Angela A. Garibaldi Week 2: Difference between revisions

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=Evolution Aipotu IV=
'''Note: Protocol adapted from [[BIOL398-01/S10:Molecular Genetics Explorer | Molecular Genetics Explorer]] Evolution Aipotu IV protocol'''
==Methods and Results==
==Methods and Results==
Evolution AipotuIV


===Select for Red===
===Select for Red===
Line 64: Line 65:
This result matches my prediction. 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.
This result matches my prediction. 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===
{{Angela A. Garibaldi}}
'''Note: This exercise was done in error and in excess of the assigned exercises.
'''
 
 
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}
 
#Choose Preferences… from the File menu and click on the Mutation Rates button. Click Enable Mutations and then click OK. Mutations are now enabled.
#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(equal fitness)
#Quit and re-start Aipotu to enable mutation.
#Go to Evolution and load the World with Green-1 from the Greenhouse.
#Click Run and let the simulation run for about 5 generations.
#'''Results:''' Colors seen were:Green, Black, Red, Orange, Yellow, Blue and White are present.
#Colors besides green that are present are: Black, Red, Orange, yellow, Blue and White are present.
#'''Other group results:''' 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 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.
 
***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
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.
 
'''Black flower'''
 
#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.
#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:
#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:
#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.
#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?
* 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. 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.

Latest revision as of 00:41, 31 January 2010

Evolution Aipotu IV

Note: Protocol adapted from Molecular Genetics Explorer Evolution Aipotu IV protocol

Methods and Results

Select for Red

  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 add both
  2. Click the Load button in the Controls to load the World with a roughly 50:50 mix of red and white organisms.Note: Resulting mix was 58 white, 42 red 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 due to the increase in fitness of the red, and the 0 fitness of other colors (including white), the next few generations should see a decrease in all colors that are not red. Eventually future generations will be all red.
  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 offspring. Each offspring flower will get two alleles randomly chosen from the gene pool.
  6. Result:The red count after one generation jumped to 80, whereas the white count dropped to 20. Overall red is increasing rapidly over generations. It takes about 9 generations to get pure red. 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.


Select for White

  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 choose both.
  2. Click the Load button in the Controls to fill the World with a roughly 50:50 mix of red and white organisms. Note: Resulting mix was 50 white and 50 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: 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.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.
  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 offspring. Each offspring flower will get two alleles randomly chosen from the gene pool.
  6. Result:My prediction was false; it took only one generation to become completely white.
  7. Question:Why does it take more generations to get to pure red than it does to get to pure white?
  • Response: 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

  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. 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. Result:The population is at Hardy-Weinberg Equilibrium based on the following calculations and reasoning:
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

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

The population is at Hardy-Weinberg Equilibrium because the frequencies of p and q add up to 1 and the frequencies translated into number of individuals of RR, Rr, and rr equate to the original population.

Part II

  1. Run one generation only. Is that population at HWE? Result: The population is still HWE.
  2. 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).
  3. Prediction:After several generations of this selection, 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, then p should increase overall and r will probably decrease.
  4. Test: Click the One Generation Only button in the Controls. Do this a few times.
  5. Result:
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

This result matches my prediction. 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.


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