Angela A. Garibaldi - Week 2

Methods and Results
Evolution AipotuIV

Select for Red.
holding the shift key, click on the White organism in the Greenhouse; now, both should be selected. and white organisms. Note the count of red and white in the Settings panel; it should be about 50 of each. (the maximum) and all the other colors to 0 (the minimum). after several generations with this selection? a decrease in all colors that are not red. Eventually future generations will be all red. 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 offspring. Each offspring flower will get two alleles randomly chosen from the gene pool. generations? Roughly how many generations does it take to get to pure red? Be careful, as some all red generations can have some white offspring (why?). Some all red generations can have white offspring because two heterozygotes (one recessive white allele, one dominant red allele) may have produced a homozygous offspring with two recessive white alleles.
 * 1) Click on the Red organism in the Greenhouse to select it; its border will turn green. While
 * 1) Click the Load button in the Controls. The World will fill with a roughly 50:50 mix of red
 * Resulting mix was 58 white, 42 red organisms.
 * 1) Set the Fitness settings in the Settings panel to select for red. Set the fitness of red to 10
 * 1) Prediction: What should happen to the number of red and the number of white flowers
 * I predict that due to the increase in fitness of the red, and the 0 fitness of other colors (including white), the next few generations should see
 * 1) Test: Click the One Generation Only button in the Controls. This will run one generation
 * 1) Result: What happens to the counts of red and white flowers as you simulate more
 * The red count after one generation jumped to 80, whereas the white count dropped to 20. Overall red is increasingly rapidly over generations. It takes about 9 generations to get pure red.

Select for White
B1) 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; now, both should be selected.

B2) Click the Load button in the Controls. The World will fill with a roughly 50:50 mix of red and white organisms. Note the count of red and white in the Settings panel; it should be about 50 of each.
 * Resulting mix was 50 white and 50 red organisms.

B3) 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). B4) Prediction: What should happen to the number of red and the number of white flowers after several generations with this selection? As more heterozygotes produce offspring, the white count will increase in numbers and eventually the population over a longer period of time than the red selected scenario will become all white.
 * With the fitness of white increased and all other colors set to 0, the number of red flowers will slowly decline over time. At first the white count will hold constant until red homozygotes are eliminated.

B5) 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 offspring. Each offspring flower will get two alleles randomly chosen from the gene pool.

B6) Result: What happens to the counts of red and white flowers as you simulate more generations? Roughly how many generations does it take to get to pure white?
 * It took only one generation to become completely white.

Hint, you can see the genotype of each flower by checking the Show colors of both alleles in the World Settings part of the Preferences….
 * 1) Why does it take more generations to get to pure red than it does to get to pure white?
 * It takes longer to get pure red in that an organism can still be red, yet carry the white allele, and therefore will still survive and have fitness when selecting for red organisms. But, this means that future generations can still produce white offspring on occasion when two heterozygotes produce offspring. On the contrary, when selecting for white, an organism cannot be white and carry a red allele because in order to be white, an organism must be homozygous because the white allele is recessive and the red allele is dominant. Therefore, if all plants with even one red allele must be red, then all organisms carrying a red allele must also have 0 fitness and will not continue on to the next generation.

Quantitative
Hardy-Weinberg Equilibrium & Natural Selection

C1) Load the World with only the Red organism from the Greenhouse. The World should be entirely red. C2) 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. C3) Set all Fitnesses to 5.

• Is this population at Hardy-Weinberg Equilibrium? Yes, there is no mutation.

C4) Calculate the allele frequencies in the starting population: Genotype Number          #R’s               #r’s RR 27                                  54                    0 Rr 51                                   51                   51 rr 22                                    0                     44 TOTAL:                               105                 95 • frequency of R (p) = 105/200=0.525 • frequency of r (q) =95/200=0.475 C5) Calculate the genotype frequencies expected at HWE: • frequency of RR = p2 =(.475)^2 (100)=22.56 • frequency of Rr = 2pq =2(.525)(.475)(100)=49.88 • frequency of rr = q2 =(.525)^2(100)=27.56 C6) Is the population at HWE? Why or why not?
 * Yes, because the frequencies of p and q add up to 1 and the frequencies of RR, Rr, and rr equate to the original population.Also, there is no mutation in this population.

C7) Run one generation only. Is that population at HWE? You may find it useful to pool the class results to get an answer that is less subject to small-sample-size fluctuations.
 * Yes,the population is still HWE.

C8) 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).

C9) Prediction: What should happen to p and q after several generations with this selection? then p should increase overall and r will probably decrease.
 * p and q should still equal 1 although the frequencies of each may distribute differently based on which alleles are being selected for. In this case, if p represents the R allele and q represents the r allele,

C10) Test: Click the One Generation Only button in the Controls. Do this a few times.

C11) Result: Calculate p and q as you did in part (d): Genotype Number        #R’s          #r’s RR 65                                130             0 Rr 30                                  30             30 rr 5                                      0               10 TOTAL:                               160           40 • frequency of R (p) = 160/200= 0.8 • frequency of r (q) = 40/200= 0.2 C12) Does the result match your prediction? Why or why not?
 * Yes it does. The frequencies of p and q still add up to 1 and the frequency of p increased as that allele is being selected for. The allele being selected against (q) decreased.

Mutations
4) Choose Preferences… from the File menu and click on the Mutation Rates button. Click Enable Mutations and then click OK. Mutations are now enabled.

List of Misconceptions about Mutations 1. Mutations always reduce the fitness of organisms. Since mutations damage genes, they can only impair their function and must therefore reduce the fitness of the organism. {In fact, mutations can be neutral, beneficial, or deleterious} 2. Selection causes mutations that are adaptive. For example, the presence of an antibiotic causes the mutations that make the bacteria antibiotic resistant. {In fact, the mutations are always random and occur before the selection} 3. All new phenotypes are equally likely to occur by mutation. For example, if you have primitive cats, a mutation that results in high speed is just as likely as a mutation that results in great strength or sharp teeth. {In fact, some phenotypes are ‘easier to evolve’ than others} 4. Mutations cannot produce new features. Since mutations are random and destructive (see 1), they cannot create new features. {In fact, that is how all the amazing diversity of life originated} 5. There is only one mutation that can cause a given phenotype. For example, there is only one particular DNA change that could change a slow cat into a faster cat. {In fact, although this is true for some phenotypes, in most cases, any given phenotype can be caused by several mutations} 6. Evolution has a goal. If the world were somehow started over, the result would be the same world we see today. {In fact, chance plays a huge role in evolution and the outcome would likely be very different}

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? suggests that evolution would result in the same "world" no matter how many times it was started over. This was clearly not the case when comparing my simulation with my classmate's. After 5 generations, evolution resulted in a few colors that my classmate did not see; Blue, Orange, and yellow. If the misconception were true, he and I would have seen the exact same colors after 5 generations. equally likely to occur, then there would have been less of a discrepancy between the number and types of colors I saw in my evolution run in comparison to that of my classmate. Furthermore, the frequency of each phenotype would have been much more similar if they were equally likely to occur. However, this was not the case in that yellow and blue were easily the rarest colors for my evolution and red and black were the rarest for my classmate's evolution.
 * Green, Black, Red, Orange, Yellow, Blue and White are present.
 * Black, Red, Orange, yellow, Blue and White are present.
 * For classmates: All colors seen were Green, white, red and black. Green was most common. Rare: red, black
 * The common colors are Green and white. The most rare were yellow and blue. Medium rarity were red, orange, and black
 * This addresses the misconception that evolution has a goal and that all new phenotypes are equally likely to occur by mutation. First, the misconception of evolution having a goal
 * Second, the misconception of all phenotypes being equally likely to occur is false for the same reason that the previous misconception was incorrect. If each phenotype were

Black flower

D5) Save one of the black flowers to the Greenhouse. To do this: choose one of the black flowers from your World, click on it to select it (its border will turn black) and click the Add… button at the top of the Greenhouse. Give it a name when the program asks you and it will appear in the Greenhouse. You can now examine it using the other tools in Aipotu. Aipotu IV-12 D6) 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 pigment protein gene in this organism along with their individual and combined color. A sample is shown below; yours will likely look different:

D7) 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:

D8) 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 – the un-mutated green allele that all the mutants started from – to the program’s memory.

D9) 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.

Make a list of the ‘red mutations’ from your class. Are they all the same? How is it possible that more than one mutation can lead to the same phenotype? How does this explain why some colors are rare and others are not? This can also happen with an insertion or a deletion mutation that may cause a frame shift that causes coding for the amino acid change that causes the new phenotype. This may explain why some colors are rare or not based on the protein and its corresponding codon that cause the phenotype. For example, if the phenotype is caused by a protein that requires an amino acid that has less possibilities for coding such as Tyr and Trp, there are fewer different options for viable mutations that could result in the same phenotype. In comparison, Leucine has many codons to produce the amino acid.
 * Mutations: C12A, A43-
 * Class mutations: 44 insertion
 * It is possible that more than one mutation can lead to the same phenotype in that one base pair change in a different location can still result in a codon that codes for the same amino acid that helps build the protein that causes that phenotype.

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

E) Starting with Green-1; with and without selection for Orange.

Here you will pool class results to see how many generations it takes for Orange to evolve with and without selection for orange. • First run; without selection for orange. E1) Load the World with Green-1 from the Greenhouse. E2) Set all the fitness values to 5 (default value). E3) Click Run and watch for the first appearance of an orange flower. Note the generation number when it appeared in the space below. If you get to Generation 10 and still have not seen an orange flower, click Pause and write “>10” in the space below. Generation # - Did it take the same number of generations for all groups? Would you expect it to? Why or why not? - Roughly how many generations did it take to get the first orange in the absence of selection for orange? • Second run; with selection for orange. E4) Load the World with Green-1 from the Greenhouse. E5) Set the fitness values to select for orange; that is, set orange to 10 and all the others to 2. E6) Click Run and watch for the first appearance of an orange flower. Note the generation number when it appeared. If you get to Generation 10 and still have not seen an orange flower, click Pause and write “>10” in the space below. Generation # - Did it take the same number of generations for all groups? Would you expect it to? Why or why not? - Roughly how many generations did it take to get the first orange in the absence of selection for orange?

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