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The first genetic study conducted on the peopling of the Americas has confirmed a truth not found in public school history books—European colonization wiped out Native American populations to extinction.

The University of Adelaide’s Australian Centre for Ancient DNA (ACAD) analyzed the DNA of pre-Columbian mummies and skeletons to reconstruct a genetic history. There is a “striking absence” of those genetic lineages in modern Native Americans, pointing to an extinction event that coincides with the European arrival.

“Surprisingly, none of the genetic lineages we found in almost 100 ancient humans were present, or showed evidence of descendants, in today’s Indigenous populations,” says joint lead author Dr. Bastien Llamas, Senior Research Associate with ACAD. “This separation appears to have been established as early as 9000 years ago and was completely unexpected, so we examined many demographic scenarios to try and explain the pattern.”

“The only scenario that fit our observations was that shortly after the initial colonisation, populations were established that subsequently stayed geographically isolated from one another, and that a major portion of these populations later became extinct following European contact. This closely matches the historical reports of a major demographic collapse immediately after the Spaniards arrived in the late 1400s.”

Francisco Pizarro’s treachery and murder in 1532 of the last Incan emperor, Atahualpa, is a symbol of that willful extermination. With the blessing of King Charles V, Pizarro marched to the Incan capital under the banner of Christianity and greed.

Pizarro invited Atahualpa to a feast in honor of the new emperor’s rise to the throne. At the feast, Pizarro had his friar, Vicente de Valverde, urge that Atahualpa convert to Christianity and accept Charles V as their king—which was a calculated move to infuriate the ruler. When Atahualpa refused, Pizarro ordered his men to open fire, whereupon they slaughtered 5,000 Incan soldiers in an hour.

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The Spanish account speaks of the event with great pride and thanks to God. Pizarro kept Atahualpa alive long enough to get a ransom of gold and silver, and then, even after Atahualpa converted to Christianity under duress, he was strangled to death.

These tales of barbarity are a common theme of European conquest all over the Americas. The accounts of torture and mass murder carried out by Columbus and his men in the Caribbean islands are truly disturbing.

There was another culprit in the death of Native Americans. Europeans, being from densely populated cities, were vectors of chronic diseases such as influenza, bubonic plague, smallpox, and measles. Indigenous Americans, on the other hand, had become genetically isolated over their thousands of years of migration from the Beringian land bridge to the farther reaches of South America. A vast number of Native American deaths were the result of diseases that were completely new to their populations.

The DNA study carried out by ACAD also adds valuable information on the timing of the first people entering the Americas, which produced this genetic isolation.

“Our genetic reconstruction confirms that the first Americans entered around 16,000 years ago via the Pacific coast, skirting around the massive ice sheets that blocked an inland corridor route which only opened much later,” says Professor Alan Cooper, Director of ACAD. “They spread southward remarkably swiftly, reaching southern Chile by 14,600 years ago.“

“Genetic diversity in these early people from Asia was limited by the small founding populations which were isolated on the Beringian land bridge for around 2400 to 9000 years,” says joint lead author Dr. Lars Fehren-Schmitz, from UCSC. “It was at the peak of the last Ice Age, when cold deserts and ice sheets blocked human movement, and limited resources would have constrained population size. This long isolation of a small group of people brewed the unique genetic diversity observed in the early Americans.”

The tale of Native Americans sadly turned out to be one of extermination by Europeans bent on conquest and riches. It will forever remain a mystery what these untold numbers of extinct, unique populations could have contributed to humanity.