Of course there is a strong possibility that the neutral theory is assumed not because it is appropriate but because the math of that theory is so very simple compared to the math applying for any selective theory.
Can I follow that up? Do you think that that has lead to models of phylogenetic change that is not very well supported by the evidence?
I think that that is quite possible. However, here we enter into another question. In mathematical population genetics theory you know from the very start that you are making big simplifying assumptions. You are in a very different position from a physicist, who might believe that his mathematical models describe reality exactly. No sensible population geneticist would make any claim along those lines. He or she is forced to simplify, because reality is so complicated that you don’t know it in any detail, and even if you did know it and used math describing it faithfully, the analysis would be impossible to carry through. So simplification is unavoidable. I do not know whether the use of the neutral theory is too much of a simplification and has lead us to incorrect and distorted views about the true evolutionary tree, it’s shape and dimensions, but I suspect that there has been quite a significant distortion.