I also greatly appreciate that evograd brought this paper to our attention. Over the next few weeks, I would like to start a discussion here of one of the deeper issues raised by the paper, namely, how to model separate ancestry, in a fashion that the model is not simply an easily-knocked-over straw man or sand bottom clown. Only within the past decade have I begun to see attempts (e.g., by Douglas Theobald, Elliott Sober and Mike Steel, David Penny [e.g., the paper under discussion], David Baum, and a few others) seriously to describe separate ancestry scenarios, so that the evidence can be evaluated in the light of competing historical geometries.
Problem is, nearly all of the modeling of separate ancestry (SA) is being done by authors who think SA is false, and who (perhaps) for various reasons want SA to be false. Genuine advocates of SA, such as YECs and OECs, and some IDers, generally speaking aren’t welcome in mainstream ev bio journals. SA models sketched out by evolutionary biologists therefore tend to be “well, this is good enough, seems reasonable” with the outcome that satisfactory (i.e., thorough and reliable) theorizing tends to suffer. Of course, pro-SA authors are cheering for their preferred outcomes, too – but the competition should occur with the best models on both sides being weighed in the light of the greatest amount of data possible.
So there is a philosophical or analytical imbalance in scientific discussions of this very important question. We can remedy that here, in the short term, although of course it would be best for the topic to migrate into the refereed literature at some point soon.
More work travel for me over the next 4 days, but contacting B. Zhong to obtain his sequence alignment files remains a top priority. Back to this discussion soon. Best to all.