E X E R C I S E S
III. How Does Your Class Compare to Other Groups?
1. Alu insertion frequencies can also be used to study relationships between human populations. The Chi-Square statistic can be used to determine if Alu genotype frequencies differ significantly between any two populations. In this question, you will use the Student Allele Server to compare your observed Alu genotype frequencies to reference data sets collected from populations around the world.
a. Point your web browser to http://www.bioservers.org/sad/. Log-into the Allele Server either as a guest, or using a registered account. (If your group is private, you will not see it if you register as a guest).
b. Click on 'Manage Groups.' Select "Your Groups" from the pulldown menu. Click the checkbox next to your workshop (you might have to scroll to see it). Click 'OK.'
c. Click on 'Manage Groups' again. Choose "Reference" from the popup menu. Click the checkboxes next to four or five reference groups drawn from around the world. Click OK. The Manage Groups window closes, and the populations you selected are loaded into the Allele Server workspace.
d. On the Sequence Server Workspace, click the checkbox next to your workshop, and then click the checkbox next to any one of the reference sets you chose. Choose "Chi-Square" from the popup menu on the left, then click 'COMPARE.'
e. On the Chi-Square page, compare the genotype frequency pie charts for the two populations. Do the populations look similar or different? Does the Chi-Square statistic and associated p-value support your visual impression?
f. Click DONE to close the Results window. Choose another reference data set from the Workspace, and run the Chi-Square test again. Record your results in a notepad.
g. To complete your analysis, uncheck your workshop, then begin checking other reference sets. Repeat these pairwise comparisons until all permutations have been performed.
h. Based on the results you recorded, how useful is the PV-92 Alu polymorphism in distinguishing populations from each other? Why do you think that the PV-92 allele frequencies differ significantly between some populations, while not between others? Do you think you could use PV-92 data to answer the questions of where humans originated and the paths by which they spread throughout the world? What other population data sets or types of information might you need to accurately answer this question?
2. Use the Heterozygozity Feature of the Analyze Function to determine the + allele frequency in a number of populations representing differing parts of the world. Select 'Heterozygosity' from the pulldown menu on the RIGHT. Click the round checkbox underneath to select a group for analysis. (You can only analyze one group at a time). Print the world map (http://www.bioservers.org/map.html) and plot the + allele frequencies on it.
a. Do you notice any pattern in the allele frequencies?
b. Suggest a hypothesis about the origin and dispersal of the Alu allele that accounts for your observation.
c. Which of these mechanisms is consistent with the statistical evidence that PV92 first inserted about 200,000 years ago?
3. Considering your results, do you think this protocol could be used forensically to link a suspect with a crime?
4. Alu can be considered parasites of retroviruses, which produce the enzyme reverse transcriptase needed for transposition. Why is this so? Propose a transposition mechanism requiring reverse transcriptase.
5. An Alu insertion has only two states: + and -. How does this relate to information stored in digital form by a computer? How much digital information is provided by an Alu genotype?
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