Uncommon or Common Descent?

[swamidass (S. Joshua Swamidass)]

@colewd

Here is the reason that it does not invalidate the paper and it also still remains a problem for the anomalies between chimps and man.

Uti- lizing gene families rather than sequences ignores small deviations from the tree easily explained by convergent evolution or incomplete lineage sorting.

I apologize for not including this in my original argument

Yeah, that turns out not to be correct if we consider deletions. Deletions can easily delete proteins, and genomic rearrangements can do this on a massive and correlated scale. Keep in mind what he says next:

@Winston_Ewert

As for 2, I do have deletions in my model. But I’m curious about how you see large scale genome rearrangement playing into this. Since I’m just looking at the presence or absence of gene families, I’d think a rearrangement wouldn’t do anything interesting there. But presumably you know something about that which I don’t.

@swamidass

Large scale genomic rearrangements can create correlated deletions in multiple branches of the tree. One test for this is to see if modules are correlated with synteny. I expect they are. If so, that gives a fairly straightforward reason for why the data shakes out this way.

And incomplete lineage sorting can also create this pattern (dependency graph vs. tree) in the human-primate data.