Tell us what you are trying to do?
I am trying to set up synonyms between the Latin names for plants. I have created custom post types for Family, Genus and Species with the appropriate relationships, effectively creating a hierarchy. One combination of Genus & Species can have one or more synonyms consisting of a different combination of Genus & Species
Is there any documentation that you are following? Relationships
Is there a similar example that we can see? hidden link
What I've set up so far doesn't really matter - bottom line is I want to set up a relationship between instances of the same post type, the relationship being that they are synonyms, but the current implementation doesn't allow relationships of that nature
The only way to setup a same CPT relationship is by using the default wordpress relationship style, where you can set a post of that CPT as the parent.
If you go to your CPT settings there should be an option name "Hierarchical", enabling this should allow you to have Parent/child relationships of the same CPT.