Sorry; maybe I'm too stupid or lazy, but I genuinely don't get your point. Is it just that when they construct the tree in "Inferring", it looks qualitatively surprising (non-modal) given any single introduction, assuming (as I do as well) that A predates B? But we've known that for literally years now. As I understand the paper, their novel contribution is to quantify how surprising that looks, whether it's p ~ 20% surprising (which wouldn't mean much) or their claimed p ~ 0.5%. That's what they do in "Separate", and it correctly and inherently depends on the epidemiological modeling that I don't trust.
Again, in the Twitter thread that you yourself linked, Worobey says:
> This [the real polytomy structure] is something that [we] DO NOT see in ~99.5% of simulations. That is the crux of the paper.
The simulations in question are the epidemiological simulations from "Separate". You've told me to disregard Worobey's comments here; but while it's possible that Worobey has misunderstood the significance of his own paper, it seems more likely to me that you have.
Again, in the Twitter thread that you yourself linked, Worobey says:
> This [the real polytomy structure] is something that [we] DO NOT see in ~99.5% of simulations. That is the crux of the paper.
The simulations in question are the epidemiological simulations from "Separate". You've told me to disregard Worobey's comments here; but while it's possible that Worobey has misunderstood the significance of his own paper, it seems more likely to me that you have.