Individual-Based Model
Formulation for Cutthroat Trout,
Little Jones Creek, California
Pacific Southwest
Research Station
Contents
In Brief
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I. Introduction.............................................................................................................
I.A. Fundamental Approach and Assumptions ............................................
I.B. Study Site.......................................................................................................
I.C. Conventions..................................................................................................
I.C.1. Units .................................................................................................
I.C.2. Parameter and Variable Names ..................................................
I.C.3 Survival Probabilities and Mortality Sources...........................
I.C.4. Dates, Days, and Fish Ages .........................................................
I.C.5. Habitat Cell Conventions.............................................................
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II. Model Initialization ...........................................................................................
II.A. Habitat Initialization ................................................................................
II.B. Fish Initialization ......................................................................................
II.C. Redd Initialization ....................................................................................
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III. Habitat Model...................................................................................................... 6
III.A. Cell Boundaries and Dimensions ........................................................... 7
III.B. Daily Flow, Temperature, and Turbidity ............................................. 7
III.C. Depth and Velocity ................................................................................... 7
III.D. Velocity Shelter Availability ................................................................... 8
III.E. Spawning Gravel Availability ................................................................ 8
III.F. Distance to Hiding Cover ........................................................................ 8
III.G. Food Production and Availability ......................................................... 8
III.G.1. Production.................................................................................... 9
III.G.2. Availability ................................................................................ 10
III.H. Day Length ............................................................................................... 10
IV. Fish Model..........................................................................................................
IV.A. Spawning ..................................................................................................
IV.A.1. Determine Spawn Readiness ..................................................
IV.A.2. Identify Redd Location ............................................................
IV.A.3. Make Redd .................................................................................
IV.B. Movement.................................................................................................
IV.B.1. Departure Rules ........................................................................
IV.B.2. Destination Rules......................................................................
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USDA Forest Service
General Technical
Report
PSW-GTR-182
June 2001
IV.C. Feeding and Growth............................................................................... 17
IV.D. Survival ..................................................................................................... 19
V. Redd Model ......................................................................................................
V.A. Survival .....................................................................................................
V.B. Development............................................................................................
V.C. Emergence ................................................................................................
V.C.1. Emergence Timing .....................................................................
V.C.2. New Fish Attributes ..................................................................
V.D. Empty Redds............................................................................................
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VI. Model Schedules...............................................................................................
VI.A. Habitat Actions........................................................................................
VI.B. Fish Actions..............................................................................................
VI.C. Redd Actions............................................................................................
VI.D. Observer Actions (Model Outputs) .....................................................
VI.E. Complete Schedule .................................................................................
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VII.Calibration..........................................................................................................
VII.A. Individual Actions .................................................................................
VII.A.1. Fish Spawning.........................................................................
VII.A.2. Fish Growth and Survival .....................................................
VII.A.3. Fish Movement ........................................................................
VII.A.4. Redd Survival ..........................................................................
VII.A.5. Redd Development and Emergence ....................................
VII.B.Short-term Population Responses........................................................
VII.B.1. Seasonal Changes in Habitat Use, Growth, and
Survival .....................................................................................
VII.B.2. Redd Scouring and Temperature-related
Mortality...................................................................................
VII.C.Long-term Population Responses ........................................................
VII.C.1. Redd Numbers and Incubation Success..............................
VII.C.2. Long-term Abundance, Growth and
Relative Abundance ...............................................................
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VIII. Habitat Data Collection Methods ...............................................................
VIII.A. Reach Location and Length ..............................................................
VIII.B. Transects and Longitudinal Cell Boundaries ................................
VIII.C. Lateral Cell Boundaries .....................................................................
VIII.D. Depths and Velocities ........................................................................
VIII.E. High-Flow Water Surface Elevations..............................................
VIII.F. Spawning Gravel Availability..........................................................
VIII.G. Velocity Shelter Availability.............................................................
VIII.H. Distance to Hiding Cover ..................................................................
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IX. Method Details ..................................................................................................
IX.A. Criteria for Day of Spawning................................................................
IX.A.1. Date Window.............................................................................
IX.A.2. Temperature Range ..................................................................
IX.A.3. Flow Limit.................................................................................
IX.A.4. Steady Flows.............................................................................
IX.A.5. Female Spawners .....................................................................
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IX.A.6. Minimum Length, Age, and Condition ................................
IX.A.7. Not Spawned This Season.......................................................
Spawning Habitat Suitability................................................................
Fish Feeding and Energetics .................................................................
IX.C.1. Activity Budget .........................................................................
IX.C.2. Food Intake ................................................................................
IX.C.3. Respiration Costs and Use of Velocity Shelters ..................
IX.C.4. Other Energy Losses ................................................................
IX.C.5. Feeding Strategy Selection, Net Energy Benefits, and
Growth........................................................................................
IX.C.6. Feeding and Growth Calibration ...........................................
Fish Survival Probabilities.....................................................................
IX.D.1. High Temperature ....................................................................
IX.D.2. High Velocity.............................................................................
IX.D.3. Stranding ....................................................................................
IX.D.4. Spawning....................................................................................
IX.D.5. Poor Condition ..........................................................................
IX.D.6. Terrestrial Predation ................................................................
IX.D.7. Aquatic Predation.....................................................................
IX.D.8. Total Survival: Parameter Estimation and Effects of
Fish Size, Depth, and Velocity................................................
Redd Survival Functions .......................................................................
IX.E.1. Dewatering.................................................................................
IX.E.2. Scouring and Deposition .........................................................
IX.E.3. Low Temperature .....................................................................
IX.E.4. High Temperature ....................................................................
IX.E.5. Superimposition........................................................................
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Model Development Priorities and Research Topics ...............................
X.A. Imposed versus Emergent Behaviors ..................................................
X.A.1. Generalization of Movement Objectives ..............................
X.A.2. Readiness to Spawn and Spawning Location......................
X.A.3. Allocation of Growth to Fish Length, Weight, and
Gonads ........................................................................................
X.A.4. Diurnal Changes in Behavior and Hiding Cover
Limitations .................................................................................
X.B. Habitat Model Issues..............................................................................
X.B.1. Habitat Cell Sizes ......................................................................
X.B.2. Accuracy of Hydraulic Simulations ......................................
X.B.3. Variation in Velocity Shelter Availability ............................
X.B.4. Spatial and Temporal Variation in Food Availability........
X.C. Fish Model Issues ....................................................................................
X.C.1. Immigration and Emigration..................................................
X.C.2. Movement Distances and Knowledge of Environment.....
X.C.3. Fitness Time Horizons for Movement ..................................
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IX.B.
IX.C.
IX.D.
IX.E.
X.
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XI. Input Parameter Index ..................................................................................... 75
XII. References........................................................................................................... 77