The argument was not that the haplogroup data was wrong — D1 is unambiguously an American haplogroup — but that it was incomplete.

Haplogroup continuity does not rule out the possibility that the nuclear genome of Naia and people like her might show differences from later Native American populations that would complicate the simple continuity narrative.

Subsequent work in ancient American genomics has provided additional data on this question, though the specific nuclear genome of Naia has not been published — the DNA preservation at Hoyo Negro, while sufficient for mitochondrial analysis, apparently did not yield enough nuclear DNA for a complete genome analysis.

The data that has emerged from other ancient American individuals — including the Anzick-1 child in Montana, the Kennewick Man in Washington State, and various ancient individuals from across the hemisphere — has consistently supported the picture of genetic continuity between the earliest Americans and later Native peoples, at least at the level of founding lineages.