Bio 475 Evolutionary Biology
Population Genetics Lab – Introductory Assignment
I.
Read background information carefully
1. Open the PopGen lab and read the information in the Background section of the lab. The goal
is to understand the terminology and the basic understanding necessary to explore the HardyWeinberg (H-W) equilibrium. This material should be review from your genetics class.
2. Read the introduction section of the lab. This lab will actually deal with material in chapters 5
and 6 of your textbook and you should read both of these chapters before beginning the lab.
Hint:
Before beginning to work with the PopGen lab make a note of the following:
 Always set the number of stands to 20 unless the assignment makes some other specific request
regarding stand size. This way as you run each experiment you will be getting 20 replicate
experiments each time.
 You will be able to see what happens to a single stand and compare different stands (replicates)
and also see what the average result is if you were to repeat the experiment several times without
having to actually do the experiment over again.
The attached assignment is to be completed by everyone.
Submit your typed answers to all parts of Questions 1 – 5. You will be emailed the file which
contains the answer sheet you are to use to submit your answers to these questions. Use this emailed
version to type in your answers and then print it out and turn it in to Dr. Firestone before the due
date. Make sure your answers are complete and include specific data from the experiments you
run. You do not need to include copies of the results but you need to mention specific examples of
what happened in your answers. Keep your answers concise but make sure you adequately answer
the questions.
A. General Instructions
Using what you learned about the PopGen lab from the in-class demonstration, explore all of the
parameters in the PopGen lab and what they do. Use any parameters or inputs you wish and
thoroughly examine what happens. Also explore the types of information that you get from an
experimental run. Play with the lab for about 10 minutes until you feel you understand how to
manipulate the simulation properly. Then proceed to the Introductory Assignment which begins on
the next page
Assignment: Testing the Hardy-Weinberg Principle:
Now that you are familiar with the basic parameters in PopGenLab, set up the following
experiment to help you understand H-W equilibrium and the factors that influence a
state of equilibrium in a population.
 Leave all input parameters at their default values, except set the number of
stands at 20.
Getting to know the PopGen Lab: testing the Hardy Weinberg Principle Page 1 of 3
Bio 475
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Check the beginning genotype frequency value and note the allele frequency
values (in the upper right corner) for comparison after you have run the
experiment.
You now have an experimental paradigm with equal allele frequencies; genotype
frequencies of 50% brown, 25% white, 25% black; equal proportions of each tree
type; 20 tree stands with a carrying capacity of 4000
This is a large population of moths; there is random mating; and because the
disaster frequency is set at "Never," the population size of these moths will
remain constant. In addition there is no migration.
Run the following experiments and place your answer to each of the questions asked on the answer sheet
provided. Each student will do this part of the experiment for him or herself and turn in their own
answers. You may consult with one another and ask questions of each other or anyone else but your
answers must reflect your own thinking and should be in your own words.
Question #1 – to be answered before beginning experiment
Based on these conditions, does each moth genotype have an equal chance of survival
or is there a selective pressure (positive or negative) on one or more genotypes?
Explain your answer.
Run Experiment #1
 Return to the initial page of the simulation if you are still in the Change Inputs
view. Find the popup menu, showing the number of generations, in the lower left
corner of the screen. Leave generation number set at its default value of 100.
 Click the Run Experiment button to run this simulation.
 When the experiment has finished running, a separate page will appear that
presents the results of your experiment.
RESULTS: Examine the following data for your experiment:
Genotype Frequency - click and drag the slider to show how genotype
frequencies for AA (black), Aa (brown), and aa (white) change for each of the
100 generations. On the bottom right side of the screen where it says stand
number you will see that the values you are viewing are an average value for all
20 tree stands. Click on the arrow there and scroll through each of the 20 stands
individually to see how the stands vary from one another.
Allele Frequency - click on the check boxes at the bottom of the screen to show a
plotted view of allele frequency for each allele (A or a or both). Data is
represented as the percentage of an allele in each generation. Don’t forget to
check the values for each of the 20 tree stands separately.
Heterozygosity - plots the percentage of heterozygous (brown) moths in each
generation over time. Check individual tree stands.
Population Size - plots the number of moths in each generation over time. Check
individual tree stands.
Allele Distribution - plots the frequency of the A allele vs. the number of
populations showing this frequency in each generation over time.
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Textual Data - text columns of raw data for allele frequencies.
Input Summary - a summary table of the input parameters for the experiment that
you carried out. You should always double check your parameters here.
*Answer questions 2 and 3 using the average values that you got for each parameter.
Question #2 Look at the allele and genotype frequencies. Is there a change in allele
frequency over time? Is there a change in genotype frequency over time?
What did you observe? Explain your answers.
Question #3
How do the actual genotype frequencies compare to the H-W
predictions?
*Answer Question #4 by viewing individual stand results.
Question #4
Compare the parameter values from the individual stands to determine if
the results from this experiment are consistent. Comment on the
consistency of your results among the different stands. Why are they not
all the same?
Run Experiment #2
Now, repeat the same experiment with a different set of initial genotype frequencies (proportions
of black, brown and white moths) by moving the sliders on the pie chart. Use any numbers that
you want but change them considerably from what you did in the default experiment. In the
upper right corner you will see the new allele frequencies depicted for the genotype proportions
you have chosen. (It would be good practice to verify these allele frequencies using the H-W
equilibrium equations).
NOTE: ….
*BEFORE YOU RUN THE EXPERIMENT, use the Hardy-Weinberg equation to predict what
the new equilibrium genotype frequencies will be for the new populations
parameters
Question #5
a) List the new genotype frequencies you chose to work with.
b) Explain how you calculated the new expected Hardy Weinberg genotype frequencies
for the newly chosen allele frequencies you chose above.
Run the Experiment
c) Did your new allele frequencies agree with your prediction? Why or why not?
d) How many generations did it take to establish the new Hardy Weinberg allele
frequencies?
Getting to know the PopGen Lab: testing the Hardy Weinberg Principle Page 3 of 3
Bio 475