Washington Post: The 500-year-old skull, found in a long-forgotten Inca cemetery outside Lima, Peru, had two round holes just across from each other. Nearby was a plug of bone, recovered intact, that carried the distinct markings of an old musket ball.

Archaeologists sensed they had unearthed an important find, but it wasn’t until months later that a powerful electron microscope scan confirmed it by finding traces of lead in the skull. The victim, who was between 18 and 22 years old when he died, had been shot by a Spanish conquistador.

Given the age of the remains, as well as the age of other remains buried nearby, the archaeologists came to the conclusion that they had identified the earliest victim of a gunshot wound ever found in the Americas.

“There may have been Incas and other native people killed by Europeans before him, but this is our oldest example so far,” said Peruvian archaeologist Guillermo Cock, who has excavated in the area for more than 20 years. “This happened at the beginning of a long and difficult history.”

Based on carbon dating, as well as analysis of the hundreds of other bodies buried in the area, Cock believes the man was shot in the 1530s, just a few years after Francisco Pizarro and his small army of conquistadors arrived in Peru.

That arrival led to one of the most disastrous population declines in recorded history up to 80 percent of the 12 million people in the Inca Empire died within 70 years.

The history of the Incas’ rapid defeat and decline, written almost entirely by the Spanish victors, has emphasized the valor and skill of the greatly outnumbered Europeans. Cock said the relatively new field of Inca archaeology is beginning to rewrite some of that story.

For instance, Cock said, there is good reason to believe the young gunshot victim died during the siege of Lima in 1536 -- one of numerous Inca uprisings following the execution of their leader, Atahualpa, by the Spanish. He also said there is archaeological and historical evidence to suggest those insurrections were put down with the help of native peoples who opposed the Incas’ rule.

“We are just now starting to really compare what was written with the material evidence being uncovered,” Cock said. “There is a lot that was never told before.”

The musket victim was one of 72 people who appear to have been hastily placed in a formal Inca burial ground where hundreds of others had been meticulously wrapped, honored and interred in the traditional Inca way. The 72 were barely wrapped, had no ceremonial offerings with them and were in shallow graves.

These signs of a speedy burial, along with tentative evidence that two others may have died of gunshot wounds and that several more had been crushed by swinging maces, led Cock to conclude they died during the little-known siege of Lima. He said relatives probably took them from the battlefield and buried them quickly in the traditional cemetery. The remains of women and children, who most likely traveled with the Inca forces, were also found.

Cock’s research was funded by National Geographic and will be the subject of a “Nova” TV special on PBS next Tuesday. The discovery of the lead deep in the bone of the skull was made at the University of New Haven’s Henry C. Lee Institute of Forensic Science.

Cock, who is trained as a historian as well as an archaeologist, said about 30 of the 72 bodies had been killed by native weapons -- lending support to his theory that Pizarro succeeded only because he enlisted the help of other tribes who were enemies of the Incas. Pizarro’s closest allies are believed to have been the Huaylas, who lived about 100 miles north of Lima, Cock said. Pizarro is known to have taken a prominent Huayla woman to be his mistress, and Huayla forces are believed to have had a decisive impact during the Lima siege.

Richard Burger, a Yale University anthropology professor, said that if the finding holds up, it will indeed represent the first example of a Native American killed by guns. He said Spanish colonists were in the Caribbean and Mexico decades before they came to Peru in 1532, and some native people were probably shot during those years. But their remains have not been unearthed.

“There hasn’t been much archaeological evidence in this area, so the finding could be very important,” Burger said. “There’s a lot of interest now in learning more about the Inca decline from sources other than the victors.”

Before the Spanish arrived, the Inca Empire controlled the entire Andean region, later earning the designation “Romans of the New World.” Highly accomplished builders, the Incas built the city of Machu Picchu on a mountaintop 8,000 feet above sea level.

The fast decline of the Incas has generally been attributed to the far more advanced Spanish weaponry, the spread of European diseases to which native people had no immunity, and malnutrition and illness caused by the harsh working conditions imposed by the colonists.

Cock said all those factors doubtless played a role, but the ability of the Spaniards to establish native allies was also important and has been generally ignored.

 “They joined Pizarro in the hope of being rewarded with more independence and freedom,” Cock said. “I believe they wanted a more equal, more horizontal relationship with the Spaniards. Clearly, that did not happen.”