Late to the party, but since I had this in Notepad during my dallying I'm not going to just dump it.
I'd say it depends on how you're using CommonName. If you mean that Acer is the botanical name for maple, and a piece in your inventory is maple then it is the same word and CommonName is not something peculiar to each table (i.e. no two CommonName values are the same in either table).
In that case I think BotanicalName is the pk in reference table. CommonNameFK is the foreign key in reference that relates back to CommonNamePK in master. This assumes that you intend to relate Acer to your many pieces of Maple in your inventory. However, if you intend to put a number id on every piece you have then that isn't right. I guess you need to clarify what common name means in each table and if you're tagging each piece with an ID. To do that I think Acer and Maple should be in botanical and common name fields in the same table and the pk from reference is the fk in your table for wood stocks.
The more we hear silence, the more we begin to think about our value in this universe.
Paraphrase of Professor Brian Cox.