1. Answer the question \"What is an outgroup (provide a definition)?\" State the
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Question
1. Answer the question "What is an outgroup (provide a definition)?" State the name of your outgroup from the tree and explain "why" this group your best choice for an outgroup based on your tree. Describe where the following sequences are found on your tree and what this means in terms of the evolution of these HIV strains: 2. How closely related are the viruses from the patient only? Are they forming monophyletic groups with one another? What does that mean? How closely related are the viruses from the victim only? Are they forming monophyletic groups with one another? What does that mean? Based on the placement of the nodes of your tree, is the sequence from the victim's HIV more closely related to the sequences from the patient, the sequences from another ransom individual in the US, or the sequences from an individual of another country? a. b. c. If you were the Chief Medical Examiner for this case, and these where the results of your study, what are the overall scientific conclusions that would you draw from this tree? What does that mean in terms of this case? Given the circumstantial evidence and the phylogenetic evidence, in your expert/professional opinion, did the doctor intentionally infect this woman with HIV? Provide here a short summary of your conclusions and final statement for court that could be provided to the jury. Feel free to refer back to the "figure" that you have created for the jury if necessary 3.Explanation / Answer
Answer 1. Outgroup serves as a reference group when determining the evolutionary relationships of the ingroup (the set of organisms under study).
In the given phylogeny, sample from Switzerland serves as a outgroup because it is located far away from the location of study samples (North America).
2. monophyletic group is a group of organisms that forms a clade, which consists of all the descendants of a common ancestor.
a. viruses from different patients are well spreaded in the phylogeny tree. hence, they do not form monophyletic groups. This indicates that their sequences have high variations which indicates less evolutionary relationship.
b. In contrast to patients, viruses of victims are closely aligned in phylogeny and exhibit high degree of evolutionary relationship.
c. Based on the given phylogeny, sequence of victim is more close to patient virus sequence (highlighted in yellow) in comparison to other samples.
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