Thanks to Alice Gaylor for pointing me at this link where Katherine Griffis-Greenberg has proposed a different family tree from that in the JAMA article. Here's a short extract from her post (part of a discussion on the subject that you can track from the above page) but see the above page for the graphic showing her proposed family tree.
The eSupplement states that the two female foetuses in KV 62 are related to Tutankhamun and Princess KV 21A. Yet, the eSupplement to the article states that it cannot be said for a certainty that this individual is Ankhsenamun.
So, finding that odd, I went back and compared the various alleles in the article's graphs. Interestingly, the alleles that Princess KV 21A has more in common is not with the KV 55 mummy, as would be expected, but with the mummy identified as Amenhotep III!
So, this raises the question which Wente and Harris proposed back in the 1990's: do we have the mummies identified correctly?