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excirse 16.1

Question 1. Is the group of the queried sequences monophyletic, paraphyletic, or polyphyletic? Explain.

Question 2. Based on your answer to Questiong 1, what inference can be drawn about how the three subjects were infected?

Question 3. What can be inferred about the Serbian infected population from the observed phylogenetic patterns?

Question 4. Do the env sequences show a similar pattern to the pol sequences

Question 5. Do any of the individual subjects have sequences that form a monopyletic group? Explain.

Question 6. Which individual has the most phylogenetically diverse sequences?

Question 7. What inference about the transmission of HIV-1 among the subjects is most likely? Why?

Question 8. Based on the timeline at the bottom, what inference can we make about when Subject 1 was infected? Explain.

Question 9. What assumption are we making in Q8 regarding the dating of the infection of Subject 1?

Question 10. Recall that Subject 1 brought a lawsuit against Subject 3 for knowingly infecting him. What type of result would have supported that claim?

Question 11. The researchers used maximum likelihood methods in their analysis. Why do you think they would have used maximum likelihood over parsimony analysis?

Explanation / Answer

Ans.1. The group queried is monophylectic.

Reason: A monophylectic group includes the set of organisms descended from a single ancestor. In the give case it can be seen that they all arise from a common root and then further bifurcates into branches and so on.

Ans. 2 . Acording to the first question, the three subjects were infected through same genetic changes as they are all descendents of common ancestors. They must carry similar set of gene that is altered during the infection.

Ans. 3. From the given data it can be seen that the subject one is infected from HIV from starting and then infected the subject 2 and 3 which suggests that the main culprit was subject 1 not subject 3. It was observed from the tree because the subject 1 branch us separated and subject 2 and 3 were derived from branch of subject 1.

Ans.4. Yes, pol and encv have shown the same pattern as both are monophylectic.

Ans. 5. Yes, subject 1 have the sequences which when get sexually active with subject 2 and 3 transfer the infected gene and we got a monophylectic group in the phylogenetic syudy.

Ans 6. Individial 1 has most diverse sequences because it has formed a separate branch in the tree.

Ans. 7. The transmission of HIV-1 is most likely in the subject 2 and 3 as they are more closely situated in the clade of phylogenetic tree.

Ans. 8. It can be seen from the timeline that the subject 1 was infected since 2005. while the subject 2 got infected first by subject 1 as they were married. and at later stage when subject 3 got sexually involved with the subject 1 it got infected after 2007.

Question 9. What assumption are we making in Q8 regarding the dating of the infection of Subject 1?

Ans. 9. The subject 1 can be seen to have the HIV-1 virus before 2005, but it got active and transmitted from year 2005 and 2007 respectively. It can be inferred that the subject 1 starts dating with subject 3 after 2007.

Ans. 10. His unawareness about the infection he has, and due to less symptoms in initial stage he might have thought that he did not have infection. But after he got engaged with the subject 3, he would have developed the symptoms and mislead the interpretation. And he claims that he got infection from the subject 3.

Ans11. The maximum parsimony is failed to account for the factors of like reversals, convergence, and homoplasy insequence evolution as it minimizes the mutations by itself while the maximum likelihood gives the correct vision of evolution without any modifications with all the factors.

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