Yes, this is the same point @T_aquaticus has brought up, that sequence level is more reliable than gene level. I don’t disagree. It is just much more difficult to analyze and simulate. I would like to get there.
Additionally, for the purpose of my argument, I don’t believe going to the sequence level is necessary to illustrate my point. So, for now, I will stick with the gene level, and then rethink things if we hit a roadblock.
But first, I just want to establish the basic methodology, to make sure everyone is tracking. Does what I’ve written make sense to you? Anything unclear? Do you see how the tree and null hypotheses are inferred from the dataset, and then pitted against each other in a tournament of champions wherein the most likely explanation is declared the winner?