Genetic Linkage Analysis in Drosophila

globals [x y p1 p2 population-size f-x f-y fly-ID list-1 list-2 list-3 list-4 list-5 list-6 list-7 list-8 list-9]    ;p1=selected parent 1, p2=selected parent 2,
turtles-own [c1 c2 genotype phenotype gender eye-shape wing-shape body-color]

breed [sperms sperm]
breed [eggs egg]
breed [flies a-fly]
breed [crosses cross]

to setup
  ca
  set-gametes
  fertilization
  set-tray
  output-results
  reset-ticks
end 

to set-gametes

set population-size 20 + random 16

(ifelse
  Cases = "Case 1" [              ;bar eyes.
  create-sperms population-size
  [gamete-trait
    set c1 item random 3 ["XEB" "XEb" "Y"]     ;given the three possoibilities, the gender ratio does not start with 1:1 at the beginning but brias to female
    set c2 "D"                               ;all flies are normal-winged
    set genotype word c1 c2                  ;form  genotype of gamete
    ]

  create-eggs population-size
  [gamete-trait
    set c1 item random 2 ["XEB" "XEb"]
    set c2 "D"
    set genotype word c1 c2
    ]
  ]

 Cases = "Case 2" [             ; dumpy wings
   create-sperms population-size
  [gamete-trait
    set c1 item random 2 ["XEb" "Y"]         ; Xb is normal eye trait
    set c2 item random 3 ["D" "d" "d"]        ; D and d are wing shape color alleles.
    set genotype word c1 c2
    ]

  create-eggs population-size
  [gamete-trait
    set c1 "XEb"
    set c2 item random 3 ["D" "d" "d"]
    set genotype word c1 c2
    ]
  ]



Cases = "Case 3" [             ;yellow body.
   create-sperms population-size
  [gamete-trait
    set c1 item random 3 ["XEb" "Xeb" "Y"]         ; XE is normal body color
    set c2 "D"                                   ; nomral wings
    set genotype word c1 c2
    ]

  create-eggs population-size
  [gamete-trait
    set c1 item random 2 ["XEb" "Xeb"]
    set c2 "D"
    set genotype word c1 c2
    ]
  ]
)
end 

to gamete-trait
  set shape "dot"
    set size 0.1
    setxy random-xcor random-ycor
end 

to express

  ;;Determine phenotypes based on the allele, then code the phenotypes
  ifelse member? "Y" genotype = true [set gender "male" set size 0.75 set phenotype "m-" ][set gender "female" set size 0.9 set phenotype "f-"]

  ifelse member? "D" genotype = true [set wing-shape "normal-winged" set phenotype word phenotype "lw-"][set wing-shape "dumpy-winged" set phenotype word phenotype "dw-"]

  ifelse member? "XE" genotype = true
  [(ifelse
    member? "B" genotype = true and member? "b" genotype = false
    [set eye-shape "bar eye" set phenotype word phenotype "b-"]

    member? "B" genotype = false and member? "b" genotype = true
    [set eye-shape "normal eye" set phenotype word phenotype "r-"]

     member? "B" genotype = true and member? "b" genotype = true
    [set eye-shape "kidney eye" set phenotype word phenotype "h-"])

    set body-color "normal body" set phenotype word phenotype "lb"]

  [(ifelse
    member? "B" genotype = true and member? "b" genotype = false
    [set eye-shape "bar eye" set phenotype word phenotype "b-"]

    member? "B" genotype = false and member? "b" genotype = true
    [set eye-shape "normal eye" set phenotype word phenotype "r-"]

     member? "B" genotype = true and member? "b" genotype = true
    [set eye-shape "kidney eye" set phenotype word phenotype "h-"])

    set body-color "yellow body" set phenotype word phenotype "yb"]





  ;;Determine the shape and color using phenotype codes
  if phenotype = "m-lw-r-lb" [set shape "fly-m-r-lw"]
  if phenotype = "m-lw-r-yb" [set shape "fly-m-r-lw" set color 48.5]  ;set yellow body color
  if phenotype = "m-dw-r-lb" [set shape "fly-m-r-dp"]
  ;if phenotype = "m-dw-r-yb" [set shape "fly-m-r-dp" set color 48.5]
  if phenotype = "m-lw-b-lb" [set shape "fly-m-b-lw"]
  ;if phenotype = "m-lw-b-yb" [set shape "fly-m-b-lw" set color 48.5]


  if phenotype = "f-lw-h-lb" [set shape "fly-f-h-lw"]
  if phenotype = "f-lw-r-lb" [set shape "fly-f-r-lw"]
  if phenotype = "f-lw-r-yb" [set shape "fly-f-r-lw" set color 48.5]
  if phenotype = "f-dw-r-lb" [set shape "fly-f-r-dp"]
 ; if phenotype = "f-dw-r-yb" [set shape "fly-f-r-dp" set color 48.5]
  if phenotype = "f-lw-b-lb" [set shape "fly-f-b-lw"]
  ;if phenotype = "f-lw-b-yb" [set shape "fly-f-b-lw" set color 48.5]
end 

to fertilization

  ask eggs
  [let mate one-of sperms
    if mate != nobody
    [hatch-flies 1
     [set color 28             ;set light body color, some will be overwritten to a black body color in express
       set heading 0
       set genotype word genotype [genotype] of mate
       express
       set-position
      ]
      ask mate [die]
      die
  ]]

  ask sperms [die]
  ask eggs [die]
end 

to set-tray
  ask patches [set pcolor 102 + random-float 0.5]
  ask patches with [pxcor >= max-pxcor - 1] [set pcolor 87]

  create-crosses 1
   [set shape "x"
    setxy max-pxcor - 0.5 max-pycor / 2
    set size 0.5
    set color 35]

  create-crosses 1 [
    set shape "female"
    set heading 45
    setxy max-pxcor + 0.25 5
    set size 0.75
    set color 0]

 create-crosses 1 [
    set shape "male"
    set heading 45
    setxy max-pxcor + 0.25 min-pycor + 0.25
    set size 0.75
    set color 0]
end 

to set-position
  setxy random 10 random 7
  if any? other flies-here [set-position]
end 

;====================================================================================

to go

  ifelse count flies != 2
[output-print ""
 output-print "Please first choose two parent flies."]
[
    gametogenesis
    fertilization
]
end 

to pick

;clear-output
  if mouse-inside? [
    if mouse-down? [
      set x round mouse-xcor set y round mouse-ycor
      ask flies with [xcor = x and ycor = y]
        [ if gender = "male"
            [ifelse count flies with [gender = "male" and pxcor >  max-pxcor - 1] > 0
            [set p1 "Opse! You have chosen a male."]
            [set size 1.25 setxy max-pxcor - 0.5 1.5

            let dad flies with [pxcor >= max-pxcor - 1 and gender = "male"]
            set p2 [eye-shape] of dad
            set p2 word p2 " "
            set p2 word p2 [wing-shape] of dad
            set p2 word p2 " "
            set p2 word p2 [body-color] of dad
          ]]

          if gender = "female"
            [ifelse count flies with [pxcor > max-pxcor - 1 and gender = "female"] > 0
            [set p2 "Opse! You have chosen a female."]
            [set size 1.25 setxy max-pxcor - 0.5 4.5

             let mom flies with [pxcor >= max-pxcor - 1 and gender = "female"]
             set p1 [eye-shape] of mom
             set p1 word p1 " "
             set p1 word p1 [wing-shape] of mom
             set p1 word p1 " "
             set p1 word p1 [body-color] of mom
          ]]
  ]]]


 if count flies with [pxcor >= max-pxcor - 1] = 2 [
  ask flies with [pxcor < max-pxcor - 1 ] [die]
  ask eggs [die]
  ask sperms [die]
  stop
  ]
end 

to gametogenesis

set population-size 4 * (14 + random 4)

  ;set eggs

  let mom one-of flies with [gender = "female"]

  (ifelse       ;set XEB gene
    member? "XEB" [genotype] of mom = true and member? "XEb" [genotype] of mom = false and member? "Xeb" [genotype] of mom = false   ;XEBXEB
     [create-eggs population-size [set genotype "XEB" gamete-trait ]]

    member? "XEB" [genotype] of mom = false and member? "XEb" [genotype] of mom = true and member? "Xeb" [genotype] of mom = false   ;XEbXEb
     [create-eggs population-size [set genotype "XEb" gamete-trait ]]

    member? "XEB" [genotype] of mom = false and member? "XEb" [genotype] of mom = false and member? "Xeb" [genotype] of mom = true   ;XebXeb
     [create-eggs population-size [set genotype "Xeb" gamete-trait ]]

    member? "XEB" [genotype] of mom = true and member? "XEb" [genotype] of mom = true and member? "Xeb" [genotype] of mom = false   ;XEBXEb
     [create-eggs 0.5 * population-size [set genotype "XEB" gamete-trait ]
      create-eggs 0.5 * population-size [set genotype "XEb" gamete-trait ]]

    member? "XEB" [genotype] of mom = true and member? "XEb" [genotype] of mom = false and member? "Xeb" [genotype] of mom = true   ;XEBXeb
     [create-eggs 0.5 * population-size [set genotype "XEB" gamete-trait ]
      create-eggs 0.5 * population-size [set genotype "Xeb" gamete-trait ]]

    member? "XEB" [genotype] of mom = false and member? "XEb" [genotype] of mom = true and member? "Xeb" [genotype] of mom = true   ;XEbXeb
     [create-eggs 0.5 * population-size [set genotype "XEb" gamete-trait ]
      create-eggs 0.5 * population-size [set genotype "Xeb" gamete-trait ]]

   )

  (ifelse        ;Set D gene
    member? "D" [genotype] of mom = true and member? "d" [genotype] of mom = false ;DD
    [ask eggs [set genotype word genotype "D"]]

    member? "D" [genotype] of mom = false and member? "d" [genotype] of mom = true ;dd
    [ask eggs [set genotype word genotype "d"]]

    member? "D" [genotype] of mom = true and member? "d" [genotype] of mom = true ;Dd
    [ask n-of (0.5 * count eggs with [genotype = "XEb"]) eggs with [genotype = "XEb"] [set genotype word genotype "D"]  ; XEbD  50%
      ask eggs with [genotype = "XEb"] [set genotype word genotype "d"]])                                                 ; XEbd 50%



   ; set sperms

   let dad one-of flies with [gender = "male"]

   (ifelse

      member? "XEB" [genotype] of dad = true and member? "XEb" [genotype] of dad = false and member? "Xeb" [genotype] of dad = false    ;XEBY
           [create-sperms 0.5 * population-size [set genotype "XEB" gamete-trait ] create-sperms 0.5 * population-size [set genotype "Y" gamete-trait ]]

      member? "XEb" [genotype] of dad = true and member? "XEB" [genotype] of dad = false and member? "Xeb" [genotype] of dad = false    ;XEbY
           [create-sperms 0.5 * population-size [set genotype "XEb" gamete-trait ] create-sperms 0.5 * population-size [set genotype "Y" gamete-trait ]]

      member? "XEb" [genotype] of dad = false and member? "XEB" [genotype] of dad = false and member? "Xeb" [genotype] of dad = true    ;XebY
           [create-sperms 0.5 * population-size [set genotype "Xeb" gamete-trait ] create-sperms 0.5 * population-size [set genotype "Y" gamete-trait ]])



  (ifelse        ;Set D gene

   member? "D" [genotype] of dad = true and member? "d" [genotype] of dad = false ;DD
    [ask sperms [set genotype word genotype "D"]]

   member? "d" [genotype] of dad = true and member? "D" [genotype] of dad = false ;dd
    [ask sperms [set genotype word genotype "d"]]

   member? "d" [genotype] of dad = true and member? "D" [genotype] of dad = true ;Dd
     [ask n-of (0.5 * count sperms with [genotype = "XEB"]) sperms with [genotype = "XEB"] [set genotype word genotype "D"]  ; XEBD  50%
      ask sperms with [genotype = "XEB"] [set genotype word genotype "d"]                                                    ; XEBd 50%

      ask n-of (0.5 * count sperms with [genotype = "XEb"]) sperms with [genotype = "XEb"] [set genotype word genotype "D"]  ; XEbD  50%
      ask sperms with [genotype = "XEb"] [set genotype word genotype "d"]                                                    ; XEbd 50%

      ask n-of (0.5 * count sperms with [genotype = "Xeb"]) sperms with [genotype = "Xeb"] [set genotype word genotype "D"]  ; XebD  50%
      ask sperms with [genotype = "Xeb"] [set genotype word genotype "d"]                                                    ; Xebd 50%

      ask n-of (0.5 * count sperms with [genotype = "Y"]) sperms with [genotype = "Y"] [set genotype word genotype "D"]  ; YD  50%
      ask sperms with [genotype = "Y"] [set genotype word genotype "d"]])                                               ; Yd 50%

  ask flies [die]
end 

to output-results

  (ifelse

   Cases = "Case 1" [
  output-print "Female flies:  Bigger in size without a dark genitalia at the tip of the abdomen."
  output-print "Male flies:  Smaller in size with a dark genitalia at the tip of the abdomen."
  output-print ""
  output-print "Guiding Questions:"
  output-print "   Are the eye shape traits inherited through incomplete dominance or multiple alleles?"
  output-print "   Are the eye shape traits sex-linked or autosomal?"
    ]

Cases = "Case 2" [
  output-print "Female flies:  Bigger in size without a dark genitalia at the tip of the abdomen."
  output-print "Male flies:  Smaller in size with a dark genitalia at the tip of the abdomen."
  output-print ""
  output-print "Guiding Questions:"
  output-print "   Is the dumpy wing trait dominant or recessive?"
  output-print "   Is the dumpy wing trait sex-linked or autosomal?"
  ]

 Cases = "Case 3" [
  output-print "Female flies:  Bigger in size without a dark genitalia at the tip of the abdomen."
  output-print "Male flies:  Smaller in size with a dark genitalia at the tip of the abdomen."
  output-print ""
  output-print "Guiding Questions:"
  output-print "   Is the yellow body trait dominant or recessive?"
  output-print "   Is the yellow body trait sex-linked or autosomal?"
  ]
    )
end 

to set-lists


  if any? flies with [xcor <= 9][
         set list-1 [who] of flies with [phenotype = "m-lw-r-lb" and xcor < max-pxcor - 1]
         set list-2 [who] of flies with [phenotype = "m-lw-r-yb" and xcor < max-pxcor - 1]
         set list-1 sentence list-1 list-2

         set list-3 [who] of flies with [phenotype = "m-dw-r-lb" and xcor < max-pxcor - 1]
         set list-4 [who] of flies with [phenotype = "m-lw-b-lb" and xcor < max-pxcor - 1]
         set list-3 sentence list-3 list-4
         set list-1 sentence list-1 list-3

         set list-5 list-1



         set list-1 [who] of flies with [phenotype = "f-lw-r-lb" and xcor < max-pxcor - 1]
         set list-2 [who] of flies with [phenotype = "f-lw-r-yb" and xcor < max-pxcor - 1]
         set list-1 sentence list-1 list-2

         set list-3 [who] of flies with [phenotype = "f-dw-r-lb" and xcor < max-pxcor - 1]
         set list-4 [who] of flies with [phenotype = "f-lw-b-lb" and xcor < max-pxcor - 1]
         set list-3 sentence list-3 list-4
         set list-1 sentence list-1 list-3

         set list-6 [who] of flies with [phenotype = "f-lw-h-lb" and xcor < max-pxcor - 1]
         set list-1 sentence list-1 list-6

         set list-1 sentence list-1 list-5



    sorting
      ]
end 

to sorting

   set f-x 0
        set f-y max-pycor
        set fly-ID 0

        repeat length list-1
        [ask flies with [who = item fly-ID list-1] [setxy f-x f-y]
          ifelse f-y > 0 [set f-y f-y - 1][set f-y max-pycor set f-x f-x + 1]
          set fly-ID fly-ID + 1 ]
end