Bobak Seddighzadeh Week 2

Methods and Results
I. 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
 * 2) 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
 * 3) 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).
 * 4) 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.
 * 5) 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.
 * 6) 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.

II. 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
 * 2) 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
 * 3) 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).
 * 4) 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.
 * 5) 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.
 * 6) 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.

III.The third protocol is to get quantitative results using the Hardy-Weingberg Equilibrium for Natural Selection: 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 * 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 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) Load the World with only the Red organism from the Greenhouse. The World should be entirely red.
 * 2) 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.
 * 3) Set all Fitnesses to 5.
 * 4) Calculate the allele frequencies in the starting population:
 * 1) Calculate the genotype frequencies expected at HWE:
 * 1) Is the population at HWE?  Why or why not?
 * 1) Run one generation only. Is that population at HWE?

C4) Calculate the allele frequencies in the starting population:  Genotype Number #R’s  #r’s       RR          21           42     0      Rr           49           49     49       rr            30           0        60           TOTAL:             91     109  • frequency of R (p) =   91/200 = 0.455  • frequency of r (q) =  109/200 = 0.545

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. 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) 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).
 * 2) 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.
 * 3) Test: Click the One Generation Only button in the Controls. Do this a few times.
 * 4) Result: Calculate p and q as you did in part (d):
 * 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. *What colors besides green are present in your World? The other colors that are present are black, white, and red *What colors are present in the World’s of the other groups in your lab? The colors that are present in my partners simulation are red, black, white, orange, and blue. Based on these class results, which colors occur often and which are rare? The color that occurs most often green and white and the rarest were yellow, blue, and red. *Which misconception(s) does this address? It addresses the misconception that all new phenotypes are equally likely to occur by mutation. If this were true then me and my partner would have more random results on the frequency of each color. It also addresses the misconception that evolution has a goal. If this were true then both me and my partner would have had a similar color set because evolution would tend towards to same goal. Instead we got very different results.\
 * 1) 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.
 * 2) Quit and re-start Aipotu to enable mutation.
 * 3) Go to Evolution and load the World with Green-1 from the Greenhouse.
 * 4) Click Run and let the simulation run for about 5 generations.
 * 5) What colors do you see? Specifically:
 * 1) Switch to Biochemistry and double-click the organism you just saved in the Greenhouse. The program will then show you the proteins encoded by the two copies of the protein gene in this organism along with their individual and combined color. Look at the black mutants of your classmates; they should almost all be red/green heterozygotes.
 * 2) Switch to Molecular Biology. In order to compare the mutant and starting sequences, you will need to save the sequence of the un-mutated green allele for comparison.  To do this, you double-click on the Green-1 in the Greenhouse.  You should see the sequences of two identical green genes appear as shown below:
 * 3) From the Edit menu, choose Copy Upper Sequence to Clipboard (be sure not to choose either of the “image” options). This copies the upper DNA sequence allele that all the mutants started from – to the program’s memory.
 * 4) Double-click on the black mutant organism you saved in the Greenhouse. You will see its two copies of the pigment protein gene in a window like the one above.  One will be green and one will be red.  You want to look at the red one – note whether it is the upper or lower sequence
 * 5) From the Compare menu, choose Compare Upper vs Clipboard (or Lower, whichever is the red one) and you will see a display of the differences between the two DNA sequences like the one shown below (if no differences are shown, you compared two identical green alleles;you tried Upper, try Lower and vice-versa). Yours will be similar, but not identical, to this. My partner got a mutation at bp 12 and 43. I got a mutation at 44.