Rare DNA of Boy Sacrificed by the Inca Reveals Lost Lineage

November 17, 2015 | Kelly Tatera

Inca child mummy
Photo credit: Scientific Reports and Gomez, Carballa et al.

Only three modern people match his DNA.

Back in 1985, scientists discovered the mummified body of a seven-year-old boy near the top of Aconcagua — the world’s tallest mountain outside of Asia. The young victim was sacrificed by the Inca more than 500 years ago, and now researchers have sequenced his genome, coming to a striking conclusion about the genetic diversity that’s been lost through time.

In fact, they believe his rare DNA might tell the story of an ancient, lost lineage. The DNA signature discovered by the researchers seems to have pretty much disappeared from modern day South Americans, but they have reason to believe that it was once very prevalent.

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In this Incan ritual sacrifice, known as capacocha, children were brought to the top of the mountain and either killed or left to die. Unfortunately, this young boy’s fate wasn’t at all pleasant. As reported by The Guardian, “Vomit stained his clothes red and archaeologists found achiote, a dye which can act as a hallucinogen, in his intestines. He was strangled and died from a blow to the head.”

But luckily for the international team of geneticists, the boy was naturally mummified by the freezing cold, enabling them to isolate and sequence the boy’s entire mitochondrial genome from just one of his lungs.

Unlike nuclear DNA, which a child inherits from both parents, mitochondrial DNA contains only 37 genes passed down from mother to child. The researchers said this was the first time that scientists had ever decoded all of the mitochondrial DNA from a Native American mummy.

Interestingly, the boy’s genetic variations suggest that he belonged to a population from Mesoamerica and the Andes dating back about 18,000 years, called C1b. However, researchers were unable to place him in one of the subgroups for C1b.

The C1b population diversified as it spread throughout Central and South America — as groups became isolated from one another, they began to develop their own unique genetic variations. Despite the fact that C1b contains a number of genetically distinct groups, the sacrificed boy’s genome still didn’t fit into any of them. Surprisingly, his mitochondrial genome had 10 distinct mutations that had never been observed together in either ancient or modern DNA.

Thus, the researchers say he was part of a native South American population that had never been identified. They dubbed his genetic group C1bi.

The scientists sifted through genetic databases in search for any traces of the boy’s unique DNA code, but just four entries surfaced that appeared to belong to C1bi. Three of these finds were modern people from Peru and Bolivia, and the fourth person belonged to the ancient Wari Empire (its prime was from 600 to 1000 CE).

Finding two ancient individuals who fit the C1bi group doesn’t sound remarkable, but the researchers contend that this hints that the lineage was once far more common. After all, what are the odds of picking two ancient samples at random that both fit this genetic group?

As Andrés Moreno-Estrada, a population geneticist from Mexico’s National Laboratory of Genomics for Biodiversity, told Science, “What are the chances you pick the rare guy? Most likely, you’re picking the common guy.”

Either way, this finding still offers an interesting look at the genetic diversity that once existed in South America. The researchers hypothesize that the diversity was lost at the hands of the Spanish colonizers who brought new diseases to South America.

“Up to 90 percent of native South Americans died very quickly,” Antonio Salas, the study’s lead from the University of Santiago Compostela, told Science. “You can imagine that a lot of genetic diversity was lost as well.”

Undoubtedly, the horrific acts that this little boy endured tug at the heart strings. But from a scientific standpoint, the findings contribute another important piece to the intricate puzzle of ancient humanity.

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