Additional Questions

• ANSWER THE QUESTIONS IN THE MAIN LAB
• NOTE: For the Drift simulation (all sections) record the difference and generation data for each experiment. These should be pasted into Excel to make your graphs. That way the graphs will all be to the same scale.
• On page 8 your should run the suggested experiments in the brackets.
  • Simulate the effects of drift by changing the population from 5,10,20,30,40 (you already did 50). Make graphs and explain the effect(s) of population size on drift. Provide a real-life example of populations that show effects similar to your experiment.
  • Simulate the effects of selection by comparing beneficial and deleterious mutations for population sizes of 10,25, and 30. Explain what you have seen.
• NOTE: BEFORE BEGINNING WITH THE NEXT SECTION GO TO THE RESET BUTTON AND MAKE SURE THE POPULATION SIZE IS SET TO 50, THE SEQUENCE LENGTH TO 100, WITH MUTATIONS BEING NEUTRAL
• On page 11 perform all the bracketed experiments at the bottom.
• NOTE: BEFORE BEGINNING WITH THE NEXT SECTION GO TO THE RESET BUTTON AND MAKE SURE THE POPULATION SIZE IS SET TO 50, THE SEQUENCE LENGTH TO 100, WITH MUTATIONS BEING NEUTRAL
• For the TREE portion of the lab be sure to make comparisons of randomly chosen virons from each of the infected patients.
• Do NOT do the bracketed exercises at the bottom of page 21
• NOTE: BEFORE BEGINNING WITH THE NEXT SECTION GO TO THE RESET BUTTON AND MAKE SURE THE POPULATION SIZE IS SET TO 50, THE SEQUENCE LENGTH TO 100, WITH MUTATIONS BEING NEUTRAL
• On page 24 DO PERFORM the suggested experiments at the bottom of the page.
• An article comparing the efficiency of the two tree-building procedures for a known HIV population is found here.
• NOTE: BEFORE BEGINNING WITH THE NEXT SECTION GO TO THE RESET BUTTON AND MAKE SURE THE POPULATION SIZE IS SET TO 50, THE SEQUENCE LENGTH TO 100, WITH MUTATIONS BEING NEUTRAL
• After reading the above article, rerun the Evolutionary Tree portion of the simulation (page 12) and duplicate the conditions in the paper. Write down your procedure and provide copies of the images. Remember: The time line in the paper is important for your simulation. How do the results differ if mutations are neutral (no treatment) or beneficial (drug cocktail)?