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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.

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.


Experiment 2. Initial Allele Frequency

Goal: to explore the effect of initial allele frequency on fixation of alleles

Run six unlinked loci simultaneously (collectively), each with an initial population size of 10. Run the simulations for 100 generations.
Explore the effect of changing the initial frequency by running this program for 4 different frequencies of allele A between 0 and 1. You will need to "SET FREQUENCIES COLLECTIVELY"
EACH TIME YOU RUN THE SIMULATION record the total number of loci fixed for allele A and allele a.
REPEAT the simulation 5 times for a total of 30 replicated for each initial allele frequency.

Calculate the proportion of loci fixed for allele A and a for each initial frequency.

Bring to discussion next week:

A table showing the relationship between initial allele frequency and the probability of fixation for allele A.

Homework


In a few short paragraphs use your results to comment on the following:

  • A polymorphism is when two alleles (or traits) are present in a population at the same time. Discuss the effects of  population size on the loss of polymorphism and time to fixation of alleles.
  • Discuss the effect of initial allele frequency on the loss of polymorphism
  • Many evolutionary biologists believe that the subdivision of populations  has ramifications for evolution (i.e. in nature , large populations are divided into smaller populations between which there is reduced gene flow). Discuss the effects of genetic drift in subdivided populations. How would subdividing a population affect the overall gene frequency for the entire species? Would all populations fix for the same allele? Is overall loss of genetic variation faster or slower when populations are subdivided?

Instructor  Hints

Populus versions can be downloaded from   http://www.cbs.umn.edu/populus/


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