Thanks for pointing out Nakhleh, 2013. It is not controversial that gene trees (and the other characters for that matter) are not congruent (i.e., they do not fit the common descent model), and this paper does nothing to dispute that fact. What the paper discusses is progress toward constructing auxiliary mechanisms to “save the theory.”
It is a good example that any Theory A can explain any Evidence B, if you try hard enough. IOW, this paper is written from an evolutionary perspective. That is what they do–try to figure out how to explain the evidence according to evolution. Nothing wrong with that, but we need to understand that this paper is not testing the theory, it is working within the theory.
The argument that CD is a fact because it explains and fits the data so well is no different than the argument that geocentrism or the flat earth are facts. So I’m not citing “remaining challenges,” I’m simply the messenger pointing out that the empirical data do not fit the theory–not from a theory-neutral perspective. It is not even close. I realize this goes against the grain, and in the past I’ve even had people attack me for simply explaining the science. I always forgive them, but the science is the science. It is just non sensical to say CD is a fact (or whatever).