Pig Check Assignment

Discuss these questions with the members of your breakout group and write concise answers in the Canvas assignment.

As we saw in class, we can use the Hardy-Weinberg Equilibrium Principle to predict the change in allele frequencies from one generation to the next. Simply by repeating the calculations over and over, we can predict how a population will change across any number of generations.

How accurate are these predictions? A first step toward finding out is to see how well our calculations based on the Hardy-Weinberg Equilibrium Principle can predict evolution in populations of virtual pigs in SimbBio’s Mendelian Pigs lab.

Open Mendelian Pigs and go to Section 3, Going Hog Wild, page 10 - Hungry Wolves. This exercise employs an individual-based model of a pig population. In other words, SimUText keeps track of individual virtual pigs as they run around, bump into each other, mate, and get eaten by wolves or die of old age. Because it tracks a finite population of individuals moving about in space, this model is much closer to real biology than are the calculations we make using the Hardy-Weinberg EP.

1. Reset the simulation, then drag all the brown pigs and all the black pigs into the experimental population. Set the death rate from wolves to 0.5 for brown pigs, and leave it where it is for all other phenotypes. Make sure the frequency graph is tracking the frequency of allele W. Note that the starting frequencies for alleles W and B are both 0.5.
    
   Before running the simulation, predict what will happen. PigCheck is a web app set up to perform Hardy-Weinberg calculations for you, using the same arithmetic you used for the bird problems.
    
   First, set up the parameters to match the scenario you just created in Mendelian Pigs. Set the starting frequency of allele A1 to 0.5. This will represent allele W in Pigs. Set the fitness of genotype A1A1 to 0.5. This reflects the fact that half the brown pigs get eaten by wolves before they reproduce. Leave all the other parameters alone. The blue line in the graph predicts how your pig population will evolve across 15 generations.
    
   Now go back to Mendelian Pigs and run your simulation for 450 months, then stop it. Because the generation time in Pigs is approximately 30 months, this is about 15 generations. You can see the frequency of allele W at any given time point by running the arrow cursor tool along the graph line. Note the frequency of W at months, 30, 60, 90, and so on, and transfer these frequencies to the Observed Frequencies column, under Mendelian Pigs Data, on the left side of the Pig Check page. As you enter the values, the orange dots on the graph will move. After you’ve entered all 16 frequency values, compare the predictions (blue) to the actual data (dots).
    
   Save a screen shot of the graph in PigCheck so that you can refer to it later.
    
   How accurate were the predictions based on Hardy-Weinberg calculations?
    
   
2. Now try this scenario: Red pigs and heavy spotted red pigs, with a starting frequency for allele R at 0.25. Use all the pure heavy spotted red pigs and as many pure reds as necessary. Be sure to track allele R in the graph. Set the death rate of red, many spotted pigs at 0.4, and all other death rates to 0.
    
   In PigCheck R will be allele A1. Set its starting frequency to 0.25. Set the fitness of genotypes A1A1, A1A2, and A2A2 to 1, 1, and 0.6. (Why does a fitness of 0.6 match a death rate of 0.4?) Run the simulation for 450 months, and transfer the frequency data to PigCheck.
    
   Save a screen shot of the graph in PigCheck so that you can refer to it later.
    
   How accurate were the predictions based on Hardy-Weinberg calculations?
    
   
3. Next try this scenario: Red and heavy spotted red pigs, with a starting frequency for allele R at 0.25. Use all the pure heavy spotted red pigs and as many pure reds as necessary. Be sure to track allele R in the graph. Set the death rate of red, many spotted pigs AND red, few spotted pigs at 0.4, and all other death rates to 0.
    
   In PigCheck R will be allele A1. Set its starting frequency to 0.25. Set the fitness of genotypes A1A1, A1A2, and A2A2 to 1, 0.6, and 0.6. Run the simulation for 450 months, and transfer the frequency data to PigCheck.
    
   Save a screen shot of the graph in PigCheck so that you can refer to it later.
    
   How accurate were the predictions based on Hardy-Weinberg calculations?
    
   Can you explain why the frequency of allele R rose to a higher value under the scenario you ran in Question 3 than under the scenario you ran in Question 2?
    
   Comparing your three screenshots, you may discover that the predictions based on the Hardy-Weinberg Equilibrium Principle were less accurate for the scenario in Question 3 than for the scenarios in Questions 1 and 2. Can you think of an explanation? Can you devise an experiment to test your explanation? Explain:
    
   
4. Make up your own scenario. You can play with different starting frequencies, different fitness, and different strengths of selection.
    
   Describe the scenario you set up in Mendelian Pigs:
    
   Describe the parameters you used in PigCheck to match your Pigs scenario:
    
   How accurate were the predictions based on Hardy-Weinberg calculations?
    
   
5. Overall, how well do calculations based on the Hardy-Weinberg Equilibrium Principle predict the evolution of virtual pig populations?
    
   
6. If you have time, explore these questions:
    
   1. What happens to allele frequencies in a population when heterozygotes have higher fitness than either homozygote?
       
      1. Use PigCheck first, using a wide variety of different starting frequencies for allele A1. Sketch a graph showing the outcomes.
          
         
      2. Does PigCheck accurately predict what happens in populations of virtual pigs where heterozygotes have higher fitness than either homozygote? Explain.
          
         
   2. What happens to allele frequencies in a population when heterozygotes have lower fitness than either homozygote?
       
      1. Use PigCheck first, using a wide variety of different starting frequencies for allele A1. Sketch a graph showing the outcomes.
          
         
      2. Does PigCheck accurately predict what happens in populations of virtual pigs when heterozygotes have lower fitness than either homozygote? Explain.
          
         
   3. Can immigration impede local adaptation?
       
      1. Use PigCheck to onsider scenarios in which selection favors one allele over the other. Set up populations in which migrants bring the other allele into the population ever generation. Look for combinations of parameters that are interesting.
          
         
      2. Once you’ve found an interesting set of parametyers in PigCheck, set up similar scenarios in Mendelian Pigs to see if PigCheck accurately predicts their behavior.
          
         
   4. In a finite population, how strongly does selection have favor a rare allele to give it a reasonable chance of rising to fixation?
       
      1. Use PigCheck to onsider scenarios in which selection in a finite population favors a rare allele. You will want to use population sizes similar to those you can set up in Mendelian Pigs. Look for combinations of parameters that are interesting.
          
         
      2. Once you’ve found an interesting set of parametyers in PigCheck, set up similar scenarios in Mendelian Pigs to see if PigCheck accurately predicts their behavior.
          
         If you want to investigate more evolutionary scenarios without worrying about virtual pigs, try Dr. Herron’s dedicated Hardy-Weinberg calculator, called AlleleA1.