You would think that as nature.com advertises itself as "Internation weekly of science", it would clearly mark fictional articles very clearly.
I read the article, and it could be fact. However, I think that due to the writing style with plenty of dialogue thrown in, it is would almost fiction.
I think it's science fiction, but I'm not sure. The reason I think this is because it's in a section called "futures", which Nature describes elsewhere as "Science fiction from the home of science".
Nature's "Futures" section is an ongoing science fiction short story series, so this is fiction. (Also, the genetic data doesn't say anything in that direction, especially not in such a simplistic way.)
The author seems to have contributed to New Scientist on the subject matter[1], therefore I'm hoping (and expecting) it to be the latter of your two possibilities.
Both would please me, but not knowing which does not.