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Phylogenetic nomenclators cannot have it both ways: They cannot claim that they can do away with all the ranks (and the problems they present) while retaining all the information that the ranks provide in our current system.
When crafting a phylogenetic definition for a taxon name, a phylogenetic nomenclator can take into consideration historical usage of the name.
In the Delta example, the phylogenetic nomenclator could have prevented the shift by originally crafting the definition to use species E and species G as specifiers.