Ending a long-standing mystery that once set the unidentified flying object community abuzz, researchers have sequenced the entire genome of a strange, 15-centimeter-tall human skeleton and identified mutations that may be responsible for its odd appearance. The specimen, discovered in the Chilean desert in 2003, had puzzled scientists because of its skeletal deformities and bone development that seemed much more advanced than its size suggested. But a comparison of its DNA to that of another human has revealed several mutations in genes involved in bone disorders—and confirmed once and for all that this being is definitely from our world.
The skeleton was apparently discovered in a small leather sack in a deserted village in Chile’s Atacama Desert (giving the specimen its name, Ata), though the study’s senior author, Garry Nolan, an immunologist at Stanford University in Palo Alto, California, acknowledges that its history is “a bit murky.” Ata eventually found its way to Spain, where it caught the attention of filmmakers producing a documentary about alien life. Nolan offered to sequence the specimen’s DNA—on the condition that if he found that it wasn’t an alien, the documentary would make that clear. As Science reported at the time, Nolan found that Ata was very clearly human, but he was left questioning what exactly caused the specimen’s odd skeletal structure.
One of the central questions was why Ata—only 15 centimeters tall and thus the size of a 5-month-old fetus—had bone development in the growth plates of its knees that would normally be seen in a 6-year-old. This led to speculation that Ata could be a child with a new form of dwarfism. But others believed that Ata was a fetus with genetic mutations that caused its advanced bone age, as well as a raft of other disorders such as having two pairs of ribs fewer than normal and an oddly shaped head.
The team took samples from Ata’s bone marrow and sequenced the DNA, mapping it against a human reference genome. They found, once again, that Ata was most definitely human, but also that she was female and, based on the preservation of her DNA, was born within the past 500 years—though her skeleton was discovered so well-preserved that she is probably mere decades old, Nolan says. Ata’s DNA also indicated that she was likely to be of Chilean origin; she had traces of European and Asian ancestry that suggests she is a product of fairly recent migrations.
The analysis of Ata’s DNA identified about 3 million single nucleotide variants (SNVs), places where a “letter” in the genetic code differs between individuals. To examine whether any of these could account for her abnormalities, the researchers focused just on SNVs in regions involved in creating proteins and filtered out variants that are commonly found in the general population, whittling them down to just 54. Many of these mutations had never been described before, but the researchers found that most of them occurred on genes known to be involved in skeletal formation, and which had previously been implicated in bone disorders, they report today in Genome Research. For example, they identified SNVs in genes encoding the collagen proteins that make up bone and cartilage, and in genes where other mutations have caused defects similar to Ata’s, such as fewer-than-normal ribs or short stature.
Nolan says the analysis reveals that Ata was almost certainly a preterm birth who had an assortment of mutations in her DNA that together could explain her unusual disorders. “This specimen had the bad luck lottery,” he says. “We all are born with multiple mutations, and that’s evolution, but sometimes the mutations all align badly.”
Not everyone agrees with these conclusions. Geneticist Michael Briggs from Newcastle University in Newcastle upon Tyne, U.K., who specializes in skeletal diseases, says it’s “highly implausible” that these variants all have detrimental effects and just happened to occur together by chance. It’s much more likely that Ata’s skeletal oddities are caused by just one or two variants, he says, but “they’ve not gone and done any functional studies, which you’d normally do to prove that [a] variant was disease-causing.” Without such studies—for example in mouse models or tissue cultures—it is impossible to know which variants are responsible, Briggs says. He also notes that several of the 54 SNVs found in Ata have been described in the human population before as benign, which rules them out as possible culprits.
Nolan acknowledges that the role of Ata’s mutations can’t be conclusively proved without experiments. But he adds that genes are “team players,” and that SNVs that are benign in isolation could cause disease when accompanied by other detrimental variants.
That debate may continue, but the one about Ata’s extraterrestrial origins should definitely end, says William Jungers, a paleoanthropologist and anatomist at the State University of New York in Stony Brook’s School of Medicine. “The alien hype was silly pseudoscience promoted for media attention,” he says. “This paper puts that nonsense and poor little Ata to bed.”