Two things to try,

1. setting genus=NULL, The logic being it doesn't know which genus to add it to. Just as a precaution setting all blank space within a taxa id to _ ...

add.species.to.genus(test_tree, "t1_polytome1", genus=NULL, where=c("root"))

Maybe replace root with random to get it working.

2. alternative using tree instead

genus.to.species.tree(test_tree, "t1_polytome1")

Two things to try,

1. setting genus=NULL, The logic being it doesn't know which genus to add it to. Just as a precaution setting all blank space within a taxa id in the tree to _ ...

add.species.to.genus(test_tree, "t1_polytome1", genus=NULL, where=c("root"))

Maybe replace root with random to get it working.

2. alternative using tree instead

genus.to.species.tree(test_tree, "t1_polytome1")