By studying the genetics of modern-day descendants from the ancient Inca nobility, researchers have been able to piece together the origin of the Inca Empire. 

While today we use the term Inca to refer to all people who were ruled under the empire – from southern Colombia to central Chile – in its strictest sense it actually refers to just the ruling class at the time, who numbered perhaps as many as 40,000 people out of the entire 10 million. In the native language of Quechua, the empire is known as Tawantinsuyu.

Despite their clear prowess in conquering and ruling such an enormous area, and by many accounts it was the largest empire anywhere in the world during the 16th century, they amazingly lacked a system of writing. This means that while we have a whole wealth of architecture and cultural artifacts to study, piecing together the history of the Inca and the people they ruled is a little trickier.

There are two foundation myths about the origin of the Inca, passed down for generations. The first tells of how Manco Capac and Mama Ocllo, the children of the Sun God, came to found the Inca Empire in Cusco valley after traveling over 500 kilometers (311 miles) from Lake Titicaca. The second talks of how the four Ayar brothers, along with four sisters, emerged from a cave in the Paccarictambo hills 50 kilometers (32 miles) south of Cusco with only one brother, Manco, making it to the valley.

The researchers wanted to use genetics to try and tease out whether there is any truth in either of these origin stories. “A unique patrilineal cluster would be expected in the first case. In the second case, two or more patrilineal patterns will be evident,” said geneticist Ricardo Fujita, co-author of this latest research published in Molecular Genetics and Genomics.

The problem arises in that even though we have quite a few South American mummies, we don’t have any from the Inca ruling families. This is because at the time they were often worshipped as gods, and so when the Spanish took over they burned and buried the remains in unknown locations. Historians have, however, been able to trace the descendants of at least 12 lineages to people surviving today.

They used markers for the Y chromosome and mitochondrial DNA (mtDNA) from these descendants and compared them to thousands of other native South Americans. From this, they were able to discern two patrilineal haplotypes, named AWKI-1 and AWKI-2, and the pattern of their inheritance reveals some interesting aspects.

The most interesting of these is that the most locations of the AWKI-1 and 2 haplotypes cluster south of Cusco, in the basin of Lake Titicaca, and the neighboring Paccarictambo hills. According to Fujita, this is “in agreement with the two foundational myths of the Inca, probably two pictures at different times of the same journey with final destination Cusco.”

The mtDNA, however, shows a much more diverse matrilineal origin, which is thought to reflect the multitude of political alliances through arranged marriages between Inca nobility and the tribes they ruled over.  

The researchers hope one day to get their hands on the remains of even just one ancient Incan mummy, to help further their understanding of the origin of the civilization, and use genetics to piece together the history of an ethnic group that was almost completely erased from the history books.