Populus Genetic Drift Computer Simulation

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Introduction for students

The Monte Carlo model simulates genetic drift using a random number generator to sample genes from a small parental population and passes them on to offspring. Population size is assumed to be constant from generation to generation and gene frequency changes the result only from the random sampling process.

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Exercise Instructions

Click on the Populus "P" icon to start
In the upper left corner, click on "Model"
From the pull-down menu choose "Genetic Drift Model" and then from that menu choose "Genetic Drift"
Make sure the page opens to the MONTE CARLO MODEL

Experiment 1. Population Size

Goal: To  investigate the effect of population size on the loss of polymorphism.

This program allows you to change the population size and initial gene frequencies of six unlinked loci.
After you run the program you will see a graphical display of the change in frequency of allele A over time in generations. Each different colored line is a separate locus. Fixation of allele A occurs when its frequency reaches 1.0. Fixation for allele a occurs when the frequency of A is 0.

Run six unlinked loci simultaneously (collectively), each with initial gene frequencies of 0.5. To run the program and view the result graph, click "VIEW". Explore the effect of changing the population size by running this program for 3 different population sizes between 2 and 200 (you choose the three sizes). Run the simulations for 10x (the population size ) generations (e.g. if your population size is 30, run the simulation for 300 generations). To change the number of generations click the circle marked "Other" under "Runtime" and you can specify an alternate value for the number of generations you would like to run the simulations.

EACH TIME YOU RUN THE SIMULATION DO THE FOLLOWING
Record the number of fixed loci for A and for a as well as the number of loci which remain polymorphic.
Approximate the number of generations until fixation for each population you explore

REPEAT the simulation 5 times for a total of 30 replicates for each population size

Bring to discussion next week:

A table showing the relationship between a) population size and time to fixation of alleles and b) population size and the number of alleles fixed for allele A and allele a.

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