A moving target—incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations


Freshwater fish move vertically and horizontally through the aquatic landscape for a variety of reasons, such as to find and exploit patchy resources or to locate essential habitats (e.g., for spawning). Inherent challenges exist with the assessment of fish populations because they are moving targets. We submit that quantifying and describing the spatial ecology of fish and their habitat is an important component of freshwater fishery assessment and management. With a growing number of tools available for studying the spatial ecology of fishes (e.g., telemetry, population genetics, hydroacoustics, otolith microchemistry, stable isotope analysis), new knowledge can now be generated and incorporated into biological assessment and fishery management. For example, knowing when, where, and how to deploy assessment gears is essential to inform, refine, or calibrate assessment protocols. Such information is also useful for quantifying or avoiding bycatch of imperiled species. Knowledge of habitat connectivity and usage can identify critically important migration corridors and habitats and can be used to improve our understanding of variables that influence spatial structuring of fish populations. Similarly, demographic processes are partly driven by the behavior of fish and mediated by environmental drivers. Information on these processes is critical to the development and application of realistic population dynamics models. Collectively, biological assessment, when informed by knowledge of spatial ecology, can provide managers with the ability to understand how and when fish and their habitats may be exposed to different threats. Naturally, this knowledge helps to better evaluate or develop strategies to protect the long-term viability of fishery production. Failure to understand the spatial ecology of fishes and to incorporate spatiotemporal data can bias population assessments and forecasts and potentially lead to ineffective or counterproductive management actions.

This is a preview of subscription content, access via your institution.

Fig. 1


  1. Allan, J. D., & Castillo, M. M. (2007). Stream ecology: structure and function of running waters. Springer.

  2. Allen, I. R. H. (1966). Counting fences for salmon and sea-trout and what can be learned from them. Salmon and Trout Magazine, 176, 19–21.

    Google Scholar 

  3. Arlinghaus, R., Klefoth, T., Cooke, S. J., Gingerich, A., & Suski, C. D. (2009). A combined laboratory and field study to understand physiological and behavioral disturbance and recovery from catch-and-release recreational angling in northern pike (Esox lucius). Fish Research, 97, 223–233.

  4. Arrhenius, F., Benneheij, B. J. A. M., Rudstam, L. G., & Boisclair D. (2000). Can stationary bottom split-beam hydroacoustics be used to measure fish swimming speed in situ? Fish Research, 45, 31–41.

  5. Bacheler, N. M., Buckel, J. A., Hightower, J. E., Paramore, L. M., & Pollock, K. H. (2009). A combined telemetry-tag return approach to estimate fishing and natural mortality rates of an estuarine fish. Canadian Journal of Fisheries and Aquatic Science, 66, 1230–1244.

  6. Baigún, C., Minotti, P., & Oldani, N. (2013). Assessment of sábalo (Prochilodus lineatus) fisheries in the lower Paraná River basin (Argentina) based on hydrological, biological and fishery indicators. Neotrop Ichthyol., 11, 199–210.

  7. Bajer, P. G., Chizinski, C. J., & Sorensen, P. W. (2011). Using the Judas technique to locate and remove wintertime aggregations of invasive common carp. Fish Manage Ecology, 18, 497–505.

  8. Beard, T. D. Jr., Arlinghaus, R., Cooke, S. J., McIntyre, P. B., De Silva, S., Bartley, D., et al. (2011). Ecosystem approach to inland fisheries: research needs and implementation strategies. Biology Letter UK, 7, 481–483.

  9. Begg, G. A., Friedland, K. D., & Pearce, J. B. (1999). Stock identification and its role in stock assessment and fisheries management: an overview. Fisheries Research, 43, 1–8.

  10. Belcher, E., Hanot, W., & Burch, J. (2002). Dual-frequency identification sonar (DIDSON). In: Underwater technology. Proceedings of the 2002 International Symposium on Underwater Technology, pp. 187–192.

  11. Bettinger, J. M., & Bettoli, P. W. (2002). Fate, dispersal, and persistence of recently stocked and resident rainbow trout in a Tennessee tailwater. North American Journal of Fisheries Management, 22, 425–432.

    Article  Google Scholar 

  12. Bird, T., Lyon, J., Nicol, S., McCarthy, M., & Barker, R. (2014). Estimating population size in the presence of temporary migration using a joint analysis of telemetry and capture–recapture data. Methos Ecology Evolution, 5, 615–625.

  13. Biro, P. A., & Post, J. R. (2008). Rapid depletion of genotypes with fast growth and bold personality traits from harvested fish populations. Proceedings of the National Academy of Sciences, 105, 2919–2922.

    CAS  Article  Google Scholar 

  14. Bolland, J. D., Cowx, I. G., & Lucas, M. C. (2009). Dispersal and survival of stocked cyprinids in a small English river: comparison with wild fishes using a multi‐method approach. Journal of Fish Biology, 74, 2313–2328.

  15. Bolland, J. D., Nunn, A. D., Lucas, M. C., & Cowx, I. G. (2012). The importance of variable lateral connectivity between artificial floodplain waterbodies and river channels. River Research Applied, 28, 1189–1199.

  16. Bravener, G. A., & McLaughlin, R. L. (2013). A behavioural framework for trapping success and its application to invasive sea lamprey. Canadian Journal of Fisheries and Aquatic Sciences, 70(10), 1438–1446.

    Article  Google Scholar 

  17. Brett, J. R. (1971). Energetic responses of salmon to temperature: a study of some thermal relations in the physiology and freshwater ecology of sockeye salmon (Oncorhynchus nerka). American Zoologist, 11, 99–113.

    Article  Google Scholar 

  18. Bronte, C. R., Holey, M. E., Madenjian, C. P., Jonas, J. L., Claramunt, R. M., McKee, P. C., et al. (2007). Relative abundance, site fidelity, and survival of adult lake trout in Lake Michigan from 1999 to 2001: implications for future restoration strategies. North American Journal of Fisheries Management, 27, 137–155.

  19. Brown, C., & Day, R. L. (2002). The future of stock enhancements: lessons for hatchery practice from conservation biology. Fish Fish and Fisheries, 3, 79–94.

    Article  Google Scholar 

  20. Casselman, J. M., & Lewis, C. A. (1996). Habitat requirements of northern pike (Essox lucius). Canadian Journal of Fisheries and Aquatic Science, 53, 161–174.

    Article  Google Scholar 

  21. Castello, L. (2007). Lateral migration of Arapaima gigas in floodplains of the Amazon. Ecology Freshw Fish, 17, 38–46.

    Article  Google Scholar 

  22. Catalano, S. R., Whittington, I. D., Donnellan, S. C., & Gillanders, B. M. (2014). Parasites as biological tags to assess host population structure: guidelines, recent genetic advances and comments on a holistic approach. International Journal for Parasitology: Parasites and Wildlife, 3, 220–226.

  23. Childress, E. S., Allan, J. D., & McIntyre, P. B. (2014). Nutrient subsidies from iteroparous fish migrations can enhance stream productivity. Ecosystems, 17(3), 522–534.

  24. Chow-Fraser, P. (2005). Ecosystem response to changes in water level of Lake Ontario marshes: lessons from the restoration of Cootes Paradise Marsh. Hydrobiologia, 539, 189–204.

    Article  Google Scholar 

  25. Christie, W. J., Goddard, C. I., Nepszy, S. J., Collins, J. J. & MacCallum, W. (1987). Problems associated with fisheries assessment methods in the Great Lakes. Canadian Journal of Fisheries and Aquatic Science, 44, s431–s438.

  26. Colotelo, A. H., Raby, G. D., Hasler, C. T., Haxton, T. J., Smokorowski, K. E., Blouin-Demers, G. et al. (2013). Northern pike bycatch in an inland commercial hoop net fishery: effects of water temperature and net tending frequency on injury, physiology, and survival. Fish Research, 137, 41–49.

  27. Cooke, S. J., & Thorstad, E. B. (2012). Is radio telemetry getting washed downstream? The changing role of radio telemetry in studies of freshwater ichthyofauna relative to other tagging and telemetry technology. American Fisheries Society Symposium, 76, 349–369.

    Google Scholar 

  28. Cooke, S. J., Hinch, S. G., Lucas, M. C., & Lutcavage, M. (2012). Biotelemetry and biologging. In A. V. Zale, D. L. Parrish, & T. M. Sutton (Eds.), Fisheries techniques (3rd ed., pp. 819–860). Bethesda: American Fisheries Society.

  29. Cooke, S. J., Midwood, J. D., Thiem, J. D., Klimley, P., Lucas, M. C., Thorstad, E. B., et al. (2013). Tracking animals in freshwater with electronic tags: past, present and future. Animal Biotelemetry, 1, 5.

  30. Cooke, S. J., Arlinghaus, R., Bartley, D. M., Beard, T. D., Cowx, I. G., Essington, T. E., et al. (2014). Where the waters meet: sharing ideas and experiences between inland and marine realms to promote sustainable fisheries management. Canadian Journal of Fisheries and Aquatic Sciences, 71, 1593–1601.

  31. Cowx, I. G. (1996). Stock assessment in inland fisheries. London: Fishing News Books.

  32. Cowx, I. G., & Welcomme, R. L. (1998). Rehabilitation of rivers for fish. Rome: Food and Agriculture Org.

  33. Crook, D. A., Lowe, W. H., Allendorf, F. W., Erős, T., Finn, D. S., Gillanders, B. M., et al. (2015). Human effects on ecological connectivity in aquatic ecosystems: integrating scientific approaches to support management and mitigation. Science of the Total Environment, 534, 52–64.

  34. Crowder, L. B., Lyman, S. J., Figueira, W. F., & Priddy, J. (2000). Source-sink population dynamics and the problem of siting marine reserves. Bulletin of Marine Science, 66(3), 799–820.

  35. Da Silva, P. S., Makrakis, M. C., Miranda, L. E., Makrakis, S., Assumpção, L., Paula, S., et al. (2014). Importance of reservoir tributaries to spawning of migratory fish in the upper Paraná river. River Research Applied, 31, 313–322.

  36. DeAngelis, D. L., & Petersen, J. H. (2001). Importance of the predator’s ecological neighborhood in modeling predation on migrating prey. Oikos, 94, 315–325.

    Article  Google Scholar 

  37. Dextrase, A. J., Mandrak, N. E., & Schaefers, J. A. (2014). Modelling occupancy of an imperilled stream fish at multiple scales while accounting for imperfect detection: implications for conservation. Freshw O Biologico, 59, 1799–1815.

  38. Dodge, S., Bohrer, G., Weinzierl, R., Davidson, S. C., Kays, R., Douglas, D., et al. (2013). The environmental-data automated track annotation (Env-DATA) system: linking animal tracks with environmental data. Movement Ecology, 1, 3.

  39. Donaldson, M. R., Arlinghaus, R., Hanson, K. C., & Cooke, S. J. (2008). Enhancing catch-and-release science with biotelemetry. Fish and Fisheries, 9, 79–105.

  40. Donaldson, M. R., Hinch, S. G., Suski, C. D., Fisk, A. T., Heupel, M. R., & Cooke, S. J. (2014). Making connections in aquatic ecosystems with acoustic telemetry monitoring. Front Ecology Environment, 12, 565–573.

  41. Drake, D. A. R., & Mandrak, N. E. (2014). Harvest models and stock co-occurrence: probabilistic methods for estimating bycatch. Fish and Fisheries, 15, 23–42.

    Article  Google Scholar 

  42. Duncan, A., & Kubecka, J. (1996). Patchiness of longitudinal fish distributions in a river as revealed by a continuous hydroacoustic survey. ICES Journals · Science and Mathematics; ICES Journal of Marine Science, 53, 161–165.

    Article  Google Scholar 

  43. Dux, A. M., Guy, C. S., & Fredenberg, W. A. (2011). Spatiotemporal distribution and population characteristics of a nonnative lake trout population, with implications for suppression. North American Journal of Fisheries Management, 31, 187–196.

  44. Ebner, B. C., & Thiem, J. D. (2009). Monitoring by telemetry reveals differences in movement and survival following hatchery or wild rearing of an endangered fish. Marine Freshwater Research, 60, 45–57.

    Article  Google Scholar 

  45. English, K. K., Koski, W. R., Sliwinski, C., Blakley, A., Cass, A., & Woodey, J. C. (2005). Migration timing and river survival of late-run Fraser River sockeye salmon estimated using radiotelemetry techniques. Trans American Fisheries Society Symposium, 134, 1342–1365.

  46. Fausch, K. D., Torgersen, C. E., Baxter, C. V., Li, H. W. (2002). Landscapes to riverscapes: bridging the gap between research and conservation of stream fishes. Bioscience, 52, 483–498.

  47. Fausch, K. D., Rieman, B. E., Dunham, J. B., Young, M. K., & Peterson, D. P. (2009). Invasion versus isolation: trade-offs in managing native salmonids with barriers to upstream movement. Conserv O Biologico, 23, 859–870.

  48. Fayram, A. H., & Sibley, T. H. (2000). Impact of predation by smallmouth bass on sockeye salmon in Lake Washington. Washington American Journal of Fisheries Management, 20, 81–89.

    Article  Google Scholar 

  49. Ferguson, J. W., Healey, M., Dugan, P., & Barlow, C. (2011). Potential effects of dams on migratory fish in the Mekong River: lessons from salmon in the Fraser and Columbia Rivers. Environment Manage, 47, 141–159.

  50. Fernandes, C. C. (1997). Lateral migration of fishes in Amazon floodplains. Ecol Fresh Fish, 6, 36–44.

    Article  Google Scholar 

  51. Figueira, W. F. (2009). Connectivity or demography: defining sources and sinks in coral reef fish metapopulations. Ecology Model, 220(8), 1126–1137.

    Article  Google Scholar 

  52. Finer, M., & Jenkins, C. N. (2012). Proliferation of hydroelectric dams in the Andean Amazon and implications for Andes-Amazon connectivity. PloS One, 7, e35126.

    CAS  Article  Google Scholar 

  53. Flecker, A. S., McIntyre, P. B., Moore, J. W., Anderson, J. T., Taylor, B. W., & Hall, R. O. Jr. (2010). Migratory fishes as material and process subsidies in riverine ecosystems. In K. B. Gido, & D. Jackson (Eds.), Community ecology of stream fishes: concepts, approaches, and techniques (pp. 559–592). Bethesda: American Fisheries Society Symposium.

  54. Fortin, M.-J., & Dale, M. (2005). Spatial analysis: a guide for ecologists. Cambridge: Cambridge University Press.

    Google Scholar 

  55. Fry, F. E. J. 1971. The effect of environmental factors on the physiology of fish. In: Hoar, W.S. and Randall, D.J. (eds.), Fish physiology. Academic Press, pp. 1–98.

  56. Garcia, S. M., & Cochrane, K. L. (2005). Ecosystem approach to fisheries: a review of implementation guidelines. ICES Journal of Marine Science, 62, 311–318.

    Article  Google Scholar 

  57. Gauld, N. R., Campbell, R. N., & Lucas, M. C. (2013). Reduced flows impact salmonid smolt emigration in a river with low-head weirs. Science of the Total Environment, 458–460, 435–443.

  58. Gerking, S. D. (1950). Stability of a stream fish population. Journal of Wildlife Management, 14, 193–202.

    Article  Google Scholar 

  59. Gerking, S. D. (1953). Evidence for the concepts of home range and territory in stream fishes. Ecology, 34, 347–365.

    Article  Google Scholar 

  60. Gjelland, K. O., Bohn, T., Horne, J. K., Jensvoll, I., Knudsen, F. R., & Amundsen, P. A. (2009). Planktivore vertical migration and shoaling under a subarctic light regime. Canadian Journal of Fisheries and Aquatic Science, 66, 525–539.

  61. Godinho, A. L., & Kynard, B. (2009). Migratory fishes of Brazil: life history and fish passage needs. River Research and Applications, 25, 702–712.

    Article  Google Scholar 

  62. Goodwin, A., Politano, M. S., Garvin, J. W., Nestler, J., Hay, D., Anderson, J. J., et al. (2014). Fish navigation of large dams emerges from their modulation of flow field experience. Proceedings of the National Academy of Sciences of the United States of America, 111(14), 5277–5282.

  63. Goulding, M. (1980). The fishes and the forest: explorations in the Amazonian natural history. Berkeley: University of California Press.

    Google Scholar 

  64. Gowan, C., Young, M. K., Fausch, K. D., & Riley, S. C. (1994). Restricted movement in resident stream salmonids: a paradigm lost? Canadian Journal of Fisheries and Aquatic Science, 51, 2626–2637.

  65. Gresswell, R. E., Suski, C. D., Parsley, M. J., Koel, T. M., Bigelow, P. E., Ertel, B. D., et al. (2012). Identifying movement patterns and spawning areas of invasive lake trout Salvelinus namaycush in Yellowstone Lake. Investigators Annual Report.

  66. Gross, M. R., Coleman, R. M., & McDowall, R. M. (1988). Aquatic productivity and the evolution of diadromous fish migration. Science, 239, 1291–1293.

  67. Gurarie, E., Bracis, C., Delgado, M., Meckley, T. D., Kojola, I., & Wagner, C. M. (2015). What is the animal doing? Tools for exploring behavioral structure in animal movements. Journal of Animal Ecology, 85(1), 69–84.

  68. Hall, M. A. (1996). On bycatches. Reviews in Fish Biology and Fisheries, 6, 319–352.

    Article  Google Scholar 

  69. Hall, C. J., Jordaan, A., & Frisk, M. G. (2012). Centuries of anadromous forage fish loss: consequences for ecosystem connectivity and productivity. Bioscience, 62, 723–731.

  70. Harris, J. H. (1995). The use of fish in ecological assessments. Aust Journal of Ecology, 20, 65–80.

    Article  Google Scholar 

  71. Hayden, T. A., Holbrook, C. M., Fielder, D. G., Vandergoot, C. S., Bergstedt, R. A., Dettmers, J. M., et al. (2014). Acoustic telemetry reveals large-scale migration patterns of walleye in Lake Huron. PloS One, 9, e114833.

  72. Hayes, D. B., Paola Ferreri, C., & Taylor, W. W. (1996). Linking fish habitat to their population dynamics. Canadian Journal of Fisheries and Aquatic Sciences, 53(S1), 383–390.

  73. Henderson, B. A., & Wong, J. L. (1991). A method for estimating gillnet selectivity of walleye (Stizostedion vitreum vitreum) in multimesh multifilament gill nets in Lake Erie, and its application. Canadian Journal of Fisheries and Aquatic Science, 48, 2420–2428.

    Article  Google Scholar 

  74. Hendry, A. P., Bohlin, T., Jonsson, B., & Berg, O. K. (2004). To sea or not to sea? Anadromy in salmonids. In A. P. Hendry, & S. C. Stearns (Eds.), Evolution illuminated: salmon and their relatives (pp. 92–125). Oxford: Oxford University Press.

  75. Hightower, J. E., Jackson, J. R., Pollock, K. H. (2001). Use of telemetry methods to estimate natural and fishing mortality of striped bass in Lake Gaston, North Carolina. Transactions of the American Fisheries Society, 130, 557–567.

  76. Hilborn, R., & Walters, C. J. (2013). Quantitative fisheries stock assessment: choice, dynamics and uncertainty. Springer Science & Business Media.

  77. Hillyard, K. A., Smith, B. B., Conallin, A. J., & Gillanders, B. M. (2010). Optimising exclusion screens to control exotic carp in an Australian lowland river. Marine Freshwater Research, 61, 418–429.

  78. Hoeinghaus, D. J., Winemiller, K. O., Layman, C. A., Arrington, D. A., & Jepsen, D. B. (2006). Effects of seasonality and migratory prey on body condition of Cichla species in a tropical floodplain river. Ecology of Freshwater Fish, 15, 398–407.

  79. Hoffnagle, T. L., Carmichael, R. W., Frenyea, K. A., & Keniry, P. J. (2008). Run timing, spawn timing, and spawning distribution of hatchery-and natural-origin spring Chinook salmon in the Imnaha River. Oregon North American Journal of Fisheries Management, 28, 148–164.

  80. Holbrook, C., Bergstedt, R., Barber, J., Bravener, G., Jones, M. L., & Krueger, C. (2016). Using acoustic telemetry to evaluate performance of sea lamprey traps in the Great Lakes. Ecological Applications. doi:10.1890/15-2251.1.

  81. Höök, T. O., McCormick, M. J., Rutherford, E. S., Mason, D. M., & Carter, G. S. (2006). Short-term water mass movements in Lake Michigan: implications for larval fish transport. Journal of Great Lakes Research, 32, 728–737.

  82. Hrabik, T. R., Jensen, O. P., Martell, S. J. D., Walters, C. J., & Kitchell, J. F. (2006). Diel vertical migration in the Lake Superior pelagic community I. Changes in vertical migration of coregonids in response to varying predation risk. Canadian Journal of Fisheries and Aquatic Sciences, 63, 2286–2295.

  83. Hughes, J. M., Schmidt, D. J., & Finn, D. S. (2009). Genes in streams: using DNA to understand the movement of freshwater fauna and their riverine habitat. BioScience, 59, 573–583.

  84. Hussey, N. E., Kessel, S. T., Aarestrup, K., Cooke, S. J., Cowley, P. D., Fisk, A. T., et al. (2015). Aquatic animal telemetry: a panoramic window into the underwater world. Science. doi:10.1126/science.1255642.

  85. Isaak, D. J., Luce, C. H., Rieman, B. E., Nagel, D. E., Peterson, E. E., Horan, D. L., et al. (2010). Effects of climate change and wildfire on stream temperatures and salmonid thermal habitat in a mountain river network. Ecological Applications, 20, 1350–1371.

  86. Jackson, D. A., & Harvey, H. H. (1997). Qualitative and quantitative sampling of lake fish communities. Can Journal of Fisheries and Aquatic Science, 54, 2807–2813.

    Article  Google Scholar 

  87. Jardine, T. D., Pusey, B. J., Hamilton, S. K., Pettit, N. E., Davies, P. M., Douglas, M. M., et al. (2011). Fish mediate high food web connectivity in the lower reaches of a tropical floodplain river. Oecologia, 168, 829–838.

  88. Jeffres, C. A., Opperman, J. J., & Moyle, P. B. (2008). Ephemeral floodplain habitats provide best growth conditions for juvenile Chinook salmon in a California river. Environmental Biology of Fishes, 83, 449–458.

  89. Junk, W. J., Bayley, P. B., & Sparks, R. E. (1989). The flood pulse concept in river floodplain systems. Canadian Special Publication of Fisheries Science, 106, 110–127.

  90. Junk, W. J., Soares, M. G. M., & Saint-Paul, U. (1997). The fish. In W. J. Junk (Ed.), The Central Amazon floodplain: ecology of a pulsing system (pp. 385–408). Berlin: Springer.

  91. Kerns, J. A., Bettoli, P. W., & Scholten, G. D. (2009). Mortality and movements of paddlefish released as bycatch in a commercial fishery in Kentucky Lake, Tennessee. In C. P. Paukert and G. D. Scholten (Eds.), Paddlefish management, propagation, and conservation in the 21st century: building from 20 years of research and management. American Fisheries Society, Symposium (vol. 66). Maryland: Bethesda.

  92. King, A. J. (2004). Ontogenetic patterns of habitat use by fishes within the main channel of an Australian floodplain river. Journal of Fish Biology, 65, 1582–1603.

    Article  Google Scholar 

  93. King, M. (2013). Fisheries biology, assessment and management. John Wiley & Sons.

  94. Kramer, D. L., & Chapman, M. R. (1999). Implications of fish home range size and relocation for marine reserve function. Environmental Biology of Fishes, 55, 65–79.

    Article  Google Scholar 

  95. Krueger, C. C. and Decker, D. J. 1999. The process of fisheries management. Inland fisheries management in North America, 2nd edition. American Fisheries Society, Bethesda, Maryland, pp. 31–59.

  96. Krueger, C. C., Swanson, B. L., & Selgeby, J. H. (1986). Evaluation of hatchery-reared lake trout for reestablishment of populations in the Apostle Islands region of Lake Superior, 1960–84. In R. H. Stroud (Ed.), Fish culture in fisheries management (pp. 93–107). Bethesda: American Fisheries Society.

  97. Lapointe, N. W. R., Thiem, J. D., Doka, S. E., & Cooke, S. J. (2013). Opportunities for improving aquatic restoration science and monitoring through the use of animal electronic-tagging technology. BioScience, 63, 390–396.

  98. Lapointe, N. W. R., Cooke, S. J., Imhof, J. G., Boisclair, D., Casselman, J. M., Curry, R. A. et al. (2014). Principles for ensuring healthy and productive freshwater ecosystems that support sustainable fisheries. Environmental Reviews, 22, 1–25.

  99. Larkin, P. A. (1977). An epitaph for the concept of maximum sustained yield. Transactions of the American Fisheries Society, 106, 1–11.

    Article  Google Scholar 

  100. Legendre, P., & Fortin, M.-J. (1989). Spatial pattern and ecological analysis. Vegetatio, 80, 107–138.

    Article  Google Scholar 

  101. Lima, S. L., & Zollner, P. A. (1996). Towards a behavioral ecology of ecological landscapes. Trends in Ecology & Evolution, 11, 131–135.

    CAS  Article  Google Scholar 

  102. Louca, V., Lindsay, S. W., Majambere, S., & Lucas, M. C. (2009). Fish community characteristics of the lower Gambia River floodplains: a study in the last major undisturbed West African River. Freshwater Biology, 54, 254–271.

  103. Lucas, M. C., & Baras, E. (2000). Methods for studying the spatial behaviour of freshwater fishes in the natural environment. Fish and Fisheries, 1, 238–316.

    Article  Google Scholar 

  104. Lucas, M. C., & Baras, E. (2001). Migration of freshwater fishes. Oxford: Blackwell Science Ltd.

    Google Scholar 

  105. Lucas, M. C., & Frear, P. A. (1997). Effects of a flow-gauging weir on the migratory behaviour of barbel, Barbus barbus, a riverine cyprinid. Journal of Fish Biology, 50, 382–396.

    Article  Google Scholar 

  106. Lyon, J. P., Bird, T., Nicol, S., Kearns, J., O’Mahony, J., Todd, C. R., et al. (2014). Efficiency of electrofishing in turbid lowland rivers: implications for measuring temporal change in fish populations. Canadian Journal of Fisheries and Aquatic Science, 71, 878–886.

  107. Mackey, G., Mclean, J. E., & Quinn, T. P. (2001). Comparisons of run timing, spatial distribution, and length of wild and newly established hatchery populations of steelhead in Forks Creek, Washington. North American Journal of Fisheries Management, 21, 717–724.

  108. Martins, E. G., Gutowsky, L. F. G., Harrison, P. M., Flemming, J. E. M., Jonsen, I. D., Zhu, D. Z., et al. (2014). Behavioral attributes of turbine entrainment risk for adult resident fish revealed by acoustic telemetry and state-space modeling. Journal Animal Biotelemetry, 2, 13.

  109. Mason, D. M., Johnson, T. B., Harvey, C. J., Kitchell, J., Schram, S., Bronte, C., et al. (2005). Hydroacoustic estimates of abundance and spatial distribution of pelagic prey fishes in western Lake Superior. Journal of Great Lakes Research, 31, 426–438.

  110. Masters, J. E. G., Jang, M. -H., Ha, K., Bird, P. D., Frear, P. A., & Lucas, M. C. (2006). The commercial exploitation of a protected anadromous species, the river lamprey (Lampetra fluviatilis (L.)), in the tidal River Ouse, north‐east England. Aquatic Conservation: Marine and Freshwater Ecosystems, 16, 77–92.

  111. McClellan, C. M., Read, A. J., Price, B. A., Cluse, W. M., & Godfrey, M. H. (2009). Using telemetry to mitigate the bycatch of long-lived marine vertebrates. Ecological Applications, 19, 1660–1671.

  112. McCusker, M. R., Mandrak, N. E., Doka, S., Gertzen, E. L., van Wieren, J. F., McKenna, J. E., et al. (2014). Estimating the distribution of the imperiled pugnose shiner (Notropis anogenus) in the St Lawrence River using a habitat model. Journal of Great Lakes Research, 40, 980–988.

  113. McRae, B. H., Hall, S. A., Beier, P., & Theobald, D. M. (2012). Where to restore ecological connectivity? Detecting barriers and quantifying restoration benefits. PloS One, 7(12), e52604.

  114. Mehner, T., & Schulz, M. (2002). Monthly variability of hydroacoustic fish stock estimates in a deep lake and its correlation to gillnet catches. Journal of Fish Biology, 61, 1109–1121.

    Article  Google Scholar 

  115. Melegari, J.L. 2015. Abundance and run timing of adult fall chum salmon in the Chandalar River, Yukon Flats National Wildlife Refuge, Alaska 2014. Alaska U.S. Fish and Wildlife Service, Fisheries Data Series 2015–9, September 2015.

  116. Meldgaard, T., Nielsen, E. E., & Loeschcke, V. (2003). Fragmentation by weirs in a riverine system: a study of genetic variation in time and space among populations of European grayling (Thymallus thymallus) in a Danish river system. Conservation Genetics, 4, 735–747.

  117. Millar, R. B., & Fryer, R. J. (1999). Estimating the size-selection curves of towed gears, traps, nets and hooks. Reviews in Fish Biology and Fisheries, 9, 89–116.

    Article  Google Scholar 

  118. Minns, C. K. (2001). Science for freshwater fish habitat management in Canada: current status and future prospects. Aquatic Ecosystem Health and Management, 4, 423–436.

    Article  Google Scholar 

  119. Morita, K., Fukuwaka, M., & Tanimata, N. (2010). Age‐related thermal habitat use by Pacific salmon Oncorhynchus spp. Journal of Fish Biology, 77, 1024–1029.

  120. Mouton, A. M., Dillen, A., Van den Neucker, T., Buysse, D., Stevens, M., & Coeck, J. (2012). Impact of sampling efficiency on the performance of data-driven fish habitat models. Ecological Modelling, 245, 94–102.

  121. Naiman, R. J., Bilby, R. E., Schindler, D. E. & Helfield, J. M. (2002). Pacific salmon, nutrients and the dynamics of freshwater and riparian ecosystems. Ecosystems, 5, 399–417.

  122. Nathan, R., Getz, W. M., Revilla, E., Holyoak, M., Kadmon, R., Saltz, D., et al. (2008). A movement ecology paradigm for unifying organismal movement research. Proceedings of the National Academy of Sciences of the United States of America, 105, 19052–19059.

  123. Nestler, J. M., Pompeu, P. S., Goodwin, R. A., Smith, D. L., Silva, L. G. M., Baigún, C. R. M., et al. (2012). The river machine: a template for fish movement and habitat, fluvial geomorphology, fluid dynamics and biogeochemical cycling. River Research and Applications, 28, 490–503.

  124. Nunn, A. D., Copp, G. H., Vilizzi, L. & Carter, M. G. (2010). Seasonal and diel patterns in the migrations of fishes between a river and a floodplain tributary. Ecology of Freshwater Fish, 19, 153–162.

  125. O’Connor, J. P., O’Mahony, D. J., O’Mahony, J. M., & Glenane, T. J. (2006). Some impacts of low and medium head weirs on downstream fish movement in the Murray–Darling Basin in southeastern Australia. Ecology of Freshwater Fish, 15, 419–427.

  126. Palmer, M. A., Bernhardt, E. S., Allan, J. D., Lake, P. S., Alexander, G., Brooks, S. et al. (2005). Standards for ecologically successful river restoration. Journal of Applied Ecology, 42, 208–217.

  127. Pelicice, F. M., & Agostinho, A. A. (2008). Fish-passage facilities as ecological traps in large Neotropical rivers. Conserv O Biologico, 22, 180–188.

    Article  Google Scholar 

  128. Pelicice, F. M., Pompeu, P. S., & Agostinho, A. A. (2016). Large reservoirs as ecological barriers to downstream movements of Neotropical migratory fish. Fish and Fisheries, 16, 697–715.

  129. Perez, A., & Fabre, N. N. (2009). Seasonal growth and life history of the catfish Calophysus macropterus (Lichtenstein, 1819) (Siluriformes: Pimelodidae) from the Amazon floodplain. Journal of Applied Ichthyology, 25, 343–349.

    Article  Google Scholar 

  130. Perkins, D. L., Fitzsimons, J. D., Marsden, J. E., Krueger, C. C., & May, B. (1995). Differences in reproduction among hatchery strains of lake trout at eight spawning areas in Lake Ontario: genetic evidence from mixed-stock analysis. Journal Great Lakes Research, 21, 364–374.

  131. Policansky, D., & Magnuson, J. J. (1998). Genetics, metapopulations, and ecosystem management of fisheries. Ecological Applications, 8(sp1), S119–S123.

    Article  Google Scholar 

  132. Polis, G. A. and Winemiller, K. O. 1996. Food webs: integration of patterns and dynamics. Springer.

  133. Polis, G. A., Anderson, W. B., & Holt, R. D. (1997). Toward an integration of landscape and food web ecology: the dynamics of spatially subsidized food webs. Annual Review of Ecological Systems, 28, 289–316.

  134. Polis, G. A., Power, M. E., & Huxel, G. R. (2004). Food webs at the landscape level. Chicago: University of Chicago Press.

  135. Pörtner, H. O., & Farrell, A. P. (2008). Physiology and climate change. Science, 322, 690–692.

    Article  Google Scholar 

  136. Power, M. 2007. Fish population bioassessment. In: Guy, C. and Brown, M.L. (eds.). Analysis and interpretation of freshwater fisheries data. American Fisheries Society, pp. 561–624.

  137. Pratt, T. C., O’Connor, L. M., Hallett, A. G., McLaughlin, R. L., Katopodis, C., Hayes, D. B., et al. (2009). Balancing aquatic habitat fragmentation and control of invasive species: enhancing selective fish passage at sea lamprey control barriers. Transactions of the American Fisheries Society, 138, 652–665.

  138. Punt, A. E., & Hilborn, R. (1997). Fisheries stock assessment and decision analysis: the Bayesian approach. Reviews in Fish Biology and Fisheries, 7, 35–63.

    Article  Google Scholar 

  139. Raby, G. D., Colotelo, A. H. A., Blouin-Demers, G., & Cooke, S. J. (2011). Freshwater commercial bycatch: an understated conservation problem. BioScience, 61, 271–280.

  140. Raby, G. D., Donaldson, M. R., Nguyen, V. M., Taylor, M. K., Sopinka, N. M., Cook, K. V., et al. (2014). Bycatch mortality of endangered coho salmon: impacts, solutions, and aboriginal perspectives. Ecological Applications, 24, 1803–1819.

  141. Rahel, F. J. (2013). Intentional fragmentation as a management strategy in aquatic systems. BioScience, 63(5), 362–372.

    Article  Google Scholar 

  142. Rapp, T., Hallermann, J., Cooke, S. J., Hetz, S. K., Wuertz, S., & Arlinghaus, R. (2014). Consequences of air exposure on the physiology and behavior of caught-and-released common carp in the laboratory and under natural conditions. North American Journal of Fisheries Management, 34, 232–246.

  143. Romine, J. G., Perry, R. W., Johnston, S. V., Fitzer, C. W., Pagliughi, S. W., & Blake, A. R. (2014). Identifying when tagged fishes have been consumed by piscivorous predators: application of multivariate mixture models to movement parameters of telemetered fishes. Animal Biotelemetry , 2(3). doi:10.1186/2050-3385-2-3.

  144. Roni, P. (2005). Habitat rehabilitation for inland fisheries: global review of effectiveness and guidance for rehabilitation of freshwater ecosystems. Issue 484. Food and Agriculture Org., 2005 - Technology and Engineering, pp 116.

  145. Roseman, E. F., Taylor, W. W., Hayes, D. B., Tyson, J. T., & Haas, R. C. (2005). Spatial patterns emphasize the importance of coastal zones as nursery areas for larval walleye in western Lake Erie. Journal Great Lakes Research, 31, 28–44.

  146. Rous, A. 2014. Behaviour and space use of sea lamprey near traps at a hydroelectric generating station. M.Sc. Thesis, University of Guelph.

  147. Rudstam, L. G., Magnuson, J. J., & Tonn, W. M. (1984). Size selectivity of passive fishing gear: a correction for encounter probability applied to gill nets. Canadian Journal of Fisheries and Aquatic Science, 41, 1252–1255.

  148. Schindler, D. E., Leavitt, P. R., Brock, C. S., Johnson, S. P., & Quay, P. D. (2005). Marine-derived nutrients, commercial fisheries, and production of salmon and lake algae in Alaska. Ecology, 86, 3225–3231.

  149. Seeb, J. E., Carvalho, G., Hauser, L., Naish, K., Roberts, S., & Seeb, L. W. (2011). Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11(s1), 1–8.

  150. Shafer, A. B. A., Northrup, J. M., Wikelski, M., Wittemyer, G., & Wolf, J. B. W. (2016). Forecasting ecological genomics: high-tech animal instrumentation meets high-throughput sequencing. PLoS Biology, 14(1), e1002350.

  151. Sheaves, M. (2009). Consequences of ecological connectivity: the coastal ecosystem mosaic. Marine Ecology: Progress Series, 391, 107–115.

    Article  Google Scholar 

  152. Shepard, E. L., Wilson, R. P., Rees, W. G., Grundy, E., Lambertucci, S. A., & Vosper, S. B. (2013). Energy landscapes shape animal movement ecology. American Naturalist, 182, 298–312.

  153. Sims, M., Cox, T., & Lewison, R. (2008). Modeling spatial patterns in fisheries bycatch: improving bycatch maps to aid fisheries management. Ecological Applications, 18, 649–661.

  154. Skalski, J. R., Lady, J., Townsend, R. L., & McDonald, R. D. (2001). Estimating in-river survival of migrating salmonid smolts using radiotelemetry. Canadian Journal of Fisheries and Aquatic Science, 58, 1987–1997.

  155. Skalski, J. R., Townsend, R., Lady, J., Giorgi, A. E., Stevenson, J. J., & McDonald, R. D. (2002). Estimating route-specific passage and survival probabilities at a hydroelectric project from smolt radiotelemetry studies. Canadian Journal of Fisheries and Aquatic Science, 59, 1385–1393.

  156. Starrs, D., Ebner, B. C., & Fulton, C. J. (2016). All in the ears: unlocking the early life history biology and spatial ecology of fishes. Biological Reviews of the Cambridge Philosophical Society, 91(1):86–105.

  157. Struthers, D. P., Danylchuk, A. J., Wilson, A. D. M., & Cooke, S. J. (2016). Action cameras: bringing aquatic and fisheries research into view. Fisheries, 40, 502–512.

  158. Svendsen, J. C., Aarestrup, K., Malte, H., Thygesen, U. H., Baktoft, H., Koed, A., et al. (2011). Linking individual behaviour and migration success in Salmo salar smolts approaching a water withdrawal site: implications for management. Aquatic Living Resources, 24, 201–209.

  159. Taylor, P. D., Fahrig, L., Henein, K., & Merriam, G. (1993). Connectivity is a vital element of landscape structure. Oikos, 68, 571–573.

  160. Thompson, L. A., Cooke, S. J., Donaldson, M. R., Hanson, K. C., Gingerich, A., Klefoth, T., et al. (2008). Physiology, behaviour, and survival of angled and air-exposed largemouth bass. North American Journal of Fisheries Management, 28, 1059–1068.

  161. Thurfjell, H., Ciuti, S., & Boyce, M. S. (2014) Applications of step-selection functions in ecology and conservation. Movement Ecology, 2, 4.

  162. Tilman, D. and Kareiva, P. M. 1997. Spatial ecology: the role of space in population dynamics and interspecific interactions (vol. 30). Princeton University Press.

  163. Vander Zanden, M. J., & Vadeboncoeur, Y. (2002). Fish as integrators of benthic and pelagic food webs in lakes. Ecology, 83, 2152–2161.

    Article  Google Scholar 

  164. Vanni, M. J. 1996. Nutrient transport and recycling by consumers in lake food webs: implications for algal communities. In: Polis, G. A. and Winemiller, K.O. (eds.) Food webs: integration of patterns and dynamics. Chapman & Hall, pp. 81–95.

  165. Vélez-Espino, L. A., & Koops, M. A. (2009). Recovery potential assessment for lake sturgeon in Canadian designatable units. North American Journal of Fisheries Management, 29, 1065–1090.

    Article  Google Scholar 

  166. Walters, C. J., & Holling, C. S. (1990). Large-scale management experiments and learning by doing. Ecology, 71, 2060–2068.

  167. Wang, H. -Y., Rutherford, E. S., Cook, H. A., Einhouse, D. W., Haas, R. C., Johnson, T. B., et al. (2007). Movement of walleyes in Lakes Erie and St Clair inferred from tag return and fisheries data. Transactions of the American Fisheries Society, 136, 539–551.

  168. Ward, J. V. (1989). The four-dimensional nature of lotic ecosystems. Journal of the North American Benthological Society, 8, 2–8.

    Article  Google Scholar 

  169. Welcomme, R. 1979. Fisheries ecology of floodplain rivers. Longman Press.

  170. Welcomme, R. L., Cowx, I. G., Coates, D., Béné, C., Funge-Smith, S., Halls, A., et al. (2010). Inland capture fisheries. Philosophical Transactions of the Royal Society of London B, 365, 2881–2896.

  171. Winemiller, K. O., & Jepsen, D. B. (1998). Effects of seasonality and fish movement on tropical river food webs. Journal of fish biology, 53, 267–296.

    Article  Google Scholar 

  172. Winfield, I. J., Fletcher, J. M., & James, J. B. (2007). Seasonal variability in the abundance of Arctic charr (Salvelinus alpinus (L.)) recorded using hydroacoustics in Windermere, UK and its implications for survey design. Ecology of Freshwater Fish, 16, 64–69.

  173. Wootton, R. J. (1998). Ecology of teleost fishes, 2nd edition. Dordrecht: Kluwer Academic Publishers.

    Google Scholar 

  174. Ziv, G., Baran, E., Rodriguez-Iturbe, I., & Levin, S. (2012). Trading-off fish biodiversity, food security and hydropower in the Mekong River Basin. Proceedings of the National Academy of Sciences of the United States of America, 109, 5609–5614.

  175. Zuur, A., Ieno, E. N., Walker, N., Saveliev, A. A., & Smith, G. M. (2009). Mixed effects models and extensions in ecology with R. Springer Science & Business Media.

  176. Žydelis, R., Lewison, R. L., Shaffer, S. A., Moore, J. E., Boustany, A. M., Roberts, J. J., et al. (2011). Dynamic habitat models: using telemetry data to project fisheries bycatch. Proceeding of the Royal Society. B. Biological Sciences, 278, 3191–3200.

Download references


Cooke is supported by the Canada Research Chairs program, the Natural Sciences and Engineering Research Council of Canada, and the Great Lakes Fishery Commission and Ocean Tracking Network Canada. This work was funded in part by the Great Lakes Fishery Commission by way of Great Lakes Restoration Initiative appropriations (GL-00E23010). This paper is Contribution 18 of the Great Lakes Acoustic Telemetry Observation System (GLATOS). This is contribution 2023 of the Great Lakes Science Center. DAC was supported by the Australian Government’s National Environmental Research Program, Northern Australia Hub. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

Author information



Corresponding author

Correspondence to Steven J. Cooke.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Cooke, S.J., Martins, E.G., Struthers, D.P. et al. A moving target—incorporating knowledge of the spatial ecology of fish into the assessment and management of freshwater fish populations. Environ Monit Assess 188, 239 (2016). https://doi.org/10.1007/s10661-016-5228-0

Download citation


  • Habitat use
  • Movement ecology
  • Behavior
  • Fisheries
  • Telemetry
  • Hydroacoustics
  • Sampling strategy
  • Trophic ecology