globals [number-of-individuals dead time death-rate percent-small percent-red percent-square]
breeds [males females ]
turtles-own [trait1 trait2 trait3 age mother father ]


to setup
  ca
  create-males (number / 2)                                    ;half the initial turtles are male, half are female
  create-females (number / 2)
ask turtles [  ifelse random 100 < percent_green [set trait1 2]               ;trait 1 is color
        [ifelse random (100 - percent_green) < (((1 - sqrt (percent_green / 100)) ^ 2) * 100) 
        [set trait1 0] [set trait1 1]]]
ask turtles [  ifelse random 100 < percent_big [set trait2 2]                 ; trait 2 is size
        [ifelse random (100 - percent_big) < (((1 - sqrt (percent_big / 100)) ^ 2) * 100) 
        [set trait2 0] [set trait2 1]]]
ask turtles [  ifelse random 100 < percent_circle [set trait3 2]               ; trait 3 is shape
        [ifelse random (100 - percent_circle) < (((1 - sqrt (percent_circle / 100)) ^ 2) * 100) 
        [set trait3 0] [set trait3 1]]]                                                        
ask turtles [ifelse trait1 = 2 [set color green] [set color red]      ; green is recessive(2), red is dominant: (0) for AA (1) for Aa
     ifelse trait2 = 2 [set size 1] [set size 0.5]                    ; big is recessive (2), small is dominant: (0) for AA (1) for Aa
     ifelse trait3 = 2 [set shape "circle"] [set shape "square"]]     ; circle is recessive(2), square is dominant: (0) for AA (1) for Aa
  ask turtles [set heading (random 360) fd random screen-edge-x] 
  ask turtles [ set age random 25]
  ask turtles [set mother nobody set father nobody]
  set dead 0
end

to go
ask turtles   [wander ]
ask turtles [set age age + 1]
set time (time + 1)
ask females [if age > 25 [find-mate]]
do-selecting
set number-of-individuals (count turtles)
ask turtles [check-pop-vs-carrying-capacity]
if number-of-individuals = 0 [stop]
setup-plots
do-plotting
end

to wander
fd 1 rt random 90 - random 90
end

to check-pop-vs-carrying-capacity
if number-of-individuals > (carrying_capacity) [
ifelse number-of-individuals > (2 * carrying_capacity)    [if random 2 = 0 [die ] ]
  [set death-rate (((number-of-individuals - carrying_capacity) / carrying_capacity) * 100) if random 100 < death-rate  [die]] ]
end

to find-mate
if mate-preference = "no one"  
    [without-interruption [
    if (mother = nobody) and ((any? males-here with [father = nobody]))
    [set-mates]]]
if mate-preference = "red"  
    [if (mother = nobody) and (any? males-here with [father = nobody])
    [ifelse any? males-here with [color = red] [set-mates] [if random 101 >= %preference [set-mates]]]]
if mate-preference = "green" 
    [if (mother = nobody) and (any? males-here with [father = nobody])
    [ifelse any? males-here with [color = green] [set-mates] [if random 101 >= %preference [set-mates]]]]
if mate-preference = "small" 
    [if (mother = nobody) and (any? males-here with [father = nobody])
    [ifelse any? males-here with [size = 0.5] [set-mates] [if random 101 >= %preference [set-mates]]]]
if mate-preference = "big" 
    [if (mother = nobody) and (any? males-here with [father = nobody])
    [ifelse any? males-here with [size = 1] [set-mates] [if random 101 >= %preference [set-mates]]]]
if mate-preference = "square" 
    [if (mother = nobody) and (any? males-here with [father = nobody])
    [ifelse any? males-here with [shape = "square"] [set-mates] [if random 101 >= %preference [set-mates]]]]
if mate-preference = "circle" 
    [if (mother = nobody) and (any? males-here with [father = nobody])
    [ifelse any? males-here with [shape = "circle"] [set-mates] [if random 101 >= %preference [set-mates]]]]
end

to set-mates
set father (random-one-of males-here with [father = nobody])
set mother self reproduce set age 0 set mother nobody set father nobody
end


to reproduce
ifelse random 2 = 1 [hatch-females 1 [ set age 0 set-trait1-of-offspring set-trait2-of-offspring set-trait3-of-offspring
    set mother nobody set father nobody
  ifelse trait1 = 2 [set color green] [set color red]
  ifelse trait2 = 2 [set size 1] [set size 0.5]
  ifelse trait3 = 2 [set shape "circle"] [set shape "square"]]]
 [ hatch-males 1 [ set age 0  set-trait1-of-offspring set-trait2-of-offspring set-trait3-of-offspring
     set mother nobody set father nobody
  ifelse trait1 = 2 [set color green] [set color red]
  ifelse trait2 = 2 [set size 1] [set size 0.5]
  ifelse trait3 = 2 [set shape "circle"] [set shape "square"]]]

end

to set-trait1-of-offspring   ; 0 is homozygous dominant (AA), 1 is heterozygous (Aa), 2 is homozygous recessive (aa)
 if (trait1-of father = 0 and trait1-of mother = 0) [set trait1 0]           ; AA x AA => AA
 if (trait1-of father = 0 and trait1-of mother = 1) [set trait1 random 2]    ; AA x Aa => 50% AA, 50% Aa
 if (trait1-of father = 0 and trait1-of mother = 2) [set trait1 1]           ; AA x aa => Aa
 if (trait1-of father = 1 and trait1-of mother = 0) [set trait1 random 2]    ; Aa X AA => 50% AA, 50% Aa
 if (trait1-of father = 1 and trait1-of mother = 1) 
  [ifelse (random 2 = 0) [set trait1 1] [ifelse random 2 = 0 [set trait1 0] [set trait1 2]]]; Aa x Aa => 50% Aa, 25% aa, 25%AA
 if (trait1-of father = 1 and trait1-of mother = 2) [set trait1 (1 + (random 2))] ; Aa x aa => 50% Aa, 50% aa
 if (trait1-of father = 2 and trait1-of mother = 0) [set trait1 1]          ; aa x AA => Aa
 if (trait1-of father = 2 and trait1-of mother = 1) [set trait1 (1 + (random 2))]          ; aa x Aa => 50% Aa, 50% aa
 if (trait1-of father = 2 and trait1-of mother = 2) [set trait1 2]          ; aa x aa => aa
end

to set-trait2-of-offspring   ; 0 is homozygous dominant (AA), 1 is heterozygous (Aa), 2 is homozygous recessive (aa)
 if (trait2-of father = 0 and trait2-of mother = 0) [set trait2 0]           ; AA x AA => AA
 if (trait2-of father = 0 and trait2-of mother = 1) [set trait2 random 2]    ; AA x Aa => 50% AA, 50% Aa
 if (trait2-of father = 0 and trait2-of mother = 2) [set trait2 1]           ; AA x aa => Aa
 if (trait2-of father = 1 and trait2-of mother = 0) [set trait2 random 2]    ; Aa X AA => 50% AA, 50% Aa
 if (trait2-of father = 1 and trait2-of mother = 1) 
  [ifelse (random 2 = 0) [set trait2 1] [ifelse random 2 = 0 [set trait2 0] [set trait2 2]]]; Aa x Aa => 50% Aa, 25% aa, 25%AA
 if (trait2-of father = 1 and trait2-of mother = 2) [set trait2 ((random 2) + 1)] ; Aa x aa => 50% Aa, 50% aa
 if (trait2-of father = 2 and trait2-of mother = 0) [set trait2 1]          ; aa x AA => Aa
 if (trait2-of father = 2 and trait2-of mother = 1) [set trait2 ((random 2) + 1)]          ; aa x Aa => 50% Aa, 50% aa
 if (trait2-of father = 2 and trait2-of mother = 2) [set trait2 2]          ; aa x aa => aa
end

to set-trait3-of-offspring   ; 0 is homozygous dominant (AA), 1 is heterozygous (Aa), 2 is homozygous recessive (aa)
 if (trait3-of father = 0 and trait3-of mother = 0) [set trait3 0]           ; AA x AA => AA
 if (trait3-of father = 0 and trait3-of mother = 1) [set trait3 random 2]    ; AA x Aa => 50% AA, 50% Aa
 if (trait3-of father = 0 and trait3-of mother = 2) [set trait3 1]           ; AA x aa => Aa
 if (trait3-of father = 1 and trait3-of mother = 0) [set trait3 random 2]    ; Aa X AA => 50% AA, 50% Aa
 if (trait3-of father = 1 and trait3-of mother = 1) 
  [ifelse (random 2 = 0) [set trait3 1] [ifelse random 2 = 0 [set trait3 0] [set trait3 2]]]; Aa x Aa => 50% Aa, 25% aa, 25%AA
 if (trait3-of father = 1 and trait3-of mother = 2) [set trait3 ((random 2) + 1)] ; Aa x aa => 50% Aa, 50% aa
 if (trait3-of father = 2 and trait3-of mother = 0) [set trait3 1]          ; aa x AA => Aa
 if (trait3-of father = 2 and trait3-of mother = 1) [set trait3 ((random 2) + 1)]          ; aa x Aa => 50% Aa, 50% aa
 if (trait3-of father = 2 and trait3-of mother = 2) [set trait3 2]          ; aa x aa => aa
end

to setup-plots                                              
;  set-current-plot "color AA          Aa          aa"
;  set-plot-x-range 0 2.1
;  set-plot-y-range 0 (int 1.1 * carrying_capacity) 
;  set-histogram-num-bars 3
  
;  set-current-plot "size BB          Bb          bb"
;  set-plot-x-range 0 2.1
;  set-plot-y-range 0 (int 1.1 * carrying_capacity) 
;  set-histogram-num-bars 3
  
;  set-current-plot "shape DD          Dd          dd"
;  set-plot-x-range 0 2.1
;  set-plot-y-range 0 (int 1.1 * carrying_capacity) 
;  set-histogram-num-bars 3                
end          
                                          
to do-plotting
  set-current-plot "% by gene"   
  set percent-red ((count turtles with [color = red]) / (number-of-individuals)* 100)
  set percent-square ((count turtles with [shape = "square"]) / (number-of-individuals) * 100)
  set percent-small ((count turtles with [size = 0.5]) / (number-of-individuals) * 100)
  set-current-plot-pen "percent-red"
  plot percent-red
  set-current-plot-pen "percent-square"
  plot percent-square
  set-current-plot-pen "percent-small"
  plot percent-small
  
;  set-current-plot "color AA          Aa          aa"               
;  histogram-from turtles [ trait1 ]

;  set-current-plot "size BB          Bb          bb"
;  histogram-from turtles [ trait2 ]
  
;  set-current-plot "shape DD          Dd          dd"
;  histogram-from turtles [ trait3 ]                                   
end

to do-selecting
if selection-against = "red" [ask turtles with [color = red] [if random 100 < (selection-against_factor / 1000)  [die] ]]
if selection-against = "green" [ask turtles with [color = green] [if random 100 < (selection-against_factor / 1000)  [die] ]]
if selection-against = "small" [ask turtles with [size = 0.5] [if random 100 < (selection-against_factor / 1000)  [die] ]]
if selection-against = "big" [ask turtles with [size = 1] [if random 100 < (selection-against_factor / 1000)  [die] ]]
if selection-against = "square" [ask turtles with [shape = "square"] [if random 100 < (selection-against_factor / 1000)  [die] ]]
if selection-against = "circle" [ask turtles with [shape = "circle"] [if random 100 < (selection-against_factor / 1000)  [die] ]]
end
@#$#@#$#@
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@#$#@#$#@
WHAT IS IT?
-----------
This is a model of population genetics. The population has three genes (size, color and shape), each with a dominant and recessive phenotype, that are passed along to offspring from a mated pair in a Mendelian fashion. The model runs in an equilibrium fashion if criteria for a Hardy-Weinberg equilibrium hold; that is, there is no mutation, no migration, no selection, random-mating and a large population. Students can manipulate the model so that there is selection against any one phenotype, there is preference by the female for one of the phenotypes, or there is a large or small population. 


HOW IT WORKS
------------
Organisms represented by colored shapes move randomly around the world. If a female of appropriate age (25) finds and unmated male, she mates and has one offspring. Offspring have 50% chance of being female, 50% chance of being a male. Traits of the mother and father are passed on to offspring in a Mendelian fashion. For each of the three genes, parents are homozygous dominant, hetrozygous or homozygous recessive. The model calculates the probability of possible allele combinations from the mother and father and assigns the genotypes to the offspring based on the calculated probability. Calculations are based on independent assortment of the genes.
After a female mates, her age is reset to zero, such that she must wait a short time (25 time steps) before mating again. Offspring can mate in a similar fashion, passing on their genes to their own offspring.

Carrying capacity is the limit to the populations size. After carrying capacity has been exceeded, al individuals have a likelihood of dying at a rate of [(population size - carrying capacity) / carrying capacity]

Students can manipulate selection against any one phenotype by choosing the phenotype and setting a "selection_against_factor" that either slowly (low) or quickly (high number) eliminates that phenotype from the population. This occurs at all times, regardless of whether the carrying capacity has been exceeded or not. Selecting a phenotype and setting the "selection_against_factor" at zero is the same as choosing "no one". 

Students can manipulate whether females have a mate preference or not by choosing a phenotype that is preferred and setting the "%preference" to determine how often the un-preferred phenotype gets to mate. Setting the "%preference" to zero is the same as the female preferring "no one"; that is mating with both phenotypes equally.


HOW TO USE IT
-------------
Students select a starting population size, as well as carrying capacity for the population.

Students can then select the approximate % of the population that will have the recessive phenotype (q2) for each gene. The model then calculates the approximate number of individuals in the population that are heterozygous (2pq) and homozygous dominant (p2) such tha the starting population is in an equilibrium. 

Students can manipulate selection against any one phenotype by choosing the phenotype and setting a "selection_against_fator" that either slowly (low) or quickly (high number) eliminates that phenotype from the population. 

Students can manipulate whether females have a mate preference or not by choosing a phenotype that is preferred and setting the "%preference" to determine how often the un-preferred phenotype gets to mate.

THINGS TO NOTICE
----------------
Note that the model runs at an equilibrium (that is, the percentages of the phenotypes do not change over time) if there is no selection, random mating, and the population is large enough.


THINGS TO TRY
-------------
Does the model run at equilibium for all starting phenotype percentages? 
What happens if the population is small?
What happens if you select against a phenotype?
What happens if you have mate preference for one phenotype over another?
What happens if you change these while the model is running? Can you reverse a trend?
How long does it take to remove a phenotype completely from the model under each circumstance?

EXTENDING THE MODEL
-------------------
How might you change the model to include mutation and migration?
How might you code the model so males have to be of a certain age to mate?
Code could be wrritten in the model to include organisms dying after a certain age or after they have had a certin number of offspring.

NETLOGO FEATURES
----------------
This section could point out any especially interesting or unusual features of NetLogo that the model makes use of, particularly in the Procedures tab.  It might also point out places where workarounds were needed because of missing features.


RELATED MODELS
--------------
Other models of population genetics can be found at
http://ccl.northwestern.edu/netlogo/models/community/sheep-selection (Ed Hazzard)
http://ccl.northwestern.edu/netlogo/models/community/sheep-fussyfemales (Ed Hazzard)
http://ccl.northwestern.edu/ProbLab/Genetics.html

After looking at the code for sheep-selection and sheep-fussyfemales, I think these models have a problem in that the offspring can inherit genes from more than one father. 

CREDITS AND REFERENCES
----------------------
This section could contain a reference to the model's URL on the web if it has one, as well as any other necessary credits or references.
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Circle -16777216 true false 24 174 42
Circle -7500403 false true 24 174 42
Circle -7500403 false true 144 174 42
Circle -7500403 false true 234 174 42

turtle
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Polygon -10899396 true false 215 204 240 233 246 254 228 266 215 252 193 210
Polygon -10899396 true false 195 90 225 75 245 75 260 89 269 108 261 124 240 105 225 105 210 105
Polygon -10899396 true false 105 90 75 75 55 75 40 89 31 108 39 124 60 105 75 105 90 105
Polygon -10899396 true false 132 85 134 64 107 51 108 17 150 2 192 18 192 52 169 65 172 87
Polygon -10899396 true false 85 204 60 233 54 254 72 266 85 252 107 210
Polygon -7500403 true true 119 75 179 75 209 101 224 135 220 225 175 261 128 261 81 224 74 135 88 99

wheel
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Circle -7500403 true true 3 3 294
Circle -16777216 true false 30 30 240
Line -7500403 true 150 285 150 15
Line -7500403 true 15 150 285 150
Circle -7500403 true true 120 120 60
Line -7500403 true 216 40 79 269
Line -7500403 true 40 84 269 221
Line -7500403 true 40 216 269 79
Line -7500403 true 84 40 221 269

x
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Polygon -7500403 true true 270 75 225 30 30 225 75 270
Polygon -7500403 true true 30 75 75 30 270 225 225 270

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NetLogo 3.0
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