Allelea 1 Exercises - notes PDF

Preview

Summary

notes...

Description

ALLELE A1 EXERCISES – Introduction Today's lab will use a computer program to simulate evolution at the population genetic level. Evolution is often defined as a change in allele frequencies over time. The program that we are using today, Allele A1, shows how the frequency of one allele in a two-allele system changes over many generations. How to start Allele A1: Allele A1 is available as freeware from: http://faculty.washington.edu/~herronjc/SoftwareFolder/software.html You can download the appropriate version for a Mac or PC. Double click on the icon (or single click on the icon in the dock), and the program will start up. Click on the ad for the textbook to get rid of it. Reading the output: Allele A1 provides a plot of each run that graphs the frequency of one allele (A1) over the specified number of generations. Note that the frequency goes from zero to 1.0. Although the frequency of the second allele (A2) is not given, it can be inferred by subtracting the frequency of A from 1.0. You can view frequencies of the other allele (A2) or of the genotypes by clicking on the arrow at the left of the display and selecting the appropriate option. Note that the alleles are given as A1 and A2, because we are not (yet) assuming that one allele is dominant to the other. Setting parameters: Allele A1 allows you to manipulate a number of parameters and other aspects of the program. Parameters include the initial frequency of A1, mutation rate of A1 (to A2) and A2 (to A1), fitness of different genotypes, and migration rate. You can also set the number of plots that will be shown on the screen simultaneously. Set this value to multiple. Each time you run the program, be sure to choose a new color from the row of colored boxes, so that you'll be able to view results of different runs more easily.

Using AlleleA1 to simulate the Hardy-Weinberg Equilibrium and its Violations The Hardy-Weinberg Equilibrium (HWE) is the prediction that populations will not change in terms of allele and genotype frequencies in the absence of evolutionary causes. Thus, HardyWeinberg equilibrium occurs if: 1. There is no mutation of alleles (the mutation rate of both alleles = 0),

2. There is no migration into the population from elsewhere (the frequency of migrants each generation = 0), 3. There is random mating between individuals in the population (the inbreeding coefficient = 0), 4. The population size is infinitely large, and 5. There is no natural selection occurring in the population (all fitness = 1.0). AlleleA1 allows us to simulate HWE by simply running the program with the parameters set as above. Set all parameters as above and record five runs of the program. a) What did you observe regarding changes in the frequency of allele A1? -There are no changes in the frequency. One parameter that we can set in the program is not explicitly mentioned in the assumptions of HWE, namely the initial frequency. If we change the initial frequency, how do you predict that the results will differ? - I think that the line will remain constant at the new frequency. Test this prediction with the following simulation: Set all parameters as above, except set the initial frequency of A1 to 0.20. Record five runs. Without clearing the screen, set the initial frequency of A1 to 0.80 and record five more runs. a) How does the frequency of A1 change? -It was a straight line at 0.20 and a straight line at 0.80. Both remain constant through all 5 runs. b) Does the initial value of the frequency of A1 affect how the frequency changes over time? -No the initial value of the frequency of Al does not affect how the frequency changes over time c) Was evolution occurring in these populations? Justify your answer!!! -No, evolution was not occurring in these populations because since there was no change in frequency there was no change in population.

Violations of Hardy-Weinberg equilibrium: Natural selection AlleleA1 allows us to test the effects of breaking the assumptions of HWE. Today we’ll examine the effect of natural selection. There are three boxes that let you set the fitnesses for the three genotypes. The fitnesses allow you to play with the effects of selection (that is, differences between the genotypes in survival and/or reproduction). Setting the values to 1.0, 1.0, and 0.2, for example, is equivalent to specifying that for every 100 individuals of genotype A1A1 that survive to reproduce, 100 individuals of genotype A1A2 survive, and 20 individuals of genotype A2A2 survive. Question 1: a). Set the frequency of A1 to 0.5 and the fitnesses of A1A1, A1A2, and A2A2 to 1.0, 1.0, and 0.2, respectively. Predict what will happen to the frequency of A1 over time by drawing a figure below. Run the simulation. Was your prediction correct? Explain.

-Our prediction is that if A2A2 has a lower strength and fitness, then A1A1 and A1A2 will have an increase in allele A1 frequency. -Our prediction was correct because the allele A1 is only present in A1A1 and A1A2. Therefore, a low fitness in A2A2 will cause the frequency of allele A1 to increase do to lower survival rates. b) Now set the initial frequency of allele A1 to 0.01, and the fitnesses to 1, 1, and 0.99. What happens when you run the simulation? Now try fitnesses of 1, 1, and 0.95. Explain the differences in what happens to the frequency of A1 in the three combinations of fitnesses. -The frequency starts at 0.01 and slowly increases into possibly the bottom of the SCurve.

-After changing the last fitness to 0.95, the graph resembles an S-Curve and shows a more dramatic increase in the frequency of the Allele A1.

Question 2: One of the two alleles is dominant in the example above. Which one was it? How do you know this? -A1 is the dominant allele in this example. We know this because A1 allele has a fitness of 1. Question 3: What appears to be the effect of selection on genetic variation in this population? -The fitness of a genotype affects the selection of variation in the population. Question 4: The setup above models the situation where selection is acting against individuals with a recessive phenotype. When this occurs, does it appear likely that the recessive allele will ever be completely eliminated from the population? Explain why your answer should be true. -Following Hardy Weinberg’s principles, the recessive allele will never be eliminated completely from the population. This is true because there is no random mating and no natural selection.

Selection against dominant phenotypes Set the fitness values of A1A1, A1A2, and A2A2 to 0.95, 0.95, and 1.0, respectively. This models the situation where selection is acting against individuals with a dominant phenotype. Question 5: Explain which allele is dominant in this setup. How do you know this? -The dominant allele is A2 because the fitness is 1.0

Question 6: If you set the initial frequency of A1 to 0.5 and run the program with the fitness values above, what happens? Explain why this result is different than the results you discussed in question 1. -The frequency starts at .5 and then continuously decreases until it approaches 0. The results are different because in this set up we chose against the dominant allele but in question 1 we chose against the recessive allele.

Question 7: When selection is acting against individuals with a dominant phenotype, will the dominant allele ever be completely eliminated from the population? Why or why not? -Following Hardy Weinberg’s principles, the dominant allele will never be eliminated completely from the population. This is true because there is no random mating and no natural selection.

Question 8: Huntington’s disease is a dominant lethal genetic disorder in humans that affects muscle function, although it does not usually affect individuals until they reach 40 years of age or older. This disorder remains fairly common, with around 1 in every 20,000 individuals of Western European descent developing it during their lifetimes (such as the folk singer Woody Guthrie). Explain why natural selection has not eliminated Huntington’s from human populations. -Natural Selection has not wiped out huntington’s disease because individuals have the ability to reproduce and pass the allele onto their offspring since it is heritable. Heterozygote advantage What if heterozygotes were the fittest in a population? What might your fitness values look like? Fitness for A1A1 = 0.5 Fitness for A1A2 = 1.0 Fitness for A2A2 = 0.5 Run this simulation a few times after setting the initial frequency of A1 to 0.5.

·

Question 9: What happens to the frequency of the allele A1? How does this change if you increase or decrease the fitness advantage of the heterozygote over the homozygotes? -

The frequency of allele A1 stays the same. When we increase or decrease the fitness advantage of the heterozygote over the homozygote the results stay the same.

Question 10: Set the initial frequency of A1 to something other than 0.5 and run the simulation. What happens? Explain the result. -If we change the frequency to 0.3 and run the simulation it starts at 0.3 but shoots back up to 0.5 and remains constant. Question 11. Sickle cell anemia is a result of being homozygous for a recessive allele (s). Heterozygous (+/s) individuals exhibit resistance to malaria. Assume that for a population in Nigeria (where malaria is present) the relative fitnesses are 0.88 for dominant homozygotes (+/ +), 1.0 for heterozygotes (+/s), and 0.14 for recessive homozygotes (s/s). If you run a simulation with these values, what is your final frequency of the recessive allele? -The final frequency for the recessive allele is 0.01499 Question 12: If we were to completely eliminate malaria in Nigeria, what would the fitness values in question 11 now look like? What effect would this have on the frequency of the recessive allele for sickle-cell anemia? -The fitness value in question 11 would look like genotype A1,A1 because there would be no benefit to a malaria resistance. The frequency of A2,A2 would decrease significantly, which would result in it approaching 0.

Question 13: Why is heterozygote advantage said to help maintain genetic variation? -Heterozygote advantage helps maintain genetic variation because it provides another trait that can be varied or maintained among the population....