No Selection

Let's quickly review the situation that occurs when no selection is operating on the three different genotypes. Begin Populus and select Selection from the first menu and Autosomal Selection from the second menu. Now read the text that appears (10 pages worth) and answer the following questions. Remember to take the Numbers Lock off by hitting the Num Lock key so that you can use the PgDn key to scroll down through the pages of text. Don't get too caught up in all the calculations, but be sure that you understand the terminology. To make sure you do understand the terms we use, answer these questions:

1. DISTINGUISH BETWEEN ABSOLUTE FITNESS AND RELATIVE FITNESS.
2. DESCRIBE HOW AVERAGE (MEAN) FITNESS FOR A POPULATION IS DETERMINED.  (Hint: You might need your text or lecture notes to answer this one).
3. WHAT IS delta p, AND HOW IS IT CALCULATED?
4. WHAT DOES THE SELECTION COEFFICIENT MEASURE?
5. WHAT DO WE MEAN WHEN WE SAY THAT AN ALLELE OR GENOTYPE HAS BECOME FIXED IN THE POPULATION?
6. IN TERMS OF FITNESS, DISTINGUISH OVERDOMINANCE FROM UNDERDOMINANCE.

Now let's try a simulation. Select your values as Fitness (relative fitness values) rather than Selection (which would use selection coefficients). Set the relative fitnesses of all three genotypes to 1.0 so that there is no selection. Use Single Frequency stability analysis, 500 generations, and an initial allele frequency of 0.2. Now run the simulation. Do you observe Hardy-Weinberg? You should see that the allele frequency remains constant and the genotypic frequencies are those predicted by Hardy-Weinberg. The rate of change of p is constant, and the average fitness remains at 1.0.

Strong Directional Selection

Now let's impose strong selection favoring the "A" allele. Set the relative fitnesses to wAA = 1.0, wAa = 0.85, and waa = 0.65. Let's make the "A" allele pretty common by setting its initial frequency to 0.4 and run 500 generations.

1. HOW MANY GENERATIONS DOES IT TAKE BEFORE "A" BECOMES FIXED IN THE POPULATION?
2. WHAT HAPPENS TO THE AA GENOTYPE? THE aa GENOTYPE? WHY DOES THE FREQUENCY OF THE HETEROZYGOUS GENOTYPE INITIALLY INCREASE AND THEN DROP TO 0?
3. WHICH FREQUENCIES OF THE p ALLELE CAUSE delta p TO CHANGE MOST RAPIDLY?
4. WHAT HAPPENS TO THE AVERAGE FITNESS OF THE POPULATION AS THE "A" ALLELE BECOMES MORE COMMON IN THE POPULATION?

Now rerun the simulation, but make the "A" allele initially extremely rare in the population.

5. WHAT WAS YOUR INITIAL ALLELE FREQUENCY FOR "A"? HOW MANY GENERATIONS DOES IT TAKE FOR THE "A" ALLELE TO BECOME FIXED IN THE POPULATION? HOW IS THIS NUMBER DIVIDED BETWEEN THE NUMBER OF GENERATIONS IT TAKES FOR THE "A" ALLELE TO GO FROM THE INITIAL VALUE YOU CHOSE TO 0.4 (THE INITIAL VALUE WE CHOSE FOR #1 ABOVE) AND THAT TO GO FROM 0.4 TO FIXATION?
6. IS THE ULTIMATE FATE OF THE "A" ALLELE AND THE AA GENOTYPE THE SAME AS BEFORE?

Weak Selection

The last simulation imposed strong selection that favored one phenotype over the other. What happens if the relative fitnesses of the three genotypes are nearly equal so that selection favoring the AA genotype is weak? You can find out by setting the following relative fitnesses: wAA = 1.0, wAa = 0.99, waa = 0.98. Set the initial frequency of the "A" allele at 0.20 and run 500 generations.

1. DOES THE "A" ALLELE STILL BECOME FIXED IN THE POPULATION? IF SO, HOW MANY GENERATIONS DOES IT TAKE UNDER THIS WEAKER SELECTION?
2. ARE THE OVERALL PATTERNS IN THE CHANGES IN THE GENOTYPE FREQUENCIES THE SAME AS THOSE UNDER STRONG SELECTION? WHAT IS DIFFERENT ABOUT THEM?
3. WHAT WOULD HAPPEN IF YOU MADE THE "A" ALLELE EXTREMELY RARE IN THE POPULATION? AGAIN HOW IS THE RESULT DIVIDED BETWEEN THE NUMBER OF GENERATIONS IT TAKES FOR THE "A" ALLELE TO GO FROM ITS INITIAL FREQUENCY TO 0.20 AND THAT FOR IT TO GO FROM 0.20 TO FIXATION?

Underdominance and Overdominance

What happens to allele and genotypic frequencies if the heterozygote is favored (overdominance) or selected against (underdominance)?

Set the relative fitnesses of the three genotypes in such a way as to simulate overdominance.

1. WHAT ARE YOUR RELATIVE FITNESSES FOR EACH GENOTYPE?
2. WHAT HAPPENS TO THE FREQUENCY OF THE "A" ALLELE? WHY? WILL THE "A" ALLELE ALWAYS HAVE THE SAME ENDING FREQUENCY REGARDLESS OF ITS INITIAL FREQUENCY IN THE POPULATION OR THE STRENGTH OF OVERDOMINANCE?
3. WHAT HAPPENS TO THE FREQUENCIES OF THE AA AND aa HOMOZYGOTES?
4. HOW DOES THE CHANGE IN AVERAGE FITNESS VARY WITH THE FREQUENCY OF THE "A" ALLELE (p)? DESCRIBE THE SHAPE OF THIS GRAPH AND EXPLAIN WHY IT HAS THE SHAPE THAT IT DOES.

Set the relative fitnesses of the three genotypes in such a way as to simulate underdominance. Set the initial frequency of the "A" allele to 0.5.

5. WHAT ARE YOUR RELATIVE FITNESSES FOR EACH GENOTYPE?
6. DOES EITHER ALLELE BECOME FIXED IN THE POPULATION? WHY OR WHY NOT?
7. WHAT HAPPENS TO THE FREQUENCY OF THE Aa GENOTYPE ACROSS GENERATIONS?
8. HOW DOES THE CHANGE IN AVERAGE FITNESS VARY WITH THE FREQUENCY OF THE "A" ALLELE (p)? DESCRIBE THE SHAPE OF THIS GRAPH AND EXPLAIN WHY IT HAS THE SHAPE THAT IT DOES.

Now set the initial frequency of "A" to 0.20 and rerun the simulation.

9. DESCRIBE ANY DIFFERENCES IN OUTCOME FROM THE PREVIOUS INITIAL ALLELE FREQUENCIES AND OFFER AN EXPLANATION FOR THOSE DIFFERENCES (OR WHY THERE AREN'T ANY DIFFERENCES).

When you have finished with the assignment, hit escape until you return to the main menu. Cursor down to Exit Populus and hit Enter. If you have finished with the computer, please do a Start->Shutdown->Close all progams and log on as a different user.