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Activity 8-Evolution by Natural Selection
This activity uses the population genetic simulation program PopGen to explore the outcomes of
evolution when there are fitness differences between genotypes.
To receive credit for this activity, do all of the following by Tuesday, Feb. 17 at 9:15 am:
1) Run the simulations specified below and answer the questions after each.
2) Report simulation results in online form (instructions at end)
3) Bring this form to class
Go to the following website:
http://www.radford.edu/~rsheehy/Gen_flash/popgen/
It should look familiar from our study of genetic drift.
General instructions for using the simulation program:
The top bar (in blue) contains boxes where you will enter values for the population. To run
simulations, use the red GO button on the bottom left. To run more generations, hit CONTINUE
Step 1: setting parameters
To explore the effects of genetic drift alone, you will be testing the effects of parameters
on the left side of the blue bar. Hold the following values constant in all simulations:
Finite Pop.
Migration
Mutation rates
Bottle Neck?
# of Populations
unchecked
unchecked
0
unchecked
5
Fitness: These values refer to the relative fitnesses of different genotypes. By convention,
the genotype with the highest probability of surviving (and reproducing) is given a fitness
of 1. The relative fitness then indicates how much less likely an individual of another genotype
is to survive and reproduce relative to the most fit genotype in the population.
REMEMBER TO HIT THE RESET BUTTON BETWEEN RUNS!
In these simulations, pay attention to the thin black line shown on the graphs; that line shows
what would happen without any effect of genetic drift. (Note: if you don’t see the line, it’s
probably because it’s right under one of your simulation lines.)
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Condition 1: Heterozygote is intermediate in fitness
Set the fitness of A1A1 to 1. Choose values for the other genotypes so that A1A2 is intermediate
in fitness and record your values below:
Make sure the following is true: fitness A1A1 > fitness A1A2 > fitness A2A2 > 0
Fitness A1A2 = _____
Fitness A2A2 = _____
Simulation 1a: Set the initial frequency of A1 to 0.5 and the initial population size to 500. Run a
simulation and record your results in the RESULTS TABLE on the last page.
How many times is the A1 allele fixed? How do these results compare to the result expected
by drift alone? (Note: rerun simulations with equal fitnesses to compare drift results.)
How fast is the A1 allele fixed? How do these results compare to the result expected by drift
alone?
How much variation is there in the path followed by different populations? What does this
variation tell you?
Simulation 1b: Effect of starting allele frequency
Is there any non-zero frequency of A1 for which there is a tendency to lose rather than fix the
A1 allele? Leaving your fitness values and population sizes the same as in Simulation 1a,
play with the starting allele frequency until you find the lowest value that gives a ca. 20%
chance of fixation. (i.e., fixation occurs in 1 of the 5 populations). You should do multiple
runs at this starting allele frequency to check—you would expect that on average, fixation
occurs in 1 population and loss in the other 4. Because of the effects of drift, there will be
some variation, of course (i.e., fixation will sometimes occur in 0 populations and sometimes
in 2). Record your results in the RESULTS TABLE on the last page.
How does this result compare to the result shown by the solid black line? Why do they
differ?
Simulation 1c: Change the population size from 500 to 50, and run the simulation 5 times (25
populations total). Keep track of the total number of times the A1 allele was fixed here and
record the total number (out of 25 runs) in the RESULTS TABLE on the last page.
Run
1
Run
2
Run
3
Run
4
Run
5
Why is the chance of fixation lower simulation 1c than in simulation 1b, even though the
fitness advantage (and therefore strength of selection) is exactly the same?
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Condition 2: Heterozygote is most fit
Keep the same three relative fitness values used above, but this time set the fitness of A1A2 = 1
and give the intermediate fitness value to A1A1.
Now the following will be true: fitness A1A2 > fitness A1A1 > fitness A2A2 > 0
Fitness A1A2 = _____
Fitness A2A2 = _____
Simulation 2a: Try a starting allele frequency of 0.9. Leave the population size at 500. Run a
simulation and record your results in the RESULTS TABLE on the last page.
In this case, no matter how long you run the simulation, it’s unlikely that the A1 allele will be
lost or fixed. Why?
Based on your results, what is the average allele frequency you expect to observe after many
generations of evolution: ______. This is the expected equilibrium frequency.
Simulation 2b: Change the starting allele frequency to 0.1. Run a simulation and record your
results in the RESULTS TABLE on the last page.
Based on your results, what is the average allele frequency you expect to observe after many
generations: ______
Given the results of simulations 2a and 2b, what is the effect of starting allele frequency in this
example?
What, ultimately, do you expect will be the genetic composition of a population experiencing
this sort of selection? How does that differ from other conditions we have examined?
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Condition 3: Heterozygote is least fit
Keep the same three relative fitness values used above. Set fitness of A1A1 = 1, and give the
lowest fitness to the heterozygote.
Now the following will be true: fitness A1A1 > fitness A2A2 > fitness A1A2 > 0
Fitness A1A2 = _____
Fitness A2A2 = _____
Simulations 3a and 3b: Test the effects of starting allele frequency. Run simulations using
starting allele frequencies of 0.1 and 0.9 and record your results in the RESULTS TABLE on the
last page.
Based on your results, what is the expected outcome of evolution in a population with a
starting allele frequency of 0.9 (i.e., what is the genetic composition of the population after
many generations)?
Based on your results, what is the expected outcome of evolution in a population with a
starting allele frequency of 0.1?
The expected outcomes of evolution probably differ for these two starting allele frequencies.
How do you explain that?
Compare the fitness of individuals in the populations that result from Simulations 3a and 3b.
Use these to explain why the following statement is incorrect: Evolution by natural selection
always leads to populations of individuals with the highest relative fitness.
Simulation 3c: Most of you probably observed the following result for 3a and 3b: fixation of
the A1 allele when the starting frequency was 0.9 and loss of the A1 allele when it was 0.1. If
so, then somewhere between 0.9 and 0.1 there is a starting allele frequency with an equal
probability of fixation or loss. Play with the starting allele frequency value until you find this
frequency (approximately). Record your results in the RESULTS TABLE on the last page
Note: If instead, you observed that fixation occurred for both 0.9 and 0.1 initial A1 frequency,
you will need to test starting allele frequencies below 0.1 to find the value with an equal chance
of fixation or loss.
Thought question: As an initial prediction, you might expect that the starting allele frequency at
which a population switches from fixing to losing the A1 allele when heterozygotes have the
lowest fitness is 0.5 (i.e., Simulation 3). Similarly, you might predict that the equilibrium allele
frequency when heterozygotes have the highest fitness (i.e., Simulation 2) is 0.5, since this
would maximize the frequency of heterozygotes in the population (remember the HardyWeinberg equilibrium!)
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RESULTS TABLE You do not need to fill in cells that are blacked out.
Fit.
Fit.
Fit.
p
N
#
Mean
A1A1 A1A2 A2A2
(A1
(pop. Fixed Generations
Freq) size)
to Fixation
Sim 1a
1
0.5
Sim 1b
1
500
Sim 1c
1
50
# Lost
Mean
Generati
ons to
Loss
NA
NA
NA
500
Sim 2a
1
0.9
500
NA
NA
NA
NA
Sim 2b
1
0.1
500
NA
NA
NA
NA
Sim 3a
1
0.9
500
Sim 3b
1
0.1
500
Sim 3c
1
500
Reporting results
Use this link http://goo.gl/XqUY4N to go to the online reporting form for your results.
Remember to bring this sheet to class. You will learn how to complete the table below in
lecture.
*********Save the table below for later—you do not need to complete it before class*******
Mean Fitness of the Population
p
2eq
2eq+
2eq3c
3c +
3c -
Freq
A1A1
Fitness
A1A1
Freq
A1A2
Fitness
A1A2
Freq
A2A2
Fitness
A2A2
Mean
Fitness