Bobak Seddighzadeh Week 2

Methods and Results

The first step was to select for a red organism:

1. Click on the Red organism in the Greenhouse to select it; its border will turn green. While

holding the shift key, click on the White organism in the Greenhouse to select for both

1. Click the Load button in the Controls. The World will fill with a roughly 50:50 mix of red

and white organisms. Specifically, I observed 51 red organisms and 49 white organisms

1. Set the Fitness settings in the Settings panel to select for red. Set the fitness of red to 10

(the maximum) and all the other colors to 0 (the minimum).

1. Prediction: I predict that within the first generation most the flowers will be red because they have the selective advantage with respect to their fitness. Also, within several generations I predict there should be no white flowers and all red flowers left because no new mutations are being introduced.

1. Test: Click the One Generation Only button in the Controls. This will run one generation

only. First, the starting flowers will contribute to the gene pool based on their fitnesses. Then the starting flowers will die off and be replaced by exactly 100 offspringflower will get two alleles randomly chosen from the gene pool.

1. Result: Within the first generation the ratio went from 51:49 to 70:30 red to white, which is 19% increase in the total amount of red flowers. After a subsequent generation, the ratio went to 90:10 red to white, which is another 20% increase in red flowers. At this rate of increase, I predicted that after three generations there should be no more white flowers left. However, it took three more generations leaving me with a total of five generations to achieve all red flowers. It took my partner nine generations to achieve the same results. I loaded a subsequent generation after I got all red flowers, and I observed one white flower. This is due to the fact that a portion of the flowers are heterozygotes meaning that the alleles for a white flower still exist in the gene pool.

The next protocol I preformed was to select for a white organism:

1. Click on the Red organism in the Greenhouse to select it; its border will turn green. While

holding the shift key, click on the White organism in the Greenhouse to select for both

1. Click the Load button in the Controls. The World will fill with a roughly 50:50 mix of red

and white organisms. Specifically, I observed 52 white organisms and 48 red organisms

1. Set the Fitness settings in the Settings panel to select for white. Set the fitness of white to 10

(the maximum) and all the other colors to 0 (the minimum).

1. Prediction: I predict that within the first generation most the flowers will be white because they have the selective advantage with respect to their fitness. Also, within several generations I predict there should be no red flowers and all white flowers left because no new mutations are being introduced.

1. Test: Click the One Generation Only button in the Controls. This will run one generation

only. First, the starting flowers will contribute to the gene pool based on their fitnesses. Then the starting flowers will die off and be replaced by exactly 100 offspringflower will get two alleles randomly chosen from the gene pool.

1. Results: I was completely shocked by how rapidly the whole population able to transform to all white flowers. It took only one generation to do so, which is four generations faster than it took me to do the same with red. This is puzzling to me because I know that red posses the dominant genes. Therefore, intuitively I believed that red would achieve a population of full red in less time than white would, but after I put some thought into it, it is relatively very simple and obvious why the whole population turned white. The white flower is recessive rr meaning it does not carry the R allele. The R allele is the dominant allele and codes for the Red flower. Therefore,white flowers (rr) are the most fit and red flowers (RR or Rr) have no fitness, then no R alleles can pass onto the subsequent generation, and it should only take one generation time to reach all white population.

The third protocol is to get quantitative results using the Hardy-Weingberg Equilibrium for Natural Selection:

1. Load the World with only the Red organism from the Greenhouse. The World should be

entirely red.

1. Show the colors of both alleles in each organism by checking the Show colors of both

alleles in the World Settings part of the Preferences… if you haven’t already. You should see little red and white rectangles in the upper left corner of each organism in the World – this indicates that each has one red and one white allele = genotype Rr.

1. Set all Fitnesses to 5.

1. Calculate the allele frequencies in the starting population:

 Genotype Number #R’s  #r’s 

Genotype: Number: R's: r's:

RR                 19                38     0

Rr                  48                48     48

rr                   33                0       66
          
               TOTAL:              86      114

 • frequency of R (p) =   86/200= 0.43

 • frequency of r (q) =  1-0.43=0.57

1. Calculate the genotype frequencies expected at HWE:

 • frequency of RR = p2 =  0.43^2 x 100 = 18

 • frequency of Rr = 2pq = 2 (0.43)(0.57)(100) = 49

 • frequency of rr = q2 = (0.57)^2 x 100 = 32

1. Is the population at HWE? Why or why not?

Yes, the population is at HWE because the expected and observed were almost dead on. The reason for this is because there are no mutations, genetic drift, or random gene flow in this simulation therefore the allele and genotype frequencies should remain constant and can be predicted using the HWE.

1. Run one generation only. Is that population at HWE?

           Number:    R's:           r's:

RR 21 42 0 Rr 49 49 49 rr 30 0 60

           Totals:        91             109

Frequency of R: 91/200 = 0.455 Frequency of r: 109/200 = 0.545

Frequency of RR: (0.455)^2 x 100 = 20.7 approx 21 Frequency of Rr: 2(0.455)(0.545)(100) = 49.5 approx 50 Frequency of rr: (0.545)^2 x 100 = 29.7 approx 30

Yes, the population is still at HWE because no mutations are introduced.

1. Set the Fitness settings in the Settings panel to select for red. Set the fitness of red to 10

(the maximum) and all the other colors to 0 (the minimum).

1. Prediction: What should happen to p and q after several generations with this selection? I predict that the frequency of p to q should change over several generations. I believe that the frequency for p will increase relative to q because selection will decrease the total amount of q alleles in the gene pool.

1. Test: Click the One Generation Only button in the Controls. Do this a few times.

1. Result: Calculate p and q as you did in part (d):

 Genotype        Number      #R’s     #r’s 

     RR                 69               138      0

     Rr                  30               30        30

     rr                   1                  0          2   
          
                          TOTAL:        168     32


 • frequency of R (p) =   168/200 = 0.84

 • frequency of r (q) =    32/200 = 0.16

1. Does the result match your prediction? Why or why not? Yes, the results do match my prediction because the selective advantage is for the red flower (Rr). With subsequent generations there should be more red flowers in the population than white flowers. Consequently, there will be less r alleles and more R alleles. Thus, the frequency for R should increase and r should decrease.

Part II: Misconceptions about Evolution. The next step is to observe the evolution of new alleles and new colors with the introduction of mutations to our simulation.

D) Starting with Green-1; no selection.

Here, you will start with Green-1, which is a homozygote – it has two identical green 

alleles. You will let it reproduce with random mutations, but no selection. That is, all colors, including white, will be equally fit.

D1) Quit and re-start Aipotu to enable mutation.

D2) Go to Evolution and load the World with Green-1 from the Greenhouse.

D3) Click Run and let the simulation run for about 5 generations.

D4) What colors do you see? Specifically:

- What colors besides green are present in your World?   
 

- What colors are present in the World’s of the other groups in your lab? Based on these  
 class results, which colors occur often and which are rare? 



- Which misconception(s) does this address?  For each, what would the result have been  
 if the misconception were true?