.
For this example you need the primate data for Pongo, Pan,
Gorilla and Homo from . Pongo is taken to be the outgroup in this
example. This exercise investigates whether Pan is more closely related to
Homo than Gorilla is.
a. Using the approach in Section 12.5.1, give the representation of the tree
in which Pan and Homo split first. Calculate the likelihood of the data
for this topology.
b. Repeat the previous problem, but for the tree in which Gorilla and Homo
split first.
c. What do you conclude about the divergence of these three species?
d. What is the effect on the estimated topology of the tree if you use more
of the cytochrome oxidase sub-unit sequence? If you use other sequences?
[Note: this exercise can be completed using likelihood software available at
www.cmb.usc.edu.]