the tree of knowledge is the proto-language whose branches grow everywhere and whose fruits bear on the tongue
Now you have "the", I read sentence as saying:
of all the proto-languages, the tree of life is the one whose branches grow everywhere ...
This does establish that there's only one proto-language with these characteristics, but not necessarily that it's the first or original one -- the ur-language -- just that it's the most successful. There could also be other, older proto-languages whose branches are almost everywhere, say.
Is that what you intend? When I suggested "the", I was thinking of it meaning:
The tree of knowledge is the proto-language. Its branches grow everywhere and its fruits bear on the tongue.
Placing a comma after "proto-language" would do that, I think, changing what follows from a restrictive to non-restrictive clause.
Anyway, quite possibly you have exactly what you want here.