BIOL3445 - Introduction

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Default-person Andrew McDevitt (Author)

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NetLogo Introduction

WHAT IS IT?

This model examines natural selection in a population of wild rabbits. Evolution, on a genetic level, is a change in the frequency of alleles in a population over a period of time. Breeders of rabbits have long been familiar with a variety of genetic traits that affect the survivability of rabbits in the wild, as well as in breeding populations. One such trait is the trait for furless rabbits (naked rabbits). This trait was first discovered in England by W.E. Castle in 1933. The furless rabbit is rarely found in the wild because the cold English winters are a definite selective force against it.

In this model, the dominant allele for normal fur is represented by F and the recessive allele for no fur is represented by f. Rabbits that inherit two F alleles or one F and one f allele have fur, while rabbits that inherit two f alleles have no fur.

HOW IT WORKS

This model follows the basic principles of the Hardy-Weinberg principles which states that allele frequencies will remain constant in a population that lacks any evolutionary influences. You are able to control the fate of a rabbit population. Using various sliders and drop-downs, you can control the following parameters:

  • Maximum population size ( max-population ) - Through this slider you can adjust the population size.

  • Percent with fur phenotype ( %-with-fur ) - Through this slider you can adjust the percent of individuals within the population that start off with the fur (brown) phenotype. Related - %-Fur-are-heterozygous

  • Percent of the fur with a heterozygous genotype ( %-fur-are-heterozygous ) - Through this slider you can adjust the percent of fur phenotypes that are resulting from the heterozygous "Ff" genotype. Related - %-with-fur.

  • Will rabbits without fur freeze to death? ( no-fur-freeze ) - This drop-down menu allows the user to change whether furless/naked rabbits will freeze over the winter (between generations). If "No" is selected, all rabbits (regardless of phenotype) will survive the winter and will pass on their alleles on to the next generation. If "Yes" is selected, a random number of furless/naked rabbits will die over the winter and will not be able to pass their alleles on to the next generation.

HOW TO USE IT

The "Setup" button creates a new population of rabbits based on the specified setup parameters. If you choose to change these parameters, you will need to press the "Setup" button again.

The "Advance Generation" button will cause the parent generation to breed and will create a new offspring generation (Note: in this scenario we only ever view one generation/cohort at a time). Each click of the "Advance Generation" button is related to a single generation (Genotypes and allele frequencies are recorded in the respective plots).

To run the simulation indefinitely, press the "Run/Stop" button. To stop or pause the continuous simulation, press the "Run/Stop" button again.

To slow-down/speed-up the simulation, adjust the program's embedded model speed slider.

THINGS TO TRY

Explore the Hardy-Weinberg equilibrium

Set no-fur-freeze as "No", and adjust the sliders. What happens?

With set no-fur-freeze as "No", do genotypes change between generation 1 and 2 (ignore the spike between 0 and 1, this is NetLogo setting up the plot)? What about allele frequencies between generation 1 and 2? What might be going on?

Deviate from Hardy-Weinberg equilibrium

Simulate a bottleneck event. Set a large population size and run it for a few generations. Then before you run another generation, slide the population size below 10. What happens to the allele frequencies.

Set no-fur-freeze as "Yes", advance 5 generations, and remember what the genotype plot looks like (possibly save it for reference). Without adjusting the sliders, click setup again and run for another 5 generations. Compare the two plots. Are they exactly the same? Why?

THINGS TO NOTICE

There are random processes underlying each simulation. In the world view, rabits are assigned corrdinates and your population may look like it changed, however you will notice that the genotypes and allele frequency reporters will remain the same.

The plots will automatically update after each new generation. The default x-max is 10 but this will also update as needed.

Error are most likely rounding errors that NetLogo Web cannot automatically adjust. Consider clicking "Setup" again or ajdusting parameters.

CREDITS AND REFERENCES

Code adapted from: http://modelingcommons.org/browse/one_model/3995

Comments and Questions

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Click to Run Model

breed [rabbit rabbits]
rabbit-own [
  dom                                             ; homozygous dominant (AA)
  rec                                             ; homozygous recessive (aa)
  hetero                                          ; hetrozygous (Aa)]\
]
globals [furallele nofurallele p q gen-size]

to count-alleles
  set furallele ((2 * count rabbit with [dom = true]) + count rabbit with [hetero = true])
  set nofurallele ((2 * count rabbit with [rec = true]) + count rabbit with [hetero = true])
  set p (furallele / (furallele + nofurallele))
  set q (nofurallele /(furallele + nofurallele))
  set gen-size count rabbit
end 

to freeze
  if no-fur-freeze = "Yes" [ask n-of random (count rabbit with [color = pink]) rabbit with [color = pink][die]] ;Kills a random number of
end 

to generation
  ct
  create-rabbit max-population [; creates alleles
    set size 2
    set dom false
    set hetero false
    set rec true
    set shape "rabbit"
    setxy random-xcor random-ycor
    set color brown
    ]
  reproduce
  ask rabbit [if rec = true [set color pink]]
  freeze
  tick
  count-alleles
end 

to go
  generation
end 

to setup
  ca
  reset-ticks
  ask patches [; create background
    set pcolor 9.9 - (random 5)
    ]
  diffuse pcolor 1
  create-rabbit max-population [; creates alleles
    set size 2
    set dom false
    set hetero false
    set rec true
    set shape "rabbit"
    setxy random-xcor random-ycor
    set color brown
    ]
   ask n-of (%-with-fur / 100 * max-population ) rabbit with [dom = false and rec = true and hetero = false] [
      set dom true
      set hetero false
      set rec false
    ]
    ask n-of ((%-fur-are-heterozygous / 100 * %-with-fur / 100) * max-population) rabbit with [dom = true] [
      set dom false
      set hetero true
    ]
    ask rabbit [if rec = true [set color pink]]
  count-alleles
  tick
end 

to reproduce
 ask rabbit [
    set dom false
    set hetero false
    set rec false
 ]
 ask n-of precision(q * q * max-population)0 rabbit [
    set dom false
    set hetero false
    set rec true
 ]
ask n-of precision((2 * p * q) * max-population)0 rabbit with [rec = false][
    set dom false
    set hetero true
    set rec false
  ]
ask n-of precision(p * p * max-population)0 rabbit with [hetero = false and rec = false][
    set dom true
    set hetero false
    set rec false
 ]
end 

There are 8 versions of this model.

Uploaded by When Description Download
Andrew McDevitt 9 months ago Reverted to older version Download this version
Andrew McDevitt 9 months ago Reverted to older version Download this version
Andrew McDevitt 9 months ago Reverted to older version Download this version
Andrew McDevitt 9 months ago graph updates Download this version
Andrew McDevitt 9 months ago graph updates Download this version
Andrew McDevitt almost 2 years ago Plot functionality Download this version
Andrew McDevitt almost 2 years ago Web friendly layout and minor bug fixes Download this version
Andrew McDevitt almost 2 years ago Initial upload Download this version

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