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.