The archaeologist has retrieved some 500 skeletons from the Puruchuco graves between 2004 and 2007.
Seventy-two of the individuals had been wrapped in simple cloth and chaotically buried in shallow graves. Their lack of traditional adornments and offerings—jewelry, pots for food, or headdresses, for example—suggests that the burials had been hastily prepared, as if during a period of civil unrest.
Many of the skeletons bore signs of violent hacking, tearing, and impalement with iron weapons.
Notably, one of the skulls bore entrance and exit wounds like those seen in shooting victims. A small piece of bone that appeared to have been shot out of the skull was found nearby.
"We thought it was a person killed recently—5, 10 or 20 years ago," Cock said. "We didn't expect the individual would have been killed by a bullet 500 years ago."
But the team soon realized that the individual was a Peru native dating to the Inca period, he said.
Moreover, the bone fragment showed evidence of a less forceful impact than a modern weapon would have made.
The skull fragment also bore a concave imprint suggestive of a musket ball.
Then Melissa Murphy of Bryn Mawr College—a scientist who studies human remains from archaeological settings—and archaeologist Elena Goycochea set out to help Cock confirm his theory.
They used a CT scanner at a Peruvian research facility to look for traces of metal from the musket ball around the wound and on the bone fragment.
No metal remnants were found.
But forensic experts at the University of Connecticut used a more powerful microscope to positively reveal traces of iron both places.
Iron was often used to make Spanish musket balls. Also, experts say the Inca did not know how to work iron, so the ball had to be Spanish.
"This gave us positive evidence that this individual died during conquest and was killed by gunfire," Cock said.
"We have traces of iron on the edges of the bullet entrance and we have exit damage in the face caused by the bullet leaving the head."
Cock and his colleagues believe the individual was killed during the siege of Lima. The 1536 uprising pitted Inca against Spanish invaders led by Francisco Pizarro.
Because women and children were found among the 72 hastily buried bodies, the team suggests that the individuals were not warriors but supporters of the warriors, such as cooks and porters."