Answers

Exercise 2

Question 1: From which African primate species did humans contract HIV-1?
> Chimpanzee.

Question 2: How many times did this occur? Explain your answer.
> 3 times producing Group M, O and N.

Question 3: How much bootstrap support is there for your conclusions?
> Generally pretty high at 80-100 although the figure for CPZ.GA.88.GAB2 AF382828 to the rest of the tree including Group M is only about 57%.

Question 4: From which African primate species did humans contract HIV-2?
> The Sooty Mangabey.

Question 5: How many times does this appear to have happened? Explain your answer.
> Twice. Once to produce Group A and B, and another producing G and U.

Question 6: How much bootstrap support do you have for your conclusions?
> There is strong support for the separation of the SIVs (including Group U and G of HIV-2) and Group A and B of HIV-2 (95%).

Question 7: From which African primate species did these Asian macaque species contract an SIV in captivity?
> The Sooty Mangabey

Exercise 3

Question 8: Calculate the mean sum from the tip of a branch to the common ancestor of Group M.
> Sum the substitutions per site from each terminal node to the root of the clade, then divide by the number of species in the clade. You should get 0.08 but your result might differ a little from this if you built your own tree.

Question 9: Assuming that the substitution rate of HIV-1 is approximately 10-5 substitutions per nucleotide site per generation, use the mean sum of branch lengths to calculate how many HIV-1 generations have elapsed since the Group M sequences diverged from a common ancestor.
> 0.08 / 0.00001 = 8000 generations (again, your value should be close to this but may not be exactly the same).

Question 10: An HIV-1 generation lasts about 2 days. This is the time it takes for a virus particle to infect a cell and produce new virus particles ready to infect new cells. From this generation time, calculate how many years ago the Group M sequences diverged from a common ancestor.
> (8000 generations X 2 days per generation) / 365 days per year = 43.8 years.

Question 11: Approximately in which year did the HIV-1 pandemic sequences originate assuming the average sampling year was 1990?
> <1990 - 43.8 = 1946.

Question 12: Which of the above hypotheses about when the pandemic sequences originated does your result support?
> Only 2 & 3 are supported. It is unlikely that HIV-1 has been circulating in humans for a long time.