The number of Native Americans quickly shrank by roughly half following European contact about 500 years ago, according to a new genetic study.

The finding supports historical accounts that Europeans triggered a wave of disease, warfare, and enslavement in the New World that had devastating effects for indigenous populations across the Americas.

Using samples of ancient and modern mitochondrial DNA—which is passed down only from mothers to daughters—the researchers calculated a demographic history for American Indians. (Get an overview of human genetics.)

Based on the data, the team estimates that the Native American population was at an all-time high about 5,000 years ago.

The population then reached a low point about 500 years ago—only a few years after Christopher Columbus arrived in the New World and before extensive European colonization began.

Study co-author Brendan O'Fallon, a population geneticist who conducted the research while at the University of Washington in Seattle, speculates that many of the early casualties may have been due to disease, which "would likely have traveled much faster than the European settlers themselves."

For instance, the Franciscan friar Toribio de Benavente—one of the first Spanish missionaries to arrive in the New World in the early 1500s—wrote that Mexico was initially "extremely full of people, and when the smallpox began to attack the Indians, it became so great a pestilence among them ... that in most provinces more than half the population died."

Some historians have questioned whether such effects were restricted to particular cities or regions, but the new study suggests mortality was widespread.

Pinpointing a Recent Native American Decline

The new analysis—published in this week's online early edition of the Proceedings of the National Academy of Sciences—found that modern Native Americans are more genetically similar to one another than those living before European contact. This suggests the population size was reduced sometime in the recent past.

Imagine "selecting two individuals from a very small village and asking them how many generations ago they first shared a common ancestor. It's likely to have not been that long," O'Fallon said.

"On the other hand, if the village is very large, you might have to go back a long way to find a common ancestor."

The results run counter to earlier genetic studies, which found no evidence of a recent population contraction among American Indians.

But those earlier studies did not include ancient DNA, which is crucial for establishing an accurate time line, O'Fallon said.

"One previous study did find a decline in population size among Native Americans but inferred the time of the decrease as around 1,000 to 2,000 years ago, [which is] hard to reconcile with what we know about Native American history," he said.

Although the new study is based on DNA, the researchers caution that their use of statistical analysis means the findings aren't conclusive and can only suggest that a particular scenario most likely occurred.

"Our methods infer thousands of genealogies," O'Fallon said. "By looking at the bulk properties of all these genealogies we can begin to get a clearer picture of what likely happened."

In addition, the margin of error for the new study is rather large, O'Fallon said, so it's possible the decline happened more recently than 500 years ago.

"I don't think it would rule out European influence at all if the bottleneck happened a bit more recently than 500 years ago," he said.

Instead, a slightly more recent time frame might change "our interpretation [of the early cause of the decline] from disease to other causes such as war, societal disruption, loss of homelands, etc."

A Short-Lived Population Bottleneck?

Despite revealing a dramatic drop, the new study suggests that Native American populations eventually recovered to their predecline levels, likely aided by the development of resistance to European diseases.

Furthermore, the genetic health of the group did not appear to suffer long-term damage.

"Our study did not find a substantial reduction in genetic diversity," O'Fallon said. "The bottleneck was fairly short-lived and, while significant, didn't appear to eliminate many lineages that were present before Europeans arrived."

Overall, the new results "are some of the most detailed information scientists have about Native American ancestral population demography based on genetic data," said Quentin Atkinson, an evolutionary anthropologist at the University of Auckland in New Zealand, who was not involved in the study.