Ewert’s paper is discussed in another thread:. The consensus is that it has a long way to go before it can show what Ewert wants it to show. However, we all give Ewert a lot of credit for tackling this data.
From what I can tell, the dependency graph requires violations of the nested hierarchy. For example, Ewert talks about zebras and zebrafish sharing a gene that other fish and mammals do not. That would be an obvious violation of the nested hierarchy. However, Ewert’s conclusions seem to depend on complete annotation of all genomes and wide coverage of species groups, which isn’t the case.