Hi @fjdisofj0ew, I don't mean to step on @jwdebelius's toes, but thought this might be useful for you:
http://scikit-bio.org/docs/0.5.6/generated/skbio.io.format.newick.html#explanation
QIIME 2 uses scikit-bio for working with trees, so all of the rules outlined in the link above are going to apply here. I'll draw your attention to this passage:
More characters can be used to create more descriptive labels. When creating a label there are some rules that must be considered due to limitations in the Newick format. The following characters are not allowed within a standard label: parenthesis, commas, square-brackets, colon, semi-colon, and whitespace.
What if these characters are needed within a label? In the simple case of spaces, an underscore (
_) will be translated as a space on read and vice versa on write.
What if a literal underscore or any of the others mentioned are needed? A label can be escaped (meaning that its contents are understood as regular text) using single-quotes ('). When a label is surrounded by single-quotes, any character is permissible. If a single-quote is needed inside of an escaped label or anywhere else, it can be escaped with another single-quote. For example,A_1is written'A_1'and'A'_1would be'''A''_1'.
Oof, no fun.