globals [popsize cullsize started bark-color dark-color light-color dom-color rec-color]
breed [moths moth]
breed [birds bird]
breed [couples couple]
breed [exes ex]

moths-own [chromosome1 chromosome2 doomed? active? chosen? flapping? partner targetx targety]
birds-own [target sated?]
couples-own [cross-type]

to-report get-cross-text [moth1 moth2]
  let result ""
  let tmp1 [chromosome1] of moth1 + [chromosome2] of moth1
  let tmp2 [chromosome1] of moth2 + [chromosome2] of moth2
  let g1 max list tmp1 tmp2
  let g2 min list tmp1 tmp2
  ifelse g1 = 0 [
    set result word result "bb x "
    ][
      ifelse g1 = 1 [set result word result "Bb x "][set result word result "BB x "]
    ]
  ifelse g2 = 0 [
    set result word result "bb"
    ][
      ifelse g2 = 1 [set result word result "Bb"][set result word result "BB"]
    ]
  report result
end

to setup
  clear-all
  set-default-shape moths "butterfly"
  set dark-color 1
  set light-color 8
  ifelse dominant-allele = "dark" [
    set dom-color dark-color
    set rec-color light-color
  ][
    set dom-color light-color
    set rec-color dark-color
  ]
  set started 1
  set popsize 50
  set cullsize 10
  lighten-bark
  create-moths popsize
  ask moths [
    set shape "butterfly"
    setxy random-pxcor random-pycor
    set size 3
    set doomed? false
    set active? false
    set chosen? false
    set flapping? false
    set color dark-color
    set chromosome1 0
    set chromosome2 0
    if random 2 = 0 [set chromosome1 1 set chromosome2 1]
    ifelse chromosome1 + chromosome2 > 0 [set color dom-color][set color rec-color]
  ]
  do-labels
  do-plot
end

to lighten-bark
  import-drawing "bark_light.png"
  set bark-color "light"
end

to darken-bark
  import-drawing "bark_dark.png"
  set bark-color "dark"
end

to mate
  ask n-of (int ((count moths) / 2 )) moths [set chosen? true]
  ask moths with [chosen?][
    ask one-of moths with [not active? and not chosen?][
      set active? true
      set partner myself
      if distance partner > 0 [set heading towards partner]
    ]
  ]
  while [count moths > 1] [
    ask moths with [active?][
      ifelse distance partner > 2 [
        forward 2
        ;wait 0.01
        ifelse flapping? [set shape "butterfly"][set shape "butterfly-flapping"]
        set flapping? (not flapping?)
        ]
      [
        move-to partner
        hatch 1 [
        set breed couples
        set cross-type (get-cross-text myself ([partner] of myself))
        set shape "heart"
        set heading 0
        set label cross-type
        set size 1
        wait 0.05
        set size 2
        wait 0.05
        set size 3
        ]
        ask partner [die]
        die
      ] ; end ifelse
    ]]
  while [count moths < popsize] [
    ask one-of couples [
      if cross-type = "BB x BB" [
        hatch 1 [
          set breed moths
          set chromosome1 1
          set chromosome2 1
        ]]
      if cross-type = "bb x bb" [
        hatch 1 [
          set breed moths
          set chromosome1 0
          set chromosome2 0
        ]]
      if cross-type = "BB x Bb" [
        hatch 1 [
          set breed moths
          set chromosome1 1
          ifelse random 2 = 0 [set chromosome2 0][set chromosome2 1] 
        ]]
      if cross-type = "Bb x bb" [
        hatch 1 [
          set breed moths
          set chromosome1 0
          ifelse random 2 = 0 [set chromosome2 0][set chromosome2 1]  
        ]]
      if cross-type = "Bb x Bb" [
        hatch 1 [
          set breed moths
          ifelse random 2 = 0 [set chromosome1 0][set chromosome1 1]
          ifelse random 2 = 0 [set chromosome2 0][set chromosome2 1]  
        ]]
      if cross-type = "BB x bb" [
        hatch 1 [
          set breed moths
          set chromosome1 1
          set chromosome2 0 
        ]]
      ]
    ]
  do-labels
  mutate
  do-plot
  ask couples [set size 3]
  ask moths [
    set active? false
    set chosen? false
    set shape "butterfly"
    set flapping? false
    set doomed? false
    set size 2
    ifelse chromosome1 + chromosome2 > 0 [set color dom-color][set color rec-color]
   ; set targetx random-pxcor
   ; set targety random-pycor
  ]
;  while [any? moths with [distancexy targetx targety > 2]] [
;    ask moths with [distancexy targetx targety > 2] [
 ;     set heading towardsxy targetx targety
 ;     forward 2
 ;     wait 0.001
      
      ;ifelse flapping? [set shape "butterfly"][set shape "butterfly-flapping"]
      ;set flapping? (not flapping?)
    
    ;set flapping? false
    ;set shape "butterfly"
 ;   ]
;  ]

foreach [1 2 3 4][ask moths [set heading random 360 fd 3 wait 0.001]]

  ask couples [die]
  ask moths [set size 3]
  wait 0.5
end

to select
  let cryptic-color dark-color
  if bark-color = "light" [set cryptic-color light-color]
  while [count moths with [doomed?] < cullsize] [
    ifelse any? moths with [color != cryptic-color and not doomed?] and any? moths with [color = cryptic-color and not doomed?][
      ifelse random 10 < 2 [ask one-of moths with [color = cryptic-color][set doomed? true]]
      [ask one-of moths with [color != cryptic-color][set doomed? true]]
    ][
      ask one-of moths [set doomed? true]
    ]
  ]
  ask moths with [doomed?] [
    hatch 1 [
      set breed exes
      set shape "x"
      set heading 0
      ifelse [color] of myself = light-color[set color 16][set color 14]
      set size 4
    ]
  ]
  wait 2
  ask moths with [doomed?][die]
  ask exes [die]
  wait 0.5
end

to do-plot
  let dom-pen-name "dark allele"
  let rec-pen-name "light allele"
  if dominant-allele = "light" [set dom-pen-name "light allele" set rec-pen-name "dark allele"]
  let dom-freq ((count moths with [chromosome1 = 1]) + (count moths with [chromosome2 = 1])) / (2 * count moths)
  set-current-plot-pen dom-pen-name
  plotxy ticks dom-freq
  set-current-plot-pen rec-pen-name
  plotxy ticks (1.0 - dom-freq)
end

to do-labels
  ifelse genotype-labels [
    ask moths [
      set label-color red
      let tmp chromosome1 + chromosome2
      ifelse tmp = 0 [set label "bb"]
        [ifelse tmp = 1 [set label "Bb"][set label "BB"]]
  ]
  ]
  [ask moths [set label ""]
  ]
end

to mutate
  ask moths [
    if random 100 = 0 [
      ifelse random 2 = 0 [ifelse chromosome1 = 0 [set chromosome1 1][set chromosome1 0]]
      [ifelse chromosome2 = 0 [set chromosome2 1][set chromosome2 0]]
    ]
  ]
end

to go-once
  tick
  ifelse started = 0 [
    ask patch 0 0 [set plabel "Please set up first."]
  ][
    do-labels
    select
    mate
    ]
end
@#$#@#$#@
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@#$#@#$#@
WHAT IS IT?
-----------
This is a simple simulation of natural selection in a trait controlled by a single gene with two alleles. It is modeled on evolution of color-morphs of the peppered moth Biston betularia.

Peppered moths rest on tree trunks. In England in the early 19th century, the most commonly seen of these moths had light-gray, speckled wings. They were well camouflaged against the light-gray lichens and bark. Occasionally one saw dark-winged morphs, but these were poorly camouflaged and tended to be eaten by birds.

As the Industrial Revolution progressed, air pollution killed many of the lichens and darkened the tree trunks with soot. As the previously cryptic light-winged moths became visible to predators -- and the dark-winged morphs became better camouflaged -- the dark-winged trait became more common.


HOW IT WORKS
------------
Each moth has a single-gene, two-allele genotype. There are two phenotypes -- light and dark -- and the user can specify whether light or dark is the dominant trait.

In every generation, the simulation starts with a population of fifty moths. Selection eliminates ten of them, preferentially eliminating dark moths if the bark is light and light moths if the bark is dark.

The surviving moths then pair off and mate. Pairs produce offspring whose genotypes are determined probabilistically by simple Mendelian genetics. Offspring phenotypes follow from their genotypes.

The plot then records the new generation's allele frequencies.


HOW TO USE IT
-------------
First, SET UP. This creates the first generation of moths. Your first time playing with the simulation, leave all the settings at their defaults.

Click GO ONCE. Watch selection eliminate moths, and note that the poorly-camouflaged moths are preferentially killed. (Selection is indicated by X's. Dark moths have dark-red X's, and light moths have light-red X's, so it's easy to make a quick visual assessment of the selection bias.)

If you have the genotype-labels turned on, watch the genotypes of the offspring as they emerge from the crosses. Either way, get a general feel for whether you see more or fewer dark moths emerging.

Click GO ONCE again, or click GO REPEATEDLY. (Click GO REPEATEDLY again to stop. Note that the simulation won't stop immediately; it will stop at the end of the current generation.) Watch the trajectories of the allele frequencies.


THINGS TO NOTICE
----------------
When the bark is light, you should see the dark allele decrease in frequency. When the bark is dark, you should see the light allele decline. It doesn't happen particularly straightforwardly, though. Does one of the elleles decline more quiickly than the other? Why? (Look at http://people.brynmawr.edu/twong/models/completedominance.html for a hint.)


THINGS TO TRY
-------------
The default settings have the light allele as recessive to dark. Try setting the light as dominant. With light bark, does the dark allele decline more or less quickly than before? (Remember, you can't make conclusions on the basis of single trials. Try running the simulation to fixation several times for each set of settings, and compare averages.)



RELATED MODELS
--------------
http://people.brynmawr.edu/twong/models/completedominance.html
http://people.brynmawr.edu/twong/models/incompletedominance.html
http://faculty.ccp.edu/faculty/twong/demos/drift.html


CREDITS AND REFERENCES
----------------------
This simulation was built by Ted Wong, November 2009. It is hosted as a web applet at http://faculty.ccp.edu/faculty/twong/demos/simple_selection.html

More detailed information on peppered-moth evolution can be found at http://en.wikipedia.org/wiki/Peppered_moth_evolution
@#$#@#$#@
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