska Sea Grant College Program, Fairbanks, Alaska; 1996. p. 559-72.
Quinn TP. The behaviour and ecology of pacific salmon and trout. 2nd ed. Seattle, WA: University of British Columbia Press; 2018.
Ahrens RNM, Walters CJ, Christensen V. Foraging arena theory. Fish Fish. 2012;13(1):41–59.
Loher T, Webster RA, Carlile D. A test of the detection range of acoustic transmitters and receivers deployed in deep waters of Southeast Alaska, USA. Anim Biotelemetry. 2017;5(1):27.
Holbrook C, Hayden T, Binder T, Pye J. Glatos: A package for the great lakes acoustic telemetry observation system. R pack vers 0.5.1. 2019.
Metzger EJ, Smedstad OM, Thoppil P, Hurlburt H, Cummings J, Walcraft A, et al. US Navy operational global ocean and arctic ice prediction systems. Oceanography. 2014;27(3):32–43.
Mass CF, Albright M, Ovens D, Steed R, Maciver M, Grimit E, et al. Regional environmental prediction over the Pacific northwest. Bull Am Meteor Soc. 2003;84(10):1353–66.
Davis KA, Banas NS, Giddings SN, Siedlecki SA, MacCready P, Lessard EJ, et al. Estuary-enhanced upwelling of marine nutrients fuels coastal productivity in the U.S. Pacific Northwest. J Geophys Res Oceans. 2014;119(12):8778–99.
Siedlecki SA, Banas NS, Davis KA, Giddings S, Hickey BM, MacCready P, et al. Seasonal and interannual oxygen variability on the Washington and Oregon continental shelves. J Geophys Res Oceans. 2015;120(2):608–33.
Hoyer S, Hamman J. Xarray: N-d labeled arrays and datasets in Python. J Open Res Softw. 2017;5(1):10.
Kowarik A, Templ M. Imputation with the R Package VIM. J Stat Softw. 2016;74(7):1–16.
Bürkner PC. Brms: an R package for Bayesian multilevel models using Stan. J Stat Softw. 2017;80(1):1–28.
Add Comment