In the documentary, Nolan says about his preliminary findings, “I can say with absolute certainty that it is not a monkey. It is human, or as close to human, closer to human than chimpanzees would be. But when you count up the number of mutations that we are observing, what we’re seeing is more than what we would expect to be caused by simple cell division.”

The rest of the discussion is meandering and technical enough that a nonexpert would come away with doubt. In the film, Nolan also says she has a Y chromosome—a mistake, he acknowledged to me, due to his inexperience with this kind of DNA analysis. (The extra mutations may also be the result of DNA degradation over the decades.) For the paper published this week, Nolan brought on experts in genetics and in paleogenomics to do the DNA analysis. They found some mutations that may explain the shape and hardness of her bones. They determined she was, in fact, a girl, and she was of both indigenous and European ancestry.

None of the paper’s coauthors are archaeologists or anthropologists though. And none of them were Chilean. By Wednesday, the Chilean Association of Archaeologists and the Chilean Society of Biological Anthropology issued statements denouncing the research. The two organizations and 11 other Chilean researchers also signed a letter to the journal that published the study. “The scientific community in Chile is deeply upset and concerned about this situation,” they wrote, adding that studies like this encouraged the looting of archaeological sites. (Full text of the letter below.)

“In the Atacama Desert, unfortunately, ancient sites are often looted. Many are not properly managed or delimited,” Bernardo Arriaza, a Chilean anthropologist who studies mummies in the Atacama Desert, wrote in an email. “It is a tragedy that a mother lost a baby, a miscarriage perhaps, but also a shame that looters got the body and sold it for a couple of dollars.”

For archaeologists and anthropologists, the ethical lapses in the handling of the girl’s body are glaring. “My first reaction as bioarchaeologist is I wasn’t happy. I was a little disgusted,” says Sabrina Agarwal at UC Berkeley. She ticked off the issues: how the girl’s body was found and sold, the lack of local stakeholders, the lack of an ethics statement in the published paper. “It’s part of the darker history of all of bioarchaeology and anthropology. It’s not like we are not part of it,” says Agarwal. “But contemporary bioarchaeologists and anthropologists are very sensitive to how they look at human remains.”

Geneticists have not had this kind of reckoning. Though they almost certainly will have to face up to this issue as the study of ancient DNA becomes a more and more common tool in anthropology. Late on Wednesday night, as outside pressure mounted, the University of California at San Francisco sent The Atlantic a statement on behalf of Nolan and his coauthor, Atul Butte, at UCSF, denying the study authors did anything inappropriate. It reads:

We affirm the need to respect the traditions of other cultures in genomic analyses. We have previously stated that we believe the skeletal remains should be returned to the country of origin and, by finding them to be human, this research supports the argument that these remains should be repatriated. This research clarifies what has been a very public and sensationalized story for a long time, and it was done out of a desire to bring some humanity to this discussion and dignity to the skeleton. The skeleton has never been in the possession of either Stanford or UCSF, and we had nothing to do with removing the skeleton from its place of origin. The DNA and images come from remains that were not known to be human when the research began. It does not provide identifiable information about a living individual, as defined by federal regulations, and does not qualify as human-subjects research, per the Federal Office of Human Research Protections. It has long been known that this skeleton was privately held in Spain, without any allegations of criminal conduct as to how it was acquired.

The authors are also writing a response that will be published in Genome Research.