Biology 32: Evolutionary Biology Computer simulations of evolutionary forces, 2010 Type your name here

1. 
   The default settings in Allele A₁ demonstrate Hardy-Weinberg equilibrium. These settings include initial frequencies of 0.5 for alleles A₁ and A₂ and the assumptions of no mutation, no selection, no migration, no genetic drift (infinite population size), and random mating. Run this simulation and convince yourself that these conditions result in no change in the allele frequencies and also that the genotype frequencies can be predicted by the allele frequencies.
   

Now, try different values for the starting frequency of allele A₁ and run several simulations. Does your experimentation verify that any starting frequencies are in Hardy-Weinberg equilibrium? Explain how you know.

2. 
   Now change the population size to 1000 and re-run this simulation (starting with an allele A₁ frequency of 0.5). Run this simulation five times. Does the same thing happen each time? Why or why not? You will probably want to select the "Multiple" button, which will allow you to compare the different simulations.
   

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3. 
   Under drift, if we track allele A₁ for long enough, eventually it will either be fixed (frequency=1) or be lost (frequency=0). Use this program to quantify how the initial frequency of an allele relates to the probability of either its fixation or its loss? Think about how you can use AlleleA1 to determine this.
   

Reset the program to the default values and then change the population size to 100. Run this simulation and record whether allele A₁ is either fixed or lost from the population. Ignore those runs in which allele A₁ neither fixes or is lost. Repeat this simulation a total of 30 times, recording each time whether allele A₁ is fixed or lost. What % of simulations fixed allele A₁? What % lost allele A₁?

4. 
   Is genetic drift a creative or destructive force with regard to genetic variation within populations? What about between a set of subpopulations?
   

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5. 
   Reset to the default parameters and then set the initial frequency of allele A₁ equal to 0.05 and the starting population size to 100. Run this simulation several times. What usually happens to the A₁ allele and why?
   

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6. 
   Set the population size to infinite, and change the number of generations to 100. Now create another case with the A₁ allele favored by natural selection. What relative fitness values did you use? Enter them below.
   

wA1A1 =	?
wA1A2 =	?
wA2A2 =	?

Given your fitness values, is allele A₁ dominant, recessive, or co-dominant?

7. 
   Reset to the default values, but change the initial frequency of allele A₁ to 0.05 and select the Multiple button so you can compare two scenarios. Next, change the fitness values to create two different cases, one where allele A₁ is beneficial and dominant and another where A₁ is beneficial and recessive. Enter your values in the table below. Compare the rate of fixation for a dominant versus a recessive beneficial allele A₁.
   

	A1 Dominant	A1 Recessive
wA1A1 =	?	?
wA1A2 =	?	?
wA2A2 =	?	?

Summarize the differences in the time to fixation (i.e., the number of generations before the beneficial A₁ allele is fixed) between the two scenarios.

8. 
   Reset to the default values before continuing, but change the number of generations to 100. Pigmentation in Gila monsters is controlled by a single locus with two alleles: Or and B. Individuals homozygous for the Or allele are mostly orange and so blend in with the reddish rock surroundings they inhabit, whereas individuals homozygous for allele B are mostly black. As a result, mostly black Gila monsters survive about three-quarters as well as do mostly orange Gila monsters.
   

Heterozygous individuals are speckled orange and black. Gila monsters advertise their toxicity by contrasting patterns of orange and black, and individuals with this patterning spend less time defending themselves and more time eating (& having babies) than do single-color individuals. On average, orange Gila monsters reproduce only about 80% as well as speckled individuals. Model this scenario in AlleleA₁, assuming allele Or is allele A₁. Fill in the fitness values you used in the Table below.

wA1A1 =	?
wA1A2 =	?
wA2A2 =	?

Run this simulation. What happens to the frequency of allele A₁?

9. 
   Use the equation in Box 6.8 on p. 202 in your text to calculate the necessary fitness values for the genotypes in order to maintain allele A₁ at a frequency of 0.2. Enter these fitness values below.
   

wA1A1 =	?
wA1A2 =	?
wA2A2 =	?

This type of scenario has a name. What is it and how can you recognize it? What is the consequence of this type of evolution for genetic variation within populations?

10. 
    Reset to the default parameters and create a case of underdominance. What fitness values did you use and how do you know it is a case of underdominance?
    

wA1A1 =	?
wA1A2 =	?
wA2A2 =	?

type your answer here

11. 
    Reset to the default parameters, but select the Multiple button. Next, set-up another case of balanced underdominance (i.e., both homozygotes have the same relative fitness values), but with no migration and no mutation. Enter your fitness values below. Start with a population size of 1000 and an initial allele frequency of A₁ = 0.5. Run this simulation several times for 500 generations. What happens?
    

wA1A1 =	?
wA1A2 =	?
wA2A2 =	?

type your answer here

12. 
    Reset the default values, but enter a population size of 2000, and set the number of generations to 1000. Use fitness values that make allele A₁ deleterious in the recessive state and enter these in the table below.
    

wA1A1 =	?
wA1A2 =	?
wA2A2 =	?

Given the values above, will allele A₁ be fixed, lost, or maintained at some equilibrium frequency? Run the above simulation for 1000 generations - were you correct?

Now change the mutation rates such that the rate from allele A₁ to allele A₂ is 0.001 and the rate from allele A₂ to allele A₁ is 0. Wait! Before you press “Run” – what will happen and why? What two forces are at work here?

13. 
    Reset the parameters to the default settings, but change the number of generations to 10,000 and a low mutation rate (0.0001) from allele A₂ to allele A₁. Now make allele A₁ slightly deleterious in the recessive state by changing the fitness of the A₁A₁ genotype to 0.9. Notice that allele A₁, although it is harmful, is not eliminated from this population but instead is maintained at a very low frequency. (Note: You can confirm this by running this simulation over 100,000 generations).
    

There are two possible hypotheses for why allele A₁ is not lost completely. First, mutation from A₂ to A₁ may be recreating allele A₁ faster than it is being eliminated by selection. How can you test this idea? Hint: Change only 1 parameter from the conditions above, then re-run the simulation to determine if allele A₁ is still maintained. Answer the following questions.