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POPULATION GENETICS SIMULATIONS By F. Frey and C. Lively, Indiana University How to get the program Go to http://evolution.gs.washington.edu/popgen/popg.html (This is correct for 2008. Use a browser other than Safari). Download the appropriate version of the popgen program for your computer. Software Notes See “Running the program” in the url above Purpose of this exercise Drawing from past courses and interactions with other faculty (especially Dr. Fortier and Dr. Dudle), Frank Frey and C. Lively developed this series of exercises. This program allows you to set parameter values (fitness of genotypes, mutation & migration rates, population size, etc.) and watch allele frequencies change through time in a series of simulated populations. These exercises should solidify your understanding of how selection, mutation, migration, and drift affect the evolutionary process. Additionally, you should come away with an understanding of how beneficial or deleterious recessive alleles may or may not persist in a population depending on the evolutionary forces at work and understand the effects of interacting evolutionary forces on the evolutionary process. How to set values in the program and start a simulation In the menu, select run, then select “new run”. With the mouse, click on the box neighboring the value you would like to set (or use the TAB button) Type in the new value. When all values are set, click the ‘run simulation’ button to start the simulation Parameters and explanations (alleles are italicized in this exercise) Initial frequency of allele A (not necessarily dominant – depends on relative fitness values) wAA, wAa, waa: Relative fitness of each genotype in the population (may vary between 0 & 1) Migration rate: Number of migrants from source population per generation to your population Mutation rate of allele A to allele a . This may vary between 0 & 1 Mutation rate of allele a to allele A . This may vary between 0 & 1 Number of different populations to simulate at the same time (may vary between 1 & 10) Number of generations the simulation will run through (may vary between 1 & 10000) Population Size: Size of each simulated population (may vary between 1 & 10000) 1
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NATURAL SELECTION Consider a simple case of overdominance alone (no other evolutionary forces) using the parameters: p = 0.01, wAA = 0.9, wAa = 1.0, and waa = 0.9, where p is the frequency of the A allele. 1) Why is this a case of overdominance? 2) Will allele A get more or less common through time? 3) Will allele A be fixed (p = 1), lost (p = 0), or maintained at some intermediate frequency? 4) On the figure below, graph your prediction of the frequency of allele A through time. Consider the shape of the curve as you do so (e.g., Is the spread or loss of the allele constant? Does the rate of spread or loss of the allele slow down or speed up over time?, etc.). Is the output from Popgen, the dashed line is the analytical prediction, assuming an infinite population size.
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