Same here. This thread will be open indefinitely though. This is a place where you can figure out what type of experiments might convince skeptics. Even if it takes months to get that analysis done, we will still be interested. Coming to agreement on the experiments ahead of time will help us understand the results when they come. And this also gives you a forum to make negative results known too, which also will build trust in your work.
I can see a few:
- Incomplete sorting (which seems to be at play in the human data).
- Deletion and large scale genome rearrangement.
- The Birthday paradox.
- Introgression and/or hybridization after speciation.
Now, there are ways to test to what extent these things are affecting your results. The primate lineages are a good place to focus, because we have the most data there, and is most salient because it deals with human origins.
Once again, there seem to be ways to test your theory on the data versus these mechanisms. However, it seems that as written that it is not specified clearly enough to do this yet (at least as a third party reviewer). Though we can, for example, start to apportion specific cases into the different classes I just mentioned based on some tests of the data.
This, also, is where the human data becomes important. I think we both agree that humans are monophyogenetic. So if your non-tree model fits better than a tree model, that is an important failed control. Without getting into the details yet, we already know that tree models fail on human diversity data. There have been several papers put out demonstrating this. We should get into the weeds on this I am sure, but that seems to indicate that common descent in the real world does not produce a tree, so your tests themselves are not demonstrating that your model is better than common descent. Where am I going wrong in that reasoning? And do you want to see some examples of what I am talking about?
Selection is not really the issue I’m referring to here. That has to be considered carefully too.
Instead, I’m referring to, for example, synonymous mutations in proteins. It seems (though I could be wrong), you’ve restricted this to gene families. If that is the case, you are glossing over mutations more likely to be neutral. That seems to be a real problem. As this is actually where the nested clade evidence is stronger (at least from my assessment).
If I am right (and I may not be), it seems this is a direct falsification of the conceptual argument being put forward. It seems that “design modules” must be defined to be non-neutral, and you may have an explanation for why they almost fit in a nested tree. However, that does not explain why more neutral mutations (it is a relative term) might fit more tightly in a nested three than design modules. That seems to be a looming problem for your proposal. I don’t think you can make your case without dealing with this head on. It seems to be a direct falsification of your proposal, unless I’m missing something here.
Thanks for the offer. I’m more interested in real dialogue with you. I want you to have the best model possible, and get credit for retracting it if its wrong. If it is wrong, maybe the next idea you come up would work. Dialogue like this, I’ve found, is a much faster way to help you out.
I’m not looking for a publication out of this, but to really help us all figure this out together. In a way, think about this forum like a “micro publication,” or a “public peer-review.” It is a public thread. If desired, I can even get a DOI for it so you can reference it.