[Q5] Phylogenetic trees: Parsimony

Given one rooted and one unrooted most parsimonious trees for the same group of species that consider only binary states, it is correct to say that:

1. The edge where an hypothetical root for the unrooted tree is placed would affect the number of changes of state of this most parsimonious tree.
2. Whether a tree is rooted or not, affects only in the possible positions of state changes for the most parsimonious tree.
3. The rooted and unrooted tree will never be able to have the same topology.¹
4. Nothing can be concluded from this, since the interpretation of a rooted and an unrooted tree is different.
5. None of the above.

¹ Assuming that two trees could be considered to have the same topology if the only difference in them is the fact that a root is present or not.

Original idea by: Juan Felipe Hernández Albarracín.

[Q4] DNA Evolution Models

According to the assumptions made for both Jukes-Cantor and Kimura 2 Parameter (K2P) models about the substitution rates (either α or β), and taking into account the restrictions for Markov models, it is correct to say about the range of possible values for them that:

1. Any of the rates α and β in K2P have a larger range than α in Jukes-Cantor.
2. The range of α in Jukes-Cantor is larger that any of the ranges for α and β in K2P.
3. Only depending on the value of α in K2P it is possible to conclude anything about the size of the ranges of β in K2P with respect to α in Jukes-Cantor.
4. Only depending on the value of β in K2P it is possible to conclude anything about the size of the ranges of α in K2P with respect to α in Jukes-Cantor.
5. None of the above

Original idea by: Juan Felipe Hernández Albarracín.