Lab #1: Population Genetics (#POPGEN-AB)by Alanna Barnett, Aziz Bajouri, Melanie Nguyen, Morgan Howell, and Robert Barker
Lab #1: Population Genetics (#POPGEN-AB) by Aziz Bajouri, Alanna Barnett, Melanie Nguyen, Morgan Howell, and Robert Barker
- Distribution of Genes in a Population
Hypotheses:
H0: Allele pairs will follow the Hardy-Weinberg Equilibrium proportions of p2+2pq+q2, with p and q being the relative frequencies of pinto (allelep) and white (alleleq) beans.
Ha: Allele pairs will not follow the Hardy-Weinberg Equilibrium proportions due to either genetic drift or natural selection.
Prediction: For group A, our prediction was that we would be left with 12.5 (12 or 13) pairs of homozygous white, 12.5 (12 or 13) pairs of homozygous speckled. and 25 pairs of heterozygous.
Results:
Figure 1: The result of Group A randomly selecting 50 beans from a cup that contained 50 speckled beans and 50 white beans. The test was run twice, once for Group A and once for Group B.
Figure 2. Expected vs. observed genotype frequencies for Group A and Group B
Conclusion:
Using a p-value of 0.05 and two degrees of freedom, both groups decided on a critical value of 5.99. Group A calculated a 𝜒2 value of 0.72, and Group B calculated a 𝜒2 value of 2.11. Because neither group obtained a 𝜒2 value greater than 5.99, both groups accepted H0, stating that there was no statistically significant change in genotype frequencies than is stated by the Hardy-Weinberg Equilibrium.
- Genetic Drift or Natural Selection
Hypotheses
H0: There will be no change in the frequency of bean types from the 1st generation to the 10th generation.
Ha: The frequency of each bean type will change from the 1st generation to the 10th because of either genetic drift or natural selection.
Prediction: The populations of the smaller beans (black and white) would get smaller through natural selection because they will be harder to grab from the cup.
Data for Group A:
Results for Group A:
| ||||||||||
Bean Color
|
Generation
| |||||||||
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
| |
Red
|
13
|
16
|
18
|
21
|
19
|
22
|
27
|
14
|
39
|
38
|
Pinto
|
14
|
16
|
16
|
18
|
23
|
25
|
21
|
34
|
11
|
12
|
Black
|
12
|
9
|
5
|
4
|
4
|
1
|
1
|
1
|
0
|
0
|
White
|
11
|
9
|
5
|
4
|
4
|
1
|
1
|
1
|
0
|
0
|
Table 1. Results for Group A
Figure 3. Allele Frequencies Represented by Different Types of Beans Over Ten Generations for Group A.
Chi-squared ( 𝜒2) Calculations for Observed vs. Expected Generations in Group A:
| |||||
Bean Color
|
Observed (O)
|
Expected (E)
|
O-E
|
(O-E)2
|
(O-E)2/E
|
Black
|
0
|
12
|
-12
|
144
|
12
|
White
|
0
|
11
|
-11
|
121
|
11
|
Pinto
|
12
|
14
|
-2
|
4
|
0.29
|
Red
|
38
|
13
|
25
|
625
|
48.07
|
Total
|
71.36
| ||||
Table 2. Chi-squared ( 𝜒2) Calculations for Observed vs. Expected Generations in Group A
Data for Group B:
Results for Group B:
| ||||||||||
Bean Color
|
Generation
| |||||||||
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
| |
Red
|
12
|
13
|
16
|
19
|
21
|
18
|
15
|
-
|
-
|
-
|
Pinto
|
11
|
17
|
19
|
22
|
18
|
21
|
20
|
-
|
-
|
-
|
Black
|
13
|
8
|
6
|
4
|
5
|
6
|
8
|
-
|
-
|
-
|
White
|
14
|
12
|
9
|
5
|
6
|
5
|
7
|
-
|
-
|
-
|
Table 3. Results for Group B
Figure 4. Allele Frequencies Represented by Different Types of Beans Over Seven Generations for Group B.
Chi-squared ( 𝜒2) Calculations for Observed vs. Expected Generations in Group B:
| |||||
Bean Color
|
Observed (O)
|
Expected (E)
|
O-E
|
(O-E)2
|
(O-E)2/E
|
Black
|
8
|
13
|
-5
|
25
|
1.9
|
White
|
7
|
14
|
-7
|
49
|
3.4
|
Pinto
|
21
|
11
|
10
|
100
|
9.1
|
Red
|
18
|
12
|
6
|
36
|
3.0
|
Total
|
17.4
| ||||
Table 4. Chi-squared ( 𝜒2) Calculations for Observed vs. Expected Generations in Group B
Error:
Group B was only able to make it to generation 7 because of time constraints.
Conclusion:
Group A had a 𝜒2 calculation of 71.36 and group B had a 𝜒2 calculation of 17.4 (Group B a was a little skewed because of error). Because we had three degrees of freedom - which combined with a p-value of 0.05 leads to a critical value of 7.82 - and because both groups obtained 𝜒2 values greater than the critical value, we must accept our hypothesis that allele frequencies in generation 10 will be significantly different than the allele frequencies in generation 1. Both our raw data and our chi-square calculations support our hypothesis.
Our two groups came to the conclusion that the data was a result of natural selection rather than genetic drift. We came to this conclusion when we noticed that the red and speckled beans had the highest frequencies in both Group A and Group B. We suspect this was because the red and pinto beans were larger and easier to grab than the black and white beans, and as a result both groups picked them more frequently. Even though Group B was unable to get to the 10th generation, the data from the 7th generation shows that the frequencies of individuals was still heavily skewed in favor of the red and pinto beans.
It is interesting how the simulation for Part A in both of our groups have the same results even when we did them separately. I also find it very fascinating that the results from Part B in your group is very different from what my group did since we picked the beads instead of the beans for the simulation. Before reading your results, I did expect the drastic change in the bean simulation because I also noticed how the size difference between the beans affected my choices in Part A. However, the increase in Group B’s black and white bean frequency after the initial dip was surprising to me since Group A’s black and white bean decreased steadily until none was left. It made me wonder if it is possible to alter the methods of this simulation to imitate genetic drift better while still using the beans.
ReplyDeleteI find it amazing that, in part A for population A, you guys actually were pretty close to the Hardy-Weinberg equilibrium! For my group we had large amount of heterozygous individuals. In addition, the very low Chi square value you calculated for population A suggests that there was not significance difference, which is impressive. For part B, our group made a similar prediction, which we stated the larger beads are more likely to be grabbed from the cup, thus causing natural selection. According to your results, your predictions are right! My group had similar results, the populations of the smaller beans dropped to zero as well. Lastly, I really like how the hypothesis and predictions are clear and scientific, good job!
ReplyDeleteOne thing I found very interesting from your results was the graphs from part B. Both graphs have a similar trend in separating the red and pinto from the black and white. I thought before that their would be a somewhat noticeable difference in selecting beans versus beads due to the size and shape differences between the different types, but this truly shows how much of an impact it has on the selection. My group used beads instead of beans and the graphs from our two populations show almost no similar trend. It seems like the pinto bean was clearly being selected for, and it would have been interesting to see over many more generations if even the red bean got eliminated from the gene pool.
ReplyDeleteNice post guys! It seem like we got a similar data from Part B of the experiment. Two out of four beans eventually went to extinction. That has to be because of the size/shape of the beans that are larger and has a much higher chance of being picked up. In the lab, red beans were definitely more prominent compare to other ones. This is a great example of "fitness" ones that are best suited to the situation survives and able to make "offspring" to the next generation and the ones that weren't as "fit" as the other eventually face extinction.
ReplyDelete