Archaeologists are astonished: the discovery of a humanoid skeleton resembling a dinosaur in the desert redefines history.

An unusual skeleton found in Chile has puzzled people for more than a decade.

Complete genome sequence revealed that caused their abnormalities

A mummified skeleton discovered in Chile’s Atacama Desert 15 years ago is unlike any you’ve ever encountered. In fact, some might say it looks… well, strange.

It is a skeletal drum made up of puzzling features. It is only 6 inches tall, but initial estimates of the drums’ age were consistent with that of a child between 6 and 8 years old.

The elongated, angular skull, flattened eye sockets and fewer ribs than normal (10 pairs instead of the normal 12) only added to the mystery.

Questions surrounding the discovery led to speculation that it was a previously identified primate or even an extraterrestrial life form.

The skeleton, nicknamed Ata, appeared on television shows and in a documentary, “Sirius,” in which a UFO researcher attempts to uncover Ata’s origins.

Now, the authors of a study based on five years of genetic analysis want to set the record straight: ATA is human, albeit with multiple mutations associated with diseases of the body. And they believe their results, published Thursday in the journal Geographic Research, could help diagnose cases of genetic mutations in living patients.

In 2003, Ata was found in an abandoned village called La Noria in Chile’s Atacama region. Initially thought to be a wreck, an initial analysis in 2012 showed the skeleton was only about 40 years old. This DNA flesh would still be intact and could be recovered for study.

Widespread speculation surrounding Ata brought the case to the attention of Gary Nolai, senior author of the new study and a professor of microbiology and immunology at Stanford University.

“I heard about this through a friend who was interested in the whole area of extraterrestrial life,” Nolaí wrote in an email. “He told me about a documentary that was coming out (‘Sirius’… you can find it on Netflix now) that was going to feature the ‘Atacama Humanoid.’”

It was claimed that it was possibly the mummy of an alien.

“That was a significant statement in itself. But what was even more shocking was the image I was given, which was part of the official publicity. I decided to contact the film’s directors (basically on a dare…) to tell them that it was possible to sequence the specimen (if it had terrestrial DNA…) to determine its origin.”

Nolap and his colleagues signed a confidentiality agreement, and the directors agreed to report Nolap’s findings even if the results indicated Ata’s DNA was human.

Nolap wanted to study Ata for several reasons. The extraordinary specimen could have been a previously recognized primate species, some kind of human deformity or something else. Nolap said he and his colleagues never believed it could be an animal.

They were expecting an answer to the basic question: “What is it?”

DNA analysis would reveal the true story. A sample taken from Ata’s ribs was used to perform a whole genome sequencing analysis.

The genomes were compared to humans and primates and it was determined that the remains were a female human, probably a fetus, with Chilean ancestry. Although the data initially estimated the skeleton’s age to be between 6 and 8 years, the researchers discovered that the remains had a rare skeletal age disorder that made them appear older than the person they belonged to.

At first, 8% of the DNA didn’t match human DNA. Researchers determined this was due to a degraded sample. An enhanced analysis matched it up to 98%, Nola said. Given the exposure and age of the skeleton, this wasn’t surprising. They then moved on to diagnose the anomalies.

Researchers were looking for something that might explain the skeleton’s small stature, as well as abnormal rib coupling and other oddities in the body and skull.

Dr. Atul Butte, another senior author on the paper, was brought in to help evaluate the genome. Butte, the Priscilla Chapé and Mark Zuckerberg Distinguished Professor and director of the Institute for Health Computational Sciences at the University of California, San Francisco, treated the analysis as if it were for a patient.

A series of mutations in seven genes were revealed that together created musculoskeletal and body deformities such as scoliosis and skeletal dysplasia, known as dwarfism.

“There are mutations in many genes, including those that evolved with collagen production (like the body and hair), joints, ribs, and arteries,” Butte wrote in an email. “We know that these genes evolve with these processes in human development, but we are still learning what all the other genes in DNA do.”

Although mutations in genes are known to cause uterine diseases, some of them had not previously been associated with growth or developmental disorders. The combination of genetic mutations explains the appearance of Ata, but what surprised scientists was the number of mutations present in the same specimen.

“It’s rare,” Butte said. “To our knowledge, no one has ever explained all of these symptoms to a patient before, and the DNA changes or mutations reflect that.”

But what could have caused this series of mutations?

“A lot of times, genetic diseases are passed down from carrier parents,” Butte said. “In this case, these mutations are so rare that we’ve never seen some of them before, so it’s hard to imagine there being carriers there. We speculate that the environment this child was developing in might have played a role. The sample was found in a village with pyridoxine-depleted microbes, and exposure to pyridoxine could have caused the mutations. But it’s just speculation.”

No other researcher has seen the remains.

The way Nola, Butte and their colleagues used their analytical tools to understand the mysteries presented by Ata’s skeleton may provide a path for multi-gene analysis to uncover the roots of the mutations.

Butte said he hopes the technology and tools used in this study can help patients and their families receive diagnoses more quickly, as well as help develop treatments for diseases that can be traced back to genetic mutations.

“Many children’s hospitals now see patients or children with common syndromes, including those that have been described before,” Butte said.

“DNA sequencing is increasingly being used to help us solve these ‘undiagnosed diseases.’ But often, we tend to look for a single genetic mutation that can explain what we see in the patient.

“What this case taught me is that sometimes there may be more than one important difference in DNA that has developed to explain a particularly difficult-to-explain patient. We should not stop a search when we have found the first relevant mutation – in fact, there may be many others that have also developed.”