# DemGenTrout 1.3

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## WHAT IS IT?

This is the version 1.3 of a brown trout demogenetic model developed by Beatrice Frank during her PhD thesis (Supervisor: Prof. Philippe Baret, Earth and Life Institute, Universite catholique de Louvain). This version includes features of DemGenTrout 1.1 (faster initialisation) and simulates stocking with hatchery trout.

## HOW IT WORKS

The model, named DemGenTrout, was designed to understand how anthropogenic disturbances can affect a brown trout (*Salmo trutta* L.) population living in a river / nursery brook system of the Lesse River network (Belgium). Changes in the demogenetic (i.e., demography and genetics) structure of the population were monitored, and at a latter stage, the model was used to predict how trout populations might respond to migration barriers and stocking with hatchery trout (Frank & Baret, 2013).

The model has been described following the ODD (Overview, Design concepts, Details) protocol (Grimm et al., 2006; 2010) in DemGenTrout 1.1. To study stocking impacts on wild brown trout, several modifications of the model structure were needed. More specifically, one submodel, two breeds, and eight parameters (stocking-start, stocking-end, stocking-coefficient, num-stocked, survival-factor, trout-spawning-prob, stocked-spawning-prob, hybrid-spawning-prob) were added. Both spawning and survival submodels were adapted to include phenotypic and genetic differences between hatchery-reared and wild trout.

The new submodel, 'intro-stocked-trout', simulates the introduction of hatchery individuals in the Lesse River (stream L). Each year at week 27 (i.e., the end of March, corresponding to the beginning of the fishing season) and during 10 years, a fixed number of stocked trout (num-stocked parameter) is introduced in stream L. This number is calculated once, at week 27 of year 1, as the product of the stocking-coefficient by the number of wild trout in stream L. The state variables of each stocked trout are defined as follows. Their length is drawn from a random normal distribution with a mean of 248.47 mm and a standard deviation of 26.71 mm. Their condition factor is set to 1.1, as hatchery fish are often larger and heavier than wild fish. The weight of each individual is calculated as its condition factor times its length cubed according to Fulton's formula. Genotypes are assigned in accordance with alleles and corresponding allelic frequencies observed for hatchery-reared individuals (see text files ''input-genotypes-stocking-12markers'' and ''input-genofreq-stocking-12markers''). All stocked individuals are of age 2.

The spawning submodel was modified to incorporate the new breeds, which correspond to stocked trout and hybrids. Both breeds have the same state variables as those defined for wild trout. Breed attribution to each offspring depends of the mating. A thirteenth locus was added in trout genotypes for breed tracking, with homozygous alleles arbitrarily fixed to '000' and '999' for wild and hatchery trout, respectively. Hybrids are identified as individuals having heterozygous alleles (i.e., either '000/999' or '999/000'). Phenotypes are thus inherited the same way as genotypes. We hypothesised that stocked trout had reduced reproductive success in comparison with wild trout, and their probability of spawning was set to 0.10 (stocked-spawning-prob parameter). For wild trout, the spawning probability was set to 1.00 (trout-spawning-prob). The spawning probability for hybrids (hybrid-spawning-prob) is given by: trout-spawning-prob * (1 - ((1 - stocked-spawning-prob) / 2)) and is thus equal to 0.55.

The survival process of trout was also adapted. We hypothesised a high mortality of hatchery-reared fish soon after their release, in comparison with wild fish. The survival rate of age-2 hatchery trout released in stream L was thus divided by the survival-factor, set to 10 (the survival of stocked trout is 10 times lower than the rate normally used for wild trout). As phenotypic differences between hatchery and wild fish often disappear after 1 year in nature, stocked trout of age strictly higher than 2 and hatchery trout born in the system have the same age-specific survival rates than wild trout. Survival of hybrids is computed from survival of wild (S_{W}) and hatchery trout (S_{S}): S_{H} = S_{W} * (1 - ((1 - S_{S}) / 2)).

## HOW TO USE IT

Click the 'Setup' button to initialise the model. In this version, the values of all variables are imported from the file ''DemGenTrout-world.csv''.

You can change the values of parameters with the sliders, then click the 'Change parameters' button, or you can keep the default values (to restore them, click the 'Restore parameters' button). Only parameters linked to stocking can be modified:

- stocking-start and stocking-end, the time period of stoking in years.
- stocking-coefficient, the intensity of stocking in relation to the number of wild trout present in stream L (typically, values from 0.50 to 0.70 reflect a moderate stoking).
- survival-factor, the division factor for survival rate of stocked individuals of age 2 living in stream L in relation to the survival rate of wild trout of the same age class.
- trout-spawning-prob, the probability of spawning for wild trout.
- stocked-spawning-prob, the probability of spawning for hatchery trout.

Click the 'go' button to start the simulation (click 'go' again to stop it). The model can also be run weekly ('step-W' button), monthly ('step-M') or yearly ('step-Y'). The two plots on the left show abundance of wild trout, stocked trout and hybrids in both streams, and is updated each year at week 1. The six plots on the right vary with time, and represent the age distribution of wild trout, stocked trout and hybrids in both streams.

## THINGS TO NOTICE AND TO TRY

You can test the following parameterizations described in Frank & Baret (2013):

- a spawning probability equal to 1 for all breeds, by setting the stocked-spawning-prob equal to 1.
- a survival rate for freshly stocked trout similar to wild trout, by setting the survival-factor equal to 1.
- the two previous modifications, by setting both stocked-spawning-prob and survival-factor equal to 1.

Stocking with hatchery fish thus shows a relatively weak impact on the demographic structure of the brook population (i.e., abundance around 3300 individuals after 35 years of simulation) provided that stocked trout had lower survival and spawning probabilities than wild trout. However, a drastic reduction in abundance of wild trout in stream C is observed (i.e., abundance around 1800 individuals after 35 years) in the latter case implementing a situation where hatchery and wild trout have similar survival and spawning probabilities.

## RELATED MODELS

DemGenTrout 1.0: This is the first version of the DemGenTrout model, as described in Frank & Baret (2013).

DemGenTrout 1.1: In comparison with DemGenTrout 1.0, the initialisation of this version is faster.

DemGenTrout 1.2: This version includes features of DemGenTrout 1.1 (faster initialisation) and simulates a barrier to upstream spawning migration.

## CREDITS AND CITATION

The development of the model was funded by the "Fonds pour la formation a la Recherche dans l'Industrie et dans l'Agriculture" (F.R.I.A.). During the formulation phase, the report describing the inSTREAM model of Railsback et al. (2009) has been an inspirational source. For the programming phase, many of the sample NetLogo models were of great use.

To refer to this model in academic publications, please use: Frank, B.M., Baret, P.V. (2013). Simulating brown trout demogenetics in a river/nursery brook system: The individual-based model DemGenTrout. Ecological Modelling 248: 184-202.

## COPYRIGHT AND LICENSE

DemGenTrout 1.3 (2012)

Beatrice M. Frank

Earth and Life Institute

Universite catholique de Louvain

beatrice.frank@gmail.com

This work is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-sa/3.0/.

## Comments and Questions

;; DemGenTrout 1.3 (2012) ;; ;; Developed by ;; Beatrice M. Frank ;; Earth and Life Institute ;; Universite catholique de Louvain ;; Beatrice.Frank@gmail.com ;; ;; Last updated: September 2012 breed[ trout ] breed[ dead ] breed[ gone ] breed[ stocked ] breed[ hybrid ] ;; trout state variables trout-own[ sex genotype natal-stream week-of-birth week-of-birth2 ;; fixed current-stream age stage status body-length body-weight condition-factor num-offspring spawned? moved-to-spawn? returned? ] ;; gone trout state variables gone-own[ sex genotype natal-stream week-of-birth week-of-birth2 ;; fixed current-stream age stage status body-length body-weight condition-factor num-offspring spawned? moved-to-spawn? returned? ] ;; dead trout state variables dead-own[ sex genotype natal-stream week-of-birth week-of-birth2 ;; fixed current-stream age stage status body-length body-weight condition-factor num-offspring spawned? moved-to-spawn? returned? ] ;; stocked state variables stocked-own[ sex genotype natal-stream week-of-birth week-of-birth2 ;; fixed current-stream age stage status body-length body-weight condition-factor num-offspring spawned? moved-to-spawn? returned? newly-stocked? ] ;; hybrid state variables hybrid-own[ sex genotype natal-stream week-of-birth week-of-birth2 ;; fixed current-stream age stage status body-length body-weight condition-factor num-offspring spawned? moved-to-spawn? returned? ] ;; stream state variables patches-own [ stream flow temperature ] globals[ week week-of-year month-of-year year ;; trout initialisation prop-C prop-L init-N prop-age0-C prop-age1-C prop-age2-C prop-age3-C prop-age0-L prop-age1-L prop-age2-L meanl-age0-C meanl-age0-L meanl-age1-C meanl-age1-L meanl-age2-C meanl-age2-L meanl-age3-C meanl-age3-L sdl-age0-C sdl-age0-L sdl-age1-C sdl-age1-L sdl-age2-C sdl-age2-L sdl-age3-C sdl-age3-L trdown-age0-C trdown-age0-L trdown-age1-C trdown-age1-L trdown-age2-C trdown-age2-L trdown-age3-C trdown-age3-L trup-age0-C trup-age0-L trup-age1-C trup-age1-L trup-age2-C trup-age2-L trup-age3-C trup-age3-L meanl-birth-C sdl-birth-C meanl-birth-L sdl-birth-L trdown-C trup-C trdown-L trup-L mean-bcf-C sd-bcf-C mean-bcf-L sd-bcf-L propC-inL ;; stream input data streamC-discharge streamL-discharge streamC-temperature streamL-temperature mean-dischargeC sd-dischargeC mean-dischargeL sd-dischargeL mean-temperatureC sd-temperatureC mean-temperatureL sd-temperatureL max-dischargeC max-dischargeL ;; survival parameters streamC-age0-survival streamC-age1-survival streamC-age2-survival streamC-age3-survival streamL-age0-survival streamL-age1-survival streamL-age2-survival streamL-age3-survival streamC-age0-survival-list streamC-age1-survival-list streamC-age2-survival-list streamC-age3-survival-list streamL-age0-survival-list streamL-age1-survival-list streamL-age2-survival-list streamL-age3-survival-list C-age0-survival C-age1-survival C-age2-survival C-age3-survival L-age0-survival L-age1-survival L-age2-survival L-age3-survival predation-factor ;; growth parameters streamC-parK streamL-parK streamC-max-length streamC-parA streamC-parB streamL-max-length streamL-parA streamL-parB ;; spawning parameters spawn-start spawn-end moved-prop spawn-mean-length spawn-mean-cond spawn-sd-length spawn-sd-cond spawn-min-age spawn-mean-temperature spawn-sd-temperature spawn-mean-flow spawn-sd-flow streamC-capacity offprod offprod-min-length offprod-max-length offprod-min offspringC-varA offspringC-varB offspringL-varA offspringL-varB offprodC-max offprodL-max length-heritability ;; hatching parameters hatch-start hatch-end ;; downstream movement parameters move-start move-end move-min-age move-max-age move-mean-length move-sd-length move-age1-prob move-age1-varB move-age1-varA move-age2-prob move-age2-varB move-age2-varA move-mean-temperature move-sd-temperature move-mean-flow move-sd-flow ;; leaving stream L forever parameters leaving-propC leaving-propL ;; stocking ; stocking-start stocking-end stocking-coefficient survival-factor num-stocked hybrid-spawning-prob ; trout-spawning-prob stocked-spawning-prob out-year out-month out-week ] to setup clear-all no-display ;; controlling the random numbers random-seed 1223251200 ;; first week of the year = 1st to 7th October included set week 1 set week-of-year 1 set month-of-year 1 set year 1 import-world "DemGenTrout-world.csv" ask trout [set genotype lput "000/000" genotype] reset-ticks restore-defaults end to restore-defaults ;; restore the default parameters linked to stocking set stocking-start 1 set stocking-end 10 set stocking-coefficient 0.50 set survival-factor 10 set trout-spawning-prob 1.00 set stocked-spawning-prob 0.10 ;; compute spawning probability for hybrids set hybrid-spawning-prob (trout-spawning-prob * (1 - ((1 - stocked-spawning-prob) / 2))) end to set-parameters ;; compute spawning probability for hybrids set hybrid-spawning-prob (trout-spawning-prob * (1 - ((1 - stocked-spawning-prob) / 2))) end ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; SCHEDULING ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; to go no-display tick ;; end at year 35 if ticks = 1820 [ user-message "Input data are only available for 35 years." stop ] ;; a year = 52 weeks set week-of-year (week mod 52) + 1 set month-of-year (int(week-of-year / 4.5) mod 52) + 1 set year (int(week / 52)) + 1 ; mod 52 ;; each week ;-- 1. Update stream hydrological conditions ---------------------------------------------------------- ask patches [ update-stream-conditions ] ;-- New. Introduce stocked trout in the system -------------------------------------------------------- ;; introduction of stocked trout if week-of-year = 27 and year >= stocking-start and year <= stocking-end [ intro-stocked-trout ] let selected-breed (list trout stocked hybrid) foreach selected-breed [ ;-- 2. Kill trout in each stream ---------------------------------------------------------------------- ask ? [ trout-die ] ;-- 3. Update trout length, weight and condition factor ----------------------------------------------- ask ? [ trout-grow ] ;-- 4. Reproduce trout in each stream ----------------------------------------------------------------- ;; spawning time window: duration = 11 weeks if week-of-year >= spawn-start and week-of-year <= spawn-end [ ;--- 4.1. Identify candidate spawners ---; ask ? [ trout-become-candidate-spawners ] ;; select some of the candidate spawners born in stream L in order to make them reproduce in C let candidate-spawners-streamL ? with [ status = "candidate-spawner" and current-stream = "L" and natal-stream = "L" and not moved-to-spawn? ] while [ (count ? with [status = "selected-candidate-spawner"]) < (moved-prop * count candidate-spawners-streamL) ] [ ask one-of candidate-spawners-streamL [ set status "selected-candidate-spawner" ] ] ;--- 4.2. Move candidate spawners upstream ---; ask ? [ trout-move-to-spawn ] ;; adapt offspring production if abundance in C is strictly higher than streamC-capacity ifelse count ? with [ current-stream = "C" ] > streamC-capacity [ set offprodC-max offprod / 10 ] [ set offprodC-max offprod ] ;--- 4.3. Produce offspring in each stream ---; trout-spawn-in-streamC trout-spawn-in-streamL ] ;-- 5. Increment trout age and update stage ----------------------------------------------------------- if week-of-year = (hatch-start - 1) ;; one week before hatching [ ask ? [ trout-update-age ] ask ? with [age > 6] [die!] ;; trout die at age 7 ] ;-- 6. Reveal offspring ------------------------------------------------------------------------------- ;; hatching time window: duration = 11 weeks if week-of-year >= hatch-start and week-of-year <= hatch-end [ (foreach sort ? with [age = -1] [ ask ? [ if (week-of-year - week-of-birth) = (hatch-start - spawn-start) ;; delay = 10 weeks [ set hidden? false set age 0 ] ]]) ] ;-- 7. Move trout of stream C downstream ---------------------------------------------------------- ;; migration time window: duration = 25 weeks if week-of-year >= move-start and week-of-year <= move-end [ ;--- 7.1. Identify candidate migrants among juveniles ---; ask ? [ trout-become-candidate-migrants ] ;--- 7.2. Update movement probabilities ---; update-move-age1-prob update-move-age2-prob ;--- 7.3. Move candidate migrants ---; ask ? [ trout-move-downstream ] ] ;-- 8. Move upswimming spawners back to stream L ----------------------------------------------------- if week-of-year = (spawn-end + 1) ;; the week after the spawning process [ ask ? [ trout-move-back ] ] ;-- 9. Remove young trout of stream L from the system ------------------------------------------------ ;; at the end of the year if week-of-year = 52 [ ;; some juveniles born in C and living in stream L do not settle and go elsewhere let bornC-in-streamL ? with [current-stream = "L" and natal-stream = "C" and status = "migrant"] let bornC-leaving (leaving-propC * count bornC-in-streamL) ask n-of bornC-leaving bornC-in-streamL [ leave-streamL ] ;; some juveniles born in L and living in stream L do not settle and go elsewhere let bornL-in-streamL ? with [current-stream = "L" and natal-stream = "L" and (age = 1 or age = 2)] let bornL-leaving (leaving-propL * count bornL-in-streamL) ask n-of bornL-leaving bornL-in-streamL [ leave-streamL ] ] ; Trout reset -------------------------------------------------------------------------------------- ;; at the end of the year if week-of-year = 52 [ ;; reset trout status and boolean state variables ask ? [ set status "non-spawner" set moved-to-spawn? false set spawned? false set returned? false ] ;; kill all hidden turtles ask gone [die] ask dead [die] ] ] ; Increment the week ------------------------------------------------------------------------------- set week week + 1 end ;;;;;;;;;;;;;;;;;;;;;;;;;;; STREAM PROCEDURE ;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ;; update water temperature and flow of each stream to update-stream-conditions ifelse ticks < (6 * 52) ;; first 6 years (2004 to 2009) [ ifelse stream = "C" [ set flow item week streamC-discharge set temperature item week streamC-temperature ] [ set flow item week streamL-discharge set temperature item week streamL-temperature ] ] ;; next years (2010 to 2038) [ ifelse stream = "C" [ set flow min (list max-dischargeC (item week streamC-discharge + random-lognormal mean-dischargeC sd-dischargeC)) set temperature (item week streamC-temperature + random-normal mean-temperatureC sd-temperatureC) ] [ set flow min (list max-dischargeL (item week streamL-discharge + random-lognormal mean-dischargeL sd-dischargeL)) set temperature (item week streamL-temperature + random-normal mean-temperatureL sd-temperatureL) ] ] end ;;;;;;;;;;;;;;;;;;;;;;;;;; TROUT PROCEDURES ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; ;; trout mortality to trout-die ;; in stream C if (breed = trout or breed = stocked) and stage = "fry" and current-stream = "C" [if random-float 1 > ((item week-of-year streamC-age0-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "fry" and current-stream = "C" [if random-float 1 > (((item week-of-year streamC-age0-survival) * (1 - ((1 - (item week-of-year streamC-age0-survival)) / 2))) ^ (1 / 52)) [die!]] if (breed = trout or breed = stocked) and stage = "juvenile" and age = 1 and current-stream = "C" [if random-float 1 > ((item week-of-year streamC-age1-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "juvenile" and age = 1 and current-stream = "C" [if random-float 1 > (((item week-of-year streamC-age1-survival) * (1 - ((1 - (item week-of-year streamC-age1-survival)) / 2))) ^ (1 / 52)) [die!]] if (breed = trout or breed = stocked) and stage = "juvenile" and age = 2 and current-stream = "C" [if random-float 1 > ((item week-of-year streamC-age2-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "juvenile" and age = 2 and current-stream = "C" [if random-float 1 > (((item week-of-year streamC-age2-survival) * (1 - ((1 - (item week-of-year streamC-age2-survival)) / 2))) ^ (1 / 52)) [die!]] if (breed = trout or breed = stocked) and stage = "adult" and age < 6 and current-stream = "C" [if random-float 1 > ((item week-of-year streamC-age3-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "adult" and age < 6 and current-stream = "C" [if random-float 1 > (((item week-of-year streamC-age3-survival) * (1 - ((1 - (item week-of-year streamC-age3-survival)) / 2))) ^ (1 / 52)) [die!]] if week-of-year >= spawn-start and week-of-year <= spawn-end and (breed = trout or breed = stocked) and moved-to-spawn? = true and current-stream = "C" [if random-float 1 > (((item week-of-year streamC-age3-survival) / predation-factor) ^ (1 / (spawn-end - spawn-start))) [die!]] if week-of-year >= spawn-start and week-of-year <= spawn-end and breed = hybrid and moved-to-spawn? = true and current-stream = "C" [if random-float 1 > ((((item week-of-year streamC-age3-survival) * (1 - ((1 - (item week-of-year streamC-age3-survival)) / 2))) / predation-factor) ^ (1 / (spawn-end - spawn-start))) [die!]] ;; in stream L if (breed = trout or breed = stocked) and stage = "fry" and current-stream = "L" [if random-float 1 > ((item week-of-year streamL-age0-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "fry" and current-stream = "L" [if random-float 1 > (((item week-of-year streamL-age0-survival) * (1 - ((1 - (item week-of-year streamL-age0-survival)) / 2))) ^ (1 / 52)) [die!]] if (breed = trout or breed = stocked) and stage = "juvenile" and age = 1 and current-stream = "L" [if random-float 1 > ((item week-of-year streamL-age1-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "juvenile" and age = 1 and current-stream = "L" [if random-float 1 > (((item week-of-year streamL-age1-survival) * (1 - ((1 - (item week-of-year streamL-age1-survival)) / 2))) ^ (1 / 52)) [die!]] if breed = stocked and newly-stocked? = true and stage = "juvenile" and age = 2 and current-stream = "L" [if random-float 1 > (((item week-of-year streamL-age2-survival) / survival-factor) ^ (1 / 52)) [die!]] if (breed = trout or breed = stocked) and stage = "juvenile" and age = 2 and current-stream = "L" [if random-float 1 > ((item week-of-year streamL-age2-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "juvenile" and age = 2 and current-stream = "L" [if random-float 1 > (((item week-of-year streamL-age2-survival) * (1 - ((1 - (item week-of-year streamL-age2-survival)) / 2))) ^ (1 / 52)) [die!]] if (breed = trout or breed = stocked) and stage = "adult" and age < 6 and current-stream = "L" [if random-float 1 > ((item week-of-year streamL-age3-survival) ^ (1 / 52)) [die!]] if breed = hybrid and stage = "adult" and age < 6 and current-stream = "L" [if random-float 1 > (((item week-of-year streamL-age3-survival) * (1 - ((1 - (item week-of-year streamL-age3-survival)) / 2))) ^ (1 / 52)) [die!]] end ;; individual growth to trout-grow ifelse current-stream = "C" [ ;; von Bertalanffy growth equation for trout in stream C set body-length (body-length + (streamC-parK * (streamC-max-length - body-length))) let healthy-weight (streamC-parA * ((body-length) ^ streamC-parB)) ;; weight-length regression set body-weight (condition-factor * healthy-weight) ] [ ;; von Bertalanffy growth equation for trout in stream L set body-length (body-length + (streamL-parK * (streamL-max-length - body-length))) let healthy-weight (streamL-parA * ((body-length) ^ streamL-parB)) ;; weight-length regression set body-weight (condition-factor * healthy-weight) ] set condition-factor max (list 0.5 (condition-factor + (- 0.008 + random-float 0.016))) ;; test for negative length and negative weight if body-length < 0 [ user-message "Negative fish length" ] if body-weight < 0 [ user-message "Negative fish weight" ] end to die! set breed dead hide-turtle end ;; identification of candidate spawners to trout-become-candidate-spawners if age >= spawn-min-age and status != "spawner" and not moved-to-spawn? [ if random-normal spawn-mean-length spawn-sd-length < body-length and random-normal spawn-mean-cond spawn-sd-cond < condition-factor [ set status "candidate-spawner" ] ] end ;; movement to stream C for reproduction to trout-move-to-spawn let temperature-streamL [temperature] of one-of patches with [ stream = "L" ] let flow-streamL [flow] of one-of patches with [ stream = "L" ] ;; spawners born in C or in L move to C if (status = "candidate-spawner" and not moved-to-spawn? and current-stream = "L" and natal-stream = "C") or (status = "selected-candidate-spawner" and not moved-to-spawn?) [ if random-lognormal spawn-mean-flow spawn-sd-flow < flow-streamL [ set current-stream "C" set xcor 1 set moved-to-spawn? true set status "candidate-spawner" ] ] end ;; update trout age and stage to trout-update-age set age age + 1 trout-update-stage end ;; update trout stage: fry, juvenile, adult to trout-update-stage if age < 1 [ set stage "fry" stop ] if age >= 1 and age <= 2 [ set stage "juvenile"stop ] if age > 2 [ set stage "adult" stop ] end ;; reproduction to trout-spawn-in-streamC let trout-spawners trout with [ status = "candidate-spawner" or status = "spawner" and current-stream = "C" ] let stocked-spawners-temp stocked with [ status = "candidate-spawner" or status = "spawner" and current-stream = "C" ] let hybrid-spawners-temp hybrid with [ status = "candidate-spawner" or status = "spawner" and current-stream = "C" ] let num-stocked-spawners (floor ((count stocked-spawners-temp) * stocked-spawning-prob)) let num-hybrid-spawners (floor ((count hybrid-spawners-temp) * hybrid-spawning-prob)) let stocked-spawners n-of num-stocked-spawners stocked-spawners-temp let hybrid-spawners n-of num-hybrid-spawners hybrid-spawners-temp let spawners (turtle-set trout-spawners stocked-spawners hybrid-spawners) ifelse count spawners < 2 [ stop ] [ ;; length of parents when born (VBLF backwards) let born-length-parents VBLF-reverse spawners ;; mean and variance of length of parents when born if length born-length-parents < 2 [ stop ] let mean-parents mean born-length-parents let var-parents variance born-length-parents let num-crossover ((count trout-spawners + count stocked-spawners + count hybrid-spawners) / 2) ;; polygamous mating with satellite males (not in good condition) repeat num-crossover [ let num-males 1 + random 4 ; number of males drawn randomly from an uniform distribution from 1 to 4 let all-parent-M spawners with [ sex = "M" ] if count all-parent-M < num-males [ stop ] let no-parent-M max-n-of num-males spawners with [ sex = "M" ] [condition-factor] let sel-parent-M all-parent-M with [ not member? self no-parent-M and not spawned? ] if count spawners with [ sex = "F" and not spawned? ] <= 1 [ stop ] if count sel-parent-M < num-males [ stop ] ;; select the parents: first, the spawners that have moved to spawn, then the other spawners let parent-M n-of num-males sel-parent-M let parent-F max-one-of spawners with [ sex = "F" and not spawned? ] [condition-factor] if (count spawners with [ sex = "M" and not spawned? and moved-to-spawn? ] - num-males) >= num-males [ if any? spawners with [ sex = "M" and not spawned? and moved-to-spawn? ] [ set all-parent-M spawners with [ sex = "M" and moved-to-spawn? ] set no-parent-M max-n-of num-males spawners with [ sex = "M" and moved-to-spawn? ] [condition-factor] set sel-parent-M all-parent-M with [ not member? self no-parent-M and not spawned? ] set parent-M n-of num-males sel-parent-M ] ] if any? spawners with [ sex = "F" and not spawned? and moved-to-spawn?] [ set parent-F max-one-of spawners with [ sex = "F" and not spawned? and moved-to-spawn?] [condition-factor] ] ;; length deviances of parents M and F from mean-parents let dummy VBLF-reverse parent-M let dev-M 0 let temp (random-normal meanl-birth-C sdl-birth-C) if temp < trdown-C [set temp trdown-C] if temp > trup-C [set temp trup-C] if length dummy = 0 [ set dev-M (mean-parents - temp) ] if length dummy = 1 [ set dev-M (mean-parents - (item 0 dummy)) ] if length dummy > 1 [ set dev-M (mean-parents - mean dummy) ] let dev-F (mean-parents - (VBLF-reverse parent-F)) ask parent-F [ set spawned? true set status "spawner" set xcor 1 let num-fry update-num-offspringC [body-length] of parent-F hatch-trout num-fry [ set hidden? true ;; hide trout until hatching set age -1 set stage "fry" ;; genotype of parent-M is a mixture of the several genotypes of males let genotype-mix mixture ([genotype] of parent-M) ;; define genotypes for eggs let egg-genotype cross-genotype (genotype-mix) ([genotype] of parent-F) set genotype egg-genotype set breed item 0 assign-breed egg-genotype set xcor 1 set current-stream "C" set natal-stream "C" set num-offspring 0 set week-of-birth week-of-year set week-of-birth2 (week + 1) ifelse random-float 1 > 0.5 [ set sex "M" ] [ set sex "F" ] set status "non-spawner" set spawned? false set moved-to-spawn? false set returned? false ;; set body-length as function of parents' length and environment let genetic-dev (sqrt length-heritability) * (dev-M + dev-F) let envi-var ((1 - length-heritability) ^ 2) * var-parents let envi-dev random-normal 0 (sqrt envi-var) set body-length mean-parents + genetic-dev + envi-dev let temp2 (random-normal meanl-birth-C sdl-birth-C) if temp2 < trdown-C [set temp2 trdown-C] if temp2 > trup-C [set temp2 trup-C] if body-length < trdown-C or body-length > trup-C [ set body-length temp2 ] ;; set body-weight and condition-factor set condition-factor (random-normal mean-bcf-C sd-bcf-C) set body-weight (condition-factor * ((body-length) ^ 3) / 100000) ] set num-offspring num-fry ] ask parent-M [ ;set spawned? true ;; shut because males can reproduce more than once set status "spawner" set xcor 1 set num-offspring [num-offspring] of parent-F ] ] ] end to trout-spawn-in-streamL let trout-spawners trout with [ status = "candidate-spawner" or status = "spawner" and current-stream = "L" ] let stocked-spawners-temp stocked with [ status = "candidate-spawner" or status = "spawner" and current-stream = "L" ] let hybrid-spawners-temp hybrid with [ status = "candidate-spawner" or status = "spawner" and current-stream = "L" ] let num-stocked-spawners (floor ((count stocked-spawners-temp) * stocked-spawning-prob)) let num-hybrid-spawners (floor ((count hybrid-spawners-temp) * hybrid-spawning-prob)) let stocked-spawners n-of num-stocked-spawners stocked-spawners-temp let hybrid-spawners n-of num-hybrid-spawners hybrid-spawners-temp let spawners (turtle-set trout-spawners stocked-spawners hybrid-spawners) ifelse count spawners < 2 [ stop ] [ let born-length-parents VBLF-reverse spawners ;; mean and variance of length of parents when born if length born-length-parents < 2 [ stop ] let mean-parents mean born-length-parents let var-parents variance born-length-parents let num-crossover ((count trout-spawners + count stocked-spawners + count hybrid-spawners) / 2) ;; polygamous mating with satellite males (not in good condition) repeat num-crossover [ let num-males 1 + random 4 ; number of males drawn randomly from an uniform distribution from 1 to 4 let all-parent-M spawners with [ sex = "M" ] if count all-parent-M < num-males [ stop ] let no-parent-M max-n-of num-males spawners with [ sex = "M" ] [condition-factor] let sel-parent-M all-parent-M with [ not member? self no-parent-M and not spawned? ] if count spawners with [ sex = "F" and not spawned? ] <= 1 [ stop ] if count sel-parent-M < num-males [ stop ] ;; select the parents: first, the spawners that have moved to spawn, then the other spawners let parent-M n-of num-males sel-parent-M let parent-F max-one-of spawners with [ sex = "F" and not spawned? ] [condition-factor] if (count spawners with [ sex = "M" and not spawned? and moved-to-spawn? ] - num-males) >= num-males [ if any? spawners with [ sex = "M" and not spawned? and moved-to-spawn? ] [ set all-parent-M spawners with [ sex = "M" and moved-to-spawn? ] set no-parent-M max-n-of num-males spawners with [ sex = "M" and moved-to-spawn? ] [condition-factor] set sel-parent-M all-parent-M with [ not member? self no-parent-M and not spawned? ] set parent-M n-of num-males sel-parent-M ] ] if any? spawners with [ sex = "F" and not spawned? and moved-to-spawn?] [ set parent-F max-one-of spawners with [ sex = "F" and not spawned? and moved-to-spawn?] [condition-factor] ] ;; length deviances of parents M and F from mean-parents let dummy VBLF-reverse parent-M let dev-M 0 let temp (random-normal meanl-birth-L sdl-birth-L) if temp < trdown-L [set temp trdown-L] if temp > trup-L [set temp trup-L] if length dummy = 0 [ set dev-M (mean-parents - temp) ] if length dummy = 1 [ set dev-M (mean-parents - (item 0 dummy)) ] if length dummy > 1 [ set dev-M (mean-parents - mean dummy) ] let dev-F (mean-parents - (VBLF-reverse parent-F)) ask parent-F [ set spawned? true set status "spawner" set xcor 0 let num-fry update-num-offspringL [body-length] of parent-F hatch-trout num-fry [ set hidden? true ;; hide trout until hatching set age -1 set stage "fry" ;; genotype of parent-M is a mixture of the several genotypes of males let genotype-mix mixture ([genotype] of parent-M) ;; define genotypes for eggs let egg-genotype cross-genotype (genotype-mix) ([genotype] of parent-F) set genotype egg-genotype set breed item 0 assign-breed egg-genotype set xcor 0 set current-stream "L" set natal-stream "L" set num-offspring 0 set week-of-birth week-of-year set week-of-birth2 (week + 1) ifelse random-float 1 > 0.5 [ set sex "M" ] [ set sex "F" ] set status "non-spawner" set spawned? false set moved-to-spawn? false set returned? false ;; set body-length as function of parents' length and environment let genetic-dev (sqrt length-heritability) * (dev-M + dev-F) let envi-var ((1 - length-heritability) ^ 2) * var-parents let envi-dev random-normal 0 (sqrt envi-var) set body-length mean-parents + genetic-dev + envi-dev let temp2 (random-normal meanl-birth-L sdl-birth-L) if temp2 < trdown-L [set temp2 trdown-L] if temp2 > trup-L [set temp2 trup-L] if body-length < trdown-L or body-length > trup-L [ set body-length temp2 ] ;; set body-weight and condition-factor set condition-factor (random-normal mean-bcf-L sd-bcf-L) set body-weight (condition-factor * ((body-length) ^ 3) / 100000) ] set num-offspring num-fry ] ask parent-M [ ;set spawned? true ;; shut because males can reproduce more than once set status "spawner" set xcor 0 set num-offspring [num-offspring] of parent-F ] ] ] end ;; stream C to-report update-num-offspringC [ female-length ] ;; linear function ;; compute the intermediate variables for the linear offspring production function for trout of stream C set offspringC-varA (offprodC-max - offprod-min) / (offprod-max-length - offprod-min-length) set offspringC-varB offprod-min - (offspringC-varA * offprod-min-length) report ((offspringC-varA * female-length) + offspringC-varB) end ;; stream L to-report update-num-offspringL [ female-length ] ;; linear function ;; compute the intermediate variables for the linear offspring production function for trout of stream C set offspringL-varA (offprodL-max - offprod-min) / (offprod-max-length - offprod-min-length) set offspringL-varB offprod-min - (offspringL-varA * offprod-min-length) report ((offspringL-varA * female-length) + offspringL-varB) end to-report cross-genotype [ genotype1 genotype2 ] let new-genotype [] let bit 0 repeat length genotype1 [ let choice random 4 if choice = 0 [ set new-genotype (lput (word(substring (item bit genotype1) 0 4)(substring (item bit genotype2) 0 3)) new-genotype)] if choice = 1 [ set new-genotype (lput (word(substring (item bit genotype1) 0 3) (substring (item bit genotype2) 3 7)) new-genotype)] if choice = 2 [ set new-genotype (lput (word(substring (item bit genotype2) 0 3) (substring (item bit genotype1) 3 7)) new-genotype)] if choice = 3 [ set new-genotype (lput (word(substring (item bit genotype1) 4 7) (substring (item bit genotype2) 3 7)) new-genotype)] set bit bit + 1 ] report new-genotype end to-report mixture [ genotype-temp ] let genotype-mix [] let bit 0 repeat length one-of genotype-temp [ let choice random (length genotype-temp) ; choose randomly one genotype among n males set genotype-mix lput item bit (item choice genotype-temp) genotype-mix set bit bit + 1 ] report genotype-mix end to-report VBLF-reverse [ trout-indiv ] ifelse is-agentset? trout-indiv [ let length-when-born [] (foreach sort trout-indiv [ let time 0 let length-diff 0 let length-when-born-temp 0 ask ? [ set time (week - week-of-birth2) ifelse natal-stream = "C" [ set length-diff (streamC-max-length - body-length) set length-when-born-temp (streamC-max-length - (length-diff / ((1 - streamC-parK) ^ (time)))) ] [ set length-diff (streamL-max-length - body-length) set length-when-born-temp (streamL-max-length - (length-diff / ((1 - streamL-parK) ^ (time)))) ] ] set length-when-born lput length-when-born-temp length-when-born ]) report length-when-born ] [ let time (week - ([week-of-birth2] of trout-indiv)) ifelse [natal-stream] of trout-indiv = "C" [ let length-when-born (streamC-max-length - ((streamC-max-length - [body-length] of trout-indiv) / ((1 - streamC-parK) ^ (time)))) report length-when-born ] [ let length-when-born (streamL-max-length - ((streamL-max-length - [body-length] of trout-indiv) / ((1 - streamL-parK) ^ (time)))) report length-when-born ] ] end to trout-become-candidate-migrants if (age = move-min-age or age = move-max-age) and current-stream = "C" and natal-stream = "C" [ if random-normal move-mean-length move-sd-length < body-length [ set status "candidate-migrant" ] ] end ;; movement from C to L to trout-move-downstream let temperature-streamC [temperature] of one-of patches with [ stream = "C" ] let flow-streamC [flow] of one-of patches with [ stream = "C" ] if status = "candidate-migrant" [ if random-normal move-mean-temperature move-sd-temperature < temperature-streamC and random-lognormal move-mean-flow move-sd-flow < flow-streamC [ ifelse age = 1 ;; juveniles age 1 [ if random-float 1 < move-age1-prob [ set xcor 0 set current-stream "L" set status "migrant" ] ] ;; juveniles age 2 [ if random-float 1 < move-age2-prob [ set xcor 0 set current-stream "L" set status "migrant" ] ] ] ] end to update-move-age1-prob ;; logistic function let nb1 count trout with [current-stream = "C" and body-length > 70] let Z1 (exp((move-age1-varA * nb1) + move-age1-varB)) set move-age1-prob (Z1 / (1 + Z1)) end to update-move-age2-prob ;; logistic function let nb2 count trout with [current-stream = "C" and body-length > 70] let Z1 (exp((move-age2-varA * nb2) + move-age2-varB)) set move-age2-prob (Z1 / (1 + Z1)) end to trout-move-back ;; candidate spawners return to previous stream if (status = "candidate-spawner" and current-stream = "C" and moved-to-spawn?) ;; effective spawners return to previous stream or (status = "spawner" and current-stream = "C" and moved-to-spawn?) [ set current-stream "L" set xcor 0 set returned? true ] end to leave-streamL set breed gone hide-turtle end to intro-stocked-trout if year = 1 [ let num-trout count trout with [current-stream = "L"] set num-stocked round (stocking-coefficient * num-trout) ;print num-stocked ] create-stocked num-stocked [ set breed stocked set newly-stocked? true setxy random-xcor -15 set shape "box" set size 0.8 set current-stream "L" set natal-stream "X" ifelse random-float 1 > 0.5 [ set sex "M" ] [ set sex "F" ] ;; attribute trout genotypes at 12 microsatellites markers (loci) let markers [] file-open "input-genotypes-stocking.txt" set markers (sentence file-read (list ["999/999"])) file-close let freq [] file-open "input-genofreq-stocking.txt" set freq (sentence file-read (list [1])) file-close set genotype [] set genotype assign-genotype (markers) (freq) set num-offspring 0 set status "non-spawner" set spawned? false set moved-to-spawn? false set returned? false set age 2 trout-update-stage ;; a trout procedure setting stage from age ;; attribute body-length, body-weight and condition-factor set body-length random-normal 248.47 26.71 set condition-factor 1.1 set body-weight (condition-factor * ((body-length) ^ 3) / 100000) ;; test for negative length and negative weight if body-length < 0 [ user-message "Negative fish length" ] if body-weight < 0 [ user-message "Negative fish weight" ] ] ;; end of create-stocked in stream L end to-report assign-genotype [markers freq] let locus [] let bit 0 repeat length markers [ set locus assign-locus (bit) (markers) (freq) set genotype lput (first locus) genotype set bit bit + 1 ] report genotype end to-report assign-locus [bit markers freq] let locus [] let q 0 let ran random-float 1.0 (foreach (item bit markers) (item bit freq) [ set q q + ?2 if ran <= q [set locus lput ?1 locus] if empty? locus and ?1 = last (item bit markers) [ set locus assign-locus (bit) (markers) (freq) ] ]) report locus end ;; breed attribution to offspring in function of 13th loci in genotype to-report assign-breed [ genotype-temp ] ;; wild trout if (last genotype-temp) = "000/000" [ report (list trout) ] ;; stocked trout if (last genotype-temp) = "999/999" [ report (list stocked)] ;; hybrids if (last genotype-temp) = "000/999" [ report (list hybrid) ] if (last genotype-temp) = "999/000" [ report (list hybrid) ] end ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; to-report random-lognormal [mu sigma] let S sqrt(ln(((sigma / mu) ^ 2) + 1)) let M ln (mu) - ((S ^ 2) / 2) report exp(random-normal M S) end

There is only one version of this model, created over 10 years ago by Béatrice Frank.

## Attached files

File | Type | Description | Last updated | |
---|---|---|---|---|

DemGenTrout-V1-3_data.zip | data | External files for 'DemGenTrout 1.3' | almost 10 years ago, by Béatrice Frank | Download |

**Parent:** DemGenTrout 1.1

This model does not have any descendants.

Béatrice Frank

## About DemGenTrout 1.3

This version includes features of DemGenTrout 1.1 (faster initialisation) and simulates stocking with hatchery trout. An applet of the model is available at: http://sites-final.uclouvain.be/gena-truites/DemGenTrout/DemGenTrout-V1-3.html

## Posted over 10 years ago