For your original question:
From what I remember, my teacher mentioned that people used to base evolutionary relationships on the anatomy of animals. However, with the development of DNA hybridisation and such, we can revise these relationships.
For example, we used to think that lizards and crocodiles were more closely related to each other than with birds. Now though, we know that crocodiles are more related to birds than lizards (I think that's right, but my memory is pretty screwy and I didn't write it down Oo You might want to check up on this example).