Individual based modeling of fish migration in a 2-D river system: model description and case study

  • Marcía N. SnyderEmail author
  • Nathan H. Schumaker
  • Joseph L. Ebersole
  • Jason B. Dunham
  • Randy L. Comeleo
  • Matthew L. Keefer
  • Peter Leinenbach
  • Allen Brookes
  • Ben Cope
  • Jennifer Wu
  • John Palmer
  • Druscilla Keenan
Research Article



Diadromous fish populations in the Pacific Northwest face challenges along their migratory routes from declining habitat quality, harvest, and barriers to longitudinal connectivity. These stressors complicate the prioritization of proposed management actions intended to improve conditions for migratory fishes including anadromous salmon and trout.


We describe a multi-scale hybrid mechanistic–probabilistic simulation model linking migration corridor conditions to fish fitness outcomes. We demonstrate the model’s utility using a case study of salmon and steelhead adults in the Columbia River migration corridor exposed to spatially- and temporally-varying stressors.


The migration corridor simulation model is based on a behavioral decision tree that governs individual interactions with the environment, and an energetic submodel that estimates the hourly costs of migration. Emergent properties of the migration corridor simulation model include passage time, energy use, and survival.


We observed that the simulated fish’s initial energy density, the migration corridor temperatures they experienced, and their history of behavioral thermoregulation were the primary determinants of their fitness outcomes. Insights gained from use of the model might be exploited to identify management interventions that increase successful migration outcomes.


This paper describes new methods that extend the suite of tools available to aquatic biologists and conservation practitioners. We have developed a 2-dimensional spatially-explicit behavioral and physiological model and illustrated how it can be used to simulate fish migration within a river system. Our model can be used to evaluate trade-offs between behavioral thermoregulation and fish fitness at population scales.


Individual based model Thermoregulation Salmon HexSim Migration 



We would like to thank two anonymous reviewers for their insightful comments. The information in this document has been funded in part by the U.S. Environmental Protection Agency. It has been subjected to review by the National Health and Environmental Effects Research Laboratory’s Western Ecology Division and approved for publication. Approval does not signify that the contents reflect the views of the Agency, nor does mention of trade names or commercial products constitute endorsement or recommendation for use. The information in this document has been approved by, and does represent the views of the USGS.

Supplementary material

10980_2019_804_MOESM1_ESM.pdf (330 kb)
Supplementary material 1 (PDF 330 kb)
10980_2019_804_MOESM2_ESM.pdf (120 kb)
Supplementary material 2 (PDF 120 kb)


  1. Arismendi I, Safeeq M, Johnson SL, Dunham JB, Haggerty R (2012) Increasing synchrony of high temperature and low flow in western North American streams: double trouble for coldwater biota? Hydrobiologia 712:61–70CrossRefGoogle Scholar
  2. Armstrong JB, Ward EJ, Schindler DE, Lisi PJ (2016) Adaptive capacity at the northern front: sockeye salmon behaviourally thermoregulate during novel exposure to warm temperatures. Conserv Physiol 4:cow039CrossRefGoogle Scholar
  3. August SM, Hicks BJ (2007) Water temperature and upstream migration of glass eels in New Zealand: implications of climate change. Environ Biol Fishes 81:195–205CrossRefGoogle Scholar
  4. Battin J (2004) When good animals love bad habitats: ecological traps and the conservation of animal populations. Conserv Biol 18:1482–1491CrossRefGoogle Scholar
  5. Bellmore RJ, Duda JJ, Craig LS, Greene SL, Torgersen CE, Collins MJ, Vittum K (2016) Status and trends of dam removal research in the United States. Wiley Interdiscip Rev 4:e1164CrossRefGoogle Scholar
  6. Berman CH, Quinn TP (1991) Behavioural thermoregulation and homing by spring chinook salmon, Oncorhynchus tshawytscha (Walbaum), in the Yakima River. J Fish Biol 39:301–312CrossRefGoogle Scholar
  7. Bowerman TE, Pinson-Dumm A, Peery CA, Caudill CC (2017) Reproductive energy expenditure and changes in body morphology for a population of Chinook salmon Oncorhynchus tshawytscha with a long distance migration. J Fish Biol 90:1960–1979CrossRefGoogle Scholar
  8. Brett JR (1971) Energetic responses of salmon to temperature. A study of some thermal relations in the physiology and freshwater ecology of Sockeye Salmon (Oncorhynchus nerkd). Am Zool 11:99–113CrossRefGoogle Scholar
  9. Busby PJ, Wainwright TC, Bryant GJ, Lierheimer LJ, Waples RS, Waknitz FW, Lagomarsino IV (1996) Status review of west coast steelhead from Washington, Idaho, Oregon, and California. U.S. Department of Commerce, National Marine Fisheries Service, Northwest Fisheries Science Center, WashingtonGoogle Scholar
  10. Connor WP, Tiffan KF, Chandler JA, Rondorf DW, Arnsberg BD, Anderson KC (2018) Upstream migration and spawning success of Chinook Salmon in a highly developed, seasonally warm river system. Rev Fish Sci Aquac 27(1):1–50Google Scholar
  11. Cooke SJ, Hinch SG, Farrell AP, Patterson DA, Miller-Saunders K, Welch DW, Donaldson MR, Hanson KC, Crossin GT, Mathes MT, Lotto AG (2008) Developing a mechanistic understanding of fish migrations by linking telemetry with physiology, behavior, genomics and experimental biology: an interdisciplinary case study on adult Fraser River sockeye salmon. Fisheries 33:321–339CrossRefGoogle Scholar
  12. Crossin GT, Hinch SG, Cooke SJ, Welch DW, Patterson DA, Jones SR, Lotto AG, Leggatt RA, Mathes MT, Shrimpton JM, Van Der Kraak G (2008) Exposure to high temperature influences the behaviour, physiology, and survival of sockeye salmon during spawning migration. Can J Zool 86:127–140CrossRefGoogle Scholar
  13. Crossin GT, Hinch SG, Farrell AP, Higgs DA, Lotto AG, Oakes JD, Healey MC (2004) Energetics and morphology of sockeye salmon: effects of upriver migratory distance and elevation. J Fish Biol 65:788–810CrossRefGoogle Scholar
  14. Crozier LG, Bowerman TE, Burke BJ, Keefer ML, Caudill CC (2017) High-stakes steeplechase: a behavior-based model to predict individual travel times through diverse migration segments. Ecosphere 8:e01965CrossRefGoogle Scholar
  15. Deslauriers D, Chipps SR, Breck JE, Rice JA, Madenjian CP (2017) Fish bioenergetics 4.0: an R-based modeling application. Fisheries 42:586–596CrossRefGoogle Scholar
  16. Dickerson BR, Brinck KW, Willson MF, Bentzen P, Quinn TP (2005) Relative importance of salmon body size and arrival time at breeding grounds to reproductive success. Ecology 86:347–352CrossRefGoogle Scholar
  17. Dietrich JP, Van Gaest AL, Strickland SA, Arkoosh MR (2014) The impact of temperature stress and pesticide exposure on mortality and disease susceptibility of endangered Pacific salmon. Chemosphere 108:353–359CrossRefGoogle Scholar
  18. Dunning JB, Danielson BJ, Ronald Pulliam H (1992) Ecological processes that affect populations in complex landscapes. Oikos 65:169CrossRefGoogle Scholar
  19. Dunning JB, Stewart DJ, Danielson BJ, Noon BR, Root TL, Lamberson RH, Stevens EE (1995) Spatially explicit population models: current forms and future uses. Ecol Appl 5(1):3–11CrossRefGoogle Scholar
  20. Ebersole JL, Liss WJ, Frissell CA (2001) Relationship between stream temperature, thermal refugia and rainbow trout Oncorhynchus mykiss abundance in arid-land streams in the northwestern United States. Ecol Freshw Fish 10:1–10CrossRefGoogle Scholar
  21. Fausch KD, Torgersen CE, Baxter CV, Li HW (2002) Landscapes to riverscapes: bridging the gap between research and conservation of stream fishes. Bioscience 52:483CrossRefGoogle Scholar
  22. Frissell CA, Liss WJ, Warren CE, Hurley MD (1986) A hierarchical framework for stream habitat classification: viewing streams in a watershed context. Environ Manage 10:199–214CrossRefGoogle Scholar
  23. Fullerton AH, Burke BJ, Lawler JJ, Torgersen CE, Ebersole JL, Leibowitz SG (2017) Simulated juvenile salmon growth and phenology respond to altered thermal regimes and stream network shape. Ecosphere 8:1–23CrossRefGoogle Scholar
  24. Geist DR, Brown RS, Cullinan VI, Mesa MG, Vanderkooi SP, McKinstry CA (2003) Relationships between metabolic rate, muscle electromyograms and swim performance of adult chinook salmon. J Fish Biol 63:970–989CrossRefGoogle Scholar
  25. Goniea TM, Keefer ML, Bjornn TC, Peery CA, Bennett DH, Stuehrenberg LC (2006) Behavioral thermoregulation and slowed migration by adult fall Chinook Salmon in response to high columbia river water temperatures. Trans Am Fish Soc 135:408–419CrossRefGoogle Scholar
  26. Healey M (2011) The cumulative impacts of climate change on Fraser River sockeye salmon (Oncorhynchus nerka) and implications for management. Can J Fish Aquat Sci 68:718–737CrossRefGoogle Scholar
  27. Isaak DJ, Wenger SJ, Young MK (2017) Big biology meets microclimatology: defining thermal niches of ectotherms at landscape scales for conservation planning. Ecol Appl 27:977–990CrossRefGoogle Scholar
  28. Isaak DJ, Wollrab S, Horan D, Chandler G (2011) Climate change effects on stream and river temperatures across the northwest U.S. from 1980–2009 and implications for salmonid fishes. Clim Change 113:499–524CrossRefGoogle Scholar
  29. Isaak DJ, Young MK, Luce CH, Hostetler SW, Wenger SJ, Peterson EE, Ver Hoef JM, Groce MC, Horan DL, Nagel DE (2016) Slow climate velocities of mountain streams portend their role as refugia for cold-water biodiversity. Proc Natl Acad Sci USA 113:4374–4379CrossRefGoogle Scholar
  30. Jager HI, DeAngelis DL (2018) The confluences of ideas leading to, and the flow of ideas emerging from, individual-based modeling of riverine fishes. Ecol Modell 384:341–352CrossRefGoogle Scholar
  31. Jepson MA, Keefer ML, Naughton GP, Peery CA, Burke BJ (2010) Population composition, migration timing, and harvest of Columbia River Chinook Salmon in late summer and fall. N Am J Fish Manage 30:72–88CrossRefGoogle Scholar
  32. Jonsson B, Jonsson N (2009a) A review of the likely effects of climate change on anadromous Atlantic salmon Salmo salar and brown trout Salmo trutta, with particular reference to water temperature and flow. J Fish Biol 75:2381–2447CrossRefGoogle Scholar
  33. Jonsson B, Jonsson N (2009b) Migratory timing, marine survival and growth of anadromous brown trout Salmo truttain the River Imsa, Norway. J Fish Biol 74:621–638CrossRefGoogle Scholar
  34. Keefer ML, Clabough TS, Jepson MA, Johnson EL, Peery CA, Caudill CC (2018) Thermal exposure of adult Chinook salmon and steelhead: diverse behavioral strategies in a large and warming river system. PLoS ONE 13:e0204274CrossRefGoogle Scholar
  35. Keefer ML, Peery CA, High B (2009) Behavioral thermoregulation and associated mortality trade-offs in migrating adult steelhead (Oncorhynchus mykiss): variability among sympatric populations. Can J Fish Aquat Sci 66:1734–1747CrossRefGoogle Scholar
  36. Keefer ML, Peery CA, Jepson MA, Stuehrenberg LC (2004) Upstream migration rates of radio-tagged adult Chinook salmon in riverine habitats of the Columbia River basin. J Fish Biol 65:1126–1141CrossRefGoogle Scholar
  37. King HR, Pankhurst NW, Watts M, Pankhurst PM (2003) Effect of elevated summer temperatures on gonadal steroid production, vitellogenesis and egg quality in female Atlantic salmon. J Fish Biol 63:153–167CrossRefGoogle Scholar
  38. Klemetsen AA, Amundsen P, Dempson JB, Jonsson N, O’connell MF, Mortensen E (2003) Atlantic salmon Salmo salar L., brown trout Salmo trutta L. and Arctic charr Salvelinus alpinus (L.): a review of aspects of their life histories. Ecol Freshw Fish 12:1–59CrossRefGoogle Scholar
  39. Landguth EL, Bearlin A, Day CC, Dunham J (2016) CDMetaPOP: an individual-based, eco-evolutionary model for spatially explicit simulation of landscape demogenetics. Methods Ecol Evol 8:4–11CrossRefGoogle Scholar
  40. Lassalle G, Rochard E (2009) Impact of twenty-first century climate change on diadromous fish spread over Europe, North Africa and the Middle East. Glob Chang Biol 15:1072–1089CrossRefGoogle Scholar
  41. Lennox RJ, Chapman JM, Souliere CM, Tudorache C, Wikelski M, Metcalfe JD, Cooke SJ (2016) Conservation physiology of animal migration. Conserv Physiol 4:cov072CrossRefGoogle Scholar
  42. McCullough DA, Bartholow JM, Jager HI, Beschta RL, Cheslak EF, Deas ML, Ebersole JL, Foott JS, Johnson SL, Marine KR, Mesa MG (2009) Research in thermal biology: burning questions for coldwater stream fishes. Rev Fish Sci 17:90–115CrossRefGoogle Scholar
  43. Mesa MG, Magie CD (2006) Evaluation of energy expenditure in adult spring Chinook salmon migrating upstream in the Columbia River Basin: an assessment based on sequential proximate analysis. River Res Appl 22:1085–1095CrossRefGoogle Scholar
  44. Montgomery D (2003) King of fish: the thousand-year run of Salmon. Basic Books, CambridgeGoogle Scholar
  45. Ohlberger J, Ward EJ, Schindler DE, Lewis B (2018) Demographic changes in Chinook salmon across the Northeast Pacific Ocean. Fish Fish 19:533–546CrossRefGoogle Scholar
  46. Penaluna BE, Dunham JB, Railsback SF, Arismendi I, Johnson SL, Bilby RE, Safeeq M, Skaugset AE (2015) Local variability mediates vulnerability of trout populations to land use and climate change. PLoS ONE 10:e0135334CrossRefGoogle Scholar
  47. Pickering AD, Pottinger TG (1989) Stress responses and disease resistance in salmonid fish: effects of chronic elevation of plasma cortisol. Fish Physiol Biochem 7:253–258CrossRefGoogle Scholar
  48. Plumb JM (2018) A bioenergetics evaluation of temperature-dependent selection for the spawning phenology by Snake River fall Chinook salmon. Ecol Evol. Google Scholar
  49. Poole GC (2002) Fluvial landscape ecology: addressing uniqueness within the river discontinuum. Freshw Biol 47:641–660CrossRefGoogle Scholar
  50. Quinn TP (2011) The Behavior and ecology of pacific Salmon and Trout. UBC Press, VancouverGoogle Scholar
  51. Railsback SF, Harvey BC, Jackson SK, Lamberson RH (2009) InSTREAM: the individual-based stream trout research and environmental assessment model. US Department of Agriculture, Forest Service, Pacific Southwest Research Station, AlbanyCrossRefGoogle Scholar
  52. Railsback SF, Harvey BC, White JL (2014) Facultative anadromy in salmonids: linking habitat, individual life history decisions, and population-level consequences. Can J Fish Aquat Sci 71:1270–1278CrossRefGoogle Scholar
  53. Richter A, Kolmes SA (2005) Maximum temperature limits for Chinook, Coho, and Chum Salmon, and Steelhead Trout in the Pacific Northwest. Rev Fish Sci 13:23–49CrossRefGoogle Scholar
  54. Robards MD, Quinn TP (2002) The migratory timing of adult summer-run steelhead in the Columbia river over six decades of environmental change. Trans Am Fish Soc 131:523–536CrossRefGoogle Scholar
  55. Roscoe DW, Hinch SG, Cooke SJ, Patterson DA (2010) 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 19:51–62CrossRefGoogle Scholar
  56. Schaffer WM, Elson PF (1975) The adaptive significance of variations in life history among local populations of Atlantic Salmon in North America. Ecology 56:577–590CrossRefGoogle Scholar
  57. Schlosser IJ (1995) Critical landscape attributes that influence fish population dynamics in headwater streams. Hydrobiologia 303:71–81CrossRefGoogle Scholar
  58. Schumaker NH, Brookes A (2018) HexSim: a modeling environment for ecology and conservation. Landscape Ecol 33:197–211CrossRefGoogle Scholar
  59. Silva AT, Lucas MC, Castro-Santos T, Katopodis C, Baumgartner LJ, Thiem JD, Aarestrup K, Pompeu PS, O’Brien GC, Braun DC, Burnett NJ (2017) The future of fish passage science, engineering, and practice. Fish Fish 19:340–362CrossRefGoogle Scholar
  60. Stewart DJ, Ibarra M (1991) Predation and production by Salmonine Fishes in Lake Michigan, 1978–88. Can J Fish Aquat Sci 48:909–922CrossRefGoogle Scholar
  61. Strange JS (2012) Migration strategies of adult Chinook Salmon runs in response to diverse environmental conditions in the Klamath River Basin. Trans Am Fish Soc 141:1622–1636CrossRefGoogle Scholar
  62. Taranger GL, Hansen T (1993) Ovulation and egg survival following exposure of Atlantic salmon, Salmo salar L., broodstock to different water temperatures. Aquac Res 24:151–156CrossRefGoogle Scholar
  63. Torgersen CE, Ebersole JL, Keenan ADM (2012) Primer for identifying cold-water refuges to protect and restore thermal diversity in riverine landscapes. U.S. Environmental Protection Agency, WashingtonGoogle Scholar
  64. Torgersen CE, Price DM, Li HW, McIntosh BA (1999) Multiscale thermal refugia and stream habitat associations of Chinook Salmon in Northeastern Oregon. Ecol Appl 9:301CrossRefGoogle Scholar
  65. University of Washington (2018) fish passage data. In: Columbia River DART (Data Access Real Time). Accessed 27 Nov 2018
  66. Vannote RL, Wayne Minshall G, Cummins KW, Sedell JR, Cushing CE (1980) The river continuum concept. Can J Fish Aquat Sci 37:130–137CrossRefGoogle Scholar
  67. Waknitz WF, Matthews GM, Wainwright T, Winans GA (1995) Status Review for Mid-Columbia River Summer Chinook Salmon. Department of Commerce, National Oceanic and Atmoospheric Administration, National Marine Fisheries Service, Northwest Fisheries Science Center, WashingtonGoogle Scholar
  68. Walter RP, Hogan JD, Blum MJ, Gagne RB, Hain EF, Gilliam JF, McIntyre PB (2012) Climate change and conservation of endemic amphidromous fishes in Hawaiian streams. Endanger Species Res 16:261–272CrossRefGoogle Scholar
  69. Waples RS, Zabel RW, Scheuerell MD, Sanderson BL (2008) Evolutionary responses by native species to major anthropogenic changes to their ecosystems: Pacific salmon in the Columbia River hydropower system. Mol Ecol 17:84–96CrossRefGoogle Scholar
  70. Wu H, Kimball JS, Elsner MM, Mantua N, Adler RF, Stanford J (2012) Projected climate change impacts on the hydrology and temperature of Pacific Northwest rivers. Water Resour Res 48:11530Google Scholar

Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2019

Authors and Affiliations

  • Marcía N. Snyder
    • 1
    Email author
  • Nathan H. Schumaker
    • 1
  • Joseph L. Ebersole
    • 1
  • Jason B. Dunham
    • 2
  • Randy L. Comeleo
    • 1
  • Matthew L. Keefer
    • 3
  • Peter Leinenbach
    • 4
  • Allen Brookes
    • 1
  • Ben Cope
    • 4
  • Jennifer Wu
    • 4
  • John Palmer
    • 4
  • Druscilla Keenan
    • 4
  1. 1.US Environmental Protection AgencyCorvallisUSA
  2. 2.Forest and Rangeland Ecosystem Science CenterUS Geological SurveyCorvallisUSA
  3. 3.Department of Fish and Wildlife Sciences, College of Natural ResourcesUniversity of IdahoMoscowUSA
  4. 4.US Environmental Protection AgencySeattleUSA

Personalised recommendations