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For example, a pond is dark in color. There are two alleles. The dark color allele is dominant over the light color one. Let's assume that the relative fitness of both the homozygous dominant and heterozygous is 1, and the relative fitness of the homozygous recessive is 0.5. When I ran the simulation, I changed no other values. enter image description here My data after 251 generations is this: enter image description here My question is that being homozygous recessive is clearly less favorable, and even though being homozygous dominant and heterozygous carry the same advantage instead of heterozygote advantage, why wouldn't the recessive allele disappear?

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    $\begingroup$ You only run your simulation for ~250 generations - what makes you think that this is enough to generalize the results. I honestly don't myself how many generations are 'enough' to be sure that the results won't change anymore (you'd probably have to check if your model converges to a stable state with your given parameters). $\endgroup$ – Nicolai Feb 21 '20 at 10:34
  • $\begingroup$ If you have a way to run a deterministic model that calculates the expected allele frequency over time, that would probably clarify things (e.g., I agree with @Nicolai that you probably just haven't run the simulation long enough) $\endgroup$ – Ben Bolker Feb 21 '20 at 16:36
  • $\begingroup$ Welcome to Biology.SE! Have you thought about what happens as the frequency of of the "r" allele drops? Take the extreme example of a population with only a single heterozygous individual being present in the population — how much selection would there be at that point against the "r" allele? ——— You may also want to take the tour and then go through the help pages starting with How to Ask questions effectively on this site. Thanks! 😊 $\endgroup$ – tyersome Feb 21 '20 at 22:01

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