Trees from the scientific literature and experts don’t always agree with one another about evolutionary relationships, and sometimes there is not enough evidence to construct the details of those relationships. This can be represented in two ways on an evolutionary tree. One is with a polytomy, and the other is to show alternative hypotheses.

If your goal is to teach about the scientific process or scientific debate, then tackle ambiguity by being explicit — e.g., you’d want to explain the meaning of a polytomy or be clear that you are showing two different hypotheses about the relationships. Keep in mind that many relationships are very well understood, so you’ll want to balance your message: uncertainty does exist because science is an ongoing process, but don’t leave the impression that evolutionary relationships are not well understood, because in many cases they are.

Now that you know what taxa and relationships you will depict, you can decide if there are other features that you want to include on the tree …