Ancient "Atacama Alien" Skeleton Reveals Bizarre Genetic Mutations

In 2003, amid the dry, desolate stones and salt lakes of Chile’s Atacama Desert, a wanderer discovered a tiny, humanoid skeleton. This six-inch-long “Atacama alien,” with its strangely elongated skull and dearth of ribs, was sold on the black market and provided plenty of fodder for alien conspiracy theories until 2013, when a Stanford University scientist showed that “Ata” was indeed human. That didn’t make it any less weird, and neither does a new Genome Research study on the strange mutations she carried in her DNA.

In a paper published Thursday, a team of researchers from the University of California San Francisco, together with members of the Stanford University team who first characterized Ata as a human female, show through genetic profiling that she carries 64 genetic mutations, many of which have never been seen. A further bioinformatics analysis showed that these genes greatly affected Ata’s skeletal system, resulting in her abnormally tiny stature and her scant 10 pairs of ribs. Most humans have 12.

Ironically, this study shows that many parts of the human genome are still alien to us. “While hundreds of thousands of individuals have had genomes sequenced now, there are still many more to go on the planet, and it’s still possible to find rare (or never before seen) mutations in people,” co-author and UC San Fransisco researcher Atul J. Butte, Ph.D., tells Inverse in an email. “This particular child appears to have several rare mutations, many of which are in genes that we know are involved in bone formation and development.”

In 2013, Ata’s genome was profiled by Stanford’s Garry P. Nolan, Ph.D., who took bits of her DNA and compared it to a reference human genome to show that she “is human, there’s no doubt about it,” as he told Science. Her mother was shown to be of Chilean origin.

Still, there were many things about Ata that seemed strange, or at least hadn’t been characterized in human studies before. In particular, she had the skeletal development of a child between the ages of six and eight, though, obviously, she was not the size of a normal human child. Nolan guessed that she either had severe dwarfism and was born that way or that she had the rare, rapid aging disease known as progeria and died that way in the womb. To confirm or refute these hypotheses, however, he had to find evidence in Ata’s genes.

In the new research, study co-author and UC San Francisco bioinformatician Sanchita Bhattacharya, Ph.D., compared Ata’s genome to data in a giant public domain database of genetic information called the Human Phenotype Ontology. The analysis linked Ata’s genes to physical abnormalities known to be caused by genetic mutations in other humans, or at least found similarities between them.

The mutations the authors found occurred in genes “previously linked with diseases of small stature, rib anomalies, cranial malformations, premature joint fusion, and osteochondrodysplasia (also known as skeletal dysplasia),” they write. They note that the effects of many of these mutations are “putative” — that is, they’re only predictions, seeing as the mutations have not been seen in any other humans before.

In any case, the mutations she carried were rare indeed, which is probably why we’ve never seen them before. Still, much of Ata’s history and her familial background remains to be explored.

“The specimen itself is not very old, and we are estimating this to have happened only several dozen years ago,” says Butte. “The population likely still lives in the region, but we do not know anything about her family.”

The researchers point out in the paper that they’ve found evidence of human children with severe osteogenesis imperfecta (a skeletal condition marked by short stature, low bone density, and severe vertebral compression fractures) linked to many of the same genetic mutations as Ata’s. Because the children in that report were born from incestuous mating, their genes confirm that super-deleterious genes like Ata’s can, in uncommon situations, be passed down through the gene pool instead of getting weeded out.

The discovery is sure to be a letdown for people hoping Ata was indeed the extraterrestrial she was purported to be, but the analysis just goes to show how alien human life can be if our genes are mutated enough. Nevertheless, Nolan asserts that Ata was indeed a human child and should be treated as such.

“We now know that it’s a child, and probably either a pre- or post-term birth and death,” he said in a statement published Thursday. “I think it should be returned to the country of origin and buried according to the customs of the local people.”