Evolution Lab 1, the best Simulation of Genetic Drift in the Universe by Ghaza Hosseini and Kevin Tang :D

In this experiment, we used beans and beads to simulate genetic drift and natural selection. An initial gene pool 100 consisting of 25 round, 25 pinto, 25 black and 25 white bean was created, from which 50 beans were randomly drawn to create the upcoming generation. This process was repeated until 10 generations were obtained and studied. We came up with the null hypothesis that the beans won’t be affected by genetic drift, as well as an alternative hypothesis that the beans will be affected genetic drift. We also thought that natural selection would act on size, favoring the bigger beans.

Figure 1. The data collected from the first set of 10 "generations" from experiment 1.

Beans	Expected	Observed	o – e	(o – e)2	(o – e)2/e
Round	10	36	26	676	67.6
Pinto	11	14	3	9	0.82
Black	13	0	13	169	13
White	16	0	16	256	16
Total	50	50	-	-	97.4

DF = 3                p = 0.05               Critical Value = 7.82

We determined that population A experienced genetic drift as both the black and white beans completely died out in figure 1, while the round beans consistently propagated to a total of 360%, and the pinto bean population rose to 200% but fell back down to almost the original size of 11. We also calculated the chi-square value to be 97.4 for population A, which is far bigger than the critical value of 7.82, so we reject null hypothesis. We also didn’t think this was natural selection because the round beans are the smallest  but came out on top while the pinto beans which are the biggest came in second.

Figure 2. Shows the data collected of the second set of 10 "generations."

Beans	Expected	Observed	o - e	(o – e)2	(o – e)2/e
Round	15	19	4	16	1.07
Pinto	14	19	5	25	1.79
Black	12	6	6	36	3
White	9	6	3	9	1
Total	50	50	-	-	6.86

DF = 3                p = 0.05               Critical Value = 7.82

Genetic drift didn't seem to have occurred in population B. The population of all beans remained relatively steady, with the most significant changes being the black beans' population dropped b 50% and the pinto bean population grew by almost 36%, but no beans died off or significantly increased in population. The chi-square test also supports the null hypothesis that the beans won't be affected by genetic drift because the chi-square value is less than the critical value.

The experiment showed us that genetic drift is completely random, as the two data sets contradicts each other. It's also worth noting that two different techniques were used to create the 10 generations of beans. In population A, beans were randomly drawn from a cup, so size will influence the chances of being picked. In population B, beans were mixed, then dumped out of a cup and the pile was cut in half to be counted and used. Perhaps in future experiments, there should be more than two sets of data and sorting techniques should be controlled to maximize accuracy.

Lab 1: Natural Selection and Genetic Drift

Evolution Lab 1:
Pinto Beanboozled!

Bio Squad
Matthew Donnelly, Bailey Longoni, Aaron Oberstadt, EJ Tilt

What would happen if 4 types of beans were taken from a cup, each type doubled, and the total were halved, over and over? Evolution operates by similar means, through random reproduction and random selection for generations on end. But is this an actually random process? And if not, what happens to such a population over time?

Hypotheses

We hypothesized that random selection of four different types of beans over the course of ten generations would lead to a statistically significant change in frequency in the type of bean selected; this is because natural selection will favor certain bean types over others. Our prediction under the conditions of this hypothesis is that speckled beans are more likely to be selected for because their larger size makes it easier to be picked up. Therefore, speckled beans will have a large increase in allele frequency.

To accurately test for this, we tested a null hypothesis, which stated that the frequency at which each bean is selected will not change significantly over time.

Figure 1.

10 generations of bean population A and the number of circle, speckled, black, and white beans during each generation. The speckled bean frequency increased to 50 of 50 in the 9th generation, accompanying the elimination of the other three beans from the population.

Figure 2.

10 generations of bean population B and the number of circle, speckled, black and white beans in each generation. The frequency of speckled beans increased to 47 of 50 at generation 10 while each other bean type was reduced to 1 of 50.

Conclusions

As seen in figures 1 and 2, there was a significant change in bean frequency from generation 1 to generation 10, demonstrating a change of allele frequency. Our data supported our hypothesis that random selection of the beans resulted in a change in allele frequency due to traits, and also supported our prediction that the speckled bean would become the dominant allele in these populations, suggesting the work of natural selection. We believe that because the speckled bean was bigger, it was easier to pick out of the cup and also rose to the top of the pile of beans.

The chi-squared value for our first data set is 88.275, and the chi-squared value for our second data set is 200. These are much larger than the critical values necessary for these results to be accepted as not random; therefore, we reject our null hypothesis. The random selection of four different types of beans over 10 generations did lead to a statistically significant change in frequency of the type of bean selected, and it is likely due to natural selection of the speckled beans.

Evolution Lab 1: Using Beads as a Model for Allelic Frequency Changes in Genetic Drift. Team Name: Biohazards

Evolution Lab 1: Using Beads as a Model for Allelic Frequency Changes in Genetic Drift.

Team Name: The Beaddazzlers
Team Members: Marisa Kemper, Michelle Le, Zach Bigelow, Eloina Rodriguez

Our team was given beads to use as a model for alleles. Each bead color represented an allele for that color. Our hypothesis was that as time went on, and generation after generation of beads came and went, bead color (allelic frequency) would not change significantly. In other words, our prediction was that after ten generations of random bead "mating", generation 10 should look the same as generation 1 in terms of bead count. If generation 10 was significantly different, we knew we had either natural selection or genetic drift occurring. In order to decide between which, we would have to look at the way in which generation 10 differed from generation 1. And so we went on our merry way, pulling beads out of cups to decide which "alleles" stuck around and made it to the next round, and which were gone forever, making sure to record each pool of beads for each generation. Our group of four scientists were split into pairs, with Michelle and Zach being "Population A" and Michelle and Marisa being "Population B". Our resulting alleles per generation are graphed for each pair below (Figure 1 and Figure 2):

Figure 1. Change in frequency of four different colors of beads in Population A over a span of ten generations as a representation of change in frequency of alleles within a population over time. Population A consisted of fifty beads randomly selected from an original pool of 100 beads.

Figure 2. Change in frequency of four different colors of beads in population B over a span of ten generations as a representation of change in frequency of alleles within a population over time. Population B consisted of fifty beads randomly selected from the same original pool of 100 beads that population A was selected.

After putting this data into graphs, we began to form some opinions. Perhaps we had genetic drift, because the allele change seemed to be random, and while some bead colors appeared to be selected for in Population A (like clear and white), others were selected for in Population B (red dominated the numbers). However, to be sure we did a chi-squared analysis for each population. The calculations and results for this are tabulated below (Table 1 and Table 2):

Chi-squared for Population A

Allele (Bead)	e	o	o-e	(o-e)²	(o-e)² e
Red	8	6	-2	4	0.5
Clear	15	16	1	1	0.07
Blue	10	12	2	4	0.4
White	17	16	-1	1	0.06
					10.03 = chi-square

Table 1. Chi-square calculations comparing the frequency of alleles in generation 10 to generation 1 of Population A to determine if it supports a change in allele frequency over time.

Chi-squared for Population B

Allele (Bead)	e	o	o-e	(o-e)²	(o-e)² e
Red	17	16	-1	1	.06
Clear	10	7	-3	9	0.9
Blue	15	11	-4	16	1.07
White	8	16	8	64	8
					1.03 = chi-square

Table 2. Chi-square calculations comparing the frequency of alleles in generation 10 to generation 1 of Population B to determine if it supports a hypothesis of change in allele frequency over time.

So what are our final thoughts? The data between Populations A and B are wildly different, but this difference helps us draw a conclusion. For population A, with 3 degrees of freedom, a p-value of 0.05, and a critical value of 7.82, the results suggest we reject our null hypothesis because our calculated value of 10.03 is greater than 7.82. For population B, also with 3 degrees of freedom, a p-value of 0.05, and critical value of 7.82, the results suggest we do not reject our null hypothesis since our calculated value of 1.03 is less than 7.82. The results in generation 10 appear to be the way they are merely by chance, otherwise Population A and B would agree more in graph shape and in chi-squared interpretation. Because the beads were identical to each other except in color, and because color was masked by the cup (the involved researchers were blind to the color they were picking), this change in bead color was completely random and based on the chance that some beads were randomly grabbed more than others. In fact, if we had selected generation 3 or generation 5 in population A as our final observed generation, we would have stated there was no change in those alleles and supported our hypothesis! To further illustrate this point, here are some images from the drift-worm simulation found on The Biology Project's website that works in the same way our bead experiment did:

Figure 3. Four different runs of the driftworm simulation. Courtesy http://www.biology.arizona.edu/evolution/act/drift/about.html

Notice that these worms are four different colors, like our beads, and go through 10 generations as well. What do we see? We see that every generation 10 was different, as if created by throwing the dice. This is exactly what we experienced with this experiment. So while we are unable to definitively support or reject our hypothesis (it depends on whether you go with Population A or B) we can at least say that our model followed the process of genetic drift, variation in a population that is due to the random chance of some alleles not being passed on.

Lab1-Evolution-AB: The Era of Pinto Beans over the Others by Supporting of Natural Selection by Amelia, Evan, Octavia and Tu

Hypothesis and Prediction:

In this lab section, we tested the effect of natural selection on the frequencies of alleles in two distinguished populations originated from the same population. There were four different types of beans used to represent for four alleles of a trait in the genotype: round, pinto, black, and white beans. The allele frequency of the populations of beans will change by the 10th generation due to natural selection because the pinto beans are larger and will, therefore, be picked more than the other beans. Our prediction was that there were changes in the frequencies of alleles in the 10th generation that were different from the beginning of each population. Particularly, the number of pinto beans would increase from generation to generation and the other beans or “alleles” would eventually die off. Our null hypothesis was there was no change in the allele frequencies between the beginning generation and the last generation. Based on this hypothesis, there would be no impact of neither natural selection or genetic drift on the allele frequencies.

Graphs:

Figure 1.  The number of beans (including round, pinto, black, and white) picked randomly in 10 generations in population A (performed by Octavia and Evan). The total number of beans picked in each generation was 50. The two populations (A and B) originated from a common population (shared ancestor) and were divided by “natural barrier”. Each type of bean was represented for an allele in the population. Data was collected in Lab 1, Jan 03 2017 by Octavia and Evan.

Figure 2.  The number of beans (including round, pinto, black, and white) picked randomly in 10 generations in population B (performed by Amelia and Tu). The total number of beans picked in each generation was 50. The two populations (A and B) originated from a common population (shared ancestor) and were divided by “natural barrier”. Each type of bean was represented for an allele in the population. Data was collected in Lab 1, Jan 03 2017 by Amelia and Tu.

Analysis:

After analyzing our data and observing the numbers of pinto beans in generation 10 of other groups, we can say that the reason for the largest number of pinto beans over the others in generation 10 (as shown in Figure 1 and 2) is due to natural selection. The calculated chi-square numbers are 187.7 and 119.9 respectively for population A and B. Through these numbers, we can reject our null hypothesis of that there would be no significant change in the allele frequencies, which were represented as the number of four types of bean (pinto, round, black, and white).

The number of pinto beans selected had changed the allele frequencies because they were getting larger and picked more often due to the larger size and advantage over the other beans. For our lab group, we picked the beans as randomly as we could by using our red cup and selected beans from it. Once our cups had more than half of pinto beans there was little probability of selecting any other kinds besides the pinto beans. That  resulted in the last generation of both populations were mostly pinto beans, where in population A it had killed off the round beans, and in population B it had killed off the round and the white beans. For this to be a result of natural selection, we would first need to have variation present in the starting population. We would also need differential reproduction and heredity. For this lab, we did start with a variation of the “alleles” by determining each bean type as a different allele in the population. We also had differential reproduction because as a result, the pinto beans were able to pass on the offspring more than the other beans due to the size advantage. Lastly, the beans that were selected, but most of them were pinto beans, were considered the next generation and heredity are shown through the pinto beans remaining the larger beans. This leads to the conclusion of natural selection which caused the variation of our population to diminish leaving little to no other beans in both populations and if continued it likely would have lead to all of our populations to be pinto beans.

Conclusion:

The chi-square values we had for Population A was approximately 187.7, and for Population B was 119.9. Both of them were greater than the probability value, which means according to Chi-Square statistics, we then rejected our null hypothesis. In both populations, there were only few pinto beans that were chosen in our first generations. However, from that point on the pinto beans had gradually increased in numbers over generations due to the fact that they were larger and therefore easier to grab from the cups. The pinto allele quickly became the dominant allele, due to our data gathered from the simulation. As a result, the pinto bean or “allele” gradually increased from the initial numbers in generation 1 to the final much larger numbers found in generation 10.