There is some controversy over whether the pronghorn is more closely related to antelopes or goats. A researcher sequences the mtDNA control region (a highly variable bit of DNA) from pronghorn, impala, domestic goat, and two outgroups, cow and horse. There are fifteen possible trees but the three most interesting are:
Fictitious sequence data (only variable sites are shown):
| Pronghorn | A | A | A | G | G | G | T | A | C |
| Impala | A | A | T | C | C | C | A | A | C |
| Goat | A | T | T | G | C | C | A | A | C |
| Cow | A | T | A | C | G | G | T | T | G |
| Horse | T | T | A | C | G | C | T | T | C |
1. Mark mutations on each of the three trees. Which tree is best supported by parsimony?
2. Horses are in a different class than the other four animals, so it is fairly safe to assume that the root of these trees should be between horse and the other four. Draw the rooted form of the tree you picked in question 1. Which hypothesis about pronghorns does it support?
3. Create a distance matrix from these data, and draw the UPGMA tree. (You may find it helpful to redraw the distance matrix after every step.) Does the UPGMA tree agree with the best unrooted parsimony tree?
4. Does the UPGMA tree agree with the rooted parsimony tree?