Interpreting the tree (step 5)

This might be the most complicated step, and it is only getting easier with experience and after failing many times. We have to remember that the phylogenetic tree that we have just inferred in the previous step is a hypothesis of the data (and model) we used, and we should always be critical to our initial hypothesis and our methods.

Briefly, you are inferring a phylogenetic tree because it is a mean to answer your scientific question. In this sense, you have several interconnected layers to pay attention to. Firstly you want to check if you have correctly built the tree from a pure methodological point of view. Then you want to understand how the tree explains your data within your study, or in other words the results of the tree. And lastly you are interested in discussing the tree in a broader evolutionary context.