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Articles

Do rearing salmonids predictably occupy physical microhabitat?

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Pages 132-150 | Received 11 Mar 2019, Accepted 20 Nov 2019, Published online: 20 Dec 2019

References

  • Ahmadi-Nedushan B, St-Hilaire A, Bérubé M, Robichaud É, Thiémonge N, Bobée B. 2006. A review of statistical methods for the evaluation of aquatic habitat suitability for instream flow assessment. River Res Appl. 22(5):503–523.
  • Al-Chokhachy R, Budy P. 2007. Summer microhabitat use of fluvial Bull Trout in eastern Oregon streams. North Am J Fish Manage. 27(4):1068–1081.
  • Allen MA. 2000. Seasonal microhabitat use by juvenile spring Chinook salmon in the Yakima River Basin, Washington. Rivers. 7:314–332.
  • Anim DO, Fletcher TD, Vietz GJ, Pasternack GB, Burns MJ. 2018. Restoring in-stream habitat in urban catchments: modify flow or the channel? Ecohydrology. 12:1–16.
  • Arif MSM, Gülch E, Tuhtan JA, Thumser P, Haas C. 2017. An investigation of image processing techniques for substrate classification based on dominant grain size using RGB images from UAV. Int J Remote Sens. 38(8–10):2639–2661.
  • Baker PF, Ligon FK, Speed TP. 1995. Estimating the influence of temperature on the survival of Chinook salmon smolts (Oncorhynchus tshawytscha) migrating through the Sacramento-San Joaquin River Delta of California. Can J Fish Aquat Sci. 52(4):855–863.
  • Beard TD, Carline RF. 1991. Influence of spawning and other stream habitat features on spatial variability of wild brown trout. Trans Am Fish Soc. 120(6):711–711.
  • Beecher HA, Caldwell BA, DeMond SB. 2002. Evaluation of depth and velocity preferences of juvenile coho salmon in Washington streams. North Am J Fish Manage. 22(3):785–795.
  • Beecher HA, Caldwell BA, DeMond SB, Seiler D, Boessow SN. 2010. An empirical assessment of PHABSIM using longterm monitoring of coho salmon smolt production in Bingham Creek, Washington. North Am J Fish Manage. 30(6):1529–1543.
  • Beecher HA, Carleton JP, Johnson TH. 1995. Notes: utility of depth and velocity preferences for predicting steelhead parr distribution at different flows. Trans Am Fish Soc. 124(6):935–938.
  • Benjanker R, Tonina D, Marzadri A, McKean J, Issak DJ. 2016. Effects of habitat quality and ambient hyporheic flows on salmon spawning site selection. J Geophys Res Biogeosci. 121:1221–1435.
  • Benjanker R, Tonina D, McKean J. 2015. One-dimensional and two-dimensional hydrodynamic modeling derived flow properties: impacts on aquatic habitat quality predictions. Earth Surf Process Landforms. 40:340–356.
  • Bovee KD. 1986. Development and evaluation of habitat suitability criteria for use in the instream flow incremental methodology. Washington (DC): US Fish and Wildlife Service. Instream Flow Information Paper #21 FWS/OBS-86/7.
  • Bugert RM, Bjornn TC. 1991. Habitat use by steelhead and coho salmon and their responses to predators and cover in laboratory streams. Trans Am Fish Soc. 120(4):486–493.
  • Dill LM, Ydenberg RC, Fraser A. 1981. Food abundance and territory size in juvenile coho salmon (Oncorhynchus kisutch). Can J Zool. 59(9):1801–1809.
  • Dixon PM. 2001. The bootstrap and the jackknife: describing the precision of ecological indices In: Scheiner SM, Gurevitch J, editors. Design and analysis of ecological experiments. New York (NY): Oxford University Press; p. 267–288.
  • Dunbar MJ, Alfredsen K, Harby A. 2012. Hydraulic-habitat modelling for setting environmental river flow needs for salmonids. Fish Manag Ecol. 19(6):500–517.
  • Efron B, Tibshirani R. 1993. An introduction to the bootstrap. Boca Raton (FL): Chapman & Hall/CRC.
  • ESRI. 2016. ArcGIS desktop: release 10.5. Redlands (CA): Environmental Systems Research Institute.
  • Everest FH, Chapman DW. 1972. Habitat selection and spatial interaction by juvenile Chinook salmon and steelhead trout in two Idaho streams. J Fish Res Bd Can. 29(1):91–100.
  • Favrot SD, Jonasson BC, Peterson JT. 2018. Fall and winter microhabitat use and suitability for spring Chinook salmon parr in a U.S. Pacific Northwest River. Trans Am Fish Soc. 147(1):151–170.
  • Fraser NHC, Metcalfe NB, Heggenes J, Thorpe JE. 1995. Low summer temperatures cause juvenile Atlantic salmon to become nocturnal. Can J Zool. 73(3):446–451.
  • Garbe J, Beevers L, Pender G. 2016. The interaction of low flow conditions and spawning brown trout (Salmo trutta) habitat availability. Ecol Eng. 88:53–63.
  • Gard M. 2006. Modeling changes in salmon spawning and rearing habitat associated with river channel restoration. Int J River Basin Manage. 4(3):201–211.
  • Gard M. 2009. Comparison of spawning habitat predictions of PHABSIM and River2D models. Int J River Basin Manage. 7(1):55–71.
  • Gard M. 2014. Modelling changes in salmon habitat associated with river channel restoration and flow-induced channel alternations. River Res Appl. 30(1):40–44.
  • Geist DR, Jones J, Murray CJ, Dauble D. 2000. Suitability criteria analysed at the spatial scale of red clusters improved estimates of fall chinook salmon (Oncorhynchus tshawytscha) spawning habitat use in the Hanford Reach, Columbia River. Can J Fish Aquat Sci. 57(8):1636–1646.
  • Geist DR, Murray CJ, Hanrahan TP, Xie Y. 2008. A model of the effects of flow fluctuation on fall Chinook salmon spawning habitat availability in the Columbia River. North Am J Fish Manage. 28(6):1894–1910.
  • Gibson SA, Pasternack GB. 2016. Selecting between one-dimensional and two-dimensional hydrodynamic models for ecohydraulic analysis. River Res Appl. 32(6):1365–1381.
  • Gilbert GK. 1917. Hydraulic-mining debris in the Sierra Nevada. Washington (DC): US Geological Survey.
  • Grant JWA, Kramer DL. 1990. Territory size as a predictor of the upper limit to population density of juvenile salmonids in streams. Can J Fish Aquat Sci. 47(9):1724–1737.
  • Guay JC, Boisclair D, Leclerc M, Lapointe M, Legendre P. 2003. Assessment of the transferability of biological habitat models for Atlantic salmon parr (Salmo salar). Can J Fish Aquat Sci. 60(11):1398–1408.
  • Guay JC, Boisclair D, Rioux D, Leclerc M, Lapointe M, Legendre P. 2000. Development and validation of numerical habitat models for juveniles of Atlantic salmon (Salmo salar). Can J Fish Aquat Sci. 57(10):2065–2075.
  • Guse B, Kail J, Radinger J, Schröder M, Kiesel J, Hering D, Wolter C, Fohrer N. 2015. Eco-hydrologic model cascades: simulating land use and climate change impacts on hydrology, hydraulics and habitats for fish and macroinvertebrates. Sci Total Environ. 533:542–556.
  • Harrison LR, Legleiter CJ, Wydzga MA, Dunne T. 2011. Channel dynamics and habitat development in a meandering, gravel bed river. Water Resour Res. 47:1–21.
  • Hatten JR, Batt TR, Skalicky JJ, Engle R, Barton GJ, Fosness RL, Warren J. 2016. Effects of dam removal on Tule fall Chinook salmon spawning habitat in the White Salmon River, Washington. River Res Appl. 32(7):1481–1492.
  • Hatten JR, Tiffan KF, Anglin DR, Haeseker SL, Skalicky JJ, Schaller H. 2009. A spatial model to assess the effects of hydropower operations on Columbia River fall Chinook salmon spawning habitat. North Am J Fish Manage. 29(5):1379–1405.
  • Heggenes J. 1988. Effect of short-term flow fluctuations on displacement of, and habitat use by brown trout in a small stream. Trans Am Fish Soc. 117(4):336–344.
  • Hellmair M, Peterson M, Mulvey B, Young K, Montgomery J, Fuller A. 2018. Physical characteristics influencing nearshore habitat use by juvenile Chinook salmon in the Sacramento River, California. North Am J Fish Manage. 38(4):959–970.
  • Hess AD, Swartz A. 1940. The forage ratio and its use in determining the food grade of streams. Trans N Am Wildl Conf. 5:162–164.
  • Hillman TW, Griffith JS, Platts WS. 1987. Summer and winter habitat selection by juvenile Chinook salmon in a highly sedimented Idaho stream. Trans Am Fish Soc. 116(2):185–195.
  • Holm CF, Armstrong JD, Gilvear DJ. 2001. Investigating a major assumption of predictive instream habitat models: is water velocity preference of juvenile Atlantic salmon independent of discharge? J Fish Biol. 59(6):1653–1666.
  • Hopkins CE, Pasternack GB. 2018. Autumn 2014 lower Yuba River TUFLOW GPU 2D model description and validation. Davis (CA): University of California at Davis. Prepared for Yuba County Water Agency.
  • Huxley C, Syme B. 2016. TUFLOW GPU – Best practice advice for hydrologic and hydraulic model simulations Paper presented at: Hydrology and Water Resources Symposium, Queenstown, New Zealand.
  • Ivlev VS. 1961. Experimental ecology of the feeding of fishes. New Haven (CT): Yale University Press.
  • Jackson JR, Pasternack GB, Wyrick JR. 2013. Substrate of the lower Yuba River. Davis (CA): University of California at Davis. Prepared for the Yuba Accord River Management Team.
  • James LA. 2005. Sediment from hydraulic mining detained by Englebright Dam and small dams in the Yuba Basin. Geomorphology. 71(1–2):202–226.
  • Johnson DH. 1980. The comparison of usage and availability measurements for evaluating resource preference. Ecology. 61(1):65–71.
  • Kammel LE, Pasternack GB, Massa DA, Bratovich PM. 2016. Near-census ecohydraulics bioverification of Oncorhynchus mykiss spawning microhabitat preferences. J Ecohydraulics. 1(1–2):62–78.
  • Lallias-Tacon S, Liébault F, Piégay H. 2017. Use of airborne LiDAR and historical aerial photos for characterising the history of braided river floodplain morphology and vegetation responses. Catena. 149:742–759.
  • Lamb BL, Sabaton C, Souchon Y. 2004. Use of the instream flow incremental methodology: introduction to the special issue. Hydroécol Appl. 14:1–7.
  • Lamouroux N, Capra H, Pouilly M. 1998. Predicting habitat suitability for lotic fish: linking statistical hydraulic models with multivariate habitat use models. Regul Rivers: Res Mgmt. 14(1):1–11.
  • Leclerc M, Boudreault A, Bechara JA, Corfa G. 1996. Two-dimensional hydrodynamic modeling: a neglected tool in the instream flow incremental methodology. Trans Am Fish Soc. 124(5):645–662.
  • Lee P, Suen J. 2013. Comparing habitat suitability indices (HSIs) based on abundance and occurrence data. North Am J Fish Manage. 33(1):89–96.
  • Mann HB, Whitney DR. 1947. On a test of whether one of two random variables is stochastically larger than the other. Ann Math Statist. 18(1):50–60.
  • Mäki-Petäys A, Huusko A, Erkinaro J, Muotka T. 2002. Transferability of habitat suitability criteria of juvenile Atlantic salmon (Salmo salar). Can J Fish Aquat Sci. 59(2):218–228.
  • Marine KR, Cech JJ. 2004. Effects of high water temperature on growth, smoltification, and predator avoidance in juvenile Sacramento River Chinook salmon. North Am J Fish Manage. 24(1):198–210.
  • Meybeck M. 2003. Global analysis of river systems: from Earth system controls to Anthropocene syndromes. Philos Trans Roy Soc B. 358(1440):1935–1955.
  • Moniz PJ, Pasternack GB. 2019a. Bioverification of microhabitat suitability models for rearing salmonids in the lower Yuba river. Davis (CA): University of California at Davis. Prepared for Yuba Water Agency.
  • Moniz PJ, Pasternack GB. 2019b. Habitat suitability curves for rearing salmonids in the lower Yuba river. Davis (CA): University of California at Davis. Prepared for Yuba Water Agency.
  • National Marine Fisheries Service. 2014. Recovery plan for the evolutionarily significant units of sacramento river winter-run chinook salmon and central valley spring-run chinook salmon and the distinct population segment of California central valley steelhead. California Central Valley Area Office.
  • Pasternack GB, Baig D, Weber MD, Brown RA. 2018. Hierarchically nested river landform sequences. Part 2: bankfull channel morphodynamics governed by valley nesting structure. Earth Surf Process Landforms. 43(12):2519–2532.
  • Pasternack GB, Hopkins CE. 2017. Near-census 2D model comparison between SRH-2D and TUFLOW GPU for use in gravel/cobble rivers. Davis (CA): University of California at Davis. Prepared for Yuba County Water Agency.
  • Pasternack GB, Tu D, Wyrick JR. 2014. Chinook adult salmon spawning physical habitat of the lower Yuba River. Final report. Davis (CA): Lower Yuba River Accord Monitoring and Evaluation Program.
  • Pasternack GB, Wang CL, Merz JE. 2004. Application of a 2D hydrodynamic model to design of reach-scale spawning gravel replenishment on the Mokelumne River, California. River Res Appl. 20:205–225.
  • Pert EJ, Erman DC. 1994. Habitat use by adult rainbow trout under moderate artificial fluctuations in flow. Trans Am Fish Soc.123(6):913–923.
  • Railsback SF. 2016. Why it is time to put PHABSIM out to pasture. Fisheries. 41(12):720–725.
  • Remington RD, Schork M. 1970. Statistics with applications to the biological and health sciences. Englewood Cliffs (NJ): Prentice-Hall.
  • Richter A, Kolmes SA. 2005. Maximum temperature limits for Chinook, coho, chum salmon, and steelhead trout in the Pacific Northwest. Rev Fish Sci. 13(1):23–49.
  • Robertson MJ, Pennell CJ, Scruton DA, Robertson GJ, Brown JA. 2004. Effect of increased flow on the behaviour of Atlantic salmon parr in winter. J Fish Biol. 65(4):1070–1079.
  • Rosenfeld J, Beecher H, Ptolemy R. 2016. Developing bioenergetics-based habitat suitability curves for instream flow models. North Am J Fish Manage. 36(5):1205–1219.
  • Schwindt S, Pasternack GB, Bratovich PM, Rabone G, Simodynes D. 2019. Hydro-morphological parameters generate lifespan maps for stream restoration management. J Environ Manage. 232:475–489.
  • Shirvell CS. 1994. Effect of changes in streamflow on the microhabitat use and movements of sympatric juvenile coho (Oncorhynchus kisutch) and Chinook salmon (O. tshawytscha) in a natural stream. Can J Fish Aquat Sci. 51(7):1644–1652.
  • Somerville PN. 1958. Tables for obtaining non-parametric tolerance limits. Ann Math Stat. 29(2):599–601.
  • Taylor EB. 1988. Water temperature and velocity as determinants of microhabitats of juvenile Chinook and coho salmon in a laboratory stream channel. Trans Am Fish Soc. 117(1):22–28.
  • Tharme RE. 2003. A global perspective on environmental flow assessment: emerging trends in the development and application of environmental flow methodologies for rivers. River Res Appl. 19(5–6):397–441.
  • Thomas JA, Bovee KD. 1993. Application and testing of a procedure to evaluate transferability of habitat suitability criteria. Regul Rivers: Res Mgmt. 8(3):285–294.
  • Tiffan KF, Garland RD, Rondorf DW. 2002. Quantifying flow-dependent changes in subyearling fall Chinook salmon rearing habitat using two-dimensional spatially explicit modeling. North Am J Fish Manage. 22(3):713–726.
  • Tiffan KF, Clark LO, Garland RD, Rondorf DW. 2006. Variables influencing the presence of subyearling fall Chinook salmon in shoreline habitats on the Hanford Reach, Columbia River. North Am J Fish Manage. 26(2):351–360.
  • Tiffan KF, Hatten JR, Trachtenbarg DA. 2016. Assessing juvenile salmon rearing habitat and associated predation risk in a lower Snake River reservoir. River Res Appl. 32(5):1030–1038.
  • US Fish and Wildlife Service. 2010. Flow-habitat relationships for juvenile fall/spring-run Chinook salmon and steelhead/rainbow trout rearing in the Yuba River. Sacramento (CA): US Fish and Wildlife Service.
  • US Fish and Wildlife Service. 2013. Flow-habitat relationships for juvenile spring-run and fall-run Chinook salmon and steelhead/rainbow trout rearing in Clear Creek between Clear Creek Road and the Sacramento River. Sacramento (CA): US Fish and Wildlife Service.
  • Vehanen T, Bjerke PL, Heggenes J, Huusko A, Mäki-Petäys A. 2000. Effect of fluctuating flow and temperature on cover type selection and behaviour by juvenile brown trout in artificial flumes. J Fish Biol. 56(4):923–937.
  • Waddle TJ. 2001. PHABSIM for Windows: user’s manual and exercises. Fort Collins (CO): US Geological Survey. Open File Report 2001-340.
  • Weber MD, Pasternack GB. 2017. Valley-scale morphology drives differences in fluvial sediment budgets and incision rates during contrasting flow regimes. Geomorphology. 288:39–51.
  • Wesche TA, Goertler CM, Hubert WA. 1987. Modified habitat suitability index for brown trout in southeastern Wyoming. North Am J Fish Manage. 7(2):232–237.
  • Williams CS, Marshall WH. 1938. Duck nesting studies, Bear River Migratory Bird Refuge, Utah, 1937. J Wildlife Manage. 2(2):29–48.
  • Wyrick JR, Pasternack GB. 2014. Geospatial organization of fluvial landforms in a gravel-cobble river: beyond the riffle-pool couplet. Geomorphology. 213:48–65.
  • Wyrick JR, Pasternack GB. 2016. Revealing the natural complexity of topographic change processes through repeat surveys and decision-tree classification. Earth Surf Process Landforms. 41(6):723–737.
  • Yuba County Water Agency. 2013. Technical memorandum 7-10: instream flow downstream of Englebright dam. Marysville (CA): Yuba River Development Project. FERC Project No. 2246.

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