globals [tmp1 tmp2 counter disp-time status clock]
breed [ diploids ]
breed [ haploids ]


diploids-own [
    zygosity
]

haploids-own [
    allele
]

to clear
    clear-turtles
    clear-patches
    cp ct
    set clock 0
end

to do-plots
    set-current-plot-pen "dom/dom"
    set-plot-pen-interval 1
    ifelse (any? diploids) [plot (count diploids with [zygosity = 2] / count diploids)] [plot 0]
    set-current-plot-pen "dom/rec"
    set-plot-pen-interval 1
    ifelse (any? diploids) [plot (count diploids with [zygosity = 1] / count diploids)] [plot 0]
    set-current-plot-pen "rec/rec"
    set-plot-pen-interval 1
    ifelse (any? diploids) [plot (count diploids with [zygosity = 0] / count diploids)] [plot 0]
end

to setup-turtles
    set status "setting up"
    clear
    set-current-plot "genotype frequencies"
    set-plot-pen-interval 10
    set-plot-y-range 0 1
    crt (init-homdom) [
        set breed diploids
        set hidden? false
        set color pink
        set zygosity 2
    ]
    crt (init-het) [
        set breed diploids
        set hidden? false
        set color pink
        set zygosity 1
    ]
    crt (init-homrec) [
        set breed diploids
        set hidden? false
        set color green
        set zygosity 0
    ]
    do-plots
end

to disperse-diploids
    set status "mixing"
    ifelse (high-dispersal) [set disp-time 10] [set disp-time 1]
    if any? diploids [
        repeat disp-time [
            ask diploids [
                right (random 360)
                fd (random-float (1.5 * max-pxcor))
            ]
        ]
    ]
end

to make-diploids
    while [any? haploids-here] [
        set status "making diploids"
        ask one-of haploids-here [
            set tmp1 allele
            ask one-of other haploids-here [
                set tmp2 allele
                die
            ]
            die
        ]
        sprout 1 [
            set breed diploids
            set hidden? false
            set zygosity (tmp1 + tmp2)
            ifelse (zygosity = 0) [set color green] [set color pink]
        ]
    ]
end

to go-one
    disperse-diploids
    while [any? diploids] [
        ask one-of diploids [
            if (zygosity = 0) [
                set tmp1 0
                set tmp2 0
            ]
            if (zygosity = 1) [
                set tmp1 0
                set tmp2 1
            ]
            if (zygosity = 2) [
                set tmp1 1
                set tmp2 1
            ]
            set status "making gametes"
            hatch 1 [
                set breed haploids
                set hidden? true
                set allele tmp1
            ]
            hatch 1 [
                set breed haploids
                set hidden? true
                set allele tmp2
            ]
            die
        ]
    ]
    while [any? haploids] [
        ask one-of patches with [any? haploids-here] [   
            make-diploids
        ]
    ]
    set clock clock + 1
    do-plots
end

to go-ten
    set counter 0
    while [counter < 11] [
        go-one
        set counter counter + 1    
    ]
end
@#$#@#$#@
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@#$#@#$#@
<ul><li>First, set up. Choose the number of individuals of each genotype. Click set-up to create a population of diploids. You'll see what looks like one individual. That's actually every individual created, all stacked up on one spot. The pink trait is dominant to green. There is full dominance, so heterozygotes are phenotypically indistinguishable from homozygous dominants.</li>
<li>In each generation, the diploids disperse, then create haploid gametes. The gametes then combine to form the next generation of diploids. Genotype frequencies are tracked on the plot.</li>
<li>Can you predict the genotype frequencies using the Hardy-Weinberg
model? Does the simulation behave as you expect? If not, what assumptions
of the Hardy-Weinberg model does the simulation violate? Does <a href=hw-sm.html>this one</a> do any better?</li>
</ul>
<hr /><BR /><BR />
The Hardy-Weinberg model of population genetics allows for the prediction of the next generation's genotype frequencies from the frequencies in the current generation, given that there is no selection, genetic drift, migration, or mutation. In other words, it describes how genotype frequencies in a population change in the absence of evolution.<BR /><BR />Individuals in this simulation vary between two alleles at a single locus. One allele is completely recessive to the other. The recessive trait is green, and the dominant trait is pink.<BR /><BR />Specify the initial genotype frequencies and create the initial population. In each generation, each diploid individual disperses, releases gametes, and dies. Gametes then combine to form the next generation of diploid individuals. The plot tracks the genotype frequencies over the generations.<BR><BR>Exercises and questions: Choose arbitrary numbers for the initial genotype numbers. Use the Hardy-Weinberg model and predict mathemtaically what the next generation's genotype frequencies should be. Does the model behave as you predicted? Probably not, because of differences between the simulation and the idealized Hardy-Weinberg population. Can you modify your initial genotype numbers to better approximate the ideal? (Also try the simulator "hw-sm." It works better. Why?) If you began with identical numbers of homozygous-recessive and homozygous-dominant individuals, one of the plot lines for the homozygous genotypes will always be completely obscured by the other. Why do the homozygote frequencies track each other so precisely in this case?<BR /><BR />(Ted Wong, Dec. 2002)
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