Asexual-Selection+Mutation

Submitted by librarian on Tue, 2006-08-15 19:23. :: Category

WHAT IS IT?

Introduction

If you have not done so, run asexual.noselection model. The rabbits in this model (as in asex-no sel model) differ in one genetically determined trait. The distribution of that trait is random over a given range. Without mutation, what happens to the distribution of that trait in the rabbit population over time? What would happen to the population if that gene experienced spontaneous and random mutation?

In this model (as in asex-no sel model) the genetically determined trait is color. Each rabbit begins the simulation with a randomly given color that is determined by a colorgene. The colorgene has a numerical value between 20 and 100. The color of the rabbit does not affect its fitness in this environment. That is, the color is cosmetic. In this model, the colorgene can mutate to a new value within the 20 – 100 range. In this model, rabbits with colorgenes <20 and >100 are never created.

HOW TO USE IT

Set up

Determine the initial population number with the number slider.

‘setup’ button will distribute rabbits and grass randomly across the land.

‘show statistics’ button will activate monitors, showing you colorgene statistics; minimum, maximum, average colorgene values; as well as the range and standard deviation of colorgene values in the population.

Run

The ‘go’ button will cause the grass to grow, the rabbits to move randomly, and eat grass. Rabbits are born with a randomly determined supply of ‘energy’. They use ‘energy’ to move, and gain ‘energy’ by eating grass. When their ‘energy’ is greater than the hatch-threshold (see below) they reproduce asexually. That is, two new rabbits are created, each with half the ‘hatch –threshold’ energy, moving randomly. If rabbit ‘energy’ goes to zero, the rabbit dies. A graph of the number of rabbits (blue) and grass (green) vs. time is activated by ‘go’ button. Average colorgene value is plotted in black.

‘stop-it’ button stops all of this.

‘grass-rate’ slider determines how fast grass will grow. The ‘hatch-threshold’ slider determines how much

‘energy’ rabbit needs to accumulate before it can reproduce.

‘drought’ button kills 75% of the grass.

‘mutation rate’ determines the relative rate of mutation

EXPLORATIONS

Set up and run model several times. Observe screen and statistics. Refer to graph. What happens to the range and standard deviation of colorgenes over time? Compare results of several runs.

Account for your results. Compare with results of asex-no sel. Account for similarities and differences.

Turtle procedures



	
turtles-own [energy species [rabbit grass] colorgene]
;turtles can be of species rabbit or species grass

to setup
  setxy random screen-width random screen-height
  ifelse who < grass-rate
   [setc black ht setspecies grass]
   [set colorgene ((random 81) + 20)
    scale-color blue colorgene 20 100 ;scale the color to reflect colorgene
    setspecies rabbit
    setenergy random 10]
  repeat 20 [grow]
end

to grow
  if species = grass [  ;only grass turtles should do this
    rt random 10 lt random 10
    fd 1
    if pc-ahead = green [stamp green]  ;grass only grows near other grass
  ]
end

to move
  if species = rabbit [       ;only rabbit turtles should do this
    takestep
    eat-grass
    reproduce
    death
  ]
end

to eat-grass  ;turn the patch to black and increase energy
  if pc = green [stamp brown setenergy energy + 1]
  if energy > 30 [setenergy  30]
end

to takestep
  rt random 50
  lt random 50
  setenergy energy - .25
  fd 1
end

to reproduce
  if energy > (hatch-threshold)
       [setenergy energy * .5
        hatch [seth random 360 jump 1]
       if  ((random 100) < mutation-rate) [setcolorgene (colorgene + (random 21) - 10)
      if colorgene < 20 [setcolorgene 20]
      if colorgene > 100 [setcolorgene 100]
      scale-color blue colorgene 20 100]

       ]
end

to death
  if energy < 0 [die]
end

Observer procedures




globals [mincolorgene maxcolorgene rangecolorgene avgcolorgene sdcolorgene temp totalcolorgene]

to setup
  ca
  clearplot
  setbg brown
  crt number + grass-rate
  ask-patches [if (random 100) < 25 [setpc green]]
  ask-turtles [setup]
  setup-graph
end

to setup-graph
  pp1 ppreset setppc green
  pp2 ppreset setppc blue
  pp3 ppreset setppc black
  setplot-title "Rabbits and Grass"
  setplot-yrange 0 300
  setplot-xrange 0 50
end

to graph-it  ;graph the amount of grass (scaled) and turtles
  pp1 ppd plot (count-pc green) / 5
  pp2 ppd plot count-turtles-with [species = rabbit]
  pp3 ppd plot avg-colorgene
end

to total-rabbits
  output count-turtles-with [species = rabbit]
end

to avg-colorgene
   output ((sum-of-turtles-with (species = rabbit) [colorgene]) / count-turtles-with [species = rabbit])
end

to go
 ;the movebutton, grassbutton, and graphbutton are pressed
  startmovebutton
  startgrassbutton
  startgraphbutton
  startextinction
end

to stop-it
  ;the movebutton, grassbutton, and graphbutton are stopped
  stopmovebutton
  stopgrassbutton
  stopgraphbutton
  stopshow-statistics
  stopextinction
end

to calcsd
  settemp 0
  ask-turtles [if color != black [settemp temp + ((colorgene - avgcolorgene) * (colorgene - avgcolorgene))]]
end

to calcstats
  setmincolorgene min-of-turtles-with (species = rabbit) [colorgene]
  setmaxcolorgene max-of-turtles-with (species = rabbit) [colorgene]
  setrangecolorgene (maxcolorgene - mincolorgene)
  settotalcolorgene sum-of-turtles-with (species = rabbit) [colorgene]
  setavgcolorgene (totalcolorgene / count-turtles-with [species = rabbit])
  calcsd
end

  setsdcolorgene sqrt ((temp / (count-turtles-with [species = rabbit])))
end

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